Methods and compositions for treating and diagnosing autoimmune disease

Abstract

The application relates to methods for the diagnosis, treatment, and prevention of autoimmune and / or inflammatory disease such as systemic lupus erythematosus (SLE) and lupus nephritis.

Description

METHODS AND COMPOSITIONS FOR TREATING AND DIAGNOSINGAUTOIMMUNE DISEASECROSS-REFERENCE TO RELATED APPLICATION

[0001] This application claims priority to U.S. Provisional Application No. 63 / 533,004, filed August 16, 2023, the disclosure of which is herein incorporated by reference in its entirety.STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

[0002] This invention was made with government support under R01 AI143313, P50 AR070591, and R21 AI180737-01 awarded by the National Institutes of Health. The government has certain rights in the invention.SEQUENCE LISTING

[0003] The instant application contains a Sequence Listing which has been submitted electronically in XML file format and is hereby incorporated by reference in its entirety. Said XML copy, created on August 15, 2024, is named 243735_000363_SL.xml and is 21,824 bytes in size.FIELD

[0004] The application relates to methods for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, as well as methods for treating a subject diagnosed with SLE or ILE, and methods of monitoring the effect of a treatment on development of a disorder in a subj ect, wherein the disorder is lupus nephritis or other forms of SLE with renal involvement or polyarthritis.BACKGROUND

[0005] Systemic lupus erythematosus (SLE) is a chronic, systemic autoimmune disease, with heterogeneous phenotypes, often with protean non-specific initial presentation that cause delayed diagnosis. SLE disproportionately strikes women, non-White groups, and those of lowsocioeconomic status. Its incidence, like that of many autoimmune diseases, appears to be rising (1-3). It is quixotic, with remissions and then flares of increased activity (4). Clinical features and organ involvement distinguish SLE from other autoimmune disease, with high rates of disfiguring rashes, disabling arthritis, infections, and cardiovascular disease. One of the most prevalent severe disease manifestations, occurring in -40% of patients is lupus nephritis (LN) (5). Patients with Class III or IV LN have poor prognoses, and more than 20% of these affected patients progress to end-stage kidney disease within 15 years of diagnosis (6-8).

[0006] Diverse pathogenic pathways are involved in the different aspects of the disease, and while insights into lupus pathogenesis have led to the development of new FDA approved therapies, there remains a great burden of disease especially for patients with LN. Especially relevant, -20 years ago the new technology of gene expression arrays was used to first show that many SLE patients displayed increases in interferon stimulated genes (ISG), and a pattern termed the interferon (IFN) signature (15). Confirming the clinical relevance of these findings, two Phase 3 RCT trials led to approval of an antibody agent that blocks to type I interferon receptor subunit 1, termed IFNAR, for patients with moderate to severe SLE disease without serious renal involvement (16). However, a more recent Phase 2 RCT, that included only active biopsy-proven Class III / IV LN failed the 1° or 2° endpoints (17). Although this was rationalized as due to patient heterogeneity, and that higher doses may be required, certainly other factors could be in play. Baseline patient lab studies primarily focused on ISG (17), but other gene expression patterns have not been as deeply considered. Indeed, LN kidneys have low IFN signatures compared to SLE skin and synovium (18). Hence, IFN may not be the only driver in every LN patient, and other pathways may have been overlooked. Importantly, many SLE patients, and LN patients in particular, have waxing-waning illness with flares, particularly of Blautia (Ruminococcus) gnavus of the family Lachnospiraceae , hereinafter referred to as Blautia (Ruminococcus) gnavus or R. gnavus, despite appropriate therapeutic interventions.

[0007] In early life, gut commensal organisms are essential for development and maintenance of the innate and adaptive immune systems, including for the normal development of peripheral T regulatory cells (Tregs) (32, 33). Imbalances, termed dysbioses, within gut commensal communities are common in patients with diverse inflammatory and autoimmune diseases (reviewed in (34)). In rheumatoid arthritis (RA), altered barrier function, due to impaired gut epithelial tight junctions, has been implicated in the transition from preclinical systemicautoimmunity to overt inflammatory joint disease (35, 36). Highly relevant, altered intestinal permeability has been documented in SLE patients, and their first-degree relatives (35, 36). The mechanisms by which dysbiosis drives disease, such as SLE and / or LN, should be studied.

[0008] Thus, there remains a need for methods for earlier and more accurate determinations of whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, as well as effective methods for treating a subject diagnosed with SLE or ILE, and methods of monitoring the effect of a treatment on development of a disorder in a subject, wherein the disorder is lupus nephritis or other forms of SLE with renal involvement or polyarthritis.SUMMARY OF THE INVENTION

[0009] As specified in the Background section above, there is a great need in the art for methods for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, as well as methods for treating a subject diagnosed with SLE or ILE, and methods of monitoring the effect of a treatment on development of a disorder in a subject, wherein the disorder is lupus nephritis or other forms of SLE with renal involvement or polyarthritis.

[0010] In one aspect, the invention provides a method for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, said method comprising: (a) determining in a sample collected from the subject the level of mRNA of two or more genes selected from integrin subunit alpha 2b (ITGA2B), multimerin 1 (MMRN1), ATP binding cassette subfamily C member 4 (ABCC4), dematin actin binding protein (DMTN), GATA binding protein 1 (GATA1), lymphocyte antigen 6 family member G6F (LY6G6F), myosin light chain 9 (MYL9), platelet factor 4 (PF4), protein S (PROS1), synuclein alpha (SNCA), secreted protein acidic and cysteinerich (SPARC), and PDGFA (platelet derived growth factor subunit A), wherein the sample comprises platelets, (b) comparing each of the mRNA levels determined in step (a) to a corresponding control mRNA level of said genes, and (c) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, when each of the mRNA levels determined in step (a) is at least 1.5-fold higher than the corresponding control mRNA level.

[0011] In some embodiments, step (a) comprises determining the mRNA levels of three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, or ten or more genes selected from ITGA2B, MMRN1, ABCC4, DMTN, GATA1, LY6G6F, MYL9, PF4, PROS1, SNCA, SPARC, and PDGFA, .

[0012] In some embodiments, step (a) comprises determining the mRNA levels of ITGA2B, MMRN1, ABCC4, DMTN, GATA1, LY6G6F, MYL9, PF4, PROS1, SNCA, SPARC, and PDGFA genes.

[0013] In some embodiments, the method further comprises: (d) determining in a sample collected from the subject the level of mRNA of two or more genes selected from interferon alpha inducible protein 27 (IFI27), interferon inducible protein 44 (IFI44), radical S-adenosyl methionine domain containing 2 (RSAD2), and interferon inducible protein 44 like (IFI44L); (e) comparing each of the mRNA levels determined in step (d) to a corresponding control mRNA level, and (f) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, when at least two of the mRNA levels determined in step (d) are statistically significantly lower than the corresponding mRNA levels in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

[0014] In some embodiments, step (d) comprises determining the mRNA levels of three or more genes selected from IFI27, IFI44, RSAD2, and IFI44L.

[0015] In some embodiments, step (d) comprises determining the mRNA levels of IFI27, IFI44, RSAD2, and IFI44L genes.

[0016] In some embodiments, the sample tested in all embodiments is the same sample. In some embodiments, the sample tested in all embodiments is the same type of sample.

[0017] In some embodiments, the control mRNA level for a given gene is (i) a predetermined standard, (ii) the mRNA level of said gene in a similarly prepared sample obtained from the same subject in the past, (iii) the mRNA level of said gene in a similarly prepared sample obtained from a healthy matched subject or a mean value of samples from several matched healthy subjects, or (iv) the mRNA level of said gene in a similarly prepared sample obtained from a subject, wherein said subject does not have a pre-existing diagnosis of lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such subjects.

[0018] In some embodiments, the predetermined standard is a value that represents a statistically validated threshold ratio of the mRNA levels of said gene equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

[0019] In some embodiments, the mRNA levels are determined by quantitative RT-PCR, nanostring technology, RNA sequencing, or representation in a bulk RNA library.

[0020] In some embodiments, the sample is whole blood, platelet-enriched plasma, or purified platelets.

[0021] In some embodiments, the method further comprises (1) determining in a blood sample collected from the subject the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments; (2) comparing the level of the protein(s) and / or NETosis fragments determined in step (1) to a control level of said protein(s) and / or of NETosis fragments, and (3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, when the level(s) of P-selectin protein, PF4 protein, and / or NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

[0022] In another aspect, the invention provides a method for determining whether a subject being evaluated for the diagnosis of systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject diagnosed with SLE or ILE, is at an increased risk for developing lupusnephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, said method comprising: (1) determining in a blood sample collected from the subject the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments; (2) comparing the level of the protein(s) and / or NETosis fragments determined in step (1) to a control level of said protein(s) and / or of NETosis fragments, and (3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, when the level(s) of P-selectin protein, of PF4 protein and / or NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

[0023] In some embodiments, step (1) comprises determining the level of both P-selectin protein, of PF4 protein, and / or NETosis fragments, and step (3) comprises determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, when the level(s) of P-selectin protein, of PF4 protein, and / or NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

[0024] In some embodiments, step (3) comprises determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, when the levels ofboth P-selectin protein and PF4 protein, and / or NETosis fragments determined in step (1) are statistically significantly higher than the corresponding control levels.

[0025] In some embodiments, the blood sample is whole blood, serum or plasma.

[0026] In some embodiments, the control protein level is (i) a predetermined standard, (ii) the level of said protein in a similarly prepared sample obtained from the same subject in the past, (iii) the level of said protein in a similarly prepared sample obtained from a healthy matched subject or a mean value of samples from several matched healthy subjects, or (iv) the level of said protein in a similarly prepared sample obtained from an SLE or ILE patient or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such patients.

[0027] In some embodiments, the control NETosis fragment level is (i) a predetermined standard, (ii) the level of said NETosis fragment in a similarly prepared sample obtained from the same subject in the past, (iii) the level of said NETosis fragment in a similarly prepared sample obtained from a healthy matched subject or a mean value of samples from several matched healthy subjects, or (iv) the level of said NETosis fragment in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such patients.

[0028] In some embodiments, the predetermined standard is a value which represents a statistically validated threshold ratio of the levels of said protein(s) and / or NETosis fragments equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

[0029] In some embodiments, the protein level is determined by an enzyme-linked immunosorbent assay (ELISA), radioimmunoassay, counterimmuno-electrophoresis (CIE), immunodiffusion, Western blotting, microscopy, or bead-based assays.

[0030] In some embodiments, the method further comprises (1) determining in a bodily fluid sample collected from the subject the level of antibodies that recognize a lipoglycan-containing antigen from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae or a derivative thereof; (2) comparing the level of the antibodies determined in step (1) to a control level of said antibodies, and (3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the level of the antibodies determined in step (1) is statistically significantly higher than the control level.

[0031] In some embodiments, the lipoglycan-containing antigen: (1) comprises a diacyl-glycerol ortriacyl-glycerol moiety and is not a capsular polysaccharide orteichoic acid, (2) has an estimated molecular weight based on Western blot between about 20,000 and about 30,000 Daltons, and (3) shares one or more antigenic determinants with or is the same as the lipoglycan-containing antigen obtained from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No:SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) using a method selected from:(i) Method 1 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) at 37°C under anaerobic conditions for 2-7 days, and b. producing bacterial extract in the presence of a lysozyme, Serratia marcescens endonuclease, Proteinase K, and a detergent under non-denaturing conditions;(ii) Method 2 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) in rich nutrient media at 37°C under anaerobic conditions (75% N2, 20% CO2, and 5% H2) for 2-7 days, b. pelleting bacteria by centrifugation, c. producing a bacterial extract in a protein extraction buffer in the presence of lysozyme, Serratia marcescens endonuclease, and a detergent under non-denaturing conditions, d. treating the extract obtained in step (c) with Proteinase K, e. incubating the treated extract obtained in step (d) at 55°C for about 10 minutes, f. removing cell debris by centrifugation, and g. using the supernatant as an antigen preparation; or(iii) Method 3 comprising the steps: a. disrupting strain CC55 001C, HM-1056 cells or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) cells with a French press, b. ultracentrifugation to obtain a precipitate and produce an ultracentrifugation supernatant, c. subjecting the ultracentrifugation supernatant obtained in step (b) to butanol -water extraction and isolating an aqueous phase, d. applying the aqueous phase from step (c) to a hydrophobic interaction chromatography matrix, and e. isolating lipoglycan-containing fractions.

[0032] In some embodiments, the level of antibodies is determined using an enzyme-linked immunosorbent assay (ELISA), radioimmunoassay, counterimmuno-electrophoresis (CIE), immunodiffusion, Western blotting, microscopy, or bead-based assays.

[0033] In some embodiments, the bodily fluid is selected from whole blood, plasma, serum, urine, and saliva.

[0034] In some embodiments, wherein the control level of said antibodies is (i) a predetermined standard, (ii) the level of said antibodies in a similarly prepared sample obtained from the same subject in the past, (iii) the level of said antibodies in a similarly prepared sample obtained from a healthy matched subject or a mean value of several matched healthy subjects, or (iv) the level of said antibodies in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such patients.

[0035] In some embodiments, the predetermined standard is a value which represents a statistically validated threshold ratio of the levels of said antibodies equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

[0036] In some embodiments, the method further comprises (1) determining in the gastrointestinal (GI) microbiota sample collected from the subject an abundance of bacteria from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or another strain from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae species that produces a lipoglycan- containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744); (2) comparing the abundance of bacteria determined in step (1) to a control abundance of said bacteria, and (3) determining that the subjectis at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, when the abundance of bacteria determined in step (1) is statistically significantly higher than the control abundance.

[0037] In some embodiments, the GI microbiota is of cecal, ileal, colonic, or fecal origin.

[0038] In some embodiments, the GI microbiota is fecal microbiota.

[0039] In some embodiments, the lipoglycan-containing antigen: (1) comprises a diacyl-glycerol or triacyl-glycerol moiety and is not a capsular polysaccharide or teichoic acid, (2) has an estimated molecular weight based on Western blot between about 20,000 and about 30,000 Daltons, and (3) shares one or more antigenic determinants with or is the same as the lipoglycan-containing antigen obtained from Blautia (Ruminococcus) gna s of the family Lachnospiraceae strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) using a method selected from:(i) Method 1 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) at 37°C under anaerobic conditions for 2-7 days, and b. producing bacterial extract in the presence of a lysozyme, Serratia marcescens endonuclease, Proteinase K, and a detergent under non-denaturing conditions;(ii) Method 2 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) in rich nutrient media at 37°C under anaerobic conditions (75% N2, 20% CO2, and 5% H2) for 2-7 days, b. pelleting bacteria by centrifugation, c. producing a bacterial extract in a protein extraction buffer in the presence of lysozyme, Serratia marcescens endonuclease, and a detergent under non-denaturing conditions, d. treating the extract obtained in step (c) with Proteinase K, e. incubating the treated extract obtained in step (d) at 55°C for about 10 minutes,f. removing cell debris by centrifugation, and g. using the supernatant as an antigen preparation; or(iii) Method 3 comprising the steps: a. disrupting strain CC55_001C, HM-1056 cells or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) cells with a French press, b. ultracentrifugating to obtain a precipitate and produce an ultracentrifugation supernatant, c. subjecting the ultracentrifugation supernatant obtained in step (b) to butanol-water extraction and isolating an aqueous phase, d. applying the aqueous phase from step (c) to a hydrophobic interaction chromatography matrix, and e. isolating lipoglycan-containing fractions.

[0040] In some embodiments, the control abundance of said bacteria is (i) a predetermined standard, (ii) the abundance of said bacteria in a similarly prepared sample obtained from the same subject in the past, (iii) the abundance of said bacteria in a similarly prepared sample obtained from a matched healthy subject or a mean value of several matched healthy subjects, or (iv) the abundance of said bacteria in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such patients.

[0041] In some embodiments, the predetermined standard is a value which represents a statistically validated threshold ratio of the abundance of said bacteria equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

[0042] In some embodiments, the lupus nephritis is proliferative lupus nephritis, membranous lupus nephritis, membranoproliferative lupus nephritis, or mesangial glomerulonephritis.

[0043] In some embodiments, the subject has been diagnosed with SLE or ILE in part by determining a decreased serum level of one or more complement components selected from Clq, C3, C4, and CH50, and / or an elevated level of C-reactive protein (CRP).

[0044] In some embodiments, the subject has been diagnosed with SLE or ILE in part by determining an elevation of the erythrocyte sedimentation rate (ESR).

[0045] In some embodiments, the subject has been diagnosed with SLE or ILE in part by determining a level of anti-nuclear antibodies (ANA) including those which recognize doublestranded DNA (dsDNA), or Smith antigen (Sm).

[0046] In some embodiments, the method further comprises conducting an assessment of the subject by determining one or more parameters selected from gut permeability, SLE Disease Activity Index (SLED Al), SLED Al modified by the Safety of Estrogens in Lupus Erythematosus National Assessment trial (SELENA- SLED Al), British Isles Lupus Activity Group (BILAG) assessment, the SLAM index, American College of Rheumatology (ACR) SLE classification criteria, and Systemic Lupus Collaborating Clinics (SLICC) criteria.

[0047] In some embodiments, the method further comprises a kidney biopsy assessment or urinalysis in the subject determined to be at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement.

[0048] In some embodiments, the urinalysis comprises determining the level of protein and / or red blood cells in the urine, and wherein the increased level of protein or red blood cells as compared to a relevant control is indicative of a kidney disease.

[0049] In some embodiments, the method further comprises recruiting the subject in a clinical trial.

[0050] In some embodiments, the method further comprises administering to the subject determined to be at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, an inhibitor of platelet activation, an inhibitor of platelet aggregation, an inhibitor of platelet adhesion, or any combinations thereof.

[0051] In some embodiments, the method further comprises administering to the subject determined to be at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, a cyclooxygenase- 1 inhibitor, a phosphodiesterase (PDE) inhibitor, an adenosine reuptake inhibitor, a Glycoprotein Ilb / IIIa (GpIIb / IIIa) receptor antagonist, an adenosine diphosphate (ADP) receptor inhibitor, caplacizumab, or any combinations thereof.

[0052] In some embodiments, the cyclooxygenase- 1 inhibitor is aspirin, masoprocol, indomethacin, nabumetone, celecoxib, tolimetin, rofecoxib, piroxicam, fenoprofen, valdecoxib, diclofenac, or etoricoxib.

[0053] In some embodiments, the PDE inhibitor is a PDE 3 inhibitor, PDE 4 inhibitor, PDE 5 inhibitor, or non-specific PDE inhibitor.

[0054] In some embodiments, the PDE 3 inhibitor is cilostazol, dipyridamole, milrinone, or amrinone.

[0055] In some embodiments, the PDE4 inhibitor is roflumilast, apremilast, or crisaborole.

[0056] In some embodiments, the PDE5 inhibitor is sildenafil, tadalafil, vardenafil, or avanafil.

[0057] In some embodiments, the non-specific PDE inhibitor is theophylline or ibudilast.

[0058] In some embodiments, the adenosine reuptake inhibitor is dipyridamole.

[0059] In some embodiments, the GpIIb / IIIa receptor antagonist is abciximab, eptifibatide, or tirofiban.

[0060] In some embodiments, the ADP receptor inhibitor is ticlopidine, clopidogrel, prasugrel, ticagrelor, or cangrelor.

[0061] In some embodiments, the method further comprises administering to the subject determined to be at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, a treatment directed to eliminating or inhibiting or reducing the level of neutrophil extracellular traps (NETs).

[0062] In some embodiments, the treatment directed to eliminating or inhibiting NETs comprises administering to the subject protease inhibitors, Deoxyribonuclease (DNase), peptidyl arginine deiminase 4 (PAD4) inhibitors, neutrophilic elastase inhibitors, myeloperoxidase (MPO) inhibitors, N-a-benzoyl-N5-(2-chloro-l-iminoethyl)-L-ornithine amide (Cl-amidine), Diphenyleneiodonium chloride, disulfiram, NADPH oxidase 2 (N0X2) inhibitor (e.g., GSK2795039), agents that aid clearance of NETosis product, or any combination thereof.

[0063] In some embodiments, the method further comprises administering to the subject determined to be at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, a treatment normalizing the functional level of permeability of the intestinal barrier and / or normalizing the composition of the intestinal microbial community.

[0064] In some embodiments, the method further comprises administering to the subject determined to be at an increased risk for developing lupus nephritis or other forms of SLE withrenal involvement, or polyarthritis, a treatment which (i) results in a decrease in the level in bodily fluid(s) of the subject of a lipogly can-containing antigen produced by Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55_001C, HM-1056 or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or a lipoglycan-containing antigen which shares one or more antigenic determinants of said lipoglycan-containing antigen, or (ii) results in a decrease in the level in bodily fluid(s) of the subject of the antibodies which recognize said lipoglycan-containing antigen, or (iii) results in a decrease in GI microbiota of the subject of an abundance of bacteria from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or another strain from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae species that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744).

[0065] In some embodiments, the treatment comprises administering an antibiotic and / or probiotic and / or prebiotic and / or bacteriophage which inhibits growth or activity of said bacteria within the GI microbiota community of the subject in one approach with an antibody or antigenbinding fragment thereof, wherein said antibody or antigen-binding fragment thereof binds to a lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or a lipoglycan-containing antigen which shares one or more antigenic determinants of said lipoglycan-containing antigen, or binds to antibodies which recognize said lipoglycan-containing antigen.

[0066] In some embodiments, the probiotic comprises one or more strains from non-pathogenic Blautia (Ruminococcus) gnavus species, and / or species Faecalibacterium prausnitzii, and / or species Bacteroides uniformis, and / or genus Lactobacillus .

[0067] In some embodiments, the method further comprises administering to the subject determined to be at an increased risk for developing lupus nephritis or other forms of SLE withrenal involvement, or polyarthritis, a compound selected from hydroxychloroquine, a glucocorticosteroid, an immunosuppressive agent, a calcineurin inhibitor, a pyrimidine synthesis inhibitor, belimumab, anifrolumab, and any combinations thereof.

[0068] In some embodiments, the glucocorticosteroid is prednisone or methylprednisolone.

[0069] In some embodiments, the immunosuppressive agent is cyclophosphamide, azathioprine, my cophenolate mofetil, cyclosporine, or chlorambucil.

[0070] In some embodiments, the calcineurin inhibitor is tacrolimus or voclosporin.

[0071] In some embodiments, the pyrimidine synthesis inhibitor is leflunomide.

[0072] In another aspect, the invention provides a method of treating a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), said method comprising: (a) determining in a sample collected from the subject the level of mRNA of two or more genes selected from integrin subunit alpha 2b (ITGA2B), multimerin 1 (MMRN1), ATP binding cassette subfamily C member 4 (ABCC4), dematin actin binding protein (DMTN), GATA binding protein 1 (GATA1), lymphocyte antigen 6 family member G6F (LY6G6F), myosin light chain 9 (MYL9), platelet factor 4 (PF4), protein S (PROS1), synuclein alpha (SNCA), secreted protein acidic and cysteine rich (SPARC), and PDGFA (platelet derived growth factor subunit A), wherein the sample comprises platelets, (b) comparing each of the mRNA levels determined in step (a) to a corresponding control mRNA level, and (c) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when each of the mRNA levels determined in step (a) is at least 1 .5-fold higher than the corresponding control mRNA level.

[0073] In some embodiments, step (a) comprises determining the mRNA levels of three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, or ten or more genes selected from ITGA2B, MMRN1, ABCC4, DMTN, GATA1, LY6G6F, MYL9, PF4, PROS1, SNCA, SPARC, and PDGFA.

[0074] In some embodiments, step (a) comprises determining the mRNA levels of ITGA2B, MMRN1, ABCC4, DMTN, GATA1, LY6G6F, MYL9, PF4, PROS1, SNCA, SPARC, and PDGFA genes.

[0075] In some embodiments, the method further comprises: (d) determining in a sample collected from the subject the mRNA level of two or more genes selected from interferon alpha inducible protein 27 (IFI27), interferon inducible protein 44 (IFI44), radical S-adenosylmethionine domain containing 2 (RSAD2), and interferon inducible protein 44 like (IFI44L); (e) comparing each of the mRNA levels determined in step (d) to a corresponding control mRNA level, and (f) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when at least two of the mRNA levels determined in step (d) are statistically significantly lower than the corresponding mRNA levels in a similarly prepared sample obtained from an SLE or ILE patient or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

[0076] In some embodiments, step (d) comprises determining the mRNA levels of three or more genes selected from IFI27, IFI44, RSAD2, and IFI44L.

[0077] In some embodiments, step (d) comprises determining the mRNA levels of IFI27, IFI44, RSAD2, and IFI44L genes.

[0078] In some embodiments, the sample tested in all embodiments is the same sample. In some embodiments, the sample tested in all embodiments is the same type of sample.

[0079] In some embodiments, the control mRNA level for a given gene is (i) a predetermined standard, (ii) the mRNA level of said gene in a similarly prepared sample obtained from the same subject in the past, (iii) the mRNA level of said gene in a similarly prepared sample obtained from a healthy matched subject or a mean value of samples from several matched healthy subjects, or (iv) the mRNA level of said gene in a similarly prepared sample obtained from a subject, wherein said subject does not have a pre-existing diagnosis of lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such subjects.

[0080] In some embodiments, the predetermined standard is a value which represents a statistically validated threshold ratio of the mRNA levels of said gene equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

[0081] In some embodiments, the mRNA levels are determined by quantitative RT-PCR, nanostring technology, RNA sequencing, or representation in a bulk RNA library made from said sample.

[0082] In some embodiments, the sample is whole blood, platelet-enriched plasma, or purified platelets.

[0083] In some embodiments, the method further comprises: (1) determining in a blood sample collected from the subject the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments; (2) comparing the level of the protein(s) and / or of NETosis fragments determined in step (1) to a control level of said protein(s) and / or said NETosis fragments, and (3) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

[0084] In an aspect, the invention provides a method of treating a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), said method comprising: (1) determining in a blood sample collected from the subject the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments; (2) comparing the level of the protein(s) and / or of the NETosis fragments determined in step (1) to a control level of said protein(s) and / or of said NETosis fragments, and (3) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

[0085] In some embodiments, step (1) comprises determining the level of P-selectin protein and PF4 protein, and / or of NETosis fragments, and step (3) comprises administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

[0086] In some embodiments, step (3) comprises administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the levels of P-selectin protein and PF4 protein, and / or of NETosis fragments determined in step (1) are statistically significantly higher than the corresponding control levels.

[0087] In some embodiments, the blood sample is whole blood, serum or plasma.

[0088] In some embodiments, the control protein level is (i) a predetermined standard, (ii) the level of said protein in a similarly prepared sample obtained from the same subject in the past, (iii) the level of said protein in a similarly prepared sample obtained from a healthy matched subject or a mean value of samples from several matched healthy subjects, or (iv) the level of said protein in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such patients.

[0089] In some embodiments, the control NETosis fragment level is (i) a predetermined standard, (ii) the level of said NETosis fragments in a similarly prepared sample obtained from the same subject in the past, (iii) the level of said NETosis fragments in a similarly prepared sample obtained from a healthy matched subject or a mean value of samples from several matched healthy subjects, or (iv) the level of said NETosis fragments in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such patients.

[0090] In some embodiments, the predetermined standard is a value which represents a statistically validated threshold ratio of the levels of said protein and / or NETosis fragments equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement, polyarthritis.

[0091] In some embodiments, the protein level is determined by an enzyme-linked immunosorbent assay (ELISA), radioimmunoassay, counterimmuno-electrophoresis (CIE), immunodiffusion, Western blotting, microscopy, or bead-based assays.

[0092] In some embodiments, the method further comprises: (1) determining in a bodily fluid sample collected from the subject the level of antibodies that recognize a lipoglycan-containing antigen from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae or a derivative thereof; (2) comparing the level of the antibodies determined in step (1) to a control level of said antibodies, and (3) administering to the subject a treatment effective for treating or preventinglupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the level of the antibodies determined in step (1) is statistically significantly higher than the control level.

[0093] In some embodiments, (1) comprises a diacyl-glycerol or triacyl-glycerol moiety and is not a capsular polysaccharide or teichoic acid, (2) has an estimated molecular weight based on Western blot between about 20,000 and about 30,000 Daltons, and (3) shares one or more antigenic determinants with or is the same as the lipoglycan-containing antigen obtained from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) using a method selected from:(i) Method 1 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) at 37°C under anaerobic conditions for 2-7 days, and b. producing bacterial extract in the presence of a lysozyme, Serratia marcescens endonuclease, Proteinase K, and a detergent under non-denaturing conditions;(ii) Method 2 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) in rich nutrient media at 37°C under anaerobic conditions (75% N2, 20% CO2, and 5% H2) for 2-7 days, b. pelleting bacteria by centrifugation, c. producing a bacterial extract in a protein extraction buffer in the presence of lysozyme, Serratia marcescens endonuclease, and a detergent under non-denaturing conditions, d. treating the extract obtained in step (c) with Proteinase K, e. incubating the treated extract obtained in step (d) at 55°C for about 10 minutes, f. removing cell debris by centrifugation, and g. using the supernatant as an antigen preparation; or(iii) Method 3 comprising the steps:a. disrupting strain CC55_001 C, HM-1056 cells or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) with a French press, b. ultracentrifugating to obtain a precipitate and produce an ultracentrifugation supernatant, c. subjecting the ultracentrifugation supernatant obtained in step (b) to butanol -water extraction and isolating an aqueous phase, d. applying the aqueous phase from step (c) to a hydrophobic interaction chromatography matrix, and e. isolating lipoglycan-containing fractions.

[0094] In some embodiments, the level of antibodies is determined using an enzyme-linked immunosorbent assay (ELISA), radioimmunoassay, counterimmuno-electrophoresis (CIE), immunodiffusion, Western blotting, microscopy, or bead-based assays.

[0095] In some embodiments, the bodily fluid is selected from whole blood, plasma, serum, urine, and saliva.

[0096] In some embodiments, the control level of said antibodies is (i) a predetermined standard, (ii) the level of said antibodies in a similarly prepared sample obtained from the same subject in the past, (iii) the level of said antibodies in a similarly prepared sample obtained from a healthy matched subject or a mean value of several matched healthy subjects, or (iv) the level of said antibodies in a similarly prepared sample obtained from an SLE or ILE patient, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such patients.

[0097] In some embodiments, the predetermined standard is a value which represents a statistically validated threshold ratio of the levels of said antibodies equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

[0098] In some embodiments, the method further comprises: (1) determining in the gastrointestinal (GI) microbiota sample collected from the subject an abundance of bacteria from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056(Human Microbiome Project (HMP) ID 1201 ; GenBank: AZJF00000000) or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or another strain from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae species that produces a lipoglycan- containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744); (2) comparing the abundance of bacteria determined in step (1) to a control abundance of said bacteria, and (3) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the abundance of bacteria determined in step (1) is statistically significantly higher than the control abundance.

[0099] In some embodiments, the GI microbiota is of cecal, ileal, colonic, or fecal origin.

[0100] In some embodiments, the GI microbiota is fecal microbiota.

[0101] In some embodiments, the lipoglycan-containing antigen: comprises a diacyl-glycerol or triacyl-glycerol moiety and is not a capsular polysaccharide or teichoic acid, (2) has an estimated molecular weight based on Western blot between about 20,000 and about 30,000 Daltons, and (3) shares one or more antigenic determinants with or is the same as the lipoglycan-containing antigen obtained from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) using a method selected from:(i) Method 1 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) at 37°C under anaerobic conditions for 2-7 days, and b. producing bacterial extract in the presence of a lysozyme, Serratia marcescens endonuclease, Proteinase K, and a detergent under non-denaturing conditions;(ii) Method 2 comprising the steps:a. culturing strain CC55_001C, HM-1056 or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) in rich nutrient media at 37°C under anaerobic conditions (75% N2, 20% CO2, and 5% H2) for 2-7 days, b. pelleting bacteria by centrifugation, c. producing a bacterial extract in a protein extraction buffer in the presence of lysozyme, Serratia marcescens endonuclease, and a detergent under non-denaturing conditions, d. treating the extract obtained in step (c) with Proteinase K, e. incubating the treated extract obtained in step (d) at 55°C for about 10 minutes, f. removing cell debris by centrifugation, and g. using the supernatant as an antigen preparation; or(iii) Method 3 comprising the steps: a. disrupting strain CC55_001C, HM-1056 cells or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) cells with a French press, b. ultracentrifugating to obtain a precipitate and produce an ultracentrifugation supernatant, c. subjecting the ultracentrifugation supernatant obtained in step (b) to butanol -water extraction and isolating an aqueous phase, d. applying the aqueous phase from step (c) to a hydrophobic interaction chromatography matrix, and e. isolating lipoglycan-containing fractions.

[0102] In some embodiments, the control abundance of said bacteria is (i) a predetermined standard, (ii) the abundance of said bacteria in a similarly prepared sample obtained from the same subject in the past, (iii) the abundance of said bacteria in a similarly prepared sample obtained from a matched healthy subject or a mean value of several matched healthy subjects, or (iv) the abundance of said bacteria in a similarly prepared sample obtained from an SLE or ILE patient or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such patients.

[0103] In some embodiments, the predetermined standard is a value which represents a statistically validated threshold ratio of the abundance of said bacteria equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

[0104] In some embodiments, the lupus nephritis is proliferative lupus nephritis, membranous lupus nephritis, membranoproliferative lupus nephritis, or mesangial glomerulonephritis.

[0105] In some embodiments, the subject has been diagnosed with SLE or ILE in part by determining a decreased serum level of one or more complement components selected from Clq, C3, C4, and CH50, and / or an elevated level of C-reactive protein (CRP).

[0106] In some embodiments, the subject has been diagnosed with SLE or ILE in part by determining an elevation of the erythrocyte sedimentation rate (ESR).

[0107] In some embodiments, the subject has been diagnosed with SLE or ILE in part by determining a level of anti-nuclear antibodies (ANA) including those which recognize doublestranded DNA (dsDNA), or Smith antigen (Sm).

[0108] In some embodiments, the method further comprises conducting an assessment of the subject by determining one or more parameters selected from gut permeability, SLE Disease Activity Index (SLED Al), SLED Al modified by the Safety of Estrogens in Lupus Erythematosus National Assessment trial (SELENA-SLEDAI), British Isles Lupus Activity Group (BILAG) assessment, the SLAM index, American College of Rheumatology (ACR) SLE classification criteria, and Systemic Lupus Collaborating Clinics (SLICC) criteria.

[0109] In some embodiments, the method further comprises a kidney biopsy assessment or urinalysis in the subject.

[0110] In some embodiments, the urinalysis comprises determining the level of protein and / or red blood cells in the urine, and wherein the increased level of protein or red blood cells as compared to a relevant control is indicative of a kidney disease.

[0111] In some embodiments, the method further comprises recruiting the subject in a clinical trial.

[0112] In some embodiments, the treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis comprises administering to thesubject an inhibitor of platelet activation, an inhibitor of platelet aggregation, an inhibitor of platelet adhesion, or any combinations thereof.

[0113] In some embodiments, the treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis comprises administering to the subject a cyclooxygenase- 1 inhibitor, a phosphodiesterase (PDE) inhibitor, an adenosine reuptake inhibitor, a Glycoprotein Ilb / IIIa (GpIIb / IIIa) receptor antagonist, an adenosine diphosphate (ADP) receptor inhibitor, caplacizumab, or any combinations thereof.

[0114] In some embodiments, the cyclooxygenase- 1 inhibitor is aspirin, masoprocol, indomethacin, nabumetone, celecoxib, tolimetin, rofecoxib, piroxicam, fenoprofen, valdecoxib, diclofenac, or etoricoxib.

[0115] In some embodiments, the PDE inhibitor is a PDE 3 inhibitor, PDE 4 inhibitor, PDE 5 inhibitor, or non-specific PDE inhibitor.

[0116] In some embodiments, the PDE 3 inhibitor is cilostazol, dipyridamole, milrinone, or amrinone.

[0117] In some embodiments, the PDE4 inhibitor is roflumilast, apremilast, or crisaborole.

[0118] In some embodiments, the PDE5 inhibitor is sildenafil, tadalafil, vardenafil, or avanafil.

[0119] In some embodiments, the non-specific PDE inhibitor is theophylline or ibudilast.

[0120] In some embodiments, the adenosine reuptake inhibitor is dipyridamole.

[0121] In some embodiments, the GpIIb / IIIa receptor antagonist is abciximab, eptifibatide, or tirofiban.

[0122] In some embodiments, the ADP receptor inhibitor is ticlopidine, clopidogrel, prasugrel, ticagrelor, or cangrelor.

[0123] In some embodiments, the treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis comprises administering to the subject a treatment directed to eliminating or inhibiting neutrophil extracellular traps (NETs).

[0124] In some embodiments, the treatment directed to eliminating or inhibiting NETs comprises administering to the subject protease inhibitors, Deoxyribonuclease (DNase), peptidyl arginine deiminase 4 (PAD4) inhibitors, neutrophilic elastase inhibitors, myeloperoxidase (MPO) inhibitors, N-a-benzoyl-N5-(2-chloro-l-iminoethyl)-L-ornithine amide (Cl-amidine), Diphenyleneiodonium chloride, disulfiram, NADPH oxidase 2 (N0X2) inhibitor (e.g., GSK2795039), agents that aid clearance of NETosis products, or any combination thereof.

[0125] In some embodiments, the treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis comprises administering to the subject a treatment normalizing the functional level of permeability of the intestinal barrier and / or normalizing the composition of the intestinal microbial community.

[0126] In some embodiments, the treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis comprises administering to the subject a treatment which (i) results in a decrease in the level in bodily fluid(s) of the subject of a lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or a lipoglycan-containing antigen which shares one or more antigenic determinants of said lipoglycan-containing antigen, or (ii) results in a decrease in bodily fluid(s) of the subject in the level of the antibodies which recognize said lipoglycan-containing antigen or (iii) results in a decrease in GI microbiota of the subject of an abundance of bacteria from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM- 1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or another strain from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae species that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744).

[0127] In some embodiments, the treatment comprises administering an antibiotic and / or probiotic and / or prebiotic and / or bacteriophage which inhibits growth or activity of said bacteria within the GI microbiota community of the subject in one approach with an antibody or antigenbinding fragment thereof, wherein said antibody or antigen-binding fragment thereof binds to a lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or a lipoglycan-containing antigen which shares one or moreantigenic determinants of said lipoglycan-containing antigen, or binds to antibodies which recognize said lipoglycan-containing antigen.

[0128] In some embodiments, the probiotic comprises one or more strains from non-pathogenic Blautia (Ruminococcus) gnavus species, and / or species Faecalibacterium prausnitzii, and / or species Bacteroides uniformis, and / or genus Lactobacillus.

[0129] In some embodiments, the treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis comprises administering to the subject a compound selected from hydroxychloroquine, a glucocorticosteroid, an immunosuppressive agent, a calcineurin inhibitor, a pyrimidine synthesis inhibitor, belimumab, anifrolumab, and any combinations thereof.

[0130] In some embodiments, the glucocorticosteroid is prednisone or methylprednisolone.

[0131] In some embodiments, the immunosuppressive agent is cyclophosphamide, azathioprine, my cophenolate mofetil, cyclosporine, or chlorambucil.

[0132] In some embodiments, the calcineurin inhibitor is tacrolimus or voclosporin.

[0133] In some embodiments, the pyrimidine synthesis inhibitor is leflunomide.

[0134] In an aspect, the invention provides a method for monitoring the effect of a treatment on development of a disorder in a subject, wherein the disorder is lupus nephritis or other forms of systemic lupus erythematosus (SLE) with renal involvement, or polyarthritis, which method comprises: (a) determining in a sample collected from the subject prior to initiation of the treatment the level of mRNA of two or more genes selected from integrin subunit alpha 2b (ITGA2B), multimerin 1 (MMRN1), ATP binding cassette subfamily C member 4 (ABCC4), dematin actin binding protein (DMTN), GATA binding protein 1 (GATA1), lymphocyte antigen 6 family member G6F (LY6G6F), myosin light chain 9 (MYL9), platelet factor 4 (PF4), protein S (PROS1), synuclein alpha (SNCA), secreted protein acidic and cysteine rich (SPARC), and PDGFA (platelet derived growth factor subunit A), wherein the sample comprises platelets, (b) determining the mRNA levels of said two or more genes in the same type of sample collected from the subject in the course of or following the treatment, (c) comparing the mRNA levels determined in steps (a) and (b), and (d) (i) determining that the treatment is effective for said disorder if each of the mRNA levels determined in step (b) is not statistically significantly higher than the corresponding mRNA level determined in step (a), or (ii) determining that the treatment is not effective for said disorderif at least one mRNA expression level determined in step (b) is at least 1.5-fold higher than the corresponding mRNA level determined in step (a).

[0135] In some embodiments, step (a) comprises determining the mRNA levels of three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, or ten or more genes selected from ITGA2B, MMRN1, ABCC4, DMTN, GATA1, LY6G6F, MYL9, PF4, PROS1, SNCA, SPARC, and PDGFA.

[0136] In some embodiments, step (a) comprises determining the mRNA levels of ITGA2B, MMRN1, ABCC4, DMTN, GATA1, LY6G6F, MYL9, PF4, PROS1, SNCA, SPARC, and PDGFA genes.

[0137] In some embodiments, the method further comprises: (e) determining in a sample collected from the subject prior to initiation of the treatment the level of mRNA of two or more genes selected from interferon alpha inducible protein 27 (IFI27), interferon inducible protein 44 (IFI44), radical S-adenosyl methionine domain containing 2 (RSAD2), and interferon inducible protein 44 like (IFI44L); (f) determining the mRNA levels of said two or more genes in the same type of sample collected from the subject in the course of or following the treatment; (g) comparing the mRNA levels determined in steps (e) and (f), and (h) (1) determining that the treatment is effective for said disorder if the mRNA levels determined in step (e) are not statistically significantly lower for more than one mRNA as compared to the corresponding mRNA levels determined in step (f), or (2) determining that the treatment is not effective for said disorder if the mRNA levels determined in step (e) are statistically significantly lower for more than one mRNA as compared to the corresponding mRNA levels determined in step (f).

[0138] In some embodiments, step (e) comprises determining the mRNA levels of three or more genes selected from IFI27, IFI44, RSAD2, and IFI44L.

[0139] In some embodiments, step (e) comprises determining the mRNA levels of IFI27, IFI44, RSAD2, and IFI44L genes.

[0140] In some embodiments, the samples tested in all embodiments are the same sample. In some embodiments, the samples tested in all embodiments are the same type of sample.

[0141] In some embodiments, the mRNA levels are determined by quantitative RT-PCR, nanostring technology, RNA sequencing, or representation in a bulk RNA library made from said sample.

[0142] In some embodiments, the sample is whole blood, platelet-enriched plasma, or purified platelets.

[0143] In some embodiments, the method further comprises: (1) determining in a blood sample collected from the subject prior to initiation of the treatment the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments; (2) determining the level of P-selectin protein, PF4 protein, and / or of NETosis fragments in the same type of sample collected from the subject in the course of or following the treatment; (3) comparing the protein levels and / or the levels of NETosis fragments determined in steps (1) and (2), and (4) (i) determining that the treatment is effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is not statistically significantly higher than the corresponding level(s) determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is statistically significantly higher than the corresponding level(s) determined in step (1).

[0144] In an aspect, the invention provides a method for monitoring the effect of a treatment on development of a disorder in a subject, wherein the disorder is lupus nephritis or other forms of systemic lupus erythematosus (SLE) with renal involvement, or polyarthritis, which method comprises: (1) determining in a blood sample collected from the subject prior to initiation of the treatment the level of P-selectin protein, of platelet factor 4 (PF4) protein and / or of NETosis fragments; (2) determining the level of P-selectin protein, of PF4 protein, and / or of NETosis fragments in the same type of sample collected from the subject in the course of or following the treatment; (3) comparing the protein levels and / or the levels of NETosis fragments determined in steps (1) and (2), and (4) (i) determining that the treatment is effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is not statistically significantly higher than the corresponding level(s) determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is statistically significantly higher than the corresponding level(s) determined in step (1).

[0145] In some embodiments, steps (1) and (2) comprise determining the level of P-selectin protein, of PF4 protein, and / or of NETosis fragments, and step (4) comprises (i) determining that the treatment is effective for said disorder if the level(s) of P-selectin protein, of PF4 protein,and / or of NETosis fragments determined in step (2) is not statistically significantly higher than the corresponding level(s) determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is statistically significantly higher than the corresponding level(s) determined in step (1).

[0146] In some embodiments, step (4) comprises (i) determining that the treatment is effective for said disorder if the levels of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) are not statistically significantly higher than the corresponding levels determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the levels of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) are statistically significantly higher than the corresponding levels determined in step (1).

[0147] In some embodiments, the blood sample is whole blood, serum or plasma.

[0148] In some embodiments, the protein level is determined by an enzyme-linked immunosorbent assay (ELISA), radioimmunoassay, counterimmuno-electrophoresis (CIE), immunodiffusion, Western blotting, microscopy, or bead-based assays.

[0149] In some embodiments, the method further comprises: (1) determining in a bodily fluid sample collected from the subject prior to initiation of the treatment the level of antibodies that recognize a lipoglycan-containing antigen from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae or a derivative thereof; (2) determining the level of said antibodies in the same type of sample collected from the subject in the course of or following the treatment; (3) comparing the antibody levels determined in steps (1) and (2), and (4) (i) determining that the treatment is effective for said disorder if the level of antibodies determined in step (2) is not statistically significantly higher than the level of antibodies determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level of antibodies determined in step (2) is statistically significantly higher than the level of antibodies determined in step (1).

[0150] In some embodiments, the lipoglycan-containing antigen: (1) comprises a diacyl-glycerol or triacyl-glycerol moiety and is not a capsular polysaccharide or teichoic acid, (2) has an estimated molecular weight based on Western blot between about 20,000 and about 30,000 Daltons, and (3) shares one or more antigenic determinants with or is the same as the lipoglycan-containing antigen obtained from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strainSI 07-48 (NCBI SRA Accession No: SRX 14861748) or SI 07-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) using a method selected from:(i) Method 1 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) at 37°C under anaerobic conditions for 2-7 days, and b. producing bacterial extract in the presence of a lysozyme, Serratia marcescens endonuclease, Proteinase K, and a detergent under non-denaturing conditions;(ii) Method 2 comprising the steps: a. culturing strain CC55 001C, HM-1056 or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) in rich nutrient media at 37°C under anaerobic conditions (75% N2, 20% CO2, and 5% H2) for 2-7 days, b. pelleting bacteria by centrifugation, c. producing a bacterial extract in a protein extraction buffer in the presence of lysozyme, Serratia marcescens endonuclease, and a detergent under non-denaturing conditions, d. treating the extract obtained in step (c) with Proteinase K, e. incubating the treated extract obtained in step (d) at 55°C for about 10 minutes, f. removing cell debris by centrifugation, and g. using the supernatant as an antigen preparation; or(iii) Method 3 comprising the steps: a. disrupting strain CC55_001C, HM-1056 cells or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) cells with a French press, b. ultracentrifugating to obtain a precipitate and produce an ultracentrifugation supernatant, c. subjecting the ultracentrifugation supernatant obtained in step (b) to butanol-water extraction and isolating an aqueous phase, d. applying the aqueous phase from step (c) to a hydrophobic interaction chromatography matrix, ande. isolating lipoglycan-containing fractions.

[0151] In some embodiments, the level of antibodies is determined using an enzyme-linked immunosorbent assay (ELISA), radioimmunoassay, counterimmuno-electrophoresis (CIE), immunodiffusion, Western blotting, microscopy, or bead-based assays.

[0152] In some embodiments, the bodily fluid is selected from whole blood, plasma, serum, urine, and saliva.

[0153] In some embodiments, the method further comprises (1) determining in the gastrointestinal (GI) microbiota sample collected from the subject prior to initiation of the treatment an abundance of bacteria from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107- 86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or another strain from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae species that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744); (2) determining the abundance of said bacteria in the same type of sample collected from the subject in the course of or following the treatment; (3) comparing the abundance of bacteria determined in steps (1) and (2), and (4) (i) determining that the treatment is effective for said disorder if the abundance of bacteria determined in step (2) is not statistically significantly higher than the abundance of said bacteria determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the abundance of bacteria determined in step (2) is statistically significantly higher than the abundance of said bacteria determined in step (1).

[0154] In some embodiments, the GI microbiota is of cecal, ileal, colonic, or fecal origin.

[0155] In some embodiments, the GI microbiota is fecal microbiota.

[0156] In some embodiments, the lipoglycan-containing antigen: (1) comprises a diacyl-glycerol or triacyl-glycerol moiety and is not a capsular polysaccharide or teichoic acid, (2) has an estimated molecular weight based on Western blot between about 20,000 and about 30,000 Daltons, and (3)shares one or more antigenic determinants with oris the same as the lipoglycan-containing antigen obtained from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) using a method selected from:(i) Method 1 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) at 37°C under anaerobic conditions for 2-7 days, and b. producing bacterial extract in the presence of a lysozyme, Serratia marcescens endonuclease, Proteinase K, and a detergent under non-denaturing conditions;(ii) Method 2 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) in rich nutrient media at 37°C under anaerobic conditions (75% N2, 20% CO2, and 5% H2) for 2-7 days, b. pelleting bacteria by centrifugation, c. producing a bacterial extract in a protein extraction buffer in the presence of lysozyme, Serratia marcescens endonuclease, and a detergent under non-denaturing conditions, d. treating the extract obtained in step (c) with Proteinase K, e. incubating the treated extract obtained in step (d) at 55°C for about 10 minutes, f. removing cell debris by centrifugation, and g. using the supernatant as an antigen preparation; or(iii) Method 3 comprising the steps: a. disrupting strain CC55 001C, HM-1056 cells or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) cells with a French press, b. ultracentrifugating to obtain a precipitate and produce an ultracentrifugation supernatant,c. subjecting the ultracentrifugation supernatant obtained in step (b) to butanol-water extraction and isolating an aqueous phase, d. applying the aqueous phase from step (c) to a hydrophobic interaction chromatography matrix, and e. isolating lipoglycan-containing fractions.

[0157] In some embodiments, lupus nephritis is proliferative lupus nephritis, membranous lupus nephritis, membranoproliferative lupus nephritis, or mesangial glomerulonephritis.

[0158] In some embodiments, the subject is human. In some embodiments, the subject is a veterinary animal.

[0159] These and other aspects of the present invention will be apparent to those of ordinary skill in the art in the following description, claims, and drawings.BRIEF DESCRIPTION OF THE DRAWINGS

[0160] Figures 1A-1D. Dysbiosis and longitudinal instability in SLE microbiota communities compared to healthy individuals. (Fig. 1A) Principal Coordinates Analysis (PCoA) was used to estimate b-diversity between groups using the Jensen-Shannon divergence (JSD) dissimilarity metric. Commensal communities from SLE patients were heterogenous, with most exhibiting significant distance variance from CTL (by multivariate distance Welch Wd* test, 2?=0.001 ). (Fig. IB) Compared to CTL, variance in diversity was greatest within the SLED Al high subgroup, and (Fig. 1C) the subset with active renal disease. (Fig. ID) To compare the overall dynamics of shifts in fecal communities sampled over time in different subjects, subject variances were computed based on JSD using an average multivariate dissimilarity estimation method. Variances between these three groups were significantly different (Kruskal Wallis ANOVA, / ?=0.03). Patients with a history of nephritis were assigned to the Lupus Nephritis (LN) group based on ACR criteria, whereas the patients in the non-renal group were without a documented history or laboratory findings of LN. Lupus patients have more unstable gut microbiota than healthy individuals. Variance of gut microbiota was significantly different in the renal Lupus group, compared to healthy subjects (two-sided Mann-Whitney test, / ?=0.02). The non-renal Lupus group was significantly different than the healthy subjects (p=Q.Q3). Notably, the overall variance in the renal group was not different from the non-renal group (p =0.379, NS).

[0161] Figure 2. Dynamic changes in Blautia (Ruminococcus) gnavus abundance were documented at sequential time points in healthy and Lupus-affected individuals. In 5 / 16 (31%) of the SLE patients evaluated over time, and the abundance of Blautia (Ruminococcus) gnavus fluctuated greatly overtime. In these cases, Blautia (Ruminococcus) gnavus abundance at much higher levels were present in fecal samples obtained proximal to visits in which disease flares were documented. In all but one of these Blautia (Ruminococcus) gnavus bloom-associated patients had documented LN. Blautia (Ruminococcus) gnavus relative abundance was evaluated for 16 SLE in 44 samples obtained at different time points, and for CTL subjects in 49 samples obtained at different time points, which ranged from 2-12 samples per donor. Clinical and demographic data are shown in Tables 1C-1D. Dotted line depicts an arbitrary 1% threshold of 16S rRNA amplicon representing Blautia (Ruminococcus) gnavus abundance that is highly above the mean 0.15% level in these healthy controls. Abundance levels above 1% were considered a bloom. Note that for patient S78 the greater range of Blautia (Ruminococcus) gnavus abundance necessitated a different scale. SLED Al > 8 was considered high disease activity. See Fig. 13 for the depiction of all healthy control subjects and the other 11 SLE patients that displayed a stable low abundance in Blautia (Ruminococcus) gnavus representation.

[0162] Figures 3A-3B. Whole genome sequencing of Blautia (Ruminococcus) gnavus isolates from two Lupus patients in a clinical flare. Type strain Blautia (Ruminococcus) gnavus 2 (designated CC55_001C and also referred to herein as RG2) as well as isolates from patients S47 and SI 07 were sequenced and de-novo assembled, while an assembly for Blautia (Ruminococcus) gnavus 1 (designated ATCC29491 and also referred to herein as RG1) was obtained from NCBI RefSeq. (Fig. 3A) Long-read assemblies of six Blautia (Ruminococcus) gnavus isolates. From inside to outside, circular tracks show average GC content across 1 kbp windows (black line); assembled contigs (gray ring sections- second innermost circle); locations of Ikbp windows with BLAST hits to type strain assemblies ATCC 29491 and CC55_001C; and gene start sites as predicted by Prokka, colored by strand (+: light black shade in the outermost circle (red in the provisional application), dark black shade in the outermost circle (blue in the provisional application)). (Fig. 3B) Complete-linkage hierarchical clustering of the gene content (orthogroup presence / absence) of newly sequenced Blautia (Ruminococcus) gnavus isolates and publicly available assemblies. Newly sequenced isolates and type strains ATCC 29491 and CC55_001C are shown in blue (dark black shade in the outermost circle).

[0163] Figures 4A-4B. Inflammatory bowel disease (IBD) genes are shared by Blautia (Ruminococcus) gnavus strains from lupus nephritis (LN) and IBD patients, but only LN strains express the cell-wall lipoglycan (LG). Within select Blautia (Ruminococcus) gnavus strains, the inventors searched for 199 IBD-associated Blautia (Ruminococcus) gnavus genes previously identified by metagenomic analysis

[0013] , Based on a 70% homology cut-off, 42 of these genes were present in one or more of the strains. Comparisons included the genomes from the nine strains from Crohn’s Disease patients (IBD), and two from infants in the source report

[0013] , with comparison to strains from a healthy donor (MSK 22.24), two Blautia (Ruminococcus) gnavus type strains, and four strains from LN patients with disease flares and concurrent Blautia (Ruminococcus) gnavus blooms. LN strains were found to commonly express a number of genes associated with IBD strains, and could not be discriminated based on expression of these genes. At far left panel, expression of the Blautia (Ruminococcus) gnavus lipoglycan (LG) (shown at far left) was detected in three of four LN strains, but neither in any of the strains from IBD, the antibiotic-treated infants nor the strain from a healthy donor. Presence or absence of designated individual genes, based on gene sequence homology (see Example 1, Methods), is indicated. Also indicated is a phenotypic readout for Blautia (Ruminococcus) gnavus lipoglycan is based on murine monoclonal IgG reactivity to antibodies 33.2.2 and 34.2.2 (Azzouz et al., Longitudinal gut microbiome analyses and blooms of pathogenic strains during lupus disease flares. Annals of the Rheumatic Diseases Published Online First: 26 June 2023) and lupus serum IgG. Fig. 4B represents the same heatmap as Fig. 4A, with specific genes labeled.

[0164] Figures 5A-5F. Conserved structural features of lipoglycans purified from Blautia (Ruminococcus) gnavus strains isolated from three donors. Mass spectrometric analyses of isolated LG preparations from (Fig. 5A) the type strain CC55_001C, (Fig. 5B) the LN strain S107- 86 (NCBI SRA Accession No: SRX14861747), and (Fig. 5C) the LN strain S47-18 (NCBI SRA Accession No: SRX 14861744) were performed as previously described [7] and charge- deconvoluted spectra are shown. Relative abundances for the depicted spectral regions were normalized to the most intense signal of the tri-acyl LG 47:0 found in all strains. Mono-acyl LGs are labeled in jet black (blue in the provisional application), di-acyl LGs in lightest shade of black (green in the provisional application), and tri-acyl LGs in charcoal black shade (red in the provisional application). Details of all detected molecular LG species for strain CC55 001C are summarized in Table 4. (Fig. 5D) Heatmap of the 100 most abundant signals of LGs from the 3strains (corresponding mass spectra are shown in panels A to C. Isotype clusters originating from the same molecular species are grouped together and the LG structural composition is assigned if applicable. (Fig. 5E) Spectral similarity score calculated from these 100 most abundant peaks, indicating a high similarity between the LG populations of these three strains (p<2xl0-12). (Fig. 5F) A structural model of the major abundant LG species consisting of tri-, di- and mono-acyl LGs. The glycoconjugate consists of a diacylglycerol-hexuronic acid linker and the next two connected sugars are hexoses. The lipid anchor can potentially include one or both of these hexoses. The third fatty acid can be either bound to the hexuronic acid, the two adjacent hexoses or to a sugar moiety of the core glycan. The core glycan composition of the purified LG of these Blautia (Ruminococcus) gnavus strains showed a remarkable conservation. Image generated with Biorender.com.

[0165] Figures 6A-6E. Conservation of immunodominant lipoglycan-associated nonprotein antigen in Blautia (Ruminococcus) gnavus strains from SLE patients. Molecular components of different Blautia (Ruminococcus) gnavus strains were separated by polyacrylamide gel electrophoresis, and transferred to membranes. (Fig. 6A) Immunoblot with serum IgG from LN patient S47, obtained during a disease flare of strains isolated from LN patient S107 (S107-48 strain (NCBI SRA Accession No: SRX14861748), S107-61 strain (NCBI SRA Accession No: SRX14861746) and S107-86 strain (NCBI SRA Accession No: SRX14861747)), and from LN patient S47 (S47-18 strain (NCBI SRA Accession No: SRX14861744)), while RJX1118 strin was from an antibiotic-treated infant and RJX1125 strain was from a patient with IBD

[0013] , ATCC29491 and MSK22.24 strains were from healthy donors. (Fig. 6B) Aliquots of these same bacterial extracts were treated with proteinase K, which reveals the immune recognition by Lupus serum IgG of oligo bands non-protein antigens that migrate akin to 20-30 kDa protein bands. (Fig. 6C) Nine different Blautia (Ruminococcus) gnavus strains from IBD patients and two Blautia (Ruminococcus) gnavus strains from antibiotic-treated infants do not contain the immunoreactive oligo bands of lipoglycan that are found in CC55_001C extract and purified CC55_001C lipoglycan. These non-lupus strains and their genomes described in

[0013] , Non-reactive ATCC29491 is also from a healthy adult. (Fig. 6D) Immunoblot reactivity of S47 serum IgG- antibodies were reactive with extracts of five Blautia (Ruminococcus) gnavus strains, and the lipoglycan purified from Lupus S47-18 (NCBI SRA Accession No: SRX14861744) strain. (Fig. 6E) A replicate immunoblot was performed after preincubation of the S47 sera with 4 mg ofpurified S47-18 (NCBI SRA Accession No: SRX14861744) LG, which resulted in complete inhibition of Lupus serum IgG reactivity with oligo bands of comparable MW in SI 07-48 (NCBI SRA Accession No: SRX14861748), S107-86 (NCBI SRA Accession No: SRX14861747) and S47-18 (NCBI SRA Accession No: SRX14861744) extracts and the purified S47-18 (NCBI SRA Accession No: SRX14861744) LG. The lower MW band in ATCC29491 from a healthy donor, which was previously shown to be protease-sensitive, was unaffected. Lipoglycan oligo bands migrate to an area delineated by the boxes indicated with broken lines (red boxes in the provisional application).

[0166] Figures 7A-7N. Serum IgG antibodies to Lupus Blautia (Ruminococcus) gnavus strain LGs, parallel gut community abundance and Blautia (Ruminococcus) gnavus blooms with concordant disease flares. To investigate the Lupus host immune response overtime to colonization with Blautia (Ruminococcus) gnavus strains, the inventors studied IgG n -Blautia (Ruminococcus) gnavus responses longitudinally obtained sera, (at multiple dilutions) from three Lupus patients. (Figs. 7A-7D) IgG responses for patient S47. (Figs. 7E-7H) IgG responses of patient 61. (Figs. 7I-7L) IgG responses of patient S78. (Figs. 7A, 7E, 71) Serum IgG-reactivity with whole bacterial extract of CC55 001C, the index Blautia (Ruminococcus) gnavus strain first identified immunogenic LG. [7], (Figs. 7B, 7F, and 7J) Reactivity with the purified LG from this same CC55_001C strain (termed CC55_001C LG or RG2 LG) had very similar reactivity patterns, confirming LG within bacterial extracts is highly immunogenic. (Figs. 7C, 7G, and 7K) Reactivity with the structurally related purified LG from the S47-18 (NCBI SRA Accession No: SRX14861744) strain (S47-18 (NCBI SRA Accession No: SRX14861744) LG). Here, the same relative reactivity patterns are seen, with uniformly stronger levels of IgG-binding curves for purified S47-18 (NCBI SRA Accession No: SRX14861744) LG. (Figs. 7D, 7H, 7L) By contrast, the lipopolysaccharide (LPS) glycan from a Pseudomonas species, displayed little or no IgG reactivity. In each panel, reactivity with serum from a representative healthy female control is shown (CTL). Samples obtained over time are indicated with a sequential designation. Studies were performed with custom bead-based MBI array (Luminex), with previously described methods [7], (Fig. 7M) Strong IgG2 predominance of serum human IgG subclass-specific reactivity with purified CC55_001C LG, detected by ELISA. Blautia (Ruminococcus) gnavus bloom group are from patients; S47 (LN), S78 (LN), S120 (LN) and S61 (polyarthritis without renal involvement); see Fig. 2). Representative data are for available sera from 7 non-renalpatients, obtained at a visit associated with highest disease activity. Mann-Whitney two-tailed test. (Fig. 7N) There is a strong correlation between serum total IgG anti-lipoglycan reactivity and IgG2 subclass restricted serum anti-LG responses, for samples also depicted in Fig. 7M (see Example 1 Methods).

[0167] Figure 8. Consistent libraries composition found in the two independently generated 16S rRNA gene amplimer Miseq batches from the same RNA sample demonstrates reproducibility of findings. To provide an inter-run technical control, Principal Coordinates Analysis (PCoA) were performed on libraries generated from samples of same individuals / samples that were sequenced in the two different 16S rRNA sequencing runs (1stand 2nd), which shows no consistent bias or batch effect.

[0168] Figures 9A-9C. Dysbiosis in in SLE microbiota communities. (Fig. 9A) The number of distinct taxa estimated based on observed ASV and alpha diversity richness was reduced in samples from Lupus patients (SLE) compared to healthy controls (CTL) (Wilcoxon, p=0.0023). (Fig. 9B) Compared to control samples (CTL), while mean alpha diversity was reduced in Lupus patients with low disease activity (based on SLED Al score), there were even greater contractions in the group with high disease activity (Wilcoxon, p=0.034, p=0.0045, respectively). (Fig. 9C) Compared to CTL, alpha diversity was reduced in those with inactive renal disease, there were further diversity contractions in those with active renal disease (Wilcoxon, p=0.0006 and p=0.0033, respectively). As the purpose was to assess greater overall correlations in this data set, these analyses did not consider statistical adjustments for multiple samples from the same patient.

[0169] Figures 10A-10B. Alpha diversity is reduced in libraries from patients with high Lupus disease activity. Analyses were performed as shown in Fig. 1. High disease activity is defined as a composite SLED Al score of >8.

[0170] Figures 11A-11B. Alpha diversity is reduced in libraries from patients with active renal disease compared to inactive renal disease. Analyses were performed as shown in Fig. 2. Active renal disease was defined by standard clinical laboratory criteria.

[0171] Figures 12A-12C. Blautia (Ruminococcus) gnavus expansions occur at the time of high Lupus disease activity and active LN. (Fig. 12A) All samples from SLE patients have a numerical but non-significant trend toward increased Blautia (Ruminococcus) gnavus abundance compared to healthy CTL (Wilcoxon, p=0.0760). (Fig. 12B) Samples from patients with high disease activity (based on SLED Al) showed a greater Blautia (Ruminococcus) gnavus abundance,compared to low disease activity and CTL (Wilcoxon, p =0.81, p =0.01, respectively). (Fig. 12C) Blautia (Ruminococcus) gnavus expansions were common in the active LN group compared to healthy CTL (Wilcoxon p=0.02), but not significantly different in the inactive LN group. Wilcoxon, p=0.27, NS. Blautia (Ruminococcus) gnavus relative abundance is shown as log 2 values.

[0172] Figures 13A-13C. Blooms of Veillonella are not concurrent with high Lupus disease activity. (Fig. 13 A) Veillonella abundance in healthy individuals. (Fig. 13B) Veillonella abundance in SLE patients. (Fig. 13C) Veillonella abundance in the same samples from SLE patients that had the above-described Blautia (Ruminococcus) gnavus blooms concordant with Lupus disease activity flares. Abundance is based on ASV representation in total amplicon libraries.

[0173] Figures 14A-14C. Blooms of Fusobacterium do not occur at time of peak flares of Lupus disease activity. (Fig. 14A) Fusobacterium abundance in healthy individuals. (Fig. 14B) Fusobacterium abundance in SLE patients. (Fig. 14C) Fusobacterium abundance in the same samples from SLE patients with above-described Blautia (Ruminococcus) gnavus blooms that were concordant with Lupus disease activity flares. Abundance is based on ASV representation in total amplicon libraries.

[0174] Figures 15A-15B. Lack of dynamic changes in Blautia (Ruminococcus) gnavus abundance documented at sequential time points in healthy and in many Lupus-affected individuals. (Fig. 15 A) All healthy control subjects displayed a stable low relative abundance in Blautia (Ruminococcus) gnavus representation. (Fig. 15B) For 11 of the 16 SLE patients under investigation, a stable low abundance in Blautia (Ruminococcus) gnavus representation was also detected. By comparison, in Fig. 2, data for 5 / 16 (31%) of the SLE patients evaluated overtime, which documented that the abundance of Blautia (Ruminococcus) gnavus fluctuated greatly overtime. In those cases, Blautia (Ruminococcus) gnavus abundance, at much higher levels, were detected in fecal samples obtained time proximal to visits in which disease flares were documented. Clinical and demographic data are shown in table S1&S3. Dotted line depicts an arbitrary 1% threshold of 16S rRNA amplicon levels representing Blautia (Ruminococcus) gnavus abundance that is highly above the mean 0.15% level in these healthy adult controls.

[0175] Figure 16. Abundance of Blautia (Ruminococcus) gnavus in SLE fecal genomic samples as determined by 16srRNA and shotgun metagenomic analysis is highly correlated.Here, the abundance of Blautia (Ruminococcus) gnavus species was determined by these two approaches for 16 SLE fecal samples. Values for Spearman analysis with p value for two-tailed analysis are shown. Fecal genomic DNA was used from 16 SLE patients was used to generate individual metagenomic sequencing runs. After quality fdtering using fastp v. 0.23.2

[0036] , the number of reads in each run ranged from 62 million to 79 million. MetaPhlAn v. 4.0.6

[0037] , which were used to quantify the relative abundance of taxa from each sequencing run. The relative abundance of Blautia (Ruminococcus) gnavus in these 16 patient samples, as determined by metagenomic shotgun sequencing, were then compared with results as determined by 16S rRNA library analysis. The calculated correlation coefficients of the relative abundances obtained with each of the two methods for Blautia (Ruminococcus) gnavus, by Pearson correlation was 0.66 and by Spearman correlation was 0.81.

[0176] Figure 17. Classical multi-dimensional analyses of whole genome sequences (WGS) of a dissimilarity matrix reveals inter-person Blautia (Ruminococcus) gnavus variability and SLE-unique clades. Within these comparisons are strains from healthy adults

[0038] , IBD-related strains

[0039] and 27 strains from SLE patients with LN flares. The LN strains are shown to be distributed into four subgroupings for which a representative strain is identified. The LN strains show differences from all other strains. Reference refers to genome sequences for ATCC29149 and CC_001C.

[0177] Figure 18. Phylogenetic tree based on core alignment of Blautia (Ruminococcus) gnavus genome assemblies downloaded from NCBI RefSeq, together with five newly generated genome assemblies. Newly sequenced isolates are shown in blue, along with the NCBI database downloaded ATCC29491 (ATCC 29149) strain for reference.

[0178] Figure 19. MS2 analysis of the basic de-O-acyl LG without hexose extension (composed of 1 Gro, 8 Hex, 5 HexNAc, 3 HexU; calc, mono-isotopic mass: 2931.963 Da) of strain CC55 001C obtained after hydrazine-treatment [1], In the experiment shown here, the double charged peak for this molecule was isolated and an NCE of 30 was applied to induce fragmentation. Full spectrum is depicted in the upper panel. A zoom into the region of m / z 140 to 650 comprising the small molecular fragments generated under these conditions is depicted in the lower panel. Fragments indicative for the presence of a glycerol-hexuronic acid unit (221.0665 Da: glycerol-hexuronic acid (decarboxylated); 249.0614 Da: glycerol-hexuronic acid, with loss of water) which is extended by at least two hexoses (545.1723 Da: glycerol-hexuronic acid(decarboxylated)-hexose-hexose) can be observed. The loss of the glycerol-hexuronic acid unit including loss of water can also be observed from the selected ion. (z=l, single charged ions [M- H]‘; z=2, double charged ions [M-2H]2-).

[0179] Figures 20A-20C. Reactivity of post-immunization murine monoclonal antibodies is restricted to conserved cross-reactive determinants on the oligobands of protease-resistant lipoglycans from Blautia (Ruminococcus) gnavus strains derived from clinically active LN patients. (Fig. 20A) Direct binding ELISA demonstrates reactivity of both mAbs, 33.2.3 and 34.2.2, with the purified CC55_001C and S47-18 (NCBI SRA Accession No: SRX14861744) LGs, and bacterial extracts from the CC55_001C strain and Lupus-derived strains; S47-18 (NCBI SRA Accession No: SRX14861744), S107-48 (NCBI SRA Accession No: SRX14861748) and S107-86 (NCBI SRA Accession No: SRX14861747). In this assay, LG or nuclease-treated Blautia (Ruminococcus) gnavus strain extracts were precoated directly onto microtiter wells, then after blocking mAbs or isotype control were incubated, then washed and developed (see methods). (Fig. 20B) Immunoblots with 33.2.3 mAb or (Fig. 20C) with the 34.2.2 mAb detect antigenically related LG oligo bands in extracts of Blautia (Ruminococcus) gnavus strains isolated from active LN patients. In each panel are shown samples of purified lipoglycan (LG) from the Lupus S47-18 (NCBI SRA Accession No: SRX14861744) strain, and the CC55_001C strain. At left, extracts of whole bacteria are shown for the ATCC29491 strain (from a healthy donor), and the Lupus-derived Blautia (Ruminococcus) gnavus strains; SI 07-48 (NCBI SRA Accession No: SRX14861748), S107-86 (NCBI SRA Accession No: SRX14861747), S47- 18 (NCBI SRA Accession No: SRX14861744), as well as the CC55_001C strain.

[0180] Figure 21A-21B. Antibody gene sequences and deduced amino acid sequences of the murine nn i-Blautia (Ruminococcus) gnavus LG antibodies. Alignments were based on Immunogenetics (IMGT) information systems web-based analysis. (Fig. 21A) VH sequences of the anti-5 awto (Ruminococcus) gnavus LG antibodies. Figure 21A discloses amino acid sequence corresponding to “33.2.2 VH_Amino acid sequence deduced” disclosed as SEQ ID NO: 5, nucleic acid sequence corresponding to “33.2.2 VH _gene” disclosed as SEQ ID NO: 6, nucleic acid sequence corresponding to “IGHV3-8*02 Nucleotide sequence” disclosed as SEQ ID NO: 7, amino acid sequence corresponding to “IGHV3-8*02 Amino acid sequence” disclosed as SEQ ID NO: 8, nucleic acid sequence corresponding to “34.2.2 VH _gene” disclosed as SEQ ID NO: 9, amino acid sequence corresponding to “34.2.2 VH Amino acid sequence deduced” disclosed asSEQ ID NO: 10, nucleic acid sequence corresponding to “IGHDl-l *01 - 94.4%” disclosed as SEQ ID NO: 17, nucleic acid sequence corresponding to “IGHJ4*01 - 95.9%” disclosed as SEQ ID NO: 18, and nucleic acid sequence corresponding to “IGHJ4*01 - 98%” disclosed as SEQ ID NO: 19. (Fig. 21B) VL sequences of the r x-Blautia (Ruminococcus) gnavus LG monoclonal antibodies. Figure 21B discloses amino acid sequence corresponding to “33.2.2 VL_ Amino acid sequence deduced” disclosed as SEQ ID NO: 11, nucleic acid sequence corresponding to “33.2.2 VL gene” disclosed as SEQ ID NO: 12, nucleic acid sequence corresponding to “IGKV15- I03*01_gene” disclosed as SEQ ID NO: 13, amino acid sequence corresponding to “IGKV15- 103*01_Amino acid deduced” disclosed as SEQ ID NO: 14, nucleic acid sequence corresponding to “34.2.2 VL _gene” disclosed as SEQ ID NO: 15, amino acid sequence corresponding to “34.2.2 VL Amino acid sequence deduced” disclosed as SEQ ID NO: 16, nucleic acid sequence corresponding to “IGKV15-103*01” disclosed as SEQ ID NO: 20, and nucleic acid sequence corresponding to “IGKJ5*01” disclosed as SEQ ID NO: 21. This reflects the influence of somatic hypermutation in which the B cell introduced a variation in residue that differences from the closest known germline gene or gene segment that is inherited by that human.

[0181] Figure 22A-B. Schematic of hypothetical Blautia (Ruminococcus) gnavus effects on patient immune systems and distribution in the number of counts of individual genes in these bulk RNA transcript libraries of SLE patients and healthy controls. (Fig. 22A) Overview of proposed mechanism of Blautia (Ruminococcus) gnavus effect on platelet activation. (Fig. 22B) Identification of differences in gene transcripts from SLE patients and healthy controls (HCs). From purified RNA samples, using a standard method, RNA was reverse transcribed, then DNA sequencing was performed. The composition of these peripheral blood transcript libraries was then analyzed. Approximately -10-20 million reads per sample were performed, and 24,319 genes passed a minimum threshold of 4 reads in >1 / 2 of libraries.

[0182] Figure 23. Unsupervised cluster analysis of transcript libraries from SLE patients and healthy controls. There were differences between healthy controls and SLE patients of the three subsets (non-renal; renal with no Blautia (Ruminococcus) gnavus bloom; and renal with Blautia (Ruminococcus) gnavus bloom).

[0183] Figure 24A-24C. Analysis of bulk RNA libraries. (Fig. 24A) Principal Coordinates analysis (PCoA) demonstrates separation between the libraries from heathy controls (•) from the SLE patients (+). (Fig. 24B) Heat map analysis and unsupervised clustering of thelibraries from the 8 patients with renal (LN) flares (clinical and demographic data in Table 1). While Blautia (Ruminococcus) gnavus bloom libraries distributed into one cluster (at left), the libraries from patients with LN flares without a detectable intestinal community bloom (i.e., nonbloom) (at right). These two gut microbiome defined groups have great differences in relative expression of specific gene transcripts. (Fig. 24C). In the transcript analysis, the bloom LN libraries compared to LN flare and no bloom had 173 upregulated and 13 downregulated genes based on differential expression analysis (padj < 0.05, log2fc > 1).

[0184] Figure 25. Heatmap of relative expression levels of 13 platelet activation associated genes, and four interferon (IFN) stimulated genes (ISG) in the NYU bulk lupus blood RNA-seq dataset. Here, for each clinical groups, relative mean transcript expression levels are depicted. High levels of all platelet activation genes were found in the LN flare with Blautia (Ruminococcus) gnavus group along with much lower levels of ISG transcripts. Notably, the highest ISG levels were in the non-renal group and in the LN flare without Blautia (Ruminococcus) gnavus bloom group, which also had relatively lower platelet activation transcript levels.

[0185] Figures 26A-26C. Relationships between platelet activation genes and ISG, from an independent published data set (57). Spearman correlations are depicted for the two genes depicted, for Z score reported for 11 LN patients. Values are R(2) values. Direct correlation indicated by outlined cells (in shades of red in the provisional application), and inverse indicated by shading (in blue in the provisional application). All values are p<0.05, indicated by intensity of color. The data show significant correlation of Type I interferon genes to each other, and platelet related genes to each other, but no inverse correlation in LN patients without RG bloom. Fig. 26C represents the same data as given in Fig. 26B to make it distinguishable in the color independent format.

[0186] Figure 27. Comparison of the LN flare libraries. Normalized enrichment scores (NES) were used to compare the two groups of LN flare libraries, which identified pathways which were significantly different in the no-bloom (without bloom) group with the Blautia (Ruminococcus) gnavus bloom group. The LN flare group without detectable expansion of an intestinal species had significantly increased levels of genes associated with interferon alpha, and interferon gamma. Other differences were also detected.

[0187] Figure 28. Mean levels of four IFN inducible genes in the different clinical groups. Groups are arranged in the same order as shown for platelet activation genes in Fig. 27.Here, the highest mean expression levels of these four interferon related genes, IFI27, IFI44, RSAD2, and IFI44L, were instead found in the no-bloom LN flare group and the non-renal SLE patient group. Lower levels were instead found in the Blautia (Ruminococcus) gnavu .sb loom LN flare group (far left). The lowest mean levels of these interferon related genes were found in the healthy control group.

[0188] Figures 29A-29C. LN patients with Blautia (Ruminococcus) gnavus (RG) gut blooms overexpress genes, including for platelet activation. ( Fig. 29A) Volcano plot of genes differentially expressed in LN patients with (LNRG) and without RG bloom (LN Not Bloom) (genes represented outside of the two vertical lines and above horizontal line at log2 (red in the provisional application)) indicates p<0.01 and log2FC>l or <-l, and genes represented within two vertical lines and above horizontal line at log2 (green in the provisional application) p<0.01 with Log2FC <1 or >-l). ( Fig. 29B) Heatmap illustrates differential gene expression in patients with LN and RG blooms, compared to control samples, for 11 genes of interest. Non renal SLE patients, (termed here SLENot LN), (panel A. of Fig. 29C, panel B. of Fig. 29C) Singscore module assessment of platelet activation (panel A. of Fig. 29C) and B cell activation (panel B. of Fig. 29C) related genes compared to SLED Al in longitudinal assessment of whole-blood RNASeq measurements in patients with (termed LNRG) and those without (termed LNNotBloom) RG blooms. Platelet gene signature compared to SLED Al is significantly different between the two groups (p =0.009, Wilcoxon rank sum test, mixed effects model; R2represent pearson R). Positive correlation of platelet gene signature at SLED Al is identifiable in LN patients with an RG bloom, while a negative correlation is identifiable between B cell gene signatures and SLEDAI in LN patients with RG bloom.

[0189] Figures 30A-30B. P-selectin levels are increased in patients with LN and RG bloom. ( Fig. 30A) P-selectin / CD62-P levels in SLE patients and (Fig. 30B) correlation of P- selectin and PF-4 in sera of patients with LN and levels of serum RG anti-LG antibodies above the level in healthy individuals, indicates p<0.05, non-parametric Mann-Whitney U analysis of LNRG vs. Control. Based on commercial ELISA of serum (P-selectin 1 :400, PF4 1 :20).

[0190] Figures 31A-31D. LN with high antibody responses to RG cell wall lipoglycan (LG) have increased platelet activation. ( Fig. 31 A) To evaluate for prior immune exposure to Ruminococcus gnavus (RG), which is the same as Blautia Ruminococcus gnavus, we determined serum anti-LG levels in Healthy-Ctrls (Controls), non-renal SLE, and SLE patients withdocumented intestinal blooms of RG by 16S rRNA sequencing (SLE RG bloom) or without blooms (Renal No-Bloom) from a NYU cohort, compared to patients with negative (<5.3xl04) or positive anti-LG levels (as a horizontal dashed line) from the validation ITN034AI = ACCESS LN and Bordeaux cohorts. (Fig. 3 IB) Heatmap of gene expression in platelet and myeloid leukocyte activation pathways in patients with negative vs positive anti-LG antibody levels from ACCESS_LN. Pathway analysis represents ordered query functional profiling gene set enrichment analysis gene ontology results (g:Profiler) (Fig. 31C) PF4 / CXCL4 levels in sera dichotomized for anti-LG level in ACCESS LN samples. Mann-Whitney U non-parametric test. (Fig. 3 ID) ELISA of serum NET fragments from active LN dichotomized by anti-LG antibody levels. Mann-Whitney U.

[0191] Figures 32A-32C. Murine RG gavage with a lipoglycan from R. gnavus drives platelet activity in whole blood RNAseq and flow cytometry studies of ex-vivo platelets 2 weeks post gavage. (Fig. 32A) Protocol for antibiotic pretreatment, gavage of RG or sham, and sample collection. (Fig. 32B) Volcano plot of gene expression 2 weeks post gavage with genes related to platelet degranulation noted. All genes above horizontal dashed line represent p<0.05, and vertical dashed lines indicate genes >1 or <-l Log2FC (RG vs. Sham). (Fig. 32C) Flow cytometry of murine ex-vivo platelet activation from whole-blood 2-weeks post RG gavage with stimulation of PBS or thrombin in C57BL / 6 (top) and C57BL / 6-Gplb tdTomato mice — non-parametric, Mann- Whitney U test. No significant differences for ADP or collagen stimulation were observed.

[0192] Figure 33. A model of the testable hypothesis that in SLE patients RG intestinal blooms cause increased gut permeability and translocation of microbial products, resulting in systemic immune exposure to RG surface lipoglycan (LG).

[0193] Figure 34. Orthologues of IBD associated Blaiitica (Ruminococcus) gnavus genes found in strains from LN patients.DETAILED DESCRIPTION

[0194] The present invention provides methods for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, as well as methods for treating a subject diagnosedwith SLE or ILE, and methods of monitoring the effect of a treatment on development of a disorder in a subject, wherein the disorder is lupus nephritis or other forms of SLE with renal involvement or polyarthritis.

[0195] SLE is a chronic inflammatory autoimmune disease with hallmarks of B-cell abnormalities and clonal expansions, in which circulating autoantibodies and immune-complexes mediate tissue injury. SLE can lead to complications such as lupus nephritis, which is an inflammation of the kidneys. Lupus nephritis can be life-threatening and / or result in renal failure. Before the present invention, a diagnosis of lupus nephritis may require a renal biopsy, which is expensive and associated with the possibility of morbidity and complications.

[0196] As lupus nephritis is a major source of early mortality and overall morbidity, a diagnostic test that provides a substantial increase in confidence in the diagnosis of lupus nephritis, as well as other forms of SLE with renal involvement or polyarthritis, would therefore be predicted to provide both medical and economic advantages. Performing the diagnostic test herein described would in itself have only very minor medical risks associated with a peripheral blood draw required to obtain a platelet-containing sample. The present invention is based on the surprising discovery that patients diagnosed with SLE or ILE experiencing disease flares can have a pattern of severe gut microbiota imbalance, associated with an expansion (20-100-fold relative increased abundance) of a bacterial species that causes increased gut permeability, inflammation and induces autoantibody production. Concurrent with these specific gut blooms (in -40% of LN patients in flare), blood transcriptomes showed multiple pathways associated with activation of their platelets, which was completely unexpected. Platelets are subcellular cell fragments that were previously viewed predominantly for their hemostatic function. Yet, in recent years platelets are recognized as possessing complex and dynamic transcriptomes that can encode for expressed proteins. Effects on megakaryocytes, the source of platelets, can alter transcriptomic profiles and affect function, from transfer of altered repertoires of RNAs and proteins into newly released platelets. Platelets mediate inflammatory pathways, best characterized during sepsis, viral infection, and transfusion reactions. Hence, platelets can serve as immune sentinels responsible for thromboinflammation, although this has not been widely recognized in SLE patients.

[0197] Therefore, detection of altered platelet transcriptomic profiles in SLE or ILE patients can be used to predict whether that patient may be at risk for suffering from effects of thromboinflammation, such as, e g., lupus nephritis, as well as other forms of SLE with renalinvolvement or polyarthritis. Such detection involves determining the expression levels of certain genes involved in the platelet activation pathway. In some embodiments, this detection involves determining the mRNA levels of certain genes involved in the platelet activation pathway.

[0198] The methods disclosed herein can be further combined with additional diagnostic methods, such as for example and not limitation, (i) detection of expression levels of certain interferon (IFN) stimulated genes (ISG), (ii) detection of certain platelet activation-associated protein levels, (iii) detection of the level of blood antibodies to a lipoglycan present on the surface of a certain bacterial strain, and (iv) detection of the abundance of the bacterial strain in the subj ect.

[0199] It has been previously discovered that a subset of patients with autoimmune disease, SLE, have high serum IgG antibodies to a novel bacterial lipoglycan antigen that was previously discovered (reference 1 below). This lipoglycan is made by some strains of the gut commensal bacterium, Ruminococcus gnavus of the Lachnospiraceae family. Individuals with anti-DNA antibodies and this antibody to lipoglycan are likely to have severe renal disease termed lupus glomerulonephritis. This antibody to lipoglycan is triggered by release of this antigen from bacteria in the intestine, and because of intestinal permeability it can enter the systemic immune system to induce these antibodies.

[0200] It is simple to sample blood for this antibody, and more technically cumbersome to sample and characterize the bacteria in the intestine and fecal samples. The data provided herein suggest the presence of this bacteria in the gut, and these antibodies causes glomerulonephritis through triggering of systemic platelet activation. This may trigger a form of neutrophil death, termed NETosis, which can injure body organs, including the kidneys in genetically susceptible individuals. There are results from experiments with human clinical samples from patients with lupus nephritis from which studies were performed indicating that there is a strong correlation between high-level serum antibodies to a lipoglycan made only by certain strains of R. gnavus which are directly correlated with raised levels of transcripts from activated platelets, and released platelet proteins reflecting in vivo platelet activation, and these are correlated with soluble proteins in the protein from neutrophils undergoing NETosis. NETosis includes a process that can cause direct injury to tissues, especially kidneys. Hence antibody test may detect a previously unsuspected pathway of tissue injury in SLE, which is associated with a worse prognosis. It may also identify patients who should be evaluated for treatment with agents that therapeutically improve platelet activation and NETosis. Such treatments are very different than current availabletherapies for SLE, which generally dismantle the immune system. Such treatments increase the risk of serious infection. It should be appreciated that despite current therapeutic interventions 10- 20% of lupus nephritis patients will develop renal failure within 15 years (potential prognostic agent). Hence there is currently great unmet need for better and more effective treatments of lupus.

[0201] As described above, there is a dire need for earlier and simpler diagnosis of renal involvement in patients with systemic autoimmunity, such as lupus. Renal disease is one of the most serious complications of lupus. Although there are treatments that are standard of care, an estimated 5-20% of patients with renal involvement, also termed lupus nephritis, will progress within 15 years to renal failure. This condition has high morbidity and mortality.

[0202] In most cases, immune-modulating agents, such as corticosteroids, mycophenolate mofetil, tacrolimus, chemotherapy, and B cell-killing agents to treat lupus nephritis are used. These treatments result in a high risk for serious and often life-threatening infection.

[0203] The invention disclosed herein can enable a determination of whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), or being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease.

[0204] The invention can also enable methods for treating a subject diagnosed with SLE or ILE. In some embodiments, the methods comprise treating lupus nephritis or other forms of SLE with renal involvement or polyarthritis, in a subject diagnosed with SLE or ILE who has an increased risk of developing lupus nephritis or other forms of SLE with renal involvement and / or at increased risk of developing polyarthritis.

[0205] The invention can also enable methods of monitoring the effect of a treatment on development of a disorder in a subject, wherein the disorder is lupus nephritis or other forms of SLE with renal involvement or polyarthritis. In some embodiments, the subject is diagnosed with SLE or ILE and is identified as having an increased risk of developing lupus nephritis or other forms of SLE with renal involvement and / or having an increased risk of developing polyarthritis.Definitions

[0206] As used herein, the terms “microbe” or “microorganism” encompass both prokaryotic organisms including bacteria and archaea, and eukaryotic organisms, including fungi, present as components of the mammalian microbiota, and viruses.

[0207] The terms “gastrointestinal microbiota”, “GI microbiota”, “intestinal microbiota”, “intestinal flora”, and “intestinal microbiome” are used interchangeably and refer to the microorganisms that colonize the intestines.

[0208] As used herein, the terms Blautia (Ruminococcus) gnavus, RG, Ruminococcus gnavus, R. gnavus, Ruminococcus (blautia) gnavus are interchangeable and refer to Blautia (Ruminococcus) gnavus of the Lachnospiraceae family.

[0209] As used herein, the term “dysbiosis” refers to a microbial imbalance within a microbiome community in a human body. Dysbiosis can result from, e.g., antibiotic exposure as well as other causes, e.g., infections with pathogens including viruses, bacteria, and eukaryotic parasites, or occurring in patients with idiopathic inflammatory or autoimmune disease due to uncertain or unknown mechanisms.

[0210] Specific taxa and changes in GI microbiota discussed herein can be detected using various methods, including without limitation, quantitative PCR or high-throughput sequencing methods which detect over- and under-represented genes in the total bacterial population (e.g., sequencing for microbial community analysis e.g., using a 454 machine, miSeq, Pacbio, or other related devices); screening of microbial 16S ribosomal RNAs (16S rRNA) or microbial 16S ribosomal DNA (16S rDNA), next generation sequencing (NGS) etc.), or transcriptomic or proteomic studies that identify lost (or under-represented) or gained microbial transcripts or proteins within total bacterial populations. See, e.g., U.S. Patent Publication No. 2010 / 0074872; Eckburg et al., Science, 2005, 308: 1635-8; Costello et al., Science, 2009, 326:1694-7; Grice et al., Science, 2009, 324: 1190-2; Li et al., Nature, 2010, 464: 59-65; Bjursell et al., Journal of Biological Chemistry, 2006, 281 :36269-36279; Mahowald et al., PNAS, 2009, 14:5859-5864; Wikoff et al., PNAS, 2009, 10:3698-3703.

[0211] As used herein, the term “16S rDNA sequencing” refers to the sequencing of 16S ribosomal DNA (rDNA) or 16S ribosomal RNA (rRNA) gene sequences by using primers such as universal primers and / or species-specific primers to identify the bacteria present in a sample. rDNA and rRNA genes contain both highly conserved sites and hypervariable regions that can provide family, genus, and / or species-specific signature sequences useful for identification of bacteria. Such universal primers are well known in the art.

[0212] As used herein, the term “operational taxonomic unit” or “OTU” refers to group of bacterial sequences that differ among each other in < 97% identity. A “type” or a plurality of“types” of bacteria includes an OTU or a plurality of different OTUs, and also encompasses differences in species, genus, family or order of bacteria. The specific genetic sequence may be the 16S rDNA or rRNA sequence or a portion of the 16S rDNA or rRNA sequence or it may be a functionally conserved housekeeping gene found broadly across the eubacterial kingdom. Alternatively, assignments are based on the related method, amplicon sequence variants, ASV, which reduces the noise associated with sequencing errors.

[0213] As used herein, the term “abundance” refers to how common or rare a particular organism (e.g., bacterial species) is relative to other organisms of the same type (e.g., other bacterial species) in a defined community. In certain embodiments, abundance is the percent composition of a particular organism (e.g., bacterial species) to the total amount of organisms in the sample. In certain embodiments, abundance refers to the total level of organism in a sample. In certain embodiments, abundances are described for a single trophic level.

[0214] As used herein, the term “probiotic” refers to a substantially pure bacteria (i.e., a single isolate, of, e.g., live bacterial cells, conditionally lethal bacterial cells, inactivated bacterial cells, killed bacterial cells, spores, recombinant carrier strains), or a mixture of desired bacteria, bacteria components or bacterial extract, or bacterially-derived products (natural or synthetic bacterially- derived products such as, e.g., bacterial antigens or metabolic products) and may also include any additional components that can be administered to a mammal. Such compositions are also referred to herein as “bacterial inoculants” or “microbiota inoculants”. Probiotics or bacterial inoculant compositions of the invention may be administered with a buffering agent to allow the bacteria to survive in the acidic environment of the stomach, i.e., to resist low pH and to grow in the intestinal environment. Such buffering agents include sodium bicarbonate, juice, milk, yogurt, infant formula, and other dairy products.

[0215] As used herein, the term “prebiotic” refers to an agent that increases the number and / or activity of one or more desired bacteria, enhancing their growth. Non-limiting examples of prebiotics useful in the methods of the present invention include fructooligosaccharides (e.g., oligofructose, inulin, inulin-type fructans), galactooligosaccharides, human milk oligosaccharides (HMO), Lacto-N-neotetraose, D-Tagatose, xylo-oligosaccharides (XOS), arabinoxylan- oligosaccharides (AXOS), N-acetylglucosamine, N-acetylgalactosamine, glucose, other five- and six-carbon sugars (such as arabinose, maltose, lactose, sucrose, cellobiose, etc.), amino acids, alcohols, resistant starch (RS), water-soluble cellulose derivatives (most preferably,methyl cellulose, methyl ethyl cellulose, hydroxyethyl cellulose, ethyl hydroxyethyl cellulose, cationic hydroxyethyl cellulose, hydroxypropyl cellulose, hydroxyethyl methylcellulose, hydroxypropyl methylcellulose, and carboxymethyl cellulose), water-insoluble cellulose derivatives (most preferably, ethyl cellulose), and mixtures thereof. See, e.g., Ramirez-Farias et al., Br J Nutr (2008) 4: 1-10; Pool-Zobel and Sauer, J Nutr (2007), 137:2580S-2584S.

[0216] The terms “treat” or “treatment” of a state, disorder or condition include: (1) preventing, delaying, or reducing the incidence and / or likelihood of the appearance of at least one clinical or sub-clinical symptom of the state, disorder or condition developing in a subject that may be afflicted with or predisposed to the state, disorder or condition but does not yet experience or display clinical or subclinical symptoms of the state, disorder or condition; or (2) inhibiting the state, disorder or condition, i.e., arresting, reducing or delaying the development of the disease or a relapse thereof (in case of maintenance treatment) or at least one clinical or sub-clinical symptom thereof; or (3) relieving the disease, i.e., causing regression of the state, disorder or condition or at least one of its clinical or sub-clinical symptoms. The benefit to a subject to be treated is either statistically significant or at least perceptible to the patient or to the physician.

[0217] As used herein, the term “therapeutically effective amount” refers to the amount of a bacterial inoculant, a compound, or a composition, including a prebiotic or a probiotic, that, when administered to a subject for treating (e.g., preventing or ameliorating) a state, disorder or condition, is sufficient to effect such treatment. The “therapeutically effective amount” will vary depending, e.g., on the compound, composition, bacteria or analogues administered as well as the disease, its severity, and physical conditions and responsiveness of the subject to be treated.

[0218] As used herein, the phrase “pharmaceutically acceptable” refers to molecular entities and compositions that are generally regarded as physiologically tolerable.

[0219] As used herein, the term “combination” of a compound, composition, bacterial inoculant, probiotic, analogue, or prebiotic and at least a second pharmaceutically active ingredient means at least two, but any desired combination of compound, composition, bacterial inoculant, probiotic, analogue, or prebiotic can be delivered simultaneously or sequentially (e.g., within a 24 hour period).

[0220] Within the meaning of the present invention, the term “conjoint biotic administration” is used to refer to administration of a probiotic and a prebiotic simultaneously in one composition, or simultaneously in different compositions, or sequentially (preferably, within a 24 hour period).

[0221] The terms “patient”, “individual”, “subject”, and “animal” are used interchangeably herein and refer to mammals, including, without limitation, human and veterinary animals (e.g., cats, dogs, cows, horses, goats, sheep, pigs, etc.) and experimental animal models. In a preferred embodiment, the subject is a human.

[0222] As used herein, the term “healthy subject” refers to a subject that is without known infections or autoimmune disorders by using conventional diagnostic methods. In certain embodiments, a healthy subject is a subject without a known first degree relative with an autoimmune disorder. In certain embodiments, a matched healthy subject is matched by age, gender, and / or ethnicity.

[0223] As used herein, the term “stimulate” when used in connection with growth and / or activity of bacteria encompasses the term “enhance”.

[0224] The term “carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the compound is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Water or aqueous solution saline solutions and aqueous dextrose and glycerol solutions are preferably employed as carriers, particularly for injectable solutions. Alternatively, the carrier can be a solid dosage form carrier, including but not limited to one or more of a binder (for compressed pills), a glidant, an encapsulating agent, a flavorant, and a colorant. Suitable pharmaceutical carriers are described in “Remington’s Pharmaceutical Sciences” by E.W. Martin.

[0225] The term “about” or “approximately” means within a statistically meaningful range of a value. Such a range can be within an order of magnitude, preferably within 50%, more preferably within 20%, still more preferably within 10%, and even more preferably within 5% of a given value or range. The allowable variation encompassed by the term “about” or “approximately” depends on the particular system under study, and can be readily appreciated by one of ordinary skill in the art.

[0226] The terms “a,” “an,” and “the” do not denote a limitation of quantity, but rather denote the presence of “at least one” of the referenced item.

[0227] The practice of the present invention employs, unless otherwise indicated, conventional techniques of statistical analysis, molecular biology (including recombinant techniques), microbiology, cell biology, and biochemistry, which are within the skill of the art. Such tools andtechniques are described in detail in e.g., Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual. 3rd ed. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, New York; Ausubel et al. eds. (2005) Current Protocols in Molecular Biology. John Wiley and Sons, Inc.: Hoboken, NJ; Bonifacino et al. eds. (2005) Current Protocols in Cell Biology. John Wiley and Sons, Inc.: Hoboken, NJ; Coligan et al. eds. (2005) Current Protocols in Immunology, John Wiley and Sons, Inc.: Hoboken, NJ; Coico et al. eds. (2005) Current Protocols in Microbiology, John Wiley and Sons, Inc.: Hoboken, NJ; Coligan et al. eds. (2005) Current Protocols in Protein Science, John Wiley and Sons, Inc.: Hoboken, NJ; and Enna et al. eds. (2005) Current Protocols in Pharmacology, John Wiley and Sons, Inc. : Hoboken, NJ. Additional techniques are explained, e.g., in U.S. Patent No. 7,912,698 and U.S. Patent Appl. Pub. Nos. 2011 / 0202322 and 2011 / 0307437.Diagnostic, Therapeutic, and Monitoring Methods of the Invention

[0228] As specified in the Background section above, there is a great need in the art for methods for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease.

[0229] There is also a need for methods for treating a subject diagnosed with SLE or ILE. In certain embodiments, the subject has been identified as being at an increased risk for lupus nephritis or other forms of SLE with renal involvement and / or as being at an increased risk for developing polyarthritis. In certain embodiments, the methods involve treating lupus nephritis or other forms of SLE with renal involvement or polyarthritis in such a subject.

[0230] Finally, there is also a need for methods of monitoring the effect of a treatment on development of a disorder in a subject, wherein the disorder is lupus nephritis or other forms of SLE with renal involvement or polyarthritis. In certain embodiments, the subject has been diagnosed with SLE or ILE and / or has been identified as being at an increased risk for lupus nephritis or other forms of SLE with renal involvement and / or as being at an increased risk for developing polyarthritis.

[0231] Complications of lupus involves, for example but not limitation, the pulmonary system, central nervous system, cardiovascular system, skin disease, joint disease, musculoskeletaldisease, depressed red cell levels, depressed white cell levels, depressed platelets, immunosuppression, severe infection, or any combination thereof.

[0232] In certain embodiments, the lupus nephritis is proliferative lupus nephritis or membranous lupus nephritis. In certain embodiments, lupus nephritis is membranoproliferative Lupus nephritis. In certain embodiments, lupus nephritis is mesangial glomerulonephritis.

[0233] Renal involvement in SLE or ILE can include, but is not limited to, glomerulonephritis (e.g., IgA nephropathy). IgA nephropathy is a specific pathologic diagnosis that is established at renal biopsy. In certain embodiments, the IgA nephropathy is Henoch Schonlein Purpura (HSP). IgA nephropathy and HSP are no different in the renal biopsy, although the former is more common in adults and the latter in children, teens, and young adults. HSP patients do have other diagnostic features outside of the kidneys. Patients with liver disease may have IgA deposits in their kidneys similar or indistinguishable from IgA nephropathy. IgA nephropathy may progress to chronic kidney failure in a subset of cases during a period of 20 years. In part it may be important to make this diagnosis to also rule out other diagnoses with even worse prognoses.

[0234] Polyarthritis, also referred to as polyarticular arthritis or inflammatory arthritis, is an arthritis in which five or more joints are affected with arthritis at the same time. Polyarthritis can be associated with systemic lupus erythematosus (SLE) or incomplete lupus (ILE).

[0235] In one aspect, the invention provides a method for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or TLE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement and / or is determined to be an increased risk for developing polyarthritis and / or renal disease, wherein the method comprises (a) determining in a sample collected from the subject the level of mRNA of two or more genes selected from integrin subunit alpha 2b (ITGA2B), multimerin 1 (MMRN1), ATP binding cassette subfamily C member 4 (ABCC4), dematin actin binding protein (DMTN), GATA binding protein 1 (GATA1), lymphocyte antigen 6 family member G6F (LY6G6F), myosin light chain 9 (MYL9), platelet factor 4 (PF4), protein S (PROS1), synuclein alpha (SNCA), secreted protein acidic and cysteine rich (SPARC), PDGFA (platelet derived growth factor subunit A), and VTI1B (vesicle transport through interaction with t-SNAREs IB), wherein the sample comprises platelets, (b) comparing each of the mRNA levels determined in step (a) to a corresponding control mRNA level of said genes, and (c) determining that the subject is at an increased risk for developing lupus nephritis orother forms of SLE with renal involvement or polyarthritis, when each of the mRNA levels determined in step (a) is at least 1.5-fold higher than the corresponding control mRNA level.

[0236] In some embodiments, step (c) can further comprise determining that the subject is not at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when one or more mRNA levels determined in step (a) are not at least 1.5-fold higher than the corresponding control mRNA levels.

[0237] In some embodiments, mRNA levels from genes selected from integrin subunit alpha 2b (ITGA2B; also referred to as GT; GT1; GTA; CD41; GP2B; HP A3; CD41B; GPIIb; BDPLT2; BDPLT16; PPP1R93), multimerin 1 (MMRN1; also referred to as elastin microfibril interfacer 4 (EMILIN-4), ECM; MMRN; GPIa*), ATP binding cassette subfamily C member 4 (ABCC4; also referred to as MRP4; MOATB; MOAT-B), CD9 (also referred to as MIC3; MRP-1; BTCC-1; DRAP-27; TSPAN29; TSP AN-29), dematin actin binding protein (DMTN; also referred to as DMT; EPB49), GATA binding protein 1 (also referred to as globin transcription factor 1; GATA1; ERYF1; GATA-1; NF-Ela), hemoglobin subunit beta (HBB; also referred to as ECYT6; CD113t- C; beta-globin), lymphocyte antigen 6 family member G6F (LY6G6F; also referred to as G6f; NG32; LY6G6; LY6G6D; C6orf21), myosin light chain 9 (MYL9; also referred to as LC20; MLC2; MRLC1; MYRL2; MLC-2C; MMIHS4), platelet factor 4 (PF4; also referred to as PF-4; CXCL4; SCYB4), protein S (PROS1; also referred to as PSA; PROS; PS21; PS22; PS23; PS24; PS25; THPH5; THPH6), synuclein alpha (SNCA; also referred to as PD1; NACP; PARK1; PARK4), secreted protein acidic and cysteine rich (SPARC; also referred to as ON; ONT; 0117; BM-40), basigin (Ok blood group; also referred to as BSG; OK; 5F7; TCSF; CD147; EMPRIN; HAbl8G; EMMPRIN), C-X-C motif chemokine ligand 5 (CXCL5; also referred to as SCYB5; ENA-78), MAGUK p55 scaffold protein 1 (MPP1; also referred to as MRG1; PEMP; AAG12; EMP55; DXS552E), platelet derived growth factor subunit A (PDGFA; also referred to as PEGF- A; PDGF1), and vesicle transport through interaction with t-SNAREs IB (VTI1B; also referred to as VTI1; VTI1-LIKE; VTI1L; VTI2; v-SNARE; vtil-rpl)are determined.

[0238] In some embodiments, the method further comprises: (d) determining in a sample collected from the subject the level of mRNA of two or more genes selected from interferon alpha inducible protein 27 (IFI27), interferon inducible protein 44 (IFI44), radical S-adenosyl methionine domain containing 2 (RSAD2), and interferon inducible protein 44 like (IFI44L); (e) comparing each of the mRNA levels determined in step (d) to a corresponding control mRNAlevel, and (f) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when at least two of the mRNA levels determined in step (d) are statistically significantly lower than the corresponding mRNA levels in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

[0239] In some embodiments, the method further comprises: (1) determining in a blood sample collected from the subject the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments; (2) comparing the level of the protein(s) and / or of NETosis fragments determined in step (1) to a control level of said protein(s) and / or of said NETosis fragments, and (3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

[0240] In some embodiments, the method further comprises: (1) determining in a bodily fluid sample collected from the subject the level of antibodies that recognize a lipoglycan-containing antigen from Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX 14861744) or a derivative thereof; (2) comparing the level of the antibodies determined in step (1g) to a control level of said antibodies, and (3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, if when the level of the antibodies determined in step (1) is statistically significantly higher than the control level.

[0241] In some embodiments, the method further comprises: (1) determining in the gastrointestinal (GI) microbiota sample collected from the subject an abundance of bacteria from Blautia (Ruminococcus) gnavus such as the strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) which have more recently been assigned to the Lachnospiraceae family, wherein said strain has 16S rDNA with at least 95% sequence identity tothe 16S rDNA of Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S 107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) over its entire length or at least 99% sequence identity to any single V region of the 16S rDNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744), or another bacterial strain from Blautia (Ruminococcus) gnavus species that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744); (2) comparing the abundance of bacteria determined in step (1) to a control abundance of said bacteria, and (3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when the abundance of bacteria determined in step (1) is statistically significantly higher than the control abundance.

[0242] In one aspect, the invention provides a method for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, said method comprising: (1) determining in a blood sample collected from the subject the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments; (2) comparing the level of the protein(s) and / or of NETosis fragments determined in step (1) to a control level of said protein(s) and / or of said NETosis fragments, and (3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis, and / or renal disease when the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

[0243] In some embodiments, the method further comprises: (d) determining in a sample collected from the subject the level of mRNA of two or more genes selected from interferon alpha inducible protein 27 (IFI27), interferon inducible protein 44 (IFI44), radical S-adenosyl methionine domain containing 2 (RSAD2), and interferon inducible protein 44 like (IFI44L); (e) comparing each of the mRNA levels determined in step (d) to a corresponding control mRNA level, and (f) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when at least two of the mRNA levels determined in step (d) are statistically significantly lower than the corresponding mRNA levels in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

[0244] In some embodiments, the method further comprises (1) determining in a bodily fluid sample collected from the subject the level of antibodies that recognize a lipoglycan-containing antigen from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae or a derivative thereof; (2) comparing the level of the antibodies determined in step (1) to a control level of said antibodies, and (3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the level of the antibodies determined in step (1) is statistically significantly higher than the control level.

[0245] In some embodiments, the method further comprises (1) determining in the gastrointestinal (GI) microbiota sample collected from the subject an abundance of bacteria from Blautia (Ruminococcus) gnavus, such as the strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) which have more recently been assigned to the Lachnospiraceae family, wherein said strain has 16S rDNA with at least 95% sequence identity to the 16S rDNA of Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) over its entire length or at least 99% sequence identity to any single V region of the 16S rDNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strainSI 07-48 (NCBI SRA Accession No: SRX 14861748) or SI 07-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744), or another bacterial strain from Blautia (Ruminococcus) gnavus species that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744); (2) comparing the abundance of bacteria determined in step (1) to a control abundance of said bacteria, and (3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when the abundance of bacteria determined in step (1) is statistically significantly higher than the control abundance.

[0246] In one aspect, the invention provides a method of treating a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), said method comprising: (a) determining in a sample collected from the subject the level of mRNA of two or more genes selected from integrin subunit alpha 2b (ITGA2B), multimerin 1 (MMRN1), ATP binding cassette subfamily C member 4 (ABCC4), dematin actin binding protein (DMTN), GATA binding protein 1 (GATA1), lymphocyte antigen 6 family member G6F (LY6G6F), myosin light chain 9 (MYL9), platelet factor 4 (PF4), protein S (PROS1), synuclein alpha (SNCA), secreted protein acidic and cysteine rich (SPARC), PDGFA (platelet derived growth factor subunit A), and VTI1B (vesicle transport through interaction with t-SNAREs IB), wherein the sample comprises platelets, (b) comparing each of the mRNA levels determined in step (a) to a corresponding control mRNA level, and (c) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when each of the mRNA levels determined in step (a) is at least 1.5-fold higher than the corresponding control mRNA level.

[0247] In some embodiments, the method further comprises: (d) determining in a sample collected from the subject the level of mRNA of two or more genes selected from interferon alpha inducible protein 27 (IFI27), interferon inducible protein 44 (IFI44), radical S-adenosyl methionine domain containing 2 (RSAD2), and interferon inducible protein 44 like (IFI44L); (e) comparing each of the mRNA levels determined in step (d) to a corresponding control mRNA level, and (I) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when at least two of themRNA levels determined in step (d) are statistically significantly lower than the corresponding mRNA levels in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

[0248] In some embodiments, the method further comprises: (1) determining in a blood sample collected from the subject the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments; (2) comparing the level of the protein(s) and / or of NETosis fragments determined in step (1) to a control level of said protein(s) and / or of said NETosis fragments, and (3) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

[0249] In some embodiments, the method further comprises: (1) determining in a bodily fluid sample collected from the subject the level of antibodies that recognize a lipogly can-containing antigen from Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or a derivative thereof; (2) comparing the level of the antibodies determined in step (1g) to a control level of said antibodies, and (3) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the level of the antibodies determined in step (1) is statistically significantly higher than the control level.

[0250] In some embodiments, the method further comprises: (1) determining in the gastrointestinal (GI) microbiota sample collected from the subject an abundance of bacteria from Blautia (Ruminococcus) gnavus, such as the strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZIF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) which have more recently been assigned to the Lachnospiraceae family, wherein said strain has 16S rDNA with at least 95% sequence identity to the 16S rDNA of Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056 (HumanMicrobiome Project (HMP) ID 1201 ; GenBank: AZJF00000000), or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) over its entire length or at least 99% sequence identity to any single V region of the 16S rDNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744), or another bacterial strain from Blautia (Ruminococcus) gnavus species that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744); (2) comparing the abundance of bacteria determined in step (1) to a control abundance of said bacteria, and (3) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the abundance of bacteria determined in step (1) is statistically significantly higher than the control abundance.

[0251] In another aspect, the invention provides a method of treating a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), said method comprising: (1) determining in a blood sample collected from the subject the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments; (2) comparing the level of the protein(s) and / or of NETosis fragments determined in step (1) to a control level of said protein(s) and / or of said NETosis fragments, and (3) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

[0252] In some embodiments, the method further comprises: (d) determining in a sample collected from the subject the level of mRNA of two or more genes selected from interferon alpha inducible protein 27 (IFI27), interferon inducible protein 44 (IFI44), radical S-adenosyl methionine domain containing 2 (RSAD2), and interferon inducible protein 44 like (IFI44L); (e) comparing each of the mRNA levels determined in step (d) to a corresponding control mRNA level, and (f) administering to the subject a treatment effective for treating or preventing lupusnephritis or other forms of SLE with renal involvement or polyarthritis, when at least two of the mRNA levels determined in step (d) are statistically significantly lower than the corresponding mRNA levels in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

[0253] In some embodiments, the method further comprises (1) determining in a bodily fluid sample collected from the subject the level of antibodies that recognize a lipoglycan-containing antigen from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae or a derivative thereof; (2) comparing the level of the antibodies determined in step (1) to a control level of said antibodies, and (3) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the level of the antibodies determined in step (1) is statistically significantly higher than the control level.

[0254] In some embodiments, the method further comprises: (1) determining in the gastrointestinal (GI) microbiota sample collected from the subject an abundance of bacteria from Blautia (Ruminococcus) gnavus, such as the strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) which have more recently been assigned to the Lachnospiraceae family, wherein said strain has 16S rDNA with at least 95% sequence identity to the 16S rDNA of Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) over its entire length or at least 99% sequence identity to any single V region of the 16S rDNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744), or another bacterial strain from Blautia (Ruminococcus) gnavus species that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056, or strainSI 07-48 (NCBI SRA Accession No: SRX 14861748) or SI 07-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744); (2) comparing the abundance of bacteria determined in step (1) to a control abundance of said bacteria, and (3) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the abundance of bacteria determined in step (1) is statistically significantly higher than the control abundance.

[0255] In another aspect, the invention provides a method for monitoring the effect of a treatment on development of a disorder in a subject, wherein the disorder is lupus nephritis or other forms of systemic lupus erythematosus (SLE) with renal involvement or polyarthritis which method comprises: (a) determining in a sample collected from the subject prior to initiation of the treatment the level of mRNA of two or more genes selected from integrin subunit alpha 2b (ITGA2B), multimerin 1 (MMRN1), ATP binding cassette subfamily C member 4 (ABCC4), dematin actin binding protein (DMTN), GATA binding protein 1 (GATA1), lymphocyte antigen 6 family member G6F (LY6G6F), myosin light chain 9 (MYL9), platelet factor 4 (PF4), protein S (PROS1), synuclein alpha (SNCA), secreted protein acidic and cysteine rich (SPARC), PDGFA (platelet derived growth factor subunit A), and VTI1B (vesicle transport through interaction with t-SNAREs IB), wherein the sample comprises platelets, (b) determining the mRNA levels of said two or more genes in the same type of sample collected from the subject in the course of or following the treatment, (c) comparing the mRNA levels determined in steps (a) and (b), and (d) (i) determining that the treatment is effective for said disorder if each of the mRNA levels determined in step (b) is not statistically significantly higher than the corresponding mRNA level determined in step (a), or (ii) determining that the treatment is not effective for said disorder if at least one mRNA expression level determined in step (b) is at least 1.5-fold higher than the corresponding mRNA level determined in step (a).

[0256] In some embodiments, the method can further comprise (e) determining in a sample collected from the subject prior to initiation of the treatment the level of mRNA of two or more genes selected from interferon alpha inducible protein 27 (IFI27), interferon inducible protein 44 (IFI44), radical S-adenosyl methionine domain containing 2 (RSAD2), and interferon inducible protein 44 like (IFI44L); (f) determining the mRNA levels of said two or more genes in the same type of sample collected from the subject in the course of or following the treatment; (g) comparing the mRNA levels determined in steps (e) and (f), and (h)(1) determining that the treatment iseffective for said disorder if the mRNA levels determined in step (e) are not statistically significantly lower for more than one mRNA as compared to the corresponding mRNA levels determined in step (f), or (2) determining that the treatment is not effective for said disorder if the mRNA levels determined in step (e) are statistically significantly lower for more than one mRNA as compared to the corresponding mRNA levels determined in step (f).

[0257] In some embodiments, the method can further comprise (1) determining in a blood sample collected from the subject prior to initiation of the treatment the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments; (2) determining the level of P- selectin protein, of PF4 protein, and / or of NETosis fragments in the same type of sample collected from the subject in the course of or following the treatment; (3) comparing the protein levels and / or the levels of NETosis fragments determined in steps (1) and (2), and (4) (i) determining that the treatment is effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is not statistically significantly higher than the corresponding level(s) determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is statistically significantly higher than the corresponding level(s) determined in step (1).

[0258] In some embodiments, the method can further comprise (1) determining in a bodily fluid sample collected from the subject prior to initiation of the treatment the level of antibodies that recognize a lipoglycan-containing antigen from Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX 14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744), or a derivative thereof; (2) determining the level of said antibodies in the same type of sample collected from the subject in the course of or following the treatment; (3) comparing the antibody levels determined in steps (1) and (2), and (4) (i) determining that the treatment is effective for said disorder if the level of antibodies determined in step (2) is not statistically significantly higher than the level of antibodies determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level of antibodies determined in step (2) is statistically significantly higher than the level of antibodies determined in step (1).

[0259] In some embodiments, the method can further comprise (1) determining in the gastrointestinal (GI) microbiota sample collected from the subject prior to initiation of the treatment an abundance of bacteria from Blautia (Ruminococcus) gnavus strain CC55 001C, HM- 1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or another strain from Blautia (Ruminococcus) gnavus species that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744); (2) determining the abundance of said bacteria in the same type of sample collected from the subject in the course of or following the treatment; (3) comparing the abundance of bacteria determined in steps (1) and (2), and (4) (i) determining that the treatment is effective for said disorder if the abundance of bacteria determined in step (2) is not statistically significantly higher than the abundance of said bacteria determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the abundance of bacteria determined in step (2) is statistically significantly higher than the abundance of said bacteria determined in step (1).

[0260] In another aspect, the invention provides a method for monitoring the effect of a treatment on development of a disorder in a subject, wherein the disorder is lupus nephritis or other forms of systemic lupus erythematosus (SLE) with renal involvement, or polyarthritis, which method comprises: (1) determining in a blood sample collected from the subject prior to initiation of the treatment the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments; (2) determining the level of P-selectin protein, of PF4 protein, and / or of NETosis fragments in the same type of sample collected from the subject in the course of or following the treatment; (3) comparing the protein levels and / or the levels of NETosis fragments determined in steps (1) and (2), and (4) (i) determining that the treatment is effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is not statistically significantly higher than the corresponding level(s) determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level(s) of P-selectinprotein, of PF4 protein, and / or of NETosis fragments determined in step (2) is statistically significantly higher than the corresponding level(s) determined in step (1).

[0261] In some embodiments, the method can further comprise (e) determining in a sample collected from the subject prior to initiation of the treatment the level of mRNA of two or more genes selected from interferon alpha inducible protein 27 (IFI27), interferon inducible protein 44 (IFI44), radical S-adenosyl methionine domain containing 2 (RSAD2), and interferon inducible protein 44 like (IFI44L); (f) determining the mRNA levels of said two or more genes in the same type of sample collected from the subject in the course of or following the treatment; (g) comparing the mRNA levels determined in steps (e) and (f), and (h)(1) determining that the treatment is effective for said disorder if the mRNA levels determined in step (e) are not statistically significantly lower for more than one mRNA as compared to the corresponding mRNA levels determined in step (f), or (2) determining that the treatment is not effective for said disorder if the mRNA levels determined in step (e) are statistically significantly lower for more than one mRNA as compared to the corresponding mRNA levels determined in step (f).

[0262] In some embodiments, the method can further comprise (1) determining in a blood sample collected from the subject prior to initiation of the treatment the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments; (2) determining the level of P- selectin protein, of PF4 protein, and / or of NETosis fragments in the same type of sample collected from the subject in the course of or following the treatment; (3) comparing the protein levels and / or the levels of NETosis fragments determined in steps (1) and (2), and (4) (i) determining that the treatment is effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is not statistically significantly higher than the corresponding level(s) determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is statistically significantly higher than the corresponding level(s) determined in step (1).

[0263] In some embodiments, the method further comprises (1) determining in a bodily fluid sample collected from the subject the level of antibodies that recognize a lipoglycan-containing antigen from Blautia (Ruminococcus) giiavus of the family Lachnospiraceae or a derivative thereof; (2) comparing the level of the antibodies determined in step (1) to a control level of said antibodies, (3) comparing the antibody levels determined in steps (1) and (2), and (4) (i)determining that the treatment is effective for said disorder if the level of antibodies determined in step (2) is not statistically significantly higher than the level of antibodies determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level of antibodies determined in step (2) is statistically significantly higher than the level of antibodies determined in step (1).

[0264] In some embodiments, the method further comprises: (1) determining in the gastrointestinal (GI) microbiota sample collected from the subject an abundance of bacteria from Blautia (Ruminococcus) gnavus such as the strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) which have more recently been assigned to the Lachnospiraceae family, wherein said strain has 16S rDNA with at least 95% sequence identity to the 16S rDNA of Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) over its entire length or at least 99% sequence identity to any single V region of the 16S rDNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744), or another bacterial strain from Blautia (Ruminococcus) gnavus species that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744); (2) comparing the abundance of bacteria determined in step (1) to a control abundance of said bacteria, (3) comparing the abundance of bacteria determined in steps (1) and (2), and (4) (i) determining that the treatment is effective for said disorder if the abundance of bacteria determined in step (2) is not statistically significantly higher than the abundance of said bacteria determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the abundance of bacteria determined in step (2) is statistically significantly higher than the abundance of said bacteria determined in step (1).

[0265] In some of the embodiments described herein, the statistical significance of the increase or decrease can be determined by conventional methods. For example and not limitation, the statistical significance can be determined by a Fisher exact test to compare groups, with a predetermined p value of 0.05 for a two-tailed Fisher exact test.

[0266] Any of the diagnostic and monitoring methods described herein can further comprise administration of a treatment according to any of the embodiments described herein. Any of the diagnostic, treatment, and monitoring methods described herein can further comprise recruiting the subject into a clinical trial.Methods of Platelet Purification and Enrichment

[0267] In some embodiments, the bodily fluid sample comprises platelets. In some embodiments, the bodily fluid sample comprises whole blood, serum, plasma, platelet-enriched plasma, purified platelets, urine, and saliva. In some embodiments, the sample comprises blood. In some embodiments, the blood sample comprises whole blood, serum, plasma, platelet-enriched plasma, or purified platelets.

[0268] Blood platelets are non-nucleated cell fragments involved in blood clotting. The platelets may be analyzed directly from a whole blood preparation. However, it is preferred that at least some purification is carried out to separate the platelets from other blood components. In one embodiment, a plasma preparation is prepared from a whole blood preparation and expression levels in the platelets are detected directly from the plasma. Methods of separating plasma from other blood components are well known in the art, for example, plasma can be prepared from anticoagulated blood by centrifugation. The platelets may be further purified from the plasma so that a platelet preparation that is substantially free from other blood components is obtained. This usually requires an initial mild centrifugation at approximately 200 g, to separate plasma from the red and white cellular blood components, followed by a strong centrifugation at approximately 2000 g, to separate the platelets from the plasma. Preferably, the platelets (that have been separated from the plasma) are then lysed and a platelet extract obtained that contains mRNA and protein. Methods of lysing cells and obtaining cell-free extracts are well known in the art.

[0269] The purification of platelets and platelet extracts from whole blood using conventional methods (involving strong centrifugation) often leads to activation of the platelets. In particular, the strong centrifugation step required to separate plasma from the platelets leads to considerable activation of the platelets. Activation of platelets is a well-known phenomenon which results inexocytosis of secretion vesicles and granules (“degranulation”) together with a number of other biochemical changes and a change in shape. Activation often leads to exocytosis of proteins of diagnostic interest and, without wishing to be bound by theory, decreases the diagnostic value of the platelets obtained. Assays to detect the level of platelet activation in a sample are known in the art. It has been found that avoiding strong centrifugation during the purification of the platelets allows non-activated platelets to be obtained. Separating platelets from red and white blood cells using sedimentation or mild centrifugation followed by a separation from plasma by size exclusion filtration (instead of the conventional method requiring strong centrifugation) allows non-activated platelet extracts to be isolated. As used herein, the term “strong centrifugation” refers to the centrifugation forces used typically to pellet platelets for separation from plasma. Strong centrifugation typically requires centrifugation at 1000 g or greater, for example 1500 g or 2000 g. “Mild centrifugation” refers to centrifugation forces that do not cause activation of platelets. In a preferred embodiment, weak centrifugation involves forces of 500 g or less, more preferably 250 g or less, for example 100 g or 50 g. In the embodiment where sedimentation is used to separate the red and white blood cells, it is preferred that, prior to sedimentation, the whole blood sample is diluted with an isotonic buffer, which may contain additives to achieve an appropriate density of plasma. For example, (anti-coagulated) blood can be mixed with phosphate buffered saline (PBS) prior to sedimentation. Alternatively, (anti-coagulated) blood can be mixed directly with Dextran 500 (in PBS, e.g., 1.25% Dextran) to a final concentration of between 0.1% and 5%, preferably 0.25%.

[0270] Using sedimentation to separate biological samples is well known in the art and any sedimentation method may be used. Preferably, the technique of dextran sedimentation is used, wherein the whole blood sample is applied to a solution containing dextran at a density suitable for separating platelets and plasma from other blood components (see, for example, Bertoluzzo et al, 1999 Blood Cell, Mol. Dis. 25(22):339-349). When left untouched, the plasma and platelets will separate from the other blood components, forming a yellowish supernatant. An advantage of using sedimentation, rather than mild centrifugation, to separate the platelets from red and white blood cells is that it avoids the need for expensive centrifuge equipment.

[0271] Sedimentation or mild centrifugation of a whole blood sample results in a supernatant containing platelets and plasma. Although this supernatant may be analyzed directly, it is preferred that further purification occurs, to separate the platelets from the plasma. Thisseparation is traditionally carried out by subjecting the platelet suspension (supernatant) to a strong centrifugation step, which leads to a substantial activation of the platelets. It has now been found that avoiding this strong centrifugation step allows the preparation of non-activated platelets. Preferably, the platelets are separated from the supernatant of the sedimentation step by size exclusion filtration, such as size exclusion gel chromatography. A size exclusion gel can be used that has a molecular weight exclusion that is capable of fractionating or excluding the platelets to separate them from plasma components. Size exclusion gels with suitable molecular weight cutoffs will be apparent to the skilled person. For example and not limitation, the size exclusion gel can have a molecular weight cutoff of 40 MDa or greater. Typically, the size exclusion gel is packed into a column and the platelet suspension resulting from the sedimentation or mild centrifugation of the whole blood sample (e.g. the supernatant of the sedimentation step) is passed through the column, providing an early column eluate containing very high molecular weight components which have been excluded by the size exclusion gel and a later column eluate containing lower molecular weight components which have been included by the chromatography gel. The platelets, which are relatively large, are present in the excluded fraction.

[0272] In a non-limiting exemplary purification method, whole blood can be centrifuged or allowed to sediment to obtain platelet-rich plasma (PRP). The centrifugation conditions can vary depending on the period of time and speed of the centrifugation (e.g., from 800 x g for 5 min to 100 x g for 20 min). The PRP is the top layer of the separated whole blood. The PRP can be removed and optionally combined with a buffer (e.g., a buffer comprising 140 mM NaCl, 2.7 mM KC1, 3.8 mM HEPES, 5 mM EGTA, pH 7.4) optionally combined with prostaglandin El (PGE1, 1 pM final concentration) to prevent platelet activation.

[0273] Optionally, contaminating red and white blood cells can be collected by centrifuging the PRP at 100 x g for 15-20 min (minutes) at room temperature. The platelets remain in the solution. The platelets can be collected by centrifuging at 800 x g for 15—20 min at room temperature.

[0274] Optionally, the collected platelets can be washed in a buffer (e.g., a buffer comprising 10 mM sodium citrate, 150 mM NaCl, 1 mM EDTA, 1% (w / v) dextrose, pH 7.4) without disturbing the pellet. The pellet can be resuspended in a buffer (e.g., a buffer comprising 134 mM NaCl, 12 mM NaHCO.3, 2.9 mM KC1, 0.34 mM Na2HPO4, 1 mM MgC12, 10 mM HEPES, pH 7.4) containing 5 mM glucose and freshly added BSA (3 mg / ml). Platelet activation can be prevented by adding PGE1 (1 pM) and / or apyrase (0.2 U / ml final concentration).

[0275] Another exemplary method of obtaining mRNA from whole blood comprises the use of PAXgene® Blood RNA Tubes.

[0276] The platelets obtained by such methods can be further purified using, e.g., filtration and / or bead-based or column-based separation techniques. For example, the bead or column can be coated with a molecule that specifically binds to contaminants such as red blood cells and / or leukocytes. In a non-limiting example, platelet pellets can be resuspended in phosphate-buffered saline (PBS), 0.5% bovine serum albumin, 2.5 mM of EDTA, and 175 ng / mL of prostaglandin El, and incubated with anti-CD45 and anti-CD235a magnetic microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) to eliminate residual leukocytes and red blood cells, respectively. Platelets can be collected by negative selection using MACS columns (Miltenyi Biotec, Bergisch Gladbach, Germany) and centrifuged at 1000* g for 10 min.

[0277] Once purified platelets are obtained, mRNA and / or protein can be extracted according to conventional methods.Detection of Expression Levels of Genes Involved in the Platelet Activation Pathway

[0278] In some embodiments, the invention provides methods for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, methods of treating those conditions, and / or methods of monitoring the effects of a treatment for those conditions that can involve determining the expression levels of certain genes involved in the platelet activation pathway. In certain embodiments, the determination of the expression levels of the genes comprises determining the mRNA levels of those genes. In certain embodiments, the determination of the expression levels of such genes can be used in combination with the methods disclosed throughout the specification such as, but not limited to, (i) detection of expression levels of certain interferon (IFN) stimulated genes (ISG), (ii) detection of certain platelet activation-associated protein levels, (iii) detection of the level of antibodies to an antigen of a bacterial strain, and (iv) detection of the abundance of the bacterial strain in the subject.

[0279] In some embodiments, the invention provides methods for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritisor other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, methods of treating those conditions, and / or methods of monitoring the effects of a treatment forthose conditions that can involve determining the levels of certain platelet activation-associated proteins in a blood sample from the patient. In certain embodiments, the determination of the levels of such proteins can be used in combination with the methods disclosed throughout the specification such as, but not limited to, (i) detection of expression levels of certain interferon (IFN) stimulated genes (ISG), (ii) detection of the level of antibodies to an antigen of a bacterial strain, and (iii) detection of the abundance of the bacterial strain in the subject.

[0280] In some embodiments, the methods for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, comprises (a) determining in a sample collected from the subject the level of mRNA of two or more genes selected from integrin subunit alpha 2b (ITGA2B), multimerin 1 (MMRN1), ATP binding cassette subfamily C member 4 (ABCC4), dematin actin binding protein (DMTN), GATA binding protein 1 (GATA1), lymphocyte antigen 6 family member G6F (LY6G6F), myosin light chain 9 (MYL9), platelet factor 4 (PF4), protein S (PROS1), synuclein alpha (SNCA), secreted protein acidic and cysteine rich (SPARC), PDGFA (platelet derived growth factor subunit A), and VTI1B (vesicle transport through interaction with t-SNAREs IB), wherein the sample comprises platelets, (b) comparing each of the mRNA levels determined in step (a) to a corresponding control mRNA level of said genes, and (c) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when each of the mRNA levels determined in step (a) is at least 1.5-fold higher than the corresponding control mRNA.

[0281] In some embodiments, step (c) can further comprise determining that the subject is not at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when one or more mRNA levels determined in step (a) are not at least 1.5-fold higher than the corresponding control mRNA levels.

[0282] In certain embodiments, the blood sample is selected from whole blood, plasma, serum, platelet-enriched plasma, and purified platelets.

[0283] In some embodiments, the method comprises determining the mRNA levels of three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, or ten or more genes selected from ITGA2B, MMRN1, ABCC4, DMTN, GATA1, LY6G6F, MYL9, PF4, PROS1, SNCA, SPARC, PDGFA, and VTI1B.

[0284] In some embodiments, the method comprises determining the mRNA levels of ITGA2B, MMRN1, ABCC4, DMTN, GATA1, LY6G6F, MYL9, PF4, PROS1, SNCA, SPARC, PDGFA, and VTI1B genes.

[0285] In some embodiments, the mRNA level is determined using any conventional methodology known to those of skill in the art. As a non-limiting example, mRNA level may be determined using, e.g., RNA-seq, real-time polymerase chain reaction (RT-PCR) (e.g., quantitative RT-PCR), Northern blot analysis, quantitative RT-PCR, nanostring technology, RNA sequencing, or representation in a bulk RNA library made from said sample (optionally using a PAXgene® RNA tube to recover RNA from whole blood), and / or a Ribonuclease protection assay.

[0286] In some embodiments, the control mRNA level for a given gene is (i) a predetermined standard, (ii) the mRNA level of said gene in a similarly prepared sample obtained from the same subject in the past, (iii) the mRNA level of said gene in a similarly prepared sample obtained from a healthy matched subject or a mean value of samples from several matched healthy subjects, or (iv) the mRNA level of said gene in a similarly prepared sample obtained from a subject, wherein said subject does not have a pre-existing diagnosis of lupus nephritis or other forms of SLE with renal involvement or polyarthritis, or a mean value of samples from several such subjects.

[0287] In some embodiments, the predetermined standard is a value which represents a statistically validated threshold ratio of the mRNA levels of said gene equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement or polyarthritis.

[0288] In some embodiments, the method comprises using a standard method for normalizing values of individual gene transcripts, and for comparing the representation of such a transcript in libraries from other individuals that are being compared. Exemplary standard methods include but are not limited to calculation of a Z score for a transcript (mRNA) level of a gene of interest, and DeSeq2 analysis. The Z score is equal to (x - Mean) / standard deviation. This calculation can beperformed across each mRNA level across all the samples. The value for each sample for that mRNA level is therefore transformed against the mean and standard deviation of that mRNA level of that gene across all the samples. DESeq2 is a statistical tool that allows identification of differentially expressed genes from RNA-Seq data. It takes into account the inherent variability in the sequencing data and corrects for library size and RNA composition bias, providing more accurate results. DeSeq2 uses the value in each sample for a specific gene transcript level divided by the geometric mean of that gene transcript level across all the samples. The geometric mean is calculated by multiplying the values together and taking the square root of the result.

[0289] In some embodiments, mRNA levels from genes selected from integrin subunit alpha 2b (ITGA2B; also referred to as GT; GT1; GTA; CD41; GP2B; HP A3; CD41B; GPIIb; BDPLT2; BDPLT16; PPP1R93), multimerin 1 (MMRN1; also referred to as elastin microfibril interfacer 4 (EMILIN-4), ECM; MMRN; GPIa*), ATP binding cassette subfamily C member 4 (ABCC4; also referred to as MRP4; MOATB; MOAT-B), CD9 (also referred to as MIC3; MRP-1; BTCC-1; DRAP-27; TSPAN29; TSPAN-29), dematin actin binding protein (DMTN; also referred to as DMT; EPB49), GATA binding protein 1 (also referred to as globin transcription factor 1; GATA1; ERYF1; GATA- 1; NF -El a), hemoglobin subunit beta (HBB; also referred to as ECYT6; CD113t- C; beta-globin), lymphocyte antigen 6 family member G6F (LY6G6F; also referred to as G6f; NG32; LY6G6; LY6G6D; C6orf21), myosin light chain 9 (MYL9; also referred to as LC20; MLC2; MRLC1; MYRL2; MLC-2C; MMIHS4), platelet factor 4 (PF4; also referred to as PF -4; CXCL4; SCYB4), protein S (PROS1 ; also referred to as PSA; PROS; PS21 ; PS22; PS23; PS24; PS25; THPH5; THPH6), synuclein alpha (SNCA; also referred to as PD1; NACP; PARK1; PARKA), secreted protein acidic and cysteine rich (SPARC; also referred to as ON; ONT; 0117; BM-40), basigin (Ok blood group; also referred to as BSG; OK; 5F7; TCSF; CD147; EMPRIN; HAbl8G; EMMPRIN), C-X-C motif chemokine ligand 5 (CXCL5; also referred to as SCYB5; ENA-78), MAGUK p55 scaffold protein 1 (MPP1; also referred to as MRG1; PEMP; AAG12; EMP55; DXS552E), platelet derived growth factor subunit A (PDGFA; also referred to as PEGF- A; PDGF1), and vesicle transport through interaction with t-SNAREs IB (VTI1B; also referred to as VTI1; VTI1-LIKE; VTI1L; VTI2; v-SNARE; vtil-rpl) are determined.

[0290] ITGA2B, or integrin alpha-IIb, is a protein that in humans is encoded by the ITGA2B gene. ITGA2B, also known as CD41, encodes integrin alpha chain 2b. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. Alpha chain 2bundergoes post-translational cleavage to yield disulfide-linked light and heavy chains that join with beta 3 to form a fibrinogen receptor expressed in platelets that plays a crucial role in coagulation. Mutations that interfere with this role result in thrombasthenia.

[0291] MMRN1, multimerin 1, also known as elastin microfibril interfacer 4 (EMILIN-4), is a protein that, in humans, is encoded by the MMRN1 gene. Multimerin is a massive, soluble protein found in platelets and in the endothelium of blood vessels. It is composed of subunits linked by interchain disulfide bonds to form large, variably sized homomultimers. Multimerin is a factor V / Va-binding protein and may function as a carrier protein for platelet factor V. It may also have functions as an extracellular matrix or adhesive protein.

[0292] ABCC4, ATP -binding cassette sub-family C member 4 (ABCC4), also known as the multidrug resistance-associated protein 4 (MRP4) or multi-specific organic anion transporter B (MOAT-B), is a protein that in humans is encoded by the ABCC4 gene. ABCC4 acts as a regulator of intracellular cyclic nucleotide levels and as a mediator of cAMP-dependent signal transduction to the nucleus. MRP4 / ABCC4 also transports prostaglandins, for example PGE2, out of the cell where they can bind receptors.

[0293] DMTN is an actin binding and bundling protein that plays a structural role in erythrocytes, by stabilizing and attaching the spectrin / actin cytoskeleton to the erythrocyte membrane in a phosphorylation-dependent manner. This protein contains a core domain in the N- terminus, and a headpiece domain in the C-terminus that binds F-actin. When purified from erythrocytes, this protein exists as a trimer composed of two 48 kDa polypeptides and a 52 kDa polypeptide. The different subunits arise from alternative splicing in the 3' coding region, where the headpiece domain is located.

[0294] GATA1 is widely expressed throughout vertebrate species. In humans and mice, it is encoded by the GATA1 and Gatal genes, respectively. These genes are located on the X chromosome in both species. GATA1 regulates the expression (i.e., formation of the genes’ products) of an ensemble of genes that mediate the development of red blood cells and platelets. Its critical roles in red blood cell formation include promoting the maturation of precursor cells, e.g., erythroblasts, to red blood cells and stimulating these cells to erect their cytoskeleton and biosynthesize their oxy gen-carrying components (hemoglobin and heme). GATA1 plays a similarly critical role in the maturation of blood platelets from megakaryoblasts,promegakaryocytes, and megakaryocytes; the latter cells then shed membrane-enclosed fragments of their cytoplasm, i .e., platelets, into the blood.

[0295] LY6G6F is a type I transmembrane protein belonging to the immunoglobin (Ig) superfamily, which is comprised of cell-surface proteins involved in the immune system and cellular recognition.

[0296] MYL9 is a myosin light chain that may regulate muscle contraction by modulating the ATPase activity of myosin heads.

[0297] PF4, or platelet factor-4, is a 70-amino acid protein that is released from the alphagranules of activated platelets, and binds with high affinity to heparin. Its major physiologic role appears to be neutralization of heparin-like molecules on the endothelial surface of blood vessels, thereby inhibiting local antithrombin activity and promoting coagulation. As a strong chemoattractant for neutrophils and fibroblasts, PF4 may play a role in inflammation and wound repair. PF4 is chemotactic for neutrophils, fibroblasts, and monocytes, and interacts with a splice variant of the chemokine receptor CXCR3, known as CXCR3-B.

[0298] PRO SI is a vitamin K-dependent plasma protein that functions as a cofactor for the anticoagulant protease, activated protein C (APC) to inhibit blood coagulation. It is found in plasma in both a free, functionally active form and also in an inactive form complexed with C4b- binding protein. Mutations in this gene result in autosomal dominant hereditary thrombophilia.

[0299] SNCA is a member of the synuclein family, which also includes beta- and gamma- synuclein. Synucleins are abundantly expressed in the brain and alpha- and beta-synuclein inhibit phospholipase D2 selectively. SNCA may serve to integrate presynaptic signaling and membrane trafficking.

[0300] SPARC is a cysteine-rich acidic matrix-associated protein. The encoded protein is required for the collagen in bone to become calcified but is also involved in extracellular matrix synthesis and promotion of changes to cell shape.

[0301] PDGFA is a platelet derived growth factor subunit A protein. The encoded protein is a member of the protein family comprised of both platelet-derived growth factors (PDGF) and vascular endothelial growth factors (VEGF). The encoded preproprotein is proteolytically processed to generate platelet-derived growth factor subunit A, that is capable to homodimerize, or alternatively, heterodimerize with the related platelet-derived growth factor subunit B. Theseproteins bind and activate PDGF receptor tyrosine kinases, which play a role in a wide range of developmental processes.

[0302] VTI1B is involved in regulation of protein localization to plasma membrane. It facilitates SNARE binding activity and chloride channel inhibitor activity.Detection of Expression Levels of Interferon (IFN)-stimulated Genes (ISG)

[0303] In some embodiments, the invention provides methods for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, methods of treating those conditions, and / or methods of monitoring the effects of a treatment for those conditions that can involve determining the expression levels of certain interferon (IFN) stimulated genes (ISG) in combination with detection of expression levels of certain genes involved in the platelet activation pathway. In certain embodiments, the determination of the expression levels of the genes comprises determining the mRNA levels of those genes. In certain embodiments, the determination of the expression levels of these genes can be used in combination with additional methods disclosed throughout the specification such as, but not limited to, (i) detection of certain platelet activation- associated protein levels, (ii) detection of the level of antibodies to an antigen of a bacterial strain, and (iii) detection of the abundance of the bacterial strain in the subject.

[0304] In some embodiments, the invention provides methods for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, methods of treating those conditions, and / or methods of monitoring the effects of a treatment forthose conditions that can involve determining the levels of certain platelet activation-associated proteins in a blood sample from the patient in combination with detection of expression levels of certain interferon (IFN) stimulated genes (ISG). In certain embodiments, the determination of the levels of such proteins can be used in combination with the methods disclosed throughout the specification such as, but not limited to, (i) detection of expression levels of certain genes involved in the platelet activation pathway, (ii) detection of the level of antibodies to an antigen of a bacterial strain, and (iii) detection of the abundance of the bacterial strain in the subject.

[0305] In some embodiments, the methods described herein further comprise (d) determining in a sample collected from the subject the level of mRNA of two or more genes selected from interferon alpha inducible protein 27 (IFI27), interferon inducible protein 44 (IFI44), radical S- adenosyl methionine domain containing 2 (RSAD2), and interferon inducible protein 44 like (IFI44L)IFI27, IFI44, RSAD2, and IFI44L; (e) comparing each of the mRNA levels determined in step (d) to a corresponding control mRNA level, and (f) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when at least two of the mRNA levels determined in step (d) are statistically significantly lower than the corresponding mRNA levels in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

[0306] In certain embodiments, the blood sample is selected from whole blood, plasma, serum, platelet-enriched plasma, and purified platelets.

[0307] In some embodiments, the method comprises determining the mRNA levels of three or more genes selected from IFI27, IFI44, RSAD2, and IFI44L.

[0308] In some embodiments, the method comprises determining the mRNA levels of IFI27, IFI44, RSAD2, and IFI44L genes.

[0309] In some embodiments, the mRNA level is determined using any conventional methodology known to those of skill in the art. As a non-limiting example, mRNA level may be determined using, e.g., RNA-seq, real-time polymerase chain reaction (RT-PCR) (e.g., quantitative RT-PCR), Northern blot analysis, quantitative RT-PCR, nanostring technology, RNA sequencing, or representation in a bulk RNA library made from said sample (optionally using a PAXgene® RNA tube), and / or a Ribonuclease protection assay.

[0310] In some embodiments, the sample collected from the subject is the same sample as used to determine the mRNA levels of ITGA2B, MMRN1, ABCC4, DMTN, GATA1, LY6G6F, MYL9, PF4, PROS1, SNCA, SPARC, PDGFA, and VTI1B genes. In some embodiments, the sample collected from the subject is the same type of sample as used to determine the mRNA levels of ITGA2B, MMRN1, ABCC4, DMTN, GATA1, LY6G6F, MYL9, PF4, PROS1, SNCA, SPARC, PDGFA, and VTI1B genes.

[0311] In some embodiments, the control mRNA level for a given gene is (i) a predetermined standard, (ii) the mRNA level of said gene in a similarly prepared sample obtained from the same subject in the past, (iii) the mRNA level of said gene in a similarly prepared sample obtained from a healthy matched subject or a mean value of samples from several matched healthy subjects, or (iv) the mRNA level of said gene in a similarly prepared sample obtained from a subject, wherein said subject does not have a pre-existing diagnosis of lupus nephritis or other forms of SLE with renal involvement or polyarthritis, or a mean value of samples from several such subjects.

[0312] In some embodiments, the predetermined standard is a value which represents a statistically validated threshold ratio of the mRNA levels of said gene equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement or polyarthritis.

[0313] In some embodiments, the method comprises using a standard method for normalizing values of levels of individual gene transcripts from different subjects, and for comparing the representation of such a transcript in libraries from other individuals that are being compared. Exemplary standard methods include but are not limited to calculation of a Z score for a transcript (mRNA) level of a gene of interest, and DeSeq2 analysis. The Z score is equal to (x - Mean) / standard deviation. This calculation can be performed across each mRNA level across all the samples. The value for each sample for that mRNA level is therefore transformed against the mean and standard deviation of that mRNA level of that gene across all the samples. DESeq2 is a statistical tool that allows identification of differentially expressed genes from RNA-Seq data. It takes into account the inherent variability in the sequencing data and corrects for library size and RNA composition bias, providing more accurate results. DeSeq2 uses the value in each sample for a specific gene transcript level divided by the geometric mean of that gene transcript level across all the samples. The geometric mean is calculated by multiplying the values together and taking the square root of the result.

[0314] In some of the embodiments described herein, the statistical significance of the increase or decrease can be determined by conventional methods. For example and not limitation, the statistical significance can be determined by a Fisher exact test to compare groups, with a predetermined p value of 0.05 for a two-tailed Fisher exact test.Detection of Platelet- Associated Protein Levels

[0315] In some embodiments, the invention provides methods for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, methods of treating those conditions, or methods of monitoring the effects of a treatment forthose conditions that can involve determining the levels of certain platelet activation-associated proteins, optionally in combination with detection of expression levels of certain genes involved in the platelet activation pathway. In certain embodiments, the determination of the expression levels of the genes involved in the platelet activation pathway comprises determining the mRNA levels of those genes. In certain embodiments, the determination of the expression levels of these genes can be used in combination with additional methods disclosed throughout the specification such as, but not limited to, (i) detection of certain platelet activation-associated protein levels, (ii) detection of the level of antibodies to an antigen of a bacterial strain, and (iii) detection of the abundance of the bacterial strain in the subject.

[0316] In some embodiments, the invention provides methods for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, methods of treating those conditions, and / or methods of monitoring the effects of a treatment for those conditions that can involve determining the levels of certain platelet activation-associated proteins in a blood sample from the patient. In certain embodiments, the determination of the levels of such proteins can be used in combination with the methods disclosed throughout the specification such as, but not limited to, (i) detection of expression levels of certain interferon (IFN) stimulated genes (ISG), (ii) detection of the level of antibodies to an antigen of a bacterial strain, (iii) detection of the abundance of the bacterial strain in the subject, and (iv) determining the levels of certain platelet activation-associated proteins, optionally the mRNA levels of such platelet activation-associated proteins.

[0317] In some embodiments, the methods further comprise (1) determining in a blood sample collected from the subject the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments; (2) comparing the level of the protein(s) and / or of NETosis fragmentsdetermined in step (1) to a control level of said protein(s) and / or of said NETosis fragments, and (3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

[0318] In some embodiments, step (1) further comprises determining the level of both P-selectin protein and PF4 protein and / or of NETosis fragments, and step (3) comprises determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, when the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

[0319] In some embodiments, step (3) comprises determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, when the levels of both P-selectin protein and PF4 protein and / or of NETosis fragments determined in step (1) are statistically significantly higher than the corresponding control levels.

[0320] In certain embodiments, the blood sample is selected from whole blood, plasma, serum, platelet-enriched plasma, and purified platelets.

[0321] In some embodiments, the control protein level is (i) a predetermined standard, (ii) the level of said protein in a similarly prepared sample obtained from the same subject in the past, (iii) the level of said protein in a similarly prepared sample obtained from a healthy matched subject or a mean value of samples from several matched healthy subjects, or (iv) the level of said protein in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement or polyarthritis; or a mean value of samples from several such patients.

[0322] In some embodiments, the control NETosis fragment level is (i) a predetermined standard, (ii) the level of said NETosis fragments in a similarly prepared sample obtained from the same subject in the past, (iii) the level of said NETosis fragments in a similarly prepared sample obtained from a healthy matched subject or a mean value of samples from several matched healthy subjects, or (iv) the level of said NETosis fragments in a similarly prepared sample obtained froman SLE or ILE patient, or a patient being evaluated for an SLE or TLE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement or polyarthritis; or a mean value of samples from several such patients.

[0323] In some embodiments, the predetermined standard is a value which represents a statistically validated threshold ratio of the levels of said protein or NETosis fragments equal to the mean value within the range of corresponding values in a cohort of healthy matched subjects or in a cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement or polyarthritis.

[0324] In some of the embodiments described herein, the statistical significance of the increase or decrease can be determined by conventional methods. For example and not limitation, the statistical significance can be determined by a Fisher exact test to compare groups, with a predetermined p value of 0.05 for a two-tailed Fisher exact test.

[0325] In some embodiments of any of the above-described methods, the protein level may be determined using any conventional methodology known to those of skill in the art. As a nonlimiting example, protein level may be determined using an enzyme-linked immunosorbent assay (ELISA), a radioimmunoassay, a Western blot, an activity assay, counterimmuno-electrophoresis (CIE), immunodiffusion, bead-based assays, and / or a multiplex electrochemiluminescence-based assay. In some embodiments, protein level may be determined using approaches comprising, e.g., Biuret methods, UV absorption, Colorimetric dye-based methods, Fluorescent dye-based methods, Turbimetric method, BCA assay, Lowry assay, and / or Bradford assay.

[0326] P-selectin is a type-1 transmembrane protein that in humans is encoded by the SELP gene. P-selectin functions as a cell adhesion molecule (CAM) on the surfaces of activated endothelial cells, which line the inner surface of blood vessels, and is expressed on activated platelets. In unactivated endothelial cells, it is stored in granules called Weibel-Palade bodies. In unactivated platelets, P-selectin is stored in a-granules.Detection of the Level of Antibodies to a Bacterial Antigen

[0327] In some embodiments, the invention provides methods for determining whether a subj ect diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE) is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, methods of treating those conditions, or methods of monitoring the effects of a treatment for those conditionsthat can involve determining the level of antibodies that recognize a bacterial antigen in combination with determining the expression levels of certain genes involved in the platelet activation pathway. In certain embodiments, the determination of the expression levels of the genes involved in the platelet activation pathway comprises determining the mRNA levels of those genes. In certain embodiments, such methods can be used in combination with additional methods disclosed throughout the specification such as, but not limited to, (i) detection of expression levels of certain interferon (IFN) stimulated genes (ISG), (ii) detection of certain platelet activation- associated protein levels, and (iii) detection of the levels of the bacterial strain in the subject.

[0328] In some embodiments, the invention provides methods for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, methods of treating those conditions, and / or methods of monitoring the effects of a treatment for those conditions that can involve detection of the level of antibodies to an antigen of a bacterial strain in combination with determining the levels of certain platelet activation-associated proteins in a blood sample from the patient. In certain embodiments, the determination of the levels of such proteins can be used in combination with the methods disclosed throughout the specification such as, but not limited to, (i) detection of expression levels of certain interferon (IFN) stimulated genes (ISG), (ii) determining the expression levels of certain genes involved in the platelet activation pathway, and (iii) detection of the abundance of the bacterial strain in the subject.

[0329] In some embodiments, the methods further comprise (1) determining in a bodily fluid sample collected from the subject the level of antibodies that recognize a lipoglycan-containing antigen from Blautia (Ruminococcus) gnavus strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX 14861744), or a derivative thereof; (2) comparing the level of the antibodies determined in step (1) to a control level of said antibodies, and (3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when the level of the antibodies determined in step (1) is statistically significantly higher than the control level.

[0330] In certain embodiments, the present invention provides for methods of detecting antibodies that recognize a bacterial antigen. In certain embodiments, the antibodies are IgA, IgD, IgE, IgG, or IgM. In certain embodiments, the antibodies are IgG. In certain embodiments, the antibodies are detected in a bodily fluid sample comprising platelets. In certain embodiments, the bodily fluid is selected from whole blood, plasma, serum, urine, platelet-enriched plasma, purified platelets, and saliva.

[0331] An antigen is a molecule capable of inducing an immune response in a host. For example, an antigen can be any protein, carbohydrate, lipid, nucleic acid, or mixture of these, or a plurality of these, to which an immune response is elicited.

[0332] In certain embodiments, the bacterial antigen is derived from Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744). This antigen is also described in WO2018209149 which is incorporated in its entirety herein. Taxonomically, Ruminococcus gnavus was originally assigned to the genus Ruminococcus in the family Ruminococcaceae . The Ruminococcus genus contained 18 species, but on the basis of 16S ribosomal gene sequencing, some of the species have been reassigned to the new genus Blautia within the family Lachnospiraceae , which, like Ruminococcaceae, is a part of the order Clostridial es. R. gnavus was reassigned due to its active fermentative ability, but R. gnavus has retained the Ruminococcus genus name.

[0333] In certain embodiments, the bacterial antigen is derived from a subset of bacterial strains from the Lachnospiraceae family, wherein the strain has 16S rDNA or rRNA with at least 95%, 96%, 97%, 98%, 99% or including 100% sequence identity to the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744), as described above, over its entire length or at least 95%, 96%, 97%, 98%, 99% or including 100% sequence identity to any single V region of the 16S rDNA or rRNA. In certain embodiments, the bacterial antigen is derived from a bacterial strain from the Lachnospiraceae family, wherein the strain has 16S rDNA or rRNA with at least 95%, sequence identity to the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) over its entire length. In certain embodiments, the bacterial antigen is derived from a bacterial strain from the Lachnospiraceae family, wherein the strain has at least 97% sequence identity to any single V region of the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744). In certain embodiments, the V region of 16S rDNA or rRNA is the V4 region. The antigen can be defined by structural glycan features and by recognition of the glycan by the above-described monoclonal antibodies. Not all Blautia (Ruminococcus) gnavus strains produce the antigen, presumably because some or all of the necessary synthetic genes are absent from the strain genome. In certain embodiments, the bacterial antigen is derived from a bacterial strain from the Lachnospiraceae family, wherein the strain has at least 99% sequence identity to any single V region of the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM- 1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744). In certain embodiments, the V region of 16S rDNA or rRNA is the V4 region.

[0334] In certain embodiments, the bacterial antigen is derived from a bacterial strain from the Blautia genus, wherein the strain has 16S rDNA or rRNA genes with at least 95%, 96%, 97%, 98%, 99% or including 100% sequence identity to the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744), as described above, over its entire length or at least 95%, 96%, 97%, 98%, 99% or including 100% sequence identity to any single V region of the 16S rDNA or rRNA. In certain embodiments, the bacterial antigen is derived from a bacterial strain from the Blautia genus, wherein the strain has 16S rDNA or rRNA with at least 95%, sequence identity to the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM- 1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) over its entire length. In certain embodiments, the bacterial antigen is derived from a bacterial strain from the Blautia genus, wherein the strain has at least 97% sequence identity to any single V region of the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, orstrain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744). In certain embodiments, the V region of 16S rDNA or rRNA is the V4 region. In certain embodiments, the bacterial antigen is derived from a bacterial strain from the Blautia genus, wherein the strain has at least 99% sequence identity to any single V region of the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744). In certain embodiments, the V region of 16S rDNA or rRNA is the V4 region.

[0335] In certain embodiments, the bacterial antigen is derived from a bacterial strain from the Blautia (Ruminococcus) gnavus species, wherein the strain has 16S rDNA or rRNA with at least 95%, 96%, 97%, 98%, 99% or including 100% sequence identity to the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S 107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744), as described above, over its entire length or at least 95%, 96%, 97%, 98%, 99% or including 100% sequence identity to any single V region of the 16S rDNA or rRNA. In certain embodiments, bacterial antigen is derived from a bacterial strain from the Blautia (Ruminococcus) gnavus species, wherein the strain has 16S rDNA or rRNA with at least 95%, sequence identity to the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107- 86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) over its entire length. In certain embodiments, the bacterial antigen is derived from a bacterial strain from the Blautia (Ruminococcus) gnavus species, wherein the strain has at least 97% sequence identity to any single V region of the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744). In certain embodiments, the V region of 16S rDNA or rRNA is the V4 region. In certain embodiments, the bacterial antigen is derived from a bacterial strain from the Blautia (Ruminococcus) gnavus species, wherein the strain has at least 99% sequence identity to any single V region of the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) orS107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744). In certain embodiments, the V region of 16S rDNA or rRNA is the V4 region.

[0336] In certain embodiments, the bacterial antigen is a non-protein, non-nucleic acid molecule. In certain embodiments, the non-protein, non-nucleic acid bacterial antigen is a carbohydrate. In certain embodiments, the bacterial antigen comprises a lipoglycan.

[0337] In addition to using full-length lipoglycan or its derivatives, the methods of the invention can use fragments of such antigens for antibody detection. Production of such fragments is disclosed, e.g., in van der Es et al., Chem Soc Rev. 201746(5): 1464-1482.

[0338] In certain embodiments, the lipoglycan or derivative thereof is derived from Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744).

[0339] In addition to using full-length lipoglycan, the methods of the invention can use lipoglycan derivatives, including lipoglycan fragments, for antibody detection. Production of such fragments is disclosed, e.g., in van der Es et al., Chem Soc Rev. 201746(5): 1464-1482.

[0340] In certain embodiments, the lipoglycan-containing antigen or derivative thereof is derived from Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744).

[0341] In certain embodiments, the lipoglycan-containing antigen or derivative thereof is derived from a bacterial strain from the Lachnospiraceae family, wherein the strain has 16S rDNA or rRNA with at least 95%, 96%, 97%, 98%, 99% or including 100% sequence identity to the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107- 48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744), as described above, over its entire length or at least 95%, 96%, 97%, 98%, 99% or including 100% sequence identity to any single V region of the 16S rDNA or rRNA. In certain embodiments, the lipoglycan-containing antigen or derivative thereof is derived from a bacterial strain from the Lachnospiraceae family, wherein the strain has 16S rDNA or rRNA with at least 95%, sequence identity to the 16S rDNAor rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) over its entire length. In certain embodiments, the lipoglycan or derivative thereof is derived from a bacterial strain from the Lachnospiraceae family, wherein the strain has at least 97% sequence identity to any single V region of the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM- 1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744). In certain embodiments, the V region of 16S rDNA or rRNA is the V4 region. In certain embodiments, the lipoglycan-containing antigen or derivative thereof is derived from a bacterial strain from the Lachnospiraceae family, wherein the strain has at least 99% sequence identity to any single V region of the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM- 1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744). In certain embodiments, the V region of 16S rDNA or rRNA is the V4 region.

[0342] In certain embodiments, the lipoglycan-containing antigen or derivative thereof is derived from a bacterial strain from the Blautia genus, wherein the strain has 16S rDNA or rRNA with at least 95%, 96%, 97%, 98%, 99% or including 100% sequence identity to the 16S rDNA or rRNA oiBlautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744), as described above, over its entire length or at least 95%, 96%, 97%, 98%, 99% or including 100% sequence identity to any single V region of the 16S rDNA or rRNA. In certain embodiments, the lipoglycan-containing antigen or derivative thereof is derived from a bacterial strain from the Blautia genus, wherein the strain has 16S rDNA or rRNA with at least 95%, sequence identity to the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) over its entire length. In certain embodiments, the lipoglycan- containing antigen or derivative thereof is derived from a bacterial strain from the Blautia genus, wherein the strain has at least 97% sequence identity to any single V region of the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain SI 07-48 (NCBISRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744). In certain embodiments, the V region of 16S rDNA or rRNA is the V4 region. In certain embodiments, the lipoglycan-containing antigen or derivative thereof is derived from a bacterial strain from the Blautia genus, wherein the strain has at least 99% sequence identity to any single V region of the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744). In certain embodiments, the V region of 16S rDNA or rRNA is the V4 region.

[0343] In certain embodiments, the lipoglycan-containing antigen or derivative thereof is derived from a bacterial strain from the Blautia (Ruminococcus) gnavus species, wherein the strain has 16S rDNA or rRNA with at least 95%, 96%, 97%, 98%, 99% or including 100% sequence identity to the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM- 1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744), as described above, over its entire length or at least 95%, 96%, 97%, 98%, 99% or including 100% sequence identity to any single V region of the 16S rDNA or rRNA. In certain embodiments, the lipoglycan-containing antigen or derivative thereof is derived from a bacterial strain from the Blautia (Ruminococcus) gnavus species, wherein the strain has 16S rDNA or rRNA with at least 95%, sequence identity to the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107- 86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) over its entire length. In certain embodiments, the lipoglycan-containing antigen or derivative thereof is derived from a bacterial strain from the Blautia (Ruminococcus) gnavus species, wherein the strain has at least 97% sequence identity to any single V region of the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107- 48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744). In certain embodiments, the V region of 16S rDNA or rRNA is the V4 region. In certain embodiments, the lipoglycan- containing antigen or derivative thereof is derived from a bacterial strain from the Blautia (Ruminococcus) gnavus species, wherein the strain has at least 99% sequence identity to any singleV region of the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM- 1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744). In certain embodiments, the V region of 16S rDNA or rRNA is the V4 region.

[0344] In certain embodiments, the bacteria have antigenic gene products other than lipoglycan- containing antigen that play key roles, individually or in combination, to drive the pathogenesis of SLE and lupus nephritis as well as other inflammatory diseases such as, but not limited to, glomerulonephritis (e.g., IgA nephropathy).

[0345] In certain embodiments, bacterial antigen is obtained by a process that integrates treating a culture of bacteria with a lysozyme, a nucleic acid digesting agent (e.g., nucleases), and / or a protease. In certain embodiments, the culture is treated with a protease after treatment with a lysozyme and / or a nucleic acid digesting agent. In certain embodiments, the culture is treated with a protease before treatment with a lysozyme and / or a nucleic acid digesting agent.

[0346] In certain embodiments, the bacteria are cultured by ordinary methods known to one of skill in the art. In certain embodiments, the bacteria are cultured in a rich nutrient media. In certain embodiments, the bacteria are cultured in chopped meat broth or other prepared media.

[0347] Lysozymes are enzymes that occur naturally in egg white, human tears, saliva, and other body fluids, capable of destroying the cell walls of certain bacteria and thereby acting as a mild antiseptic. Exemplary lysozymes include, but are not limited to, animal based lysozymes (e.g., human, turkey, chicken, dog, rat), egg white lysozymes (e.g., chickens, ducks, quails, turkeys, and geese), and plant lysozymes.

[0348] Nucleic acid fragmentation can be achieved by any method of polynucleotide fragmentation known to those of skill in the art including, but not limited to, nuclease digestion (e.g., restriction enzymes, non-sequence-specific nucleases such as DNase I, micrococcal nuclease, SI nuclease and mung bean nuclease), and physical methods such as shearing and sonication. Isolation is accomplished by any technique that allows for the selective purification of marked fragments from unmarked fragments (e.g., size or affinity separation techniques and / or purification on the basis of a physical property).

[0349] Random cleavage can be achieved by enzymatic methods including: a single or a combination of nucleases such as Serratia marcescens, Fragmentase® (New England Biolabs, Ipswich, MA), DNAse I, and Benzonase® (EMD, Gibbstown, NI), or other types of nucleases.Fragmentase is an endonuclease that generates dsDNA breaks in a time-dependent manner to yield 100bp-800bp DNA fragments. Benzonase is genetically engineered endonuclease from Serratia marcescens that can effectively cleave both DNAs and RNAs. Other enzymatic methods include the use of Vvn nuclease alone or Serratia nuclease, or DNase I, or other nuclease in the art such as Shearase™ (Zymo Research, Irvine, CA) or Ion Shear™ (Life Technologies, Grand Island, NY). Nicking enzymes can be used since the DNA is denatured after fragmentation.

[0350] Exemplary proteases include, but are not limited to, proteinase K, gelatinase A, gelatinase B, trypsin, trypsin (Arg blocked), trypsin (Lys blocked), clostripain, endoproteinase (e.g., microvillar, Asp-N), chymotrypsin, cyanogen bromide, iodozobenzoate, Myxobacter P., Armillaria, pepsin (e.g., luminal), dipeptidyl peptidase, enteropeptidase, hydrolase, bromelain, ficin, papain, pepsin, plasmin, thermolysin, thrombi, and cathepsins.

[0351] In certain embodiments, the bacterial antigen is obtained by a) pelleting a bacterial culture; b) producing a bacterial extract by treating the bacteria with a protein extraction buffer in the presence of a lysozyme, a nuclease, and / or a protease, and a detergent under non-denaturing conditions; c) incubating the mixture; d) removing cell debris (e.g., centrifugation), and using the supernatant as the antigen preparation. In certain embodiments, the bacterial extract is incubated in the presence of a lysozyme, a nuclease, and a protease. In certain embodiments, the nuclease is Serratia marcescens. In certain embodiments, the protease is Proteinase K.

[0352] In certain embodiments, the sample may be purified using size exclusion chromatography. In certain embodiments, the sample is enriched for specific characteristic polymers and oligomers and to remove irrelevant components.

[0353] In certain embodiments, the bacteria are incubated at 37°C under anaerobic (75% N2, 20% CO2, and 5% H2) conditions for at least 2, at least 3, at least 4, at least 5, at least 6, or at least 7 days. In certain embodiments, the cells are incubated for about 2 to about 7 days.

[0354] In certain embodiments, the lipoglycan-containing antigen comprises a diacyl-glycerol or triacyl-glycerol moiety and is not a capsular polysaccharide or teichoic acid.

[0355] In certain embodiments, the lipoglycan-containing antigen has an estimated molecular weight based on Western blot between about 20,000 and about 30,000 Daltons.

[0356] In certain embodiments, the lipoglycan-containing antigen shares one or more antigenic determinants with or is the same as the lipoglycan-containing antigen obtained from Blautia (Ruminococcus) gnavus strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID1201 ; GenBank: AZJF00000000), or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744), using a method selected from:

[0357] (i) Method 1 comprising the steps: a. culturing Blautia (Ruminococcus) guavas strain CC55 001C, HM-1056, or strain S107- 48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) at 37°C under anaerobic conditions for 2-7 days, and b. producing bacterial extract in the presence of a lysozyme, Serratia marcescens endonuclease, Proteinase K, and a detergent under non-denaturing conditions;

[0358] (ii) Method 2 comprising the steps: a. culturing Blautia (Ruminococcus) gnavus strain CC55 001C, HM-1056, or strain S107- 48 (NCBI SRA Accession No: SRX14861748) or S 107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) in rich nutrient media at 37°C under anaerobic conditions (75% N2, 20% CO2, and 5% H2) for 2-7 days, b. pelleting bacteria by centrifugation, c. producing a bacterial extract in a protein extraction buffer in the presence of lysozyme, Serratia marcescens endonuclease, and a detergent under non-denaturing conditions, d. treating the extract obtained in step (c) with Proteinase K, e. incubating the treated extract obtained in step (d) at 55°C for about 10 minutes, f. removing cell debris by centrifugation, and g. using the supernatant as an antigen preparation; or

[0359] (iii) Method 3 comprising the steps: a. disrupting Blautia (Ruminococcus) gnavus strain CC55 001C, HM-1056, or strain S107- 48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) cells with a French press, b. ultracentrifugating to obtain a precipitate and produce an ultracentrifugation supernatant, c. subjecting the ultracentrifugation supernatant obtained in step (b) to butanol -water extraction and isolating an aqueous phase,d. applying the aqueous phase from step (c) to a hydrophobic interaction chromatography matrix, and e. isolating lipoglycan-containing fractions.

[0360] In certain embodiments, the level of antibodies is determined using an assay such as, but not limited to, a bead-based assay, an enzyme-linked immunosorbent assay (ELISA), a radioimmunoassay, counterimmuno-electrophoresis (CIE), immunodiffusion, Western blotting, microscopy, and / or any variant of an assay that detects these same antigen-reactive antibodies. In certain embodiments, the bacterial antigen, lipoglycan, or derivative thereof, is coated onto a bead or onto the surface of an ELISA plate or other solid phase used for detection.

[0361] In certain embodiments, the control level of antibodies can be obtained from, for example, (i) a predetermined standard; (ii) the level in a similarly prepared sample obtained from the same subject in the past; (iii) the level in a similarly prepared sample obtained from a matched healthy subject or an average or mean value of several matched healthy subjects; or (iv) the level of the antibodies in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein the patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement or polyarthritis, or an average or mean value of samples from several such patients.

[0362] In certain embodiments, the average / mean is obtained by testing at least two, at least three, at least four, at least five, at least 10, at least 20, at least 25, at least 50, at least 75, or at least 100 healthy subjects. In certain embodiments, the average is the mean plus one, two, or three standard deviations of a group of healthy matched subjects. In certain embodiments, the level of the antibodies is determined to be statistically significantly higher than the control level if the level is higher than the mean value of normal plus one standard deviation. In certain embodiments, the level of the antibodies is determined to be statistically significantly higher than the control level if the level is higher than the mean value of normal plus two standard deviations. In certain embodiments, the level of the antibodies is determined to be statistically significantly higher than the control level if the level is higher than the mean value of normal plus three standard deviations. In certain embodiments, the level of the antibodies is determined to be statistically significantly higher than the control level if the level is higher than the mean value calculated for at least 40 healthy matched subjects plus three standard deviations. In one embodiment a level is measuredin the serum of an individual and we reevaluate over time to determine if there are patterns of increases over time.

[0363] In certain embodiments, the predetermined standard is a value which represents a statistically validated threshold ratio of the levels of the antibodies equal to the highest possible value within the range of corresponding values in a large cohort of matched healthy subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement or polyarthritis. In certain embodiments, the predetermined standard is a value which represents a statistically validated threshold cut-off of the levels of the antibodies equal to the highest possible value within the range of corresponding values in a large cohort of matched healthy subjects.

[0364] In certain embodiments, the level of antibodies is determined in a sample of bodily fluid selected from whole blood, plasma, serum, urine, platelet-enriched plasma, purified platelets, and saliva.

[0365] In some of the embodiments described herein, the statistical significance of the increase or decrease can be determined by conventional methods. For example and not limitation, the statistical significance can be determined by a Fisher exact test to compare groups, with a predetermined p value of 0.05 for a two-tailed Fisher exact test.Detection of the Abundance of a Bacterial Strain

[0366] In certain embodiments, the invention provides methods for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, methods of treating those conditions, or methods of monitoring the effects of a treatment for those conditions that can involve determining the abundance of a bacterial strain in combination with determining the expression levels of certain genes involved in the platelet activation pathway. In certain embodiments, the method of determining the expression levels of the genes comprises determining the mRNA levels of those genes. In certain embodiments, such methods can be used in combination with additional methods disclosed throughout the specification such as, but not limited to, (i) detection of expression levels of certain interferon (IFN) stimulated genes (ISG), (ii) detection of certain platelet activation-associated protein levels, and (iii) detection of the level of antibodies to an antigen of a bacterial strain.

[0367] In some embodiments, the invention provides methods for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, methods of treating those conditions, and / or methods of monitoring the effects of a treatment for those conditions that can involve determining the abundance of a bacterial strain in combination with determining the levels of certain platelet activation-associated proteins in a blood sample from the patient. In certain embodiments, the determination of the levels of such proteins can be used in combination with the methods disclosed throughout the specification such as, but not limited to, (i) detection of expression levels of certain interferon (IFN) stimulated genes (ISG), (ii) detection of the level of antibodies to an antigen of a bacterial strain, and (iii) determining the expression levels of certain genes involved in the platelet activation pathway.

[0368] In certain embodiments, the present invention provides methods for treatment or methods of monitoring the effects of a treatment that can involve determining the abundance of gastrointestinal (GI) bacteria. In certain embodiments, the detection of GI bacteria can be used in combination with the methods disclosed throughout the specification such as, but not limited to,(i) determining the expression levels of certain genes involved in the platelet activation pathway,(ii) detection of expression levels of certain interferon (IFN) stimulated genes (ISG), (iii) detection of certain platelet activation-associated protein levels, and (iv) detection of the level of antibodies to an antigen of a bacterial strain. In certain embodiments, determining the expression levels of the genes comprises determining the mRNA levels of those genes.

[0369] In certain embodiments, the method for determining the abundance of a bacterial strain comprises (1) determining in the gastrointestinal (GI) microbiota sample collected from the subject an abundance of bacteria from Blautia (Ruminococcus) gnavus strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or another strain from Blautia (Ruminococcus) gnavus species that produces a lipoglycan-containing antigen or aderivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus strain CC55 001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744); (2) comparing the abundance of bacteria determined in step (1) to a control abundance of said bacteria, and (3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when the abundance of bacteria determined in step (1) is statistically significantly higher than the control abundance.

[0370] In certain embodiments, the GI microbiota sample can be taken from the stomach, duodenumjejunum, ileum, cecum, colon, and feces. In certain embodiments, the GI microbiota sample can be taken from the feces or intestines.

[0371] In certain embodiments, the method involves testing for the abundance of bacteria that produces a bacterial antigen associated with autoimmune disease such as, but not limited to, systemic lupus erythematosus (SLE) and lupus nephritis as well as inflammatory diseases. In certain embodiments, the method involves testing for the abundance of bacteria that produces a bacterial antigen as disclosed above.

[0372] In certain embodiments, the lipoglycan-containing antigen comprises a diacyl-glycerol or triacyl-glycerol moiety and is not a capsular polysaccharide or teichoic acid.

[0373] In certain embodiments, the lipoglycan-containing antigen has an estimated molecular weight based on Western blot between about 20,000 and about 30,000 Daltons.

[0374] In certain embodiments, the lipoglycan-containing antigen shares one or more antigenic determinants with or is the same as the lipoglycan-containing antigen obtained from Blautia (Ruminococcus) gnavus strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744), using a method selected from:

[0375] (i) Method 1 comprising the steps: a. culturing Blautia (Ruminococcus) gnavus strain CC55 001C, HM-1056, or strain S107- 48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) at 37°C under anaerobic conditions for 2-7 days, andb. producing bacterial extract in the presence of a lysozyme, Serratia marcescens endonuclease, Proteinase K, and a detergent under non-denaturing conditions;

[0376] (ii) Method 2 comprising the steps: a. culturing Blautia (Ruminococcus) gnavus strain CC55 001C, HM-1056, or strain S107- 48 (NCBI SRA Accession No: SRX14861748) or S 107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744)in rich nutrient media at 37°C under anaerobic conditions (75% N2, 20% CO2, and 5% H2) for 2-7 days, b. pelleting bacteria by centrifugation, c. producing a bacterial extract in a protein extraction buffer in the presence of lysozyme, Serratia marcescens endonuclease, and a detergent under non-denaturing conditions, d. treating the extract obtained in step (c) with Proteinase K, e. incubating the treated extract obtained in step (d) at 55°C for about 10 minutes, f. removing cell debris by centrifugation, and g. using the supernatant as an antigen preparation; or

[0377] (iii) Method 3 comprising the steps: a. disrupting Blautia (Ruminococcus) gnavus strain CC55 001C, HM-1056, or strain S107- 48 (NCBI SRA Accession No: SRX14861748) or S 107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) cells with a French press, b. ultracentrifugating to obtain a precipitate and produce an ultracentrifugation supernatant, c. subjecting the ultracentrifugation supernatant obtained in step (b) to butanol-water extraction and isolating an aqueous phase, d. applying the aqueous phase from step (c) to a hydrophobic interaction chromatography matrix, and e. isolating lipoglycan-containing fractions.

[0378] In certain embodiments, the level of antibodies is determined using an assay such as, but not limited to, a bead-based assay, an enzyme-linked immunosorbent assay (ELISA), a radioimmunoassay, counterimmuno-electrophoresis (CIE), immunodiffusion, Western blotting, microscopy, and / or any variant of an assay that detects these same antigen-reactive antibodies. In certain embodiments, the bacterial antigen, lipoglycan, or derivative thereof, is coated onto a bead or onto the surface of an ELISA plate or other solid phase used for detection.

[0379] In certain embodiments, the method involves testing for the abundance of Blautia (Ruminococcus) gnaws strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) (as described above). In certain embodiments, the method involves testing for a strain from the Lachnospiraceae family, wherein said strain has 16S rDNA or rRNA with at least 95%, 96%, 97%, 98%, 99% or including 100% sequence identity to the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107- 48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) over its entire length or at least 95%, 96%, 97%, 98%, 99% or including 100% sequence identity to any single V region of the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744). In certain embodiments, the bacteria share antigenic determinants with Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or SI 07-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744). In certain embodiments, the bacterial strain is from the Lachnospiraceae family, wherein the strain has 16S rDNA or rRNA with at least 95%, sequence identity to the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) over its entire length. In certain embodiments, the bacterial strain is from the Lachnospiraceae family, wherein the strain has at least 97% sequence identity to any single V region of the 16S rDNA or rRNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744). In certain embodiments, the V region of 16S rDNA or rRNA is the V4 region. In certain embodiments, the bacterial strain is from the Lachnospiraceae family, wherein the strain has at least 99% sequence identity to any single V region of the 16S rDNA or rRNA oiBlautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S47-18 (NCBI SRA Accession No: SRX14861744), or S47-48. In certain embodiments, the V region of 16S rDNA or rRNA is the V4 region.

[0380] In certain embodiments, an abundance of bacteria in step b) of at least about 1 -fold, at least about 2-fold, at least about 3-fold, at least about 4-fold, or at least about 5-fold lower than the abundance of step a) indicates that treatment is effective. In certain embodiments, an abundance of bacteria in step b) of between about 1.2-fold to about 5-fold or about 2-fold to about 4-fold lower than in step a) indicates that treatment is effective. In certain embodiments, the abundance of bacteria in step b) is at least about 2-fold lower than the abundance of step a).

[0381] In certain embodiments, the control abundance of bacteria can be obtained from, for example, (i) a predetermined standard; (ii) the abundance in a similarly prepared sample obtained from the same subject in the past; (iii) the abundance in a similarly prepared sample obtained from a matched healthy subject or an average or mean value of several matched healthy subjects; or (iv) the abundance in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein the SLE or ILE patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement or polyarthritis, or a mean value of samples from several such patients.

[0382] In certain embodiments, the average / mean is obtained by testing at least two, at least three, at least four, at least five, at least 10, at least 20, at least 25, at least 50, at least 75, or at least 100 healthy subjects. In certain embodiments, the average is the mean plus one, two, or three standard deviations of a group of healthy matched subjects. In certain embodiments, the abundance of bacteria is determined to be statistically significantly higher than the control abundance if the abundance is higher than the mean value of normal plus one standard deviation. In certain embodiments, the abundance of bacteria is determined to be statistically significantly higher than the control abundance if the abundance is higher than the mean value of normal plus two standard deviations. In certain embodiments, the abundance of the bacteria is determined to be statistically significantly higher than the control abundance if the abundance is higher than the mean value of normal plus three standard deviations. In certain embodiments, the abundance of the bacteria is determined to be statistically significantly higher than the control abundance if the abundance is higher than the mean value calculated for at least 40 matched healthy subjects plus three standard deviations.

[0383] In certain embodiments, the predetermined standard is a value which represents a statistically validated threshold ratio of the abundances of the bacteria equal to the highest possible value within the range of corresponding values in a large cohort of matched healthy subjects or ina large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein the SLE or ILE patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement or polyarthritis.

[0384] Values will vary based on the methods for quantitation and should be normalized for the assay.

[0385] Non-limiting examples of the methods which can be used for determining the relative abundance of the bacterial strains include, e.g., quantitative polymerase chain reaction (qPCR), sequencing of bacterial 16S rDNA or rRNA, shotgun metagenome sequencing, bacterial genotype pattern based fingerprinting (DNA fingerprinting) and metabolomics. In certain embodiments, the bacterial strain is identified by high-throughput sequencing of one or more genes selected from the group consisting of 16S rDNA or rRNA, LtaS, TagB, TagF, TagE, TagG, TagH, TagH, RumA, and RumC to identify the abundance of the strain-specific nucleic acid sequence(s) (Formstone A, Carballido-Lopez J. Bacteriology 2008 190(5): 1812-21).

[0386] Additional methods include methods of evaluating the microbiota population in a subject or diagnosing an abnormal microbiota development. Methods include monitoring the subject’s microbiota after the administration of the microbiota inoculum or probiotic by: a) determining a relative abundance of one or more bacterial taxa in a microbiota sample obtained from the subject, and b) comparing the relative abundance(s) determined in step a) to (i) a predetermined standard value or (ii) to the abundance(s) of the same taxa in a control subject or (iii) to the average value of abundances of the same taxa in several control subjects.

[0387] The determination of relative abundance of the taxa may involve, for example, a method selected from the group consisting of quantitative polymerase chain reaction (qPCR), sequencing of bacterial 16S rDNA or rRNA, shotgun metagenome sequencing, bacterial genotype pattern based fingerprinting (DNA fingerprinting), and metabolomic analysis.

[0388] In some of the embodiments described herein, the statistical significance of the increase or decrease can be determined by conventional methods. For example and not limitation, the statistical significance can be determined by a Fisher exact test to compare groups, with a predetermined p value of 0.05 for a two-tailed Fisher exact test.Additional Diagnostic Criteria

[0389] In certain embodiments, additional diagnostic steps may be combined with the methods above (i.e., detection of expression levels of genes involved in the platelet activation pathway,optionally in combination with one or more of the other described methods). In certain embodiments, the additional diagnostic tests are performed before the methods described above. In certain embodiments, the additional diagnostic tests are performed after the methods described above. In certain embodiments, the additional diagnostic tests are performed in conjunction / simultaneously with the methods described above. In certain embodiments, each of the diagnostic tests is being performed simultaneously with other diagnostic methods for SLE and / or LN. In certain embodiments, the diagnostic methods being performed simultaneously are being performed on the same panel. For assays using bodily fluid samples, the same or different sample may be used for two or more different assays.

[0390] In certain embodiments, the tests above are performed after the appearance of clinical features indicative of the disorder.

[0391] In certain embodiments, the diagnostic or monitoring methods can further comprise a separate diagnosis of SLE or lupus nephritis (LN). In certain embodiments, the diagnostic or monitoring methods can further comprise determining in a bodily fluid sample collected from the subject the level of antibodies against one or more additional antigens. In certain embodiments, the additional antigens can be double-stranded DNA (dsDNA), Clq, glomerular extract, nucleosomes, Smith Antibody (Sm), U1RNP, Ro / SSA, La / SSB, histone(s), and any combination thereof.

[0392] Autoantibodies can be detected in the serum prior to the onset of clinical disease, with the number and complexity of these antibodies increasing up to the point of diagnosis (Egner W. J Clin Pathol. 2000;53:424-32; Arbuckle MR, et al. N Engl J Med. 2003;349: 1526-33.) This result raises the possibility that risk profiles for lupus could be detected prior to onset of clinical symptoms. Autoantibody complexity is increased in patients with incomplete lupus (ILE) syndromes defined as having at least one but less than four of the criteria needed for a diagnosis of SLE (Wandstrat AE, et al. J Autoimmun. 27:153-60], Detection of IgG antibodies to LG of Blautia (Ruminococcus) gnavus may aid this diagnosis, establish prognosis, and also enable early and effective treatment.

[0393] In certain embodiments, the level of the antibodies against said one or more additional antigen(s) is determined in the same sample as the level of the antibodies to the bacterial antigen. In certain embodiments, the level of antibodies can be determined using a method selected from the group consisting of enzyme-linked immunosorbent assay (ELISA), Crithidia hiciliaeimmunofluorescence test, radioimmunoassay, counterimmunoelectrophoresis (CIE), immunodiffusion, Western blotting, microscopy, bead based assays, and / or hemagglutination.

[0394] In certain embodiments, the diagnostic or monitoring methods can further comprise determining in a bodily fluid sample collected from the subject the level of analytes including Clq, C3, C4, CH50, C-reactive protein (CRP), a non-complement protein of the innate immune system, and any combination thereof.

[0395] In certain embodiments the increased level of the antibodies against said one or more additional antigen(s) or analytes as compared to a relevant control is indicative of SLE, lupus nephritis, or SLE with renal involvement, as well as inflammatory diseases such as, but not limited to, glomerulonephritis (e.g., mesangial or membranoproliferative nephropathy), or polyarthritis.

[0396] In certain embodiments, the diagnostic or monitoring methods can further comprise testing the erythrocyte sedimentation rate (ESR). ESR is the rate at which red blood cells sediment in a period of one hour. ESR is increased in inflammation, pregnancy, anemia, autoimmune disorders (such as rheumatoid arthritis and lupus), infections, and some kidney diseases. In certain embodiments, the test is performed by placing anti coagulated blood in an upright tube (e.g., a Westergren tube), and the rate at which the red blood cells fall is measured and reported in mm / h. In certain embodiments, an elevated ESR supports a diagnosis of SLE or ILE.

[0397] In certain embodiments, the diagnostic or monitoring methods can further comprise determining a level of anti-nuclear antibodies (ANA) including those which can be due to antibodies recognizing double-stranded DNA (dsDNA), or antibodies to Smith antigen (Sm).

[0398] In certain embodiments, the diagnostic or monitoring methods further comprise determining one or more of gut permeability, SLE Disease Activity Index (SLEDAI), SLEDAI modified by the Safety of Estrogens in Lupus Erythematosus National Assessment trial (SELENASLED Al), British Isles Lupus Activity Group (BILAG) assessment, the SLAM index, American College of Rheumatology (ACR) SLE classification criteria, and Systemic Lupus Collaborating Clinics (SLICC) criteria. Currently the diagnosis of SLE is based on either ACR criteria (1) or SLICC criteria (2). 1. Hochberg MC. Arthritis Rheum. 1997;40(9):1725. 2. Petri M, et al. Arthritis Rheum. 2012;64(8):2677-2686.

[0399] In certain embodiments, the diagnostic or monitoring methods further comprise conducting a kidney assessment or urinalysis in the subject having SLE or ILE who is determined to be at an increased risk for developing lupus nephritis or other forms of SLE with renalinvolvement. In certain embodiments, the kidney assessment entails a kidney biopsy. In certain embodiments, the urinalysis comprises determining the level of protein, and / or the presence or absence of red and white blood cells in the urine, and wherein the increased level of protein (e.g., proteinuria) and / or the presence of red and / or white blood cells, as compared to a relevant control, is indicative of a kidney disease. In certain embodiments, the protein in the urine can be albumin. In certain embodiments, the total level of protein in the urine is determined. In certain embodiment, the total protein in a 24 hour urine collection is determined and the ratio to creatinine in serum or urine is determined.Treatments of the Invention

[0400] In one aspect, the invention provides a method of treating a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), said method comprising: (a) determining in a sample collected from the subject the level of mRNA of two or more genes selected from integrin subunit alpha 2b (ITGA2B), multimerin 1 (MMRN1), ATP binding cassette subfamily C member 4 (ABCC4), dematin actin binding protein (DMTN), GATA binding protein 1 (GATA1), lymphocyte antigen 6 family member G6F (LY6G6F), myosin light chain 9 (MYL9), platelet factor 4 (PF4), protein S (PROS1), synuclein alpha (SNCA), secreted protein acidic and cysteine rich (SPARC), platelet derived growth factor subunit A (PDGFA), and vesicle transport through interaction with t-SNAREs IB (VTI1B), wherein the sample comprises platelets, (b) comparing each of the mRNA levels determined in step (a) to a corresponding control mRNA level, and (c) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when each of the mRNA levels determined in step (a) is at least 1.5-fold higher than the corresponding control mRNA level.

[0401] In some embodiments, the method further comprises: (d) determining in a sample collected from the subject the level of mRNA of two or more genes selected from interferon alpha inducible protein 27 (IFI27), interferon inducible protein 44 (IFI44), radical S-adenosyl methionine domain containing 2 (RSAD2), and interferon inducible protein 44 like (IFI44L); (e) comparing each of the mRNA levels determined in step (d) to a corresponding control mRNA level, and (f) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when at least two of the mRNA levels determined in step (d) are statistically significantly lower than the corresponding mRNA levels in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated foran SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

[0402] In some embodiments, the method further comprises: (1) determining in a blood sample collected from the subject the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments; (2) comparing the level of the protein(s) and / or of NETosis fragments determined in step (1) to a control level of said protein(s) and / or of NETosis fragments, and (3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

[0403] In some embodiments, the method further comprises: (1) determining in a bodily fluid sample collected from the subject the level of antibodies that recognize a lipogly can-containing antigen from Blautia (Ruminococcus) gnavus strains CC55_001C, UM- 1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or a derivative thereof; (2) comparing the level of the antibodies determined in step (1g) to a control level of said antibodies, and (3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when the level of the antibodies determined in step (1) is statistically significantly higher than the control level.

[0404] In some embodiments, the method further comprises: (1) determining in the gastrointestinal (GI) microbiota sample collected from the subject an abundance of bacteria from Blautia (Ruminococcus) gnavus, such as the strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) which have more recently been assigned to the Lachnospiraceae family, wherein said strain has 16S rDNA with at least 95% sequence identity to the 16S rDNA of Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) over its entire length or at least 99% sequence identityto any single V region of the 16S rDNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744), or another bacterial strain from Blautia (Ruminococcus) gnavus species that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744); (2) comparing the abundance of bacteria determined in step (1) to a control abundance of said bacteria, and (3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis when the abundance of bacteria determined in step (1 ) is statistically significantly higher than the control abundance.

[0405] In another aspect, the invention provides a method of treating a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), said method comprising: (1) determining in a blood sample collected from the subject the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments; (2) comparing the level of the protein(s) and / or of NETosis fragments determined in step (1) to a control level of said protein(s) and / or of NETosis fragments, and (3) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

[0406] In some embodiments, the method further comprises: (d) determining in a sample collected from the subject the level of mRNA of two or more genes selected from interferon alpha inducible protein 27 (IFI27), interferon inducible protein 44 (IFI44), radical S-adenosyl methionine domain containing 2 (RSAD2), and interferon inducible protein 44 like (IFI44L); (e) comparing each of the mRNA levels determined in step (d) to a corresponding control mRNA level, and (f) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when at least two of the mRNA levels determined in step (d) are statistically significantly lower than the corresponding mRNA levels in a similarly prepared sample obtained from an SLE or ILE patient, or a patientbeing evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

[0407] In some embodiments, the method further comprises (1) determining in a bodily fluid sample collected from the subject the level of antibodies that recognize a lipoglycan-containing antigen from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae or a derivative thereof; (2) comparing the level of the antibodies determined in step (1) to a control level of said antibodies, and (3) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the level of the antibodies determined in step (1) is statistically significantly higher than the control level.

[0408] In some embodiments, the method further comprises: (1) determining in the gastrointestinal (GI) microbiota sample collected from the subject an abundance of bacteria from Blautia (Ruminococcus) gnavus, such as the strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) which have more recently been assigned to the Lachnospiraceae family, wherein said strain has 16S rDNA with at least 95% sequence identity to the 16S rDNA of Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) over its entire length or at least 99% sequence identity to any single V region of the 16S rDNA of Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744), or another bacterial strain from Blautia (Ruminococcus) gnavus species that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744); (2) comparing the abundance of bacteria determined in step (1) to a control abundance of said bacteria, and (3)administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the abundance of bacteria determined in step (1) is statistically significantly higher than the control abundance.

[0409] In another aspect, the invention provides a method for monitoring the effect of a treatment on development of a disorder in a subject, wherein the disorder is lupus nephritis or other forms of systemic lupus erythematosus (SLE) with renal involvement or polyarthritis which method comprises: (a) determining in a sample collected from the subject prior to initiation of the treatment the level of mRNA of two or more genes selected from integrin subunit alpha 2b (ITGA2B), multimerin 1 (MMRN1), ATP binding cassette subfamily C member 4 (ABCC4), dematin actin binding protein (DMTN), GATA binding protein 1 (GATA1), lymphocyte antigen 6 family member G6F (LY6G6F), myosin light chain 9 (MYL9), platelet factor 4 (PF4), protein S (PROS1), synuclein alpha (SNCA), secreted protein acidic and cysteine rich (SPARC), platelet derived growth factor subunit A (PDGFA), and vesicle transport through interaction with t- SNAREs IB (VTI1B), wherein the sample comprises platelets, (b) determining the mRNA levels of said two or more genes in the same type of sample collected from the subject in the course of or following the treatment, (c) comparing the mRNA levels determined in steps (a) and (b), and(d) (i) determining that the treatment is effective for said disorder if each of the mRNA levels determined in step (b) is not statistically significantly higher than the corresponding mRNA level determined in step (a), or (ii) determining that the treatment is not effective for said disorder if at least one mRNA expression level determined in step (b) is statistically significantly higher than the corresponding mRNA level determined in step (a).

[0410] In some embodiments, the method further comprises: (d) determining in a sample collected from the subject the level of mRNA of two or more genes selected from interferon alpha inducible protein 27 (IFI27), interferon inducible protein 44 (IFI44), radical S-adenosyl methionine domain containing 2 (RSAD2), and interferon inducible protein 44 like (IFI44L);(e)comparing each of the mRNA levels determined in step (d) to a corresponding control mRNA level, and (f) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, when at least two of the mRNA levels determined in step (d) are statistically significantly lower than the corresponding mRNA levels in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated foran SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

[0411] In some embodiments, the method can further comprise (1) determining in a blood sample collected from the subject prior to initiation of the treatment the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments; (2) determining the level of P- selectin protein and / or PF4 protein and / or of NETosis fragments in the same type of sample collected from the subject in the course of or following the treatment; (3) comparing the protein levels and / or the levels of NETosis fragments determined in steps (1) and (2), and (4) (i) determining that the treatment is effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is not statistically significantly higher than the corresponding level(s) determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is statistically significantly higher than the corresponding level(s) determined in step (1).

[0412] In some embodiments, the method can further comprise (1) determining in a bodily fluid sample collected from the subject prior to initiation of the treatment the level of antibodies that recognize a lipoglycan-containing antigen from Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain SI 07-48 (NCBI SRA Accession No: SRX 14861748) or S 107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or a derivative thereof; (2) determining the level of said antibodies in the same type of sample collected from the subject in the course of or following the treatment; (3) comparing the antibody levels determined in steps (1) and (2), and (4) (i) determining that the treatment is effective for said disorder if the level of antibodies determined in step (2) is not statistically significantly higher than the level of antibodies determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level of antibodies determined in step (2) is statistically significantly higher than the level of antibodies determined in step (1).

[0413] In some embodiments, the method can further comprise (1) determining in the gastrointestinal (GI) microbiota sample collected from the subject prior to initiation of the treatment an abundance of bacteria from Blautia (Ruminococcus) gnavus strain CC55 OO1C, HM- 1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48(NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or another strain from Blautia (Ruminococcus) gnavus species that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744); (2) determining the abundance of said bacteria in the same type of sample collected from the subject in the course of or following the treatment;(3) comparing the abundance of bacteria determined in steps (1) and (2), and (4) (i) determining that the treatment is effective for said disorder if the abundance of bacteria determined in step (2) is not statistically significantly higher than the abundance of said bacteria determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the abundance of bacteria determined in step (2) is statistically significantly higher than the abundance of said bacteria determined in step (1).

[0414] In another aspect, the invention provides a method for monitoring the effect of a treatment on development of a disorder in a subject, wherein the disorder is lupus nephritis or other forms of systemic lupus erythematosus (SLE) with renal involvement, or polyarthritis, which method comprises: (1) determining in a blood sample collected from the subject prior to initiation of the treatment the level of P-selectin protein, of platelet factor 4 (PF4) protein and / or of NETosis fragments; (2) determining the level of P-selectin protein and / or PF4 protein and / or of NETosis fragments in the same type of sample collected from the subject in the course of or following the treatment; (3) comparing the protein levels and / or of NETosis fragments determined in steps (1) and (2), and (4) (i) determining that the treatment is effective for said disorder if the level(s) of P- selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is not statistically significantly higher than the corresponding level(s) determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is statistically significantly higher than the corresponding level(s) determined in step (1).

[0415] In some embodiments, the method can further comprise (e) determining in a sample collected from the subject prior to initiation of the treatment the level of mRNA of two or more genes selected from interferon alpha inducible protein 27 (IFI27), interferon inducible protein 44(IFI44), radical S-adenosyl methionine domain containing 2 (RSAD2), and interferon inducible protein 44 like (IFI44L); (f) determining the mRNA levels of said two or more genes in the same type of sample collected from the subject in the course of or following the treatment; (g) comparing the mRNA levels determined in steps (e) and (f), and (h)(1) determining that the treatment is effective for said disorder if the mRNA levels determined in step (e) are not statistically significantly lower for more than one mRNA as compared to the corresponding mRNA levels determined in step (f), or (2) determining that the treatment is not effective for said disorder if the mRNA levels determined in step (e) are statistically significantly lower for more than one mRNA as compared to the corresponding mRNA levels determined in step (f).

[0416] In some embodiments, the method can further comprise (1) determining in a blood sample collected from the subject prior to initiation of the treatment the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments; (2) determining the level of P- selectin protein and / or PF4 protein and / or of NETosis fragments in the same type of sample collected from the subject in the course of or following the treatment; (3) comparing the protein levels and / or the levels of NETosis fragments determined in steps (1) and (2), and (4) (i) determining that the treatment is effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is not statistically significantly higher than the corresponding level(s) determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is statistically significantly higher than the corresponding level(s) determined in step (1).

[0417] In some embodiments, the method further comprises (1) determining in a bodily fluid sample collected from the subject the level of antibodies that recognize a lipoglycan-containing antigen from Blautia (Riiminococcus) gnavus of the family Lachnospiraceae or a derivative thereof; (2) comparing the level of the antibodies determined in step (1) to a control level of said antibodies, (3) comparing the antibody levels determined in steps (1) and (2), and (4) (i) determining that the treatment is effective for said disorder if the level of antibodies determined in step (2) is not statistically significantly higher than the level of antibodies determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level of antibodies determined in step (2) is statistically significantly higher than the level of antibodies determined in step (1).

[0418] In some embodiments, the method further comprises: (1) determining in the gastrointestinal (GI) microbiota sample collected from the subject an abundance of bacteria from Blautia (Ruminococcus) gnavus, such as the strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) which have more recently been assigned to the Lachnospiraceae family, wherein said strain has 16S rDNA with at least 95% sequence identity to the 16S rDNA of Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) over its entire length or at least 99% sequence identity to any single V region of the 16S rDNA of Blautia (Ruminococcus) gnavus strains CC55_001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000), or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744), or another bacterial strain from Blautia (Ruminococcus) gnavus species that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus strains CC55 001C, HM-1056, or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744); (2) comparing the abundance of bacteria determined in step (1) to a control abundance of said bacteria, (3) comparing the abundance of bacteria determined in steps (1) and (2), and (4) (i) determining that the treatment is effective for said disorder if the abundance of bacteria determined in step (2) is not statistically significantly higher than the abundance of said bacteria determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the abundance of bacteria determined in step (2) is statistically significantly higher than the abundance of said bacteria determined in step (1).

[0419] In some embodiments of any of methods described herein, if the subject having SLE or ILE is determined to be at risk of developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, the subject can be administered a treatment to (i) inhibit one or more of platelet adhesion, activation, and / or aggregation as described herein; (ii) inhibit or eliminate formation of neutrophil extracellular traps (NETs) as described herein; and / or (iii) normalize theI l lfunction of the intestinal barrier to reduce increased permeability and / or normalize the composition of the intestinal microbial community, or defined component species therein, as described herein.

[0420] In some embodiments of any of methods described herein, if the subject having SLE or ILE is determined to be at risk of developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis, the subject can also be treated with glucocorticosteroids (e.g., prednisone, methylprednisolone); immunosuppressive therapies (e.g., hydroxychloroquine, cyclophosphamide, azathioprine, and mycophenolate mofetil); calcineurin inhibitors (e.g., tacrolimus or voclosporin); and / or pyrimidine synthesis inhibitors (e.g., leflunomide). Additional therapies include belimumab (Benlysta), an anti -B -lymphocyte stimulator [BLyS] monoclonal antibody), which is approved for parenteral administration by the US Food and Drug Administration (FDA) to treat adults with active lupus nephritis who are receiving standard therapy. Voclosporin (Lupkynis), a calcineurin inhibitor, is the first FDA-approved oral therapy used in combination with immunosuppressive therapy for lupus nephritis. Anifrolumb (SAPHNELO®; also known as anifrolumab-fnia), an anti-INFARl subunit 1 binding antibody, which is approved for parenteral administration by the US Food and Drug Administration (FDA) to treat adult patients with moderate to severe systemic lupus erythematosus (SLE), who are receiving standard therapy.

[0421] In some embodiments of any of the methods described herein, the lupus nephritis is proliferative lupus nephritis, membranous lupus nephritis, membranoproliferative lupus nephritis, or mesangial glomerulonephritis.Treatments for Inhibition of Platelet Adhesion. Activation, and / or Aggregation

[0422] Platelet activation evidenced by specific transcriptomic functional pathways may be triggered in patients due to increased intestinal permeability and systemic release of microbial components. Such a process may be triggered by intestinal expansion of certain commensal bacterial species, and by certain strains of Blautia (Ruminococcus) gnavus. This intestinal expansion and release of Blautia (Ruminococcus) gnavus may induce the platelet activation pathway, and such activated platelets may in turn trigger a further downstream neutrophilic Neutrophil Extracellular Traps (NETs) by a process termed NETosis, which has potential therapeutic inhibitors.

[0423] A patient experiencing induction of the platelet activation pathway as determined by the diagnostic methods described herein can be administered therapeutic compositions or treatmentsto mitigate the effects of activated platelets. Non-limiting exemplary therapeutic compositions or treatments include therapeutic compositions that comprise platelet inhibitors, e g., therapeutic compositions or treatments that can alter, inhibit, and / or modify one or more of platelet adhesion, activation, and / or aggregation.

[0424] In some embodiments, the methods described herein include administration to the subject determined to be at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement or polyarthritis of a therapeutic compound or treatment that can inhibit one or more of platelet adhesion, activation, and / or aggregation. In some embodiments, the methods include administration of caplacizumab, which is an anti-von Willebrand factor (coagulation factor) recombinant nanobody that inhibits the interaction of this factor with platelets. In some embodiments, the methods include administration of a cyclooxygenase- 1 inhibitor, a phosphodiesterase (PDE) inhibitor, an adenosine reuptake inhibitor, a Glycoprotein Ilb / IIIa (GpIIb / IIIa) receptor antagonist, an adenosine diphosphate (ADP) receptor inhibitor, caplacizumab, or any combinations thereof.

[0425] In some embodiments, the cyclooxygenase- 1 inhibitor is aspirin, masoprocol, indomethacin, nabumetone, celecoxib, tolimetin, rofecoxib, piroxicam, fenoprofen, valdecoxib, diclofenac, or etoricoxib.

[0426] In some embodiments, the PDE inhibitor is a PDE 3 inhibitor, PDE 4 inhibitor, PDE 5 inhibitor, or non-specific PDE inhibitor. In some embodiments, the PDE 3 inhibitor is cilostazol, dipyridamole, milrinone, or amrinone. In some embodiments, the PDE4 inhibitor is roflumilast, apremilast, or crisaborole. In some embodiments, the PDE5 inhibitor is sildenafil, tadalafil, vardenafil, or avanafil. In some embodiments, the non-specific PDE inhibitor is theophylline or ibudilast.

[0427] In some embodiments, the adenosine reuptake inhibitor is dipyridamole.

[0428] In some embodiments, the ADP receptor inhibitor is ticlopidine, clopidogrel, prasugrel, ticagrelor, or cangrelor.

[0429] In some embodiments, the GpIIb / IIIa receptor antagonist is abciximab, eptifibatide, or tirofiban.

[0430] Pharmacologic platelet inhibitors consist of several different agents that each act differently in the platelet adhesion-activation-aggregation progression. Interruption of platelet intracellular signaling pathways and blockade of ligand receptors on the platelet membrane aresome of the primary mechanisms of action of medications in this class. Individually or collaboratively, these medications can function to alter, inhibit, and / or modify one or more of platelet adhesion, activation, and / or aggregation.Cyclooxygenase -1 inhibitors

[0431] Cyclooxygenase- 1 inhibitors are known to inhibit platelet aggregation. Non-limiting examples of cyclooxygenase- 1 inhibitors include aspirin, masoprocol, indomethacin, nabumetone, celecoxib, tolimetin, rofecoxib, piroxicam, fenoprofen, valdecoxib, diclofenac, and etori coxib. In the setting of lupus renal involvement, there should be consideration of benefits from protection from platelet activation, while some agents may be undesirable due to direct effects on renal function. Aspirin is the most used platelet inhibitor globally due to its efficacy, availability, and affordability. The Food and Drug Administration (FDA) has approved aspirin for use in patients as secondary prevention in several different cardiovascular disease states. Additionally, aspirin may be used...

Claims

CLAIMSWHAT IS CLAIMED IS:

1. A method for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE or ILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, said method comprising:(a) determining in a sample collected from the subj ect the level of mRNA of two or more genes selected from integrin subunit alpha 2b (ITGA2B), multimerin 1 (MMRN1), ATP binding cassette subfamily C member 4 (ABCC4), dematin actin binding protein (DMTN), GATA binding protein 1 (GATA1), lymphocyte antigen 6 family member G6F (LY6G6F), myosin light chain 9 (MYL9), platelet factor 4 (PF4), protein S (PROS1), synuclein alpha (SNCA), secreted protein acidic and cysteine rich (SPARC), and PDGFA (platelet derived growth factor subunit A), wherein the sample comprises platelets,(b) comparing each of the mRNA levels determined in step (a) to a corresponding control mRNA level of said genes, and(c) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, when each of the mRNA levels determined in step (a) is at least 1.5-fold higher than the corresponding control mRNA level.

2. The method of claim 1, wherein step (a) comprises determining the mRNA levels of three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, or ten or more genes selected from ITGA2B, MMRN1, ABCC4, DMTN, GATA1, LY6G6F, MYL9, PF4, PROS!, SNCA, SPARC, and PDGFA.

3. The method of claim 2, wherein step (a) comprises determining the mRNA levels of ITGA2B, MMRN1, ABCC4, DMTN, GATA1, LY6G6F, MYL9, PF4, PROS1, SNCA, SPARC, and PDGFA genes.

4. The method of any one of claims 1-3, wherein the method further comprises:(d) determining in a sample collected from the subject the level of mRNA of two or more genes selected from interferon alpha inducible protein 27 (IFI27), interferon inducible protein 44 (IFI44), radical S-adenosyl methionine domain containing 2 (RSAD2), and interferon inducible protein 44 like (IFI44L);(e) comparing each of the mRNA levels determined in step (d) to a corresponding control mRNA level, and(f) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease when at least two of the mRNA levels determined in step (d) are statistically significantly lower than the corresponding mRNA levels in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

5. The method of claim 4, wherein step (d) comprises determining the mRNA levels of three or more genes selected from IFI27, IFI44, RSAD2, and IFI44L.

6. The method of claim 5, wherein step (d) comprises determining the mRNA levels of IFI27, IFI44, RSAD2, and IFI44L genes.

7. The method of any one of claims 4-6, wherein the sample collected from the subject is the same sample as in claim 1.

8. The method of any one of claims 4-6, wherein the sample collected from the subject is the same type of sample as in claim 1.

9. The method of any one of claims 1-8, wherein the control mRNA level for a given gene is (i) a predetermined standard, (ii) the mRNA level of said gene in a similarly prepared sample obtained from the same subject in the past, (iii) the mRNA level of said gene in a similarly prepared sample obtained from a healthy matched subject or a mean value of samples from several matched healthy subjects, or (iv) the mRNA level of said gene in a similarly prepared sample obtained froma subject, wherein said subject does not have a pre-existing diagnosis of lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such subjects.

10. The method of claim 9, wherein the predetermined standard is a value which represents a statistically validated threshold ratio of the mRNA levels of said gene equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

11. The method of any one of claims 1-10, wherein the mRNA levels are determined by quantitative RT-PCR, nanostring technology, RNA sequencing, or representation in a bulk RNA library.

12. The method of any one of claims 1-11, wherein the sample is whole blood, platelet- enriched plasma, or purified platelets.

13. The method of any one of claims 1-12, further comprising:(1) determining in a blood sample collected from the subject the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments;(2) comparing the level of the protein(s) and / or of the NETosis fragments determined in step (1) to a control level of said protein(s) and / or of said NETosis fragments, and(3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, when the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

14. A method for determining whether a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), and / or a subject being evaluated for an SLE orILE diagnosis, is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, said method comprising:(1) determining in a blood sample collected from the subject the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments;(2) comparing the level of the protein(s) determined in step (1) to a control level of said protein(s) and / or of NETosis fragments, and(3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, when the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

15. The method of claim 13 or claim 14, wherein step (1) comprises determining the level of both P-selectin protein, of PF4 protein, and / or of NETosis fragments, and step (3) comprises determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is at an increased risk for developing polyarthritis and / or renal disease, when the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

16. The method of claim 15, wherein step (3) comprises determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, when the levels of both P-selectin protein and PF4 protein, and / or of NETosis fragments determined in step (1) are statistically significantly higher than the corresponding control levels.

17. The method of any one of claims 13-16, wherein the blood sample is whole blood, serum or plasma.

18. The method of any one of claims 13-17, wherein the control protein level is (i) a predetermined standard, (ii) the level of said protein in a similarly prepared sample obtained from the same subject in the past, (iii) the level of said protein in a similarly prepared sample obtainedfrom a healthy matched subject or a mean value of samples from several matched healthy subjects, or (iv) the level of said protein in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such patients; and / or wherein the control NETosis fragment level is (i) a predetermined standard, (ii) the level of said NETosis fragments in a similarly prepared sample obtained from the same subject in the past, (iii) the level of said NETosis fragments in a similarly prepared sample obtained from a healthy matched subject or a mean value of samples from several matched healthy subjects, or (iv) the level of said NETosis fragments in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such patients.

19. The method of claim 18, wherein the predetermined standard is a value which represents a statistically validated threshold ratio of the levels of said protein(s) and / or of said NETosis fragments equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

20. The method of any one of claims 13-19, wherein the protein level is determined by an enzyme-linked immunosorbent assay (ELISA), radioimmunoassay, counterimmuno- electrophoresis (CIE), immunodiffusion, Western blotting, microscopy, or bead-based assays.

21. The method of any one of claims 1-20, further comprising:(1) determining in a bodily fluid sample collected from the subject the level of antibodies that recognize a lipoglycan-containing antigen from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae or a derivative thereof;(2) comparing the level of the antibodies determined in step (1) to a control level of said antibodies, and(3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the level of the antibodies determined in step (1) is statistically significantly higher than the control level.

22. The method of claim 21, wherein the lipogly can-containing antigen:(1) comprises a di acyl -glycerol ortriacyl-glycerol moiety and is not a capsular polysaccharide or teichoic acid,(2) has an estimated molecular weight based on Western blot between about 20,000 and about 30,000 Daltons, and(3) shares one or more antigenic determinants with or is the same as the lipoglycan-containing antigen obtained from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107- 86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX 14861744) using a method selected from:(i) Method 1 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain SI 07-48 (NCBI SRA Accession No: SRX 14861748) or S 107-86 (NCBI SRA Accessi on No: SRX14861747) or S47- 18 (NCBI SRA Accession No: SRX14861744) at 37°C under anaerobic conditions for 2-7 days, and b. producing bacterial extract in the presence of a lysozyme, Serratia marcescens endonuclease, Proteinase K, and a detergent under non-denaturing conditions;(ii) Method 2 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) of R. gnavus in rich nutrient media at 37°C under anaerobic conditions (75% N2, 20% CO2, and 5% H2) for 2-7 days, b. pelleting bacteria by centrifugation, c. producing a bacterial extract in a protein extraction buffer in the presence of lysozyme, Serratia marcescens endonuclease, and a detergent under non-denaturing conditions,d. treating the extract obtained in step (c) with Proteinase K, e. incubating the treated extract obtained in step (d) at 55°C for about 10 minutes, f. removing cell debris by centrifugation, and g. using the supernatant as an antigen preparation; or(iii) Method 3 comprising the steps: a. disrupting strain CC55_001C, HM-1056 cells or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) cells with a French press, b. ultracentrifugation to obtain a precipitate and produce an ultracentrifugation supernatant, c. subjecting the ultracentrifugation supernatant obtained in step (b) to butanol-water extraction and isolating an aqueous phase, d. applying the aqueous phase from step (c) to a hydrophobic interaction chromatography matrix, and e. isolating lipoglycan-containing fractions.

23. The method of claim 21 or claim 22, wherein the level of antibodies is determined using an enzyme-linked immunosorbent assay (ELISA), radioimmunoassay, counterimmuno- electrophoresis (CIE), immunodiffusion, Western blotting, microscopy, or bead-based assays.

24. The method of any one of claims 21-23, wherein the bodily fluid is selected from whole blood, plasma, serum, urine, and saliva.

25. The method of any one of claims 21-24, wherein the control level of said antibodies is (i) a predetermined standard, (ii) the level of said antibodies in a similarly prepared sample obtained from the same subject in the past, (iii) the level of said antibodies in a similarly prepared sample obtained from a healthy matched subject or a mean value of several matched healthy subjects, or (iv) the level of said antibodies in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such patients.

26. The method of claim 25, wherein the predetermined standard is a value which represents a statistically validated threshold ratio of the levels of said antibodies equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

27. The method of any one of claims 1-26, further comprising:(1) determining in the gastrointestinal (GI) microbiota sample collected from the subject an abundance of bacteria from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or another strain from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae species that produces a lipoglycan- containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744);(2) comparing the abundance of bacteria determined in step (1) to a control abundance of said bacteria, and(3) determining that the subject is at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, and / or is determined to be at an increased risk for developing polyarthritis and / or renal disease, when the abundance of bacteria determined in step (1) is statistically significantly higher than the control abundance.

28. The method of claim 27, wherein the GI microbiota is of cecal, ileal, colonic, or fecal origin.

29. The method of claim 28, wherein the GI microbiota is fecal microbiota.

0. The method of any one of claims 27-29, wherein the lipoglycan-containing antigen:(1) comprises a diacyl-glycerol ortriacyl-glycerol moiety and is not a capsular polysaccharide or teichoic acid,(2) has an estimated molecular weight based on Western blot between about 20,000 and about 30,000 Daltons, and(3) shares one or more antigenic determinants with or is the same as the lipoglycan-containing antigen obtained from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107- 86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX 14861744) using a method selected from:(i) Method 1 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) at 37°C under anaerobic conditions for 2-7 days, and b. producing bacterial extract in the presence of a lysozyme, Serratia marcescens endonuclease, Proteinase K, and a detergent under non-denaturing conditions;(ii) Method 2 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or SI 07-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) in rich nutrient media at 37°C under anaerobic conditions (75% N2, 20% CO2, and 5% H2) for 2-7 days, b. pelleting bacteria by centrifugation, c. producing a bacterial extract in a protein extraction buffer in the presence of lysozyme, Serratia marcescens endonuclease, and a detergent under non-denaturing conditions, d. treating the extract obtained in step (c) with Proteinase K, e. incubating the treated extract obtained in step (d) at 55°C for about 10 minutes, f removing cell debris by centrifugation, and g. using the supernatant as an antigen preparation; or(iii) Method 3 comprising the steps:a. disrupting strain CC55_001 C, HM-1056 cells or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) cells with a French press, b. ultracentrifugating to obtain a precipitate and produce an ultracentrifugation supernatant, c. subjecting the ultracentrifugation supernatant obtained in step (b) to butanol -water extraction and isolating an aqueous phase, d. applying the aqueous phase from step (c) to a hydrophobic interaction chromatography matrix, and e. isolating lipoglycan-containing fractions.

31. The method of any one of claims 27-30, wherein the control abundance of said bacteria is (i) a predetermined standard, (ii) the abundance of said bacteria in a similarly prepared sample obtained from the same subject in the past, (iii) the abundance of said bacteria in a similarly prepared sample obtained from a matched healthy subject or a mean value of several matched healthy subjects, or (iv) the abundance of said bacteria in a similarly prepared sample obtained from an SLE or ILE patient, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such patients.

32. The method of claim 31, wherein the predetermined standard is a value which represents a statistically validated threshold ratio of the abundance of said bacteria equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

33. The method any one of claims 1-32, wherein the lupus nephritis is proliferative lupus nephritis, membranous lupus nephritis, membranoproliferative lupus nephritis, or mesangial gl omerulonephriti s.

34. The method of any one of claim 1-33, wherein the subject has been diagnosed with SLE or ILE in part by determining a decreased serum level of one or more complement components selected from Clq, C3, C4, and CH50, and / or an elevated level of C-reactive protein (CRP).

35. The method of any one of claims 1-34, wherein the subject has been diagnosed with SLE or ILE in part by determining an elevation of the erythrocyte sedimentation rate (ESR).

36. The method of any one of claims 1-35, wherein the subject has been diagnosed with SLE or ILE in part by determining a level of anti-nuclear antibodies (ANA) including those which recognize double-stranded DNA (dsDNA), or Smith antigen (Sm).

37. The method of any one of claims 1-36, wherein the method further comprises conducting an assessment of the subject by determining one or more parameters selected from gut permeability, SLE Disease Activity Index (SLEDAI), SLEDAI modified by the Safety of Estrogens in Lupus Erythematosus National Assessment trial (SELENA-SLEDAI), British Isles Lupus Activity Group (BILAG) assessment, the SLAM index, American College of Rheumatology (ACR) SLE classification criteria, and Systemic Lupus Collaborating Clinics (SLICC) criteria.

38. The method of any one of claims 1 -37, wherein the method further comprises a kidney biopsy assessment or urinalysis in the subject determined to be at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement.

39. The method of claim 38, wherein the urinalysis comprises determining the level of protein and / or red blood cells in the urine, and wherein the increased level of protein or red blood cells as compared to a relevant control is indicative of a kidney disease.

40. The method of any one of claims 1-39, further comprising recruiting the subject in a clinical trial.41 . The method of any one of claims 1-40, comprising administering to the subject determined to be at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, an inhibitor of platelet activation, an inhibitor of platelet aggregation, an inhibitor of platelet adhesion, or any combinations thereof.

42. The method of any one of claims 1-41, comprising administering to the subject determined to be at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, a cyclooxygenase- 1 inhibitor, a phosphodiesterase (PDE) inhibitor, an adenosine reuptake inhibitor, a Glycoprotein Ilb / IIIa (GpIIb / IIIa) receptor antagonist, an adenosine diphosphate (ADP) receptor inhibitor, caplacizumab, or any combinations thereof.

43. The method of claim 42, wherein the cyclooxygenase- 1 inhibitor is aspirin, masoprocol, indomethacin, nabumetone, celecoxib, tolimetin, rofecoxib, piroxicam, fenoprofen, valdecoxib, diclofenac, or etoricoxib.

44. The method of claim 42, wherein the PDE inhibitor is a PDE 3 inhibitor, PDE 4 inhibitor, PDE 5 inhibitor, or non-specific PDE inhibitor.

45. The method of claim 44, wherein the PDE 3 inhibitor is cilostazol, dipyridamole, milrinone, or amrinone.

46. The method of claim 44, wherein the PDE4 inhibitor is roflumilast, apremilast, or crisaborole.

47. The method of claim 44, wherein the PDE5 inhibitor is sildenafil, tadalafil, vardenafil, or avanafil.

48. The method of claim 44, wherein the non-specific PDE inhibitor is theophylline or ibudilast.

49. The method of claim 42, wherein the adenosine reuptake inhibitor is dipyridamole.

50. The method of claim 42, wherein the GpIIb / IIIa receptor antagonist is abciximab, eptifibatide, or tirofiban.

51. The method of claim 42, wherein the ADP receptor inhibitor is ticlopidine, clopidogrel, prasugrel, ticagrelor, or cangrelor.

52. The method of any one of claims 1-51, comprising administering to the subject determined to be at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, a treatment directed to eliminating or inhibiting neutrophil extracellular traps (NETs).

53. The method of claim 52, wherein the treatment directed to eliminating or inhibiting NETs comprises administering to the subject protease inhibitors, Deoxyribonuclease (DNase), peptidyl arginine deiminase 4 (PAD4) inhibitors, neutrophilic elastase inhibitors, myeloperoxidase (MPO) inhibitors, N-a-benzoyl-N5-(2-chloro-l-iminoethyl)-L-ornithine amide (Cl-amidine), Diphenyleneiodonium chloride, disulfiram, NADPH oxidase 2 (N0X2) inhibitor (e.g., GSK2795039), or agents that aid clearance of NETosis products, or any combination thereof.

54. The method of any one of claims 1-53, comprising administering to the subject determined to be at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, a treatment normalizing the functional level of permeability of the intestinal barrier and / or normalizing the composition of the intestinal microbial community.

55. The method of any one of claims 1-53, comprising administering to the subject determined to be at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, a treatment which (i) results in a decrease in the level in bodily fluid(s) of the subject of a lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or a lipoglycan-containing antigen which shares one or more antigenic determinants of said lipoglycan-containing antigen, or (ii) results ina decrease in the level in bodily fluid(s) of the subject of the antibodies which recognize said lipoglycan-containing antigen, or (iii) results in a decrease in GI microbiota of the subject of an abundance of bacteria from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55_001C, HM-1056 or strain SI 07-48 (NCBI SRA Accession No: SRX 14861748) or SI 07-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or another strain from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae species that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744).

56. The method of claim 55, wherein the treatment comprises administering an antibiotic and / or probiotic and / or prebiotic and / or bacteriophage which inhibits growth or activity of said bacteria within the GI microbiota community of the subject in one approach with an antibody or antigen-binding fragment thereof, wherein said antibody or antigen-binding fragment thereof binds to a lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or a lipoglycan-containing antigen which shares one or more antigenic determinants of said lipoglycan-containing antigen, or binds to antibodies which recognize said lipoglycan-containing antigen.

57. The method of claim 56, wherein said probiotic comprises one or more strains from non- pathogenic Blautia (Ruminococcus) gnavus species, and / or species Faecalibacterium prausnitzii, and / or species Bacteroides uniformis, and / or genus Lactobacillus.

58. The method of any one of claims 1 -57, comprising administering to the subject determined to be at an increased risk for developing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, a compound selected from hydroxychloroquine, a glucocorticosteroid, an immunosuppressive agent, a calcineurin inhibitor, a pyrimidine synthesis inhibitor, belimumab, anifrolumab, and any combinations thereof.

59. The method of claim 58, wherein the glucocorticosteroid is prednisone or methylpredni solone .

60. The method of claim 58, wherein the immunosuppressive agent is cyclophosphamide, azathioprine, my cophenol ate mofetil, cyclosporine, or chlorambucil.

61. The method of claim 58, wherein the calcineurin inhibitor is tacrolimus or voclosporin.

62. The method of claim 58, wherein the pyrimidine synthesis inhibitor is leflunomide.

63. A method of treating a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), said method comprising:(a) determining in a sample collected from the subj ect the level of mRNA of two or more genes selected from integrin subunit alpha 2b (ITGA2B), multimerin 1 (MMRN1), ATP binding cassette subfamily C member 4 (ABCC4), dematin actin binding protein (DMTN), GATA binding protein 1 (GATA1), lymphocyte antigen 6 family member G6F (LY6G6F), myosin light chain 9 (MYL9), platelet factor 4 (PF4), protein S (PROS1), synuclein alpha (SNCA), secreted protein acidic and cysteine rich (SPARC), and PDGFA (platelet derived growth factor subunit A, wherein the sample comprises platelets,(b) comparing each of the mRNA levels determined in step (a) to a corresponding control mRNA level, and(c) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when each of the mRNA levels determined in step (a) is at least 1.5-fold higher than the corresponding control mRNA level.

64. The method of claim 63, wherein step (a) comprises determining the mRNA levels of three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, or ten or more genes selected from ITGA2B, MMRN1, ABCC4, DMTN, GATA1, LY6G6F, MYL9, PF4, PROS1, SNCA, SPARC, and PDGFA.

65. The method of claim 64, wherein step (a) comprises determining the mRNA levels of ITGA2B, MMRN1, ABCC4, DMTN, GATA1, LY6G6F, MYL9, PF4, PROS1, SNCA, and SPARC, and PDGFA genes.

66. The method of any one of claims 63-65, wherein the method further comprises:(d) determining in a sample collected from the subject the mRNA level of two or more genes selected from interferon alpha inducible protein 27 (IFI27), interferon inducible protein 44 (IFI44), radical S-adenosyl methionine domain containing 2 (RSAD2), and interferon inducible protein 44 like (IFI44L);(e) comparing each of the mRNA levels determined in step (d) to a corresponding control mRNA level, and(f) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when at least two of the mRNA levels determined in step (d) are statistically significantly lower than the corresponding mRNA levels in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

67. The method of claim 66, wherein step (d) comprises determining the mRNA levels of three or more genes selected from IFI27, IFI44, RSAD2, and IFI44L.

68. The method of claim 67, wherein step (d) comprises determining the mRNA levels of IFI27, IFI44, RSAD2, and IFI44L genes.

69. The method of any one of claims 66-68, wherein the sample collected from the subject is the same sample as in claim 63.

70. The method of any one of claims 66-68, wherein the sample collected from the subject is the same type of sample as in claim 63.71 . The method of any one of claims 63-70, wherein the control mRNA level for a given gene is (i) a predetermined standard, (ii) the mRNA level of said gene in a similarly prepared sample obtained from the same subject in the past, (iii) the mRNA level of said gene in a similarly prepared sample obtained from a healthy matched subject or a mean value of samples from several matched healthy subjects, or (iv) the mRNA level of said gene in a similarly prepared sample obtained from a subject, wherein said subject does not have a pre-existing diagnosis of lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such subjects.

72. The method of claim 71, wherein the predetermined standard is a value which represents a statistically validated threshold ratio of the mRNA levels of said gene equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

73. The method of any one of claims 63-72, wherein the mRNA levels are determined by quantitative RT-PCR, nanostring technology, RNA sequencing, or representation in a bulk RNA library made from said sample.

74. The method of any one of claims 63-73, wherein the sample is whole blood, platelet- enriched plasma, or purified platelets.

75. The method of any one of claims 63-74, further comprising:(1) determining in a blood sample collected from the subject the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments;(2) comparing the level of the protein(s) and / or of NETosis fragments determined in step (1) to a control level of said protein(s) and / or of said NETosis fragments, and(3) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the level(s) of P-selectinprotein, of PF4 protein and / or of NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

76. A method of treating a subject diagnosed with systemic lupus erythematosus (SLE) or incomplete lupus (ILE), said method comprising:(1) determining in a blood sample collected from the subject the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments;(2) comparing the level of the protein(s) and / or of NETosis fragments determined in step (1) to a control level of said protein(s) and / or of NETosis fragments, and(3) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

77. The method of claim 75 or claim 76, wherein step (1) comprises determining the level of P-selectin protein and PF4 protein, and / or of NETosis fragments, and step (3) comprises administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (1) is statistically significantly higher than the corresponding control level(s).

78. The method of claim 77, wherein step (3) comprises administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the levels of P-selectin protein and PF4 protein, and / or of NETosis fragments determined in step (1) are statistically significantly higher than the corresponding control levels.

79. The method of any one of claims 75-78, wherein the blood sample is whole blood, serum or plasma.

80. The method of any one of claims 75-79, wherein the control protein level is (i) a predetermined standard, (ii) the level of said protein in a similarly prepared sample obtained fromthe same subject in the past, (iii) the level of said protein in a similarly prepared sample obtained from a healthy matched subject or a mean value of samples from several matched healthy subjects, or (iv) the level of said protein in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such patients; and / or wherein the control NETosis fragment level is (i) a predetermined standard, (ii) the level of said NETosis fragments in a similarly prepared sample obtained from the same subject in the past, (iii) the level of said NETosis fragments in a similarly prepared sample obtained from a healthy matched subject or a mean value of samples from several matched healthy subjects, or (iv) the level of said NETosis fragments in a similarly prepared sample obtained from an SLE or ILE patient, or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such patients.

81. The method of claim 80, wherein the predetermined standard is a value which represents a statistically validated threshold ratio of the levels of said protein and / or of said NETosis fragments equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement, polyarthritis.

82. The method of any one of claims 75-81, wherein the protein level is determined by an enzyme-linked immunosorbent assay (ELISA), radioimmunoassay, counterimmuno- electrophoresis (CIE), immunodiffusion, Western blotting, microscopy, or bead-based assays.

83. The method of any one of claims 63-82, further comprising:(1) determining in a bodily fluid sample collected from the subject the level of antibodies that recognize a lipoglycan-containing antigen from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae or a derivative thereof;(2) comparing the level of the antibodies determined in step (1) to a control level of said antibodies, and(3) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the level of the antibodies determined in step (1) is statistically significantly higher than the control level.

84. The method of claim 83, wherein the lipoglycan-containing antigen:(1) comprises a di acyl -glycerol ortriacyl-glycerol moiety and is not a capsular polysaccharide or teichoic acid,(2) has an estimated molecular weight based on Western blot between about 20,000 and about 30,000 Daltons, and(3) shares one or more antigenic determinants with or is the same as the lipoglycan-containing antigen obtained from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107- 86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX 14861744) using a method selected from:(i) Method 1 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or SI 07-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) at 37°C under anaerobic conditions for 2-7 days, and b. producing bacterial extract in the presence of a lysozyme, Serratia marcescens endonuclease, Proteinase K, and a detergent under non-denaturing conditions;(ii) Method 2 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) in rich nutrient media at 37°C under anaerobic conditions (75% N2, 20% CO2, and 5% H2) for 2-7 days, b. pelleting bacteria by centrifugation, c. producing a bacterial extract in a protein extraction buffer in the presence of lysozyme, Serratia marcescens endonuclease, and a detergent under non-denaturing conditions,d. treating the extract obtained in step (c) with Proteinase K, e. incubating the treated extract obtained in step (d) at 55°C for about 10 minutes, f. removing cell debris by centrifugation, and g. using the supernatant as an antigen preparation; or(iii) Method 3 comprising the steps: a. disrupting strain CC55_001C, HM-1056 cells or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) with a French press, b. ultracentrifugation to obtain a precipitate and produce an ultracentrifugation supernatant, c. subjecting the ultracentrifugation supernatant obtained in step (b) to butanol-water extraction and isolating an aqueous phase, d. applying the aqueous phase from step (c) to a hydrophobic interaction chromatography matrix, and e. isolating lipoglycan-containing fractions.

85. The method of claim 83 or claim 84, wherein the level of antibodies is determined using an enzyme-linked immunosorbent assay (ELISA), radioimmunoassay, counterimmuno- electrophoresis (CIE), immunodiffusion, Western blotting, microscopy, or bead-based assays.

86. The method of any one of claims 83-85, wherein the bodily fluid is selected from whole blood, plasma, serum, urine, and saliva.

87. The method of any one of claims 83-86, wherein the control level of said antibodies is (i) a predetermined standard, (ii) the level of said antibodies in a similarly prepared sample obtained from the same subject in the past, (iii) the level of said antibodies in a similarly prepared sample obtained from a healthy matched subject or a mean value of several matched healthy subjects, or (iv) the level of said antibodies in a similarly prepared sample obtained from an SLE or ILE patient, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such patients.

88. The method of claim 87, wherein the predetermined standard is a value which represents a statistically validated threshold ratio of the levels of said antibodies equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

89. The method of any one of claims 63-88, further comprising:(1) determining in the gastrointestinal (GI) microbiota sample collected from the subject an abundance of bacteria from Blautia (Runrinococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or another strain from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae species that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM- 1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744);(2) comparing the abundance of bacteria determined in step (1) to a control abundance of said bacteria, and(3) administering to the subject a treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, when the abundance of bacteria determined in step (1) is statistically significantly higher than the control abundance.

90. The method of claim 89, wherein the GI microbiota is of cecal, ileal, colonic, or fecal origin.

91. The method of claim 90, wherein the GI microbiota is fecal microbiota.

92. The method of any one of claims 89-91, wherein the lipoglycan-containing antigen:(1) comprises a diacyl-glycerol ortriacyl-glycerol moiety and is not a capsular polysaccharide or teichoic acid,(2) has an estimated molecular weight based on Western blot between about 20,000 and about 30,000 Daltons, and(3) shares one or more antigenic determinants with or is the same as the lipoglycan-containing antigen obtained from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107- 86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) using a method selected from:(i) Method 1 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX 14861744) at 37°C under anaerobic conditions for 2-7 days, and b. producing bacterial extract in the presence of a lysozyme, Serratia marcescens endonuclease, Proteinase K, and a detergent under non-denaturing conditions;(ii) Method 2 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) in rich nutrient media at 37°C under anaerobic conditions (75% N2, 20% CO2, and 5% H2) for 2-7 days, b. pelleting bacteria by centrifugation, c. producing a bacterial extract in a protein extraction buffer in the presence of lysozyme, Serratia marcescens endonuclease, and a detergent under non-denaturing conditions, d. treating the extract obtained in step (c) with Proteinase K, e. incubating the treated extract obtained in step (d) at 55°C for about 10 minutes, f. removing cell debris by centrifugation, and g. using the supernatant as an antigen preparation; or(iii) Method 3 comprising the steps:a. disrupting strain CC55_001 C, HM-1056 cells or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) cells with a French press, b. ultracentrifugating to obtain a precipitate and produce an ultracentrifugation supernatant, c. subjecting the ultracentrifugation supernatant obtained in step (b) to butanol -water extraction and isolating an aqueous phase, d. applying the aqueous phase from step (c) to a hydrophobic interaction chromatography matrix, and e. isolating lipoglycan-containing fractions.

93. The method of any one of claims 89-92, wherein the control abundance of said bacteria is (i) a predetermined standard, (ii) the abundance of said bacteria in a similarly prepared sample obtained from the same subject in the past, (iii) the abundance of said bacteria in a similarly prepared sample obtained from a matched healthy subject or a mean value of several matched healthy subjects, or (iv) the abundance of said bacteria in a similarly prepared sample obtained from an SLE or ILE patient or a patient being evaluated for an SLE or ILE diagnosis, wherein said patient does not have or is not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis, or a mean value of samples from several such patients.

94. The method of claim 93, wherein the predetermined standard is a value which represents a statistically validated threshold ratio of the abundance of said bacteria equal to the mean value within the range of corresponding values in a large cohort of healthy matched subjects or in a large cohort of SLE or ILE patients, or patients being evaluated for an SLE or ILE diagnosis, wherein said patients do not have or are not previously known to have lupus nephritis or other forms of SLE with renal involvement, or polyarthritis.

95. The method any one of claims 63-94, wherein the lupus nephritis is proliferative lupus nephritis, membranous lupus nephritis, membranoproliferative lupus nephritis, or mesangial glomerulonephritis.

96. The method of any one of claim 63-95, wherein the subject has been diagnosed with SLE or ILE in part by determining a decreased serum level of one or more complement components selected from Clq, C3, C4, and CH50, and / or an elevated level of C-reactive protein (CRP).

97. The method of any one of claims 63-96, wherein the subject has been diagnosed with SLE or ILE in part by determining an elevation of the erythrocyte sedimentation rate (ESR).

98. The method of any one of claims 63-97, wherein the subject has been diagnosed with SLE or ILE in part by determining a level of anti-nuclear antibodies (ANA) including those which recognize double-stranded DNA (dsDNA), or Smith antigen (Sm).

99. The method of any one of claims 63-98, wherein the method further comprises conducting an assessment of the subject by determining one or more parameters selected from gut permeability, SLE Disease Activity Index (SLEDAI), SLEDAI modified by the Safety of Estrogens in Lupus Erythematosus National Assessment trial (SELENA-SLEDAI), British Isles Lupus Activity Group (BILAG) assessment, the SLAM index, American College of Rheumatology (ACR) SLE classification criteria, and Systemic Lupus Collaborating Clinics (SLICC) criteria.

100. The method of any one of claims 63-99, wherein the method further comprises a kidney biopsy assessment or urinalysis in the subject.

101. The method of claim 100, wherein the urinalysis comprises determining the level of protein and / or red blood cells in the urine, and wherein the increased level of protein or red blood cells as compared to a relevant control is indicative of a kidney disease.

102. The method of any one of claims 63-101, further comprising recruiting the subject in a clinical trial.

103. The method of any one of claims 63-102, wherein the treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritiscomprises administering to the subject an inhibitor of platelet activation, an inhibitor of platelet aggregation, an inhibitor of platelet adhesion, or any combinations thereof.

104. The method of any one of claims 63-103, wherein the treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis comprises administering to the subject a cyclooxygenase- 1 inhibitor, a phosphodiesterase (PDE) inhibitor, an adenosine reuptake inhibitor, a Glycoprotein Ilb / IIIa (GpIIb / IIIa) receptor antagonist, an adenosine diphosphate (ADP) receptor inhibitor, caplacizumab, or any combinations thereof.

105. The method of claim 104, wherein the cyclooxygenase- 1 inhibitor is aspirin, masoprocol, indomethacin, nabumetone, celecoxib, tolimetin, rofecoxib, piroxicam, fenoprofen, valdecoxib, diclofenac, or etoricoxib.

106. The method of claim 104, wherein the PDE inhibitor is a PDE 3 inhibitor, PDE 4 inhibitor, PDE 5 inhibitor, or non-specific PDE inhibitor.

107. The method of claim 106, wherein the PDE 3 inhibitor is cilostazol, dipyridamole, milrinone, or amrinone.

108. The method of claim 106, wherein the PDE4 inhibitor is roflumilast, apremilast, or crisaborole.

109. The method of claim 106, wherein the PDE5 inhibitor is sildenafil, tadalafil, vardenafil, or avanafil.

110. The method of claim 106, wherein the non-specific PDE inhibitor is theophylline or ibudilast.

111. The method of claim 104, wherein the adenosine reuptake inhibitor is dipyridamole.

112. The method of claim 104, wherein the GpIIb / IIIa receptor antagonist is abciximab, eptifibatide, or tirofiban.

113. The method of claim 104, wherein the ADP receptor inhibitor is ticlopidine, clopidogrel, prasugrel, ticagrelor, or cangrelor.

114. The method of any one of claims 63-113, wherein the treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis comprises administering to the subject a treatment directed to eliminating or inhibiting neutrophil extracellular traps (NETs).

115. The method of claim 114, wherein the treatment directed to eliminating or inhibiting NETs comprises administering to the subject protease inhibitors, Deoxyribonuclease (DNase), peptidyl arginine deiminase 4 (PAD4) inhibitors, neutrophilic elastase inhibitors, myeloperoxidase (MPO) inhibitors, N-a-benzoyl-N5-(2-chloro-l-iminoethyl)-L-ornithine amide (Cl-amidine), Diphenyleneiodonium chloride, disulfiram, NADPH oxidase 2(NOX2) inhibitor (c. ., GSK2795039), agents that aid clearance of NETosis products, or any combination thereof.

116. The method of any one of claims 63-115, wherein the treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis comprises administering to the subject a treatment normalizing the functional level of permeability of the intestinal barrier and / or normalizing the composition of the intestinal microbial community.

117. The method of any one of claims 63-115, wherein the treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis comprises administering to the subject a treatment which (i) results in a decrease in the level in bodily fluid(s) of the subject of a lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or a lipoglycan-containing antigen which shares one or more antigenic determinants of said lipoglycan-containing antigen, or (ii) results in a decrease in bodily fluid(s) of the subject in the level of the antibodies which recognize said lipoglycan-containing antigen or (iii) results in a decrease in GI microbiota of thesubject of an abundance of bacteria from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or another strain from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae species that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744).

118. The method of claim 117, wherein the treatment comprises administering an antibiotic and / or probiotic and / or prebiotic and / or bacteriophage which inhibits growth or activity of said bacteria within the GI microbiota community of the subject in one approach with an antibody or antigen-binding fragment thereof, wherein said antibody or antigen-binding fragment thereof binds to a lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or a lipoglycan-containing antigen which shares one or more antigenic determinants of said lipoglycan-containing antigen, or binds to antibodies which recognize said lipoglycan-containing antigen.

119. The method of claim 118, wherein said probiotic comprises one or more strains from non- pathogenic Blautia (Ruminococcus) gnavus species, and / or species Faecalibacterium prausnitzii, and / or species Bacteroides uniformis, and / or genus Lactobacillus.

120. The method of any one of claims 63-119, wherein the treatment effective for treating or preventing lupus nephritis or other forms of SLE with renal involvement, or polyarthritis comprises administering to the subject a compound selected from hydroxychloroquine, a glucocorticosteroid, an immunosuppressive agent, a calcineurin inhibitor, a pyrimidine synthesis inhibitor, belimumab, anifrolumab, and any combinations thereof.

121. The method of claim 120, wherein the glucocorticosteroid is prednisone or methylpredni solone .

122. The method of claim 120, wherein the immunosuppressive agent is cyclophosphamide, azathioprine, my cophenol ate mofetil, cyclosporine, or chlorambucil.

123. The method of claim 120, wherein the calcineurin inhibitor is tacrolimus or voclosporin.

124. The method of claim 120, wherein the pyrimidine synthesis inhibitor is leflunomide.

125. A method for monitoring the effect of a treatment on development of a disorder in a subject, wherein the disorder is lupus nephritis or other forms of systemic lupus erythematosus (SLE) with renal involvement, or polyarthritis, which method comprises: a. determining in a sample collected from the subject prior to initiation of the treatment the level of mRNA of two or more genes selected from integrin subunit alpha 2b (ITGA2B), multimerin 1 (MMRN1), ATP binding cassette subfamily C member 4 (ABCC4), dematin actin binding protein (DMTN), GATA binding protein 1 (GATA1), lymphocyte antigen 6 family member G6F (LY6G6F), myosin light chain 9 (MYL9), platelet factor 4 (PF4), protein S (PROS1), synuclein alpha (SNCA), secreted protein acidic and cysteine rich (SPARC), and PDGFA (platelet derived growth factor subunit A), wherein the sample comprises platelets, b. determining the mRNA levels of said two or more genes in the same type of sample collected from the subject in the course of or following the treatment, c. comparing the mRNA levels determined in steps (a) and (b), and d. (i) determining that the treatment is effective for said disorder if each of the mRNA levels determined in step (b) is not statistically significantly higher than the corresponding mRNA level determined in step (a), or (ii) determining that the treatment is not effective for said disorder if at least one mRNA expression level determined in step (b) is at least 1.5-fold higher than the corresponding mRNA level determined in step (a).

126. The method of claim 125, wherein step (a) comprises determining the mRNA levels of three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, or ten or more genes selected from ITGA2B, MMRN1, ABCC4, DMTN, GATA1, LY6G6F, MYL9, PF4, PROS1, SNCA, SPARC, and PDGFA.

127. The method of claim 126, wherein step (a) comprises determining the mRNA levels of ITGA2B, MMRN1, ABCC4, DMTN, GATA1, LY6G6F, MYL9, PF4, PROS1, SNCA, SPARC, and PDGFA genes.

128. The method of any one of claims 125-127, wherein the method further comprises:(e) determining in a sample collected from the subject prior to initiation of the treatment the level of mRNA of two or more genes selected from interferon alpha inducible protein 27 (IFI27), interferon inducible protein 44 (IFI44), radical S-adenosyl methionine domain containing 2 (RSAD2), and interferon inducible protein 44 like (IFI44L);(f) determining the mRNA levels of said two or more genes in the same type of sample collected from the subject in the course of or following the treatment;(g) comparing the mRNA levels determined in steps (e) and (f), and(h) (1) determining that the treatment is effective for said disorder if the mRNA levels determined in step (e) are not statistically significantly lower for more than one mRNA as compared to the corresponding mRNA levels determined in step (f), or (2) determining that the treatment is not effective for said disorder if the mRNA levels determined in step (e) are statistically significantly lower for more than one mRNA as compared to the corresponding mRNA levels determined in step (f).

129. The method of claim 128, wherein step (e) comprises determining the mRNA levels of three or more genes selected from IFI27, IFI44, RSAD2, and IFI44L.

130. The method of claim 129, wherein step (e) comprises determining the mRNA levels of IFI27, IFI44, RSAD2, and IFI44L genes.

131. The method of any one of claims 128-130, wherein the samples collected from the subject are the same samples as in claim 125.

132. The method of any one of claims 128-130, wherein the samples collected from the subject are the same type of samples as in claim 125.

133. The method of any one of claims 125-132, wherein the mRNA levels are determined by quantitative RT-PCR, nanostring technology, RNA sequencing, or representation in a bulk RNA library made from said sample.

134. The method of any one of claims 125-133, wherein the sample is whole blood, platelet- enriched plasma, or purified platelets.

135. The method of any one of claims 125-134, further comprising:(1) determining in a blood sample collected from the subject prior to initiation of the treatment the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments;(2) determining the level of P-selectin protein, of PF4 protein, and / or of NETosis fragments in the same type of sample collected from the subject in the course of or following the treatment;(3) comparing the protein levels and / or the levels of NETosis fragments determined in steps (1) and (2), and(4) (i) determining that the treatment is effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is not statistically significantly higher than the corresponding level(s) determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is statistically significantly higher than the corresponding level(s) determined in step (1).

136. A method for monitoring the effect of a treatment on development of a disorder in a subj ect, wherein the disorder is lupus nephritis or other forms of systemic lupus erythematosus (SLE) with renal involvement, or polyarthritis, which method comprises:(1 ) determining in a blood sample collected from the subject prior to initiation of the treatment the level of P-selectin protein, of platelet factor 4 (PF4) protein, and / or of NETosis fragments;(2) determining the level of P-selectin protein, of PF4 protein, and / or of NETosis fragments in the same type of sample collected from the subject in the course of or following the treatment;(3) comparing the protein levels and / or the levels of NETosis fragments determined in steps (1) and (2), and(4) (i) determining that the treatment is effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is not statistically significantly higher than the corresponding level(s) determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is statistically significantly higher than the corresponding level(s) determined in step (1).

137. The method of claim 135 or claim 136, wherein steps (1) and (2) comprise determining the level of P-selectin protein, of PF4 protein and / or of NETosis fragments, and step (4) comprises (i) determining that the treatment is effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is not statistically significantly higher than the corresponding level(s) determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level(s) of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) is statistically significantly higher than the corresponding level(s) determined in step (1).

138. The method of claim 137, wherein step (4) comprises (i) determining that the treatment is effective for said disorder if the levels of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) are not statistically significantly higher than the corresponding levels determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the levels of P-selectin protein, of PF4 protein, and / or of NETosis fragments determined in step (2) are statistically significantly higher than the corresponding levels determined in step (1).

139. The method of any one of claims 135-138, wherein the blood sample is whole blood, serum or plasma.

140. The method of any one of claims 135-139, wherein the protein level is determined by an enzyme-linked immunosorbent assay (ELISA), radioimmunoassay, counterimmuno- electrophoresis (CIE), immunodiffusion, Western blotting, microscopy, or bead-based assays.

141. The method of any one of claims 125-140, further comprising:(1) determining in a bodily fluid sample collected from the subject prior to initiation of the treatment the level of antibodies that recognize a lipoglycan-containing antigen from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae or a derivative thereof;(2) determining the level of said antibodies in the same type of sample collected from the subject in the course of or following the treatment;(3) comparing the antibody levels determined in steps (1) and (2), and(4) (i) determining that the treatment is effective for said disorder if the level of antibodies determined in step (2) is not statistically significantly higher than the level of antibodies determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the level of antibodies determined in step (2) is statistically significantly higher than the level of antibodies determined in step (1).

142. The method of claim 141, wherein the lipoglycan-containing antigen:(1) comprises a diacyl-glycerol ortriacyl-glycerol moiety and is not a capsular polysaccharide or teichoic acid,(2) has an estimated molecular weight based on Western blot between about 20,000 and about 30,000 Daltons, and(3) shares one or more antigenic determinants with or is the same as the lipoglycan-containing antigen obtained from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107- 86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX 14861744) using a method selected from:(i) Method 1 comprising the steps:a. culturing strain CC55_001C, HM-1056 or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) at 37°C under anaerobic conditions for 2-7 days, and b. producing bacterial extract in the presence of a lysozyme, Serratia marcescens endonuclease, Proteinase K, and a detergent under non-denaturing conditions;(ii) Method 2 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) in rich nutrient media at 37°C under anaerobic conditions (75% N2, 20% CO2, and 5% H2) for 2-7 days, b. pelleting bacteria by centrifugation, c. producing a bacterial extract in a protein extraction buffer in the presence of lysozyme, Serratia marcescens endonuclease, and a detergent under non-denaturing conditions, d. treating the extract obtained in step (c) with Proteinase K, e. incubating the treated extract obtained in step (d) at 55°C for about 10 minutes, f. removing cell debris by centrifugation, and g. using the supernatant as an antigen preparation; or(iii) Method 3 comprising the steps: a. disrupting strain CC55_001C, HM-1056 cells or strain S107-48 (NCBI SRA Accession No: SRX14861748) or SI 07-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) cells with a French press, b. ultracentrifugating to obtain a precipitate and produce an ultracentrifugation supernatant, c. subjecting the ultracentrifugation supernatant obtained in step (b) to butanol-water extraction and isolating an aqueous phase, d. applying the aqueous phase from step (c) to a hydrophobic interaction chromatography matrix, and e. isolating lipoglycan-containing fractions.

143. The method of claim 141 or claim 142, wherein the level of antibodies is determined using an enzyme-linked immunosorbent assay (ELISA), radioimmunoassay, counterimmuno- electrophoresis (CIE), immunodiffusion, Western blotting, microscopy, or bead-based assays.

144. The method of any one of claims 141-143, wherein the bodily fluid is selected from whole blood, plasma, serum, urine, and saliva.

145. The method of any one of claims 125-145, further comprising:(1) determining in the gastrointestinal (GI) microbiota sample collected from the subject prior to initiation of the treatment an abundance of bacteria from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) or another strain from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae species that produces a lipoglycan-containing antigen or a derivative thereof and shares one or more antigenic determinants of the lipoglycan-containing antigen produced by Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107- 86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744);(2) determining the abundance of said bacteria in the same type of sample collected from the subject in the course of or following the treatment;(3) comparing the abundance of bacteria determined in steps (1) and (2), and(4) (i) determining that the treatment is effective for said disorder if the abundance of bacteria determined in step (2) is not statistically significantly higher than the abundance of said bacteria determined in step (1), or (ii) determining that the treatment is not effective for said disorder if the abundance of bacteria determined in step (2) is statistically significantly higher than the abundance of said bacteria determined in step (1).

146. The method of claim 145, wherein the GI microbiota is of cecal, ileal, colonic, or fecal origin.

147. The method of claim 146, wherein the GI microbiota is fecal microbiota.

148. The method of any one of claims 145-147, wherein the lipoglycan-containing antigen:(1) comprises a diacyl-glycerol ortriacyl-glycerol moiety and is not a capsular polysaccharide or teichoic acid,(2) has an estimated molecular weight based on Western blot between about 20,000 and about 30,000 Daltons, and(3) shares one or more antigenic determinants with or is the same as the lipoglycan-containing antigen obtained from Blautia (Ruminococcus) gnavus of the family Lachnospiraceae strain CC55 001C, HM-1056 (Human Microbiome Project (HMP) ID 1201; GenBank: AZJF00000000) or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or SI 07- 86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX 14861744) using a method selected from:(i) Method 1 comprising the steps: a. culturing strain CC55_001C, HM-1056 or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) at 37°C under anaerobic conditions for 2-7 days, and b. producing bacterial extract in the presence of a lysozyme, Serratia marcescens endonuclease, Proteinase K, and a detergent under non-denaturing conditions;(ii) Method 2 comprising the steps: a. culturing strain CC55 001C, HM-1056 or strain SI 07-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) in rich nutrient media at 37°C under anaerobic conditions (75% N2, 20% CO2, and 5% H2) for 2-7 days, b. pelleting bacteria by centrifugation, c. producing a bacterial extract in a protein extraction buffer in the presence of lysozyme, Serratia marcescens endonuclease, and a detergent under non-denaturing conditions, d. treating the extract obtained in step (c) with Proteinase K, e. incubating the treated extract obtained in step (d) at 55°C for about 10 minutes, f. removing cell debris by centrifugation, andg. using the supernatant as an antigen preparation; or(iii) Method 3 comprising the steps: a. disrupting strain CC55 001C, HM-1056 cells or strain S107-48 (NCBI SRA Accession No: SRX14861748) or S107-86 (NCBI SRA Accession No: SRX14861747) or S47-18 (NCBI SRA Accession No: SRX14861744) cells with a French press, b. ultracentrifugating to obtain a precipitate and produce an ultracentrifugation supernatant, c. subjecting the ultracentrifugation supernatant obtained in step (b) to butanol-water extraction and isolating an aqueous phase, d. applying the aqueous phase from step (c) to a hydrophobic interaction chromatography matrix, and e. isolating lipoglycan-containing fractions.

149. The method of any one of claims 1-148, wherein the lupus nephritis is proliferative lupus nephritis, membranous lupus nephritis, membranoproliferative lupus nephritis, or mesangial glomerulonephritis.

150. The method of any one of claims 1-149, wherein the subject is human.151 . The method of any one of claims 1-149, wherein the subject is a veterinary animal.

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