Follicular lymphoma transcriptomic classifier

Abstract

The present disclosure relates to a method for classifying a subject diagnosed with follicular lymphoma (FL) into 7 FL subtypes (FL1-FL7) and related methods of treating a subject diagnosed with FL. The present disclosure further includes related compositions, e.g., isolated probes and primers, as well as kits and arrays comprising same. A therapy guidance software tool is also disclosed.

Description

Attorney Docket No: 243735.000396 FOLLICULAR LYMPHOMA TRANSCRIPTOMIC CLASSIFIER CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to U.S. Provisional Patent Application No.63 / 542,611, filed October 5, 2023, and U.S. Provisional Patent Application No. 63 / 547,505, filed November 6, 2023, the disclosures of both of which are herein incorporated by reference in their entireties. FIELD OF THE INVENTION

[0002] The present disclosure relates to a method for classifying a subject diagnosed with follicular lymphoma (FL) into 7 FL subtypes (FL1-FL7) and related methods of treating a subject diagnosed with FL. The present disclosure further includes related compositions, e.g., isolated probes and primers, as well as kits and arrays comprising same. A therapy guidance software tool is also disclosed. BACKGROUND

[0003] Follicular lymphoma (FL) is an indolent B-cell lymphoma that is virtually incurable despite advances in chemoimmunotherapy regimens. FL is a biologically and clinically heterogenous disease. While most FL patients achieve long-term survival rates similar to the general population, a subset (~20%) experience early disease progression within 24 months of frontline therapy initiation (POD24), often involving histologic transformation (HT), and face a dismal prognosis with an associated 5-year overall survival (OS) of 50% (Casulo 2016; Freeman 2019; Sarkozy 2016). While early progressors respond better to more aggressive front-line treatment (Casulo 2016), currently there are no sufficiently reliable robust predictive biomarkers to guide risk-adapted front-line therapy.

[0004] Although the genomic landscape of FL has been well-characterized, genetic alterations alone are limited with regard to identifying patients likely to experience early progression, even when integrated into well-established clinical risk models such as the Follicular Lymphoma International Prognostic Index (FLIPI) (Jurinovic 2016). Currently, even the most accurate clinico-genetic risk model for the prediction of early progression, the m7-FLIPI (Pastore 2015), performs with only 77% accuracy and a positive predictive value of 38-48% (Jurinovic 2016), indicating that the drivers of treatment failure are more heterogeneous than B-cell exome alterations. Moreover, as the landscape of pathway-directed therapies continues to expand, novelAttorney Docket No: 243735.000396 risk stratification strategies that account for FL biological heterogeneity are increasingly needed to guide optimal frontline therapy.

[0005] A growing body of evidence has established the critical role of the tumor microenvironment (TME) in driving FL pathogenesis (Beguelin 2020; Lamaison 2021; Riedel 2016; Sahai 2020). FL is associated with extensive phenotypic alterations in TME immune and stromal cell populations and certain TME alterations have been shown to be predictive of patient survival (Dave 2004, Mourcin 2021; Abe 2022; Han 2022). Unlike FL B-cell mutations, microenvironment alterations occur at the transcriptional level and are not captured by exome sequencing.

[0006] Accordingly, there remains a need for sufficiently sensitive and accurate predictive biomarkers to guide risk-adapted front-line therapy for patients likely to experience an aggressive disease course. SUMMARY OF THE INVENTION

[0007] In one aspect, provided herein is a method for classifying a subject diagnosed with follicular lymphoma (FL) into 7 FL subtypes (FL1-FL7), the method comprising: (a) determining in a biological sample obtained from the subject the expression level of at least 4 genes from each of 7 groups of genes provided in Table 1, wherein the 7 groups of genes correspond to 7 FL subtypes (FL1-FL7) as listed in Table 1; (b) calculating a gene expression score for the biological sample for each of the 7 groups of genes of step (a); (c) comparing the 7 gene expression scores calculated in step (b) to each other and determining the highest gene expression score among the 7 gene expression scores; and (d) classifying the subject into the FL subtype which corresponds to the highest gene expression score determined in step (c).

[0008] In some embodiments, the subject has been diagnosed with FL based on evaluation of histology and / or immunophenotypic features.

[0009] In certain embodiments, step (b) comprises: generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 1;Attorney Docket No: 243735.000396 generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreases when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

[0010] In certain embodiments, step (b) comprises: representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative; performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes provided in Table 1, and resulting in a mixture coefficient matrix; and determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.

[0011] In certain embodiments, step (c) comprises: determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

[0012] In certain embodiments, step (a) comprises determining the expression level of at least 4 genes from each of the 7 groups of genes provided in Table 3, wherein the 7 groups of genes correspond to the 7 FL subtypes (FL1-FL7) as listed in Table 3.

[0013] In certain embodiments, step (b) comprises: generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 3; generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreasesAttorney Docket No: 243735.000396 when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

[0014] In certain embodiments, step (b) comprises: representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative; performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes provided in Table3, and resulting in a mixture coefficient matrix; and determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.

[0015] In certain embodiments, step (c) comprises: determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

[0016] In certain embodiments, the genes for group 1 corresponding to FL1 comprise DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF.

[0017] In certain embodiments, the genes for group 2 corresponding to FL2 comprise GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK.

[0018] In certain embodiments, the genes for group 3 corresponding to FL3 comprise ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3.

[0019] In certain embodiments, the genes for group 4 corresponding to FL4 comprise GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX.

[0020] In certain embodiments, the genes for group 5 corresponding to FL5 comprise PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1.

[0021] In certain embodiments, the genes for group 6 corresponding to FL6 comprise PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK.

[0022] In certain embodiments, the genes for group 7 corresponding to FL7 comprise SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

[0023] In certain embodiments, the genes for group 1 corresponding to FL1 comprise DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF, the genes for group 2 corresponding to FL2 comprise GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK, the genes for group 3 corresponding to FL3 comprise ACTA2, IGFBP6, ABCA8,Attorney Docket No: 243735.000396 DCN, TAGLN, CAV2, ANXA1, and GPX3, the genes for group 4 corresponding to FL4 comprise GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX, the genes for group 5 corresponding to FL5 comprise PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1, the genes for group 6 corresponding to FL6 comprise PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK, and the genes for group 7 corresponding to FL7 comprise SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

[0024] In certain embodiments, the method further comprises administering to the subject classified in step (d) a treatment effective for the subject’s determined FL subtype.

[0025] In certain embodiments, the treatment for the subject classified as FL1 comprises administering a therapeutically effective amount of a compound selected from an inhibitor of Bruton’s tyrosine kinase (BTK), an anti-CD79b agent (e.g., Polatuzumab vedotin), an anti- CD19 agent (e.g., Tafasitamab), an inhibitor of PD1, an agent targeting neutrophilic myeloid- derived suppressor cells (PMN-MDSCs), or any combinations thereof.

[0026] In certain embodiments, the treatment for the subject classified as FL2 comprises administering a therapeutically effective amount of a compound selected from Lenalidomide, an inhibitor of Bruton’s tyrosine kinase (BTK), Ipilimumab, an inhibitor of PD-L1, an inhibitor of Janus kinase (JAK), or any combinations thereof.

[0027] In certain embodiments, the treatment for the subject classified as FL3 comprises administering a therapeutically effective amount of an inhibitor of Janus kinase (JAK).

[0028] In certain embodiments, the treatment for the subject classified as FL4 comprises administering a therapeutically effective amount of an inhibitor of enhancer of zeste homolog 2 (EZH2), or an inhibitor of polyadenosine 5'-diphosphoribose polymerase (PARP), or a combination thereof. In certain embodiments, the treatment for the subject classified as FL4 comprises administering a therapeutically effective amount of Tazemostat, or Olaparib, or a combination thereof.

[0029] In certain embodiments, the treatment for the subject classified as FL5 comprises administering a therapeutically effective amount of a compound selected from Lenalidomide, an inhibitor of Bruton’s tyrosine kinase (BTK), an anti-CD19 agent (e.g., Tafasitamab), an inhibitor of Janus kinase (JAK), an agent targeting neutrophilic myeloid-derived suppressor cells (PMN- MDSCs), or any combinations thereof.Attorney Docket No: 243735.000396

[0030] In certain embodiments, the treatment for the subject classified as FL6 comprises administering a therapeutically effective amount of a compound selected from a proteosome inhibitor, an anti-CD79b agent (e.g., Polatuzumab vedotin), an agent targeting neutrophilic myeloid-derived suppressor cells, or any combinations thereof.

[0031] In certain embodiments, the treatment for the subject classified as FL7 comprises administering a therapeutically effective amount of Lenalidomide, or an inhibitor of Janus kinase (JAK), or a combination thereof.

[0032] In certain embodiments, the treatment further comprises administering a standard immunochemotherapy.

[0033] In certain embodiments, the standard immunochemotherapy comprises administering a therapeutically effective amount of a compound selected from rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP); rituximab, cyclophosphamide, vincristine, and prednisone (R-CVP); rituximab and bendamustine (BR); obinutuzumab, cyclophosphamide, doxorubicin, vincristine, and prednisone; obinutuzumab, cyclophosphamide, vincristine, and prednisone; obinutuzumab and bendamustine; and any combinations thereof.

[0034] In certain embodiments, the treatment for the subject’s determined FL subtype is administered before, simultaneously with, or after the administration of the standard immunochemotherapy.

[0035] In certain embodiments, the inhibitor of Bruton’s tyrosine kinase (BTK) is ibrutinib, acalabrutinib, or pirtobrutinib.

[0036] In certain embodiments, the inhibitor of PD1 is nivolumab, pembrolizumab, cemiplimab, dostarlimab, or retifanlimab.

[0037] In certain embodiments, the agent targeting neutrophilic myeloid-derived suppressor cells (PMN-MDSCs) is all-trans retinoic acid (ATRA).

[0038] In certain embodiments, the inhibitor of PD-L1 is atezolizumab, avelumab or durvalumab.

[0039] In certain embodiments, the inhibitor of Janus kinase (JAK) is ruxolitinib, baricitinib, tofacitinib, fedratinib, itacitinib, momelotinib, or patricinib.

[0040] In certain embodiments, the proteosome inhibitor is bortezomib, carfilzomib or ixazomib.Attorney Docket No: 243735.000396

[0041] In another aspect, provided herein is a method of treating a subject diagnosed with follicular lymphoma (FL), the method comprising: (a) determining in a biological sample obtained from the subject the expression level of at least 4 genes from each of 7 groups of genes provided in Table 1, wherein the 7 groups of genes correspond to 7 FL subtypes (FL1-FL7) as listed in Table 1; (b) calculating a gene expression score for the biological sample for each of the 7 groups of genes of step (a); (c) comparing the 7 gene expression scores calculated in step (b) to each other and determining the highest gene expression score among the 7 gene expression scores; (d) classifying the subject into the FL subtype which corresponds to the highest gene expression score determined in step (c); and (e) administering to the subject classified in step (d) a treatment effective for the subject’s determined FL subtype.

[0042] In certain embodiments, the subject has been diagnosed with FL based on evaluation of histology and / or immunophenotypic features.

[0043] In certain embodiments, step (b) comprises: generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 1; generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreases when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

[0044] In certain embodiments, step (b) comprises: representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative;Attorney Docket No: 243735.000396 performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes provided in Table 1, and resulting in a mixture coefficient matrix; and determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.

[0045] In certain embodiments, step (c) comprises: determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

[0046] In certain embodiments, step (a) comprises determining the expression level of at least 4 genes from each of the 7 groups of genes provided in Table 3 wherein the 7 groups of genes correspond to the 7 FL subtypes (FL1-FL7) as listed in Table 3.

[0047] In certain embodiments, step (b) comprises: generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 3; generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreases when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

[0048] In certain embodiments, step (b) comprises: representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative; performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes provided in Table 3, and resulting in a mixture coefficient matrix; and determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.

[0049] In certain embodiments, step (c) comprises:Attorney Docket No: 243735.000396 determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

[0050] In certain embodiments, the genes for group 1 corresponding to FL1 comprise DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF.

[0051] In certain embodiments, the genes for group 2 corresponding to FL2 comprise GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK.

[0052] In certain embodiments, the genes for group 3 corresponding to FL3 comprise ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3.

[0053] In certain embodiments, the genes for group 4 corresponding to FL4 comprise GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX.

[0054] In certain embodiments, the genes for group 5 corresponding to FL5 comprise PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1.

[0055] In certain embodiments, the genes for group 6 corresponding to FL6 comprise PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK.

[0056] In certain embodiments, the genes for group 7 corresponding to FL7 comprise SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

[0057] In certain embodiments, the genes for group 1 corresponding to FL1 comprise DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF, the genes for group 2 corresponding to FL2 comprise GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK, the genes for group 3 corresponding to FL3 comprise ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3, the genes for group 4 corresponding to FL4 comprise GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX, the genes for group 5 corresponding to FL5 comprise PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1, the genes for group 6 corresponding to FL6 comprise PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK, and the genes for group 7 corresponding to FL7 comprise SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

[0058] In certain embodiments, the treatment for the subject classified as FL1 comprises administering a therapeutically effective amount of a compound selected from an inhibitor of Bruton’s tyrosine kinase (BTK), an anti-CD79b agent (e.g., Polatuzumab vedotin), an anti-Attorney Docket No: 243735.000396 CD19(e.g., Tafasitamab), an inhibitor of PD1, an agent targeting neutrophilic myeloid-derived suppressor cells (PMN-MDSCs), or any combinations thereof.

[0059] In certain embodiments, the treatment for the subject classified as FL2 comprises administering a therapeutically effective amount of a compound selected from Lenalidomide, an inhibitor of Bruton’s tyrosine kinase (BTK), Ipilimumab, an inhibitor of PD-L1, an inhibitor of Janus kinase (JAK), or any combinations thereof.

[0060] In certain embodiments, the treatment for the subject classified as FL3 comprises administering a therapeutically effective amount of an inhibitor of Janus kinase (JAK).

[0061] In certain embodiments, the treatment for the subject classified as FL4 comprises administering a therapeutically effective amount of an inhibitor of enhancer of zeste homolog 2 (EZH2), or an inhibitor of polyadenosine 5'-diphosphoribose polymerase (PARP), or a combination thereof. In certain embodiments, the treatment for the subject classified as FL4 comprises administering a therapeutically effective amount of Tazemostat, or Olaparib, or a combination thereof.

[0062] In certain embodiments, the treatment for the subject classified as FL5 comprises administering a therapeutically effective amount of a compound selected from Lenalidomide, an inhibitor of Bruton’s tyrosine kinase (BTK), an anti-CD19 agent (e.g., Tafasitamab), an inhibitor of Janus kinase (JAK), an agent targeting neutrophilic myeloid-derived suppressor cells (PMN- MDSCs), or any combinations thereof.

[0063] In certain embodiments, the treatment for the subject classified as FL6 comprises administering a therapeutically effective amount of a compound selected from a proteosome inhibitor, an anti-CD79b agent (e.g., Polatuzumab vedotin), an agent targeting neutrophilic myeloid-derived suppressor cells, or any combinations thereof.

[0064] In certain embodiments, the treatment for the subject classified as FL7 comprises administering a therapeutically effective amount of Lenalidomide, or an inhibitor of Janus kinase (JAK), or a combination thereof.

[0065] In certain embodiments, the treatment further comprises administering a standard immunochemotherapy.

[0066] In certain embodiments, the standard immunochemotherapy comprises administering a therapeutically effective amount of a compound selected from rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP); rituximab, cyclophosphamide, vincristine,Attorney Docket No: 243735.000396 and prednisone (R-CVP); rituximab and bendamustine (BR); obinutuzumab, cyclophosphamide, doxorubicin, vincristine, and prednisone; obinutuzumab, cyclophosphamide, vincristine, and prednisone; obinutuzumab and bendamustine; and any combinations thereof.

[0067] In certain embodiments, the treatment for the subject’s determined FL subtype is administered before, simultaneously with, or after the administration of the standard immunochemotherapy.

[0068] In certain embodiments, the inhibitor of Bruton’s tyrosine kinase (BTK) is ibrutinib, acalabrutinib, or pirtobrutinib.

[0069] In certain embodiments, the inhibitor of PD1 is nivolumab, pembrolizumab, cemiplimab, dostarlimab, or retifanlimab.

[0070] In certain embodiments, the agent targeting neutrophilic myeloid-derived suppressor cells (PMN-MDSCs) is all-trans retinoic acid (ATRA).

[0071] In certain embodiments, the inhibitor of PD-L1 is atezolizumab, avelumab or durvalumab.

[0072] In certain embodiments, the inhibitor of Janus kinase (JAK) is ruxolitinib, baricitinib, tofacitinib, fedratinib, itacitinib, momelotinib, or patricinib.

[0073] In certain embodiments, the proteosome inhibitor is bortezomib, carfilzomib or ixazomib.

[0074] In certain embodiments, the anti-CD79b agent is Polatuzumab vedotin.

[0075] In certain embodiments, the anti-CD19 agent is Tafasitamab.

[0076] In certain embodiments, the inhibitor of EZH2 is Tazemostat.

[0077] In certain embodiments, the inhibitor of PARP is Olaparib.

[0078] In certain embodiments, the gene expression level is determined by measuring mRNA level.

[0079] In certain embodiments, the mRNA level is determined using RNA sequencing, qPCR, panel sequencing, or array-based gene expression profiling.

[0080] In certain embodiments, the subject is a newly diagnosed patient.

[0081] In certain embodiments, the subject is a patient at relapse after a treatment.

[0082] In a further aspect, provided herein is a composition comprising a plurality of isolated probes and / or primers which hybridize to at least 4 genes from each of 7 groups of genes provided in Table 1.Attorney Docket No: 243735.000396

[0083] In certain embodiments, the plurality of isolated probes and / or primers hybridize to at least 4 genes from each of the 7 groups of genes provided in Table 3.

[0084] In certain embodiments, the plurality of isolated probes and / or primers hybridize to DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF.

[0085] In certain embodiments, the plurality of isolated probes and / or primers hybridize to GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK.

[0086] In certain embodiments, the plurality of isolated probes and / or primers hybridize to ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3.

[0087] In certain embodiments, the plurality of isolated probes and / or primers hybridize to GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX.

[0088] In certain embodiments, the plurality of isolated probes and / or primers hybridize to PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1.

[0089] In certain embodiments, the plurality of isolated probes and / or primers hybridize to PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK.

[0090] In certain embodiments, the plurality of isolated probes and / or primers hybridize to SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

[0091] In another aspect, provided herein is a kit comprising: (i) a plurality of isolated probes and / or primers which hybridize to at least 4 genes from each of 7 groups of genes provided in Table 1, (ii) optionally, one or more reagents for determining mRNA level, and (iii) optionally, instructions for use.

[0092] In certain embodiments, the kit comprises: (i) a plurality of isolated probes and / or primers which hybridize to at least 4 genes from each of the 7 groups of genes provided in Table 3, (ii) optionally, one or more reagents for determining mRNA level, and (iii) optionally, instructions for use.

[0093] In certain embodiments, the plurality of isolated probes and / or primers hybridize to DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF.

[0094] In certain embodiments, the plurality of isolated probes and / or primers hybridize to GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK.Attorney Docket No: 243735.000396

[0095] In certain embodiments, the plurality of isolated probes and / or primers hybridize to ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3.

[0096] In certain embodiments, the plurality of isolated probes and / or primers hybridize to GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX.

[0097] In certain embodiments, the plurality of isolated probes and / or primers hybridize to PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1.

[0098] In certain embodiments, the plurality of isolated probes and / or primers hybridize to PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK.

[0099] In certain embodiments, the plurality of isolated probes and / or primers hybridize to SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

[0100] In a further aspect, provided herein is an array comprising a plurality of probes complementary to and / or hybridizable to at least 4 genes from each of 7 groups of genes provided in Table 1.

[0101] In certain embodiments, the array comprises a plurality of probes complementary to and / or hybridizable to at least 4 genes from each of 7 groups of genes provided in Table 3.

[0102] In certain embodiments, the plurality of isolated probes and / or primers hybridize to DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF.

[0103] In certain embodiments, the plurality of isolated probes and / or primers hybridize to GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK.

[0104] In certain embodiments, the plurality of isolated probes and / or primers hybridize to ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3.

[0105] In certain embodiments, the plurality of isolated probes and / or primers hybridize to GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX.

[0106] In certain embodiments, the plurality of isolated probes and / or primers hybridize to PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1.

[0107] In certain embodiments, the plurality of isolated probes and / or primers hybridize to PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK.

[0108] In certain embodiments, the plurality of isolated probes and / or primers hybridize to SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.Attorney Docket No: 243735.000396

[0109] In another aspect, provided herein is a therapy guidance software tool for a subject diagnosed with follicular lymphoma (FL) comprising non-transitory computer readable medium with instructions thereon, that when executed by a processor, cause the processor to: (a) receive a plurality of gene expression values for at least 4 genes from each of 7 groups of genes provided in Table 1, wherein the 7 groups of genes correspond to 7 FL subtypes (FL1-FL7); (b) calculate a gene expression score for each of the 7 groups of genes based at least in part on the plurality of gene expression values; (c) classify the subject into one FL subtype of the 7 FL subtypes based at least in part on the gene expression score for each of the 7 groups of genes; and (d) provide a patient diagnosis based at least in part on the one FL subtype into which the subject is classified.

[0110] In certain embodiments, step (b) comprises: generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 1; generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreases when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

[0111] In certain embodiments, step (b) comprises: representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative; performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes provided in Table 1, and resulting in a mixture coefficient matrix; and determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.Attorney Docket No: 243735.000396

[0112] In certain embodiments, step (c) comprises: determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

[0113] In certain embodiments, the non-transitory computer readable medium includes instructions thereon, that when executed by a processor, cause the processor to: provide a treatment recommendation based at least in part on the one FL subtype into which the subject is classified.

[0114] In certain embodiments, the non-transitory computer readable medium includes instructions thereon, that when executed by a processor, cause the processor to: provide a prognosticated failure free survival based at least in part on the one FL subtype into which the subject is classified.

[0115] In certain embodiments, the non-transitory computer readable medium includes instructions thereon, that when executed by a processor, cause the processor to: provide a prognosticated overall survival based at least in part on the one FL subtype into which the subject is classified.

[0116] In certain embodiments, step (a) comprises determining the expression level of at least 4 genes from each of the 7 groups of genes provided in Table 3 wherein the 7 groups of genes correspond to the 7 FL subtypes (FL1-FL7) as listed in Table 3.

[0117] In certain embodiments, step (b) comprises: generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 3; generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreases when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

[0118] In certain embodiments, step (b) comprises:Attorney Docket No: 243735.000396 representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative; performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes provided in Table3, and resulting in a mixture coefficient matrix; and determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.

[0119] In certain embodiments, step (c) comprises: determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

[0120] In certain embodiments, the biological sample comprises tumor cells.

[0121] In certain embodiments, the biological sample is a biopsy sample.

[0122] In certain embodiments, the subject is human.

[0123] In certain embodiments, the subject is a veterinary animal. BRIEF DESCRIPTION OF THE DRAWINGS

[0124] Figures 1A-1H show follicular lymphoma (FL) encompasses biologically and clinically unique subtypes. Figure 1A shows the study workflow. Figure 1B shows a uniform manifold approximation and projection (UMAP) of discovery cohort FL subtypes (n=302). Figure 1C shows a heatmap of top differentially expressed genes in discovery cohort FL transcriptomes. Figure 1D shows heatmaps of top differentially expressed genes from discovery cohort in validation transcriptomic datasets. Figure 1E shows the bulk FL transcriptomic datasets used in discovery and validation analyses (n=1152). Figure 1F shows stacked barplots depicting the relative distribution of FL subtypes in each validation study cohort. Figure 1G shows Gene Set Enrichment Analysis (GSEA) performed on discovery cohort transcriptomes using Molecular Signatures Database (MsigDB) Hallmark signatures. Figure 1H shows a heatmap of exome alterations in 169 FL cases with paired transcriptome profiling and exome sequencing (Dreval 2023; Ma 2022).

[0125] Figures 2A-2M show FL subtypes are associated with distinct B-cell genetic alterations and transcriptional states. Figure 2A shows the FL B-cell transcriptional states imputed by Ecotyper from discovery cohort bulk transcriptomes. Figure 2B shows UMAP ofAttorney Docket No: 243735.000396 discovery cohort B-cell transcriptional states. Figure 2C shows failure-free survival (FFS) and overall survival (OS) by predominant B-cell transcriptional state recovered from bulk transcriptomic profiles of pre-treatment samples from patients treated with frontline immunochemotherapy (GSE119214). B-cell transcriptional states were assigned to samples using the Ecotyper bulk recovery algorithm. Figure 2D shows a stacked barplot showing the distribution of FL B-cell states according to each FL subtype in the discovery cohort. Figure 2E shows a stacked barplot showing the distribution of discovery cohort B-cell transcriptional states assigned to malignant B-cells in patient-level single-cell RNA sequencing (scRNA-seq) samples. Clonality for all samples (n=24) was confirmed by single cell V(D)J sequencing. Figure 2F shows a heatmap of top differentially expressed genes between B-cell transcriptional states in 61,781 malignant B-cell transcriptomes. Figure 2G shows average expression of canonical FL markers in 61,781 malignant FL B-cell single-cell transcriptomes. Figure 2H shows differentiation state ordering of B-cell states determined by CytoTRACE using malignant B-cell single-cell transcriptomes. Higher scores indicate lower differentiation, lower scores indicate higher differentiation. Figure 2I shows single-cell geneset enrichment scores for FL B-cell states using the single-cell cell-of-origin classification of Holmes et al. Normalized enrichment scores were computed using the ‘escape’ R package. Figure 2J shows single-cell GSEA of malignant FL B-cell transcriptomes using MSigDB hallmark signature collection. Figures 2K-2L show UMAPs of single-cell malignant B-cell transcriptomes annotated by transcriptional state and pseudotime trajectory analysis (Monocle3). Figure 2M shows bulk GSEA from the discovery cohort.

[0126] Figures 3A-3J show FL subtypes are enriched for transcriptionally-distinct microenvironment immune and stromal cell subsets. Figure 3A shows the relative frequency of immunophenotypically-defined tumor microenvironment (TME) populations imputed by digital cytometry using CIBERSORTx. Figure 3B shows discovery cohort (n=302) TME transcriptional state abundances ordered by co-association patterns (left bar). Top bar indicates the FL subtype assignment of each FL sample (column). Figure 3C shows the relative frequency of TME immune and stromal cell transcriptional states in discovery cohort FL subtypes imputed by Ecotyper. Figure 3D shows immune and stromal cell transcriptional states associated with each FL ecotype. Thickness of edges connecting cell states is proportionate to Jaccrd index co- association strength. Figure 3E shows a correlation plot demonstrating the associations betweenAttorney Docket No: 243735.000396 bulk FL subtype and specific ecotypes across all FL transcriptomes in discovery and validation cohorts (n=1,158). Figure 3F shows UMAP of integrated FL sc-RNAseq atlas. Figure 3G shows TME cell state-specific overall survival associations in GSE119214 based on univariate Cox proportional hazards analyses. Figure 3H shows a heatmap of regulatory T cell (Treg) single-cell GSEA scores depicting significant differentially enriched pathways between Treg transcriptional states. Significance values were determined by the Wilcoxon rank sum method using an FDR q-value threshold of <0.05. Figure 3I shows a heatmap of follicular helper T-cell (Tfh) single-cell GSEA scores depicting significant differentially enriched pathways between Tfh transcriptional states. Significance values were determined by the Wilcoxon rank sum method using an FDR q-value threshold of <0.05. Figure 3J shows an alluvial plot depicting the associations between FL subtypes, B-cell transcriptional state, and TME ecotype.

[0127] Figures 4A-4J show FL subtypes are enriched for transcriptionally-distinct myeloid subsets. Figure 4A shows top differentially expressed genes in single-cell MF transcriptomes assigned to a discrete transcriptional state from the discovery cohort. Figure 4B shows a heatmap of MF single-cell GSEA scores depicting significant differentially enriched Gene Ontology (GO) pathways between molecular function (MF) transcriptional states. Significance values were determined by the Wilcoxon rank sum method using an FDR q-value threshold of <0.05. Figure 4C shows failure-free survival (FFS) and overall survival (OS) by imputed S03 MF transcriptional state abundance and m7FLIPI score in GSE119214 (n=137). Significance was determined by two-sided log-rank tests. Figure 4D shows an hematoxylin and eosin (H&E) section and CODEX multiplex imaging that depict spatial co-association between CD163+ macrophages and FoxP3+ regulatory T-cells. Figure 4E shows single-cell ligand-receptor communication modeling using the CellphoneDB repository show predicted interactions between S03 Mfs and S01TREGs and S01 NK cells. Figure 4F shows top differentially expressed genes between single-cell polymorphonuclear leukocytes (PMN) transcriptomes (n=19,368) assigned to a discrete transcriptional state. Figure 4G shows a heatmap of PMN single-cell GSEA normalized enrichment scores depicting significant differentially enriched pathways between PMN transcriptional states. Significance values were determined by the Wilcoxon rank sum method using an false discovery rate (FDR) q-value threshold of < 0.05. Figure 4H shows H&E staining and CODEX multiplex imaging of FL biopsy enriched for neutrophilic myeloid-derived suppressor cells (PMN-MDSCs) demonstrates perifollicularAttorney Docket No: 243735.000396 localization and co-association with CD8+ T-cells. Figure 4I shows Kaplan Meier plots of overall survival (OS) by S01 and S03 PMN transcriptional state abundance in GSE119214 (n=137). Pro-inflammatory PMNs (S01) are significantly associated with longer OS while PMN- MDSCs (PMN S03) are significantly associated with inferior OS. Significance was determined by two-sided log-rank tests. Figure 4J shows single-cell ligand-receptor communication modeling using the CellphoneDB repository shows predicted interactions between PMN-MDSCs (S03 PMN) and dysfunctional / exhausted effector T-cell states (S03 TCD8 and S03 TGD).

[0128] Figures 5A-5H show FL lymph node stromal cells (LNSCs) encompass heterogeneous transcriptional subtypes. Figure 5A shows top differentially expressed genes in blood endothelial cell (BEC) sc-RNAseq transcriptomes are assigned to a discrete transcriptional state. Figure 5B shows a heatmap of BEC single-cell GSEA scores depicting significant differentially enriched Gene Ontology (GO) pathways between BEC transcriptional states. Significance values were determined by the Wilcoxon rank sum method using an FDR q-value threshold of <0.05. Figure 5C shows top differentially expressed genes in fibroblastic reticular cell (FRC) sc- RNAseq transcriptomes are assigned to a discrete transcriptional state. Figure 5D shows a heatmap of FRC single-cell GSEA scores depicting significant differentially enriched Gene Ontology (GO) pathways between BEC transcriptional states. Significance values were determined by the Wilcoxon rank sum method using an FDR q-value threshold of < 0.05. Figure 5E shows top differentially expressed genes in lymphatic endothelial cell (LEC) sc-RNAseq transcriptomes assigned to a discrete transcriptional state. Figure 5F shows a heatmap of LEC single-cell GSEA scores depicting significant differentially enriched Gene Ontology (GO) pathways between LEC transcriptional states. Significance values were determined by the Wilcoxon rank sum method using an FDR q-value threshold of <0.05. Figure 5G shows top differentially expressed genes in LEC sc-RNAseq transcriptomes assigned to a discrete transcriptional state. Figure 5H shows a heatmap of follicular dendritic cell (FDC) single-cell GSEA scores depicting significant differentially enriched Gene Ontology (GO) pathways between FDC transcriptional states. Significance values were determined by the Wilcoxon rank sum method using an FDR q-value threshold of <0.05.

[0129] Figures 6A-6G show transcriptionally-distinct LNSC states co-occur with PMN- MDSCs. Figure 6A shows a correlation plot of PMN and LNSC transcriptional state abundances from discovery cohort (n=302). FRC, fibroblastic reticular cell; LEC, lymphatic endothelial cell;Attorney Docket No: 243735.000396 BEC, blood endothelial cell; FDC, follicular dendritic cell. Figure 6B shows a heatmap of log- count intercellular ligand-receptor interactions (CellPhoneDB) in the E4 interactome based on single-cell RNAseq samples from integrated atlas. Figures 6C-6F show CODEX multiplex imaging of FL biopsies enriched for PMNs that show close spatial co-association with LNSC subsets. Figure 6G shows a dot plot of predicted interactions between S03 PMNs and E4 LNSC transcriptional states from intercellular ligand-receptor communication modeling using the CellphoneDB repository.

[0130] Figures 7A-7J show FL transcriptional signatures are independently predictive of survival following frontline immunochemotherapy. Figure 7A shows a Kaplan-Meier plot of failure-free survival (FFS) by FL bulk subtype in GSE119214. Significance was determined by two-sided log-rank tests. Figure 7B shows a Kaplan-Meier plot of overall survival (OS) by FL bulk subtype in GSE119214. Significance was determined by two-sided log-rank tests. Figure 7C shows a forest plot of univariate hazard ratios for FFS by bulk FL subtype. Figure 7D shows a forest plot of univariate hazard ratios for OS by bulk FL subtype. Figure 7E shows a Kaplan- Meier plot of failure-free survival (FFS) by FL bulk subtype and m7FLIPI score in GSE119214. Significance was determined by two-sided log-rank test. Figure 7F shows a Kaplan-Meier plot of overall survival (OS) by FL bulk subtype and m7FLIPI score in GSE119214. Significance was determined by a two-sided log-rank test. Figure 7G shows a forest plot of multivariate hazard ratios for FFS by bulk FL subtype. Figure 7H shows a forest plot of multivariate hazard ratios for OS by bulk FL subtype. Figure 7I shows a Kaplan-Meier plot of failure-free survival (FFS) by FL bulk subtype in GSE66166. Figure 7J shows a Kaplan-Meier plot of failure-free survival (FFS) by FL bulk subtype among patients classified as m7FLIPI low in GSE66166.

[0131] Figure 8 shows the summary of single-cell RNA-seq datasets used in the integrated atlas.

[0132] Figure 9 shows the copy number alterations frequencies by whole genome sequencing in Dreval et al.

[0133] Figure 10 shows targeted exome alterations in GSE66166 by FL subtype.

[0134] Figures 11A-11B show FL subtypes are enriched for transcriptionally-distinct microenvironment immune and stromal cell subsets. Figure 11A shows relative frequency of B- cells, reactive TME leukocytes, and stromal cells by FL subtype imputed by digital cytometry (CIBERSORTx). Data are presented as box plots (center line, median; box limits, upper andAttorney Docket No: 243735.000396 lower quartiles; whiskers, largest and smallest values within 1.5 × interquartile range [IQR] of the box limits). Significance was assessed by a two-sided Wilcoxon rank-sum test. Figure 11B shows Kaplan-Meier plots of FFS by FL subtypes with high TME leukocyte fraction (FL4 and FL2) compared to low TME leukocyte fractions (FL5 and FL6) based on digital cytometry analyses (GSE119214). Significance was determined by two-sided log-rank tests.

[0135] Figures 12A-12G show digital cytometry with transcriptional subtyping revealed unique T follicular helper (Tfh) states with opposing survival associations not apparent by immunophenotypically-defined digital cytometry signature. Figures 12A-12B show the FFS and OS for immunophenotypically-defined Tfh signatures. Figure 12C shows a heatmap of imputed Tfh transcriptional states. Figures 12D-12E show the Kaplan Meier curves for FFS and OS associated with high versus low abundance of Tfh transcriptional subtypes. Figure 12F shows a heatmap of the top differentially expressed genes in single-cell RNAseq samples of Tfh cells assigned to a discrete transcriptional state. Figure 12G shows a heatmap of Tfh single-cell GSEA scores depicting significant differentially enriched Gene Ontology (GO) pathways between MF transcriptional states. Significance values determined by the Wilcoxon rank sum method using an FDR q-value threshold of <0.05.

[0136] Figures 13A-13H show digital cytometry with transcriptional subtyping revealed unique T-reg states with opposing survival associations not apparent by immunophenotypically- defined digital cytometry signature. Figures 13A-13B show FFS and OS for immunophenotypically-defined T-reg signatures. Figure 13C shows a heatmap of imputed Treg transcriptional states. Figures 13D-13G show the Kaplan Meier curves for FFS and OS associated with high versus low abundance of Treg transcriptional subtypes. Figure 13H shows a heatmap of top differentially expressed genes in single-cell RNAseq samples of Treg cells assigned to a discrete transcriptional state.

[0137] Figures 14A-14G show digital cytometry with transcriptional subtyping revealed unique T cells CD8 (TCD8) states with opposing survival associations not apparent by immunophenotypically-defined digital cytometry signature. Figures 14A-14B show FFS and OS for immunophenotypically-defined TCD8 signatures. Figure 14C shows a heatmap of imputed TCD8 transcriptional states. Figures 14D-14E show the Kaplan Meier curves for FFS and OS associated with high versus low abundance of TCD8 transcriptional subtypes. Figure 14F shows a heatmap of top differentially expressed genes in single-cell RNAseq samples of Treg cellsAttorney Docket No: 243735.000396 assigned to a discrete transcriptional state. Figure 14G shows a heatmap of TCD8 single-cell GSEA scores depicting significant differentially enriched Gene Ontology (GO) pathways between MF transcriptional states. Significance values determined by the Wilcoxon rank sum method using an FDR q-value threshold of <0.05.

[0138] Figures 15A-15G show digital cytometry with transcriptional subtyping revealed unique gamma delta T-cell (Tgd) states with opposing survival associations not apparent by immunophenotypically-defined digital cytometry signature. Figures 15A-15B show the FFS and OS for immunophenotypically-defined Tgd signatures. Figure 15C shows a heatmap of imputed Tgd transcriptional states. Figures 15D-15E show the Kaplan Meier curves for FFS and OS associated with high versus low abundance of Tgd transcriptional subtypes. Figure 15F shows heatmap of top differentially expressed genes in single-cell RNAseq samples of Treg cells assigned to a discrete transcriptional state. Figure 15G shows a heatmap of Tgd single-cell GSEA scores depicting significant differentially enriched Gene Ontology (GO) pathways between Tgd transcriptional states. Significance values determined by the Wilcoxon rank sum method using an FDR q-value threshold of <0.05.

[0139] Figures 16A-16B show MF enrichment scores and MF-Treg co-association. Figure 16A shows MF single-cell GSEA scores for canonical MF phenotypes. The S03 MF state was enriched for the M1 / pro-inflammatory MF phenotype. M0, M1, and M2 MF signatures were obtained from the Staudt Laboratory database. Figure 16B shows a correlation plot between imputed MF and Treg transcriptional state abundance in the discovery cohort (n=302) showed strong co-association between S03 MF and S01 TREG states.

[0140] Figures 17A-17E show data related to PMN transcriptional states. Figure 17A shows UMAP of PMN transcriptional states imputed from discovery cohort. Figure 17B shows heatmaps of imputed PMN transcriptional states from discovery cohort and recovered across validation cohort transcriptomes profiled by diverse platforms including Affymetrix microarray (GSE16131), Illumina Whole-Genome DASL HT (GSE119214), and RNA-seq (Dreval 2023). Figure 17C shows UMAP of 19,368 single-cell RNA-seq neutrophil transcriptomes assigned to a discrete transcriptional state. Figure 17D shows S03 PMN relative abundance by FL subtype in the discovery cohort. Data are presented as box plots (center line, median; box limits, upper and lower quartiles; whiskers, largest and smallest values within 1.5 x interquartile range [IQR] of the box limits). Significance was assessed relative to FL5 by a two-sided Wilcoxon rank-sumAttorney Docket No: 243735.000396 test. Figure 17E shows correlation plot between PMN, cytotoxic T-cell (TCD8), and gamma- delta T-cell (TGD) transcriptional state abundance in discovery cohort bulk transcriptomes (n=302).

[0141] Figures 18A-18H show heatmaps of discovery cohort imputed LNSC transcriptional states and the relative abundance of select states between FL subtypes. Figure 18A shows LEC transcriptional states imputed by Ecotyper from discovery cohort transcriptomes. Figure 18B shows box plots depicting relative S03 LEC abundance across FL subtypes. Box plot center line, median; box limits, upper and lower quartiles; whiskers, largest and smallest values within 1.5 x interquartile range [IQR] of the box limits. Significance was assessed relative to FL6 by two- sided Wilcoxon rank-sum tests. Figure 18C shows FDC transcriptional states imputed by Ecotyper from discovery cohort transcriptomes. Figure 18D shows box plots depicting relative S01 FDC abundance across FL subtypes. Box plot center line, median; box limits, upper and lower quartiles; whiskers, largest and smallest values within 1.5 x interquartile range [IQR] of the box limits. Significance was assessed relative to FL5 by two-sided Wilcoxon rank-sum tests. Figure 18E shows BEC transcriptional states imputed by Ecotyper from discovery cohort transcriptomes. Figure 18F shows box plots depicting relative S01 BEC abundance across FL subtypes. Box plot center line, median; box limits, upper and lower quartiles; whiskers, largest and smallest values within 1.5 x interquartile range [IQR] of the box limits. Significance was assessed relative to FL1 by two-sided Wilcoxon rank-sum tests. Figure 18G shows FRC transcriptional states imputed by Ecotyper from discovery cohort transcriptomes. Figure 18H shows relative abundance of S02 FRCs across FL subtypes in discovery. Significance was assessed relative to FL1 by two-sided Wilcoxon rank-sum tests. DETAILED DESCRIPTION

[0142] Gene expression profiling of whole tumors has the ability to robustly capture biological perturbations in both malignant cells and the TME (Newman 2015; Dave 2004) since novel computational tools have been developed to deconvolute TME transcriptional states with prognostic and predictive associations that are otherwise masked by standard lineage-based immunophenotyping approaches (Steen 2021; Luca 2021). Therefore, it was investigated herein whether evaluation of FL transcriptomes that account for the biological features of bothAttorney Docket No: 243735.000396 malignant B-cells and the microenvironment could be utilized to develop a robust and clinically useful FL transcriptomic classifier that could improve current FL clinicogenetic risk models.

[0143] Follicular lymphoma (FL) is characterized by transcriptionally-distinct subtypes which predict frontline immunochemotherapy treatment response and overall survival independent of clinicogenetic risk classification. The results presented herein used bulk transcriptional profiling to identify 7 biologically and clinically unique FL subtypes which were predictive of frontline immuno-chemotherapy response (FFS and OS) independent of clinicogenetic risk-classification and enhanced discriminative power for both endpoints when integrated with m7-FLIPI. High- resolution deconvolution of FL TME transcriptional states revealed that the host anti-tumor immune response and survival outcomes following frontline immunochemotherapy are shaped by cytologically diverse and transcriptionally-distinct TME ecosystems.

[0144] These findings included a subset of pro-inflammatory macrophages which contributed to superior survival outcomes independent of m7FLIPI score and uncovered a novel role for neutrophilic myeloid-derived suppressor cells (PMN-MDSCs) in high-risk FL as mediators of inferior overall survival. PMN-MDSCs co-associated with dysfunctional / exhausted CD8 T-cells. Recruitment was promoted by lymph node stromal cells.

[0145] Deconstruction of the FL transcriptional landscape at the bulk tumor level and by digital cytometry revealed an extensive and diverse panorama of biologically and clinically distinct FL subtypes which significantly associated with widely disparate frontline treatment outcomes that were difficult to parse at high resolution by clinicogenetic profiling alone. These findings support incorporating transcriptional signatures into existing risk models in order to advance frontline precision medicine strategies in FL.

[0146] Further evaluation of the transcriptional classifier will be performed in larger independent FL cohorts. In vivo characterization of FL subtype biological features and therapeutic vulnerabilities will be investigated. Definitions

[0147] To facilitate an understanding of the principles and features of the various embodiments of the invention, various illustrative embodiments are explained below. Although exemplary embodiments of the invention are explained in detail, it is to be understood that other embodiments are contemplated. Accordingly, it is not intended that the invention is limited in its scope to the details of construction and arrangement of components set forth in the followingAttorney Docket No: 243735.000396 description or examples. The invention is capable of other embodiments and of being practiced or carried out in various ways. Also, in describing the exemplary embodiments, specific terminology will be resorted to for the sake of clarity.

[0148] Unless otherwise defined herein, scientific and technical terms used in connection with the present invention shall have the meanings that are commonly understood by those of ordinary skill in the art. Further, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. Generally, nomenclatures used in connection with, and techniques of, cell and tissue culture, molecular biology, immunology, microbiology, genetics and protein and nucleic acid chemistry and hybridization described herein are those well-known and commonly used in the art.

[0149] It must also be noted that, as used in the specification and the appended claims, the singular forms “a,” “an” and “the” include plural references unless the context clearly dictates otherwise. For example, reference to a component is intended also to include composition of a plurality of components. References to a composition containing “a” constituent is intended to include other constituents in addition to the one named. In other words, 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.

[0150] As used herein, the term “and / or” may mean “and,” it may mean “or,” it may mean “exclusive-or,” it may mean “one,” it may mean “some, but not all,” it may mean “neither,” and / or it may mean “both.” The term “or” is intended to mean an inclusive “or.”

[0151] Also, in describing the exemplary embodiments, terminology will be resorted to for the sake of clarity. It is intended that each term contemplates its broadest meaning as understood by those skilled in the art and includes all technical equivalents which operate in a similar manner to accomplish a similar purpose. It is to be understood that embodiments of the disclosed technology may be practiced without these specific details. In other instances, well-known methods, structures, and techniques have not been shown in detail in order not to obscure an understanding of this description. References to “one embodiment,” “an embodiment,” “example embodiment,” “some embodiments,” “certain embodiments,” “various embodiments,” etc., indicate that the embodiment(s) of the disclosed technology so described may include a particular feature, structure, or characteristic, but not every embodiment necessarily includes theAttorney Docket No: 243735.000396 particular feature, structure, or characteristic. Further, repeated use of the phrase “in one embodiment” does not necessarily refer to the same embodiment, although it may.

[0152] As used herein, the term "about" or “approximately” should be construed to refer to both of the numbers specified as the endpoint (s) of any range. Any reference to a range should be considered as providing support for any subset within that range. Ranges may be expressed herein as from “about” or “approximately” or “substantially” one particular value and / or to “about” or “approximately” or “substantially” another particular value. When such a range is expressed, other exemplary embodiments include from the one particular value and / or to the other particular value. Further, the term “about” means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, i.e., the limitations of the measurement system. For example, “about” can mean within an acceptable standard deviation, per the practice in the art. Alternatively, “about” can mean a range of up to ±20%, preferably up to ±10%, more preferably up to ±5%, and more preferably still up to ±1% of a given value. Alternatively, particularly with respect to biological systems or processes, the term can mean within an order of magnitude, preferably within 2-fold, of a value. Where particular values are described in the application and claims, unless otherwise stated, the term “about” is implicit and in this context means within an acceptable error range for the particular value.

[0153] Throughout this disclosure, various aspects of the invention can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 3, 4, 5, and 6. This applies regardless of the breadth of the range.

[0154] By “comprising” or “containing” or “including” is meant that at least the named compound, element, particle, or method step is present in the composition or article or method, but does not exclude the presence of other compounds, materials, particles, method steps, even ifAttorney Docket No: 243735.000396 the other such compounds, material, particles, method steps have the same function as what is named.

[0155] It is noted that terms like “specifically,” “preferably,” “typically,” “generally,” and “often” are not utilized herein to limit the scope of the claimed invention or to imply that certain features are critical, essential, or even important to the structure or function of the claimed invention. Rather, these terms are merely intended to highlight alternative or additional features that may or may not be utilized in a particular embodiment of the present invention.

[0156] The dimensions and values disclosed herein are not to be understood as being strictly limited to the exact numerical values recited. Instead, unless otherwise specified, each such dimension is intended to mean both the recited value and a functionally equivalent range surrounding that value. For example, a dimension disclosed as “80%” is intended to mean “about 80%.”

[0157] As used herein, the term “subject” or “patient” refers to mammals and includes, without limitation, humans, animals, veterinary animals e.g., horses, cats, and dogs, and experimental animals or animal models, e.g., mice and non-human primates. In a preferred embodiment, the subject is human, and most preferably a human that has been diagnosed with FL.

[0158] The terms “sample”, “subject sample” and “test sample” are used herein to refer to any fluid, cell, or tissue sample from a subject which can be assayed for determining gene expression level. In some embodiments, the sample may include a blood sample or a tumor sample.

[0159] The term “biological sample” as used herein includes any biological specimen obtained from a subject or patient. Samples that can be used in the methods of the present disclosure include, without limitation, serum, plasma, an immunoglobulin fraction of the blood, whole blood, red blood cells, white blood cells (e.g., peripheral blood mononuclear cells (PBMC), polymorphonuclear (PMN) cells, ductal lavage fluid, nipple aspirate, lymph (e.g., disseminated tumor cells of the lymph node), bone marrow aspirate, saliva, urine, stool (i.e., feces), sputum, bronchial lavage fluid, tears, fine needle aspirate (e.g., harvested by random periareolar fine needle aspiration), tumor sample, any other bodily fluid, a tissue sample such as a biopsy of a site of the tumor (e.g., needle biopsy), and cellular extracts thereof. In some embodiments, a sample described herein comprises tumor cells and may be a biopsy sample.Attorney Docket No: 243735.000396

[0160] As used herein, the term “expression score” or “enrichment score” is calculated based on the degree to which the genes from each of the 7 groups of genes as described herein are overrepresented at the top or bottom of a ranked list.

[0161] The term “overall survival (OS)” as used herein in connection with FL refers to a risk of death from FL.

[0162] The term “failure-free survival (FFS)” as used herein in connection with FL refers to the length of time after the end of the primary treatment for FL that the patient remains free of certain complications or events that the treatment was intended to prevent or delay, which include non-relapse mortality, relapse, and systemic treatment change.

[0163] The term “nucleic acid” includes DNA and RNA, and can be double stranded or single stranded.

[0164] The term “hybridize” or “hybridizable” refers to the sequence specific non-covalent binding interaction with a complementary nucleic acid. In some embodiments, the hybridization is under high stringency conditions. Appropriate stringency conditions which promote hybridization can be appreciated by those skilled in the art, or can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989), 6.3.16.3.6. For example, 6.0 × sodium chloride / sodium citrate (SSC) at about 45° C, followed by a wash of 2.0 × SSC at 50° C may be employed.

[0165] The term “probe” as used herein refers to a nucleic acid molecule that can hybridize to a target nucleic acid sequence. The length of probe may depend on the hybridization conditions and the sequences of the probe and the target nucleic acid sequence. In some embodiments, the probe may be at least 8, 10, 15, 20, 25, 50, 75, 100, 150, 200, 250, 400, 500 or more nucleotides in length.

[0166] The term “primer” as used herein refers to a nucleic acid molecule which is capable of acting as a point of synthesis when placed under conditions in which synthesis of a primer extension product, which is complementary to a nucleic acid sequence, is induced (e.g., in the presence of nucleotides and a polymerase, and at a suitable temperature and pH). The primer can be sufficiently long to prime the synthesis of the desired extension product in the presence of the inducing agent. The exact length of the primer may depend upon one or more factors, including temperature, sequences of the primer, and the methods used. A primer may contain 10-25 orAttorney Docket No: 243735.000396 more nucleotides, although it can contain less or more. Those of ordinary skill in the art will appreciate the factors involved in determining the appropriate length of a primer.

[0167] The terms “treat” or “treatment” of a state, disorder or condition include: (1) preventing or delaying 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.

[0168] The terms “inhibit” or “inhibition” as used herein refer to reducing a function or activity to an extent sufficient to achieve a desired biological or physiological effect. Inhibition may be complete or partial.

[0169] The term “therapeutic” as used herein means a treatment and / or prophylaxis. A therapeutic effect is obtained by suppression, diminution, remission, or eradication of a disease state.

[0170] As used herein the term “therapeutically effective” applied to a dose or amount refers to that quantity of a compound or pharmaceutical composition 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 on the compound administered as well as the disease and its severity and the age, weight, physical condition and responsiveness of the subject to be treated.

[0171] In the context of the field of medicine, the term “prevent” encompasses any activity which reduces the burden of mortality or morbidity from a disease. Prevention can occur at primary, secondary and tertiary prevention levels. While primary prevention avoids the development of a disease, secondary and tertiary levels of prevention encompass activities aimed at preventing the progression of a disease and the emergence of symptoms as well as reducing the negative impact of an already established disease by restoring function and reducing disease- related complications.Attorney Docket No: 243735.000396

[0172] Also, in describing the exemplary embodiments, terminology will be resorted to for the sake of clarity. It is intended that each term contemplates its broadest meaning as understood by those skilled in the art and includes all technical equivalents that operate in a similar manner to accomplish a similar purpose.

[0173] It is also to be understood that the mention of one or more method steps does not preclude the presence of additional method steps or intervening method steps between those steps expressly identified. Similarly, it is also to be understood that the mention of one or more components in a composition does not preclude the presence of additional components than those expressly identified.

[0174] The materials described hereinafter as making up the various elements of the present invention are intended to be illustrative and not restrictive. Many suitable materials that would perform the same or a similar function as the materials described herein are intended to be embraced within the scope of the invention. Such other materials not described herein can include, but are not limited to, materials that are developed after the time of the development of the invention, for example. Any dimensions listed in the various drawings are for illustrative purposes only and are not intended to be limiting. Other dimensions and proportions are contemplated and intended to be included within the scope of the invention. Methods of the Invention

[0175] In an exemplary embodiment, the invention provides a method for subtype classification of an FL patient. The method may include determining an expression level of a plurality of genes from each of the 7 groups corresponding to 7 follicular lymphoma (FL) subtypes, calculating a gene expression score for the tumor sample for each of the 7 groups of genes, comparing the 7 gene expression scores, and classifying the subject into the FL subtype.

[0176] In an exemplary embodiment, the method for classifying a subject diagnosed with follicular lymphoma (FL) into 7 FL subtypes (FL1-FL7) comprises (a) determining in a biological sample obtained from the subject the expression level of at least 4 genes from each of 7 groups of genes provided in Table 1, wherein the 7 groups of genes correspond to 7 FL subtypes (FL1-FL7) as listed in Table 1; (b) calculating a gene expression score for the biological sample for each of the 7 groups of genes of step (a); (c) comparing the 7 gene expression scores calculated in step (b) to each other and determining the highest geneAttorney Docket No: 243735.000396 expression score among the 7 gene expression scores; and (d) classifying the subject into the FL subtype which corresponds to the highest gene expression score determined in step (c).

[0177] In an exemplary embodiment, without wishing to be bound by theory, follicular lymphoma (FL) can be a B-cell lymphoma. FL can be a type of low-grade non-Hodgkin lymphoma. FL can be a biologically and clinically heterogenous disease.

[0178] In an exemplary embodiment, the plurality of genes may include at least 4 genes selected from each of 7 groups of genes listed in Table 1 or Table 3. In an exemplary embodiment, the plurality of genes may include at least 4 genes selected from each of 7 groups of genes listed in Table 1. In an exemplary embodiment, the plurality of genes may include at least 4 genes selected from each of 7 groups of genes listed in Table 3.

[0179] In an exemplary embodiment, the subject has been diagnosed with FL based on evaluation of histology and / or immunophenotypic features.

[0180] In an exemplary embodiment, the method comprises generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes, generating a ranked gene list based on the gene expression count matrix, and calculating the gene expression score based in part on a running-sum statistic for each of the 7 groups of genes.

[0181] In an exemplary embodiment, step (b) of the method comprises: generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 1; generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreases when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

[0182] In an exemplary embodiment, step (b) of the method comprises: representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative; performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes providedAttorney Docket No: 243735.000396 in Table 1, and resulting in a mixture coefficient matrix; and determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.

[0183] In an exemplary embodiment, step (c) of the method comprises: determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

[0184] In an exemplary embodiment, step (a) of the method comprises determining the expression level of at least 4 genes from each of the 7 groups of genes provided in Table 3 wherein the 7 groups of genes correspond to the 7 FL subtypes (FL1-FL7) as listed in Table 3.

[0185] In an exemplary embodiment, step (b) of the method comprises: generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 3; generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreases when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

[0186] In an exemplary embodiment, step (b) of the method comprises: representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative; performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes provided in Table 3, and resulting in a mixture coefficient matrix; and determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.

[0187] In an exemplary embodiment, step (c) of the method comprises: determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

[0188] In an exemplary embodiment, the plurality of genes may include any four or more genes corresponding to FL1 selected from DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF.

[0189] In an exemplary embodiment, the genes are at least 1, 2, 3, or 4 genes from Table 3. In an exemplary embodiment, the at least 4 genes are at least 4, 5, 6, 7, 8, or 9 genes from Table 3.Attorney Docket No: 243735.000396 In another exemplary embodiment, the at least 4 genes selected from any of the genes in Table 3 are at least 4, 5, 6, 7, 8, or 9 genes.

[0190] In an exemplary embodiment, the at least 4, 5, 6, 7, 8, or 9 genes may include DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and / or TNF.

[0191] In an exemplary embodiment, the genes for group 1 corresponding to FL1 comprise DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF.

[0192] In an exemplary embodiment, the genes are at least 1, 2, 3, or 4 genes from Table 1. In an exemplary embodiment, the at least 4 genes are at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, or 93 genes from Table 1. In another exemplary embodiment, the at least 4 genes selected from any of the genes in Table 1 are at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, or 93 genes.

[0193] In an exemplary embodiment, the at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, or 93 genes may include DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, TNF, ACTBP9, FCRLA, MAD1L1, P2RX5, CPNE5, H2BC12, H1-2, KLF2, GCHFR, SNORA64, SEMA4B, H2BC7, FOSB, GNG7, RPPH1, LOC105373430, BFSP2, CCDC24, FOS, CD72, NIBAN3, VPREB3, H4C6, HSPA1B, HLA-DPB1, CAMP, MIR5195, TUBB2A, H1-4, ZC3H12A, PKM, FCGR2B, H2BC5, RPL29P5, HBG2, ZNF836, IL4R, MAP3K2-DT, H1-3, HTR3A, C16orf74, BEX2, KANSL1-AS1, HBD, H2AC17, SYBU, PPBP, PMAIP1, HNRNPCL1, TNFRSF14-AS1, GNLY, MIOX, CD69, IGHD, S100A8, FCRLB, FOXD1, NR4A2, S100A9, ZNF414, DOK7, ACTR3-AS1, HMGA1, IGHV3-23, POLR1G, RGS1, IGHV4-28, HBB, CHI3L2, SUGCT, FCER2, RAB1B, MAP3K7CL, LINC01095, HLA-DQB1, DTNB-AS1, IGHE, PVALB, TOX4P1, KRT14, IGLV6-57, LOC105374258, LOC107987303, and / or LINC02367.Attorney Docket No: 243735.000396

[0194] In an exemplary embodiment, the genes for group 1 corresponding to FL1 comprise DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, TNF, ACTBP9, FCRLA, MAD1L1, P2RX5, CPNE5, H2BC12, H1-2, KLF2, GCHFR, SNORA64, SEMA4B, H2BC7, FOSB, GNG7, RPPH1, LOC105373430, BFSP2, CCDC24, FOS, CD72, NIBAN3, VPREB3, H4C6, HSPA1B, HLA-DPB1, CAMP, MIR5195, TUBB2A, H1-4, ZC3H12A, PKM, FCGR2B, H2BC5, RPL29P5, HBG2, ZNF836, IL4R, MAP3K2-DT, H1-3, HTR3A, C16orf74, BEX2, KANSL1-AS1, HBD, H2AC17, SYBU, PPBP, PMAIP1, HNRNPCL1, TNFRSF14-AS1, GNLY, MIOX, CD69, IGHD, S100A8, FCRLB, FOXD1, NR4A2, S100A9, ZNF414, DOK7, ACTR3-AS1, HMGA1, IGHV3-23, POLR1G, RGS1, IGHV4-28, HBB, CHI3L2, SUGCT, FCER2, RAB1B, MAP3K7CL, LINC01095, HLA-DQB1, DTNB-AS1, IGHE, PVALB, TOX4P1, KRT14, IGLV6-57, LOC105374258, LOC107987303, and LINC02367.

[0195] In an exemplary embodiment, the plurality of genes may include any four or more genes corresponding to FL2 selected from GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK.

[0196] In an exemplary embodiment, the genes are at least 1, 2, 3, or 4 genes from Table 3. In an exemplary embodiment, the at least 4 genes are at least 4, 5, 6, 7, or 8 genes from Table 3. In another exemplary embodiment, the at least 4 genes selected from any of the genes in Table 3 are at least 4, 5, 6, 7, or 8 genes.

[0197] In an exemplary embodiment, the at least 4, 5, 6, 7, or 8 genes may include GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK.

[0198] In an exemplary embodiment, the genes for group 2 corresponding to FL2 comprise GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK.

[0199] In an exemplary embodiment, the genes are at least 1, 2, 3, or 4 genes from Table 1. In an exemplary embodiment, the at least 4 genes are at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, or 140 genes from Table 1. In another exemplary embodiment, the at least 4 genes selected from any of the genes in Table 1 are at least 4, 5, 6, 7, 8, 9, 10, 11, 12,Attorney Docket No: 243735.000396 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, or 140 genes.

[0200] In an exemplary embodiment, the at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, or 140 genes may include GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, GZMK, CXCL10, LOC105369151, GBP1, DDX60, LYZ, CRTAM, CXCL9, CPVL, FGL2, STAT1, CD8A, GPR171, ATP9A, CXCL11, GBP3, PMCH, DDX60L, ICOS, CCL4, PLA1A, SLFN11, CTSL, KCNJ2, C1QA, CHN1, PLAC8, EPB41L3, IL18, TARP, TNFSF11, LGMN, C1QB, HERC5, PLA2G4A, SMPDL3A, TBC1D4, MIR3142HG, TNFSF13B, ZC3H12C, FCHO2, MNDA, IL3RA, ADAMDEC1, SAMD9L, CLIC2, NCEH1, LINC01943, CP, CADM1, CCL5, RGS18, DMXL2, CH25H, LGALS2, PARP14, CLEC4M, ENPP2, UBD, NTS, PLA2G7, MIR155HG, P2RY13, GZMB, APOE, CLEC4G, IRX3, CCR6, CHIT1, SHISA3, FZD6, TNFRSF11B, CHI3L1, TRAJ41, TYMP, ANKRD29, TDO2, NLRC5, CXCL5, TMEM150C, CYSLTR1, MIAT, SLC40A1, LIFR, CCL18, ALPK2, ANKRD12, ZNF267, KLRF1, CR1L, GZMH, PLA2G2D, CXCL13, NELL2, VCAM1, DNASE1L3, RADX, IGKV4-1, MARCO, ZNF300, CCL21, S1PR1, MYO6, SERPINA5, HPGD, TMSB15A, GPR34, DMRT3, IQCG, P2RY14, ERAP2, CR2, CETP, FCGR3B, FCAMR, IGHV3-21, ADGRG2, JADE3, TRAV8-3, TNFRSF21, CX3CR1, AHR, USP9Y, LILRA4, GTSF1, KDM5D, GPR82, DDX3Y, RPS4Y1, TTTY15, ZFY, EIF1AY, and / or HLA-DRB6.

[0201] In an exemplary embodiment, the genes for group 2 corresponding to FL2 comprise GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, GZMK, CXCL10, LOC105369151, GBP1, DDX60, LYZ, CRTAM, CXCL9, CPVL, FGL2, STAT1, CD8A, GPR171, ATP9A, CXCL11, GBP3, PMCH, DDX60L, ICOS, CCL4, PLA1A, SLFN11, CTSL,Attorney Docket No: 243735.000396 KCNJ2, C1QA, CHN1, PLAC8, EPB41L3, IL18, TARP, TNFSF11, LGMN, C1QB, HERC5, PLA2G4A, SMPDL3A, TBC1D4, MIR3142HG, TNFSF13B, ZC3H12C, FCHO2, MNDA, IL3RA, ADAMDEC1, SAMD9L, CLIC2, NCEH1, LINC01943, CP, CADM1, CCL5, RGS18, DMXL2, CH25H, LGALS2, PARP14, CLEC4M, ENPP2, UBD, NTS, PLA2G7, MIR155HG, P2RY13, GZMB, APOE, CLEC4G, IRX3, CCR6, CHIT1, SHISA3, FZD6, TNFRSF11B, CHI3L1, TRAJ41, TYMP, ANKRD29, TDO2, NLRC5, CXCL5, TMEM150C, CYSLTR1, MIAT, SLC40A1, LIFR, CCL18, ALPK2, ANKRD12, ZNF267, KLRF1, CR1L, GZMH, PLA2G2D, CXCL13, NELL2, VCAM1, DNASE1L3, RADX, IGKV4-1, MARCO, ZNF300, CCL21, S1PR1, MYO6, SERPINA5, HPGD, TMSB15A, GPR34, DMRT3, IQCG, P2RY14, ERAP2, CR2, CETP, FCGR3B, FCAMR, IGHV3-21, ADGRG2, JADE3, TRAV8-3, TNFRSF21, CX3CR1, AHR, USP9Y, LILRA4, GTSF1, KDM5D, GPR82, DDX3Y, RPS4Y1, TTTY15, ZFY, EIF1AY, and HLA-DRB6.

[0202] In an exemplary embodiment, the plurality of genes may include any four or more genes corresponding to FL3 selected from ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3.

[0203] In an exemplary embodiment, the genes are at least 1, 2, 3, or 4 genes from Table 3. In an exemplary embodiment, the at least 4 genes are at least 4, 5, 6, 7, or 8 genes from Table 3. In another exemplary embodiment, the at least 4 genes selected from any of the genes in Table 3 are at least 4, 5, 6, 7, or 8 genes.

[0204] In an exemplary embodiment, the at least 4, 5, 6, 7, or 8 genes may include ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and / or GPX3.

[0205] In an exemplary embodiment, the genes for group 3 corresponding to FL3 comprise ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3.

[0206] In an exemplary embodiment, the genes are at least 1, 2, 3, or 4 genes from Table 1. In an exemplary embodiment, the at least 4 genes are at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152,Attorney Docket No: 243735.000396 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, or 357 genes from Table 1. In another exemplary embodiment, the at least 4 genes selected from any of the genes in Table 1 are at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, or 357 genes.Attorney Docket No: 243735.000396

[0207] In an exemplary embodiment, the at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, or 357 genes may include ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, SELENBP1, RNASE1, ANXA1, SRPX, GPX3, AEBP1, MGST1, MANSC1, CAV1, ADIRF, PDZRN3, RNASE4, MYLK, RCAN2, SH3BGRL2, CRIM1, CD36, CRISPLD2, PLSCR4, TGFBR3, NUAK1, CHRDL1, ID1, CRYAB, FAM13C, NXN, TPBG, PAM, FAT1, CILP, LAMB2, LHFPL6, GGTA1, TM4SF1, PLK2, NID2, PODXL, TIMP3, KIT, SFRP2, TENT5A, PDGFRA, OSBPL1A, AKR1C2, ATP1B1, OLFML3, EPS8, ADGRF5, NUPR1, APOD, EFNA1, CFD, DAB2, EFEMP1, PMP22, EMCN, RIN2, CCDC80, DPT, LTBP2, SASH1, ARMCX1, MMP2, TSPAN8, PLIN1, AQP1, MRC1, HTRA1, HMCN1, TGFBI, COL6A3, CD93, RBP7, LAMB1, PXDN, C11orf96, ECSCR, ADIPOQ, PDGFRB, CCDC3, CXCL2, COL16A1, PKDCC, ECM2, OLFML1, FRMD6, AOC3, LDB2, SPOCK1, SERPINH1, NTN4, TMEM47, ZNF423, COL15A1, FABP4, SERPING1, PLS3, PLPP3, ZNF462, SHANK3, NEURL1B, COL1A1, MPDZ, FRZB, CFB, ALDH1A1, YES1, ADH1B, FERMT2, IFI27, ADAMTS1, SSPN, COL4A2, NCKAP1, CTSK, DNM3OS, MGP, OLFML2B, IFI44L, EPAS1, RGS5, IGF1, COL5A2, SLPI, MAP1B,Attorney Docket No: 243735.000396 TGFB1I1, DOCK4, DEPTOR, A2M, FSTL1, CDH5, NR2F2, NR2F1, CCN2, SPARC, NFIA, CXCL12, COL4A1, YAP1, COL1A2, IFIT1, SEPTIN10, CD14, INMT, PTPRM, SIGLEC1, IL11RA, CYYR1, G0S2, VWF, TJP1, PLCB4, FMOD, MXRA5, ASAP2, THBS2, ASS1, SFRP4, COX7A1, CFI, CSGALNACT1, PPIC, C1R, FNBP1L, NFIB, CALD1, EDNRB, PLOD2, GATA6, PRSS23, IGLV2-14, COL3A1, ZNF521, CFH, SNAI2, IGDCC4, ABI3BP, CYBRD1, TCIM, ARHGAP29, FMO2, VCAN, CLEC10A, FRMD4B, SNX7, ACKR1, KCTD12, PCK1, TIMP1, PALLD, PCOLCE, LUM, TM4SF18, AMOTL2, FBN1, NDN, NNMT, IER3, CPE, LIMA1, HSPA1A, FGF7, CCN1, PTPRK, FN1, HSPB8, CLDN5, CRISPLD1, GUCY1A1, MFAP4, CNN3, LPL, SLCO2A1, TSPAN7, ADGRL4, CSRP2, C1orf115, MAOB, FILIP1L, CCL2, SPARCL1, CNRIP1, PAPLN, RGL1, MEOX2, C1QC, RSPO3, WLS, VEGFC, CAVIN3, SLC22A3, CLEC3B, LOC105370792, MS4A4A, DSP, TMEM176A, RBMS3, ACKR3, DPYSL3, CYP1B1, MATN2, CTHRC1, IL33, ITIH5, GLIS2, ITGAV, ALDH7A1P1, CPA3, FAM114A1, C1S, C7, TF, MEIS2, TCEAL9, RND3, LINC02381, EBF3, APLNR, TMEM176B, CCL19, MYO1B, GJA4, LGALS1, ADRA2A, CEMIP, ANK2, PRKAR2B, TMEM255A, F13A1, ZFPM2, IGFBP7, FMNL2, GEM, NRN1, CXCL14, MICU3, IGFBP3, SELENOP, EGR1, IGLL3P, STATH, PRRX1, LAMP3, ZNF667- AS1, THY1, OLFM1, CCL26, RAI14, LOXL1, SERPINA3, GUSBP11, LTF, FAM30A, ANOS1, H1-0, RARRES2, GJA1, RAMP3, ARRDC4, IGLV1-40, SEMA5A, TNC, SPP1, FAM149A, RBP5, IGLV3-10, SYNM, RARRES1, NPY1R, GREM1, IGLV3-1, EFNB2, IGLV5-45, NINL, C3, ITGAX, ANKDD1A, PLA2G2A, MMP9, USP53, NCCRP1, MT2A, EYA2, MT4, GPRASP1, IGLV3-19, TMEM119, PDCL3P2, HTN3, PF4, ROBO1, HOXC6, RAB25, FAM153B, CST1, FAM3B, CKB, SERPINE2, ALKAL2, LINC00408, PAX8-AS1, IGKC, SLC16A4, PSG4, ZNF835, LINC01638, MIR548XHG, HTN1, NLRP7, NLRP2, and / or SCGB3A1.

[0208] In an exemplary embodiment, the genes for group 3 corresponding to FL3 comprise ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, SELENBP1, RNASE1, ANXA1, SRPX, GPX3, AEBP1, MGST1, MANSC1, CAV1, ADIRF, PDZRN3, RNASE4, MYLK, RCAN2, SH3BGRL2, CRIM1, CD36, CRISPLD2, PLSCR4, TGFBR3, NUAK1, CHRDL1, ID1, CRYAB, FAM13C, NXN, TPBG, PAM, FAT1, CILP, LAMB2, LHFPL6, GGTA1, TM4SF1, PLK2, NID2, PODXL, TIMP3, KIT, SFRP2, TENT5A, PDGFRA, OSBPL1A, AKR1C2, ATP1B1, OLFML3, EPS8, ADGRF5, NUPR1, APOD, EFNA1, CFD, DAB2, EFEMP1,Attorney Docket No: 243735.000396 PMP22, EMCN, RIN2, CCDC80, DPT, LTBP2, SASH1, ARMCX1, MMP2, TSPAN8, PLIN1, AQP1, MRC1, HTRA1, HMCN1, TGFBI, COL6A3, CD93, RBP7, LAMB1, PXDN, C11orf96, ECSCR, ADIPOQ, PDGFRB, CCDC3, CXCL2, COL16A1, PKDCC, ECM2, OLFML1, FRMD6, AOC3, LDB2, SPOCK1, SERPINH1, NTN4, TMEM47, ZNF423, COL15A1, FABP4, SERPING1, PLS3, PLPP3, ZNF462, SHANK3, NEURL1B, COL1A1, MPDZ, FRZB, CFB, ALDH1A1, YES1, ADH1B, FERMT2, IFI27, ADAMTS1, SSPN, COL4A2, NCKAP1, CTSK, DNM3OS, MGP, OLFML2B, IFI44L, EPAS1, RGS5, IGF1, COL5A2, SLPI, MAP1B, TGFB1I1, DOCK4, DEPTOR, A2M, FSTL1, CDH5, NR2F2, NR2F1, CCN2, SPARC, NFIA, CXCL12, COL4A1, YAP1, COL1A2, IFIT1, SEPTIN10, CD14, INMT, PTPRM, SIGLEC1, IL11RA, CYYR1, G0S2, VWF, TJP1, PLCB4, FMOD, MXRA5, ASAP2, THBS2, ASS1, SFRP4, COX7A1, CFI, CSGALNACT1, PPIC, C1R, FNBP1L, NFIB, CALD1, EDNRB, PLOD2, GATA6, PRSS23, IGLV2-14, COL3A1, ZNF521, CFH, SNAI2, IGDCC4, ABI3BP, CYBRD1, TCIM, ARHGAP29, FMO2, VCAN, CLEC10A, FRMD4B, SNX7, ACKR1, KCTD12, PCK1, TIMP1, PALLD, PCOLCE, LUM, TM4SF18, AMOTL2, FBN1, NDN, NNMT, IER3, CPE, LIMA1, HSPA1A, FGF7, CCN1, PTPRK, FN1, HSPB8, CLDN5, CRISPLD1, GUCY1A1, MFAP4, CNN3, LPL, SLCO2A1, TSPAN7, ADGRL4, CSRP2, C1orf115, MAOB, FILIP1L, CCL2, SPARCL1, CNRIP1, PAPLN, RGL1, MEOX2, C1QC, RSPO3, WLS, VEGFC, CAVIN3, SLC22A3, CLEC3B, LOC105370792, MS4A4A, DSP, TMEM176A, RBMS3, ACKR3, DPYSL3, CYP1B1, MATN2, CTHRC1, IL33, ITIH5, GLIS2, ITGAV, ALDH7A1P1, CPA3, FAM114A1, C1S, C7, TF, MEIS2, TCEAL9, RND3, LINC02381, EBF3, APLNR, TMEM176B, CCL19, MYO1B, GJA4, LGALS1, ADRA2A, CEMIP, ANK2, PRKAR2B, TMEM255A, F13A1, ZFPM2, IGFBP7, FMNL2, GEM, NRN1, CXCL14, MICU3, IGFBP3, SELENOP, EGR1, IGLL3P, STATH, PRRX1, LAMP3, ZNF667- AS1, THY1, OLFM1, CCL26, RAI14, LOXL1, SERPINA3, GUSBP11, LTF, FAM30A, ANOS1, H1-0, RARRES2, GJA1, RAMP3, ARRDC4, IGLV1-40, SEMA5A, TNC, SPP1, FAM149A, RBP5, IGLV3-10, SYNM, RARRES1, NPY1R, GREM1, IGLV3-1, EFNB2, IGLV5-45, NINL, C3, ITGAX, ANKDD1A, PLA2G2A, MMP9, USP53, NCCRP1, MT2A, EYA2, MT4, GPRASP1, IGLV3-19, TMEM119, PDCL3P2, HTN3, PF4, ROBO1, HOXC6, RAB25, FAM153B, CST1, FAM3B, CKB, SERPINE2, ALKAL2, LINC00408, PAX8-AS1, IGKC, SLC16A4, PSG4, ZNF835, LINC01638, MIR548XHG, HTN1, NLRP7, NLRP2, and SCGB3A1.Attorney Docket No: 243735.000396

[0209] In an exemplary embodiment, the plurality of genes may include any four or more genes corresponding to FL4 selected from GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX.

[0210] In an exemplary embodiment, the genes are at least 1, 2, 3, or 4 genes from Table 3. In an exemplary embodiment, the at least 4 genes are at least 4, 5, 6, 7, 8, 9, or 10 genes from Table 3. In another exemplary embodiment, the at least 4 genes selected from any of the genes in Table 3 are at least 4, 5, 6, 7, 8, 9, or 10 genes.

[0211] In an exemplary embodiment, the at least 4, 5, 6, 7, 8, 9, or 10 genes may include GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX.

[0212] In an exemplary embodiment, the genes for group 4 corresponding to FL4 comprise GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX.

[0213] In an exemplary embodiment, the genes are at least 1, 2, 3, or 4 genes from Table 1. In an exemplary embodiment, the at least 4 genes are at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, or 129 genes from Table 1. In another exemplary embodiment, the at least 4 genes selected from any of the genes in Table 1 are at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, or 129 genes.

[0214] In an exemplary embodiment, the at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, or 129 genes may includeAttorney Docket No: 243735.000396 GMDS, SHCBP1, RASL11A, QPCT, LMO2, LINC00487, SHISA8, MUC16, PDGFD, ACY3, FNDC1, TOX, FAP, DNER, IL4I1, RRAS2, LOC100505501, ASB13, SLC12A8, ENPP3, P2RY12, CRACD, SYTL4, FGD6, SDR16C5, LHX8, ATF5, MMP7, SULF1, GCNT1, ITGB8- AS1, LOC102724517, LOC107986513, C2orf88, AATBC, SGK1, ATP10D, LRRC4, PKHD1L1, GRAMD1C, BCAR3, CMPK2, TFEC, C17orf99, LOC105376412, STXBP6, HMMR, NLRP4, POSTN, MARCKSL1, LOC100507006, MACC1-DT, HOPX, DLGAP5, CDCA7, HEG1, SULT1A1, LINC00877, DMD, MMP12, RMI2, CENPE, DEPDC1B, SYT17, SCARA5, NUF2, MYBL1, ODAM, ARL14, GPR18, PXDNL, ARHGAP44, SERPINA9, SGO2, ABCA6, GALNT14, GPNMB, DHRS9, TTK, NIBAN1, LOC105377468, RAB42, RGS7, ARHGAP11B, SOX9, DIP2C, COMP, KCNH8, RNGTT, MAP3K8, SLCO5A1, LINC02562, KIFC1, SPINK2, LRRK2, LYPD6B, RGS13, TEX9, NLRP11, PCDHGA8, NMU, TNFRSF17, BTNL9, LRRC37A3, FHOD3, COX7BP1, TUBB3, HTRA4, GATM, LOC105375172, LINC01102, PARM1, DDX19A-DT, CYP27A1, DNAJC5B, ZNF185, SPA17P1, JUP, STAG3, LINC01857, GDF7, TSPYL5, PIP, PNMA8A, UGT2B17, PRAMEF11, MAB21L1, PSMA8, and / or TRGV5P.

[0215] In an exemplary embodiment, the genes for group 4 corresponding to FL4 comprise GMDS, SHCBP1, RASL11A, QPCT, LMO2, LINC00487, SHISA8, MUC16, PDGFD, ACY3, FNDC1, TOX, FAP, DNER, IL4I1, RRAS2, LOC100505501, ASB13, SLC12A8, ENPP3, P2RY12, CRACD, SYTL4, FGD6, SDR16C5, LHX8, ATF5, MMP7, SULF1, GCNT1, ITGB8- AS1, LOC102724517, LOC107986513, C2orf88, AATBC, SGK1, ATP10D, LRRC4, PKHD1L1, GRAMD1C, BCAR3, CMPK2, TFEC, C17orf99, LOC105376412, STXBP6, HMMR, NLRP4, POSTN, MARCKSL1, LOC100507006, MACC1-DT, HOPX, DLGAP5, CDCA7, HEG1, SULT1A1, LINC00877, DMD, MMP12, RMI2, CENPE, DEPDC1B, SYT17, SCARA5, NUF2, MYBL1, ODAM, ARL14, GPR18, PXDNL, ARHGAP44, SERPINA9, SGO2, ABCA6, GALNT14, GPNMB, DHRS9, TTK, NIBAN1, LOC105377468, RAB42, RGS7, ARHGAP11B, SOX9, DIP2C, COMP, KCNH8, RNGTT, MAP3K8, SLCO5A1, LINC02562, KIFC1, SPINK2, LRRK2, LYPD6B, RGS13, TEX9, NLRP11, PCDHGA8, NMU, TNFRSF17, BTNL9, LRRC37A3, FHOD3, COX7BP1, TUBB3, HTRA4, GATM, LOC105375172, LINC01102, PARM1, DDX19A-DT, CYP27A1, DNAJC5B, ZNF185, SPA17P1, JUP, STAG3, LINC01857, GDF7, TSPYL5, PIP, PNMA8A, UGT2B17, PRAMEF11, MAB21L1, PSMA8, and TRGV5P.Attorney Docket No: 243735.000396

[0216] In an exemplary embodiment, the plurality of genes may include any four or more genes corresponding to FL5 selected from PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1.

[0217] In an exemplary embodiment, the genes are at least 1, 2, 3, or 4 genes from Table 3. In an exemplary embodiment, the at least 4 genes are at least 4, 5, 6, or 7 genes from Table 3. In another exemplary embodiment, the at least 4 genes selected from any of the genes in Table 3 are at least 4, 5, 6, or 7 genes.

[0218] In an exemplary embodiment, the at least 4, 5, 6, or 7 genes may include PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and / or CLK1.

[0219] In an exemplary embodiment, the genes for group 5 corresponding to FL5 comprise PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1.

[0220] In an exemplary embodiment, the genes are at least 1, 2, 3, or 4 genes from Table 1. In an exemplary embodiment, the at least 4 genes are at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, or 120 genes from Table 1. In another exemplary embodiment, the at least 4 genes selected from any of the genes in Table 1 are at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, or 120 genes.

[0221] In an exemplary embodiment, the at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, or 120 genes may include PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, CLK1, SEC31B, ADCY10P1, GOLGA8A, TTC14, PABPC1L,Attorney Docket No: 243735.000396 FCRL1, ACCS, ACYP1, WDR19, RUNX1-IT1, INTS6L, GABBR1, ERMN, ZNF83, PNN, ZBTB20, PWAR6, AHSA2P, GSAP, AMY2B, ZNF439, NACA, BTAF1, LOC286437, CCNL1, UICLM, LINC00926, SNORA25, NSUN5P1, ZNF600, SLC6A16, OGT, ASAP1-IT1, BOD1L1, ABCA5, DKFZP586I1420, MIR29B2CHG, SNORA72, ZNF605, FAM24B, FCRL5, SUZ12P1, GDPD3, LINC00653, PCF11-AS1, CROCCP2, LOC145474, BANK1, CCDC18, GEN1, LILRB1, ADAM28, LOC101927432, MALAT1, PHIP, CEP290, ITGB2-AS1, ZNF302, SUGT1-DT, MIR223HG, MIR6755, ZBTB41, LINC00494, TDRD6, ZDBF2, MIR3682, KTN1, KLHL5, SNHG10, COL4A4, PLEKHA8P1, CCDC191, MIR17HG, DBH-AS1, RESF1, STXBP5-AS1, LOC730101, PSMD6-AS2, ANKRD42-DT, SLC9A3-AS1, CCDC112, TCTN1, ZNF680, AIM2, LOC105377891, IL17RB, GALNT3, LOC613266, LOC105370834, LOC101927069, NPIPB15, VGF, MGARP, LINC00566, XAGE3, TXLNGY, MICA-AS1, UTY, SULT1A2, NSUN7, NOL4, PRKY, PALD1, LOC102723381, IFNA16, IL13RA2, MT3, LERFS, TUBA3C, LINC01013, LOC105374809, PTPN20, and / or HLA-DQA1.

[0222] In an exemplary embodiment, the genes for group 5 corresponding to FL5 comprise PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, CLK1, SEC31B, ADCY10P1, GOLGA8A, TTC14, PABPC1L, FCRL1, ACCS, ACYP1, WDR19, RUNX1-IT1, INTS6L, GABBR1, ERMN, ZNF83, PNN, ZBTB20, PWAR6, AHSA2P, GSAP, AMY2B, ZNF439, NACA, BTAF1, LOC286437, CCNL1, UICLM, LINC00926, SNORA25, NSUN5P1, ZNF600, SLC6A16, OGT, ASAP1-IT1, BOD1L1, ABCA5, DKFZP586I1420, MIR29B2CHG, SNORA72, ZNF605, FAM24B, FCRL5, SUZ12P1, GDPD3, LINC00653, PCF11-AS1, CROCCP2, LOC145474, BANK1, CCDC18, GEN1, LILRB1, ADAM28, LOC101927432, MALAT1, PHIP, CEP290, ITGB2-AS1, ZNF302, SUGT1-DT, MIR223HG, MIR6755, ZBTB41, LINC00494, TDRD6, ZDBF2, MIR3682, KTN1, KLHL5, SNHG10, COL4A4, PLEKHA8P1, CCDC191, MIR17HG, DBH-AS1, RESF1, STXBP5-AS1, LOC730101, PSMD6- AS2, ANKRD42-DT, SLC9A3-AS1, CCDC112, TCTN1, ZNF680, AIM2, LOC105377891, IL17RB, GALNT3, LOC613266, LOC105370834, LOC101927069, NPIPB15, VGF, MGARP, LINC00566, XAGE3, TXLNGY, MICA-AS1, UTY, SULT1A2, NSUN7, NOL4, PRKY, PALD1, LOC102723381, IFNA16, IL13RA2, MT3, LERFS, TUBA3C, LINC01013, LOC105374809, PTPN20, and HLA-DQA1.Attorney Docket No: 243735.000396

[0223] In an exemplary embodiment, the plurality of genes may include any four or more genes corresponding to FL6 selected from PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK.

[0224] In an exemplary embodiment, the genes are at least 1, 2, 3, or 4 genes from Table 3. In an exemplary embodiment, the at least 4 genes are at least 4, 5, 6, 7, or 8 genes from Table 3. In another exemplary embodiment, the at least 4 genes selected from any of the genes in Table 3 are at least 4, 5, 6, 7, or 8 genes.

[0225] In an exemplary embodiment, the at least 4, 5, 6, 7, or 8 genes may include PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and / or BIK.

[0226] In an exemplary embodiment, the genes for group 6 corresponding to FL6 comprise PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK.

[0227] In an exemplary embodiment, the genes are at least 1, 2, 3, or 4 genes from Table 1. In an exemplary embodiment, the at least 4 genes are at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, or 120 genes from Table 1. In another exemplary embodiment, the at least 4 genes selected from any of the genes in Table 1 are at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, or 120 genes.

[0228] In an exemplary embodiment, the at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, or 120 genes may include PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, LINC02901, ZNF215, ZNF385B, BIK, LINC01725, RUBCNL, ZNF804A, CHST15,Attorney Docket No: 243735.000396 LINC00525, ANKRD36BP2, FCRL2, TOP2A, CXXC5, EML6, MTCL1, TCF4, PBK, ST14, CDK1, TCL1A, PCDH9, GNAZ, HRK, FCRL4, FAM111B, BCL7A, MZB1, OAS1, HJURP, GUCY2C, KIF11, AICDA, RGS16, TJP2, CYB5R2, CEP55, CRYM, LOC105372217, ASPM, KIF20A, ID3, BACH2, WNT5A, SOX5, FBP1, MME, UBE2C, RASSF6, CDC20, LOC105374869, NCAPG, CCL22, KIF4A, FAM169A, CDCA8, CCNB2, MYBL2, RRM2, MPEG1, MAP2K6, CD9, S100Z, ELL3, SLC22A15, CCL17, BEX3, E2F8, SCAT1, IGF2BP3, UCHL1, LOC644656, BEND4, CD1C, GNG11, CCL20, SERHL2, FCRL3, FAM167A, JCHAIN, GPR160, CORO2B, ABCB4, SMAD1, LOC112268421, EPCAM, ADA, VPREB1, IGKV1D-8, CD1D, CD24, IGHM, IGLL1, TUBA1C, LINC02397, TCL1B, KCNK12, CPXM1, ZBED2, C12orf75, ECHDC3, ARMCX2, TFPI2, ZCCHC18, CAMTA1-DT, CCDC85A, SOX2- OT, HOXA10, EPHB1, UBXN7-AS1, CRNDE, PLA2G10, XIST, KRT1, and / or LINC02002.

[0229] In an exemplary embodiment, the genes for group 6 corresponding to FL6 comprise PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, LINC02901, ZNF215, ZNF385B, BIK, LINC01725, RUBCNL, ZNF804A, CHST15, LINC00525, ANKRD36BP2, FCRL2, TOP2A, CXXC5, EML6, MTCL1, TCF4, PBK, ST14, CDK1, TCL1A, PCDH9, GNAZ, HRK, FCRL4, FAM111B, BCL7A, MZB1, OAS1, HJURP, GUCY2C, KIF11, AICDA, RGS16, TJP2, CYB5R2, CEP55, CRYM, LOC105372217, ASPM, KIF20A, ID3, BACH2, WNT5A, SOX5, FBP1, MME, UBE2C, RASSF6, CDC20, LOC105374869, NCAPG, CCL22, KIF4A, FAM169A, CDCA8, CCNB2, MYBL2, RRM2, MPEG1, MAP2K6, CD9, S100Z, ELL3, SLC22A15, CCL17, BEX3, E2F8, SCAT1, IGF2BP3, UCHL1, LOC644656, BEND4, CD1C, GNG11, CCL20, SERHL2, FCRL3, FAM167A, JCHAIN, GPR160, CORO2B, ABCB4, SMAD1, LOC112268421, EPCAM, ADA, VPREB1, IGKV1D-8, CD1D, CD24, IGHM, IGLL1, TUBA1C, LINC02397, TCL1B, KCNK12, CPXM1, ZBED2, C12orf75, ECHDC3, ARMCX2, TFPI2, ZCCHC18, CAMTA1-DT, CCDC85A, SOX2-OT, HOXA10, EPHB1, UBXN7-AS1, CRNDE, PLA2G10, XIST, KRT1, and LINC02002.

[0230] In an exemplary embodiment, the plurality of genes may include any four or more genes corresponding to FL7 selected from SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

[0231] In an exemplary embodiment, the genes are at least 1, 2, 3, or 4 genes from Table 3. In an exemplary embodiment, the at least 4 genes are at least 4, 5, 6, 7, 8, 9, or 10 genes from TableAttorney Docket No: 243735.000396 3. In another exemplary embodiment, the at least 4 genes selected from any of the genes in Table 3 are at least 4, 5, 6, 7, 8, 9, or 10 genes.

[0232] In an exemplary embodiment, the at least 4, 5, 6, 7, 8, 9, or 10 genes may include SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and / or TET2.

[0233] In an exemplary embodiment, the genes for group 7 corresponding to FL7 comprise SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

[0234] In an exemplary embodiment, the genes are at least 1, 2, 3, or 4 genes from Table 1. In an exemplary embodiment, the at least 4 genes are at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, or 41 genes from Table 1. In another exemplary embodiment, the at least 4 genes selected from any of the genes in Table 1 are at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, or 41 genes.

[0235] In an exemplary embodiment, the at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, or 41 genes may include RN7SKP187, SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, LINC00597, CEBPZ, NRIP1, PTGDS, DHX9P1, TET2, CCDC186, ZNF292, FAM151A, APOC1, TIMD4, SUPT16H, A2M-AS1, ATRX, EGFLAM, PSD3, HS3ST3A1, PCOLCE2, CSTA, IL32, CLU, ITIH3, SOX8, GAPT, FDCSP, VDAC1P3, MMP1, TRIM48, TSIX, LOC105375222, MACROD2, LOC102723684, and / or LOC105374042.

[0236] In an exemplary embodiment, the genes for group 7 corresponding to FL7 comprise RN7SKP187, SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, LINC00597, CEBPZ, NRIP1, PTGDS, DHX9P1, TET2, CCDC186, ZNF292, FAM151A, APOC1, TIMD4, SUPT16H, A2M-AS1, ATRX, EGFLAM, PSD3, HS3ST3A1, PCOLCE2, CSTA, IL32, CLU, ITIH3, SOX8, GAPT, FDCSP, VDAC1P3, MMP1, TRIM48, TSIX, LOC105375222, MACROD2, LOC102723684, and LOC105374042.

[0237] In an exemplary embodiment, the human subject may be diagnosed with FL, and the gene expression score may be configured to classify the subject into one of seven FL subtypes.

[0238] In an exemplary embodiment, the genes corresponding to FL1 comprise DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF, the genes corresponding toAttorney Docket No: 243735.000396 FL2 comprise GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK, the genes corresponding to FL3 comprise ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3, the genes corresponding to FL4 comprise GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX, the genes corresponding to FL5 comprise PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1, the genes corresponding to FL6 comprise PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK, and the genes corresponding to FL7 comprise SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

[0239] In an exemplary embodiment, the genes for group 1 correspond to FL1, the genes for group 2 correspond to FL2, the genes for group 3 correspond to FL3, the genes for group 4 correspond to FL4, the genes for group 5 correspond to FL5, the genes for group 6 correspond to FL6, and the genes for group 7 correspond to FL7.

[0240] In an exemplary embodiment, the genes for group 1 corresponding to FL1 comprise DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF, the genes for group 2 corresponding to FL2 comprise GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK, the genes for group 3 corresponding to FL3 comprise ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3, the genes for group 4 corresponding to FL4 comprise GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX, the genes for group 5 corresponding to FL5 comprise PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1, the genes for group 6 corresponding to FL6 comprise PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK, and the genes for group 7 corresponding to FL7 comprise SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

[0241] In an exemplary embodiment, the determination of the expression level for genes from each of the 7 groups may be used to classify the human subject into one of 7 FL subtypes.

[0242] In an exemplary embodiment, the determination of the biological subtype of FL may be based on the level of one or more RNA transcripts in a biological sample containing tumor cells.

[0243] In an exemplary embodiment, the method may further include assigning one or more RNA transcripts to 1 of 7 FL subtypes, calculating a quantitative score representing the relative level of RNA expression of the tumor cells for the genes defining each of the 7 subtypes, andAttorney Docket No: 243735.000396 classifying unfractionated tumor samples as 1 of the 7 subtypes based on the highest of the 7 scores.

[0244] In an exemplary embodiment, the enrichment score for each of the 7 FL signatures is calculated based on the degree to which the genes from each gene set are overrepresented at the top or bottom of the ranked list, given a ranked gene list derived from a normalized gene expression matrix of an FL sample.

[0245] In an exemplary embodiment, the enrichment score represents a running-sum statistic which increases when a gene is encountered by walking down the ranked list and decreases when the gene is not encountered and samples are assigned to 1 of the 7 transcriptional subtype classifications based on the highest enrichment score.

[0246] In an exemplary embodiment, the method of classifying a human subject diagnosed with follicular lymphoma (FL) into 7 FL subtypes (FL1-FL7) comprises: a) determining in a tumor sample obtained from the subject the expression level of at least 4 genes from each of 7 groups of genes provided in Table 1, wherein the 7 groups of genes correspond to 7 FL subtypes (FL1-FL7) as listed in Table 1; b) calculating a gene expression score for the tumor sample for each of the 7 groups of genes of step (a); c) comparing the 7 gene expression scores calculated in step (b) to each other and determining the highest gene expression score among the 7 gene expression scores; and d) classifying the subject into the FL subtype which corresponds to the highest gene expression score determined in step (c).

[0247] In an exemplary embodiment, the method of classifying a human subject diagnosed with follicular lymphoma (FL) into 7 FL subtypes (FL1-FL7) comprises: a) determining in a tumor sample obtained from the subject the expression level of at least 4 genes from each of 7 groups of genes provided in Table 3, wherein the 7 groups of genes correspond to 7 FL subtypes (FL1-FL7) as listed in Table 3; b) calculating a gene expression score for the tumor sample for each of the 7 groups of genes of step (a); c) comparing the 7 gene expression scores calculated in step (b) to each other and determining the highest gene expression score among the 7 gene expression scores; and d) classifying the subject into the FL subtype which corresponds to the highest gene expression score determined in step (c).

[0248] In an exemplary embodiment, a method for classifying a human subject diagnosed with follicular lymphoma (FL) into 7 FL subtypes (FL1-FL7), comprises: determining in a tumor sample obtained from the subject the expression level of at least 4 genes from each of 7 groupsAttorney Docket No: 243735.000396 of genes, wherein the genes are selected from DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF, corresponding to FL1; GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK, corresponding to FL2; ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3, corresponding to FL3; GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX, corresponding to FL4; PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1, corresponding to FL5; PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK, corresponding to FL6; and SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2 corresponding to FL7.

[0249] In an exemplary embodiment, a method for classifying a human subject diagnosed with follicular lymphoma (FL) into 7 FL subtypes (FL1-FL7), comprises: (a) determining in a tumor sample obtained from the subject the expression level of at least 4 genes from each of 7 groups of genes, wherein the genes are selected from DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF, corresponding to FL1; GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK, corresponding to FL2; ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3, corresponding to FL3; GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX, corresponding to FL4; PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1, corresponding to FL5; PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK, corresponding to FL6; and SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2 corresponding to FL7, (b) calculating a gene expression score for the tumor sample for each of the 7 groups of genes of step (a), (c) comparing the 7 gene expression scores calculated in step (b) to each other and determining the highest gene expression score among the 7 gene expression scores, and (d) classifying the subject into the FL subtype which corresponds to the highest gene expression score determined in step (c).

[0250] In an exemplary embodiment, the method may include administering to the subject a treatment effective for the subject’s determined FL subtype.

[0251] In an exemplary embodiment, the treatment for the subject classified as FL1 comprises administering a therapeutically effective amount of a compound selected from an inhibitor of Bruton’s tyrosine kinase (BTK), an anti-CD79b agent (e.g., Polatuzumab vedotin), anti-CD19Attorney Docket No: 243735.000396 (e.g., Tafasitamab), an inhibitor of PD1, an agent targeting neutrophilic myeloid-derived suppressor cells (PMN-MDSCs), or any combinations thereof.

[0252] In an exemplary embodiment, the treatment for the subject classified as FL2 comprises administering a therapeutically effective amount of a compound selected from Lenalidomide, an inhibitor of Bruton’s tyrosine kinase (BTK), Ipilimumab, an inhibitor of PD-L1, an inhibitor of Janus kinase (JAK), or any combinations thereof.

[0253] In an exemplary embodiment, the treatment for the subject classified as FL3 comprises administering a therapeutically effective amount of an inhibitor of Janus kinase (JAK).

[0254] In an exemplary embodiment, the treatment for the subject classified as FL4 comprises administering a therapeutically effective amount of an inhibitor of enhancer of zeste homolog 2 (EZH2), or an inhibitor of polyadenosine 5'-diphosphoribose polymerase (PARP), or a combination thereof.In an exemplary embodiment, the treatment for the subject classified as FL4 comprises administering a therapeutically effective amount of Tazemostat, or Olaparib, or a combination thereof.

[0255] In an exemplary embodiment, the treatment for the subject classified as FL5 comprises administering a therapeutically effective amount of a compound selected from Lenalidomide, an inhibitor of Bruton’s tyrosine kinase (BTK), anti-CD19 (e.g., Tafasitamab), an inhibitor of Janus kinase (JAK), an agent targeting neutrophilic myeloid-derived suppressor cells (PMN-MDSCs), or any combinations thereof.

[0256] In an exemplary embodiment, the treatment for the subject classified as FL6 comprises administering a therapeutically effective amount of a compound selected from a proteosome inhibitor, an anti-CD79b agent (e.g., Polatuzumab vedotin), an agent targeting neutrophilic myeloid-derived suppressor cells, or any combinations thereof.

[0257] In an exemplary embodiment, the treatment for the subject classified as FL7 comprises administering a therapeutically effective amount of Lenalidomide, or an inhibitor of Janus kinase (JAK), or a combination thereof.

[0258] In an exemplary embodiment, the treatment further comprises administering a standard immunochemotherapy.

[0259] In an exemplary embodiment, the standard immunochemotherapy comprises administering a therapeutically effective amount of a compound selected from rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP); rituximab,Attorney Docket No: 243735.000396 cyclophosphamide, vincristine, and prednisone (R-CVP); rituximab and bendamustine (BR); obinutuzumab, cyclophosphamide, doxorubicin, vincristine, and prednisone; obinutuzumab, cyclophosphamide, vincristine, and prednisone; obinutuzumab and bendamustine; and any combinations thereof.

[0260] As used herein, the term "combination" is used by the combination agents as defined above dependently or independently, or by the use of different fixed combinations with different amounts of combination agents, i.e. simultaneously or at different times. Refers to a kit of compositions or parts that can be administered. The combination agents can then be administered, for example, simultaneously or staggered in time (i.e., at different times and at equal or different time intervals for any part of the kit). The ratio of the total amount of combination agents administered in a combination can vary, e.g., to address the needs of a subpopulation of patients to be treated or the needs of a single patient, and different needs are the age of the patient, it can be due to gender, weight, etc.

[0261] In an exemplary embodiment, the treatment for the subject’s determined FL subtype is administered before, simultaneously with, or after the administration of the standard immunochemotherapy.

[0262] In some embodiments, the treatment for the subject’s determined FL subtype is administered to the subject simultaneously or sequentially with the standard immunochemotherapy. As a non-limiting example, the treatment for the subject’s determined FL subtype can be administered to the subject simultaneously with the standard immunochemotherapy in one composition. As another non-limiting example, the treatment for the subject’s determined FL subtype can be administered to the subject simultaneously with the standard immunochemotherapy in different compositions. As yet another non-limiting example, the treatment for the subject’s determined FL subtype can be administered to the subject sequentially with the standard immunochemotherapy in different compositions.

[0263] In some embodiments, when the treatment for the subject’s determined FL subtype and the standard immunochemotherapy are administered to the subject sequentially (e.g., in different compositions), the treatment for the subject’s determined FL subtype may be administered as a first component of a dosing regimen and the standard immunochemotherapy may be administered as a second component of a dosing regimen (i.e., the treatment for the subject’s determined FL subtype may be administered before the standard immunochemotherapy).Attorney Docket No: 243735.000396

[0264] In some embodiments, when the treatment for the subject’s determined FL subtype and the standard immunochemotherapy are administered to the subject sequentially (e.g., in different compositions), the standard immunochemotherapy may be administered as a first component of a dosing regimen and the treatment for the subject’s determined FL subtype may be administered as a second component of a dosing regimen (i.e., the standard immunochemotherapy may be administered before the treatment for the subject’s determined FL subtype).

[0265] In an exemplary embodiment, the inhibitor of Bruton’s tyrosine kinase (BTK) is ibrutinib, acalabrutinib, or pirtobrutinib.

[0266] In an exemplary embodiment, the inhibitor of PD1 is nivolumab, pembrolizumab, cemiplimab, dostarlimab, or retifanlimab.

[0267] In an exemplary embodiment, the agent targeting neutrophilic myeloid-derived suppressor cells (PMN-MDSCs) is all-trans retinoic acid (ATRA).

[0268] In an exemplary embodiment, the inhibitor of PD-L1 is atezolizumab, avelumab or durvalumab.

[0269] In an exemplary embodiment, the inhibitor of Janus kinase (JAK) is ruxolitinib, baricitinib, tofacitinib, fedratinib, itacitinib, momelotinib, or patricinib.

[0270] In an exemplary embodiment, the proteosome inhibitor is bortezomib, carfilzomib or ixazomib.

[0271] Any of the various methods or compositions (e.g., pharmaceutical compositions) described herein may be used in the practice of various therapeutic applications (in vivo and ex vivo) and as research tools.

[0272] In an exemplary embodiment, a method of treating a subject diagnosed with follicular lymphoma (FL) comprises: a) determining in a biological sample obtained from the subject the expression level of at least 4 genes from each of 7 groups of genes provided in Table 1, wherein the 7 groups of genes correspond to 7 FL subtypes (FL1-FL7) as listed in Table 1; b) calculating a gene expression score for the biological sample for each of the 7 groups of genes of step (a); c) comparing the 7 gene expression scores calculated in step (b) to each other and determining the highest gene expression score among the 7 gene expression scores; d) classifying the subject into the FL subtype which corresponds to the highest gene expression score determined in step (c); and (e) administering to the subject classified in step (d) a treatment effective for the subject’s determined FL subtype.Attorney Docket No: 243735.000396

[0273] In an exemplary embodiment, the subject has been diagnosed with FL based on evaluation of histology and / or immunophenotypic features.

[0274] In some embodiments, the subject is human. The human can be a patient.

[0275] In an exemplary embodiment, step (b) of the method comprises: generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 1; generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreases when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

[0276] In an exemplary embodiment, step (b) of the method comprises: representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative; performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes provided in Table 1, and resulting in a mixture coefficient matrix; and determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.

[0277] In an exemplary embodiment, step (c) of the method comprises: determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

[0278] In an exemplary embodiment, step (a) of the method comprises: determining the expression level of at least 4 genes from each of the 7 groups of genes provided in Table 3 wherein the 7 groups of genes correspond to the 7 FL subtypes (FL1-FL7) as listed in Table 3.

[0279] In an exemplary embodiment, the method of treating a subject diagnosed with follicular lymphoma comprises: a) determining in a biological sample obtained from the subject the expression level of at least 4 genes from each of 7 groups of genes provided in Table 3, wherein the 7 groups of genes correspond to 7 FL subtypes (FL1-FL7) as listed in Table 3; b) calculating a gene expression score for the biological sample for each of the 7 groups of genes of step (a); c) comparing the 7 gene expression scores calculated in step (b) to each other and determining the highest gene expression score among the 7 gene expression scores; d) classifying the subject intoAttorney Docket No: 243735.000396 the FL subtype which corresponds to the highest gene expression score determined in step (c); and (e) administering to the subject classified in step (d) a treatment effective for the subject’s determined FL subtype.

[0280] In an exemplary embodiment, step (b) of the method comprises: generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 3; generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreases when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

[0281] In an exemplary embodiment, step (b) of the method comprises: representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative; performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes provided in Table 3, and resulting in a mixture coefficient matrix; and determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.

[0282] In an exemplary embodiment, step (c) of the method comprises: determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

[0283] In an exemplary embodiment, the genes for group 1 corresponding to FL1 comprise DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF.

[0284] In an exemplary embodiment, the genes for group 2 corresponding to FL2 comprise GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK.

[0285] In an exemplary embodiment, the genes for group 3 corresponding to FL3 comprise ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3.

[0286] In an exemplary embodiment, the genes for group 4 corresponding to FL4 comprise GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX.

[0287] In an exemplary embodiment, the genes for group 5 corresponding to FL5 comprise PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1.Attorney Docket No: 243735.000396

[0288] In an exemplary embodiment, the genes for group 6 corresponding to FL6 comprise PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK.

[0289] In an exemplary embodiment, the genes for group 7 corresponding to FL7 comprise SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

[0290] In an exemplary embodiment, the genes for group 1 corresponding to FL1 comprise DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF, the genes for group 2 corresponding to FL2 comprise GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK, the genes for group 3 corresponding to FL3 comprise ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3, the genes for group 4 corresponding to FL4 comprise GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX, the genes for group 5 corresponding to FL5 comprise PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1, the genes for group 6 corresponding to FL6 comprise PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK, and the genes for group 7 corresponding to FL7 comprise SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

[0291] In an exemplary embodiment, the treatment for the subject classified as FL1 comprises administering a therapeutically effective amount of a compound selected from an inhibitor of Bruton’s tyrosine kinase (BTK), an anti-CD79b agent (e.g., Polatuzumab vedotin), anti-CD19 (e.g., Tafasitamab), an inhibitor of PD1, an agent targeting neutrophilic myeloid-derived suppressor cells (PMN-MDSCs), or any combinations thereof.

[0292] In an exemplary embodiment, the treatment for the subject classified as FL2 comprises administering a therapeutically effective amount of a compound selected from Lenalidomide, an inhibitor of Bruton’s tyrosine kinase (BTK), Ipilimumab, an inhibitor of PD-L1, an inhibitor of Janus kinase (JAK), or any combinations thereof.

[0293] In an exemplary embodiment, the treatment for the subject classified as FL3 comprises administering a therapeutically effective amount of an inhibitor of Janus kinase (JAK).

[0294] In an exemplary embodiment, the treatment for the subject classified as FL4 comprises administering a therapeutically effective amount of an inhibitor of enhancer of zeste homolog 2 (EZH2)), or an inhibitor of polyadenosine 5'-diphosphoribose polymerase (PARP), or a combination thereof. In an exemplary embodiment, the treatment for the subject classified asAttorney Docket No: 243735.000396 FL4 comprises administering a therapeutically effective amount of Tazemostat, or Olaparib, or a combination thereof.

[0295] In an exemplary embodiment, the treatment for the subject classified as FL5 comprises administering a therapeutically effective amount of a compound selected from Lenalidomide, an inhibitor of Bruton’s tyrosine kinase (BTK), an anti-CD19 agent (e.g., Tafasitamab), an inhibitor of Janus kinase (JAK), an agent targeting neutrophilic myeloid-derived suppressor cells (PMN- MDSCs), or any combinations thereof.

[0296] In an exemplary embodiment, the treatment for the subject classified as FL6 comprises administering a therapeutically effective amount of a compound selected from a proteosome inhibitor, an anti-CD79b agent (e.g., Polatuzumab vedotin), an agent targeting neutrophilic myeloid-derived suppressor cells, or any combinations thereof.

[0297] In an exemplary embodiment, the treatment for the subject classified as FL7 comprises administering a therapeutically effective amount of Lenalidomide, or an inhibitor of Janus kinase (JAK), or a combination thereof.

[0298] In an exemplary embodiment, the treatment further comprises administering a standard immunochemotherapy.

[0299] In an exemplary embodiment, the standard immunochemotherapy comprises administering a therapeutically effective amount of a compound selected from rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP); rituximab, cyclophosphamide, vincristine, and prednisone (R-CVP); rituximab and bendamustine (BR); obinutuzumab, cyclophosphamide, doxorubicin, vincristine, and prednisone; obinutuzumab, cyclophosphamide, vincristine, and prednisone; obinutuzumab and bendamustine; and any combinations thereof.

[0300] An immunochemotherapeutic or immunochemotherapeutic agent (i.e., an anti-cancer agent), is used according to its ordinary meaning, referring to a chemical composition, biologic, protein, nucleic acid, drug, inhibitor, antagonist, modulator, and / or compound having the ability to inhibit the growth or proliferation of cells and / or antineoplastic properties. In some aspects, an anti-cancer agent is a therapeutic agent approved by the FDA or equivalent or similar regulatory agency, for treating cancer.Attorney Docket No: 243735.000396

[0301] In an exemplary embodiment, the treatment for the subject’s determined FL subtype is administered before, simultaneously with, or after the administration of the standard immunochemotherapy.

[0302] In some embodiments, the treatment for the subject’s determined FL subtype is administered to the subject simultaneously or sequentially with the standard immunochemotherapy. As a non-limiting example, the treatment for the subject’s determined FL subtype can be administered to the subject simultaneously with the standard immunochemotherapy in one composition. As another non-limiting example, the treatment for the subject’s determined FL subtype can be administered to the subject simultaneously with the standard immunochemotherapy in different compositions. As yet another non-limiting example, the treatment for the subject’s determined FL subtype can be administered to the subject sequentially with the standard immunochemotherapy in different compositions.

[0303] In some embodiments, when the treatment for the subject’s determined FL subtype and the standard immunochemotherapy are administered to the subject sequentially (e.g., in different compositions), the treatment for the subject’s determined FL subtype may be administered as a first component of a dosing regimen and the standard immunochemotherapy may be administered as a second component of a dosing regimen (i.e., the treatment for the subject’s determined FL subtype may be administered before the standard immunochemotherapy).

[0304] In some embodiments, when the treatment for the subject’s determined FL subtype and the standard immunochemotherapy are administered to the subject sequentially (e.g., in different compositions), the standard immunochemotherapy may be administered as a first component of a dosing regimen and the treatment for the subject’s determined FL subtype may be administered as a second component of a dosing regimen (i.e., the standard immunochemotherapy may be administered before the treatment for the subject’s determined FL subtype).

[0305] In some embodiments, the treatment for the subject’s determined FL subtype and / or the standard immunochemotherapy can be administered to the subject by way of any route of administration of the present disclosure. As a non-limiting example, the treatment for the subject’s determined FL subtype and / or the standard immunochemotherapy can be administered orally or intravenously.

[0306] The route of administration and the type of pharmaceutically acceptable carrier will depend on the condition being treated and the type of mammal. Formulations containing theAttorney Docket No: 243735.000396 active compound may be prepared such that the activity of the compound is not disrupted during the process and the compound can reach its site of action without disruption. In some cases, it may be necessary to protect the compound by means known in the art, such as microencapsulation. Similarly, the route of dosing selected should be such that the compound reaches its site of action.

[0307] The compounds or pharmaceutically acceptable salts thereof described herein can be prepared in parenteral dosage forms such as those suitable for, e.g., intravascular (intravenous or intraarterial), intraperitoneal, subcutaneous, intradermal, intratumoral, intraventricular, intrapleural or intramuscular administration delivery. Suitable pharmaceutical forms for injectable use include sterile injectable or dispersions and sterile powders for the immediate preparation of sterile injectable solutions. They must be stable under manufacturing and storage conditions and protected from reduction or oxidation and the contaminating effects of microorganisms such as bacteria or fungi.

[0308] Other pharmaceutical forms include the oral and enteral formulations, where the active compound can be formulated with an inert diluent or an assimilated edible carrier, or encapsulated in hard or softshell gelatin capsules. The formulations can also be tableted, or it can be incorporated directly into diet foods. For oral therapeutic administration, the active compound is taken up with excipients and used in the form of ingestible tablets, buccal or sublingual tablets, troches, capsules, elixirs, suspensions, syrups, wafers, etc. The amount of active compound in such a therapeutically useful composition is such that an appropriate dose can be obtained.

[0309] Liquid formulations can also be administered enterally via the stomach or esophageal canal. The enteral preparation can be prepared in the form of a suppository by mixing with a suitable base such as an emulsifying base or a water-soluble base. It is possible, but not necessary, to administer the compound of the present disclosure topically, intranasally, intravaginally, intraocularly or the like.

[0310] In certain embodiments, the method of treating disease is in a patient that has received no prior treatment. In certain embodiments, the method of treating disease is in a patient that has received a prior treatment with therapeutic agent(s), (e.g., immunochemotherapeutic agent(s)). In certain embodiments, the patent has developed an acquired resistance to the previous treatment of one or more chemotherapeutic agents or immunotherapies. In further embodiments, the patentAttorney Docket No: 243735.000396 has developed bypass resistance to the previous treatment of one or more chemotherapeutic agents or immunotherapies.

[0311] In the methods of treatment described herein, additional therapeutic agents can be used in combination with the therapeutic agents described herein that are suitable to the disease being treated (e.g., cancer). In some aspects, the provided methods of treatment further include administering an additional therapeutic agent to the subject. The additional therapeutic agent may be a drug, compound, inhibitor, modulator, or antagonist, having the ability to inhibit the growth or proliferation of cells and / or having antineoplastic properties. In some aspects, the additional therapeutic agent can be an immunochemotherapeutic agent. In further aspects, the additional therapeutic agent is a therapeutic agent approved by the FDA or an equivalent or similar regulatory agency, for treating cancer. In certain aspects, the additional therapeutic agent is radiation therapy. Suitable additional therapeutic agents include, but are not limited to anesthetics, anticonvulsants, analgesics, allosteric inhibitors, antihelmintics, analeptics, antifungals, antirheumatic agents, anticholinesterases, anticholinergic agents, antibiotics, antineoplastic agents, antimuscarinic agents, growth factors, anabolic steroids, hematological agents, antimycobacterial agents, psychotherapeutic agents, antiviral agents, neural blocking agents, immunological agents, anti-inflammatory agents, protease inhibitors, corticosteroids, anticoagulants, antihistamines, antiprotozoal agents, dopaminergics, muscarinics, vitamins, and hormones. The choice of agent and dosage can be determined by one of skill in the art based on several factors, primarily the given disease being treated.

[0312] In some embodiments, the treatment for the subject’s determined FL subtype and / or the standard immunochemotherapy, or pharmaceutical composition thereof, is administered as a weight-based dose to a subject.

[0313] A "weight-based dose" (e.g., a dose measured in mg / kg) as used herein, is a dose of the treatment for the subject’s determined FL subtype and / or the standard immunochemotherapy that will vary depending on the subject's weight.

[0314] In other embodiments, the treatment for the subject’s determined FL subtype and / or the standard immunochemotherapy, or pharmaceutical composition thereof, is administered as a fixed dose to a subject.Attorney Docket No: 243735.000396

[0315] A "fixed dose" (e.g., a dose measured in mg) means that one dose of the treatment for the subject’s determined FL subtype and / or the standard immunochemotherapy, is used consistently for all subjects regardless of any subject-specific factors, e.g., weight.

[0316] In some embodiments, the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype is administered at a dose of about 0.05 mg / kg to about 1 g / kg. In some embodiments, the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype is administered at a dose of about 10 mg to about 100 mg,

[0317] In certain embodiments, the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype is administered to a subject at a dosing frequency of about five times a week, about four times a week, about twice a week, about once a week, about once every two weeks, about once every three weeks, about once a month, about once every five weeks, about once every six weeks, about once every seven weeks, about once every two months, about once every three months, or less frequently so long as an effective therapeutic response is achieved. In certain embodiments, the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype can be administered to a subject at a dosing frequency of about six times a year, about four times a year, about twice a year, about once a year, about once every two years, about once every three years, about once every four years, about once every five years, about once every six years, about once every eight years, about once a decade, about once every twelve years, about once every fifteen years, or less frequently so long as an effective therapeutic response is achieved.

[0318] Dosage ranges and frequency of administration of a standard immunochemotherapy and / or a treatment for the subject’s determined FL subtype as described herein can vary depending on the parameters of a specific subject, the route of administration, the type of medical condition, and / or the severity of the medical condition. A more accurate dose may depend on the subject in which it is administered, e.g., a lower dose may be used if the subject in which it is administered is juvenile and a higher dose may be used if the subject is adult. In some embodiments, a more accurate dose may depend on the subject weight.

[0319] In some embodiments, the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype may be administered following a repeated dosing regimen wherein the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype may be administered an initial time (e.g., as an initial dose) and then may be re-Attorney Docket No: 243735.000396 administered at any amount for any number of subsequent times thereafter over the time course of treatment. For example, the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype may be re-administered one time, two times, three times, four times, five times, six times, seven times, eight times, nine times, ten times, fifteen times, twenty times, or more, over the time course of treatment which may occur over any amount of time (e.g., days, weeks, or years). In certain embodiments, when the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype, the treatment which is / are administered first in a repeat dosing regimen may comprise the same treatment which is / are re- administered second or thereafter in the regimen, for any number of subsequent times thereafter. In certain embodiments, when the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype, the treatment which is / are administered first in a repeat dosing regimen may comprise a different treatment than is / are re-administered second or thereafter in the regimen, for any number of subsequent times thereafter.

[0320] In certain embodiments, the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype, may be administered using a stepwise dosing regimen. Stepwise dosing can refer to dividing dosing of the same treatment over multiple administrations. In certain embodiments, the dosing of the same treatment is / are broken up one time, two times, three times, four times, five times, six times, seven times, eight times, nine times, ten times, fifteen times, twenty times, or more, over the time course of the treatment which can occur over any period of time (e.g., over any number of days, weeks, or years). In certain embodiments, when a stepwise dose regimen is used in the administration of the treatment, the regimen may encompass an increase or decrease in dosage levels with each administration of the treatment.

[0321] In certain embodiments, multiple doses of a standard immunochemotherapy and / or a treatment for the subject’s determined FL subtype are administered over a defined time course.

[0322] In some embodiments, the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype are administered simultaneously.

[0323] In some embodiments, the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype are administered simultaneously in one composition.

[0324] In some embodiments, the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype are administered simultaneously in different compositions.Attorney Docket No: 243735.000396

[0325] In some embodiments, the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype are administered sequentially.

[0326] In certain embodiments, the standard immunochemotherapy is administered to a subject in combination with a treatment for the subject’s determined FL subtype. The standard immunochemotherapy can be administered prior to, simultaneously with, and / or after the treatment for the subject’s determined FL subtype.

[0327] In certain embodiments, when the standard immunochemotherapy is administered prior to, simultaneously with, and / or after the treatment for the subject’s determined FL subtype, the standard immunochemotherapy is administered one time, two times, three times, four times, five times, six times, seven times, eight times, nine times, ten times, twelve times, fourteen times, fifteen times, eighteen times, or twenty times or more, prior to, simultaneously with, and / or after the administration of the treatment for the subject’s determined FL subtype. In certain embodiments, when a standard immunochemotherapy is administered with a repeat dosing regimen, a treatment for the subject’s determined FL subtype may be administered once, twice, or any number of times prior to, simultaneously with, and / or after a first, second, and / or any number of subsequent administrations of the standard immunochemotherapy thereafter.

[0328] In some embodiments, a standard immunochemotherapy may be administered to a subject separately from a treatment for the subject’s determined FL subtype.

[0329] In some embodiments, when a standard immunochemotherapy and a treatment for the subject’s determined FL subtype are administered separately, the standard immunochemotherapy may also be administered simultaneously with the treatment for the subject’s determined FL subtype. In certain embodiments, the standard immunochemotherapy is administered one or multiple times during the administration of the treatment for the subject’s determined FL subtype. In another embodiment, the treatment for the subject’s determined FL subtype is administered one or multiple times during the administration of the standard immunochemotherapy.

[0330] In certain embodiments, a standard immunochemotherapy and a treatment for the subject’s determined FL subtype may be administered separately over a defined time period. In some embodiments, multiple doses of a standard immunochemotherapy and / or a treatment for the subject’s determined FL subtype may be administered to a subject through a defined time course. The methods may comprise sequentially administering to a subject multiple doses of aAttorney Docket No: 243735.000396 standard immunochemotherapy and / or a treatment for the subject’s determined FL subtype. In certain embodiments, when the standard immunochemotherapy and treatment for the subject’s determined FL subtype are administered sequentially, the standard immunochemotherapy can be administered either before and / or in between each of the administrations of the treatment for the subject’s determined FL subtype.

[0331] The term “sequentially administering”, as used herein, means that each dose of the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype, is administered to the subject at various points in time, e.g., on different days separated by an interval that may comprise hours, days, weeks, months, or years. In certain embodiments, the methods comprise sequentially administering to the subject a single initial dose of the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype, followed by one or multiple secondary doses of the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype, and optionally followed by one or multiple tertiary doses of the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype.

[0332] As used herein, the terms "initial dose," "secondary dose(s)," and "tertiary dose(s)" refer to the sequential sequence of administration of the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype. Thus, the "initial dose" is the dose administered at the beginning of the treatment regimen schedule (i.e., the "loading dose"), the "secondary dose(s)” is / are the dose(s) which are administered after the “initial dose”, and the "tertiary dose(s)” is / are the dose(s) which are administered after the “secondary dose(s)”.

[0333] In certain embodiments, the initial, secondary, and tertiary doses may all contain the same amount of the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype but may differ from one another in the frequency of administration. In another embodiment, the amounts of the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype contained in the initial, secondary, and / or tertiary doses varies from one another (e.g., increased or decreased as appropriate) during the course of treatment. In some embodiments, one or multiple (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) doses are administered in the beginning of the treatment regimen as loading doses (i.e., initial doses) followed by subsequent doses (e.g., secondary or tertiary doses) that are administered less frequently, known as "maintenance doses". In certain embodiments, the initial dose and the one or more subsequent doses (i.e., secondary or tertiary doses) each contain the same amount of theAttorney Docket No: 243735.000396 standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype. In some embodiments, the initial dose comprises an initial amount of the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype and the one or multiple secondary doses each comprise a different amount of the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype. In one embodiment, the first amount of the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype can be 1.5x, 2x, 2.5x, 3x, 3.5x, 4x, 4.5x, 5x, 10x, or more than the second amount of the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype.

[0334] In certain embodiments, each secondary dose(s) and / or tertiary dose(s) is / are administered 1 to 20 (e.g., 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5, 11, 11.5, 12, 12.5, 13, 13.5, 14, 14.5, 15, 15.5, 16, 16.5, 17, 17.5, 18, 18.5, 19, 19.5, 20, 20.5 or more) weeks after the immediately preceding dose. As used herein, the phrase "the immediately preceding dose," means, in a sequence of multiple administrations, the dose of the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype that is administered to a subject before the administration of the very next subsequent dose in the sequence with no intervening doses.

[0335] The methods may comprise administering to a subject any number of secondary doses and / or tertiary doses of a standard immunochemotherapy and / or a treatment for the subject’s determined FL subtype. In some embodiments, only one secondary dose is administered to the subject. In certain embodiments, two or more secondary doses are administered to the subject. Likewise, in some embodiments, only one tertiary dose is administered to the subject. In some embodiments, two or more tertiary doses are administered to the subject.

[0336] In certain embodiments that involve multiple secondary doses, all secondary doses are administered at the same frequency as one another (e.g., each secondary dose may be administered 1, 2, 3, or 4 weeks, or some other frequency, after the immediately preceding dose). Similarly, in certain embodiments that involve multiple tertiary doses, all tertiary doses are administered at the same frequency as one another. Alternatively, the frequency at which the secondary doses and / or tertiary doses are administered can vary over the treatment regimen course. The frequency of administration may be adjusted during the treatment regimen course by a physician depending on the subject needs following clinical examination.Attorney Docket No: 243735.000396

[0337] In certain embodiments, when a standard immunochemotherapy and / or a treatment for the subject’s determined FL subtype are sequentially administered, the treatment for the subject’s determined FL subtype may be a first component of the dosing regimen and the standard immunochemotherapy may be a second component of the dosing regimen (i.e., the treatment for the subject’s determined FL subtype may be administered before the standard immunochemotherapy). In certain embodiments, the treatment for the subject’s determined FL subtype may be a second component of the dosing regimen and the standard immunochemotherapy may be a first component of a dosing regimen (i.e., the treatment for the subject’s determined FL subtype may be administered after the standard immunochemotherapy). In other embodiments, a treatment for the subject’s determined FL subtype and a standard immunochemotherapy may be sequentially administered, by using either of the above-described orders with variable time intervals between administrations. For example, the time interval between administration of the treatment for the subject’s determined FL subtype and the standard immunochemotherapy may be at least about 30 seconds, at least about 45 seconds, at least about 1 minute, at least about 2 minutes, at least about 5 minutes, at least about 10 minutes, at least about 15 minutes, at least about 20 minutes, at least about 30 minutes, at least about 45 minutes, at least about 1 hour, at least about 2 hours, at least about 3 to 4 hours, at least about 5 hours, at least about 6 to 7 hours, at least about 8 to 9 hours, at least about 10 hours, at least about 11 to 12 hours, at least about 13 to 14 hours, at least about 15 hours, at least about 16 to 17 hours, at least about 18 to 19 hours, at least about 20 hours, at least about 21 to 24 hours, at least about 1 day, at least about 2 days, at least about 3 to 4 days, at least about 5 days, at least about 6 to 7 days, at least about 8 to 9 days, at least about 10 days, at least about 11 to 12 days, at least about 13 to 14 days, at least about 15 days, at least about 16 to 17 days, at least about 18 to 19 days, at least about 20 days, at least about 21 to 25 days, at least about 26 to 31 days, at least about 1 month, at least about 2 to 5 months, at least about 6 months, at least about 7 to 11 months, at least about 1 year, at least about 2 to 4 years, at least about 5 years, at least about 6 to 9 years, at least about 10 years, or more.

[0338] Any of the methods of administration as described herein can further comprise any of various subsequent administration steps as described herein. For example, the subsequent administration step can comprise administering the standard immunochemotherapy and / or aAttorney Docket No: 243735.000396 treatment for the subject’s determined FL subtype to the subject one or more subsequent times until a desired clinical outcome and / or measurement of interest is achieved in the subject.

[0339] For example, the subsequent administration step(s) can be at least about 1 week, at least about 2 to 4 weeks, at least about 5 weeks, at least about 6 to 9 weeks, at least about 10 weeks, at least about 11 to 15 weeks, or at least about 16 to 20 weeks after the initial dosing.

[0340] In some embodiments, the subsequent administration step can comprise administering a second standard immunochemotherapy and / or a treatment for the subject’s determined FL subtype (e.g., that is different from a first standard immunochemotherapy and / or a treatment for the subject’s determined FL subtype administered in an initial administration step) to the subject one or more subsequent times until a desired clinical outcome and / or measurement of interest is achieved in the subject.

[0341] For example, the subsequent administration step(s) can be at least about 1 week, at least about 2 to 4 weeks, at least about 5 weeks, at least about 6 to 9 weeks, at least about 10 weeks, at least about 11 to 15 weeks, or at least about 16 to 20 weeks after the initial dosing.

[0342] In some embodiments, the subsequently administered standard immunochemotherapy and / or treatment for the subject’s determined FL subtype is administered via the same administration route as the originally administered standard immunochemotherapy and / or treatment for the subject’s determined FL subtype.

[0343] In some embodiments, the subsequently administered standard immunochemotherapy and / or treatment for the subject’s determined FL subtype is administered via a different administration route as the originally administered standard immunochemotherapy and / or treatment for the subject’s determined FL subtype.

[0344] In certain embodiments, the standard immunochemotherapy is administered before the administration of the treatment for the subject’s determined FL subtype.

[0345] In certain embodiments, the standard immunochemotherapy is administered simultaneously with the administration of the treatment for the subject’s determined FL subtype.

[0346] In certain embodiments, the standard immunochemotherapy is administered after the administration of the treatment for the subject’s determined FL subtype.

[0347] In some embodiments, the treatment for the subject’s determined FL subtype are administered two or more times and the standard immunochemotherapy is administered beforeAttorney Docket No: 243735.000396 and / or between each of the administrations of the treatment for the subject’s determined FL subtype.

[0348] In some embodiments, the standard immunochemotherapy is administered simultaneously with the treatment for the subject’s determined FL subtype or not simultaneously (e.g., sequentially in any combination). For example, in a method comprising administering a standard immunochemotherapy and a treatment for the subject’s determined FL subtype, they can be administered separately (e.g., the standard immunochemotherapy separately from treatment for the subject’s determined FL subtype). Further, the standard immunochemotherapy can be administered prior to, subsequent to, prior to and subsequent to, or at the same time as the treatment for the subject’s determined FL subtype.

[0349] In certain embodiments, the standard immunochemotherapy can be administered about 2 hours to about 72 hours, about 2 hours to about 48 hours, about 2 hours to about 24 hours, about 2 hours to about 12 hours, about 2 hours to about 6 hours, about 2 hours to about 4 hours, about 1 hour to about 72 hours, about 1 hour to about 48 hours, about 1 hour to about 24 hours, about 1 hour to about 12 hours, about 1 hour to about 6 hours, about 1 hour to about 4 hours, about 1 hour to about 2 hours, about 6 hours to about 48 hours, about 6 hours to about 24 hours, about 12 hours to about 48 hours, or about 24 hours to about 48 hours prior to and / or subsequent to administration of the treatment for the subject’s determined FL subtype.

[0350] In some embodiments, the standard immunochemotherapy is administered at least about 2 hours, at least about 4 hours, at least about 6 hours, at least about 8 hours, at least about 12 hours, at least about 16 hours, at least about 18 hours, at least about 1 day, at least about 1.5 days, at least about 2 days, at least about 3 days, at least about 4 days, at least about 5 days, at least about 6 days, at least about 1 week, or at least about 2 weeks prior to administering the treatment for the subject’s determined FL subtype. In another embodiment, the standard immunochemotherapy is administered about 2 hours to about 48 hours, about 4 hours to about 24 hours, about 4 hours to about 12 hours, about 8 hours to about 24 hours, about 12 hours to about 24 hours, about 1 day to about 14 days, about 1 day to about 7 days, about 1 day to about 6 days, about 1 day to about 5 days, about 1 day to about 3 days, about 1 day to about 2 days, about 2 days to about 7 days, about 4 days to about 7 days, or about 5 days to about 7 days prior to and / or subsequent to administering the treatment for the subject’s determined FL subtype.Attorney Docket No: 243735.000396

[0351] In some embodiments, the standard immunochemotherapy is administered at least about 2 hours, at least about 4 hours, at least about 6 hours, at least about 8 hours, at least about 12 hours, at least about 16 hours, at least about 18 hours, at least about 1 day, at least about 1.5 days, at least about 2 days, at least about 3 days, at least about 4 days, at least about 5 days, at least about 6 days, at least about 1 week, or at least about 2 weeks prior to and subsequent to administering the treatment for the subject’s determined FL subtype. In another embodiment, the standard immunochemotherapy is administered about 2 hours to about 48 hours, about 4 hours to about 24 hours, about 4 hours to about 12 hours, about 8 hours to about 24 hours, about 12 hours to about 24 hours, about 1 day to about 14 days, about 1 day to about 7 days, about 1 day to about 6 days, about 1 day to about 5 days, about 1 day to about 3 days, about 1 day to about 2 days, about 2 days to about 7 days, about 4 days to about 7 days, or about 5 days to about 7 days prior to and subsequent to administering the treatment for the subject’s determined FL subtype.

[0352] In some embodiments, the standard immunochemotherapy is administered at least 2 hours, at least about 4 hours, at least 6 hours, at least about 8 hours, at least about 12 hours, at least 16 hours, at least about 18 hours, at least about 1 day, at least about 1.5 days, at least about 2 days, at least about 3 days, at least about 4 days, at least about 5 days, at least about 6 days, at least about 1 week, or at least about 2 weeks after administering treatment for the subject’s determined FL subtype. In another embodiment, the standard immunochemotherapy is administered about 2 hours to about 48 hours, about 4 hours to about 24 hours, about 4 hours to about 12 hours, about 8 hours to about 24 hours, about 12 hours to about 24 hours, about 1 day to about 14 days, about 1 day to about 7 days, about 1 day to about 6 days, about 1 day to about 5 days, about 1 day to about 3 days, about 1 day to about 2 days, about 2 days to about 7 days, about 4 days to about 7 days, or about 5 days to about 7 days after administering the treatment for the subject’s determined FL subtype.

[0353] Administration in vivo can be by any suitable route including, but not limited to, oral, parenteral, intrathecal, intra-arterial, intraperitoneal, intravenous, subcutaneous, topical, intracranial, intratumoral, intranasal, or intramuscular. Systemic modes of administration include, but are not limited to, parenteral and oral routes. Parenteral routes include, but are not limited to, subcutaneous, intraosseous, intravenous, intranasal, intradermal, intraarterial, intramuscular, and intraperitoneal routes. Some specific examples are intravenous infusion, nasal instillation, and intravitreal injection. Local modes of administration include, but are not limitedAttorney Docket No: 243735.000396 to, intracerebroventricular, intrathecal, intraparenchymal (e.g., localized intraparenchymal delivery to the cerebral cortex, temporal cortex, striatum, tegmentum, precentral gyrus, hippocampus, thalamus, frontal cortex, hypothalamus, cerebellum, amygdala, medulla, tectum, or substantia nigra), intravitreal, subconjunctival, intraocular, subretinal, intraorbital, and transscleral routes. Significantly smaller amounts of the active components may elicit an effect(s) when administered locally (e.g., intravitreal or intraparenchymal) compared to when administered systemically (e.g., intravenously). Administration locally may also reduce or eliminate the prevalence of potentially toxic side effects that may occur when the component(s) are administered systemically.

[0354] The number of dosages and the frequency of administration can depend on several factors. The administration of a standard immunochemotherapy and / or a treatment for the subject’s determined FL subtype into the cell or subject can be performed one or more times over a specific period of time. In some embodiments, the administration can be performed only once over a period of time, at least two to three times over a period of time, at least four to five times over a period of time, at least six to seven times over a period of time, at least eight to nine times over a period of time, at least ten times over a period of time, at least eleven to twelve times over a period of time, at least thirteen to fourteen times over a period of time, at least fifteen times over a period of time, at least sixteen to nineteen times over a period of time, at least twenty times over a period of time, or at least twenty-two to thirty times over a period of time. In some methods, a single administration of the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype, is sufficient to achieve the desired effect(s). In some embodiments, more than one administration may be beneficial to maximize desired therapeutic effect.

[0355] In some embodiments, the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype is administered orally or intravenously.

[0356] In some embodiments, the standard immunochemotherapy and / or the treatment for the subject’s determined FL subtype may be carried out in combination with one or more of a known therapy including, but not limited to, surgery, radiation therapy, chemotherapy, photodynamic therapy, and / or immunotherapy.

[0357] In an exemplary embodiment, the inhibitor of Bruton’s tyrosine kinase (BTK) is ibrutinib, acalabrutinib, or pirtobrutinib.Attorney Docket No: 243735.000396

[0358] In an exemplary embodiment, the inhibitor of PD1 is nivolumab, pembrolizumab, cemiplimab, dostarlimab, or retifanlimab.

[0359] In an exemplary embodiment, the agent targeting neutrophilic myeloid-derived suppressor cells (PMN-MDSCs) is all-trans retinoic acid (ATRA).

[0360] In an exemplary embodiment, the inhibitor of PD-L1 is atezolizumab, avelumab or durvalumab.

[0361] In an exemplary embodiment, the inhibitor of Janus kinase (JAK) is ruxolitinib, baricitinib, tofacitinib, fedratinib, itacitinib, momelotinib, or patricinib.

[0362] In an exemplary embodiment, the proteosome inhibitor is bortezomib, carfilzomib or ixazomib.

[0363] In an exemplary embodiment, the treatment for the subject’s determined FL subtype may be a first and second treatment. In an exemplary embodiment, the first and second treatments may be different. In an exemplary embodiment, the treatments may be a first treatment and any concurrent treatment. In an exemplary embodiment, the any concurrent treatment may be a second treatment, a third treatment, and more. In an exemplary embodiment, the first treatment and the any concurrent treatment may be different.

[0364] In an exemplary embodiment, the gene expression level is determined by measuring mRNA level.

[0365] In an exemplary embodiment, the mRNA level is determined using RNA sequencing (e.g., single-cell RNA sequencing (sc-RNA-seq)), qPCR, panel sequencing, array-based gene expression profiling, or any combination thereof.

[0366] In an exemplary embodiment, the subject is a newly diagnosed patient.

[0367] In an exemplary embodiment, the subject is a patient at relapse after a treatment. Compositions of the Invention

[0368] In an exemplary embodiment, the invention provides a composition comprising a plurality of isolated probes and / or primers which hybridize to at least 4 genes from each of 7 groups of genes provided in Table 1.

[0369] In an exemplary embodiment, the composition comprises a plurality of isolated probes and / or primers which hybridize to at least 4 genes from each of the 7 groups of genes provided in Table 3.Attorney Docket No: 243735.000396

[0370] Any of various compositions, e.g., any of various isolated probes and / or primers which hybridize to the genes as described herein, can be present in a pharmaceutical composition (such as a formulation) that can include other agents, excipients, or stabilizers. In various embodiments, a pharmaceutical composition described herein may comprise any of various isolated probes and / or primers which hybridize to the genes as described herein. In various embodiments, a pharmaceutical composition described herein may comprise any of various isolated probes and / or primers which hybridize to the genes as described herein.

[0371] It is understood that any the compounds of the present disclosure can be present in one or more stereoisomers (e.g., diastereomers). The disclosure includes, within its scope, all of these stereoisomers, either isolated (e.g., in enantiomeric isolation) or in combination (including racemic and diastereomeric mixtures).

[0372] If the compounds of the disclosure require purification, chromatographic techniques such as high-performance liquid chromatography (HPLC) and reverse phase HPLC can be used. The compounds may be characterized by mass spectrometry and / or other suitable methods.

[0373] If the compound contains one or more functional groups that can be protonated or deprotonated (e.g., at physiological pH), the compound can be prepared and / or isolated as a pharmaceutically acceptable salt. It will be appreciated that the compound can be zwitterion at a given pH. As used herein, the expression "pharmaceutically acceptable salt" refers to a salt of a given compound, which salt is suitable for pharmaceutical administration. Such salts can be formed, for example, by reacting an acid or base with an amine or carboxylic acid group, respectively.

[0374] Pharmaceutically acceptable acid addition salts can be prepared from inorganic and organic acids. Examples of inorganic acids include hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid and the like. Examples of organic acids include acetic acid, propionic acid, glycolic acid, pyruvate, oxalic acid, malic acid, malonic acid, succinic acid, maleic acid, fumaric acid, tartrate acid, citrate, benzoic acid, cinnamic acid, mandelic acid, Examples thereof include methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid and salicylic acid.

[0375] Pharmaceutically acceptable base addition salts can be prepared from inorganic and organic bases. Corresponding counterions derived from inorganic bases include salts of sodium, potassium, lithium, ammonium, calcium and magnesium. Organic bases include isopropylamine,Attorney Docket No: 243735.000396 trimethylamine, diethylamine, triethylamine, tripropylamine, ethanolamine, 2- dimethylaminoethanol, tromethamine, lysine, arginine, histidine, caffeine, prokine, hydrabamine, choline, betaine, ethylenediamine, glucosamine, Substituted amines such as primary, secondary and tertiary amines such as N-alkylglucamine, theobromine, purines, piperazine, piperazine and N-ethylpiperidine, substituted amines such as natural substituted amines and cyclic amines can be mentioned.

[0376] Acid / base addition salts tend to be more soluble in aqueous solvents than the corresponding free acid / base forms.

[0377] The appropriate formulation for the compound of the disclosure can be adjusted for pH. Buffer systems are routinely used to provide pH values in the desired range and include carboxylic acid buffers such as acetates, citrates, lactates and succinates. In some embodiments, the composition is formulated to have a pH range of about 4.5 to about 9.0, including for example pH ranges of about any of 5.0 to about 8.0, about 6.5 to about 7.5, and about 6.5 to about 7.0. In some embodiments, the pH of the composition is formulated to no less than about 6, including for example no less than about any of 6.5, 7, or 8 (such as about 8). The composition can also be made to be isotonic with blood by the addition of a suitable tonicity modifier, such as glycerol.

[0378] The formulation may also include suitable excipients, such as antioxidants. Examples of antioxidants include phenolic compounds such as BHT or Vitamin E, reducing agents such as methionine or sulfites, and metal chelating agents such as EDTA.

[0379] In an exemplary embodiment, the composition comprises a plurality of isolated probes and / or primers which hybridize to DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF.

[0380] In an exemplary embodiment, the composition comprises a plurality of isolated probes and / or primers which hybridize to GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK.

[0381] In an exemplary embodiment, the composition comprises a plurality of isolated probes and / or primers which hybridize to ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3.Attorney Docket No: 243735.000396

[0382] In an exemplary embodiment, the composition comprises a plurality of isolated probes and / or primers which hybridize to GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX.

[0383] In an exemplary embodiment, the composition comprises a plurality of isolated probes and / or primers which hybridize to PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1.

[0384] In an exemplary embodiment, the composition comprises a plurality of isolated probes and / or primers which hybridize to PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK.

[0385] In an exemplary embodiment, the composition comprises a plurality of isolated probes and / or primers which hybridize to SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2. Kits of the Invention

[0386] In an exemplary embodiment, the invention provides a kit comprising (i) a plurality of isolated probes and / or primers which hybridize to at least 4 genes from each of 7 groups of genes provided in Table 1, (ii) optionally, one or more reagents for determining mRNA level, and (iii) optionally, instructions for use.

[0387] In an exemplary embodiment, the kit comprises (i) a plurality of isolated probes and / or primers which hybridize to at least 4 genes from each of 7 groups of genes provided in Table 3, (ii) optionally, one or more reagents for determining mRNA level, and (iii) optionally, instructions for use.

[0388] In an exemplary embodiment, the kit comprises a plurality of isolated probes and / or primers which hybridize to DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF.

[0389] In an exemplary embodiment, the kit comprises a plurality of isolated probes and / or primers which hybridize to GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK.

[0390] In an exemplary embodiment, the kit comprises a plurality of isolated probes and / or primers which hybridize to ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3.Attorney Docket No: 243735.000396

[0391] In an exemplary embodiment, the kit comprises a plurality of isolated probes and / or primers which hybridize to GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX.

[0392] In an exemplary embodiment, the kit comprises a plurality of isolated probes and / or primers which hybridize to PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1.

[0393] In an exemplary embodiment, the kit comprises a plurality of isolated probes and / or primers which hybridize to PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK.

[0394] In an exemplary embodiment, the kit comprises a plurality of isolated probes and / or primers which hybridize to SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

[0395] In some embodiments, a kit can comprise: (a) a container that contains a pharmaceutical composition described herein, for example, a pharmaceutical composition in solution or in lyophilized form; (b) optionally, a second container containing a diluent or reconstituting solution for the lyophilized formulation; and / or (c) optionally, instructions for (i) use of the solution or (ii) reconstitution and / or use of the lyophilized formulation.

[0396] In some embodiments, a kit may further comprise, one or more of (i) a diluent, (ii) a buffer, (iii) a filter (iv) a syringe, and / or (v) a needle.

[0397] In some embodiments, the components of the kit may be provided in one or more liquid solutions. A liquid solution described herein may be an aqueous solution such as a sterile aqueous solution. The components of the kit may also be provided as solids, which may be converted into liquids such as by addition of suitable solvents, which may be provided in another distinct container.

[0398] In some aspects, a pharmaceutical composition described herein may be lyophilized.

[0399] In some embodiments, kits may comprise a lyophilized formulation described herein in a suitable container and instructions for its reconstitution and / or use. Non-limiting examples of suitable containers include, e.g., syringes (such as dual chamber syringes), vials (such as dual chamber vials), bottles, and test tubes. In various embodiments, a container may be a multi-use container. The container may be formed from a variety of materials such as plastic or glass. The kit and / or container may contain instructions upon or accompanying the container which canAttorney Docket No: 243735.000396 denote directions for reconstitution of, e.g., a lyophilized formulation and / or use of the kit. In some embodiments, a label may denote that the lyophilized formulation is to be reconstituted to an appropriate concentration. The label may denote that the formulation is useful or intended for any route of administration disclosed herein.

[0400] The container containing the formulation may be a multi-use vial, which may allow for repeat administrations (e.g., from 2-6 administrations) of a reconstituted formulation. The kit may further comprise a second container comprising a suitable diluent (e.g., sodium bicarbonate solution).

[0401] Upon mixing of the diluent and a lyophilized formulation, a final concentration in the reconstituted formulation can reached. The kit may further include other materials desirable from a commercial and / or user perspective, including, e.g., other filters, needles, syringes, buffers, diluents, and / or package inserts which may comprise, e.g., instructions for use.

[0402] Kits may contain a single container that contains the formulation of the pharmaceutical composition with or without other components (e.g., other compounds or pharmaceutical compositions of such other compounds) or may have a separate container for each component.

[0403] Kits may include a formulation of the disclosure packaged for use in combination with the co-administration of a second compound (such as adjuvants (e.g., GM-CSF, a natural product, a hormone or antagonist, an anti-angiogenesis agent or inhibitor, an apoptosis-inducing agent or a chelator a chemotherapeutic agent) or a pharmaceutical composition thereof. The components of the kit may pre-mixed and / or pre-complexed or each component of the kit may be in a separate distinct container prior to administration to a patient.

[0404] In some embodiments, the container of a therapeutic kit may be a vial, flask, test tube, bottle, syringe, or any other means of enclosing a solid or liquid. When there is more than one component, the kit may contain a second vial or other container, which may allow for separate dosing. The kit may also contain another container for a pharmaceutically acceptable liquid. In some embodiments, a kit may contain an apparatus (e.g., syringes, one or more needles, pipettes, eye droppers, etc.) which may permit administration of agents of the disclosure which are components of the kit. Arrays of the InventionAttorney Docket No: 243735.000396

[0405] In an exemplary embodiment, the invention provides an array comprising a plurality of probes complementary to and / or hybridizable to at least 4 genes from each of 7 groups of genes provided in Table 1.

[0406] In an exemplary embodiment, the array comprises a plurality of probes complementary to and / or hybridizable to at least 4 genes from each of 7 groups of genes provided in Table 3.

[0407] In an exemplary embodiment, the array comprises a plurality of isolated probes and / or primers which hybridize to DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF.

[0408] In an exemplary embodiment, the array comprises a plurality of isolated probes and / or primers which hybridize to GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK.

[0409] In an exemplary embodiment, the array comprises a plurality of isolated probes and / or primers which hybridize to ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3.

[0410] In an exemplary embodiment, the array comprises a plurality of isolated probes and / or primers which hybridize to GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX.

[0411] In an exemplary embodiment, the array comprises a plurality of isolated probes and / or primers which hybridize to PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1.

[0412] In an exemplary embodiment, the array comprises a plurality of isolated probes and / or primers which hybridize to PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK.

[0413] In an exemplary embodiment, the array comprises a plurality of isolated probes and / or primers which hybridize to SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2. Software Tool of the Invention

[0414] In an exemplary embodiment, the invention provides a therapy guidance software tool for a subject diagnosed with follicular lymphoma (FL) comprising non-transitory computer readable medium with instructions thereon, that when executed by a processor, cause the processor to: (a) receive a plurality of gene expression values for at least 4 genes from each of 7Attorney Docket No: 243735.000396 groups of genes provided in Table 1, wherein the 7 groups of genes correspond to 7 FL subtypes (FL1-FL7); (b) calculate a gene expression score for each of the 7 groups of genes based at least in part on the plurality of gene expression values; (c) classify the subject into one FL subtype of the 7 FL subtypes based at least in part on the gene expression score for each of the 7 groups of genes; and (d) provide a patient diagnosis based at least in part on the one FL subtype into which the subject is classified.

[0415] In an exemplary embodiment, the plurality of genes may include at least 4 genes selected from each of 7 groups of genes listed in Table 1 or Table 3. In an exemplary embodiment, the plurality of genes may include at least 4 genes selected from each of 7 groups of genes listed in Table 1. In an exemplary embodiment, the plurality of genes may include at least 4 genes selected from each of 7 groups of genes listed in Table 3.

[0416] In an exemplary embodiment, step (b) of the therapy guidance software tool comprises: generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 1; generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreases when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

[0417] In an exemplary embodiment, step (b) of the therapy guidance software tool comprises: representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative; performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes provided in Table 1, and resulting in a mixture coefficient matrix; and determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.

[0418] In an exemplary embodiment, step (c) of the therapy guidance software tool comprises: determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

[0419] In an exemplary embodiment, the non-transitory computer readable medium includes instructions thereon, that when executed by a processor, cause the processor to: provide aAttorney Docket No: 243735.000396 treatment recommendation based at least in part on the one FL subtype into which the subject is classified.

[0420] In an exemplary embodiment, wherein the non-transitory computer readable medium includes instructions thereon, that when executed by a processor, cause the processor to: provide a prognosticated failure free survival based at least in part on the one FL subtype into which the subject is classified.

[0421] In an exemplary embodiment, the non-transitory computer readable medium includes instructions thereon, that when executed by a processor, cause the processor to: provide a prognosticated overall survival based at least in part on the one FL subtype into which the subject is classified.

[0422] In an exemplary embodiment, step (a) of the therapy guidance software tool comprises determining the expression level of at least 4 genes from each of the 7 groups of genes provided in Table 3 wherein the 7 groups of genes correspond to the 7 FL subtypes (FL1-FL7) as listed in Table 3.

[0423] In an exemplary embodiment, step (b) of the therapy guidance software tool comprises: generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 3; generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreases when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

[0424] In an exemplary embodiment, step (b) of the therapy guidance software tool comprises: representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative; performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes provided in Table 3, and resulting in a mixture coefficient matrix; and determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.Attorney Docket No: 243735.000396

[0425] In an exemplary embodiment, step (c) of the therapy guidance software tool comprises: determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

[0426] In an exemplary embodiment, the subject has been diagnosed with FL based on evaluation of histology and / or immunophenotypic features.

[0427] In an exemplary embodiment, the determination of the expression level for genes from each of the 7 groups may be used to classify the human subject into one of 7 FL subtypes.

[0428] In an exemplary embodiment, the determination of the biological subtype of FL may be based on the level of one or more RNA transcripts in a biological sample containing tumor cells.

[0429] In an exemplary embodiment, the biological sample comprises tumor cells.

[0430] In an exemplary embodiment, the biological sample is a biopsy sample.

[0431] In an exemplary embodiment, the subject is human.

[0432] In an exemplary embodiment, the subject is a veterinary animal.

[0433] In an exemplary embodiment, the therapy guidance software tool may further include assigning one or more RNA transcripts to 1 of 7 FL subtypes, calculating a quantitative score representing the relative level of RNA expression of the tumor cells for the genes defining each of the 7 subtypes, and classifying unfractionated tumor samples as 1 of the 7 subtypes based on the highest of the 7 scores.

[0434] In an exemplary embodiment, the enrichment score for each of the 7 FL signatures is calculated based on the degree to which the genes from each gene set are overrepresented at the top or bottom of the ranked list, given a ranked gene list derived from a normalized gene expression matrix of an FL sample.

[0435] In an exemplary embodiment, the enrichment score represents a running-sum statistic which increases when a gene is encountered by walking down the ranked list and decreases when the gene is not encountered and samples are assigned to 1 of the 7 transcriptional subtype classifications based on the highest enrichment score.

[0436] Certain transcriptional subtype classifications may be combined / merged or omitted, creating a simplified prognostic model and / or a commercial assay identifying shared therapeutic vulnerabilities between subtypes characterized herein. Any one or more subtype classifications of FL1-FL7 as described herein may be merged in any combination. Any subtype combination or omission may reduce the total number of subtype classifications.Attorney Docket No: 243735.000396

[0437] Subtype classifier FL1 may be combined with any one or more of subtypes FL2, FL3, FL4, FL5, FL6, and FL7. Subtype classifier FL2 may be combined with any one or more of subtypes FL1, FL3, FL4, FL5, FL6, and FL7. Subtype classifier FL3 may be combined with any one or more of subtypes FL1, FL2, FL4, FL5, FL6, and FL7. Subtype classifier FL4 may be combined with any one or more of subtypes FL1, FL2, FL3, FL5, FL6, and FL7. Subtype classifier FL5 may be combined with any one or more of subtypes FL1, FL2, FL3, FL4, FL6, and FL7. Subtype classifier FL6 may be combined with any one or more of subtypes FL1, FL2, FL3, FL4, FL5, and FL7. Subtype classifier FL7 may be combined with any one or more of subtypes FL1, FL2, FL3, FL4, FL5, and FL6. The subtypes FL1, FL2, FL3, FL4, FL5, FL6, and FL7 may be merged in any combinations thereof.

[0438] The gene list corresponding to FL1 in Table 3 may be combined with any one or more of the gene lists corresponding to FL2, FL3, FL4, FL5, FL6, and FL7 in Table 3. The gene list corresponding to FL2 in Table 3 may be combined with any one or more of the gene lists corresponding to FL1, FL3, FL4, FL5, FL6, and FL7 in Table 3. The gene list corresponding to FL3 in Table 3 may be combined with any one or more of the gene lists corresponding to FL1, FL2, FL4, FL5, FL6, and FL7 in Table 3. The gene list corresponding to FL4 in Table 3 may be combined with any one or more of the gene lists corresponding to FL1, FL2, FL3, FL5, FL6, and FL7 in Table 3. The gene list corresponding to FL5 in Table 3 may be combined with any one or more of the gene lists corresponding to FL1, FL2, FL3, FL4, FL6, and FL7 in Table 3. The gene list corresponding to FL6 in Table 3 may be combined with any one or more of the gene lists corresponding to FL1, FL2, FL3, FL4, FL5, and FL7 in Table 3. The gene list corresponding to FL7 in Table 3 may be combined with any one or more of the gene lists corresponding to FL1, FL2, FL3, FL4, FL5, and FL6 in Table 3.

[0439] The gene list corresponding to FL1 in Table 1 may be combined with any one or more of the gene lists corresponding to FL2, FL3, FL4, FL5, FL6, and FL7 in Table 1. The gene list corresponding to FL2 in Table 1 may be combined with any one or more of the gene lists corresponding to FL1, FL3, FL4, FL5, FL6, and FL7 in Table 1. The gene list corresponding to FL3 in Table 1 may be combined with any one or more of the gene lists corresponding to FL1, FL2, FL4, FL5, FL6, and FL7 in Table 1. The gene list corresponding to FL4 in Table 1 may be combined with any one or more of the gene lists corresponding to FL1, FL2, FL3, FL5, FL6, and FL7 in Table 1. The gene list corresponding to FL5 in Table 1 may be combined with any one orAttorney Docket No: 243735.000396 more of the gene lists corresponding to FL1, FL2, FL3, FL4, FL6, and FL7 in Table 1. The gene list corresponding to FL6 in Table 1 may be combined with any one or more of the gene lists corresponding to FL1, FL2, FL3, FL4, FL5, and FL7 in Table 1. The gene list corresponding to FL7 in Table 1 may be combined with any one or more of the gene lists corresponding to FL1, FL2, FL3, FL4, FL5, and FL6 in Table 1.

[0440] The therapeutic regimens described herein for each of the 7 subtypes may subsequently be combined upon combination of the subtype classifiers. This may include using a combination of treatments for a patient and / or performing a treatment that only applies to a subtype upon merging of two or more of the subtype classifiers FL1-FL7. Treatments may be beneficial in combination with or possibly as an alternative to standard frontline immunochemotherapy regimens. Treatment associated with subtype classifier FL1 may be combined with any one or more treatments associated with subtypes FL2, FL3, FL4, FL5, FL6, and FL7. Treatment associated with subtype classifier FL2 may be combined with any one or more treatments associated with subtypes FL1, FL3, FL4, FL5, FL6, and FL7. Treatment associated with subtype classifier FL3 may be combined with any one or more treatments associated with subtypes FL1, FL2, FL4, FL5, FL6, and FL7. Treatment associated with subtype classifier FL4 may be combined with any one or more treatments associated with subtypes FL1, FL2, FL3, FL5, FL6, and FL7. Treatment associated with subtype classifier FL5 may be combined with any one or more treatments associated with subtypes FL1, FL2, FL3, FL4, FL6, and FL7. Treatment associated with subtype classifier FL6 may be combined with any one or more treatments associated with subtypes FL1, FL2, FL3, FL4, FL5, and FL7. Treatment associated with subtype classifier FL7 may be combined with any one or more treatments associated with subtypes FL1, FL2, FL3, FL4, FL5, and FL6.

[0441] The following examples are illustrative, but not limiting, of the methods, kits, arrays, and compositions described herein. Other suitable modifications and adaptations known to those skilled in the art are within the scope of the following embodiments. EXAMPLES

[0442] The present invention is also described and demonstrated by way of the following examples. However, the use of these and other examples anywhere in the specification is illustrative only and in no way limits the scope and meaning of the invention or of anyAttorney Docket No: 243735.000396 exemplified term. Likewise, the invention is not limited to any particular preferred embodiments described here. Indeed, many modifications and variations of the invention may be apparent to those skilled in the art upon reading this specification, and such variations can be made without departing from the invention in spirit or in scope. The invention is therefore to be limited only by the terms of the appended claims along with the full scope of equivalents to which those claims are entitled. Example 1. Follicular lymphoma encompasses seven distinct subtypes.

[0443] To investigate the transcriptional landscape in FL, non-negative matrix factorization (NMF) was performed on 302 pre-treatment bulk FL transcriptomes, which identified 7 transcriptionally-distinct subtypes (FL1-7) (Figures 1A-1C) characterized by unique biological features (Figure 1G). These subtypes were subsequently recovered in 850 FL samples from 7 independent microarray gene expression profiling datasets and 3 bulk RNAseq datasets (Figures 1D-1F). Although the transcriptomic datasets were generated using different platforms and tissue processing methods, the 7 signatures were identified in all datasets, supporting the reproducibility and cross-platform scalability of bulk FL transcriptional signatures. Example 2. FL transcriptional subtypes are enriched for distinct B-cell states.

[0444] Having demonstrated the reproducibility of the transcriptomic classifier across multiple independent datasets and gene expression profiling platforms, next the clinical and biological features of the malignant B-cell population associated with each FL transcriptional subtype were studied. Digital cytometry with transcriptional subtyping using the Ecotyper platform identified 7 transcriptionally-distinct B-cell states (Figures 2A-2B). FL transcriptional subtypes exhibited consistent enrichment for a unique B-cell state (Figure 2D). In order to evaluate the clinical significance of the 7 B-cell states in FL patients treated with frontline immunochemotherapy, bulk transcriptomes from GSE119214 were classified according to their most prevalent B-cell states using the Ecotyper state assignment algorithm and performed survival analyses using the method of Kaplan and Meier (Figure 2C). The S01 B-cell state was significantly associated with inferior failure-free survival (FFS) compared to the S03 and S04 B-cell states while S01 and S05 B-cell states were significantly associated with inferior OS compared to the S03 B-cell state, indicating that certain FL B-cell transcriptional states are predictive of response to frontline immunochemotherapy (Figure 2C).Attorney Docket No: 243735.000396

[0445] Given these observations, the 7 B-cell states at single-cell resolution were further delineated. In order to ensure geneset enrichment analyses were not confounded by residual benign follicular B-cells, 61,781 malignant FL B-cell transcriptomes from 24 patients for which clonality had been confirmed by V(D)J rearrangement sequencing were analyzed (Figures 2E- 2G). Consistent with bulk transcriptome digital cytometry analyses, patient-level scRNA-seq samples were enriched for a dominant B-cell state but harbored a mixture of the other B-cell states (Figure 2E), suggesting that FL B-cells may transit through the germinal center reaction. Consistent with this possibility, while most B-cell states were present to varying extents across individual FL subtypes, in both bulk digital cytometry analyses and patient-level scRNA-seq samples, it was observed that tumors enriched for the S02 B-state largely lacked S01 and S07 B- cell states but not vice versa. Collectively, these observations would be consistent with a developmental hierarchy in which S01 and S07 B-cells have the capacity to differentiate into more mature B-cell developmental states, including S02 B-state, while S02 B-cells arise downstream of the S01 and S07 B-states.

[0446] To investigate this hypothesis, the CytoTRACE algorithm, which utilizes transcriptional diversity to predict cellular differentiation trajectories, was applied to malignant FL B-cell transcriptomes (Gulati 2020). These analyses revealed that S01 and S07 B-cell states represented the lowest B-cell differentiation states while S02 B-state was the most differentiated (Figure 2H). These findings were recapitulated by pseudotime trajectory analyses (Figures 2K- 2L). To determine whether the 7 B-cell states correspond to specific stages of B-cell development and the germinal center reaction, single cell geneset enrichment analyses was performed using the single-cell cell-of-origin classifier developed by Holmes, et al. (Figure 2I). Consistent with CytoTRACE differentiation state ordering, S01 and S07 B-cells were enriched for features consistent with dark zone germinal center B-cells while the S02 B-state was distinctly enriched for an activated B-cell-like phenotype which most closely aligned with plasmablasts (Figures 2I-2J). Thus, FL transcriptional subtypes arise from heterogeneous and temporally distinct points in the germinal center reaction. Example 3. FL subtypes are associated with distinct genetic alterations.

[0447] Having identified 7 FL B-cells states, their relationship to underlying genetic alterations was investigated. In order to do so, bulk FL signatures were recovered from 169 pre-treatment FL patient samples which had been characterized by paired transcriptional profiling and exomeAttorney Docket No: 243735.000396 sequencing.104 cases were profiled by RNA-seq and whole genome sequencing (WGS), which included copy number and structural alterations (Dreval 2023), and 65 cases were evaluated by microarray gene expression profiling and a targeted exome sequencing of 308 lymphoid genes (Ma 2022) (Figure 1H). The prevalence of select alterations was confirmed in a paired cohort of 107 pre-treatment FL samples profiled by paired WG-DASL HT and a 7 gene targeted exome sequencing panel (GSE66166) (Figure 10 vs. Tables 5-13). The complete gene list for the FL classifier by subtype is listed in Table 1. Table 1. Gene list for FL classifier. Gene Sub- Gene Sub- Gene Sub- Gene Sub- e 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3Attorney Docket No: 243735.000396 b- e 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3Attorney Docket No: 243735.000396 b- e 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 6 6 6 6Attorney Docket No: 243735.000396 b- e 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6Attorney Docket No: 243735.000396 b- e 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7Attorney Docket No: 243735.000396 b- e 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7

[0448] These analyses revealed that FL1 was associated with a significantly increased frequency of 7q22.1 amplifications (P=0.04), 9q21.11 deletions (P=0.025), and recurrent alterations in KMT2D (P=0.02), ATP6V1B2 (P=0.01), and PIM1 (P=0.015), while FL6 was significantly associated with an increased frequency of deletions of 5q23.2 (P=0.03) and 6q25.3 (P=0.05), uniform KMT2D alterations (P=0.0025), and an increased frequency of alterations in BCL7A (P=0.006) and DTX1 (P=0.02).

[0449] FL2 was significantly associated with a lower frequency of t(14;8) translocations by fluorescence in-situ hybridization (FISH) (P=0.025), frequent deletions of 1p36 (62.5%, p=0.03), amplifications of the BCL6 locus, 3q27.3 (60%, P=0.006), the MYC locus, 8q24.21 (50%; P=0.04), and 12q12 (50%; P=0.035), as well as an increased frequency of RYR1 alterations (P=0.02), and a uniform absence of BCL2 exome alterations (P=0.001). Based on these genetic features, at least a subset of FL2 is likely to represent the diffuse growth pattern variant of FL with uncommon features, a recently introduced FL subtype which is frequently negative forAttorney Docket No: 243735.000396 t(14;18) and associated with deletion of 1p36 (Alaggio 2022). By immunohistochemistry, the diffuse variant is characteristically positive for CD23 (Alaggio 2022; Nann 2020) and, consistently, in single cell analyses, the predominant FL2 B-cell state, S07 B-cell state, was marked by significantly increased differential expression of CD23 / FCER2 (Figure 2G).

[0450] FL5 and FL4 were enriched for the S01 and S03 B-cell states, respectively, which were associated with significant differences in both FFS and OS (Figure 2C). Accordingly, it was further studied whether and to what extent these differences in clinical outcomes were attributable to specific genetic alterations. FL5 was associated with 5q23.2 deletions (P=0.03) and recurrent mutations of IGHV1-69 in 11 / 33 cases profiled by WGS (P=0.005), but was not significantly associated with an increased frequency of any additional specific exome alterations. Notably, however, in both bulk and single-cell GSEA of its predominant B-cell state, S01 B- state, FL5 was characterized by significant enrichment for multiple aberrant RNA processing pathways including splicing and intronic polyadenylation (IPA) (Figures 8-18). As IPA has been shown to have a similar functional impact on protein translation as genetic alterations (Lee 2018), the phenotype of FL5 may be driven in part by protein-level alterations that are not predicted by exome sequencing. In contrast, FL4 was characterized by a significantly increased frequency of 18q23 deletions (P=0.01) and alterations in EZH2 (P=0.0002), BCL2 (P=0.0016), MEF2B (P=0.003), NALCN (P=0.02), SGK1 (P=0.01), BTG1 (P=0.04), BCL7A (P=0.01), and SOCS1 (P=0.028). The association with alternations in EZH2 and MEF2B were confirmed in a third independent dataset profiled by targeted exome sequencing of 7 genes (GSE66166, Figures 8-18). EZH2 and MEF2B have previously been shown to be predictive of longer FFS (Pastore 2015; additional references), though neither has been linked to superior overall survival. These findings suggest that the prognostic associations of the S01 and S03 B-states likely reflect factors other than exome alterations such as non-coding alterations and changes in microenvironment composition and phenotype. Example 4. FL subtypes are enriched for distinct microenvironment ecosystems composed of transcriptionally-defined immune and stromal cell populations.

[0451] It has been previously shown that the extent of immune cell infiltration in FL inversely correlates with early disease progression in patients treated with frontline immunochemotherapy. Favorable-risk FL was associated with a higher abundance of immune cell infiltrates with enrichment for macrophages and T-cells, while POD24 events were associated with a lowerAttorney Docket No: 243735.000396 abundance of infiltrating immune cells (Tobin 2019). These findings were confirmed by others, who found that relative depletion of all T-cell subsets was associated with inferior FFS (Ma 2022). A role of non-hematopoietic cells in the FL TME was shown in patients treated with CHOP therapy in the pre-rituximab era, as the expression of marker genes for transcriptionally- defined fibroblastic reticular cell (FRC) and blood endothelial cell (BEC) and subsets were predictive of inferior OS (Abe 2022). Having characterized the 7 FL bulk transcriptomic subtypes and their associated B-cell states, next their corresponding microenvironment compositions were delineated.

[0452] Given the established association between hematopoietic and non-hematopoietic components of the TME and FFS, the relative fraction of infiltrating leukocytes, LNSCs, and B- cells associated with the seven FL subtypes were evaluated using digital cytometry (CIBERSORTx). In order to faithfully recapitulate the FL stromal cell landscape, a novel lymph node stromal cell signature matrix was developed, which included signature matrices for BECs, FRCs, LECs, and FDCs (Figure 11). These analyses revealed that FL5 and FL6 subtypes were associated with significantly depleted leukocyte compartments compared to other FL subtypes while FL4 and FL2 were associated with expanded reactive leukocyte compartments (Figure 11). Consistent with previous studies (Tobin 2019; Ma 2022), FL5 and FL6 subtypes were significantly associated with inferior FFS (FL5 HR 3.35, p=0.016; FL6 HR 3.44, p=0.007) while FL4, which was enriched for regulatory T-cells and macrophages (Figure 3A), was significantly associated with longer FFS (HR 0.3, P=0.016) and a significantly lower risk of POD24 (OR 0.155, P=0.0046). However, unlike FL4, FL2 was significantly associated with shorter FFS. Thus, while TME leukocyte depletion is consistently associated with a poor response to frontline immunochemotherapy, the prognostic significance of high leukocyte infiltration appears to vary based on immune infiltrate composition.

[0453] Having demonstrated that the bulk transcriptional subtypes identified by NMF recapitulate known prognostic associations of FL TME composition, the specific immune and stromal cell transcriptional states associated with each of the seven FL subtypes were deconvoluted. The Ecotyper platform (Steen 2021) was therefore leveraged to perform digital cytometry with transcriptional subtyping using signature matrices for 18 immune and stromal cell states (Tables 5-13). This approach identified 44 transcriptionally-distinct TME immune and stromal cell states across the FL subtypes in the discovery cohort which clustered into 6Attorney Docket No: 243735.000396 multicellular ecosystems (“ecotypes”) (Figures 3B-3D). Across 1,158 transcriptomes, FL subtypes associated with distinct ecotypes (Figure 3E).

[0454] To dissect the features of the imputed TME states at single cell resolution, a novel FL single-cell RNA-seq atlas was constructed, derived from 40 FL 10x single-cell RNAseq datasets spanning 5 independent studies (Han 2021; Abe 2022; Zhang 2019; Roider 2020; Steen 2021), as well as an atlas of lung cancer-associated TME myeloid populations (Salcher 2022) (Figure 3F and Figure 8). Using Ecotyper, more than 160,000 single-cell transcriptomes were annotated with the transcriptional states identified in the discovery cohort for downstream differential gene expression and gene set enrichment analyses. Example 5. Digital cytometry with transcriptional subtyping of immunophenotypically-defined T-cell populations reveals biologically distinct states with opposing prognostic associations.

[0455] In order to identify prognostic associations across the 44 transcriptionally-defined TME immune and stromal cell states, imputed was the relative abundance of the cell states identified in the discovery cohort in FL transcriptomes from pre-treatment patients managed with frontline immunochemotherapy (GSE119214). Survival analyses were then performed using proportional hazards regression models with individual cell state abundance as a continuous variable (Figure 3G) and by the method of Kaplan and Meier with relative abundance dichotomized into high and low groups. In order to compare the prognostic associations of the transcriptional states to those of their immunophenotypically-defined parent signatures, imputed TME fractions were used, generated by CIBERSORTx using LM22 and the LNSC signature matrices (Table 2). These analyses revealed prognostic associations that were not apparent when cell type abundance was imputed using immunophenotypically-defined signatures. Notably, multiple immunophenotypically-defined T-cell populations harbored transcriptional states with divergent survival associations which were variably enriched in the different FL subtypes and characterized by distinct biological features in single-cell analyses (Figures 3G-3I; Figures 12- 15). Among the immunophenotypically-defined CD4+ T-cell signatures, the LM22 included signatures for regulatory T-cells and follicular helper T-cells. In digital cytometry analyses with CIBERSORTx, neither immunophenotypically-defined Treg or Tfh abundance were predictive of overall survival while the abundance of Tfh but not Treg cells was predictive of superior FFS. In contrast, transcriptional subtyping of imputed cell type signatures using Ecotyper identified two transcriptionally-distinct regulatory T-cell states (S01 and S02 TREG) and three Tfh states (S01,Attorney Docket No: 243735.000396 S02, and S03 TFH), each of which was associated with distinct survival outcomes and biological features (Figures 3G-3I). Table 2. LM22 and LNSC signature matrix IDs. LM22 Cell Type Merged phenotype IDFollicular dendritic cells FDCn FL4, was significantly associated with superior FFS and OS while the S02 Treg state, which was enriched in FL1 (Figures 3B-3C), was significantly associated with inferior OS. To gain insight into the biological basis of these prognostic associations, single-cell GSEA was performed on 1,674 Treg transcriptomes that had been assigned a discrete transcriptional state by Ecotyper (Figure 3H). S01 Tregs were enriched for a resting Treg signature (Figure 3H) and, consistent with their co- association with S03 macrophages (ecotype 6) (Figure 3D), multiple transcriptional modules contributing to macrophage recruitment and pro-inflammatory phenotypic skewing (Figure 3H).Attorney Docket No: 243735.000396 Compared to S01 Tregs, S02 Tregs were characterized by significant positive enrichment for proliferation, reactive oxygen species, oxidative phosphorylation, and apoptosis genesets as well as positive regulation of B-cell activation and proliferation (Figure 3H). Treg oxidative stress within the tumor microenvironment has been shown to induce Treg apoptosis and promote adenosine-mediated myeloid-derived suppressor cell (MDSC) recruitment (Maj 2017; Del Barrio 2016; Groth 2019; Ryzhov 2011). Consistent with this model, S02 Tregs co-associated with S02 PMNs (ecotype 1) (Figures 3B and 3D) and, compared to S01 Tregs, were characterized by lower expression of the master transcription factor regulating antioxidant gene expression, NFE2L2 / NRF2, indicating a greater vulnerability to oxidative stress, and increased expression of the cell surface nucleotidase NT5E / CD73, which converts AMP to adenosine (Tables 5-13). Thus, FL-associated regulatory T-cells encompass at least two distinct subtypes which differentially influence TME composition, host anti-tumor immunity, and sensitivity to frontline immunochemotherapy.

[0457] In single cell analyses of 3,002 Tfh transcriptomes, S01 TFH, which was enriched in FL1 (Figure 3C), was significantly associated with inferior FFS and OS while S02 and S03 were significantly associated with superior FFS and OS (Figure 12). S01 TFH co-associated with S01 Tregs and S02 PMNs (ecotype 1) (Figure 3D) and, compared to other Tfh transcriptional states, exhibited higher enrichment scores for transcriptional modules regulating B-cell activation and proliferation as well as lower enrichment for pathways positively regulating myeloid leukocyte activation (Figure 3H; Tables 5-13). In contrast, S02 and S03 TFH were enriched for a Th17- type immune response signature (Figure 3H; Tables 5-13). S01 TFH expressed significantly less IL-21 (Figures 8-18), a mediator of effector T-cell cytotoxicity and anti-tumor immunity (Niogret 2021) and, consistently co-occurred with two dysfunctional / exhausted effector T-cell states, S01 CD8+ T-cells (TCD8) and S01 gamma-delta T-cells (TGD) (ecotype 1) (Figure 3D; Figures 8-18), which were characterized by significantly lower enrichment scores for proliferation and cytotoxicity compared to other transcriptional states (Figures 8-18).

[0458] Collectively, these findings underscore the clinical relevance of accounting for transcriptional and functional heterogeneity among immunophenotypically-defined immune cell populations in the characterization of lymphoma-associated microenvironment populations.Attorney Docket No: 243735.000396 Example 6. Myeloid cell populations drive patient outcomes after frontline rituximab and chemotherapy.

[0459] In univariate proportional hazards models of the individual TME states, S03 macrophages (E6) and S03 PMNs (E4) emerged as the strongest predictors of superior and inferior overall survival, respectively (Figure 3G). Enrichment for S03 macrophages was significantly associated with superior 5-year FFS (76.4% [95% CI 67.0-87.2] vs.47.1% [95% CI 36.6-60.6], P=2.2E-4) as well as 5-year OS 88.2% [95% CI 80.9-96.2] vs.66.2% [95% CI 55.8- 78.4], P=5.0E-3) and independently contributed to both FFS and OS in multivariate analyses with m7-FLIPI score (multivariate FFS HR 0.01, P=0.038; multivariate OS HR 0.0062, P=0.045) (Figure 4C). In contrast, enrichment for the S03 PMN state was characterized by a 5-year overall survival of 64.3% (95% CI 48.8-84.7) compared to 80.5% (95% CI 73.3-88.3, P=0.031) among patients not enriched for S03 PMNs (Figure 4I). Collectively, these findings demonstrate that transcriptionally defined myeloid cell types are significant predictors of FL treatment outcomes.

[0460] The prognostic significance of macrophages in FL has been difficult to resolve due to varying reports from the pre- and post-rituximab eras and heterogenous immunophenotypically- based macrophage subtype classification criteria across studies (Kridel 2015; Marques-Piebelli 2022; Gouni 2021; Stevens 2017; Chen 2019; Canioni 2008; Farinha 2005). In the analyses described herein, digital cytometry with transcriptional subtyping identified three distinct macrophage subsets that were characterized in single cell gene set enrichment analyses by distinct signaling pathways and biological features (Figures 4A-4B). Favorable-risk S03 macrophages (S03 MF) were distinguished by significantly increased differential expression of the G protein-coupled receptor GPR183 (EBI2) and characterized by a pro-inflammatory (M1) gene expression signature with significant positive enrichment for chemotaxis, phagocytosis, activated FC receptor signaling, and complement-induced cytotoxicity pathways as well as positive regulation of NK cell chemotaxis and NK-mediated anti-tumor immunity (Figures 4A- 4B, 4E; Figure 16). GPR183 has previously been associated with a pro-inflammatory macrophage phenotype and is activated by oxysterol ligands (Preuss 2014; Spann 2013; Rutkowska 2013), the production of which was upregulated in the co-occurring S01 regulatory T-cell state (TREG S01) (Figure 3H). S02 macrophages were similarly enriched for multiple phagocytosis pathways but also expressed transcriptional modules positively regulating B-cellAttorney Docket No: 243735.000396 proliferation and were not enriched for positive regulation of NK-mediated anti-tumor immunity pathways, while S01 macrophages were negatively enriched for phagocytic gene expression programs and pathways activating immune effector processes (Figure 4B). Thus, FL-associated macrophages exhibit shared and unique gene expression programs that likely variably mediate lymphoma clearance. These findings support a model in which macrophages that contribute to favorable responses to immunochemotherapy synchronously leverage innate and adaptive arms of the host immune response.

[0461] Neutrophilic myeloid-derived suppressor cells (PMN-MDSCs) were previously identified as drivers of inferior outcomes in multiple malignancies (Steen 2021; Veglia 2021; Jaillon 2020; Kim 2022), but have not been well-described in FL. Digital cytometry analyses of multiple independent FL cohorts revealed that the S03 PMN state co-occurred with dysfunctional effector T-cell states (S03 TCD8 and S03 TGD) (Figure 3D; Figure 17E), suggesting that S03 PMNs may represent PMN-MDSCs. Consistent with this possibility, at the single cell level, S03 PMNs were characterized by significantly increased differential expression of canonical PMN- MDSC marker genes including VEGFA and OLR1 (Condamine 2016) (Figure 4F). Single-cell gene set enrichment analyses revealed that, compared to other PMN transcriptional states, S03 PMNs are characterized by significantly lower enrichment scores for neutrophil chemotaxis, extravasation, and degranulation as well as lymphocyte activation and host anti-tumor immunity gene modules (Figure 4G), supporting their characterization as PMN-MDSCs (Condamine 2016). In order to determine whether S03 PMNs interact with co-associated effector T-cell states identified in digital cytometry analyses, we performed single cell intercellular ligand-receptor communication modeling using the CellPhoneDB repository, which predicted multiple interactions associated with suppression of T-cell effector function including engagement of the S03 PMN co-inhibitory T-cell ligand, CCL4L2, with its cognate T-cell receptor, VSIR (VISTA), which inhibits T-cell activation and cytokine production, and promotes peripheral tolerance (Yuan 2021) (Figure 4K). Consistently, in comparison to other FL-associated effector T-cell states, single cell gene set enrichment analyses of S03 TCD8 and S03 TGD states revealed hallmark characteristics of effector dysfunction including significantly lower enrichment scores for cytotoxicity and proliferation genes (Figures 14-15). These findings indicate that suppression of host anti-tumor immunity by PMN-MDSCs is a novel and potentially targetable driver of inferior survival in FL.Attorney Docket No: 243735.000396 Example 7. Transcriptionally-defined LNSC subsets are implicated in the expansion of myeloid- derived suppressor cells.

[0462] After having identified a significant association between PMN-MDSCs and high-risk FL, insight was then gained into microenvironment cellular communication networks that might contribute to PMN-MDSC enrichment. Single-cell ligand-receptor communication modeling was performed of the E4 microenvironment which included transcriptionally-defined lymph node stromal cell subsets (S02 FRCs, S03 LECs, S01 FDCs) (Figures 5A-5H) as well as mast cells and dysfunctional T-cell subsets. Within the E4 interactome, bidirectional crosstalk between S03 PMNs and S01 FDCs, S02 FRCs, and S03 LECs accounted for the most frequent interaction pairs (Figures 6A-6B), implicating these LNSC states as mediators of PMN recruitment and polarization toward an immunosuppressive phenotype. Consistent with an established role in MDSC recruitment (Zhang 2017; Wang 2023; Kumar 2017), CXCL2 was expressed by S01 FDCs, S02 FRCs, and S03 LECs (E4 LNSCs) and was predicted to bind to its cognate receptor, CXCR2, on S03 PMNs (Figure 6G). E4 LNSCs also were characterized by increased expression of TGFB1, which has an established role in polarization of PMNs toward an immunosuppressive, pro-tumoral state (Fridlender 2009) (Figure 6G). In addition, E4 LNSCs expressed major histocompatibility complex (MHC) molecules including HLA-F which was predicted to bind S03 PMNs via the inhibitory leukocyte immunoglobulin-like receptor B2 (LILRB2 / ILT4) (Favier 2016; Chen 2018) (Figure 6G). S01 FDCs also expressed TNF, which has been shown to induce T-cell suppressive activity in PMN-MDSCs (Aarts 2019) (Figures 5G and 6G). Notably, S03 LECs and S02 FRCs expressed CD47, which was predicted to bind the inhibitory myeloid- specific checkpoint signal regulatory protein-α (SIRPα) (Figure 6G), blockade of which has been demonstrated in vitro and in vivo to enhance neutrophil anti-tumor activity against Burkitt lymphoma B-cells opsonized with rituximab (Ring 2017) and as such may represent a novel therapeutic target. Together, these findings support the hypothesis that transcriptionally defined LNSC subsets contribute to FL TME immunosuppression through dynamic intercellular signaling circuits with neutrophilic MDSCs.

[0463] TME spatial co-association patterns were validated in primary patient samples using a CODEX imaging platform. CODEX was used to illustrate TME immunosuppression in high-risk transcriptional subtype FL using biopsy samples of pre-treatment FL grade 1-2. These samples were transformed to DLBCL within a year of frontline R-CHOP. Blood endothelial cellsAttorney Docket No: 243735.000396 mediated recruitment of PMN-MDSC as predicted by single cell ligand-receptor modeling. Increased FoxP3+ Tregs and exhausted / dysfunctional CD8 T-cells were closely associated with PMN-MDSCs (Figures 6C, 6F). Example 8. FL transcriptional signatures are independently predictive of FFS and OS in patients treated with frontline immunochemotherapy.

[0464] Bulk transcriptional signatures reflect the collective transcriptomic features of the malignant B-cell population and the TME. After having characterized significant differences in biology and microenvironment composition between the 7 FL subtypes, next was studied whether the FL subtypes were associated with significant variation in response to standard frontline immunochemotherapy. In order to evaluate possible survival associations, the transcriptomic classifier was run on a cohort of 137 pre-treatment FL transcriptomes from patients treated with frontline immunochemotherapy (GSE119214) and survival analyses were performed using subtype assignments as a discrete variable. Strikingly, these analyses revealed that the FL signatures widely stratified pre-treatment FL patients for both failure-free and overall survival.

[0465] FL4 was significantly associated with a reduced risk of POD24 (OR 0.155, P=0.0046) while five FL subtypes (FL1, FL2, FL3, FL5, and FL6) were significantly associated with an increased risk of POD24 (OR 7.1, P=0.0025). FL4 was associated with 90% 5-year FFS (95% CI 79.9-100) compared to 53.8% (95% CI 45.0-64.2) among all other subtypes (P=0.002) and in a multivariate analysis with m7-FLIPI score was independently predictive of superior FFS (HR 0.29, P=0.017) (Figures 7A, 7C, 7E, and 7G). The favorable outcomes predicted by the FL4 signature align with prior studies which identified alterations of EZH2 and MEF2B as predictors of longer FFS following frontline immunochemotherapy (Mottok 2018). Mottok et al. found negative FOXP1 IHC expression to mark FL with EZH2 and MEF2B alterations and, indeed, in GSE119214, FL4 was frequently characterized by low FOXP1 IHC expression (OR 0.29, P=0.0065). In contrast to the FL4 signature, however, the prognostic impact of FOXP1 expression was not independent of m7FLIPI (Mottok 2018), suggesting that the independent predictive value of the FL4 signature may be linked to its representation of TME transcriptional features. In support of this hypothesis, a hallmark feature of the FL4 TME (E6) was enrichment for S03 macrophages, which prognosticated for FFS and OS independent of m7FLIPI (Figure 4C).Attorney Docket No: 243735.000396

[0466] In contrast to FL4, the FL1 and FL5 signatures independently contributed to inferior FFS in multivariate analyses with m7FLIPI (FL1 HR 3.2, P=0.016; FL5 HR 3.48, P=0.017) (Figures 7A, 7C, 7E, and 7G). FL5 was associated with 61.5% 2-year FFS (95% CI 40.0-94.6) while FL1 was associated with 66.7% 2-year FFS (95% CI 51.1-87.0) (Figure 7A). Notably, in the Dreval et al. dataset (n=106; Dreval 2023), the FL1 signature was significantly associated with subsequent histologic transformation (15.6% of FL1 cases versus 0% all remaining cases, P=0.002), a finding which merits validation in a larger independent dataset.

[0467] Historically, predictive biomarkers of overall survival in FL following frontline immunochemotherapy have been elusive. While the m7FLIPI and PRIMA prognosticate for FFS, neither is predictive of OS independent of clinical risk factors. To this extent, in addition to FFS, we found that FL transcriptional signatures significantly stratified patients for overall survival (Figures 7B and 7D). FL4 and FL3 were significantly associated with superior 5-year OS (FL4: 93.3% [95% CI 84.8-100], FL3: 85% [95%CI 70.7-100]) while FL5, FL2, and FL6 were significantly associated with inferior 5-year OS (FL5: 46.2% [95% CI 25.7-83.0], FL2: 66.3% [95%CI 50.5-86.9], FL6: 70.6% [95%CI 51.9-95.9]). Moreover, in a multivariate model with m7-FLIPI score, FL4 independently contributed to superior OS (HR 0.21, P=0.008) while FL5 independently contributed to inferior OS (HR 4.68, P=0.008) (Figures 7F and 7H). Notably, FL5 was not associated with a distinct mutational signature compared to other FL subtypes, underscoring the utility of profiling unfractionated FL transcriptomes.

[0468] When the performance of FL transcriptional signatures was compared to current clinical and genetic risk stratification models, the clinically-agnostic transcriptional classifier in isolation modestly outperformed m7-FLIPI for predictions of FFS (C-index 62.9 vs.62.5) and OS (C-index 65.8 vs.64.8) and, importantly, when integrated with m7-FLIPI score, markedly improved discriminative power for both FFS (integrated C-index 68.0) and OS (integrated C- index 72.8). Collectively, these data demonstrate the importance of the FL TME in promoting disease progression and the potential utility of integrating bulk transcriptional data into current FL risk models to guide risk-adapted frontline therapy. Example 9. Patient classification of FL subtypes and treatments.

[0469] The FL classifier provides a scheme for identifying distinct biological subtypes of follicular lymphoma based on the level of one or more RNA transcripts in a biological sample containing tumor cells. The method comprises assigning one or more RNA transcripts to 1 of 7Attorney Docket No: 243735.000396 FL subtypes, calculating a quantitative score representing the relative level of RNA expression of the tumor cells for the genes defining each of the 7 subtypes, and classifying unfractionated tumor samples as 1 of the 7 subtypes based on the highest of the 7 scores. Given a ranked gene list derived from a normalized gene expression matrix of an FL sample, an enrichment score for each of the 7 FL signatures is calculated based on the degree to which the genes from each gene set are overrepresented at the top or bottom of the ranked list. The score represents a running- sum statistic which increases when a gene is encountered by walking down the ranked list and decreases when the gene is not encountered. Samples are assigned to 1 of the 7 transcriptional subtype classifications based on the highest enrichment score. The minimal essential gene set sufficient for patient classification is shown in Table 3. Table 3. Minimal essential gene set sufficient for patient classification. Subtype Gene Subtype Gene Subtype Gene Subtype Genevulnerabilities, enabling a transcriptionally-informed “precision medicine” approach to the selection of frontline therapy protocols. Treatments that may be beneficial in combination with or possibly as an alternative to standard frontline immunochemotherapy regimens for each of theAttorney Docket No: 243735.000396 7 subtypes are shown in Table 4, which is not exhaustive and may change based on current or future clinical trials in FL. Table 4. Potential treatments for each of the 7 FL subtypes. ^ ’ l- it t l- l-studies herein have utilized bulk tumor transcriptional profiling to gain new insights into FL biology and clinical behavior which are based not only on the malignant clonal population but also on the cellular elements of the microenvironment, enabling the identification of tumor- intrinsic and extrinsic determinants of treatment response and failure. Decomposition ofAttorney Docket No: 243735.000396 unfractionated FL transcriptomes revealed seven distinct FL subtypes characterized by distinct B-cell states, microenvironment compositions, and responses to frontline immunochemotherapy, supporting the concept that FL represents multiple biologically and clinically distinct disease entities.

[0472] High-resolution deconvolution of FL TME transcriptional states revealed that the host anti-tumor immune response and survival outcomes following frontline immunochemotherapy are shaped by diverse and transcriptionally-distinct microenvironment ecosystems and uncovered significant prognostic associations that were otherwise obscured when evaluated using traditional immunophenotypic definitions of cellular identity (Steen 2021). Notably, the analyses herein implicate expanded compartments of transcriptionally-defined and functionally distinct myeloid cell subtypes as potent drivers of clinical outcomes in FL patients treated with frontline immunochemotherapy. A subset of pro-inflammatory macrophages that contribute to superior survival outcomes independent of m7-FLIPI score were identified and also a novel role for neutrophilic myeloid-derived suppressor cells as mediators of inferior OS in FL was uncovered, which was linked to bidirectional crosstalk with transcriptionally-defined LNSC subsets. These findings reinforce the notion that transcriptional plasticity within the FL TME is clinically relevant and introduce a cohesive blueprint for investigating novel pathway-directed treatment strategies in FL based on therapeutic vulnerabilities associated with specific transcriptional subtypes.

[0473] Here, bulk transcriptional profiling using NMF was leveraged to identify multiple signatures which were predictive of FFS and OS independent of clinicogenetic risk classification and enhanced discriminative power for both endpoints when integrated with m7FLIPI.

[0474] Transcriptional subtyping identified a very favorable risk subset of FL (FL4). FL4 was defined by enrichment for transcriptionally-distinct subsets of pro-inflammatory macrophages and regulatory T-cells. In addition to identifying markers of longer FFS, the FL4 signature adds to the existing data by capturing a unified biological portrait of an FL subtype which is significantly associated with favorable overall survival independent of clinicogenetic risk classification.

[0475] Bulk transcriptional profiling also identified multiple biologically distinct FL subtypes which were predictive of inferior FFS and OS independent of clinicogenetic risk classification. The FL1 signature was predictive of inferior FFS independent of m7FLIPI and was significantlyAttorney Docket No: 243735.000396 associated with histologic transformation. In addition, the FL5 subtype, which was also characterized by enrichment for neutrophilic MDSCs, was independently predictive of inferior FFS as well as OS but did not harbor a unique mutational signature. Collectively, these findings demonstrate that frontline immunochemotherapy treatment outcomes are mediated by heterogeneous tumor intrinsic and TME-associated biological pathways which are not fully captured by exome alterations but are readily discernible at the bulk transcriptomic level.

[0476] In summary, deconstruction of the FL transcriptional landscape at the bulk tumor level and by digital cytometry revealed an extensive and diverse panorama of biologically distinct FL subtypes which significantly associated with disparate frontline treatment outcomes. These findings support incorporating transcriptional signatures into existing risk models in order to advance frontline precision medicine strategies in FL.

[0477] Below are the methods used in the Examples described above. Bulk FL transcriptional signature discovery.

[0478] To delineate the biological heterogeneity of FL at the bulk tumor level, non-negative matrix factorization (NMF) was performed on 302 FL bulk microarray transcriptomes (GSE127462) that were profiled with the Affymetrix Human Genome U133 Plus 2.0 Array (Steen 2021; Luca 2021; Newman 2019). Raw CEL files were processed with the ‘affy’ R package using a BrainArray (v25) custom chip definition file (CDF) and mas5 normalization based on the workflow originally described by Newman et al. (Newman 2015). Bulk NMF was performed using the ‘NMF’ R package (v0.20.0). All cases were pre-treatment FL grade 1-3a with no additional clinical information provided and as such, the discovery cohort analysis was agnostic to clinical outcomes. FL bulk signature mutational profiling.

[0479] In order to gain insight into the genetic alterations associated with the 7 bulk transcriptional subtypes, bulk signatures were recovered from 169 pre-treatment FL patient samples that had paired exome-level data.104 cases were profiled by RNA-seq and whole genome sequencing (WGS) (Dreval 2023) and 65 by microarray gene expression profiling and targeted exome sequencing of 308 lymphoid genes (Ma 2022) using the originally published variant cells. Associations between FL transcriptional subtypes and recurrent genetic alterations were evaluated for the 308 genes profiled by Ma et al by the Fisher exact test using the ‘maftools’ R package. In addition, the prevalence of select recurrent alterations was validated inAttorney Docket No: 243735.000396 a paired cohort of 107 pre-treatment FL samples profiled by paired WG-DASL HT and a 7 gene targeted exome sequencing panel (GSE66166). Associations between copy number alterations from the Dreval et al dataset and FL subtypes were evaluated by Fisher’s with the ‘GAMBLR’ R package using the original GISTIC2.0 output files. FL bulk signature gene set enrichment analysis.

[0480] Bulk gene set enrichment analyses (GSEA) were performed on the discovery microarray cohort with GSEA v4.3.2 using the Human Molecular Signatures Database (MsigDB) collection and the Staudt Lab SignatureDB (1 / 24 / 2022 update; lymphochip.nih.gov / signaturedb / ). Normalized enrichment scores (NES) reflect comparisons between samples assigned to the transcriptional state specified and all remaining samples. Deconvolution of microenvironment features associated with FL subtypes by digital cytometry with transcriptional subtyping.

[0481] To determine the TME features associated with the transcriptional signatures identified in bulk transcriptome analyses and gain insight into the role of specific TME cell transcriptional states in shaping FL clinical behavior, digital cytometry was performed with transcriptional subtyping using CIBERSORTx and Ecotyper (Newman 2015; Steen 2021). To recapitulate the unique stromal landscape of follicular lymphoma, a novel lymph node stromal cell (LNSC) signature matrix was developed which accounts for follicular dendritic cells (FDCs), fibroblastic reticular cells (FRCs), lymphatic endothelial cells (LECs), and blood endothelial cells (BECs) in place of the default Ecotyper TR4 stroma signature matrix. To generate the LNSC signature matrix, transcriptomes of FACS-sorted FDCs, FRCs, LECs, and BECs which had been profiled with the Clariom S Human microarray platform (GSE178272; Heesters 2021) were used, and bulk transcriptomes of human whole blood sample controls which had also been profiled with the Clariom S Human platform (GSE116835) were used. Raw CEL files were processed with the ‘affy’ R package using BrainArray CDF files (v25) for input into the CIBERSORTx Create Signature Matrix module. Imputation of cell fractions and gene expression with the CIBERSORTx Docker desktop implementation was performed separately for LNSC and LM22 populations according to the standard EcoTyper workflow, substituting the LNSC matrix for TR4 and removing the LNSC “leukocyte” profile from downstream Ecotyper analyses. The 22 cell types from the LM22 matrix were merged to form 14 high-level cell identity classes (Tables 5-13). LM22 cell profiles were imputed without batch correction as both LM22 and theAttorney Docket No: 243735.000396 discovery cohort were profiled with Affymetrix U133 platforms while the LNSC matrix was processed using the B-mode batch correction function to account for implicit technical differences between the Clariom S and U133 platforms. For each cell type, purified digital transcriptomes were subsequently passed to Ecotyper for transcriptional state and ecotype discovery using the Presorted Bulk Discovery module. Single-cell FL atlas.

[0482] To analyze the imputed TME transcriptional states at single cell resolution, an integrated FL single cell atlas was constructed using 40 FL 10x single-cell RNAseq datasets from 5 independent studies (Han 2021; Abe 2022; Zhang 2019; Roider 2020; Steen 2021) and single cell transcriptomes were annotated with discrete transcriptional states from the discovery cohort (Figure 8). Datasets from each study were uniformly processed according to the standard Seurat workflow in R prior to integration. In order to ensure low quality cells, empty droplets, and doublets were filtered out, only transcriptomes with unique gene counts greater than 200 and less than 2500 with <10% mitochondrial genes were passed forward with the exception of macrophages, which have been shown to have a mean mitochondrial DNA proportion greater than 10% (Osorio 2021). In order to recover additional cell types (neutrophils, macrophages, dendritic cells, and mast cells), an integrated single cell atlas of myeloid cells (Salcher 2022) using the originally published integrated count matrix and high-level annotations was drawn upon (Figure 8).

[0483] Prior to integration, single cell count matrices for each sample were passed to the Ecotyper single cell recovery module for transcriptional state assignment using the originally published high-level annotations from each study with the exception of EGAD00001008311, which was not annotated. In this case, annotation was performed using the canonical marker- based criteria used in the original publication (Abe 2022). Only single cell transcriptomes that were assigned a discrete transcriptional state by Ecotyper were integrated into the atlas. Integration of annotated samples was performed according to the standard Seurat canonical correlation analysis (CCA) integration workflow using the NormalizeData, FindVariableFeatures, and IntegrateData functions (Stuart 2019). The Seurat FindMarkers function was used for differential gene expression analyses using the Wilcox rank sum method with an FDR q value threshold of <0.05 used to define significant differences. Differential gene expression analyses reflect comparisons of individual immunophenotypically-defined cellAttorney Docket No: 243735.000396 transcriptional states to the remaining transcriptional states within the corresponding identity class. Single cell gene set enrichment analyses.

[0484] Single cell gene set enrichment analysis (scGSEA) was performed with the ‘escape’ R package (Borcherding 2021) using the mSigDB and Staudt Laboratory SignatureDB gene set collections (Liberzon 2015). Enrichment for B-cell developmental stages was evaluated using the following signatures from the single-cell cell-of-origin gene sets from Holmes et al: "DZ-A UP", "DZ-A DWN", "DZ-b UP", ""DZ-b DWN", "DZ-c UP", "DZ-c DWN", "INT-a UP", "INT-a DWN", "INT-b UP", "INT-b DWN", "INT-c UP", "INT-c DWN", "INT-d UP", "INT-d DWN", "INT-e UP", "INT-e DWN", "LZ-a UP", "LZ-a DWN", "LZ-b UP", "LZ-b DWN", "PreM UP", "PreM DWN", "PBL-a UP", "PBL-a DWN", "PBL-b UP", "PBL-b DWN". Normalized single cell enrichment scores were calculated in ‘escape’ and comparisons between individual transcriptional states to all remaining transcriptional states of that particular cell type were performed using the Seurat FindAllMarkers functions using the Wilcoxon rank sum method with the minimum threshold set to 0.01. Only log2fold NES differences with q-values <0.05 were considered significant and reported. Predicted intercellular ligand-receptor interactions.

[0485] The python implementation of CellPhone DB 4.0 (Garcia-Alonso 2022) was used to predict intercellular ligand-receptor interactions using single cell transcriptomes from the integrated atlas which had been annotated with a discrete transcriptional state using the ‘statistical_analysis’ method. Dot plots and circos plots representing the CellPhoneDB output were generated with the ‘ktplots’ R package and only interactions with adjusted P-values <0.05 by the method of Benjamini and Hochberg were considered significant. Evaluating the prognostic significance of FL TME transcriptional state abundance and bulk signatures in patients treated with frontline immunochemotherapy.

[0486] To identify possible associations with clinical outcomes in patients treated with frontline immunochemotherapy, clinically-annotated transcriptomes from the BC Cancer Agency cohort (GSE119214) was drawn upon, which includes gene expression profiles for 137 FL patients treated with frontline rituximab in combination with chemotherapy (cyclophosphamide, vincristine and prednisone) (Pastore 2015). Within this group, 113 received rituximab maintenance with intention to treat (Pastore 2015).Attorney Docket No: 243735.000396

[0487] Associations between imputed cell type abundance and survival were evaluated by univariate and multivariate Cox proportional hazards regression models using the relative frequency of TME transcriptional states imputed by Ecotyper as a continuous variable using the survminer R package. Associations between bulk FL transcriptional signatures and survival were evaluated by univariate and multivariate Cox proportional hazards regression models with FL signatures as a discrete variable. Survival time probabilities associated with enrichment for specific TME cell states and bulk signatures were computed using the method of Kaplan and Meier with significance determined by two-sided log rank tests. Enrichment for individual TME transcriptional states was defined based on the most abundant transcriptional state using the Ecotyper state assignment algorithm. All analyses were performed with the ‘survival’ and ‘survminer’ R packages. Table 5. Mutations. Significant associations between gene mutations and FL transcriptional subtypes from Dreval 2023 and Ma 2022 46 31 62 76 99 2 49 04 9 28 51 88 35 7 66 78Attorney Docket No: 243735.000396 66 26 22a e . opy umer era ons y u ype rom oe- enome equencng. ) n() en(3 6 4Attorney Docket No: 243735.000396 3 5 3 3 5 7 8Attorney Docket No: 243735.000396 7Table 7. LNSC signature matrix. Gene BEC FDC FRC LEC CD45Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396State Holmes scCOO geneset NES_avgLog2FC p_val p_val_adjAttorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396a e . sc . State Gene avg_log2FC pct.1 pct.2 p_val p_val_adj BS01 MZB1 0457352636 024 0155 779452E-68 37932E-63 7 6 9 5 6 3 7 4 8 0 0 9 1 0 8 6 5 0 0 3Attorney Docket No: 243735.000396 9 3 4 9 2 0 9 1 7 6 8 6 7 7 9 6 5 0 6 7 3 2 4 8 0 3 7 8 6 2 5 7 1 3 8 3Attorney Docket No: 243735.000396 4 5 7 1 8 4 8 8 4 5 8 2 4 1 6 3 4 0 9 1 6 9 7 8 4 5 7 2 6 8 9 5 2 3 6 9Attorney Docket No: 243735.000396 4 7 8 0 5 5 8 4 6 7 0 7 1 0 2 5 2 2 7 3 8 0 1 1 3 2 5 3 1 4 9 5 1 3 4 9 6 2 8Attorney Docket No: 243735.000396 9 7 8 2 8 0 4 2 0 6 5 0 4 7 0 5 7 8 7 4 7 4 2 3 7 6 3 5 2 5 3 5 6 5 0Attorney Docket No: 243735.000396 2 5 0 5 3 6 4 8 9 2 0 5 7 1 5 6 0 8 5 7 1 8 2 7 4 7 1 0 1 0 6 7 2 7 7 6 4Attorney Docket No: 243735.000396 0 6 3 5 3 4 3 2 7 0 5 6 9 3 3 0 0 3 8 4 7 3 9 1 1 3 0 1 8 0 5 1 2 8 6 7Attorney Docket No: 243735.000396 6 7 2 9 1 6 3 8 6 1 7 8 0 5 4 1 6 4 4 5 8 9 6 9 8 9 7 4 1 9 5 3Attorney Docket No: 243735.000396 7 2 0 2 7 4 2 4 7 7 2 9 4 7 4 6 5 5 3 9 7 2 5 8 7 2 6 6 1 8 2 5 2 1 4Attorney Docket No: 243735.000396 1 5 4 3 0 0 7 4 4 1 2 2 1 7 7 8 7 6 2 6 9 1 0 6 2 0 5 9 3 7 6 9 6 4 4Attorney Docket No: 243735.000396 5 2 0 6 5 7 5 4 4 0 3 9 4 7 7 9 6 9 6 5 7 7 0 3 8 5 1 4 0 9 8 3 5 6 1 6 0Attorney Docket No: 243735.000396 1 6 6 0 5 6 5 0 0 5 8 5 8 5 2 9 0 3 8 4 0 7 2 9 4 9 3 1 3 9 2 7 0 0Attorney Docket No: 243735.000396 0 7 6 1 4 6 4 4 5 3 8 9 9 9 3 4 3 8 3 2 7 8 2 8 9 3 5 8 3 7 6 2 0 2 8 1 2Attorney Docket No: 243735.000396 4 2 8 1 5 5 3 7 7 8 9 9 8 2 6 3 3 5 1 0 2 4 0 9 7 9 6 7 0 5 8 4 9 1 4 6 7Attorney Docket No: 243735.000396 0 5 0 7 7 1 6 9 3 1 5 6 1 4 8 2 5 9 7 0 2 5 8 2 0 9 3 4 1 3 7 2 3 4 6 4 0Attorney Docket No: 243735.000396 1 5 3 0 2 2 8 3 3 1 5 6 8 6 8 6 9 3 7 5 8 1 3 1 2 1 7 4 5 2 3 4 0 3 6Attorney Docket No: 243735.000396 9 6 2 7 5 3 8 8 5 6 5 8 2 5 1 2 0 7 5 8 5 2 7 7 9 4 2 3 0 6 3 1 7 6 0 5 0 7 8Attorney Docket No: 243735.000396 7 0 5 4 3 4 9 3 1 1 7 1 8 2 8 4 6 6 0 8 5 1 7 7 4 6 4 3 6 8 3 8 1 6 7 3 1 2Attorney Docket No: 243735.000396 4 6 2 8 2 1 5 0 7 7 7 1 2 8 7 0 3 5 5 4 9 8 3 6 7 5 6 6 6 1 4 6 5 4 3Attorney Docket No: 243735.000396 0 4 1 0 6 1 4 8 1 4 7 6 6 9 4 2 2 0 2 7 2 6 0 2 4 9 2 8 4 3 8 5 4 6 1 0 1Attorney Docket No: 243735.000396 8 4 5 3 2 3 3 0 9 9 8 2 4 2 7 6 7 3 0 0 4 9 2 4 1 2 5 4 6 9 8 7 9 3 2Attorney Docket No: 243735.000396 7 9 9 1 9 4 8 5 3 7 2 2 8 4 6 8 5 7 1 6 9 6 8 0 6 0 7 9 8 6 7 4 5 8 2 3 2Attorney Docket No: 243735.000396 8 9 6 9 0 3 8 5 1 6 2 4 0 5 6 7 4 9 5 1 6 3 8 5 5 5 5 5 8 8 8 1 3 4 6 3Attorney Docket No: 243735.000396 2 3 8 9 5 0 3 4 2 0 4 6 5 2 5 2 2 9 0 2 7 7 6 8 8 7 5 7 5 3 6 7 6Attorney Docket No: 243735.000396 9 3 3 9 6 7 7 6 8 8 3 7 8 3 3 9 6 2 1 9 2 1Attorney Docket No: 243735.000396 4 5 4 2 2 3 9 3 2 7 2 7 5 5 4 6 5 5 9 6 7 1 0 0 0 6 8Attorney Docket No: 243735.000396 5 6 6 7 6 6 5 5 3 3 4 3 9 3 9 2 8 3 1 7 4 3 2 4 0 9 7 1 2 5 6 5 9Attorney Docket No: 243735.000396 7 7 5 0 0 4 6 6 8 9 7 1 9 6 5 6 6 5 7 6 1 8 5 3 8 9 4 5 7 9 8 0 5Attorney Docket No: 243735.000396 5 5 8 2 6 2 8 4 3 1 3 6 2 5 6 2 6 5 2 3 3 1 3 9 3 4Attorney Docket No: 243735.000396 5 5 5 6 7 7 8 9 4 2 2 9 2 5 6 5 5 3 3 5 3 5 5 7 1 7 5 8 5 9 5 6 0Attorney Docket No: 243735.000396 8 5 0 0 5 4 1 4 2 7 1 2 4 8 1 0 9 9 8 9 3 5 5 2 3 5 0 9 5 9 6 3 5 6 5 9 0 2 7 3Attorney Docket No: 243735.000396 5 1 5 7 4 3 8 0 9 8 1 5 5 6 3 7 3 9 0 9 2 7 2 9 8 2 3 7 6 9 2 9 0 9 5Attorney Docket No: 243735.000396 3 3 4 6 8 1 9 1 6 7 3 6 9 4 5 6 5 5 4 0 6 8 2 5 7 5 6 5 6 4 7 5 8Attorney Docket No: 243735.000396 5 8 5 5 4 6 7 9 2 1 6 5 5 1 5 3 1 1 9 4 4 8 8 5 0 6Attorney Docket No: 243735.000396 1 6 9 6 5 7 7 8Attorney Docket No: 243735.000396 5 9 5 2 9 8 1 9 9 8 8 3 8 1 0 6 5 5 7 8 3 7Attorney Docket No: 243735.000396 3 1 6 5 1 7 5 9 7 5 6 7 8 6 7 8 6 4 1 6 5 6Attorney Docket No: 243735.000396 2 8 6 9 5 5 6 0 8 0 9 4 8 1 1 8 8 6 1 5 2 2 8 0 3 7 3 0 1 1Attorney Docket No: 243735.000396 0 3 4 8 7 2 4 0 6 6 4 4 8 9 5 3 1 9 1 7 9 4 5 2 9Attorney Docket No: 243735.000396 1 4 0 3 2 3 4 4 9 3 5 4 8 1 3 5 7 2 8 7 6 4 4 8 4 3 8 7 3 7 5 5 2 8 3 7 0Attorney Docket No: 243735.000396 0 0 1 4 3 7 1 6 2 6 5 2 5 9 5 4 3 1 6 7 0 4 8 4 7 4 0 7 6 0 7 4 0 1 9 3 8 8Attorney Docket No: 243735.000396 0 7 1 5 5 7 2 2 2 5 6 2 1 3 1 7 1 3 9 7 3 0 4 4 5 1 2 5 9 8 0 8 9 6 5 2 8Attorney Docket No: 243735.000396 6 1 2 0 6 3 7 8 5 9 4 1 1 2 5 2 1 4 6 5 5 5 8 0 4 1 4 8 0 6 9 6 6 4 4 1Attorney Docket No: 243735.000396 8 2 0 8 8 0 4 7 9 8 4 9 1 2 4 5 0 4 0 5 3 5 5 1 9 8 1 4 2 1 2 4 9 6 4 0 5Attorney Docket No: 243735.000396 1 1 7 4 6 1 3 6 3 3 3 0 3 8 8 0 8 4 5 6 1 8 5 0 4 1 4 8 5Attorney Docket No: 243735.000396 7 1 2 7 9 7 4 6 7 7 7 8 5 8 1 9 0 5 7 1 7 0 7 4 2 7 5 6 1 6 2Attorney Docket No: 243735.000396 6 9 6 7 7 5 9 5 8 8 3 3 5 1 1 3 5 8 8 8 5 3 6 0 7 8 8Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396. . . . SYMBOL avg_log2FC pct.1 pct.2 p_val p_val_adj PLIN2 2.146581002 0.272 0.097 2.5582E-220 4.5564E-216Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Table 12. Bulk GSEA (msigdb). Subtype Pathway NES FDR q-valAttorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396Attorney Docket No: 243735.000396 Table 13. GSEA. Sbt Pthw (hllmrk) NES FDR Sbt GENESET (St dt Lb) NES FDR q- 4 3 0 9 6 7 1 7 8 7 4 9 4 3 3 2 6 6 3 9 4 1 7 3 0 0 9 7 7 8 0 7 0 8 1 8 8 9 1 8 6 5 7 8 8 7 8 9 0 7Attorney Docket No: 243735.000396 4 2 2 3 7 5 8 9 9 6 7 6 8 4 3 6 3 0 5 2 6 5 4 7 R q- 8 7 0 3 1 3 6 6 0 6 8 1 9 0 6 1 1 1 9 5 0 9 9 4 6 3 1 9Attorney Docket No: 243735.000396 57 6 2 1 1 3 0 1 5 7 7 4 8 7 9 8 3 5 7 5 9 5 7 9 6 7 1 8 8 9 2 6 1 2 9 4 3 7 8 9 4 9 4 6 7 9 8 5 3 0 2 8 2 7 3Attorney Docket No: 243735.000396 51 8 9 7 2 9 1 7 2 3 0 8 4 4 4 4 4 3 7 3 3 5 3 3 6 9 5 4 2 2 8 6 3 4 2 8 0 8 3 1 9 3 4 1 7 7 4 0 2 2 5Attorney Docket No: 243735.000396 52 0 9 2 6 6 4 2 4 3 9 5 0 9 3 6 9 8 0 6 4 1 8 2 6 8 1 6 9 7 0 9 2 7 8 8 4 5 0 8 6 4 8 7 7 8 1 3 8 0 0 0 8Attorney Docket No: 243735.000396 27 8 0 1 8 7 8 7 6 5 3 6 9 9 9 0 3 4 8 8 1 1 1 9 4 3 4 4 5 0 0 0 4 7 8 0 8 0 0 8 9 3 4 4 3 3 3 5Attorney Docket No: 243735.000396 86 1 3 7 1 1 0 2 1 6 7 2 1 3 7 7 1 2 9 7 7 8 0 9 3 3 2 0 7 2 1 9 7 8 0 3 3 9 2 2 2 1 0 7Attorney Docket No: 243735.000396 9 3 1 0 6 5 5 0 9 6 7 7 5 0 1 1 0 9 9 9 5 1 5 6 0 3 2 8 8 6 0 7 8 7 1 0 2 1 2 5 6 4Attorney Docket No: 243735.000396 08 0 5 3 6 5 7 8 6 2 8 9 0 9 0 6 7 2 4 8 9 8 0 2 4 2 0 2 1 8 9 4 9 5 4 3 5 5 4 9 0 1 5 6 5 2Attorney Docket No: 243735.000396 97 5 0 9 5 5 0 0 8 0 1 3 1 2 2 9 9 9 1 8 2 7 8 9 0 9 3 6 6 7 4 6 6 4 1 9 5 4 2 3 0 5 6 6 1 1 9Attorney Docket No: 243735.000396 41 6 1 1 9 0 3 2 5 4 7 8 0 9 5 0 0 0 0 0 0 2 1 2 2 2 2 3 3 2 2 2 3 4 3 3 4 4 6 8 9 9 9 9Attorney Docket No: 243735.000396 09 9 0 0 1 1 1 1 2 4 4 4 5 6 9 9 1 2 1 1 1 3 7 6 8 8 9 9 0 0 1 0 0 0 1 3 6 7 8 7 8 8 9 9 0 2 4 5Attorney Docket No: 243735.000396 46 6 7 6 1 2 2 4 4 4 5 7 0 0 1 1 4 5 5 8 9 9 8 9 1 5 4 0 6 0 3 4 4 4 4 4 3 4 5 5 4 3 3Attorney Docket No: 243735.000396 26 9 1 6 5 8 8 0 4 6 1 0 0 0 9 9 8 8 9 0 5 4 3 3 2 2 1 7 3 4 4 0 3 0 4 3 2 8 1 2 5 0 8Attorney Docket No: 243735.000396 1 3 7 2 2 2 4 4 1 2 0 1 1 1 1 0 4 7 1 8 8 8 4 3 4 4 7 7 6 6 8 8 4 1 9 1 0 7 7 4 8 5 4 3Attorney Docket No: 243735.000396 10 0 9 3 0 8 7 8 8 7 3 2 7 6 9 9 0 9 9 7 3 4 1 2 8 4 4 2 1 1 2 0 9 6 7 5 3 0 8 8 1 7 7Attorney Docket No: 243735.000396 81 5 0 5 3 7 1 5 5 3 1 6 4 2 2 6 5 6 7 2 1 2 7 8 7 6 7 6 7 7 0 0 5 4 5 9 2 0 3 4 4 1 2 3 5 7 9 0 6 2 8Attorney Docket No: 243735.000396 52 9 7 4 7 3 1 2 9 5 0 8 2 4 8 3 9 2 3 4 5 7 0 9 4 1 8 4 2 7 4 3 0 5 0 0 6 3 8 4 1 5 1 5 2 8 6 3 6 5 1 9Attorney Docket No: 243735.000396 67 4 9 1 7 3 0 6 1 1 2 2 6 4 6 1 1 1 8 9 6 8 3 0 1 0 5 4 9 4 0 1 9 3 3 9 2 9 6 2 7 5 4 5 7 5 0 6 9 5 3 9 8 4 8 3Attorney Docket No: 243735.000396 8 9 0 7 8 0 0 5 1 8 8 3 7 5 1 6 4 7 4 8 2 3 3 2 3 4 3 4 4 5 5 6 6 6 6 6 6 7 8 8 7 7 7 0 0 0 0 2 3 3 3 2Attorney Docket No: 243735.000396 3 3 3 3 4 4 7 7 9 2 3 4 5 8 8 8 9 0 0 9 2 8 9 0 0 0 2 1 1 1 4 6 8 9 1 0 1 5 7 9 9 3 0 9 0 9 1 3 6Attorney Docket No: 243735.000396 75 5 7 3 9 2 1 1 5 1 5 1 1 1 2 1 9 2 4 4 3 4 5 4 3 3 2 3 2 8 0 0 4 5 5 9 6 1 6 7 2 6 1 9 4 3Attorney Docket No: 243735.000396 41 4 4 7 3 3 5 4 3 1 4 3 4 0 0 1 8 0 8 8 4 4 2 9 0 9 1 6 0 6 8 7 0 1 0 2 9 7 5 6 8 8 4 6 9 7 5 7Attorney Docket No: 243735.000396 58 1 6 3 1 3 6 8 0 8 2 8 6 4 3 5 3 4 5 8 9 0 2 8 6 2 8 1 9 3 9 3 1 3 7 9 4 3 3 5 7 4 6 3 1 8 9 0 3Attorney Docket No: 243735.000396 96 1 6 4 3 7 1 4 6 2 2 3 3 2 3 4 3 4 4 5 5 6 6 6 6 6 6 7 8 8 7 7 7 0 0 0 0 2 3 3 3 2 3 3 3 3 4Attorney Docket No: 243735.000396 14 7 7 9 2 3 4 5 8 8 8 9 0 0 9 2 8 9 0 0 0 2 1 1 1 4 6 8 9 1 0 1 5 7 9 9 3 0 9 0 9 1 3 6 5 5 7 3Attorney Docket No: 243735.000396 89 2 1 1 5 1 5 1 1 1 2 1 9 2 4 4 3 4 5 4 3 3 2 3 2 8 0 0 4 5 5 9 6 1 6 7 2 6 1 9 4 3 1 4 4 7Attorney Docket No: 243735.000396 73 3 5 4 3 1 4 3 4 0 0 1 8 0 8 8 4 4 2 9 0 9 1 6 0 6 8 7 0 1 0 2 9 7 5 6 8 8 4 6 9 7 5 7 8 1 6 3 1 3Attorney Docket No: 243735.000396 96 8 0 8 2 8 6 4 3 5 3 4 5 8 9 0 2 8 6 2 8 1 9 3 9 3 1 3 7 9 4 3 3 5 7 4 6 3 1 8 9 0 3 6 1 6 4Attorney Docket No: 243735.000396 13 7 1 4 6 2 0 1 0 0 0 0 0 0 1 2 2 3 4 4 5 7 8 8 0 2 2 4 3 5 5 6 7 7 8 8 9 9 9 2 2 1 4 6 8 9 9 9 0 4Attorney Docket No: 243735.000396 4 8 7 9 2 3 3 4 9 0 6 6 5 6 7 6 8 8 8 9 9 4 6 2 0 7 5 0 9 6 6 9 6 4 3 2 8 0 8 7 4 4 7 6 8 8 9 9 3 8 3 2Attorney Docket No: 243735.000396 1 8 1 8 9 1 9 7 4 8 3 2 1 1 3 0 1 0 9 3 2 4 2 8 3 0 8 2 0 8 6 1 6 1 1 7 3 4 7 6 1 0 5 1 0 9 4Attorney Docket No: 243735.000396 53 2 5 2 3 2 2 4 8 1 4 0 8 6 7 7 6 2 1 7 4 1 5 0 0 2 5 1 9 8 8 9 9 6 7 8 6 4 4 1 3 8 3 7 8 0 1 8 4Attorney Docket No: 243735.000396 1 6 6 0 0 0 0 0 0 1 1 4 6 6 7 9 9 4 7 7 7 6 8 6 9 8 3 4 8 7 8 0 8 9 7 5 7 9 1 8 4 5 4 9 0 4 4 2 1 7Attorney Docket No: 243735.000396 73 0 4 5 2 1 1 8 5 0 2 0 7 3 3 9 3 9 1 7 0 9 9 1 0 0 3 7 2 7 8 7 4 8 7 1 4 9 3 6 5 5 4 4 3Attorney Docket No: 243735.000396 9 0 6 2 8 8 0 5 1 8 2 3 3 3 9 8 6 2 8 7 9 5 3 9 7 4 0 7 7 6 4 2 1 8 3 9 6 1 8 8 2 7 3 0 3 1 7 3 1 0Attorney Docket No: 243735.000396 25 0 5 9 0 4 9 4 3 6 7 4 8 5 4 8 7 2 7 4 4 3 8 7 8 5 9 7 0 8 8 8 2 1 9 9 9 1 3 1 5 8 3 0 2Attorney Docket No: 243735.000396 61 1 2 5 2 2 2 6 5 2 8 2 0 7 2 6 6 5 3 6 0 7 6 9 3 2 6 2 6 2 3 2 1 0 6 0 0 3 1 2 9 8 4 6 3 7 6Attorney Docket No: 243735.000396 8 6 0 2 5 7 5 7 4 7 3 5 4 9 4 9 7 5 0 9 0 7 3 3 4 9 7 6 2 8 9 8 5 2 2 2 3 0 0 3 3 6 0 3Attorney Docket No: 243735.000396 88 7 5 2 4 2 4 7 4 5 3 7 0 6 5 4 2 1 3 0 9 6 9 3 8 5 3 1 3 0 6 1 8 6 3 9 3 0 8 3 0 3 8Attorney Docket No: 243735.000396 49 0 8 7 5 3 2 2 3 3 1 4 5 8 5 4 6 3 1 9 7 3 8 7 6 6 6 8 5 2 8 5 6 3 3 3 9 8 6 5 2 4 1 1 8 7 2 5 3Attorney Docket No: 243735.000396 02 6 5 3 4 2 4 3 3 8 5 6 4 2 3 3 9 1 7 5 1 9 2 2 0 9 7 6 9 8 7 1 7 5 7 4 6 7 3 6 9 6 6 2 8 6 3Attorney Docket No: 243735.000396 51 4 6 9 4 1 8 8 9 0 0 8 8 1 5 8 2 8 3 1 2 5 2 1 5 1 5 2 4 1 9 2 6 0 8 2 3 4 6 9 1 7 3 9 7 0 4 4 7 2Attorney Docket No: 243735.000396 6 1 7 2 3 2 7 5 9 8 0 7 4 2 3 8 9 2 7 2 3 2 7 2 0 4 9 3 6 3 3 4 4 5 3 7 9 5 7 7 8 6 5 4 9 8 9 6 6Attorney Docket No: 243735.000396 6 2 5 8 8 5 0 6 1 0 3 8 2 5 0 0 6 3 2 0 9 8 4 8 8 7 6 8 9 3 2 1 2 1 1 1 0 6 7 9 8 8 8 0 9Attorney Docket No: 243735.000396 29 9 9 9 8 3 3 4 6 1 0 7 9 0 5 7 6 6 7 0 1 3 3 6 3 7 7 5 9 3 9 3 4 5 4 4 6 5 8 2 6 8 1 1 9 1 4 5Attorney Docket No: 243735.000396 82 8 7 4 4 4 4 2 4 3 2 0 1 9 2 2 3 1 1 7 0 3 3 2 1 2 4 5 1 2 5 3 4 2 2 1 9 5 7 6 8 7 8 7 0 8 6Attorney Docket No: 243735.000396 51 5 6 9 4 8 7 7 8 8 8 2 1 5 3 5 9 1 0 8 6 6 2 5 8 4 8 7 6 7 6 5 3 6 9 2 5 8 7 5 0 8 1 9 0 0 9 7Attorney Docket No: 243735.000396 95 8 6 0 9 6 1 4 1 2 9 1 0 9 7 0 4 4 2 3 7 8 3 9 9 6 6 6 9 9 2 9 3 2 0 9 3 3 1 2 0 0 9 7 5 6 3 3Attorney Docket No: 243735.000396 13 0 0 7 0 9 7 9 3 1 1 9 5 3 4 5 7 6 6 0 9 9 4 3 4 2 4 8 2 3 3 3 1 3 4 2 4 6 7 5 5 1 1 4Attorney Docket No: 243735.000396 2 6 0 0 5 8 7 8 7 7 6 5 2 4 2 1 0 4 3 1 6 8 3 1 2 4 7 7 5 3 6 4 5 2 6 3 8 6 9 1 9 4 7 5 5 5 1 9 6Attorney Docket No: 243735.000396 23 0 1 1 7 9 6 7 5 6 8 8 9 0 0 0 0 0 0 0 0 0 1 1 2 3 7 0 3 5 4 3 3 3 7 7 4 4 3 2 4 6 6 4 6 8 8 2 0 7 8Attorney Docket No: 243735.000396 99 0 3 6 4 2 4 3 1 5 8 5 1 6 4 2 3 1 0 2 1 6 3 7 0 0 1 9 7 0 3 1 2 3 6 5 5 2 1 6 2 2 1 6 4 1 8 7Attorney Docket No: 243735.000396 54 2 0 0 9 3 3 0 8 0 9 8 7 3 8 9 6 8 8 0 0 8 5 3 8 9 3 8 0 1 2 5 5 0 8 9 1 2 1 8 7 0 0 2 0 3 9 4 6 7Attorney Docket No: 243735.000396 1 1 1 6 2 2 9 2 9 1 0 7 0 0 9 7 9 7 5 4 5 4 6 5 1 0 1 0 9 7 0 3 4 4 3 6 6 8 0 0 0 0 9 0 4Attorney Docket No: 243735.000396 9 9 8 7 7 7 6 6 5 4 6 5 4 8 8 8 9 9 2 7 7 2 2 2 3 3 1 3 4 5 5 5 4 5 0 3 3 3 2 1 0 1 2 1 6 6 7 4 6Attorney Docket No: 243735.000396 27 9 0 3 0 0 1 2 2 4 8 0 9 5 1 1 2 3 2 2 1 1 1 4 3 4 3 3 2 1 4 8 3 2 9 0 9 2 0 9 9 0 9 6Attorney Docket No: 243735.000396 09 0 0 9 9 8 8 8 9 0 1 6 5 4 5 7 6 4 3 4 3 3 2 4 3 3 2 9 6 5 7 0 0 1 3 2 2 7 6 5 5 5 1 5 3 3 2Attorney Docket No: 243735.000396 80 1 0 9 0 7 5 8 9 0 3 4 4 3 2 1 3 4 5 6 1 4 5 3 1 2 5 4 6 6 4 7 5 4 9 9 0 1 6 1 1 1 2 6 8 9 9 9 1Attorney Docket No: 243735.000396 93 3 2 7 6 7 5 9 9 0 4 6 9 7 6 5 4 1 8 9 9 8 7 1 9 0 1 4 4 0 0 1 1 1 1 4 3 6 8 7 8 7 1 9 8 5Attorney Docket No: 243735.000396 21 9 3 3 0 6 6 9 7 8 3 7 0 2 9 2 1 0 0 6 3 1 0 0 3 0 0 0 0 0 0 0 0 0 0 0 0 6 8 4 6 2 5 8 3 3 3 0 7 2 9Attorney Docket No: 243735.000396 71 6 1 6 3 4 1 7 1 7 4 4 8 3 0 3 7 9 4 5 3 3 7 2 8 8 2 0 0 1 8 2 4 0 1 2 4 3 5 1 9 9 6 8 3 1Attorney Docket No: 243735.000396 14 3 2 5 5 5 2 2 4 0 1 8 5 8 0 6 4 0 3 7 5 1 6 8 1 0 8 3 0 5 7 0 9 0 9 0 9 6 8 2 7 1 7 2 7 9 4 7 3Attorney Docket No: 243735.000396 6 7 1 7 1 6 4 4 2 0 4 4 0 7 4 1 1 9 4 8 2 2 6 3 4 1 9 9 1 9 5 7 5 4 7 9 4 2 7 3 3 9 2 9 5 2 8 4Attorney Docket No: 243735.000396 99 0 7 8 1 2 4 6 5 6 7 4 9 1 4 4 3 7 8 6 7 8 2 0 0 7 3 9 3 0 8 8 1 3 0 4 0 8 6 0 0 6 9 2 2Attorney Docket No: 243735.000396 08 7 0 8 2 3 3 3 7 8 6 0 6 7 1 3 0 2 0 0 1 9 9 1 0 9 2 5 9 3 4 7 1 3 5 7 0 3 5 4 3 6 1 3 3 6 1 7 5 7 5Attorney Docket No: 243735.000396 25 3 5 6 5 8 2 5 4 1 3 2 5 9 6 3 2 7 5 4 3 7 3 1 4 2 7 6 0 9 1 8 3 8 9 7 4 1 2 6 4 5 6 1 7 2 7Attorney Docket No: 243735.000396 09 0 6 0 5 0 2 7 3 9 6 3 9 6 3 9 4 4 4 4 9 7 7 4 0 2 2 9 6 7 6 4 3 0 9 6 7 1 7 8 7 4 9 4 3 3 2 6 6 3 9Attorney Docket No: 243735.000396 44 1 7 3 0 0 9 7 7 8 0 7 0 8 1 8 8 9 1 8 6 5 7 8 8 7 8 9 0 7 4 2 2 3 7 5 8 9 9 6 7 6 8 4 3Attorney Docket No: 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N Engl J Med. 2004;351(21):2159-2169.Attorney Docket No: 243735.000396 Dreval K, Hilton LK, Cruz M, et al. Genetic Subdivisions of Follicular Lymphoma Defined by Distinct Coding and non-coding Mutation Patterns [published online ahead of print, 2023 Apr 21]. Blood.2023;blood.2022018719. Farinha P, Masoudi H, Skinnider BF, et al. Analysis of multiple biomarkers shows that lymphoma-associated macrophage (LAM) content is an independent predictor of survival in follicular lymphoma (FL). Blood.2005;106(6):2169-2174. Freeman CL, Kridel R, Moccia AA, et al. Early progression after bendamustine-rituximab is associated with high risk of transformation in advanced stage follicular lymphoma. Blood.2019;134(9):761-764. Fridlender ZG, Sun J, Kim S, et al. Polarization of tumor-associated neutrophil phenotype by TGF-beta: "N1" versus "N2" TAN. Cancer Cell.2009;16(3):183-194. Gouni S, Marques-Piubelli ML, Strati P. Follicular lymphoma and macrophages: impact of approved and novel therapies. Blood Adv.2021;5(20):4303-4312. Han G, Deng Q, Marques-Piubelli ML, et al. Follicular Lymphoma Microenvironment Characteristics Associated with Tumor Cell Mutations and MHC Class II Expression. Blood Cancer Discov.2022;3(5):428-443. Jaillon S, Ponzetta A, Di Mitri D, Santoni A, Bonecchi R, Mantovani A. Neutrophil diversity and plasticity in tumour progression and therapy. Nat Rev Cancer.2020;20(9):485-503. Jurinovic V, Kridel R, Staiger AM, et al. Clinicogenetic risk models predict early progression of follicular lymphoma after first-line immunochemotherapy. Blood.2016;128(8):1112- 1120. Khan O, Giles JR, McDonald S, et al. TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion. Nature.2019;571(7764):211-218. Kim R, Hashimoto A, Markosyan N, et al. Ferroptosis of tumour neutrophils causes immune suppression in cancer. Nature.2022;612(7939):338-346. Kridel R, Xerri L, Gelas-Dore B, et al. The Prognostic Impact of CD163-Positive Macrophages in Follicular Lymphoma: A Study from the BC Cancer Agency and the Lymphoma Study Association. Clin Cancer Res.2015;21(15):3428-3435. Lamaison C, Tarte K. B cell / stromal cell crosstalk in health, disease, and treatment: Follicular lymphoma as a paradigm. Immunol Rev.2021;302(1):273-285.Attorney Docket No: 243735.000396 Marques-Piubelli ML, Parra ER, Feng L, et al. SIRPα+ macrophages are increased in patients with FL who progress or relapse after frontline lenalidomide and rituximab. Blood Adv.2022;6(11):3286-3293. Mourcin F, Verdière L, Roulois D, et al. Follicular lymphoma triggers phenotypic and functional remodeling of the human lymphoid stromal cell landscape [published correction appears in Immunity.2021 Aug 10;54(8):1901]. Immunity.2021;54(8):1788-1806.e7. Newman AM, Liu CL, Green MR, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods.2015;12(5):453-457. Niogret J, Berger H, Rebe C, et al. Follicular helper-T cells restore CD8+-dependent antitumor immunity and anti-PD-L1 / PD-1 efficacy. J Immunother Cancer.2021;9(6):e002157. Okosun J, Bödör C, Wang J, et al. Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma. Nat Genet.2014;46(2):176-181 Osorio D, Cai JJ. Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control. Bioinformatics. 2021;37(7):963-967. Pandey S, Mourcin F, Marchand T, et al. IL-4 / CXCL12 loop is a key regulator of lymphoid stroma function in follicular lymphoma. Blood.2017;129(18):2507-2518. Pasqualucci L, Khiabanian H, Fangazio M, Vasishtha M, Messina M, Holmes AB, et al. Genetics of follicular lymphoma transformation. Cell Rep.2014 Jan 16;6(1):130-40. Pastore A, Jurinovic V, Kridel R, et al. Integration of gene mutations in risk prognostication for patients receiving first-line immunochemotherapy for follicular lymphoma: a retrospective analysis of a prospective clinical trial and validation in a population- based registry. Lancet Oncol.2015;16(9):1111-1122. Preuss I, Ludwig MG, Baumgarten B, et al. Transcriptional regulation and functional characterization of the oxysterol / EBI2 system in primary human macrophages. Biochem Biophys Res Commun.2014;446(3):663-668. Riedel A, Shorthouse D, Haas L, Hall BA, Shields J. Tumor-induced stromal reprogramming drives lymph node transformation. Nat Immunol.2016;17(9):1118-1127. Sahai E, Astsaturov I, Cukierman E, et al. A framework for advancing our understanding of cancer-associated fibroblasts. Nat Rev Cancer.2020;20(3):174-186.Attorney Docket No: 243735.000396 Salcher S, Sturm G, Horvath L, et al. High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer. Cancer Cell. 2022;40(12):1503-1520.e8. Sarkozy C, Trneny M, Xerri L, et al. Risk Factors and Outcomes for Patients With Follicular Lymphoma Who Had Histologic Transformation After Response to First-Line Immunochemotherapy in the PRIMA Trial [published correction appears in J Clin Oncol.2016 Sep 10;34(26):3230]. J Clin Oncol. Spann NJ, Glass CK. Sterols and oxysterols in immune cell function. Nat Immunol. 2013;14(9):893-900. Steen CB, Liu CL, Alizadeh AA, Newman AM. Profiling Cell Type Abundance and Expression in Bulk Tissues with CIBERSORTx. Methods Mol Biol.2020;2117:135-157. Steen CB, Luca BA, Esfahani MS, et al. The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma. Cancer Cell.2021;39(10):1422-1437.e10. Stevens WBC, Mendeville M, Redd R, et al. Prognostic relevance of CD163 and CD8 combined with EZH2 and gain of chromosome 18 in follicular lymphoma: a study by the Lunenburg Lymphoma Biomarker Consortium. Haematologica.2017;102(8):1413- 1423. Tobin JWD, Keane C, Gunawardana J, et al. Progression of Disease Within 24 Months in Follicular Lymphoma Is Associated With Reduced Intratumoral Immune Infiltration. J Clin Oncol.2019;37(34):3300-3309. Veglia F, Hashimoto A, Dweep H, et al. Analysis of classical neutrophils and polymorphonuclear myeloid-derived suppressor cells in cancer patients and tumor- bearing mice. J Exp Med.2021;218(4):e20201803. Wang T, Zhou Y, Zhou Z, et al. Secreted protease PRSS35 suppresses hepatocellular carcinoma by disabling CXCL2-mediated neutrophil extracellular traps. Nat Commun. 2023;14(1):1513. Wang X, Nissen M, Gracias D, et al. Single-cell profiling reveals a memory B cell-like subtype of follicular lymphoma with increased transformation risk. Nat Commun. 2022;13(1):6772.Attorney Docket No: 243735.000396 Yang ZZ, Kim HJ, Wu H, et al. T-cell phenotype including CD57+ T follicular helper cells in the tumor microenvironment correlate with a poor outcome in follicular lymphoma. Blood Cancer J.2023;13(1):124. Zhang H, Ye YL, Li MX, et al. CXCL2 / MIF-CXCR2 signaling promotes the recruitment of myeloid-derived suppressor cells and is correlated with prognosis in bladder cancer. Oncogene.2017;36(15):2095-2104. * * *

[0488] The present invention is not to be limited in scope by the specific embodiments described herein. Indeed, various modifications of the invention in addition to those described herein will become apparent to those skilled in the art from the foregoing description. Such modifications are intended to fall within the scope of the appended claims.

[0489] All patents, applications, publications, test methods, literature, and other materials cited herein are hereby incorporated by reference in their entirety as if physically present in this specification.

Claims

Attorney Docket No: 243735.000396 Claims 1. A method for classifying a subject diagnosed with follicular lymphoma (FL) into 7 FL subtypes (FL1-FL7), the method comprising: (a) determining in a biological sample obtained from the subject the expression level of at least 4 genes from each of 7 groups of genes provided in Table 1, wherein the 7 groups of genes correspond to 7 FL subtypes (FL1-FL7) as listed in Table 1; (b) calculating a gene expression score for the biological sample for each of the 7 groups of genes of step (a); (c) comparing the 7 gene expression scores calculated in step (b) to each other and determining the highest gene expression score among the 7 gene expression scores; and (d) classifying the subject into the FL subtype which corresponds to the highest gene expression score determined in step (c).

2. The method of claim 1, wherein the subject has been diagnosed with FL based on evaluation of histology and / or immunophenotypic features.

3. The method of claim 1 or claim 2, wherein step (b) comprises: generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 1; generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreases when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

4. The method of claim 1 or claim 2, wherein step (b) comprises: representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative;Attorney Docket No: 243735.000396 performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes provided in Table 1, and resulting in a mixture coefficient matrix; and determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.

5. The method of claim 4, wherein step (c) comprises: determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

6. The method of claim 1 or claim 2, wherein step (a) comprises determining the expression level of at least 4 genes from each of the 7 groups of genes provided in Table 3, wherein the 7 groups of genes correspond to the 7 FL subtypes (FL1-FL7) as listed in Table 3.

7. The method of claim 6, wherein step (b) comprises: generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 3; generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreases when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

8. The method of any one of claims 1-2 and 6, wherein step (b) comprises: representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative;Attorney Docket No: 243735.000396 performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes provided in Table 3, and resulting in a mixture coefficient matrix; and determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.

9. The method of claim 8, wherein step (c) comprises: determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

10. The method of any one of claims 1-9, wherein the genes for group 1 corresponding to FL1 comprise DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF.

11. The method of any one of claims 1-10, wherein the genes for group 2 corresponding to FL2 comprise GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK.

12. The method of any one of claims 1-11, wherein the genes for group 3 corresponding to FL3 comprise ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3.

13. The method of any one of claims 1-12, wherein the genes for group 4 corresponding to FL4 comprise GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX.

14. The method of any one of claims 1-13, wherein the genes for group 5 corresponding to FL5 comprise PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1.

15. The method of any one of claims 1-14, wherein the genes for group 6 corresponding to FL6 comprise PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK.Attorney Docket No: 243735.000396 16. The method of any one of claims 1-15, wherein the genes for group 7 corresponding to FL7 comprise SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

17. The method of any one of claims 1-16, wherein the genes for group 1 corresponding to FL1 comprise DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF, the genes for group 2 corresponding to FL2 comprise GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK, the genes for group 3 corresponding to FL3 comprise ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3, the genes for group 4 corresponding to FL4 comprise GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX, the genes for group 5 corresponding to FL5 comprise PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1, the genes for group 6 corresponding to FL6 comprise PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK, and the genes for group 7 corresponding to FL7 comprise SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

18. The method of any one of claims 1-17, wherein the method further comprises administering to the subject classified in step (d) a treatment effective for the subject’s determined FL subtype.

19. The method of claim 18, wherein the treatment for the subject classified as FL1 comprises administering a therapeutically effective amount of a compound selected from an inhibitor of Bruton’s tyrosine kinase (BTK), an anti-CD79b agent, an anti-CD19 agent, an inhibitor of PD1, an agent targeting neutrophilic myeloid-derived suppressor cells (PMN-MDSCs), or any combinations thereof.

20. The method of claim 18, wherein the treatment for the subject classified as FL2 comprises administering a therapeutically effective amount of a compound selected from Lenalidomide, an inhibitor of Bruton’s tyrosine kinase (BTK), Ipilimumab, an inhibitor of PD-L1, an inhibitor of Janus kinase (JAK), or any combinations thereof.Attorney Docket No: 243735.000396 21. The method of claim 18, wherein the treatment for the subject classified as FL3 comprises administering a therapeutically effective amount of an inhibitor of Janus kinase (JAK).

22. The method of claim 18, wherein the treatment for the subject classified as FL4 comprises administering a therapeutically effective amount of an inhibitor of enhancer of zeste homolog 2 (EZH2), or an inhibitor of polyadenosine 5'-diphosphoribose polymerase (PARP), or a combination thereof.

23. The method of claim 18, wherein the treatment for the subject classified as FL5 comprises administering a therapeutically effective amount of a compound selected from Lenalidomide, an inhibitor of Bruton’s tyrosine kinase (BTK), an anti-CD19 agent, an inhibitor of Janus kinase (JAK), an agent targeting neutrophilic myeloid-derived suppressor cells (PMN-MDSCs), or any combinations thereof.

24. The method of claim 18, wherein the treatment for the subject classified as FL6 comprises administering a therapeutically effective amount of a compound selected from a proteosome inhibitor, an anti-CD79b agent, an agent targeting neutrophilic myeloid- derived suppressor cells, or any combinations thereof.

25. The method of claim 18, wherein the treatment for the subject classified as FL7 comprises administering a therapeutically effective amount of Lenalidomide, or an inhibitor of Janus kinase (JAK), or a combination thereof.

26. The method of any one of claims 18-25, wherein the treatment further comprises administering a standard immunochemotherapy.

27. The method of claim 26, wherein the standard immunochemotherapy comprises administering a therapeutically effective amount of a compound selected from rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP); rituximab,Attorney Docket No: 243735.000396 cyclophosphamide, vincristine, and prednisone (R-CVP); rituximab and bendamustine (BR); obinutuzumab, cyclophosphamide, doxorubicin, vincristine, and prednisone; obinutuzumab, cyclophosphamide, vincristine, and prednisone; obinutuzumab and bendamustine; and any combinations thereof.

28. The method of claims 26 or claim 27, wherein the treatment for the subject’s determined FL subtype is administered before, simultaneously with, or after the administration of the standard immunochemotherapy.

29. The method of any one of claims 19, 20, and 23, wherein the inhibitor of Bruton’s tyrosine kinase (BTK) is ibrutinib, acalabrutinib, or pirtobrutinib.

30. The method of claim 19, wherein the inhibitor of PD1 is nivolumab, pembrolizumab, cemiplimab, dostarlimab, or retifanlimab.

31. The method of claim 19 or claim 23, wherein the agent targeting neutrophilic myeloid- derived suppressor cells (PMN-MDSCs) is all-trans retinoic acid (ATRA).

32. The method of claim 20, wherein the inhibitor of PD-L1 is atezolizumab, avelumab or durvalumab.

33. The method of any one of claims 20-21, 23, and 25, wherein the inhibitor of Janus kinase (JAK) is ruxolitinib, baricitinib, tofacitinib, fedratinib, itacitinib, momelotinib, or patricinib.

34. The method of claim 24, wherein the proteosome inhibitor is bortezomib, carfilzomib or ixazomib.

35. A method of treating a subject diagnosed with follicular lymphoma (FL), the method comprising:Attorney Docket No: 243735.000396 (a) determining in a biological sample obtained from the subject the expression level of at least 4 genes from each of 7 groups of genes provided in Table 1, wherein the 7 groups of genes correspond to 7 FL subtypes (FL1-FL7) as listed in Table 1; (b) calculating a gene expression score for the biological sample for each of the 7 groups of genes of step (a); (c) comparing the 7 gene expression scores calculated in step (b) to each other and determining the highest gene expression score among the 7 gene expression scores; (d) classifying the subject into the FL subtype which corresponds to the highest gene expression score determined in step (c); and (e) administering to the subject classified in step (d) a treatment effective for the subject’s determined FL subtype.

36. The method of claim 35, wherein the subject has been diagnosed with FL based on evaluation of histology and / or immunophenotypic features.

37. The method of claim 35 or claim 36, wherein step (b) comprises: generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 1; generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreases when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

38. The method of claim 35 or claim 36, wherein step (b) comprises: representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative;Attorney Docket No: 243735.000396 performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes provided in Table 1, and resulting in a mixture coefficient matrix; and determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.

39. The method of claim 38, wherein step (c) comprises: determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

40. The method of claim 35 or claim 36, wherein step (a) comprises determining the expression level of at least 4 genes from each of the 7 groups of genes provided in Table 3 wherein the 7 groups of genes correspond to the 7 FL subtypes (FL1-FL7) as listed in Table 3.

41. The method of claim 40, wherein step (b) comprises: generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 3; generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreases when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

42. The method of any one of claims 35-36 and 40, wherein step (b) comprises: representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative;Attorney Docket No: 243735.000396 performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes provided in Table 3, and resulting in a mixture coefficient matrix; and determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.

43. The method of claim 42, wherein step (c) comprises: determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

44. The method of any one of claims 35-43, wherein the genes for group 1 corresponding to FL1 comprise DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF.

45. The method of any one of claims 35-44, wherein the genes for group 2 corresponding to FL2 comprise GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK.

46. The method of any one of claims 35-45, wherein the genes for group 3 corresponding to FL3 comprise ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3.

47. The method of any one of claims 35-46, wherein the genes for group 4 corresponding to FL4 comprise GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX.

48. The method of any one of claims 35-47, wherein the genes for group 5 corresponding to FL5 comprise PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1.

49. The method of any one of claims 35-48, wherein the genes for group 6 corresponding to FL6 comprise PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK.Attorney Docket No: 243735.000396 50. The method of any one of claims 35-49, wherein the genes for group 7 corresponding to FL7 comprise SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

51. The method of any one of claims 35-50, wherein the genes for group 1 corresponding to FL1 comprise DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF, the genes for group 2 corresponding to FL2 comprise GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK, the genes for group 3 corresponding to FL3 comprise ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3, the genes for group 4 corresponding to FL4 comprise GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX, the genes for group 5 corresponding to FL5 comprise PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1, the genes for group 6 corresponding to FL6 comprise PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK, and the genes for group 7 corresponding to FL7 comprise SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

52. The method of any one of claims 35-51, wherein the treatment for the subject classified as FL1 comprises administering a therapeutically effective amount of a compound selected from an inhibitor of Bruton’s tyrosine kinase (BTK), an anti-CD79b agent, an anti-CD19 agent, an inhibitor of PD1, an agent targeting neutrophilic myeloid-derived suppressor cells (PMN-MDSCs), or any combinations thereof.

53. The method of any one of claims 35-52, wherein the treatment for the subject classified as FL2 comprises administering a therapeutically effective amount of a compound selected from Lenalidomide, an inhibitor of Bruton’s tyrosine kinase (BTK), Ipilimumab, an inhibitor of PD-L1, an inhibitor of Janus kinase (JAK), or any combinations thereof.

54. The method of any one of claims 35-53, wherein the treatment for the subject classified as FL3 comprises administering a therapeutically effective amount of an inhibitor of Janus kinase (JAK).Attorney Docket No: 243735.000396 55. The method of any one of claims 35-54, wherein the treatment for the subject classified as FL4 comprises administering a therapeutically effective amount of an inhibitor of enhancer of zeste homolog 2 (EZH2), or an inhibitor of polyadenosine 5'- diphosphoribose polymerase (PARP), or a combination thereof.

56. The method of any one of claims 35-55, wherein the treatment for the subject classified as FL5 comprises administering a therapeutically effective amount of a compound selected from Lenalidomide, an inhibitor of Bruton’s tyrosine kinase (BTK), an anti- CD19 agent, an inhibitor of Janus kinase (JAK), an agent targeting neutrophilic myeloid- derived suppressor cells (PMN-MDSCs), or any combinations thereof.

57. The method of any one of claims 35-56, wherein the treatment for the subject classified as FL6 comprises administering a therapeutically effective amount of a compound selected from a proteosome inhibitor, an anti-CD79b agent, an agent targeting neutrophilic myeloid-derived suppressor cells, or any combinations thereof.

58. The method of any one of claims 35-57, wherein the treatment for the subject classified as FL7 comprises administering a therapeutically effective amount of Lenalidomide, or an inhibitor of Janus kinase (JAK), or a combination thereof.

59. The method of any one of claims 35-58, wherein the treatment further comprises administering a standard immunochemotherapy.

60. The method of claim 59, wherein the standard immunochemotherapy comprises administering a therapeutically effective amount of a compound selected from rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP); rituximab, cyclophosphamide, vincristine, and prednisone (R-CVP); rituximab and bendamustine (BR); obinutuzumab, cyclophosphamide, doxorubicin, vincristine, and prednisone; obinutuzumab, cyclophosphamide, vincristine, and prednisone; obinutuzumab and bendamustine; and any combinations thereof.Attorney Docket No: 243735.000396 61. The method of claims 59 or claim 60, wherein the treatment for the subject’s determined FL subtype is administered before, simultaneously with, or after the administration of the standard immunochemotherapy.

62. The method of any one of claims 52, 53, and 56, wherein the inhibitor of Bruton’s tyrosine kinase (BTK) is ibrutinib, acalabrutinib, or pirtobrutinib.

63. The method of claim 52, wherein the inhibitor of PD1 is nivolumab, pembrolizumab, cemiplimab, dostarlimab, or retifanlimab.

64. The method of claim 52 or claim 56, wherein the agent targeting neutrophilic myeloid- derived suppressor cells (PMN-MDSCs) is all-trans retinoic acid (ATRA).

65. The method of claim 53, wherein the inhibitor of PD-L1 is atezolizumab, avelumab or durvalumab.

66. The method of any one of claims 53-54, 56, and 58, wherein the inhibitor of Janus kinase (JAK) is ruxolitinib, baricitinib, tofacitinib, fedratinib, itacitinib, momelotinib, or patricinib.

67. The method of claim 57, wherein the proteosome inhibitor is bortezomib, carfilzomib or ixazomib.

68. The method of any one of claims 19, 24, 52, and 57, wherein the anti-CD79b agent is Polatuzumab vedotin.

69. The method of any one of claims 19, 23, 52, and 56, wherein the anti-CD19 agent is Tafasitamab.Attorney Docket No: 243735.000396 70. The method of any one of claims 22 and 55, wherein the inhibitor of EZH2 is Tazemostat.

71. The method of any one of claims 22 and 55, wherein the inhibitor of PARP is Olaparib.

72. The method of any one of claims 1-71, wherein the gene expression level is determined by measuring mRNA level.

73. The method of claim 72, wherein the mRNA level is determined using RNA sequencing, qPCR, panel sequencing, or array-based gene expression profiling.

74. The method of any one of claims 1-73, wherein the subject is a newly diagnosed patient.

75. The method of any one of claims 1-73, wherein the subject is a patient at relapse after a treatment.

76. A composition comprising a plurality of isolated probes and / or primers which hybridize to at least 4 genes from each of 7 groups of genes provided in Table 1.

77. The composition of claim 76, wherein said plurality of isolated probes and / or primers hybridize to at least 4 genes from each of the 7 groups of genes provided in Table 3.

78. The composition of claim 77, wherein said plurality of isolated probes and / or primers hybridize to DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF.

79. The composition of claim 77 or claim 78, wherein said plurality of isolated probes and / or primers hybridize to GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK.Attorney Docket No: 243735.000396 80. The composition of any one of claims 77-79, wherein said plurality of isolated probes and / or primers hybridize to ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3.

81. The composition of any one of claims 77-80, wherein said plurality of isolated probes and / or primers hybridize to GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX.

82. The composition of any one of claims 77-81, wherein said plurality of isolated probes and / or primers hybridize to PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1.

83. The composition of any one of claims 77-82, wherein said plurality of isolated probes and / or primers hybridize to PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK.

84. The composition of any one of claims 77-83, wherein said plurality of isolated probes and / or primers hybridize to SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

85. A kit comprising: (i) a plurality of isolated probes and / or primers which hybridize to at least 4 genes from each of 7 groups of genes provided in Table 1, (ii) optionally, one or more reagents for determining mRNA level, and (iii) optionally, instructions for use.

86. The kit of claim 85, comprising: (i) a plurality of isolated probes and / or primers which hybridize to at least 4 genes from each of the 7 groups of genes provided in Table 3, (ii) optionally, one or more reagents for determining mRNA level, and (iii) optionally, instructions for use.Attorney Docket No: 243735.000396 87. The kit of claim 86, wherein said plurality of isolated probes and / or primers hybridize to DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF.

88. The kit of claim 86 or claim 87, wherein said plurality of isolated probes and / or primers hybridize to GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK.

89. The kit of any one of claims 86-88, wherein said plurality of isolated probes and / or primers hybridize to ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3.

90. The kit of any one of claims 86-89, wherein said plurality of isolated probes and / or primers hybridize to GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX.

91. The kit of any one of claims 86-90, wherein said plurality of isolated probes and / or primers hybridize to PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1.

92. The kit of any one of claims 86-91, wherein said plurality of isolated probes and / or primers hybridize to PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK.

93. The kit of any one of claims 86-92, wherein said plurality of isolated probes and / or primers hybridize to SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.

94. An array comprising a plurality of probes complementary to and / or hybridizable to at least 4 genes from each of 7 groups of genes provided in Table 1.Attorney Docket No: 243735.000396 95. The array of claim 94, comprising a plurality of probes complementary to and / or hybridizable to at least 4 genes from each of 7 groups of genes provided in Table 3.

96. The array of claim 95, wherein said plurality of isolated probes and / or primers hybridize to DUSP1, TSC22D3, JUNB, PNOC, JUN, FADS3, H3C4, RGS2, and TNF.

97. The array of claim 95 or claim 96, wherein said plurality of isolated probes and / or primers hybridize to GBP5, SMIM43, IDO1, TRAT1, THEMIS, IFNG, GIMAP7, and GZMK.

98. The array of any one of claims 95-97, wherein said plurality of isolated probes and / or primers hybridize to ACTA2, IGFBP6, ABCA8, DCN, TAGLN, CAV2, ANXA1, and GPX3.

99. The array of any one of claims 95-98, wherein said plurality of isolated probes and / or primers hybridize to GMDS, SHCBP1, RASL11A, QPCT, LMO2, SHISA8, MUC16, PDGFD, FNDC1, and TOX.

100. The array of any one of claims 95-99, wherein said plurality of isolated probes and / or primers hybridize to PNISR, FAM13A-AS1, ZMAT1, PSMA3-AS1, LOC100289230, HNRNPA1, and CLK1.

101. The array of any one of claims 95-100, wherein said plurality of isolated probes and / or primers hybridize to PRDM15, GPM6A, GABRB2, BMP7, RGCC, E2F5, ZNF215, and BIK.

102. The array of any one of claims 95-101, wherein said plurality of isolated probes and / or primers hybridize to SUMO4, TOP1, LOC105377320, SMC3, IL6ST, KLRB1, ESCO1, CEBPZ, DHX9P1, and TET2.Attorney Docket No: 243735.000396 103. A therapy guidance software tool for a subject diagnosed with follicular lymphoma (FL) comprising non-transitory computer readable medium with instructions thereon, that when executed by a processor, cause the processor to: (a) receive a plurality of gene expression values for at least 4 genes from each of 7 groups of genes provided in Table 1, wherein the 7 groups of genes correspond to 7 FL subtypes (FL1-FL7); (b) calculate a gene expression score for each of the 7 groups of genes based at least in part on the plurality of gene expression values; (c) classify the subject into one FL subtype of the 7 FL subtypes based at least in part on the gene expression score for each of the 7 groups of genes; and (d) provide a patient diagnosis based at least in part on the one FL subtype into which the subject is classified.

104. The therapy guidance software tool of claim 103, wherein step (b) comprises: generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 1; generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreases when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

105. The therapy guidance software tool of claim 103, wherein step (b) comprises: representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative; performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes provided in Table 1, and resulting in a mixture coefficient matrix; andAttorney Docket No: 243735.000396 determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.

106. The therapy guidance software tool of claim 105, wherein step (c) comprises: determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

107. The therapy guidance software tool of any one of claims 103-106, wherein the non-transitory computer readable medium includes instructions thereon, that when executed by a processor, cause the processor to: provide a treatment recommendation based at least in part on the one FL subtype into which the subject is classified.

108. The therapy guidance software tool of any one of claims 103-107, wherein the non-transitory computer readable medium includes instructions thereon, that when executed by a processor, cause the processor to: provide a prognosticated failure free survival based at least in part on the one FL subtype into which the subject is classified.

109. The therapy guidance software tool of any one of claims 103-108, wherein the non-transitory computer readable medium includes instructions thereon, that when executed by a processor, cause the processor to: provide a prognosticated overall survival based at least in part on the one FL subtype into which the subject is classified.

110. The therapy guidance software tool of any one of claims 103 and 107-109, wherein step (a) comprises determining the expression level of at least 4 genes from each of the 7 groups of genes provided in Table 3 wherein the 7 groups of genes correspond to the 7 FL subtypes (FL1-FL7) as listed in Table 3.

111. The therapy guidance software tool of claim 110, wherein step (b) comprises:Attorney Docket No: 243735.000396 generating a gene expression count matrix including the expression level of the at least 4 genes from each of the 7 groups of genes provided in Table 3; generating a ranked gene list based on the gene expression count matrix such that overrepresented genes are at the top of the ranked gene list; and calculating the gene expression score based at least in part on a running-sum statistic for each of the 7 groups of genes such that the running-sum statistic for a respective group of the 7 groups of genes increases when a gene of the at least 4 genes of the respective group is encountered by walking down the ranked gene list and decreases when a gene of the at least 4 genes of the respective group is not encountered by walking down the ranked gene list.

112. The therapy guidance software tool of any one of claims 103 and 107-110, wherein step (b) comprises: representing the expression level of the at least 4 genes as a gene expression count matrix, wherein the gene expression count matrix is non-negative; performing nonnegative matrix factorization on the gene expression count matrix, using a basis matrix representing the 7 groups of genes provided in Table3, and resulting in a mixture coefficient matrix; and determining the 7 gene expression scores based at least in part on the mixture coefficient matrix.

113. The therapy guidance software tool of claim 112, wherein step (c) comprises: determining the highest score value among the 7 gene expression scores based at least in part in a maximum coefficient value in the mixture coefficient matrix.

114. The method of any one of claims 1-75, wherein the biological sample comprises tumor cells.

115. The method of any one of claims 1-75 and 114, wherein the biological sample is a biopsy sample.Attorney Docket No: 243735.000396 116. The method of any one of claims 1-75 and 103-115, wherein the subject is human.

117. The method of any one of claims 1-75 and 103-115, wherein the subject is a veterinary animal.

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