Targeting il1r1, MEOX1, and MAFF for treatment of inflammatory bowel disease

Abstract

The disclosure provides compositions and methods for treating inflammatory bowel disease (IBD) by inhibiting signaling molecules of the IL1 signaling pathway. Specifically, methods for treating IBD are provided, the methods comprising administering to subjects having IBD inhibitors of IL1 receptor 1 (IL1R1), inhibitors of transcription factors MEOX1 and MAFF to block MEOX1 and MAFF signaling in intestinal stroma cells.

Description

[0001] TARGETING IL1R1, MEOX1, AND MAFF FOR TREATMENT OF INFLAMMATORY BOWEL DISEASE RELATED APPLICATIONS

[0002] This application claims the benefit under 35 U.S.C. § 119(e) to U.S. Provisional Application No. 63 / 721,347, filed November 15, 2024, entitled “TARGETING MEOX1 AND MAFF FOR TREATMENT OF INFLAMMATORY BOWEL DISEASE,” the entire contents of which are incorporated herein by reference.

[0003] FEDERALLY SPONSORED RESEARCH

[0004] This invention was made with government support under Grant Numbers DK118640 and DK131321, awarded by the National Institutes of Health. The Government has certain rights in the invention.

[0005] BACKGROUND

[0006] Inflammatory bowel disease (IBD), including ulcerative colitis and Crohn’s disease, is a chronic intestinal inflammatory disorder associated with significant morbidity for patients. There are multiple therapeutics on the market for IBD including biologic agents or small molecules targeting specific cytokine pathways or cell trafficking. However, a substantial proportion of patients do not gain remission, or lose remission, to these available therapies. There is a need for new treatments.

[0007] SUMMARY

[0008] Provided are methods for treating inflammatory bowel disease by inhibiting signaling molecules of the interleukin 1 (IL1) signaling pathway. In some embodiments, described herein are compounds and compositions comprising inhibitors of interleukin- 1 receptor type 1 (IL1R1). Further described are compounds and compositions comprising inhibitors of transcription factors MEOX1 and MAFF, which are transcription factors associated with the IL1 signaling pathway. Provided are methods, compounds, and compositions that inhibit IL1R1, MEOX1, and MAFF signaling in intestinal stroma cells to treat inflammatory bowel disease.

[0009] Accordingly, in some aspects, the present disclosure provides methods of treating an autoimmune disease (e.g., inflammatory bowel disease), the method comprising administering to a subject in need thereof a composition comprising an IL1R1 inhibitor in an

[0010] 1

[0011] #14601190vl effective amount to treat the disease. In some embodiments, an IL1R1 inhibitor is or is part of an antibody, an antibody-drug conjugate (ADC), a nanoparticle, a small molecule, an inhibitor nucleic acid, or some combination thereof.

[0012] In some embodiments, the IL1R1 inhibitor is an antibody that binds IL1R1. In some embodiments, the antibody is a bispecific antibody that also binds ACKR1. In some embodiments, the inhibitor is an antibody drug conjugate (ADC) that comprises an IL1R1 inhibitor and a molecule that binds ACKR1. In some embodiments, the IL1R1 inhibitor is a small molecule or an inhibitory nucleic acid.

[0013] In some embodiments, the molecule that binds ACKR1 is an ACKR1 antibody. In some embodiments, the inhibitor is a nanoparticle comprising an inhibitor nucleic acid.

[0014] In some embodiments, the administering is by oral administration or rectal administration. In some embodiments, the rectal administration is by enema.

[0015] In some embodiments, the inflammatory bowel disease is ulcerative colitis or Crohn’s disease.

[0016] In some aspects, provided herein is a method of inhibiting IL1R1 in an intestinal endothelial cell, the method comprising contacting an intestinal endothelial cell with a composition comprising a IL1R1 inhibitor in an effective amount to inhibit IL1R1 in the intestinal endothelial cell.

[0017] In some embodiments, the intestinal endothelial cell is a venular endothelial cell.

[0018] In some embodiments, the IL1R1 inhibitor is an antibody that binds IL1R1. In some embodiments, the antibody is a bispecific antibody that also binds ACKR1.

[0019] In some embodiments, the inhibitor is an antibody drug conjugate (ADC) that comprises an IL1R1 inhibitor and a molecule that binds ACKR1. In some embodiments, the IL1R1 inhibitor is a small molecule or an inhibitory nucleic acid.

[0020] In some embodiments, the molecule that binds ACKR1 is an ACKR1 antibody. In some embodiments, the inhibitor is a nanoparticle comprising an inhibitor nucleic acid.

[0021] In some embodiments, the intestinal endothelial cell is in vivo.

[0022] BRIEF DESCRIPTION OF THE DRAWINGS

[0023] The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present disclosure, which can be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein. The patent or application file contains at least one

[0024] 2

[0025] #14601190vl drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

[0026] FIGs. 1A-1D shows that interleukin 1 (IL1) bioactivity is a hallmark of inflammatory bowel disease (IBD) ulcers, and that ME0X1 and MAFF are ulcer-associated transcription factors. FIG. 1A shows an IL1 bioactivity assay applied to an IBD cohort’s intestinal mucosa. FIG. IB shows a weighted gene network correlation analysis (WGCNA) of the cellular fractions’ bulk RNA-seq of the samples in FIG. 1A demonstrating a gene module (“brown module”) that was correlated with ulcerated IBD colon. FIG. 1C shows ME0X1 as an ulcer-associated transcription factors identified in the brown module. FIG. ID shows MAFF as an ulcer associated transcription factors identified in the brown module.

[0027] FIGs. 2A-2C shows bulk RNA sequencing data in pediatric patients with ileal Crohn’s disease (RISK cohort). FIG. 2A shows enrichment of the brown module in ulcerated ileal mucosa in the RISK cohort. FIG. 2B shows ME0X1 enrichment in ulcerated ileal mucosa of the RISK cohort. FIG. 2C shows MAFF enrichment in ulcerated ileal mucosa of the RISK cohort.

[0028] FIGs. 3A-3B shows that ME0X1, MAFF, and associated genes are expressed in postcapillary venule endothelium and are upregulated in a ILlB-specific manner. FIG. 3A shows single cell RNA sequencing data in ulcerative colitis patient samples. FIG. 3B shows human umbilical vein endothelial cells (HUVECs) incubated for 24 hours with IL1B, TGFB + / - JQ1.

[0029] FIG. 4 shows ACKR1, ME0X1, and IL1R expression in an ulcerated tissue sample of a patient with inflammatory bowel disease using a combination of immune-histochemistry (probe for protein) as well as RNAscope (probe for transcripts).

[0030] FIGs. 5A-5B show antibody targeting of IL1R1. FIG. 5A shows a diagram of a bispecific antibody that binds and inhibits IL1R1 activity and binds ACKR1. FIG. 5B shows diagrams of antibody drug conjugates (ADCs) that inhibit IL1R activity and bind ACKR1.

[0031] FIG. 6 shows a diagram of nanoparticles to deliver inhibitory oligonucleotides. The nanoparticles comprise anti-ACKRl antibodies that bind ACKR1 on the surface of cells. The nanoparticles may encapsulate inhibitory oligonucleotides that inhibit IL1R1 expression, ME0X1 expression, or IL1R1 expression and ME0X1 expression.

[0032] DETAILED DESCRIPTION

[0033] Interleukin- 1 (IL1) cytokines mediate innate immune reactions. IL1 family cytokines activate intracellular signaling pathways by binding to a primary receptor subunit, such as IL1REIL1R1, IL18Ra / ILlR5, ILlRrp2 / ILlR6, or ST2 / IL1R4, and the primary receptor

[0034] #14601190vl 3 subunit then recruits an accessory receptor to form the active receptor complex. Signaling cascades triggered by ILla, ILip, IL-18, IL-33, IL36a, IL36P, or IL36y activate MAPKs and NFKP, leading to the expression of pro-inflammatory cytokines, chemokines, and secondary mediators of the inflammatory response. Inhibiting IL1 signaling therefore inhibits the inflammatory response by, for example, reducing expression of pro-inflammatory cytokines, chemokines, and secondary mediators of the inflammatory response. Inhibiting IL1 signaling will therefore inhibit inflammatory responses in conditions such as autoimmune diseases (e.g., inflammatory bowel disease) fibrosis, or fibrotic diseases.

[0035] IL1 signaling increases pro-inflammatory signaling and is associated with autoimmune diseases, fibrotic diseases, and fibrosis. Provided herein are methods for treating an autoimmune disease (e.g., inflammatory bowel disease (IBD)), a fibrotic disease, or fibrosis the methods comprising administering to a subject in need thereof an inhibitor of IL1 signaling. Interleukin- 1 receptor type 1 (IL1R1) is a receptor for cytokines such as interleukin- 1 alpha (IL- la) and interleukin- 1 beta (IL- ip), and signaling downstream of IL1R1 increases transcription factor activity. Mesenchymal Homeobox 1 (ME0X1) and MAF BZIP Transcription Factor F (MAFF) are transcription factors associated with the IL1 signaling pathway. ME0X1 has been reported to be associated with cancer progression (see, e.g., Sun et al., Int. J. Med. Sci., 16: 68-74, 2019). MAFF is a member of the small Maf family of transcription factors that lacks an obvious transactivation domain but can heterodimerize with other bZIP proteins to modulate transcription (see, e.g., Wu et al., Oncol. Res., 28: 299-309, 2020).

[0036] Accordingly, in some embodiments, the present disclosure provides a method for treating an autoimmune disease (e.g., an inflammatory bowel disease), the method comprising administering to a subject in need thereof an effective amount of an IL1R1 inhibitor, a MEOX1 inhibitor, and / or a MAFF inhibitor. In additional embodiments, the present disclosure provides a method for treating fibrosis (e.g., cardiac fibrosis), the method comprising administering to a subject in need thereof an effective amount of an IL1R1 inhibitor, a MEOX1 inhibitor, and / or a MAFF inhibitor. In preferred embodiments, an IL1R1 inhibitor, a MEOX1 inhibitor, and / or MAFF inhibitor is administered to a subject to target an intestinal stroma cell in the subject. Intestinal stroma cells include intestinal endothelial cells, intestinal fibroblasts, intestinal myofibroblasts and intestinal pericytes. In some embodiments, an intestinal stroma cell targeted by the methods and compounds described herein is an intestinal post-capillary venule endothelial cell. Inventors demonstrated that intestinal postcapillary venule endothelial cells present in intestinal lesions of subjects with inflammatory

[0037] 4

[0038] #14601190vl bowel disease express ACKR1. Therefore, in preferred embodiments, methods, compounds, and compositions are described that target ACKR1 expressing post-capillary venule endothelial cells.

[0039] I. Methods of Treatment

[0040] Autoimmune Disease

[0041] In some embodiments, provided are methods of treating an autoimmune disease associated with interleukin 1 (IL1) signaling. An autoimmune disease associated with IL1 signaling may be any autoimmune disease in which elevated IL1 activity, expression, or some combination thereof, has been detected. Elevated IL1 activity and / or expression is activity and / or expression that is increased by 10% to 100%, 20% to 90%, 30% to 80%, 40% to 70%, or 50% to 60% compared to a control. In some embodiments, elevated IL1 activity and / or expression is activity and / or expression that is by 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% or more compared to a control. A control may be a subject with an autoimmune disease that is not associated with elevated IL1 expression and / or signaling.

[0042] Non-limiting examples of autoimmune diseases associated with IL1 signaling include: inflammatory bowel disease (IBD), rheumatoid arthritis (RA), cryopyrin-associated periodic syndromes (CAPS), familial Mediterranean fever (FMF), and Behget’s disease. In some embodiments, an autoimmune disease associated with IE1 signaling is inflammatory bowel disease (e.g., ulcerative colitis or Crohn’s disease).

[0043] A method of treating an autoimmune disease associated IE1 signaling may be by administering a compound or composition described herein to a subject in need thereof. The term “treating,” as used herein, refers to reducing the frequency or severity of at least one sign or symptom of a disease, e.g., an inflammatory bowel disease in a subject. Treatment includes prophylactic treatment and therapeutic treatment. Prophylactic treatment includes preventing the onset of a disease or condition, e.g., inflammatory bowel disease. Prophylactic treatment can include treatment of a subject known to have an inflammatory bowel disease and being in remission, where the prophylactic treatment prevents the recurrence of an active disease. Therapeutic treatment includes delaying or slowing the progression of a disease or condition, e.g., inflammatory bowel disease or reducing the severity of at least one sign or symptom of the disease. A “sign or symptom” of inflammatory bowel disease includes, e.g., diarrhea, abdominal pain, rectal bleeding, intestinal cramps, and / or muscle spasms, and, in

[0044] 5

[0045] #14601190vl some cases, anemia. Methods of monitoring effects of treatments of inflammatory bowel diseases are well known to healthcare practitioners.

[0046] The term “administering” or “administration,” as used herein, refers to providing a material to a subject in a manner that is pharmacologically useful and includes contacting a subject with an effective amount of a compound or composition described herein.

[0047] Administering includes injecting or infusing a compound or composition into a subject. The injection or infusion can be systemic or local into an area of the intestine. In some embodiments, administering comprises contacting an intestine of a subject with a compound or composition described herein through endoscopic means. For example, administering includes providing, infusing, or injecting a compound or composition into an intestinal tract of a subject, e.g., by endoscopic deposition, infusion or injection. Endoscopy can be performed through a peroral access or through rectal access.

[0048] An “effective amount,” as used herein, refers to an amount of a compound or composition that is capable of reducing the severity of at least one sign or symptom of inflammatory bowel disease when administered to a subject in need thereof. An effective amount of a compound or composition is also an amount that delays the progression of inflammatory bowel disease in a subject. The effective amount will vary with the age and physical condition of the subject being treated, the severity of the condition, the duration of the treatment, the nature of the concurrent therapy (if any), the specific route of administration, and like factors are within the knowledge and expertise of the healthcare practitioner. An effective amount can depend upon the duration the individual has had the disease.

[0049] Non-Autoimmune Inflammation

[0050] In some embodiments, provided are methods of treating IL-1 mediated inflammation not associated with an autoimmune disease. IL-1 mediated inflammation not associated with an autoimmune disease, as provided herein, means that IL- 1 mediated inflammation is present in a subject that is not diagnosed with or suspected of having an autoimmune disease. IL-1 mediated inflammation may be detected by measuring levels of any cytokines associated with IL-1 signaling. Non-limiting examples of cytokines associated with IL-1 signaling include: IL- la, IL-ip, interleukin-6 (IL-6), prostaglandins (e.g., PGE2, nitric oxide), and acute-phase proteins (e.g., C-reactive protein, serum amyloid A). In some embodiments, IL-1 mediated inflammation is a level of one or more cytokines associated with IL-1 signaling that is increased by 10% to 100%, 20% to 90%, 30% to 80%, 40% to 70%, or 50% to 60% compared to a control. In some embodiments, IL- 1 mediated inflammation is a level of one

[0051] 6

[0052] #14601190vl or more cytokines associated with IL-1 signaling that is increased by 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% compared to a control. A control may be a level of the one or more cytokines in a subject that is not present in a subject that is not diagnosed with or suspected of having an autoimmune disease.

[0053] Non-limiting examples of IL-1 mediated inflammation not associated with an autoimmune disease include: fibrosis, type 2 diabetes mellitus, cardiovascular disease (e.g., heart failure, myocarditis, coronary artery disease, cardiac ischemic injury), cancer, and neurodegenerative disease (e.g., Alzheimer’s disease, Parkinson’s disease). In some embodiments, IL-1 mediated inflammation not associated with autoimmune disease is fibrosis.

[0054] A method of treating IL- 1 mediated inflammation not associated with autoimmune disease may be by administering a compound or composition described herein to a subject in need thereof. The term “treating,” as used herein, refers to reducing the frequency or severity of at least one sign or symptom of a disease, e.g., IL-1 mediated inflammation not associated with autoimmune disease in a subject. Treatment includes prophylactic treatment and therapeutic treatment. Prophylactic treatment includes preventing the onset of a disease or condition, e.g., IL-1 mediated inflammation not associated with autoimmune disease.

[0055] Prophylactic treatment can include treatment of a subject known to have a disorder having IL-1 mediated inflammation not associated with autoimmune disease and being in remission, where the prophylactic treatment prevents the recurrence of an active disease. Therapeutic treatment includes delaying or slowing the progression of a disease or condition, e.g., a disorder having IL-1 mediated inflammation not associated with autoimmune disease or reducing the severity of at least one sign or symptom of the disease. A “sign or symptom” of a disorder having IL- 1 mediated inflammation not associated with autoimmune disease may be: fever, aches, high blood pressure, swelling, dementia, extreme tiredness or fatigue, aching muscles and joints, and unexplained weight loss. Methods of monitoring effects of treatments of disorders having IL- 1 mediated inflammation not associated with autoimmune disease are well known to healthcare practitioners.

[0056] An “effective amount,” as used herein, refers to an amount of a compound or composition that is capable of reducing the severity of at least one sign or symptom of a disorder having IL-1 mediated inflammation not associated with autoimmune disease when administered to a subject in need thereof. An effective amount of a compound or composition is also an amount that delays the progression of a disorder having IL-1 mediated

[0057] 7

[0058] #14601190vl inflammation not associated with autoimmune disease in a subject. The effective amount will vary with the age and physical condition of the subject being treated, the severity of the condition, the duration of the treatment, the nature of the concurrent therapy (if any), the specific route of administration, and like factors are within the knowledge and expertise of the healthcare practitioner. An effective amount can depend upon the duration the individual has had the disease.

[0059] Interleukin 1 Signaling

[0060] Interleukin- 1 (IL 1) cytokines are major mediators of innate immune reactions. IL1 family cytokines activate intracellular signaling pathways by binding to a primary receptor subunit, such as IL1RI / IL1R1, IL18Ra / ILlR5, ILlRrp2 / ILlR6, or ST2 / IL1R4, which then recruits an accessory receptor to form the active receptor complex. Signaling cascades triggered by IL-1 alpha, IL-1 beta, IL- 18, IL-33, IL-36 alpha, IL-36 beta, or IL-36 gamma activate MAPKs and NF-kappa B, leading to the expression of pro-inflammatory cytokines, chemokines, and secondary mediators of the inflammatory response. Inhibiting IL1 signaling therefore inhibits the inflammatory response by, for example, reducing expression of pro-inflammatory cytokines, chemokines, and secondary mediators of the inflammatory response.

[0061] In some aspects, provided herein is a method of treating a disorder associated with IL-1 signaling (e.g., autoimmune disease, a disorder having IL-1 mediated inflammation that is not autoimmune disease) in a subject in need thereof, the method comprising administering a compound that inhibits IL1 signaling. IL1 signaling through cytokines IL1 alpha (ILla), IL1 beta (ILip), IL18, IL1F5, and IL1F11, is a mediator of innate immune reactions and controls proinflammatory reactions to tissue injury by bacterial or viral products, uric acid crystals, or adenosine 5 ’-triphosphate.

[0062] In some embodiments, inhibiting IL1 signaling is inhibiting IL1 signaling by 10% to 100%, 20% to 90%, 30% to 80%, 40% to 70%, or 50% to 60% compared to a control. In some embodiments, inhibiting IL1 signaling is inhibiting IL1 signaling by 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% or more compared to a control. A control may be a subject with a disorder associated with IL-1 signaling (e.g., autoimmune disease, a disorder having IL-1 mediated inflammation that is not autoimmune disease) in whom IL1 signaling is not inhibited or IL1 signaling in a subject before an inhibitor of IL1 signaling is administered.

[0063] IL1R1 Inhibitor

[0064] 8

[0065] #14601190vl In some embodiments, a method of inhibiting IL1 signaling provided herein comprises administering an interleukin 1 receptor, type 1 (IL1R1) inhibitor to a subject. IL1R1, also known as CD121a, is a receptor for IL1 alpha (ILla), IL1 beta (IL1 ), and IL1 receptor antagonist (IL1RA). Blockade of ILla and IL10 signaling through IL1R1 by IL-1RA occurs in a number of human diseases associated with IL-1 signaling (e.g., autoimmune diseases, disorders having IL-1 mediated signaling that are not autoimmune diseases). In some embodiments, an autoimmune disease includes, but not limited to, inflammatory bowel disease, rheumatoid arthritis, cryopyrin-associated periodic syndromes (CAPS), familial Mediterranean fever (FMF), and Behget’s disease. ILla and IL10 rapidly increase mRNA expression of genes in numerous cell types including monocytes, macrophages, epithelial cells, endothelial cells, chondrocytes, and fibroblasts. ILla and IL 10 also induce mRNA expression of their genes (ILIA and 1L1B, respectively), acting in a positive-feedback loop that increases signaling through IL1R1.

[0066] A method of inhibiting IL1 signaling provided herein therefore inhibits innate immune signaling. An IL1R1 inhibitor that reduces (e.g., inhibits) IL1R1 signaling may: (1) inhibit binding and signaling through IL1R1 by ILla, (2) inhibit binding and signaling through IL1R1 by IL10; (3) inhibit binding of IL1RA to IL1R1; or (4) some combination of (1), (2), and / or (3).

[0067] An IL1R1 inhibitor provided herein may be an antibody or part of an antibody, an antibody-drug conjugate (ADC), a nanoparticle, a small molecule, an inhibitor nucleic acid, or some combination thereof. In some embodiments, an IL1R1 inhibitor is an antibody or part of an antibody. An antibody that is an IL1R1 inhibitor may be a monospecific antibody or a bispecific antibody. A “monospecific antibody,” as provided herein, is an antibody that binds to a single, specific antigen or epitope. In some embodiments, a monospecific antibody provided herein is an anti-ILlRl antibody. In some embodiments, a monospecific anti-IL1R1 antibody is antibody disclosed in JP7114460B2, US10005842B2, MA5-38544 (ThermoFisher), 84094-6-RR (Proteintech).

[0068] In some embodiments, an antibody provided herein is a bispecific antibody. A “bispecific antibody,” as provided herein is an antibody that comprises antigen binding sites that bind two distinct antigens simultaneously (FIG. 5A). In some embodiments, a bispecific antibody provided herein binds two distinct epitopes on IL1R1. In some embodiments, a bispecific antibody provided herein binds an epitope on IL1R1 and an antigen on another protein (e.g., ME0X1, MAFF, ACKR1).

[0069] 9

[0070] #14601190vl In some embodiments, an IL1R1 inhibitor is an antibody drug conjugate (ADC). An “antibody-drug conjugate” or “ADC,” as provided herein, is an engineered molecule that combines a monospecific antibody with a therapeutic agent (FIG. 5B). A monospecific antibody may bind an antigen on any protein provided herein (e.g., IL1R1, ME0X1, MAFF, ACKR1). A therapeutic agent may be any agent that may be used to treat a disease or disorder provided herein (e.g., IBD, fibrosis, cardiovascular disease). Non-limiting examples of therapeutic agents include: a cytotoxic drug, anti-inflammatory compounds, steroids, immune modulator agents (e.g., azathioprine, 6-mercaptopurine, methotrexate, cyclosporine, tacrolimus), biologic agents (e.g., anti-TNF agents, anti-integrin agents), and / or Bromodomain-containing protein 4 (BRD4) inhibitor. In some embodiments, the BRD4 inhibitor is JQ1 (see, e.g., US 2023 / 0078089).

[0071] In some embodiments, an IL1R1 inhibitor is an inhibitor nucleic acid. An “inhibitor nucleic acid,” as provided herein, is a nucleic acid that inhibits gene expression associated with IL1R1. Gene expression associated with IL1R1 may be expression of IL1R1, expression of a gene upstream of IL1R1 in IL1 signaling (e.g., ILla, ILip), or some combination thereof. An inhibitor nucleic acid may be a short hairpin RNA (shRNA), microRNA (miRNA), artificial microRNA (amiRNA), small interfering RNA (siRNA), or circular RNA (circRNA). In some embodiments, an inhibitor nucleic acid is a siRNA. In some embodiments, an inhibitor nucleic acid is a nucleic acid as disclosed in Burch and Mahan, J Clin Invest, 88(4): 1190-1196 (1991); and Miraglia et al., Int. Jour. Immunopharmacology, 18(4): 227-240 (1996);

[0072] In some embodiments, an IL1R1 inhibitor is a nanoparticle. A “nanoparticle” as used herein, is a particle with at least one dimension between 1 nanometer to 100 nanometers in size. A nanoparticle may be an organic nanoparticle (e.g., polymer, liposome, dendrimer), a metal nanoparticle (e.g., gold, silver, copper), a metal oxide (titanium dioxide, zinc oxide), a carbon nanoparticle (e.g., carbon nanotube). Non-limiting examples of nanoparticles include: polymeric nanosphere, polymeric nanocapsule, polymeric micelles, liposomes, dendrimers, gold nanoparticles, and iron oxide nanoparticles. In some embodiments, a nanoparticle is a polymeric nanocapsule that can carry and deliver a therapeutic payload to a target cell. A polymeric nanocapsule may be made of any material known in the art including, but not limited to, poly(lactic-co-glycolic acid) (PLGA), poly(amidoamine) (PAMAM),

[0073] poly ethoxy lethylglycinamide (PEE-G), polyethylene glycol (PEG), or some combination thereof.

[0074] 10

[0075] #14601190vl In some embodiments, a therapeutic payload is an inhibitor nucleic acid provided herein. A nanoparticle may comprise a targeting agent that promotes delivery of a nanoparticle to a cell that expresses a molecule that binds to the targeting agent. In some embodiments, a targeting agent is a monospecific antibody whose antigen is expressed on the surface of a target cell. In some embodiments, a monospecific antibody is an anti-ACKRl antibody that binds ACRK1 on endothelial cells.

[0076] An IL1R1 inhibitor provided herein may inhibit IL1R1 activity by 10% to 100%, 20% to 90%, 30% to 80%, 40% to 70%, or 50% to 60% compared to a control. In some embodiments, an IL1R1 inhibitor provided herein inhibits IL1R1 activity by 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% or more compared to a control. A control may be a subject with a disease or disorder provided herein (e.g., IBD, fibrosis, cardiovascular disease) that has not been administered an IL1R1 inhibitor or IL1R1 signaling in a subject before an inhibitor of IL1R1 signaling is administered.

[0077] MEOX1 Inhibitor

[0078] In some aspects, provided is a method of treating inflammatory bowel disease in a subject in need thereof, the method comprising administering a compound that inhibits IL1 downstream signaling, e.g., a MEOX1 inhibitor. The term “MEOX1 inhibitor,” as used herein, refers to a molecule or composition that interferes with a function of a MEOX1 transcription factor, e.g., a binding function, a transcriptional activation function or an interaction between MEOX1 and another protein involved in a transcriptional control function of MEOXl.

[0079] A MEOX1 inhibitor provided herein may be an antibody or part of an antibody, an antibody-drug conjugate (ADC), a nanoparticle, a small molecule, an inhibitor nucleic acid, or some combination thereof. In some embodiments, a MEOX1 inhibitor is an inhibitory nucleic acid, e.g., a short hairpin RNA (shRNA), microRNA (miRNA), artificial microRNA (amiRNA), small interfering RNA (siRNA), or circular RNA (circRNA). In some embodiments, a MEOX1 inhibitory nucleic acid interacts with a MEOX1 mRNA. In some embodiments, a MEOX1 inhibitor is an inhibitory nucleic acid, e.g., a MEOX1 shRNA (see, e.g., Shen et al., Scientific Reports, 14: 5183, 2024). In some embodiments, a MEOX1 inhibitor is a small molecule. In some embodiments, a MEOX1 inhibitor is a Bromodomaincontaining protein 4 (BRD4) inhibitor. In some embodiments, the BRD4 inhibitor is JQ1 (see, e.g., Patent Publication US2023 / 0078089). In some embodiments, a MEOX1 inhibitor is

[0080] 11

[0081] #14601190vl an anti-MEOXl antibody. In some embodiments, a ME0X1 inhibitor is an inhibitory anti-ME0X1 antibody.

[0082] A ME0X1 inhibitor provided herein may inhibit ME0X1 activity by 10% to 100%, 20% to 90%, 30% to 80%, 40% to 70%, or 50% to 60% compared to a control. In some embodiments, a MEOX1 inhibitor provided herein inhibits MEOX1 activity by 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% or more compared to a control. A control may be a subject with a disease or disorder provided herein (e.g., IBD, fibrosis, cardiovascular disease) that has not been administered a MEOX1 inhibitor or MEOX1 signaling in a subject before an inhibitor of MEOX1 signaling is administered.

[0083] MAFF Inhibitor

[0084] In some aspects, provided is a method of treating inflammatory bowel disease in a subject in need thereof comprises inhibiting MAFF by administering a MAFF inhibitor to a cell of an intestine of a subject having inflammatory bowel disease (e.g., ulcerative colitis or Crohn’s disease). The term “MAFF inhibitor,” as used herein, refers to a molecule or composition that interferes with a function of a MAFF transcription factor, e.g., a binding function, a transcriptional activation function or an interaction between MAFF and other proteins involved in a transcriptional control function of MAFF. In some embodiments, a method of treating an inflammatory bowel disease comprises administering a composition comprising a MAFF inhibitor to a subject having an inflammatory bowel disease.

[0085] A MAFF inhibitor provided herein may be an antibody or part of an antibody, an antibody-drug conjugate (ADC), a nanoparticle, a small molecule, an inhibitor nucleic acid, or some combination thereof. In some embodiments, a MAFF inhibitor is an inhibitory nucleic acid, e.g., a short hairpin RNA (shRNA), microRNA (miRNA), artificial microRNA (amiRNA), small interfering RNA (siRNA), or circular RNA (circRNA). In some embodiments, a MAFF inhibitory nucleic acid interacts with a MAFF mRNA. In some embodiments, a MAFF inhibitory nucleic acid is, e.g., hsa-miR-224-5p (see, e.g., Wu et al., Oncology Research, 28: 299-309, 2020), miR-320a (see, e.g., Du et al., Mol Ther., 26: 444-457, 2021), or MAFF an anti-sense oligonucleotide (see, e.g., Chen et al., JC1, 131: el48020, 2021). In some embodiments, a MAFF inhibitor is a small molecule. In some embodiments, a MAFF inhibitor is an inhibitory antibody or fragment thereof that binds MAFF and prevents MAFF from executing its transcription factor activity, e.g., by inhibiting MAFF’s heterodimerization function.

[0086] #14601190vl 12 A MAFF inhibitor provided herein may inhibit MAFF activity by 10% to 100%, 20% to 90%, 30% to 80%, 40% to 70%, or 50% to 60% compared to a control. In some embodiments, a MAFF inhibitor provided herein inhibits MAFF activity by 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% or more compared to a control. A control may be a subject with a disease or disorder provided herein (e.g., IBD, fibrosis, cardiovascular disease) that has not been administered a MAFF inhibitor or MAFF signaling in a subject before an inhibitor of MAFF signaling is administered.

[0087] ACKR1

[0088] Intestinal endothelial cells, e.g., post-capillary venule endothelial cells are involved in IL-1 signaling in lesions of patients with inflammatory bowel disease. Moreover, postcapillary venule endothelial cells that express ACKR1 were identified as important targets for methods described herein. Therefore, in some embodiments, a method of treating an inflammatory bowel disease (e.g., ulcerative colitis or Crohn’s disease) in a subject in need thereof comprises administering a composition that comprises a compound described herein and a molecule that binds ACKR1. For example, a molecule that binds ACKR1 can be an ACKR1 antibody (see, e.g., Thiriot et al., BMC Biology, 15:45 (2017). Accordingly in preferred embodiments, a composition used in the methods described herein comprises an IL1R1 inhibitor, a MEOX1 inhibitor and / or a MAFF inhibitor and a molecule that binds ACKR1, e.g., an ACKR1 antibody or an ACKR1 aptamer.

[0089] In some embodiments, the methods described comprise systemic administration. In some embodiments, the methods described comprise local administration. Systemic administration includes, but is not limited to, oral, intravenous, subcutaneous, intramuscular, intraperitoneal, or by inhalation. Local administration includes, but is not limited to, intestinal administration, e.g., orally or by enema or administration, e.g., through contacting, infusing, depositing, or injecting a composition into a tissue, e.g., an intestinal tissue.

[0090] A compound or composition can be infused, deposited, or injected using an endoscope. Endoscopic administration can be by oral endoscopy, e.g., an endoscope is placed into an intestine following oral insertion of the endoscope. Alternatively, endoscopic administration can be by rectal endoscopy, e.g., an endoscope is placed into an intestine following anal insertion of the endoscope.

[0091] In some embodiments, a method of treating an inflammatory bowel disease (e.g., ulcerative colitis or Crohn’s disease) in a subject in need thereof comprises administering a

[0092] 13

[0093] #14601190vl compound or composition described herein to the subject by endoscopic administration to an inflamed intestine, e.g., an intestinal tissue that contains an ulcer. For example, an ulcerated intestinal tissue can contain granulation tissue, e.g., at the base of the ulcer. Inventors demonstrated that certain cells in granulation tissue, e.g., post-capillary venule endothelial cells express ACKR1. Thus, the administration of an IL1R1 inhibitor, a ME0X1 inhibitor and / or a MAFF inhibitor in a composition with a molecule that binds ACKR1, e.g., a ACKR1 antibody can be targeted to post-capillary venule endothelial cells, e.g., in a granulation tissue of an ulcer. It is also contemplated that a composition that comprises an IL1R1 inhibitor, a ME0X1 inhibitor and / or a MAFF inhibitor and a molecule that binds ACKR1 can be administered adjacent to an intestinal ulcer to target, e.g., post-capillary venule endothelial cells in the tissue adjacent to the ulcer.

[0094] In some embodiments, a method is provided that comprises contacting an intestinal cell with a compound or composition described herein. The term “contacting a cell,” as used herein, refers to depositing adjacent to, applying to, or injecting into a cell a compound or composition described herein, e.g., using an endoscopic device. A method of contacting a cell can include visually locating a cell or a tissue that contains the cell, e.g., an inflamed intestinal mucosa that contains ACKR1 -positive post-capillary venule endothelial cells using an endoscopic device having a camera and applying, depositing, or injecting the compound or composition into the cell or intestinal mucosa and / or submucosa. Intestinal cells that can be contacted using methods described herein include intestinal stroma cells, e.g., intestinal endothelial cells, intestinal fibroblasts, intestinal myofibroblast and / or intestinal pericytes.

[0095] In some embodiments, a method of treating inflammatory bowel disease in a subject in need thereof comprises administering an IL1R1 inhibitor to a subject that is otherwise free of indications calling for treatment with an IL1R1 inhibitor. The phrase “otherwise free of indications calling for treatment with an IL1R1 inhibitor,” refers to a subject that has no other signs or symptoms calling for treatment with an IL1R1 inhibitor. IL1R1 inhibitors are indicated for the treatment of autoimmune disorders, fibrosis, cardiovascular disease, neurodegenerative disorders, and cancer.

[0096] In some embodiments, a method of treating inflammatory bowel disease in a subject in need thereof comprises administering a ME0X1 inhibitor to a subject that is otherwise free of indications calling for treatment with a ME0X1 inhibitor. The phrase “otherwise free of indications calling for treatment with a ME0X1 inhibitor,” refers to a subject that has no other signs or symptoms calling for treatment with a ME0X1 inhibitor. ME0X1 inhibitors are indicated for the treatment of cardiac fibrosis (see, e.g., Patent Publication

[0097] 14

[0098] #14601190vl US2023 / 0078089), and cancer. The phrase “otherwise free of indications calling for treatment with a MAFF inhibitor,” refers to a subject that has no other signs or symptoms calling for treatment with a MAFF inhibitor. MAFF inhibitors are indicated for the treatment of cancer.

[0099] In some embodiments, a composition comprising an IL1R1 inhibitor, a composition comprising a ME0X1 inhibitor and a composition comprising a MAFF inhibitor are administered to a subject at the same time or at different times. For example, an IL1R1 inhibitor can be administered before a ME0X1 inhibitor or vice versa; a ME0X1 inhibitor can be administered before a MAFF inhibitor, or vice versa. An IL1R1 inhibitor can be administered between about 1 minute to about 12 hours prior to a ME0X1 inhibitor; or about 2 minutes, about 3 minutes, about 5 minutes, about 10 minutes, about 12 minutes, about 15 minutes, about 20 minutes, about 25 minutes, about 30 minutes, about 35 minutes, about 40 minutes, about 45 minutes, about 50 minutes, about 1 hour, about 1.5 hours, about 2 hours, about 2.5 hours, about 3 hours, about 3.5 hours, about 4 hours, about 4.5 hours, about 5 hours, about 5.5 hours, about 6 hours, about 6.5 hours, about 7 hours, about 7.5 hours, about 8 hours, about 8.5 hours, about 9 hours, about 9.5 hours, about 10 hours, about 10.5 hours, about 11 hours, about 11.5 hours, or about 12 hours or longer prior to administering a composition comprising a MEOX1 inhibitor or vice versa.

[0100] In some embodiments, a MEOX1 inhibitor can be administered between about 1 minute to about 12 hours prior to a MAFF1 inhibitor; or about 2 minutes, about 3 minutes, about 5 minutes, about 10 minutes, about 12 minutes, about 15 minutes, about 20 minutes, about 25 minutes, about 30 minutes, about 35 minutes, about 40 minutes, about 45 minutes, about 50 minutes, about 1 hour, about 1.5 hours, about 2 hours, about 2.5 hours, about 3 hours, about 3.5 hours, about 4 hours, about 4.5 hours, about 5 hours, about 5.5 hours, about 6 hours, about 6.5 hours, about 7 hours, about 7.5 hours, about 8 hours, about 8.5 hours, about 9 hours, about 9.5 hours, about 10 hours, about 10.5 hours, about 11 hours, about 11.5 hours, or about 12 hours or longer prior to administering a composition comprising a MAFF1 inhibitor or vice versa.

[0101] In some embodiments, an IL1R1 inhibitor and a composition comprising a MAFF inhibitor are administered to a subject at the same time or at different times. For example, an IL1R1 inhibitor can be administered before a MAFF inhibitor or vice versa; an IL1R1 inhibitor can be administered before a MAFF inhibitor, or vice versa. An IL1R1 inhibitor can be administered between about 1 minute to about 12 hours prior to a MAFF inhibitor; or about 2 minutes, about 3 minutes, about 5 minutes, about 10 minutes, about 12 minutes,

[0102] 15

[0103] #14601190vl about 15 minutes, about 20 minutes, about 25 minutes, about 30 minutes, about 35 minutes, about 40 minutes, about 45 minutes, about 50 minutes, about 1 hour, about 1.5 hours, about 2 hours, about 2.5 hours, about 3 hours, about 3.5 hours, about 4 hours, about 4.5 hours, about 5 hours, about 5.5 hours, about 6 hours, about 6.5 hours, about 7 hours, about 7.5 hours, about 8 hours, about 8.5 hours, about 9 hours, about 9.5 hours, about 10 hours, about 10.5 hours, about 11 hours, about 11.5 hours, or about 12 hours or longer prior to administering a composition comprising a MAFF inhibitor or vice versa.

[0104] Furthermore, an IL1R1 inhibitor, a MEOX1 inhibitor and a MAFF inhibitor can be administered via the same route of administration or via different routes of administration. For example, a composition comprising an IL1R1 inhibitor can be administered by intravenous administration and a composition comprising a MEOX1 inhibitor can be administered by enteral administration or vice versa. In a preferred embodiment, an IL1R1 inhibitor and / or a MEOX1 inhibitor is administered by enteral administration, e.g., oral or rectal administration. For example, an IL1R1 inhibitor can be administered by enema and a MEOX1 inhibitor can be administered by oral administration.

[0105] For example, an effective amount of a compound or composition is an amount that, when administered blocks or reduces IL1 downstream signaling in an intestinal cell, e.g., an intestinal stroma cell of a subject having inflammatory bowel disease, fibrosis, cardiovascular disease, neurodegenerative disease, or any other disease or disorder provided herein.

[0106] As is well known in the medical arts, a dosage for any one subject depends on many factors, including the subject's size, body surface area, age, the particular composition to be administered, the active ingredient(s) in the composition, time and route of administration, general health, and other drugs being administered concurrently.

[0107] In some embodiments, a method of treating an disease or disorder provided herein (e.g., inflammatory bowel disease (e.g., ulcerative colitis or Crohn’s disease)) comprises administering an IL1R1 inhibitor, a MEOX1 inhibitor, and / or a MAFF inhibitor or a composition comprising the same once to a subject. In preferred embodiments, an IL1R1 inhibitor, a MEOX1 inhibitor and / or a MAFF inhibitor or a composition comprising the same is administering to a subject multiple times (e.g., twice, three times, four times, five times, six times, or more). Repeated administration to a subject may be conducted at a regular interval (e.g., daily, every other day, twice per week, weekly, twice per month, monthly, every six months, once per year, or less or more frequently) as necessary to treat (e.g., improve or alleviate) one or more symptoms of an inflammatory bowel disease (e.g., ulcerative colitis or Crohn’s disease) in the subject.

[0108] 16

[0109] #14601190vl II. Subjects

[0110] In some embodiments, a subject treated by a method described herein is a subject having an autoimmune disease associated with IL1 signaling. An autoimmune disease associated with IL1 signaling may be any autoimmune disease provided herein including, but not limited to, inflammatory bowel disease (IBD), rheumatoid arthritis (RA), cryopyrin-associated periodic syndromes (CAPS), familial Mediterranean fever (FMF), and Behget’s disease. In some embodiments, a subject treated with a method described herein is a subject having inflammatory bowel disease (e.g., ulcerative colitis or Crohn’s disease).

[0111] In some embodiments, a subject is suspected of having an inflammatory bowel disease. In some embodiments, the subject is otherwise free of indications calling for treatment with a ME0X1 inhibitor, e.g., cardiac fibrosis, cardiac fibrosis, or cancer.

[0112] In some embodiments, a subject treated by a method described herein has an inflammatory bowel disease characterized by inflammatory lesions in the intestine and / or intestinal ulcers, e.g., containing granulation tissue. In some embodiments, the subject has intestinal ulcers with granulation tissue that contains post-capillary venule endothelial cells that express ACKR1.

[0113] In some embodiments, a subject with an inflammatory bowel disease (e.g., ulcerative colitis or Crohn’s disease) is in remission and is prophylactically administered a compound or composition described herein, e.g., in an amount that is lower than an amount administered to a subject having an active inflammatory bowel disease. A subject in remission can also be administered a compound or composition described herein at a time interval that is larger than a time interval that is used for administration of a compound or composition described herein to a subject with an active inflammatory bowel disease.

[0114] In some embodiments, a subject is a mammal, e.g., a human, non-human primate, dog, cat, horse, cow, pig, sheep, goat, chicken, mouse, rat, guinea pig, or hamster.

[0115] III. Compositions

[0116] Provided are compositions for treating inflammatory bowel disease in a subject, the compositions comprising an IL1R1 inhibitor, a ME0X1 inhibitor and / or a MAFF inhibitor. In some embodiments, a composition comprises an IL1R1 inhibitor and a molecule that binds ACKR1, e.g., an ACKR1 binding antibody. In some embodiments, a composition comprises a ME0X1 inhibitor and a molecule that binds ACKR1, e.g., an ACKR1 binding antibody. In some embodiments, a composition comprises a MAFF inhibitor and a molecule that binds

[0117] 17

[0118] #14601190vl ACKR1, e.g., an ACKR1 binding antibody. In some embodiments, a composition further comprises an excipient, e.g., a pharmaceutically-acceptable excipient. In some embodiments, a pharmaceutically-acceptable excipient includes a buffer. Exemplary buffers include, but are not limited to, borate buffer, citrate buffer, tartrate buffer, phosphate buffer, acetate buffer or Tris-HCl buffer (containing tris(hydroxymethyl)aminomethane and HC1). In some embodiments, a composition comprises an isotonic agent to prepare a composition that is isotonic with blood. In some embodiments, a composition comprises an isotonic agent to prepare a composition that is isotonic with intestinal fluid. Exemplary isotonic agents include, but are not limited to sugars, such as dextrose, glucose, sucrose, and fructose; sugar alcohols, such as mannitol and sorbitol; polyols, such as glycerin, polyethylene glycol, and propylene glycol; and salts, such as chlorinated sodium, sodium citrate, benzalkonium chloride, phedrine chloride, potassium chloride, procaine chloride, chloramphenicol and sodium succinate. In some embodiments, a composition is prepared by aseptic operation, or alternatively, sterilized at a suitable preparation stage.

[0119] IV. Kits

[0120] In some embodiments, provided are kits that comprise a compound or composition described herein. In some embodiments, a kit further comprises a solution to prepare a compound or composition described herein. In some embodiments, a kit further comprises instructions on how to prepare and administer a compound or composition described herein.

[0121] Unless specifically stated or obvious from context, as used herein, the term "or" is understood to be inclusive. Unless specifically stated or obvious from context, as used herein, the terms “a”, “an”, and “the” are understood to be singular or plural.

[0122] Unless specifically stated or obvious from context, as used herein, the term “about” is understood as within a range of normal tolerance in the art, for example within 2 standard deviations of the mean. About can be understood as within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, or 0.01% of the stated value. Unless otherwise clear from context, all numerical values provided herein are modified by the term about.

[0123] The recitation of a listing of chemical groups in any definition of a variable herein includes definitions of that variable as any single group or combination of listed groups. The recitation of an embodiment for a variable or embodiment herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.

[0124] 18

[0125] #14601190vl Any compositions or methods provided herein can be combined with one or more of any of the other compositions and methods provided herein.

[0126] EXAMPLES

[0127] Example 1:

[0128] It was demonstrated that in the IBD intestine, ME0X1 was robustly expressed in ACKR1+ endothelial cells, also known as post-capillary venules (PCV), and that PCV express IL1R1 (FIG. 4). The PCV is a highly specialized endothelium and is surrounded by pericytes, a vascular smooth muscle cell-like cell type that also has specialized functions. An assay that measures bioactive IL1 was applied to a cohort of IBD patients’ intestinal mucosa. It was found that IL1 protein (both ILIA and IL1B) bioactivity was an ulcer- specific hallmark with highest levels in Crohn’s disease patients with deep ulcers (FIG. 1A). Bulk RNA-sequencing of matched cellular fractions of Crohn’s disease patient samples was performed and an ulcer specific gene module (“brown module”) that included ILIA, IL1B as well as the transcription factors ME0X1 and MAFF was identified. A weighted gene network correlation analysis (WGCNA) of bulk RNA sequencing (RNA-seq) of the same samples as in FIG. 1A demonstrated that the ulcer specific gene module (“brown module”) correlated with an ulcerated IBD colon. The brown module factors ILIA, IL IB, ME0X1 and MAFF were specifically enriched in ulcerated colon lesions compared to uninflamed colon and inflamed but not ulcerated colon lesions (FIG. IB). ME0X1 and MAFF were enriched in ulcerated colon lesions compared to uninflamed colon and inflamed but not ulcerated colon lesions (FIG. 1C and ID).

[0129] Bulk RNA-sequencing was also performed on samples of pediatric patients with ileal Crohn’s disease (RISK cohort) and the brown module was found to be enriched in ulcerated intestinal samples of the RISK cohort (FIG. 2A). ME0X1 (FIG. 2B) and MAFF (FIG. 2A) were also enriched in bulk RNA-seq dataset of ulcerated ileum mucosa of the RISK cohort.

[0130] Publicly available as well as unpublished single cell RNA-seq (scRNA-seq) datasets of human IBD intestinal mucosa were assessed and it was demonstrated that IL1R1 as well as both ME0X1 and MAFF were expressed robustly in ACKR1+ post-capillary venule endothelium (FIG. 3A). Single-cell sequencing (scRNA-seq) data from colon samples of ulcerative colitis patients (Smilie et al., Cell, 178: 714-730, 2019) further demonstrated expression of MEOX1, MAFF, IL1R1, and ACKR1 in post-capillary venule endothelium (FIG. 2A). Although MAFF was expressed in other stromal cell types; MEOX1 was highly specific for venular endothelium (FIG. 2A).

[0131] 19

[0132] #14601190vl Incubation of human umbilical vein endothelial cells (HUVECs) for 24 hours with IL1B, TGFB + / - JQ1 demonstrated ILlB-associated increase in expression of MAFF, JAG1, EGAES9 and TGFBR2 (FIG. 3B) and morphologic change to a spindle-like (fibroblast) phenotype (data not shown). Further, IE1B induced the expression of genes including MAFF, putative downstream targets of ME0X1 (i.e. EGAES9), genes downstream of IE1B known to be associated with mesenchymal transition (i.e. JAG1), as well as the TGFb receptor TGFBR2 in a manner that was highly specific to IE1 stimulation (rather than TGFb stimulation alone) (FIG. 3B). The IE1- induced expression of ME0X1, MAFF, EGAES9, and JAG1 was abrogated in HUVEC with incubation of JQ1, a BRD4 inhibitor known to interfere with IE 1 -driven fibrosis in cardiac ischemic injury. Furthermore, ME0X1 and ACKR1 expression could be induced in HUVECs after 7 days of incubation with IE1B (data not shown).

[0133] Given that IL1B stimulation induced expression of ME0X1 and ACKR1 in HUVECs, and given that IE1 was a hallmark of ulcers, ulcerated tissue samples from IBD patients were stained for ACKR1, ME0X1, and the IE1 receptor using a combination of immune-histochemistry (probe for protein) as well as RNAscope (probe for transcripts). It was found that the endothelial cells of granulation tissue (the ulcer bed stroma) uniformly expressed ACKR1 (FIG. 4). The data further indicated that these endothelial cells also expressed ME0X1 and IL1R1 transcripts (FIG. 4). Taken together the results indicated that IE1 signaling at the site of ulcers, in endothelial cells, related to ME0X1 and downstream differentiation programs.

[0134] Based on the results described above, provided herein are methods and compositions that interfere with IL1 signaling, ME0X1 expression, MAFF expression in stromal cells (e.g., endothelial including post-capillary venule endothelial cells or fibroblasts / pericytes) to treat IBD. Specifically, these compositions can inhibit mesenchymal transition of endothelial cells or other associated stromal cells like pericytes or resident fibroblasts, into inflammatory / fibrotic subsets that contribute to tissue fibrosis after ulceration and reduce or prevent intestinal fibroses in IBD patients.

[0135] Example 2: Use of Bispecific Antibody to Target IL1R1 and ACKR1

[0136] A bispecific antibody that binds and blocks IL1R1 and binds, but does not necessarily inhibit ACKR1, will be used to modulate IL1R1 function in endothelial cells that express ACKR1. Such a bispecific antibody may be used to decrease IL1R1 function in a condition associated with increased IE1 signaling, such as inflammatory bowel disease. (FIG. 5A).

[0137] 20

[0138] #14601190vl Example 3: Use of Antibody-drug Conjugate (ADC) Systems to Target ACKR1 Expressing Cells

[0139] An antibody drug conjugate system that comprises an antigen-binding domain that targets ACKR1 and an ILIRa drug payload or a JQ1 drug payload will be used to modulate IL1 and / or ME0X1 function in ACKR1 expressing cells. Such an ADC will be used in a condition associated with increased IL1 signaling or / or increased ME0X1 signaling in intestinal endothelial cells and / or cardiac fibroblasts. (FIG. 5B).

[0140] Example 4: Nanoparticle-based Therapy to Deliver IL1R1,MEOX1, or MAFF Silencing RNA

[0141] Poly(lactic-co-glycolic acid) (PLGA) nanoparticles coated with an ACKRl-targeting antibody and / or an ACKR1 aptamer will be used to deliver a small interfering RNA (siRNA) to IL1R1, ME0X1, or both to cells expressing ACKRl-expressing cells in a condition associated with increased IL1 signaling or / or increased ME0X1 signaling in intestinal endothelial cells and / or cardiac fibroblasts. These nanoparticles will be used to target siRNA delivery to inflamed / ulcerated regions of intestine in a subject by enteric administration.

[0142] Example 5: Use of Proteolysis Targeting Chimera (PROTAC) to Induce Degradation of Tregs

[0143] Proteolysis targeting chimera (PROTAC) technology will be used to induce degradation of interleukin 1 receptor 1 (IL1R1) or ME0X1 in cells. PROTACs are small molecules that link a target protein to the cell’s proteolytic machine to selectively degrade the target protein. A PROTAC encapsulating or conjugated to inhibitory nucleic acids specific for IL1R1 or ME0X1 will be fused to an ACKRl-targeting antibody. This will enable targeting of the PROTAC to ACKRl-expressing cells (e.g., intestinal endothelial cells). This targeting of PROTAC to ACKRl-expressing cells will promote degradation of 1L1R1 or ME0X1 in ACKRl-expressing cells (FIG. 6).

[0144] In an additional example, a PROTAC encapsulating or conjugate to a small molecule inhibitor of IL1R1 and / or ME0X1 will be fused to an ACKRl-targeting antibody.

[0145] Example 6: Nanoparticle-based Therapy to Deliver IL1R1 or ME0X1 Small Molecule Inhibitors

[0146] 21

[0147] #14601190vl Poly(lactic-co-glycolic acid) (PLGA) nanoparticles coated with an ACKRl-targeting antibody and / or an ACKR1 aptamer will be used to deliver a small molecule inhibitor of 1L1R1, ME0X1, or both to cells expressing ACKR1 -expressing cells in a condition associated with increased IL1 signaling or / or increased ME0X1 signaling in intestinal endothelial cells and / or cardiac fibroblasts.

[0148] ADDITIONAL EMBODIMENTS

[0149] 1. A method of treating an inflammatory bowel disease, the method comprising administering to a subject in need thereof a composition comprising a ME0X1 inhibitor in an effective amount to treat the disease.

[0150] 2. The method of claim 1, wherein the ME0X1 inhibitor is a small molecule, an inhibitory nucleic acid, or an antibody or fragment thereof.

[0151] 3. The method of claim 2, wherein the ME0X1 inhibitor is a the Bromodomaincontaining protein 4 (BRD4) inhibitor.

[0152] 4. The method of claim 3, wherein the BRD4 inhibitor is JQ1.

[0153] 5. The method of any one of claims 1-4, wherein the composition further comprises a molecule that binds ACKR1.

[0154] 6. The method of claim 5, wherein the molecule that binds ACKR1 is an ACKR1 antibody.

[0155] 7. The method of any one of claims 1-6, wherein the administering is by oral administration or rectal administration.

[0156] 8. The method of claim 7, wherein the rectal administration is by enema.

[0157] 9. The method of any one of claims 1-8, wherein the inflammatory bowel disease is ulcerative colitis or Crohn’s disease.

[0158] 22

[0159] #14601190vl 10. The method of any one of claims 1-9, wherein the subject is otherwise free of indications calling for treatment with a MEOX1 inhibitor.

[0160] 11. A method of treating an inflammatory bowel disease, the method comprising administering to a subject in need thereof a composition comprising a MAFF inhibitor in an effective amount to treat the disease.

[0161] 12. The method of claim 11, wherein the MAFF inhibitor is an inhibitory nucleic acid, or an antibody or fragment thereof.

[0162] 13. The method of claim 12, wherein the inhibitory nucleic acid comprises a microRNA.

[0163] 14. The method of claim 13, wherein the microRNA comprises hsa-miR-224-5p.

[0164] 15. The method of any one of claims 11-14, wherein the composition further comprises a molecule that binds ACKR1.

[0165] 16. The method of claim 15, wherein the molecule that binds ACKR1 is an ACKR1 antibody.

[0166] 17. The method of any one of claims 11-16, wherein the administering is by oral administration or rectal administration.

[0167] 18. The method of claim 17, wherein the rectal administration is by enema.

[0168] 19. The method of any one of claims 11-18, wherein the inflammatory bowel disease is ulcerative colitis or Crohn’s disease.

[0169] 20. The method of any one of claims 11-19, wherein the subject is otherwise free of indications calling for treatment with a MAFF inhibitor.

[0170] 21. A method of inhibiting MEOX1 in an intestinal endothelial cell, the method comprising contacting an intestinal endothelial cell with a composition comprising a

[0171] #14601190vl 23 ME0X1 inhibitor in an effective amount to inhibit ME0X1 in the intestinal endothelial cell.

[0172] 22. The method of claim 21, wherein the intestinal endothelial cell is a venular endothelial cell.

[0173] 23. The method of claim 21 or 22, wherein the ME0X1 inhibitor is a small molecule, an inhibitory nucleic acid, or an antibody or fragment thereof.

[0174] 24. The method of claim 23, wherein the ME0X1 inhibitor is a the Bromodomaincontaining protein 4 (BRD4) inhibitor.

[0175] 25. The method of claim 24, wherein the BRD4 inhibitor is JQ1.

[0176] 26. The method of any one of claims 21-25, wherein the composition further comprises a molecule that binds ACKR1.

[0177] 27. The method of claim 26, wherein the molecule that binds ACKR1 is an ACKR1 antibody.

[0178] 28. The method of any one of claims 21-27, wherein the cell is in vivo.

[0179] 29. The method of claim 28, wherein the in vivo cell is in an intestine of a subject.

[0180] 30. The method of claim 29, wherein the contacting comprises administering the composition to an intestine of the subject.

[0181] 31. The method of claim 30, wherein the administering is by oral administration or rectal administration.

[0182] 32. The method of claim 31, wherein the rectal administration is by enema.

[0183] 24

[0184] #14601190vl 33. A method of inhibiting MAFF in an intestinal endothelial cell, the method comprising contacting a cell with a composition comprising a MAFF inhibitor in an effective amount to inhibit MAFF in the cell.

[0185] 34. The method of claim 33, wherein the intestinal endothelial cell is a venular endothelial cell.

[0186] 35. The method of claim 33 or 34, wherein the MAFF inhibitor is a small molecule, an inhibitory nucleic acid, or an antibody or fragment thereof.

[0187] 36. The method of claim 35, wherein the inhibitory nucleic acid comprises a microRNA.

[0188] 37. The method of claim 36, wherein the microRNA comprises hsa-miR-224-5p.

[0189] 38. The method of any one of claims 33-37, wherein the composition further comprises a molecule that binds ACKR1.

[0190] 39. The method of claim 38, wherein the molecule that binds ACKR1 is an ACKR1 antibody.

[0191] 40. The method of any one of claims 33-39, wherein the cell is in vivo.

[0192] 41. The method of claim 40, wherein the in vivo cell is in an intestine of a subject.

[0193] 42. The method of claim 41, wherein the contacting comprises administering the composition to an intestine of the subject.

[0194] 43. The method of claim 42, wherein the administering is by oral administration or rectal administration.

[0195] 44. The method of claim 43, wherein the rectal administration is by enema.

[0196] #14601190vl 25

Claims

CLAIMSWhat is claimed is:

1. A method of treating an inflammatory bowel disease, the method comprising administering to a subject in need thereof a composition comprising an IL1R1 inhibitor in an effective amount to treat the disease.

2. The method of claim 1, wherein the IL1R1 inhibitor is an antibody or fragment thereof, an antibody-drug conjugate (ADC), an inhibitory nucleic acid, or nanoparticle, or a combination thereof.

3. The method of claim 2, wherein the IL1R1 inhibitor is an antibody that binds IL1R1.

4. The method of claim 3, wherein the antibody is a bispecific antibody that also binds ACKR1.

5. The method of claim 1, wherein the inhibitor is an antibody drug conjugate (ADC) that comprises an IL1R1 inhibitor and a molecule that binds ACKR1.

6. The method of claim 5, wherein the IL1R1 inhibitor is a small molecule or an inhibitory nucleic acid.

7. The method of claim 5 or claim 6, wherein the molecule that binds ACKR1 is an ACKR1 antibody.

8. The method of claim 1, wherein the inhibitor is a nanoparticle comprising an inhibitor nucleic acid.

9. The method of any one of claims 1-8, wherein the administering is by oral administration or rectal administration.

10. The method of claim 9, wherein the rectal administration is by enema.#14601190vl 2611. The method of any one of claims 1-10, wherein the inflammatory bowel disease is ulcerative colitis or Crohn’s disease.

12. The method of any one of claims 1-11, wherein the method further comprises administering a MEOX1 inhibitor.

13. The method of any one of claims 1-12, wherein the method further comprises administering a MAFF inhibitor.

14. A method of inhibiting IL1R1 in an intestinal endothelial cell, the method comprising contacting an intestinal endothelial cell with a composition comprising a IL1R1 inhibitor in an effective amount to inhibit IL1R1 in the intestinal endothelial cell.

15. The method of claim 14, wherein the intestinal endothelial cell is a venular endothelial cell.

16. The method of claim 14 or claim 15, wherein the IL1R1 inhibitor is an antibody that binds IL1R1.

17. The method of claim 16, wherein the antibody is a bispecific antibody that also binds ACKR1.

18. The method of claim 14 or claim 15, wherein the inhibitor is an antibody drug conjugate (ADC) that comprises an IL1R1 inhibitor and a molecule that binds ACKR1.

19. The method of claim 18, wherein the IL1R1 inhibitor is a small molecule or an inhibitory nucleic acid.

20. The method of claim 18 or claim 19, wherein the molecule that binds ACKR1 is an ACKR1 antibody.

21. The method of claim 14 or claim 15, wherein the inhibitor is a nanoparticle comprising an inhibitor nucleic acid.

22. The method of any one of claims 14-21, wherein the cell is in vivo.#14601190vl 27

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