METHODS AND SYSTEMS FOR CHARACTERIZING SEVERE CROHN'S DISEASE

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy created Apr. 22, 2019, is named 52388-736_601_SL.txt and is 364,884 bytes in size.

BACKGROUND

Inflammatory bowel disease (IBD) has two common forms, Crohn's disease (CD) and ulcerative colitis (UC), which are chronic, relapsing inflammatory disorders of the gastrointestinal tract. Genetic factors play an important role in IBD pathogenesis, and CD and UC are thought to be related disorders that share some genetic susceptibility loci but differ at others.

The high clinical heterogeneity and genetic complexity of CD and UC suggest that the underlying biological pathways driving disease differ in subgroups of patients. Significant efficacious responses to IBD therapies are difficult to achieve due to disease heterogeneity. Thus, the development of early and targeted therapeutics requires subgroup stratification and prognostic biomarker identification, particularly in predicting an overall mild, compared to severe, disease course.

There is a number of aggravating subclinical phenotypes of IBD that are present in certain sub-populations of CD and UC patients. One such condition is intestinal stricturing disease, which can result from long term intestinal inflammation or intestinal fibrosis that leads to the formation of scar tissue in the intestinal wall (fibrostenosis) or swelling. Both outcomes can cause narrowing, or obstruction, and are known as either fibrotic or inflammatory strictures. Severe strictures can lead to blockage of the intestine, leading to abdominal pain, bloating, nausea and the inability to pass stool. Another example is penetrating disease, which is the formation of fistula or extraluminal abscesses of the intestine.

Stricturing and penetrating CD results in significant morbidity. Intestinal strictures represent a common complication of CD; nearly 40% of CD patients develop clinically apparent strictures. Subclinical phenotypes like stricturing and penetrating disease are thought to be driven by a combination of clinical, serologic, and genetic factors. Due to the clinical, serologic and genetic heterogeneity of stricturing and penetrating disease, and IBD generally, conventional treatments such as immunomodulatory (e.g., anti-TNF therapies) are efficacious in only some of the patient population. A significant portion of the population experiences non-response to the conventional treatment or loss-of-response after a successful induction of the treatment. Surgery, in the form of structureplasty (reshaping of the intestine) or resection (removal of the intestine), is the only treatment option for patients that do not respond to first line therapies. Surgical treatments for IBD are invasive, causing post-operative risks for an estimated third of patients undergoing surgery, such as anastomotic leak, infection, and bleeding.

Thus, there is a need for methods and systems that identify subjects at risk for developing severe forms of CD in order to prescribe personalized treatment strategies that obviate a need for surgery and improve patient outcomes. Targeted therapeutic strategies alternative to general immunomodulatory approaches are needed to better address the underlying disease pathology unique to severe forms of CD characterized by subclinical phenotypes such as stricturing and penetrating disease.

SUMMARY

Aspects disclosed herein provide methods and systems for characterizing severe forms of Crohn's disease (CD) in a subject, as well as identifying a risk that a subject will develop the severe forms of CD. Targeted therapeutic approaches are also described herein, that may be suitable for subjects determined to be at risk of developing severe forms of CD. The methods and systems disclosed herein involve characterizing and identifying a risk of developing severe forms of CD based on a presence of certain genotypes, serological markers, or other biomarkers that are associated with subclinical phenotypes of severe forms of CD (e.g., stricturing and penetrating disease). The genotypes and biomarkers disclosed herein are further associated with disease location, which in some cases, can be used to target therapeutic strategies to the predominantly affected area. Exemplary therapeutic agents useful for this purpose are those that target pathways such as Prolactin signaling, autophagy, and Janus Kinase (JAK)/(Signal Transducer and Activator of Transcription (STAT) pathway.

Non-limiting practical applications of the associations between the genotypes, serological markers and other biomarkers described herein and incidences of clinical and subclinical phenotypes in certain populations of subjects are provided herein. For example, the genotypes and biomarkers of the present disclosure can be used to predict a risk that a subject will develop CD. The genotypes and biomarkers are also useful to predict whether a patient diagnosed with CD will develop a severe form of the disease, such as a subclinical phenotype thereof (e.g., stricturing/penetrating disease), and in some cases, also predict where in the intestine the subclinical phenotype will present. In addition, or alternatively, the genotypes and biomarkers disclosed herein are associated with an variation in an expression of certain genes or gene expression products involved in the pathogenesis and pathology of CD, which in some cases, means the genotypes and biomarkers can be used to identify a patient who may be suitable for treatment with therapy targeting that gene or gene expression product (e.g., a patient carrying a genotype associated with an increase in the gene expression product may be suitable for a treatment with an inhibitor of that gene expression product). In some cases, a subject is administered a therapeutic agent, provided the genotype disclosed herein is detected in a sample obtained from the subject. A further example of practical applications disclosed herein include laboratory-based methods of detecting the instant genotypes and biomarkers. Exemplary methodologies of detecting the genotype include genotyping devices and sequencing. Exemplary methodologies of detecting biomarkers (e.g., serological markers) include enzyme-linked immunosorbent assays (ELISA).

Aspects disclosed provide methods of treating a severe form of Crohn's disease (CD) in a subject, the method comprising administering to the subject a therapeutically effective amount of a therapeutic agent, provided the a genotype comprising at least one polymorphism associated with at least one of stricturing disease and internal penetrating disease that is characteristic of severe CD as indicated by a P value of at most 1.0E⁻⁵is detected in a sample obtained from the subject. In some embodiments, the at least one polymorphism is associated with stricturing disease and is selected from the group consisting of rs7416358G, rs1070444A, rs11749180A, 12-54819630-G-INSERTION, rs12496281G, rs11171747C, rs116714418A, rs111455641G, rs9480689G, rs6879067A, rs11128532A, rs177665C, rs10775375A, rs6801634A, rs6962616A, rs7220814G, rs4325270T, rs768755T, rs17758350A, rs9480689G, rs525850A, rs4325270T, rs6962616A, rs10265554G, rs634641G, rs1493871G, rs12669698G, rs4332037A, rs17697480G, rs9480689G, rs6074737A, rs904910G, rs12972487A, rs445417A, rs63562C, rs7416358G, rs177665C, rs1070444A, rs10912583A, rs12914919G, rs2854725C, rs9480689G, rs71472147A, rs72939578A, rs658795A, rs17758350A, rs144260901A, rs10801129C, rs1702870A, rs10912583A, rs2452822C, rs7774349A, rs4705272G, rs117946479A, rs936126A, rs634641G, rs2314737G, rs3002685G, rs634641G, rs10134119T, rs3808240C, rs1890843G, and rs11829981A. In some embodiments, the at least one polymorphism is associated with internal penetrating disease and is selected from the group consisting of rs12496281G, rs2383184G, rs144260901A, rs6801634A, rs2383184G, and rs2954756G. In some embodiments, the at least one polymorphism is located at nucleoposition 26 or 31 within any one of SEQ ID NOS: 1-82. In some embodiments, the genotype is detected by a process comprising: (a) contacting the sample obtained from the subject with a nucleic acid sequence comprising a detectable moiety, the nucleic acid sequence capable of hybridizing to at least 20 contiguous nucleobases between nucleobase 16 and nucleobase 46 of at least one of SEQ ID NOS: 13-82; and (b) detecting binding between the nucleic acid sequence and the at least 20 contiguous nucleobases between nucleobase 16 and nucleobase 46 of at least one of SEQ ID NOS: 13-82. In some embodiments, the genotype is detected by sequencing genetic information contained in the sample obtained from the subject. In some embodiments, the methods further comprise determining whether the subject has or will develop at least one of a non-response and a loss-of-response to a standard treatment. In some embodiments, the standard treatment is selected from the group consisting of glucocorticosteriods, anti-TNF therapy, anti-a4-b7 therapy (vedolizumab), anti-IL12p40 therapy (ustekinumab), Thalidomide, and Cytoxin. In some embodiments, the therapeutic agent is a modulator of a gene or gene expression product expressed from the gene, the gene selected from group consisting of X—C Motif Chemokine Ligand 1 (XCL1), Dermatopontin (DPT), TNF Superfamily Member 4 (TNFSF4), C-Type Lectin Like 1 (CLECL1), CD69 Molecule (CD69), Fms Related Tyrosine Kinase 1 (FLT1), Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 (MAP4K4), Prostaglandin E Receptor 4 (PTGER4), interleukin 18 receptor 1 (IL18R1). 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 3 (PFKFB3), Interleukin 18 Receptor Accessory Protein (IL18RAP), Adenylate Cyclase 7 (ADCY7), B Lymphoid Tyrosine Kinase (BLK), G Protein-Coupled Receptor 65 (GPR65), Sprouty Related EVH1 Domain Containing 2 (SPRED2), Src Kinase Associated Phosphoprotein 2 (SKAP2), CD30 ligand (CD30L), Receptor Interacting Serine/Threonine Kinase 2 (RIPK2), and TNF Ligand Superfamily Member 15 (TL1A), an a combination thereof. In some embodiments, the modulator of the gene or gene expression product is selected from the group consisting of an antibody or antigen-binding fragment thereof, a small molecule, or a peptide. In some embodiments, the modulator of the gene or gene expression product is an agonist or a partial agonist. In some embodiments, the modulator of the gene or gene expression product is an antagonist or a partial antagonist. In some embodiments, the modulator of the gene or gene expression product is an allosteric modulator.

Aspects disclosed herein provide methods of characterizing an inflammatory bowel disease in a subject, the method comprising: (a) assaying genetic material in a sample obtained from a subject with an inflammatory bowel disease to detect a presence or an absence of a genotype comprising at least one polymorphism associated with at least one of stricturing disease and internal penetrating disease that is characteristic of severe CD as indicated by a P value of at most 1.0E⁻⁵; and (b) characterizing the inflammatory disease as a Crohn's disease (CD) provided the presence of the genotype is detected in step (a). In some embodiments, the at least one polymorphism is selected from the group consisting of rs2726797, rs7108993, rs79665096, rs7604404, rs73085878, rs78727269, rs2736352, rs4924935, rs11227112, rs2285043, rs6989059, rs3807552, rs111455641, rs9480689, rs7416358, rs6879067, rs11128532, rs177665, rs11171747, rs10775375, rs6801634, rs1070444, rs116714418, rs6962616, rs7220814, rs4325270, rs768755, rs17758350, rs9480689, rs525850, rs4325270, rs11749180, rs6962616, rs116714418, rs10265554, rs634641, rs1493871, rs12669698, rs4332037, rs17697480, rs9480689, rs6074737, rs904910, rs12972487, rs445417, rs635624, rs7416358, 12-54819630-G-INSERTION, rs177665, rs1070444, rs10912583, rs12914919, rs2854725, rs948068, rs71472147, rs72939578, rs658795, rs17758350, rs144260901, rs10801129, rs1702870, rs10912583, rs2452822, rs7774349, rs4705272, rs117946479, rs936126, rs634641, rs2314737, rs3002685, rs634641, rs12496281, rs10134119, rs3808240, rs1890843, rs11829981, rs12496281, rs2383184, rs144260901, rs6801634, rs2383184, and rs2954756. In some embodiments, the genotype is detected by a process comprising: (a) contacting the sample obtained from the subject with a nucleic acid sequence comprising a detectable moiety, the nucleic acid sequence capable of hybridizing to at least 20 contiguous nucleobases between nucleobase 16 and nucleobase 46 of at least one of SEQ ID NOS: 1-82; and (b) detecting binding between the nucleic acid sequence and the at least 20 contiguous nucleobases between nucleobase 16 and nucleobase 46 of at least one of SEQ ID NOS: 1-82. In some embodiments, the genotype is detected by sequencing genetic information contained in the sample obtained from the subject. In some embodiments, the further comprising characterizing the CD as a severe form of CD, the severe form of CD comprising stricturing disease or stricturing and internal penetrating disease, provided that the genotype detected in step (a) comprises at least one polymorphism selected from the group consisting of rs7416358G, rs1070444A, rs11749180A, 12-54819630-G-INSERTION, rs12496281G, rs11171747C, rs116714418A, rs111455641G, rs9480689G, rs6879067A, rs11128532A, rs177665C, rs10775375A, rs6801634A, rs6962616A, rs7220814G, rs4325270T, rs768755T, rs17758350A, rs9480689G, rs525850A, rs4325270T, rs6962616A, rs10265554G, rs634641G, rs1493871G, rs12669698G, rs4332037A, rs17697480G, rs9480689G, rs6074737A, rs904910G, rs12972487A, rs445417A, rs63562C, rs7416358G, rs177665C, rs1070444A, rs10912583A, rs12914919G, rs2854725C, rs9480689G, rs71472147A, rs72939578A, rs658795A, rs17758350A, rs144260901A, rs10801129C, rs1702870A, rs10912583A, rs2452822C, rs7774349A, rs4705272G, rs117946479A, rs936126A, rs634641G, rs2314737G, rs3002685G, rs634641G, rs10134119T, rs3808240C, rs1890843G, and rs11829981A. In some embodiments, methods further comprise characterizing the CD as a severe form of CD, the severe form of CD comprising internal penetrating disease, provided that the genotype detected in step (a) comprises at least one polymorphism selected from the group consisting of rs12496281G, rs2383184G, rs144260901A, rs6801634A, rs2383184G, and rs2954756G. In some embodiments, methods further comprise characterizing the severe form of CD by a disease location of the stricturing disease in the subject, the disease location selected from the group consisting of an ileum, an ilealcolonic region, and a colon. In some embodiments, methods further comprise characterizing the severe form of CD by a disease location of the internal penetrating disease in the subject, the disease location selected from the group consisting of an ileum, an ilealcolonic region, and a colon. In some embodiments, methods further comprise characterizing the CD as refractory. In some embodiments, the therapeutic agent is a modulator of a gene or gene expression product expressed from the gene, the gene selected from group consisting of X—C Motif Chemokine Ligand 1 (XCL1), Dermatopontin (DPT), TNF Superfamily Member 4 (TNFSF4), C-Type Lectin Like 1 (CLECL1), CD69 Molecule (CD69), Fms Related Tyrosine Kinase 1 (FLT1), Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 (MAP4K4), Prostaglandin E Receptor 4 (PTGER4), interleukin 18 receptor 1 (IL18R1). 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 3 (PFKFB3), Interleukin 18 Receptor Accessory Protein (IL18RAP), Adenylate Cyclase 7 (ADCY7), B Lymphoid Tyrosine Kinase (BLK), G Protein-Coupled Receptor 65 (GPR65), Sprouty Related EVH1 Domain Containing 2 (SPRED2), Src Kinase Associated Phosphoprotein 2 (SKAP2), CD30 ligand (CD30L), Receptor Interacting Serine/Threonine Kinase 2 (RIPK2), and TNF Ligand Superfamily Member 15 (TL1A), an a combination thereof. In some embodiments, the modulator of the gene or gene expression product is selected from the group consisting of an antibody or antigen-binding fragment thereof, a small molecule, or a peptide. In some embodiments, the modulator of the gene or gene expression product is an agonist or a partial agonist. In some embodiments, the modulator of the gene or gene expression product is an antagonist or a partial antagonist. In some embodiments, the modulator of the gene or gene expression product is an allosteric modulator.

Aspects disclosed herein provide kits comprising: (a) at least one nucleic acid sequence comprising a detectable moiety, the at least one nucleic acid sequence comprising at least 20 contiguous nucleobases between nucleobase 16 and nucleobase 46 of at least one of SEQ ID NOS: 13-82, or a reverse complement thereof; and (b) at least one primer pair comprising a forward primer and a reverse primer, the forward primer comprising any one of SEQ ID NOS: 392-624 or a reverse complement thereof, the reverse primer comprising any one of SEQ ID NOS: 625-857 or a reverse complement thereof.

Aspects disclosed here provide methods of treating a severe form of Crohn's disease using the kit of the present disclosure, the method comprising: (a) introducing the at least one nucleic acid sequence and the at least one primer pair from the kit of the present disclosure to a sample obtained from a subject; (b) amplifying at least a portion of a target nucleic acid sequence contained in the sample, the target nucleic acid sequence provided in at least one of SEQ ID NOS: 1-82, to produce a detectable target nucleic acid sequence; (c) detecting a presence or an absence of the detectable target nucleic acid sequence; and (d) administering to the subject a therapeutically effective amount of a therapeutic agent, provided the a target nucleic acid sequence is detected in (c). In some embodiments, the methods further comprise determining whether the subject has or will develop at least one of a non-response and a loss-of-response to a standard treatment. In some embodiments, the standard treatment is selected from the group consisting of glucocorticosteriods, anti-TNF therapy, anti-a4-b7 therapy (vedolizumab), anti-IL12p40 therapy (ustekinumab), Thalidomide, and Cytoxin. In some embodiments, the therapeutic agent is a modulator of a gene or gene expression product expressed from the gene, the gene selected from group consisting of X—C Motif Chemokine Ligand 1 (XCL1), Dermatopontin (DPT), TNF Superfamily Member 4 (TNFSF4), C-Type Lectin Like 1 (CLECL1), CD69 Molecule (CD69), Fms Related Tyrosine Kinase 1 (FLT1), Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 (MAP4K4), Prostaglandin E Receptor 4 (PTGER4), interleukin 18 receptor 1 (IL18R1). 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 3 (PFKFB3), Interleukin 18 Receptor Accessory Protein (IL18RAP), Adenylate Cyclase 7 (ADCY7), B Lymphoid Tyrosine Kinase (BLK), G Protein-Coupled Receptor 65 (GPR65), Sprouty Related EVH1 Domain Containing 2 (SPRED2), Src Kinase Associated Phosphoprotein 2 (SKAP2), CD30 ligand (CD30L), Receptor Interacting Serine/Threonine Kinase 2 (RIPK2), and TNF Ligand Superfamily Member 15 (TL1A), an a combination thereof. In some embodiments, the modulator of the gene or gene expression product is selected from the group consisting of an antibody or antigen-binding fragment thereof, a small molecule, or a peptide. In some embodiments, the modulator of the gene or gene expression product is an agonist or a partial agonist. In some embodiments, the modulator of the gene or gene expression product is an antagonist or a partial antagonist. In some embodiments, the modulator of the gene or gene expression product is an allosteric modulator.

Aspects disclosed herein provide methods of characterizing an inflammatory bowel disease as Crohn's disease using the kit of the present disclosure, the method comprising: (a) introducing the at least one nucleic acid sequence and the at least one primer pair from the kit of the present disclosure to a sample obtained from a subject; (b) amplifying at least a portion of a target nucleic acid sequence contained in the sample, the target nucleic acid sequence provided in at least one of SEQ ID NOS: 1-82, to produce a detectable target nucleic acid sequence; (c) detecting a presence or an absence of the detectable target nucleic acid sequence; and (d) characterizing the inflammatory disease as Crohn's disease (CD) provided the presence of the detectable target nucleic acid sequence is detected in step (c). In some embodiments, methods further comprise characterizing the severe form of CD by a disease location of the stricturing disease in the subject, the disease location selected from the group consisting of an ileum, an ilealcolonic region, and a colon. In some embodiments, methods further comprise characterizing the severe form of CD by a disease location of the internal penetrating disease in the subject, the disease location selected from the group consisting of an ileum, an ilealcolonic region, and a colon. In some embodiments, methods further comprise characterizing the CD as refractory. In some embodiments, the therapeutic agent is a modulator of a gene or gene expression product expressed from the gene, the gene selected from group consisting of X—C Motif Chemokine Ligand 1 (XCL1), Dermatopontin (DPT), TNF Superfamily Member 4 (TNFSF4), C-Type Lectin Like 1 (CLECL1), CD69 Molecule (CD69), Fms Related Tyrosine Kinase 1 (FLT1), Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 (MAP4K4), Prostaglandin E Receptor 4 (PTGER4), interleukin 18 receptor 1 (IL18R1). 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 3 (PFKFB3), Interleukin 18 Receptor Accessory Protein (IL18RAP), Adenylate Cyclase 7 (ADCY7), B Lymphoid Tyrosine Kinase (BLK), G Protein-Coupled Receptor 65 (GPR65), Sprouty Related EVH1 Domain Containing 2 (SPRED2), Src Kinase Associated Phosphoprotein 2 (SKAP2), CD30 ligand (CD30L), Receptor Interacting Serine/Threonine Kinase 2 (RIPK2), and TNF Ligand Superfamily Member 15 (TL1A), an a combination thereof. In some embodiments, the modulator of the gene or gene expression product is selected from the group consisting of an antibody or antigen-binding fragment thereof, a small molecule, or a peptide. In some embodiments, the modulator of the gene or gene expression product is an agonist or a partial agonist. In some embodiments, the modulator of the gene or gene expression product is an antagonist or a partial antagonist. In some embodiments, the modulator of the gene or gene expression product is an allosteric modulator.

Aspects disclosed provide methods of treating a severe form of Crohn's disease (CD) in a subject, the method comprising: (a) obtaining a sample from a subject; (b) contacting the sample with an assay adapted to detect a genotype in the sample; and (c) administering to the subject a therapeutically effective amount of a therapeutic agent, provided the a genotype is detected in the sample obtained from the subject, the genotype comprising at least one polymorphism associated with at least one of stricturing disease and internal penetrating disease that is characteristic of severe CD as indicated by a P value of at most 1.0E⁻⁵. In some embodiments, the assay is a genotyping device. In some embodiments, the genotyping device is a sequencer. In some embodiments, the genotyping device is quantitative polymerase chain reaction (qPCR). In some embodiments, the at least one polymorphism is associated with stricturing disease and is selected from the group consisting of rs7416358G, rs1070444A, rs11749180A, 12-54819630-G-INSERTION, rs12496281G, rs11171747C, rs116714418A, rs111455641G, rs9480689G, rs6879067A, rs11128532A, rs177665C, rs10775375A, rs6801634A, rs6962616A, rs7220814G, rs4325270T, rs768755T, rs17758350A, rs9480689G, rs525850A, rs4325270T, rs6962616A, rs10265554G, rs634641G, rs1493871G, rs12669698G, rs4332037A, rs17697480G, rs9480689G, rs6074737A, rs904910G, rs12972487A, rs445417A, rs63562C, rs7416358G, rs177665C, rs1070444A, rs10912583A, rs12914919G, rs2854725C, rs9480689G, rs71472147A, rs72939578A, rs658795A, rs17758350A, rs144260901A, rs10801129C, rs1702870A, rs10912583A, rs2452822C, rs7774349A, rs4705272G, rs117946479A, rs936126A, rs634641G, rs2314737G, rs3002685G, rs634641G, rs10134119T, rs3808240C, rs1890843G, and rs11829981A. In some embodiments, the genotype device is a microarray. In some embodiments, the at least one polymorphism is associated with internal penetrating disease and is selected from the group consisting of rs12496281G, rs2383184G, rs144260901A, rs6801634A, rs2383184G, and rs2954756G. In some embodiments, the at least one polymorphism is located at nucleoposition 26 or 31 within any one of SEQ ID NOS: 1-82. In some embodiments, the genotype is detected by a process comprising: (a) contacting the sample obtained from the subject with a nucleic acid sequence comprising a detectable moiety, the nucleic acid sequence capable of hybridizing to at least 20 contiguous nucleobases between nucleobase 16 and nucleobase 46 of at least one of SEQ ID NOS: 13-82; and (b) detecting binding between the nucleic acid sequence and the at least 20 contiguous nucleobases between nucleobase 16 and nucleobase 46 of at least one of SEQ ID NOS: 13-82. In some embodiments, the genotype is detected by sequencing genetic information contained in the sample obtained from the subject. In some embodiments, the methods further comprise determining whether the subject has or will develop at least one of a non-response and a loss-of-response to a standard treatment. In some embodiments, the standard treatment is selected from the group consisting of glucocorticosteriods, anti-TNF therapy, anti-a4-b7 therapy (vedolizumab), anti-IL12p40 therapy (ustekinumab), Thalidomide, and Cytoxin. In some embodiments, the therapeutic agent is a modulator of a gene or gene expression product expressed from the gene, the gene selected from group consisting of X—C Motif Chemokine Ligand 1 (XCL1), Dermatopontin (DPT), TNF Superfamily Member 4 (TNFSF4), C-Type Lectin Like 1 (CLECL1), CD69 Molecule (CD69), Fms Related Tyrosine Kinase 1 (FLT1), Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 (MAP4K4), Prostaglandin E Receptor 4 (PTGER4), interleukin 18 receptor 1 (IL18R1). 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 3 (PFKFB3), Interleukin 18 Receptor Accessory Protein (IL18RAP), Adenylate Cyclase 7 (ADCY7), B Lymphoid Tyrosine Kinase (BLK), G Protein-Coupled Receptor 65 (GPR65), Sprouty Related EVH1 Domain Containing 2 (SPRED2), Src Kinase Associated Phosphoprotein 2 (SKAP2), CD30 ligand (CD30L), Receptor Interacting Serine/Threonine Kinase 2 (RIPK2), and TNF Ligand Superfamily Member 15 (TL1A), an a combination thereof. In some embodiments, the modulator of the gene or gene expression product is selected from the group consisting of an antibody or antigen-binding fragment thereof, a small molecule, or a peptide. In some embodiments, the modulator of the gene or gene expression product is an agonist or a partial agonist. In some embodiments, the modulator of the gene or gene expression product is an antagonist or a partial antagonist. In some embodiments, the modulator of the gene or gene expression product is an allosteric modulator.

Aspects disclosed provide methods of treating a severe form of Crohn's disease (CD) in a subject, the method comprising: (a) contacting a sample obtained from a subject with an assay adapted to detect a genotype in the sample; and (b) administering to the subject a therapeutically effective amount of a therapeutic agent, provided the a genotype is detected in the sample obtained from the subject, the genotype comprising at least one polymorphism associated with at least one of stricturing disease and internal penetrating disease that is characteristic of severe CD as indicated by a P value of at most 1.0E⁻⁵. In some embodiments, the assay is a genotyping device. In some embodiments, the genotyping device is a sequencer. In some embodiments, the genotyping device is quantitative polymerase chain reaction (qPCR). In some embodiments, the genotype device is a microarray. In some embodiments, the at least one polymorphism is associated with stricturing disease and is selected from the group consisting of rs7416358G, rs1070444A, rs11749180A, 12-54819630-G-INSERTION, rs12496281G, rs11171747C, rs116714418A, rs111455641G, rs9480689G, rs6879067A, rs11128532A, rs177665C, rs10775375A, rs6801634A, rs6962616A, rs7220814G, rs4325270T, rs768755T, rs17758350A, rs9480689G, rs525850A, rs4325270T, rs6962616A, rs10265554G, rs634641G, rs1493871G, rs12669698G, rs4332037A, rs17697480G, rs9480689G, rs6074737A, rs904910G, rs12972487A, rs445417A, rs63562C, rs7416358G, rs177665C, rs1070444A, rs10912583A, rs12914919G, rs2854725C, rs9480689G, rs71472147A, rs72939578A, rs658795A, rs17758350A, rs144260901A, rs10801129C, rs1702870A, rs10912583A, rs2452822C, rs7774349A, rs4705272G, rs117946479A, rs936126A, rs634641G, rs2314737G, rs3002685G, rs634641G, rs10134119T, rs3808240C, rs1890843G, and rs11829981A. In some embodiments, the at least one polymorphism is associated with internal penetrating disease and is selected from the group consisting of rs12496281G, rs2383184G, rs144260901A, rs6801634A, rs2383184G, and rs2954756G. In some embodiments, the at least one polymorphism is located at nucleoposition 26 or 31 within any one of SEQ ID NOS: 1-82. In some embodiments, the genotype is detected by a process comprising: (a) contacting the sample obtained from the subject with a nucleic acid sequence comprising a detectable moiety, the nucleic acid sequence capable of hybridizing to at least 20 contiguous nucleobases between nucleobase 16 and nucleobase 46 of at least one of SEQ ID NOS: 13-82; and (b) detecting binding between the nucleic acid sequence and the at least 20 contiguous nucleobases between nucleobase 16 and nucleobase 46 of at least one of SEQ ID NOS: 13-82. In some embodiments, the genotype is detected by sequencing genetic information contained in the sample obtained from the subject. In some embodiments, the methods further comprise determining whether the subject has or will develop at least one of a non-response and a loss-of-response to a standard treatment. In some embodiments, the standard treatment is selected from the group consisting of glucocorticosteriods, anti-TNF therapy, anti-a4-b7 therapy (vedolizumab), anti-IL12p40 therapy (ustekinumab), Thalidomide, and Cytoxin. In some embodiments, the therapeutic agent is a modulator of a gene or gene expression product expressed from the gene, the gene selected from group consisting of X—C Motif Chemokine Ligand 1 (XCL1), Dermatopontin (DPT), TNF Superfamily Member 4 (TNFSF4), C-Type Lectin Like 1 (CLECL1), CD69 Molecule (CD69), Fms Related Tyrosine Kinase 1 (FLT1), Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 (MAP4K4), Prostaglandin E Receptor 4 (PTGER4), interleukin 18 receptor 1 (IL18R1). 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 3 (PFKFB3), Interleukin 18 Receptor Accessory Protein (IL18RAP), Adenylate Cyclase 7 (ADCY7), B Lymphoid Tyrosine Kinase (BLK), G Protein-Coupled Receptor 65 (GPR65), Sprouty Related EVH1 Domain Containing 2 (SPRED2), Src Kinase Associated Phosphoprotein 2 (SKAP2), CD30 ligand (CD30L), Receptor Interacting Serine/Threonine Kinase 2 (RIPK2), and TNF Ligand Superfamily Member 15 (TL1A), an a combination thereof. In some embodiments, the modulator of the gene or gene expression product is selected from the group consisting of an antibody or antigen-binding fragment thereof, a small molecule, or a peptide. In some embodiments, the modulator of the gene or gene expression product is an agonist or a partial agonist. In some embodiments, the modulator of the gene or gene expression product is an antagonist or a partial antagonist. In some embodiments, the modulator of the gene or gene expression product is an allosteric modulator.

Aspects disclosed provide methods of treating a severe form of Crohn's disease (CD) in a subject, the method comprising: (a) obtaining a sample from a subject; (b) contacting the sample with an assay adapted to detect a genotype in the sample; and (c) administering to the subject a therapeutically effective amount of a therapeutic agent, provided the a genotype is detected in the sample obtained from the subject, the genotype comprising at least one polymorphism selected from the group consisting of rs7416358G, rs1070444A, rs11749180A, 12-54819630-G-INSERTION, rs12496281G, rs11171747C, rs116714418A, rs111455641G, rs9480689G, rs6879067A, rs11128532A, rs177665C, rs10775375A, rs6801634A, rs6962616A, rs7220814G, rs4325270T, rs768755T, rs17758350A, rs9480689G, rs525850A, rs4325270T, rs6962616A, rs10265554G, rs634641G, rs1493871G, rs12669698G, rs4332037A, rs17697480G, rs9480689G, rs6074737A, rs904910G, rs12972487A, rs445417A, rs63562C, rs7416358G, rs177665C, rs1070444A, rs10912583A, rs12914919G, rs2854725C, rs9480689G, rs71472147A, rs72939578A, rs658795A, rs17758350A, rs144260901A, rs10801129C, rs1702870A, rs10912583A, rs2452822C, rs7774349A, rs4705272G, rs117946479A, rs936126A, rs634641G, rs2314737G, rs3002685G, rs634641G, rs10134119T, rs3808240C, rs1890843G, and rs11829981A, and a combination thereof. In some embodiments, the assay is a genotyping device. In some embodiments, the genotyping device is a sequencer. In some embodiments, the genotyping device is quantitative polymerase chain reaction (qPCR). In some embodiments, the genotype device is a microarray. In some embodiments, the at least one polymorphism is associated with stricturing disease and is selected from the group consisting of rs7416358G, rs1070444A, rs11749180A, 12-54819630-G-INSERTION, rs12496281G, rs11171747C, rs116714418A, rs111455641G, rs9480689G, rs6879067A, rs11128532A, rs177665C, rs10775375A, rs6801634A, rs6962616A, rs7220814G, rs4325270T, rs768755T, rs17758350A, rs9480689G, rs525850A, rs4325270T, rs6962616A, rs10265554G, rs634641G, rs1493871G, rs12669698G, rs4332037A, rs17697480G, rs9480689G, rs6074737A, rs904910G, rs12972487A, rs445417A, rs63562C, rs7416358G, rs177665C, rs1070444A, rs10912583A, rs12914919G, rs2854725C, rs9480689G, rs71472147A, rs72939578A, rs658795A, rs17758350A, rs144260901A, rs10801129C, rs1702870A, rs10912583A, rs2452822C, rs7774349A, rs4705272G, rs117946479A, rs936126A, rs634641G, rs2314737G, rs3002685G, rs634641G, rs10134119T, rs3808240C, rs1890843G, and rs11829981A. In some embodiments, the at least one polymorphism is associated with stricturing disease and is selected from the group consisting of rs7416358G, rs1070444A, rs11749180A, 12-54819630-G-INSERTION, rs12496281G, rs11171747C, rs116714418A, rs111455641G, rs9480689G, rs6879067A, rs11128532A, rs177665C, rs10775375A, rs6801634A, rs6962616A, rs7220814G, rs4325270T, rs768755T, rs17758350A, rs9480689G, rs525850A, rs4325270T, rs6962616A, rs10265554G, rs634641G, rs1493871G, rs12669698G, rs4332037A, rs17697480G, rs9480689G, rs6074737A, rs904910G, rs12972487A, rs445417A, rs63562C, rs7416358G, rs177665C, rs1070444A, rs10912583A, rs12914919G, rs2854725C, rs9480689G, rs71472147A, rs72939578A, rs658795A, rs17758350A, rs144260901A, rs10801129C, rs1702870A, rs10912583A, rs2452822C, rs7774349A, rs4705272G, rs117946479A, rs936126A, rs634641G, rs2314737G, rs3002685G, rs634641G, rs10134119T, rs3808240C, rs1890843G, and rs11829981A. In some embodiments, the genotype device is a microarray. In some embodiments, the at least one polymorphism is associated with internal penetrating disease and is selected from the group consisting of rs12496281G, rs2383184G, rs144260901A, rs6801634A, rs2383184G, and rs2954756G. In some embodiments, the at least one polymorphism is located at nucleoposition 26 or 31 within any one of SEQ ID NOS: 1-82. In some embodiments, the genotype is detected by a process comprising: (a) contacting the sample obtained from the subject with a nucleic acid sequence comprising a detectable moiety, the nucleic acid sequence capable of hybridizing to at least 20 contiguous nucleobases between nucleobase 16 and nucleobase 46 of at least one of SEQ ID NOS: 13-82; and (b) detecting binding between the nucleic acid sequence and the at least 20 contiguous nucleobases between nucleobase 16 and nucleobase 46 of at least one of SEQ ID NOS: 13-82. In some embodiments, the genotype is detected by sequencing genetic information contained in the sample obtained from the subject. In some embodiments, the methods further comprise determining whether the subject has or will develop at least one of a non-response and a loss-of-response to a standard treatment. In some embodiments, the standard treatment is selected from the group consisting of glucocorticosteriods, anti-TNF therapy, anti-a4-b7 therapy (vedolizumab), anti-IL12p40 therapy (ustekinumab), Thalidomide, and Cytoxin. In some embodiments, the therapeutic agent is a modulator of a gene or gene expression product expressed from the gene, the gene selected from group consisting of X—C Motif Chemokine Ligand 1 (XCL1), Dermatopontin (DPT), TNF Superfamily Member 4 (TNFSF4), C-Type Lectin Like 1 (CLECL1), CD69 Molecule (CD69), Fms Related Tyrosine Kinase 1 (FLT1), Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 (MAP4K4), Prostaglandin E Receptor 4 (PTGER4), interleukin 18 receptor 1 (IL18R1). 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 3 (PFKFB3), Interleukin 18 Receptor Accessory Protein (IL18RAP), Adenylate Cyclase 7 (ADCY7), B Lymphoid Tyrosine Kinase (BLK), G Protein-Coupled Receptor 65 (GPR65), Sprouty Related EVH1 Domain Containing 2 (SPRED2), Src Kinase Associated Phosphoprotein 2 (SKAP2), CD30 ligand (CD30L), Receptor Interacting Serine/Threonine Kinase 2 (RIPK2), and TNF Ligand Superfamily Member 15 (TL1A), an a combination thereof. In some embodiments, the modulator of the gene or gene expression product is selected from the group consisting of an antibody or antigen-binding fragment thereof, a small molecule, or a peptide. In some embodiments, the modulator of the gene or gene expression product is an agonist or a partial agonist. In some embodiments, the modulator of the gene or gene expression product is an antagonist or a partial antagonist. In some embodiments, the modulator of the gene or gene expression product is an allosteric modulator.

Aspects disclosed provide methods of treating a severe form of Crohn's disease (CD) in a subject, the method comprising: (a) contacting a sample obtained from a subject with an assay adapted to detect a genotype in the sample; and (b) administering to the subject a therapeutically effective amount of a therapeutic agent, provided the a genotype is detected in the sample obtained from the subject, the genotype comprising at least one polymorphism selected from the group consisting of rs7416358G, rs1070444A, rs11749180A, 12-54819630-G-INSERTION, rs12496281G, rs11171747C, rs116714418A, rs111455641G, rs9480689G, rs6879067A, rs11128532A, rs177665C, rs10775375A, rs6801634A, rs6962616A, rs7220814G, rs4325270T, rs768755T, rs17758350A, rs9480689G, rs525850A, rs4325270T, rs6962616A, rs10265554G, rs634641G, rs1493871G, rs12669698G, rs4332037A, rs17697480G, rs9480689G, rs6074737A, rs904910G, rs12972487A, rs445417A, rs63562C, rs7416358G, rs177665C, rs1070444A, rs10912583A, rs12914919G, rs2854725C, rs9480689G, rs71472147A, rs72939578A, rs658795A, rs17758350A, rs144260901A, rs10801129C, rs1702870A, rs10912583A, rs2452822C, rs7774349A, rs4705272G, rs117946479A, rs936126A, rs634641G, rs2314737G, rs3002685G, rs634641G, rs10134119T, rs3808240C, rs1890843G, and rs11829981A, and a combination thereof. In some embodiments, the assay is a genotyping device. In some embodiments, the genotyping device is a sequencer. In some embodiments, the genotyping device is quantitative polymerase chain reaction (qPCR). In some embodiments, the genotype device is a microarray. In some embodiments, the at least one polymorphism is associated with stricturing disease and is selected from the group consisting of rs7416358G, rs1070444A, rs11749180A, 12-54819630-G-INSERTION, rs12496281G, rs11171747C, rs116714418A, rs111455641G, rs9480689G, rs6879067A, rs11128532A, rs177665C, rs10775375A, rs6801634A, rs6962616A, rs7220814G, rs4325270T, rs768755T, rs17758350A, rs9480689G, rs525850A, rs4325270T, rs6962616A, rs10265554G, rs634641G, rs1493871G, rs12669698G, rs4332037A, rs17697480G, rs9480689G, rs6074737A, rs904910G, rs12972487A, rs445417A, rs63562C, rs7416358G, rs177665C, rs1070444A, rs10912583A, rs12914919G, rs2854725C, rs9480689G, rs71472147A, rs72939578A, rs658795A, rs17758350A, rs144260901A, rs10801129C, rs1702870A, rs10912583A, rs2452822C, rs7774349A, rs4705272G, rs117946479A, rs936126A, rs634641G, rs2314737G, rs3002685G, rs634641G, rs10134119T, rs3808240C, rs1890843G, and rs11829981A. In some embodiments, the at least one polymorphism is associated with internal penetrating disease and is selected from the group consisting of rs12496281G, rs2383184G, rs144260901A, rs6801634A, rs2383184G, and rs2954756G. In some embodiments, the at least one polymorphism is located at nucleoposition 26 or 31 within any one of SEQ ID NOS: 1-82. In some embodiments, the genotype is detected by a process comprising: (a) contacting the sample obtained from the subject with a nucleic acid sequence comprising a detectable moiety, the nucleic acid sequence capable of hybridizing to at least 20 contiguous nucleobases between nucleobase 16 and nucleobase 46 of at least one of SEQ ID NOS: 13-82; and (b) detecting binding between the nucleic acid sequence and the at least 20 contiguous nucleobases between nucleobase 16 and nucleobase 46 of at least one of SEQ ID NOS: 13-82. In some embodiments, the genotype is detected by sequencing genetic information contained in the sample obtained from the subject. In some embodiments, the methods further comprise determining whether the subject has or will develop at least one of a non-response and a loss-of-response to a standard treatment. In some embodiments, the standard treatment is selected from the group consisting of glucocorticosteriods, anti-TNF therapy, anti-a4-b7 therapy (vedolizumab), anti-IL12p40 therapy (ustekinumab), Thalidomide, and Cytoxin. In some embodiments, the therapeutic agent is a modulator of a gene or gene expression product expressed from the gene, the gene selected from group consisting of X—C Motif Chemokine Ligand 1 (XCL1), Dermatopontin (DPT), TNF Superfamily Member 4 (TNFSF4), C-Type Lectin Like 1 (CLECL1), CD69 Molecule (CD69), Fms Related Tyrosine Kinase 1 (FLT1), Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 (MAP4K4), Prostaglandin E Receptor 4 (PTGER4), interleukin 18 receptor 1 (IL18R1). 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 3 (PFKFB3), Interleukin 18 Receptor Accessory Protein (IL18RAP), Adenylate Cyclase 7 (ADCY7), B Lymphoid Tyrosine Kinase (BLK), G Protein-Coupled Receptor 65 (GPR65), Sprouty Related EVH1 Domain Containing 2 (SPRED2), Src Kinase Associated Phosphoprotein 2 (SKAP2), CD30 ligand (CD30L), Receptor Interacting Serine/Threonine Kinase 2 (RIPK2), and TNF Ligand Superfamily Member 15 (TL1A), an a combination thereof. In some embodiments, the modulator of the gene or gene expression product is selected from the group consisting of an antibody or antigen-binding fragment thereof, a small molecule, or a peptide. In some embodiments, the modulator of the gene or gene expression product is an agonist or a partial agonist. In some embodiments, the modulator of the gene or gene expression product is an antagonist or a partial antagonist. In some embodiments, the modulator of the gene or gene expression product is an allosteric modulator.

DETAILED DESCRIPTION

The present disclosure provides methods and systems for characterizing severe forms of CD that involve at least one stricturing, penetrating, and stricturing and penetrating disease phenotypes. Multiple case-control univariate analyses were performed comparing these subclinical phenotypes of CD that revealed genotypes and serological markers useful for characterizing severe forms of CD. The genotypes and serologies described can be detected in genetic material in a sample obtained from a subject. The genotypes and serologies detected in a sample obtained from a subject can be used to identify a risk that the subject may develop a severe form of CD, and in some cases, to pinpoint where in the subject the severe CD may manifest. The subjects identified to be at risk for developing severe forms of CD using the methods described herein are prescribed or administered a targeted therapeutic therapy (e.g., targeting Prolactin signaling, autophagy, and JAK/STAT pathways).

Subject

The subject disclosed herein can be a mammal, such as for example a mouse, rat, guinea pig, rabbit, non-human primate, or farm animal. In some instances, the subject is human. In some instances, the subject is a patient who is diagnosed with the disease or condition disclosed herein. In some instances, the subject is not diagnosed with the disease or condition. In some instances, the subject is suffering from a symptom related to a disease or condition disclosed herein (e.g., abdominal pain, cramping, diarrhea, rectal bleeding, fever, weight loss, fatigue, loss of appetite, dehydration, and malnutrition, anemia, or ulcers).

In some embodiments, the subject is susceptible to, or is inflicted with, thiopurine toxicity, or a disease caused by thiopurine toxicity (such as pancreatitis or leukopenia). The subject may experience, or is suspected of experiencing, non-response or loss-of-response to a standard treatment (e.g., anti-TNF alpha therapy, anti-a4-b7 therapy (vedolizumab), anti-IL12p40 therapy (ustekinumab), Thalidomide, or Cytoxin).

Disease or Condition

The disease or condition disclosed herein is an inflammatory bowel disease, such as Crohn's disease (CD) or ulcerative colitis (UC). A subject may suffer from fibrosis, fibrostenosis, or a fibrotic disease, either isolated or in combination with an inflammatory disease. In some cases, the CD is severe CD. The severe CD may result from inflammation that has led to the formation of scar tissue in the intestinal wall (fibrostenosis) and/or swelling. In some cases, the severe CD is characterized by the presence of fibrotic and/or inflammatory strictures. The strictures may be determined by computed tomography enterography (CTE), and magnetic resonance imaging enterography (MRE). The disease or condition may be characterized as refractory, which in some cases, means the disease is resistant to a standard treatment (e.g., anti-TNF therapy). Non-limiting examples of standard treatment include glucocorticosteriods, anti-TNF therapy, anti-a4-b7 therapy (vedolizumab), anti-IL12p40 therapy (ustekinumab), Thalidomide, and Cytoxin.

Genotypes

Disclosed herein, in some embodiments are genotypes that are detected in a sample obtained from a subject by analyzing the genetic material in the sample. In some instances, the subject may be human. In some embodiments, the genetic material is obtained from a subject having a disease or condition disclosed herein. In some cases, the genetic material is obtained from blood, serum, plasma, sweat, hair, tears, urine, and other techniques known by one of skill in the art. In some cases, the genetic material is obtained for a biopsy, e.g., from the intestinal track of the subject.

The genotypes of the present disclosure comprise genetic material that is deoxyribonucleic acid (DNA). In some instances, the genotype comprises a denatured DNA molecule or fragment thereof. In some instances, the genotype comprises DNA selected from: genomic DNA, viral DNA, mitochondrial DNA, plasmid DNA, amplified DNA, circular DNA, circulating DNA, cell-free DNA, or exosomal DNA. In some instances, the DNA is single-stranded DNA (ssDNA), double-stranded DNA, denaturing double-stranded DNA, synthetic DNA, and combinations thereof. The circular DNA may be cleaved or fragmented.

The genotypes disclosed herein comprise at least one polymorphisms at a gene or genetic locus described herein. In some instances, the gene or genetic locus is selected from the group consisting of Microtubule Associated Protein Tau (MAPT), Ankyrin 3 (ANK3), Somatostatin Receptor 3 (SSTR3), N(Alpha)-Acetyltransferase 80, NatH Catalytic Subunit (NAT6), Serine/Threonine Kinase 33 (STK33), Importin 5 (IMP5), Teneurin Transmembrane Protein 3 (ODZ3), RNA Polymerase III Subunit A (POLS), Integrin Subunit Alpha 6 (ITGA6), Fatty Acyl-CoA Reductase 1 (MLSTD2), Prokineticin 2 (PROK2), RING1 And YY1 Binding Protein (RYBP), Thyroid Stimulating Hormone Receptor (TSHR), RAS Guanyl Releasing Protein 3 (RASGRP3), Pyruvate Dehydrogenase E1 Beta Subunit (PDHB), Potassium Channel Tetramerization Domain Containing 6 (KCNQ1DN), Cyclin Dependent Kinase Inhibitor 1C (CDKN1C), CUB And Sushi Multiple Domains 1 (CSMD1), Nudix Hydrolase 12 (NUDT12), XK Related 6 (XKR6), Solute Carrier Family 2 Member 13 (SLC2A13), Beta-1,4-N-Acetyl-Galactosaminyltransferase 1 (B4GALNT1), OS9, Endoplasmic Reticulum Lectin (OS9), CTD Small Phosphatase 2 (CTDSP2), ATP23 Metallopeptidase And ATP Synthase Assembly Factor Homolog (XRCC6BP1), N-Acetylated Alpha-Linked Acidic Dipeptidase Like 1 (NAALADL1), Cell Division Cycle Associated 5 (CDCA5), Epidermal Growth Factor (EGF), Methionine Sulfoxide Reductase A (MSRA), Phosphoribosyl Pyrophosphate Synthetase Associated Protein 2 (PRPSAP2), Cytochrome P450 Family 2 Subfamily R Member 1 (CYP2R1), Calcitonin Related Polypeptide Alpha (CALCA), Dopa Decarboxylase (DDC), Calcium Voltage-Gated Channel Auxiliary Subunit Alpha2delta 2 (CACNA2D2), Proline Rich 20B (FLJ40296), Pvt1 Oncogene (PVT1), Zinc Finger Protein 184 (ZNF184), Tyrosine Kinase Non Receptor 1 (TNK1), Metaxin 1 (MTX1), TNF Alpha Induced Protein 3 (TNFAIP3), PERP, TP53 Apoptosis Effector (PERP), Stromal Antigen 3-Like 4 (Pseudogene) (STAG3L4), AUTS2, Activator Of Transcription And Developmental Regulator (AUTS2), Phosphatidylinositol Transfer Protein Beta (PITPNB), Ribosomal Protein L37 (RPL37), Caspase Recruitment Domain Family Member 6 (CARD6), Tetratricopeptide Repeat Domain 33 (TTC33), SPARC (Osteonectin), Cwcv And Kazal Like Domains Proteoglycan 3 (SPOCK3), Annexin A10 (ANXA10), Apolipoprotein B (APOB), BicC Family RNA Binding Protein 1 (BICC1), Nuclear Receptor Coactivator 2 (NCOA2), Programmed Cell Death 11 (PDCD11), Reticulon 4 Interacting Protein 1 (RTN4IP1), Engulfment And Cell Motility 1 (ELMO1), RNA Binding Motif Protein 6 (RBM6), Xylosyltransferase 1 (XYLT1), Neuropilin 2 (NRP2), Myeloma Overexpressed (MYEOV), Cyclin D1 (CCND1), Olfactory Receptor Family 51 Subfamily G Member 1 (Gene/Pseudogene) (OR51G1), Olfactory Receptor Family 51 Subfamily A Member 4 (OR51A4), Potassium Voltage-Gated Channel Subfamily H Member 7 (KCNH7), Cell Adhesion Associated, Oncogene Regulated (CDON), RNA Pseudouridine Synthase D4 (RPUSD4), Interferon Epsilon (IFNE1), Methylthioadenosine Phosphorylase (MTAP), Elongator Acetyltransferase Complex Subunit 3 (ELP3), ZFP1 Zinc Finger Protein (ZFP1), Chymotrypsinogen B2 (CTRB2), Tektin 3 (TEKT3), CMT1A Duplicated Region Transcript 4 (CDRT4), SET Domain And Mariner Transposase Fusion Gene (SETMAR), TNF Superfamily Member 4 (TNFSF4), Ribosomal Protein S26 (RPS26), Erb-B2 Receptor Tyrosine Kinase 3 (ERBB3), Ryanodine Receptor 3 (RYR3), Solute Carrier Family 16 Member 10 (SLC16A10), Achaete-Scute Family BHLH Transcription Factor 2 (ASCL2), ATPase Phospholipid Transporting 8A1 (ATP8A1), Regulator Of G Protein Signaling 21 (RGS21), Regulator Of G Protein Signaling 1 (RGS1), Late Cornified Envelope 3E (LCE3E), Late Cornified Envelope 3D (LCE3D), Sulfite Oxidase (SUOX), IKAROS Family Zinc Finger 4 (IKZF4), Ribosomal Protein S26 (RPS26), Extended Synaptotagmin 1 (FAM62A), Myosin Light Chain 6B (MYL6B), SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin Subfamily C Member 2 (SMARCC2), UDP-GlcNAc:BetaGal Beta-1,3-N-Acetylglucosaminyltransferase Like 1 (B3GNTL1), Interleukin 22 Receptor Subunit Alpha 2 (IL22RA2), PR/SET Domain 16 (PRDM16), Cutaneous T Cell Lymphoma-Associated Antigen 1 (CTAGE1), RB Binding Protein 8, Endonuclease (RBBP8), EH Domain Containing 3 (EHD3), Xanthine Dehydrogenase (XDH), BARX Homeobox 2 (BARX2), Methylcrotonoyl-CoA Carboxylase 1 (MCCC1), Solute Carrier Family 38 Member 3 (SLC38A3), G Protein Subunit Alpha 12 (GNAI2), Syntrophin Gamma 1 (SNTG1), Human Immunodeficiency Virus Type I Enhancer Binding Protein 2 (HIVEP2), Androgen Induced 1 (AIG1), BTB Domain Containing 3 (BTBD3), Serine Palmitoyltransferase Long Chain Base Subunit 3 (SPTLC3), RAB3 GTPase Activating Protein Catalytic Subunit 1 (RAB3GAP1), Zinc Finger RANBP2-Type Containing 3 (ZRANB3), Mitogen-Activated Protein Kinase Kinase Kinase 19 (YSK4), RAB3 GTPase Activating Protein Catalytic Subunit 1 (RAB3GAP1), Discoidin Domain Receptor Tyrosine Kinase 2 (DDR2), Fibronectin Leucine Rich Transmembrane Protein 3 (FLRT3), MACRO Domain Containing 2 (MACROD2), Spen Family Transcriptional Repressor (SPEN), Pituitary Tumor-Transforming 1 (PTTG1), ATPase Phospholipid Transporting 10B (Putative) (ATP10B), Solute Carrier Family 6 Member 11 (SLC6A11), X—C Motif Chemokine Ligand 1 (XCL1), Dermatopontin (DPT), Dishevelled Associated Activator Of Morphogenesis 1 (DAAM1), Dimethylarginine Dimethylaminohydrolase 1 (DDAH1), FYVE, RhoGEF And PH Domain Containing 5 (FGD5), Cyclin Dependent Kinase 14 (PFTK1), Splicing Factor 3b Subunit 3 (SF3B3), Inositol 1,4,5-Trisphosphate Receptor Type 2 (ITPR2), Hedgehog Acyltransferase (HHAT), Solute Carrier Family 14 Member 2 (SLC14A2), C-Type Lectin Like 1 (CLECL1), CD69 Molecule (CD69), Mitotic Arrest Deficient 1 Like 1 (MAD1L1), SH3 Domain Containing 19 (SH3D19), BR Serine/Threonine Kinase 1 (BRSK1), R-Spondin 2 (RSPO2), Eukaryotic Translation Initiation Factor 3 Subunit E (EIF3E), Adrenoceptor Beta 2 (ADRB2), SH3 Domain And Tetratricopeptide Repeats 2 (SH3TC2), Heparan Sulfate 6-O-Sulfotransferase 1 (HS6ST1), DNA Methyltransferase 3 Alpha (DNMT3A), Neurotrophic Receptor Tyrosine Kinase 1 (NTRK1), Platelet Endothelial Aggregation Receptor 1 (PEAR1), TEK Receptor Tyrosine Kinase (TEK), Extended Synaptotagmin 1 (FAM62A), Myosin Light Chain 6B (MYL6B), Zinc Finger CCCH-Type Containing 10 (ZC3H10), Extended Synaptotagmin 1 (FAM62A), Nucleic Acid Binding Protein 2 (OBFC2B), Heparan Sulfate-Glucosamine 3-Sulfotransferase 3A1 (HS3ST3A1), CMT1A Duplicated Region Transcript 15 Pseudogene 1 (CDRT15P) Thyroid Stimulating Hormone Receptor (TSHR), General Transcription Factor IIA Subunit 1 (GTF2A1), Fms Related Tyrosine Kinase 1 (FLT1), Ring Finger Protein 5 Pseudogene 1 (RNF5P1), and Marker Of Proliferation Ki-67 (MKI67). The genotypes disclosed herein are, in some cases, a haplotype. In some instances, the genotype comprises a particular polymorphism, a polymorphism in linkage disequilibrium (LD) therewith, or a combination thereof. In some cases, LD is defined by an r²of at least or about 0.70, 0.75, 0.80, 0.85, 0.90, or 0.1. The genotypes disclosed herein can comprise at least or about 1, 2, 3, 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, or more polymorphisms.

The polymorphisms described herein can be a single nucleotide polymorphism, such as a single nucleotide polymorphism (SNP). In some instances, the polymorphism is an insertion or a deletion of at least one nucleobase (e.g., an indel). In some instances, the genotype may comprise a copy number variation (CNV), which is a variation in a number of a nucleic acid sequence between individuals in a given population. In some instances, the CNV comprises at least or about two, three, four, five, six, seven, eight, nine, ten, twenty, thirty, forty or fifty nucleic acid molecules. In some instances, the genotype is heterozygous. In some instances, the genotype is homozygous.

The genotypes presented herein, in some cases, are associated with a presence of a serological marker. A serological marker is a type of biomarker, such as an autoantigen, that represent a serological response to microbial antigens in the body of a subject. Non-limiting examples of serological markers include anti-neutrophil cytoplasmic antibody (ANCA), anti-Saccharomyces cerevisiae antibody (ASCA), anti-flagellin (CBir1) antibody, and E. coli outer membrane porin protein C (OmpC). The serological markers disclosed herein are useful for patient selection for treatment either alone, or in combination with the genotypes disclosed herein. The serological markers disclosed herein are also useful for the diagnosis, prognosis, prevention, treatment, and/or monitoring of the disease or conditions disclosed herein either alone, or in combination with the genotypes disclosed herein.

Genotype Embodiments

Disclosed herein, in some embodiments, are the following genotypes:

1. A genotype comprising at least one polymorphism at a gene or genetic locus.

2. The genotype of embodiment 1, wherein the gene or genetic locus is selected from the group consisting of MAPT, ANK3, C1QTNF6, SSTR3, NAT6, WBSCR16, LOC653375, STK33, IMP5, LOC728191, ODZ3, POLS, ITGA6, MLSTD2, LOC729147, PROK2, RYBP, C14orf145, TSHR, RASGRP3, PDHB, KCTD6, KCNQ1DN, CDKN1C, CSMD1, C5orf30, NUDT12, XKR6, LOC157740, SLC2A13, B4GALNT1, OS9, LOC100130776, CTDSP2, XRCC6BP1, NAALADL1, CDCA5, EGF, MSRA, LOC100132391, PRPSAP2, CYP2R1, CALCA, LOC100129427, DDC, LOC100129060, CACNA2D2, LOC100128485, FLJ40296, LOC100130336, LOC100131830, PVT1, LOC728724, ZNF184, LOC100131289, TNK1, MTX1, TNFAIP3, PERP, STAG3L4, AUTS2, PITPNB, RPL37, CARD6, TTC33. SPOCK3, ANXA10, APOB, LOC728640, BICC1, C6orf58, C6orf190, NCOA2, LOC100130862, PDCD11, C6orf199, FLJ42177, RTN4IP1, LOC64694, ELMO1, RBM6, XYLT1, LOC728222, NRP2, FLJ20309, MYEOV, CCND1, OR51G1, OR51A4, KCNH7, LOC259308, LOC100128556, CDON, RPUSD4, IFNE1, MTAP, ELP3, ZFP1, CTRB2, TEKT3, CDRT4, SETMAR, TNFSF4, LOC730070, RPS26, ERBB3, RYR3, SLC16A10, TH, ASCL2, ATP8A1, LOC389207, RGS21, RGS1, LCE3E, LCE3D, SUOX, IKZF4, FAM62A, MYL6B, SMARCC2, B3GNTL1, IL22RA2, PRDM16, CTAGE1, RBBP8, EHD3, XDH, BARX2, MCCC1, SLC38A3, GNAI2, SNTG1, HIVEP2, AIG1, BTBD3, SPTLC3, RAB3GAP1, ZRANB3, YSK4, DDR2, FLRT3, MACROD2, SPEN, PTTG1, ATP10B, SLC6A11, XCL1, DPT, LOC440181, DAAM1, DDAH1, FGD5, PFTK1, SF3B3, C16orf77, ITPR2, C12orf11, LOC100129235, HHAT, LOC100131669, SLC14A2, CLECL1, CD69, MAD1L1, LOC729979, LOC730018, SH3D19, BRSK1, RSPO2, EIF3E, ADRB2, SH3TC2, HS6ST1, LOC100130768, DNMT3A, NTRK1, PEAR1, TEK, FAM62A, ZC3H10, OBFC2B, LOC100129289, HS3ST3A1, CDRT15P, GTF2A1, FLT, LOC727894. LOC728544, FLJ43582, RNF5P1, MKI67, and LOC728327.

3. The genotype embodiments 1-2, wherein the polymorphism is selected from Table 1.

4. The genotype of embodiments 1-3, wherein the genotype comprises at least 2, 3, 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, or 30 polymorphisms selected from Table 1.

5. The genotype of embodiments 1-4, wherein the polymorphism is in linkage disequilibrium (LD) with a polymorphism in Table 1.

6. The genotype of embodiment 5, wherein LD is defined by (i) a D′ value of at least about 0.70, or (ii) a D′ value of 0 and an r²value of at least about 0.70.

7. The genotype of embodiment 5, wherein LD is defined by (i) a D′ value of at least about 0.80, or (ii) a D′ value of 0 and an r²value of at least about 0.80.

8. The genotype of embodiment 5, wherein LD is defined by (i) a D′ value of at least about 0.90, or (ii) a D′ value of 0 and an r²value of at least about 0.90.

9. The genotype of embodiment 5, wherein LD is defined by (i) a D′ value of at least about 0.95, or (ii) a D′ value of 0 and an r²value of at least about 0.95.

10. The genotype of embodiments 5-9, wherein the polymorphism is associated with Crohn's disease (CD) as indicated by a P value of at most 1.0×10⁻⁴.

11. The genotype of embodiment 10, wherein the polymorphism is associated with CD as indicated by a P value of at most 1.0×10⁻⁵.

12. The genotype of embodiments 10-11, wherein the polymorphism is associated with stricturing disease as indicated by a P value of at most 1.0×10⁻⁵.

13. The genotype of embodiments 10-12, wherein the polymorphism is associated with penetrating disease as indicated by a P value of at most 1.0×10⁻⁵.

14. The genotype of embodiments 1-13, wherein the genotype is heterozygous.

15. The genotype of embodiments, 1-13, wherein the genotype is homozygous.

16. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting of rs2726797, rs7108993, rs79665096, rs7604404, rs73085878, rs78727269, rs2736352, rs4924935, rs11227112, rs2285043, rs6989059, rs3807552, rs111455641, rs9480689, rs7416358, rs6879067, rs11128532, rs177665, rs11171747, rs10775375, rs6801634, rs1070444, rs116714418, rs6962616, rs7220814, rs4325270, rs768755, rs17758350, rs9480689, rs525850, rs4325270, rs11749180, rs6962616, rs116714418, rs10265554, rs634641, rs1493871, rs12669698, rs4332037, rs17697480, rs9480689, rs6074737, rs904910, rs12972487, rs445417, rs635624, rs7416358, 12-54819630-G-INSERTION, rs177665, rs1070444, rs10912583, rs12914919, rs2854725, rs948068, rs71472147, rs72939578, rs658795, rs17758350, rs144260901, rs10801129, rs1702870, rs10912583, rs2452822, rs7774349, rs4705272, rs117946479, rs936126, rs634641, rs2314737, rs3002685, rs634641, rs12496281, rs10134119, rs3808240, rs1890843, rs11829981, rs12496281, rs2383184, rs144260901, rs6801634, rs2383184, rs2954756, and a polymorphism in LD therewith.

17. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting of rs2726797, rs7108993, rs79665096, rs7604404, and any combination thereof.

18. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs73085878, rs78727269, rs2736352, rs4924935, rs11227112, rs2285043, rs6989059, rs3807552, and any combination thereof.

19. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs111455641, rs9480689, and any combination thereof.

20. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs7416358, rs6879067, rs11128532, and any combination thereof.

21. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs177665, rs11171747, and any combination thereof.

22. The genotype of the previous embodiments, wherein the polymorphism is rs10775375.

23. The genotype of the previous embodiments, wherein the polymorphism is rs6801634.

24. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs1070444, rs116714418, rs6962616, rs7220814, rs4325270, rs768755, and any combination thereof.

25. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs17758350, rs9480689, rs525850, rs4325270, and any combination thereof.

26. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs11749180, rs6962616, rs116714418, rs10265554, rs634641, rs1493871, rs12669698, and any combination thereof.

27. The genotype of the previous embodiments, wherein the polymorphism is rs4332037.

28. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs17697480, rs9480689, and any combination thereof.

29. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs6074737, rs904910, rs12972487, rs445417, and any combination thereof.

30. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs635624, rs7416358, and any combination thereof.

31. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting 12-54819630-G-INSERTION, rs177665, and any combination thereof.

32. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs1070444, rs10912583, rs12914919, rs2854725, and any combination thereof.

33. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs948068, rs71472147, rs72939578, rs658795, rs17758350, rs144260901, and any combination thereof.

34. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs10801129, rs1702870, rs10912583, rs2452822, rs7774349, and any combination thereof.

35. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs4705272, rs117946479, and any combination thereof.

36. The genotype of the previous embodiments, wherein the polymorphism is rs936126.

37. The genotype of the previous embodiments, wherein the polymorphism is rs634641.

38. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs2314737, rs3002685, rs634641, and any combination thereof.

39. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs12496281, rs10134119, rs3808240, and any combination thereof.

40. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs1890843, rs11829981, and any combination thereof.

41. The genotype of the previous embodiments, wherein the polymorphism is rs12496281.

42. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs2383184, rs144260901, and any combination thereof.

43. The genotype of the previous embodiments, wherein the polymorphism is selected from the group consisting rs6801634, rs2383184, rs2954756, and any combination thereof.

44. The genotype of embodiment 16-43, wherein the polymorphism at rs2726797 comprises a C allele at nucleoposition 26 within SEQ ID NO: 1.

45. The genotype of embodiment 16-43, wherein the polymorphism at rs7108993 comprises a C allele at nucleoposition 26 within SEQ ID NO: 2.

46. The genotype of embodiment 16-43, wherein the polymorphism at rs79665096 comprises an A allele at nucleoposition 26 within SEQ ID NO: 3.

47. The genotype of embodiment 16-43, wherein the polymorphism at rs7604404 comprises an A allele at nucleoposition 26 within SEQ ID NO: 4.

48. The genotype of embodiment 16-43, wherein the polymorphism at rs73085878 comprises an A allele at nucleoposition 26 within SEQ ID NO: 5.

49. The genotype of embodiment 16-43, wherein the polymorphism at rs78727269 comprises an A allele at nucleoposition 26 within SEQ ID NO: 6.

50. The genotype of embodiment 16-43, wherein the polymorphism at rs2736352 comprises an A allele at nucleoposition 26 within SEQ ID NO: 7.

51. The genotype of embodiment 16-43, wherein the polymorphism at rs4924935 comprises a G allele at nucleoposition 26 within SEQ ID NO: 8.

52. The genotype of embodiment 16-43, wherein the polymorphism at rs11227112 comprises a G allele at nucleoposition 26 within SEQ ID NO: 9.

53. The genotype of embodiment 16-43, wherein the polymorphism at rs2285043 comprises an A allele at nucleoposition 26 within SEQ ID NO: 10.

54. The genotype of embodiment 16-43, wherein the polymorphism at rs6989059 comprises an A allele at nucleoposition 26 within SEQ ID NO: 11.

55. The genotype of embodiment 16-43, wherein the polymorphism at rs3807552 comprises an A allele at nucleoposition 26 within SEQ ID NO: 12.

56. The genotype of embodiment 16-43, wherein the polymorphism at rs111455641 comprises a G allele at nucleoposition 26 within SEQ ID NO: 13.

57. The genotype of embodiment 16-43, wherein the polymorphism at rs9480689 comprises a G allele at nucleoposition 26 within SEQ ID NO: 14.

58. The genotype of embodiment 16-43, wherein the polymorphism at rs7416358 comprises a G allele at nucleoposition 26 within SEQ ID NO: 15.

59. The genotype of embodiment 16-43, wherein the polymorphism at rs6879067 comprises an A allele at nucleoposition 26 within SEQ ID NO: 16.

60. The genotype of embodiment 16-43, wherein the polymorphism at rs11128532 comprises an A allele at nucleoposition 26 within SEQ ID NO: 17.

61. The genotype of embodiment 16-43, wherein the polymorphism at rs177665 comprises a C allele at nucleoposition 26 within SEQ ID NO: 18.

62. The genotype of embodiment 16-43, wherein the polymorphism at rs11171747 comprises a C allele at nucleoposition 26 within SEQ ID NO: 19.

63. The genotype of embodiment 16-43, wherein the polymorphism at rs10775375 comprises an A allele at nucleoposition 26 within SEQ ID NO: 20.

64. The genotype of embodiment 16-43, wherein the polymorphism at rs6801634 comprises an A allele at nucleoposition 26 within SEQ ID NO: 21.

65. The genotype of embodiment 16-43, wherein the polymorphism at rs1070444 comprises an A allele at nucleoposition 26 within SEQ ID NO: 22.

66. The genotype of embodiment 16-43, wherein the polymorphism at rs116714418 comprises an A allele at nucleoposition 26 within SEQ ID NO: 23.

67. The genotype of embodiment 16-43, wherein the polymorphism at rs6962616 comprises an A allele at nucleoposition 26 within SEQ ID NO: 24.

68. The genotype of embodiment 16-43, wherein the polymorphism at rs7220814 comprises a G allele at nucleoposition 26 within SEQ ID NO: 25.

69. The genotype of embodiment 16-43, wherein the polymorphism at rs4325270 comprises a T allele at nucleoposition 26 within SEQ ID NO: 26.

70. The genotype of embodiment 16-43, wherein the polymorphism at rs768755 comprises a T allele at nucleoposition 26 within SEQ ID NO: 27.

71. The genotype of embodiment 16-43, wherein the polymorphism at rs17758350 comprises an A allele at nucleoposition 31 within SEQ ID NO: 28.

72. The genotype of embodiment 16-43, wherein the polymorphism at rs9480689 comprises a G allele at nucleoposition 26 within SEQ ID NO: 29.

73. The genotype of embodiment 16-43, wherein the polymorphism at rs525850 comprises an A allele at nucleoposition 26 within SEQ ID NO: 30.

74. The genotype of embodiment 3116-43, wherein the polymorphism at rs4325270 comprises a T allele at nucleoposition 26 within SEQ ID NO: 31.

75. The genotype of embodiment 16-43, wherein the polymorphism at rs11749180 comprises an A allele at nucleoposition 26 within SEQ ID NO: 32.

76. The genotype of embodiment 16-43, wherein the polymorphism at rs6962616 comprises an A allele at nucleoposition 26 within SEQ ID NO: 33.

77. The genotype of embodiment 16-43, wherein the polymorphism at rs116714418 comprises an A allele at nucleoposition 26 within SEQ ID NO: 34.

78. The genotype of embodiment 16-43, wherein the polymorphism at rs10265554 comprises a G allele at nucleoposition 26 within SEQ ID NO: 35.

79. The genotype of embodiment 16-43, wherein the polymorphism at rs634641 comprises a G allele at nucleoposition 26 within SEQ ID NO: 36.

80. The genotype of embodiment 16-43, wherein the polymorphism at rs1493871 comprises a G allele at nucleoposition 26 within SEQ ID NO: 37.

81. The genotype of embodiment 16-43 wherein the polymorphism at rs12669698 comprises a G allele at nucleoposition 26 within SEQ ID NO: 38.

82. The genotype of embodiment 16-43, wherein the polymorphism at rs4332037 comprises an A allele at nucleoposition 26 within SEQ ID NO: 39.

83. The genotype of embodiment 16-43, wherein the polymorphism at rs17697480 comprises a G allele at nucleoposition 26 within SEQ ID NO: 40.

84. The genotype of embodiment 16-43, wherein the polymorphism at rs9480689 comprises a G allele at nucleoposition 26 within SEQ ID NO: 41.

85. The genotype of embodiment 16-43, wherein the polymorphism at rs6074737 comprises an A allele at nucleoposition 26 within SEQ ID NO: 42.

86. The genotype of embodiment 16-43, wherein the polymorphism at rs904910 comprises a G allele at nucleoposition 26 within SEQ ID NO: 43.

87. The genotype of embodiment 16-43, wherein the polymorphism at rs12972487 comprises an A allele at nucleoposition 26 within SEQ ID NO: 44.

88. The genotype of embodiment 16-43, wherein the polymorphism at rs445417 comprises an A allele at nucleoposition 26 within SEQ ID NO: 45.

89. The genotype of embodiment 16-43, wherein the polymorphism at rs635624 comprises a C allele at nucleoposition 26 within SEQ ID NO: 46.

90. The genotype of embodiment 16-43, wherein the polymorphism at rs7416358 comprises a G allele at nucleoposition 26 within SEQ ID NO: 47.

91. The genotype of embodiment 16-43, wherein the polymorphism at 12-54819630-G-INSERTION comprises an insertion of a G at nucleoposition 26 within SEQ ID NO: 48.

92. The genotype of embodiment 16-43, wherein the polymorphism at rs177665 comprises a C allele at nucleoposition 26 within SEQ ID NO: 49.

93. The genotype of embodiment 16-43, wherein the polymorphism at rs1070444 comprises an A allele at nucleoposition 26 within SEQ ID NO: 50.

94. The genotype of embodiment 16-43, wherein the polymorphism at rs10912583 comprises an A allele at nucleoposition 26 within SEQ ID NO: 51.

95. The genotype of embodiment 3116-43, wherein the polymorphism at rs12914919 comprises a G allele at nucleoposition 26 within SEQ ID NO: 52.

96. The genotype of embodiment 16-43, wherein the polymorphism at rs2854725 comprises a C allele at nucleoposition 26 within SEQ ID NO: 53.

97. The genotype of embodiment 16-43, wherein the polymorphism at rs9480689 comprises a G allele at nucleoposition 26 within SEQ ID NO: 54.

98. The genotype of embodiment 16-43, wherein the polymorphism at rs71472147 comprises an A allele at nucleoposition 26 within SEQ ID NO: 55.

99. The genotype of embodiment 16-43, wherein the polymorphism at rs72939578 comprises an A allele at nucleoposition 31 within SEQ ID NO: 56.

100. The genotype of embodiment 16-43, wherein the polymorphism at rs658795 comprises an A allele at nucleoposition 26 within SEQ ID NO: 57.

101. The genotype of embodiment 16-43, wherein the polymorphism at rs17758350 comprises an A allele at nucleoposition 31 within SEQ ID NO: 58.

102. The genotype of embodiment 16-43, wherein the polymorphism at rs144260901 comprises an A allele at nucleoposition 31 within SEQ ID NO: 59.

103. The genotype of embodiment 16-43, wherein the polymorphism at rs10801129 comprises a C allele at nucleoposition 26 within SEQ ID NO: 60.

104. The genotype of embodiment 16-43, wherein the polymorphism at rs1702870 comprises an A allele at nucleoposition 26 within SEQ ID NO: 61.

105. The genotype of embodiment 16-43, wherein the polymorphism at rs10912583 comprises an A allele at nucleoposition 26 within SEQ ID NO: 62.

106. The genotype of embodiment 16-43, wherein the polymorphism at rs2452822 comprises a C allele at nucleoposition 31 within SEQ ID NO: 63.

107. The genotype of embodiment 16-43, wherein the polymorphism at rs7774349 comprises an A allele at nucleoposition 26 within SEQ ID NO: 64.

108. The genotype of embodiment 16-43, wherein the polymorphism at rs4705272 comprises a G allele at nucleoposition 26 within SEQ ID NO: 65.

109. The genotype of embodiment 16-43, wherein the polymorphism at rs117946479 comprises an A allele at nucleoposition 31 within SEQ ID NO: 66.

110. The genotype of embodiment 16-43, wherein the polymorphism at rs936126 comprises an A allele at nucleoposition 26 within SEQ ID NO: 67.

111. The genotype of embodiment 16-43, wherein the polymorphism at rs634641 comprises a G allele at nucleoposition 26 within SEQ ID NO: 68.

112. The genotype of embodiment 16-43, wherein the polymorphism at rs2314737 comprises a G allele at nucleoposition 26 within SEQ ID NO: 69.

113. The genotype of embodiment 16-43, wherein the polymorphism at rs3002685 comprises a G allele at nucleoposition 26 within SEQ ID NO: 70.

114. The genotype of embodiment 16-43, wherein the polymorphism at rs634641 comprises a G allele at nucleoposition 26 within SEQ ID NO: 71.

115. The genotype of embodiment 16-43, wherein the polymorphism at rs12496281 comprises a G allele at nucleoposition 26 within SEQ ID NO: 72.

116. The genotype of embodiment 16-43, wherein the polymorphism at rs10134119 comprises a T allele at nucleoposition 26 within SEQ ID NO: 73.

117. The genotype of embodiment 16-43, wherein the polymorphism at rs3808240 comprises a C allele at nucleoposition 26 within SEQ ID NO: 74.

118. The genotype of embodiment 16-43, wherein the polymorphism at rs1890843 comprises a G allele at nucleoposition 26 within SEQ ID NO: 75.

119. The genotype of embodiment 16-43, wherein the polymorphism at rs11829981 comprises an A allele at nucleoposition 26 within SEQ ID NO: 76.

120. The genotype of embodiment 16-43, wherein the polymorphism at rs12496281 comprises a G allele at nucleoposition 26 within SEQ ID NO: 77.

121. The genotype of embodiment 16-43, wherein the polymorphism at rs2383184 comprises a G allele at nucleoposition 26 within SEQ ID NO: 78.

122. The genotype of embodiment 16-43, wherein the polymorphism at rs144260901 comprises an A allele at nucleoposition 31 within SEQ ID NO: 79.

123. The genotype of embodiment 16-43, wherein the polymorphism at rs6801634 comprises an A allele at nucleoposition 26 within SEQ ID NO: 80.

124. The genotype of embodiment 16-43, wherein the polymorphism at rs2383184 comprises a G allele at nucleoposition 26 within SEQ ID NO: 81.

125. The genotype of embodiment 16-43, wherein the polymorphism at rs2954756 comprises a G allele at nucleoposition 26 within SEQ ID NO: 82.

Aspects disclosed herein provide genotypes that are associated with, and therefore, indicative of, a subject having or being susceptible (e.g., at risk of) to developing a particular disease or condition, or a subclinical phenotype thereof. Table 1 provides polymorphisms significantly associated with non-stricturing and non-penetrating diseases (B1), stricturing (B2a), stricturing and internal penetrating (B2b), and isolated internal penetrating (B3). In some cases, associations between the polymorphism and the disease location in the ileal region of the intestine (L1), colon (L2), and colonic region of the intestine are also provided in Table 1. “CH” as used herein refers to the human chromosome on which the polymorphism is located. “BP” as used herein refers to the base pair location of the polymorphism on the human chromosome provided. “A1” as used herein refers to the minor allele of the polymorphism. “OR” as used herein refers to the odds ratio. An odds ratio provides a quantification of a strength of an association between the polymorphism and the subclinical phenotype within the studied population using a logistic regression. If OR<1, the minor allele correlates to a reduced risk of a patient exhibiting the listed phenotype. If OR>1 the minor allele correlates to an increased risk of a patient exhibiting the listed phenotype. “MAF” as used herein refers to the minor allele frequency in the studied population.

TABLE 1

Polymorphisms Associated with Subclinical Phenotypes of Severe CD

ss to rs

Orien-
5′
3′

Loca-

Gene/
tation/
SEQ
SEQ

tion
rs_id
SNP
CHR
BP
A1
OR
P
MAF
Locus
Strand
ID NO
ID NO

B1 vs Ctrl

all
rs7108993
rs7108993
11
8447193
C
0.771
<1.0E−5
0.4187
STK33
fwd/T
400
633

all
rs7604404
rs7604404
2
173308318
A
1.407
<1.0E−5
0.1433
ITGA6
fwd/T
413
646

all
rs9880789
rs9880789
3
71987258
G
1.418
<1.0E−5
0.1027
PROK2 |
fwd/B
421
654

RYBP

all
rs2726797
rs2726797
4
183230887
C
0.7326
<1.0E−5
0.2522
LOC728191 |
rev/B
450
683

ODZ3

all
rs79665096
imm_10_61734528
10
62064522
A
0.2747
<1.0E−5
0.01858
ANK3
rev/
485
718

all
rs2675534
rs2675534
4
183239761
A
0.703
<1.0E−5
0.2059
LOC728191 |
rev/T
503
736

ODZ3

all
rs10769905
rs10769905
11
8441716
G
0.774
<1.0E−5
0.4172
STK33
fwd/B
504
737

all
rs2675537
rs2675537
4
183237891
C
0.7388
<1.0E−5
0.2091
LOC728191 |
rev/
505
738

ODZ3

all
rs7069191
imm_10_62066379
10
62396373
A
0.7453
<1.0E−5
0.204
LOC729184
fwd/B
506
739

all
rs17690703
rs17690703
17
43925297
A
0.7606
<1.0E−5
0.2497
IMP5 |
fwd/B
507
740

MAPT

all
rs64547
imm_22_35922450
22
37592504
A
1.255
<1.0E−5
0.4321
C1QTNF6 |
fwd/B
508
741

SSTR3

all
rs920644
imm_10_62111562
10
62441556
A
0.7555
<1.0E−5
0.2023
LOC729184
fwd/B
509
742

all
rs2285043
imm_3_50311059
3
50336055
A
6.318
<1.0E−5
0.04332
NAT6 |
fwd/B
510
743

all
rs7926320
rs7926320
11
13782568
A
1.253
<1.0E−5
0.4115
MLSTD2 |
fwd/T
511
744

LOC729147

all
rs274700
rs274700
5
6728995
G
0.6888
<1.0E−5
0.1335
POLS
rev/T
512
745

all
rs76090253
chr17: 41358797
17
44002969
C
0.7648
<1.0E−5
0.2176
LOC100130148 |
fwd/T
513
746

MAPT

all
rs4731019
imm_7_74118166
7
74480230
G
0.7964
<1.0E−5
0.4533
WBSCR16
rev/B
514
747

all
rs4731019
imm_7_74604123
7
74766187
G
0.7964
<1.0E−5
0.4533
LOC653375
rev/B
515
748

all
rs7596259
rs7596259
2
173305731
A
1.386
<1.0E−5
0.1423
ITGA6
fwd/B
516
749

B1 vs Ctrl L1

L1
rs78727269
imm_2_33520650
2
33667146
A
2.62
<1.0E−5
0.05436
RASGRP3
fwd/B
401
634

L1
rs73085878
imm_3_58418103
3
58443063
A
3.751
<1.0E−5
0.02285
PDHB |
fwd/T
451
684

KCTD6

L1
rs13439849
rs13439849
8
4049489
C
2.155
<1.0E−5
0.08199
CSMD1
fwd/
517
750

L1
rs76339876
1kg_14_80498007
14
81428254
C
2.399
<1.0E−5
0.0556
TSHR
fwd/
518
751

L1
rs12786533
rs12786533
11
2896313
A
2.449
<1.0E−5
0.0874
KCNQ1DN |
fwd/T
519
752

CDKN1C

L1
rs45535733
1kg_14_80329007
14
81259254
T
2.334
<1.0E−5
0.05809
C14orf145
fwd/
520
753

L2
rs77065481
imm_12_56403034
12
58116767
G
3.093
<1.0E−5
0.0206
OS9 |
fwd/B
422
655

LOC100130776

L2
rs12507356
rs12507356
4
110923328
A
4.702
<1.0E−5
0.03315
EGF
fwd/T
423
656

L2
rs2736352
1kg_8_11133963
8
11096553
A
0.6064
<1.0E−5
0.3746
XKR6 |
fwd/T
452
685

LOC157740

L2
rs4924935
rs4924935
17
18753870
G
1.536
<1.0E−5
0.2966
LOC100132391 |
fwd/B
472
705

PRPSAP2

L2
rs11227112
rs11227112
11
64836816
G
2.354
<1.0E−5
0.03531
NAALADL1 |
fwd/B
486
719

CDCA5

L2
rs11564222
imm_12_38645596
12
40359329
G
11.59
<1.0E−5
0.01296
SLC2A13
fwd/T
521
754

L2
rs77505508
imm_12_56356895
12
58070628
A
3.073
<1.0E−5
0.02087
B4GALNT1 |
fwd/
522
755

OS9

L2
rs11774569
1kg_8_11133464
8
11096054
G
0.6078
<1.0E−5
0.3452
XKR6 |
fwd/B
523
756

LOC157740

L2
rs117135945
imm_12_56544697
12
58258430
G
2.594
<1.0E−5
0.02797
CTDSP2 |
fwd/
524
757

XRCC6BP1

L2
rs116402229
1kg_5_102724875
5
102696976
A
3.644
<1.0E−5
0.0102
C5orf30 |
fwd/T
525
758

NUDT12

L2
rs13273009
rs13273009
8
10234303
G
1.585
<1.0E−5
0.2457
MSRA
fwd/B
526
759

L2
rs59536295
seq-rs59536295
11
14956391
A
2.953
<1.0E−5
0.0451
CYP2R1 |
fwd/B
527
760

CALCA

B1 vs Ctrl L3

L3
rs6989059
rs6989059
8
130118208
A
1.494
<1.0E−5
0.1314
PVT1 |
fwd/T
402
635

LOC728724

L3
rs2285043
imm_3_50311059
3
50336055
A
9.215
<1.0E−5
0.04332
NAT6 |
fwd/B
453
686

L3
rs3807552
1kg_7_50578236
7
50610742
A
1.437
<1.0E−5
0.2188
LOC100129427 |
rev/T
487
720

DDC

L3
rs12490809
imm_3_50389408
3
50414404
A
6.634
<1.0E−5
0.0385
CACNA2D2
fwd/B
528
761

L3
rs4731019
imm_7_74118166
7
74480230
G
0.7499
<1.0E−5
0.4533
WBSCR16
rev/B
529
762

L3
rs4731019
imm_7_74604123
7
74766187
G
0.7499
<1.0E−5
0.4533
LOC653375
rev/B
530
763

L3
rs3774736
imm_3_50165114
3
50190110
A
5.041
<1.0E−5
0.04005
LOC100129060
fwd/T
531
764

L3
rs4831929
rs4831929
12
76340526
A
1.381
<1.0E−5
0.229
LOC100130336 |
rev/B
532
765

LOC100131830

L3
NA
rs2262121
9
78909677
C
0.1058
<1.0E−5
0.4478
NA
rev/B
533
766

L3
rs1832696
rs1832696
13
55107650
G
1.31
<1.0E−5
0.4574
LOC100128485 |
fwd/B
534
767

FLJ40296

L3
rs7926320
rs7926320
11
13782568
A
1.317
<1.0E−5
0.4115
MLSTD2 |
fwd/T
535
768

LOC729147

L3
rs9468159
rs9468159
6
27522374
A
1.565
<1.0E−5
0.08056
ZNF184 |
fwd/T
536
769

LOC100131289

B2a + B2b vs B1

all
rs111455641
rs6741481
2
135874622
G
0.6735
<1.0E−5
0.1756
RAB3GAP1
fwd/
454
687

all
rs4954221
rs4954221
2
135909462
A
0.6756
<1.0E−5
0.1746
RAB3GAP1
fwd/T
537
770

all
rs57829242
chr2: 135700642
2
135984172
G
0.6758
<1.0E−5
0.202
ZRANB3
fwd/T
538
771

all
rs17293519
rs17293519
2
135803766
G
0.6825
<1.0E−5
0.1763
YSK4 |
fwd/T
539
772

RAB3GAP1

all
NA
rs6999925
8
80786648
A
6.283
<1.0E−5
0.3797
NA
fwd/T
540
773

all
NA
rs17456596
8
80783998
G
7.926
<1.0E−5
0.4425
NA
fwd/T
541
774

all
rs7568525
rs7568525
2
135849613
A
0.6459
<1.0E−5
0.1554
RAB3GAP1
fwd/T
542
775

all
rs61087958
chr2: 135590508
2
135874038
A
0.6815
<1.0E−5
0.1743
RAB3GAP1
fwd/B
543
776

B2a + B2b vs B1 L1

L1
rs9480689
rs9480689
6
107024432
G
2.915
<1.0E−5
0.1226
RTN4IP1
fwd/T
455
688

B2a + B2b vs B1 L2

L2
rs2684866
rs2684866
1
162726281
A
3.44
<1.0E−5
0.2454
DDR2
fwd/T
544
777

L2
rs6074737
rs6074737
20
14420556
A
2.893
<1.0E−5
0.4654
FLRT3 |
fwd/T
545
778

MACROD2

L2
rs904910
rs904910
1
16200163
G
2.925
<1.0E−5
0.3161
SPEN
fwd/T
546
779

L3
rs7416358
rs7416358
1
168653857
G
0.6526
<1.0E−5
0.328
XCL1 |
fwd/B
392
625

DPT

L3
rs6879067
1kg_5_159872373
5
159939795
A
1.725
<1.0E−5
0.1964
PTTG1 |
fwd/
473
706

ATP 10B

L3
rs11128532
rs11128532
3
10977277
A
1.487
<1.0E−5
0.3482
SLC6A11
fwd/B
488
721

B2a + B2b vs B3

all
rs11171747
imm_12_54804675
12
56518408
C
0.5949
<1.0E−5
0.3825
ZC3H10 |
fwd/B
403
636

FAM62A

all
rs177665
rs177665
7
90102196
C
0.5855
<1.0E−5
0.4917
LOC100129289
rev/
456
689

all
12-54819630-
12-54819630-
12
56533363
I
0.5963
<1.0E−5
0.3705
FAM62A
fwd/
547
780

G-INSERTION
G-INSERTION

all
rs112668709
imm_12_54907064
12
56620797
A
0.5735
<1.0E−5
0.4204
OBFC2B
fwd/B
548
781

B2a + B2b vs B3 L1

L1
rs10775375
rs10775375
17
13544722
A
0.2593
<1.0E−5
0.2867
HS3ST3A1 |
fwd/T
457
690

CDRT15P

B2a + B2b vs B3 L3

L3
rs6801634
rs6801634
3
4354697
A
0.4949
<1.0E−5
0.141
SETMAR
fwd/T
458
691

L3
rs7143837
rs7143837
14
81640722
T
0.4588
<1.0E−5
0.1032
TSHR |
fwd/
549
782

GTF2A1

B2a + B2b vs Ctrl

all
rs1070444
rs1070444
5
40839644
A
1.502
<1.0E−5
0.1343
RPL37 |
rev/B
393
626

CARD6

all
rs116714418
rs1062731
22
28248840
A
0.707
<1.0E−5
0.223
PITPNB
fwd/B
404
637

all
rs4325270
rs4325270
10
60515468
T
0.7802
<1.0E−5
0.4591
LOC728640 |
fwd/
416
649

BICC1

all
rs768755
imm_6_138303642
6
138261949
T
0.7769
<1.0E−5
0.4307
TNFAIP3 |
fwd/
419
652

PERP

all
rs11749180
rs11749180
5
40745746
A
1.458
<1.0E−5
0.14
TTC33
fwd/T
424
657

all
rs6962616
rs6962616
7
68060815
A
0.5406
<1.0E−5
0.08535
STAG3L4 |
fwd/B
489
722

AUTS2

all
rs7220814
17_7231419
17
7290695
G
1.556
<1.0E−5
0.06822
TNK1
fwd/T
495
728

all
rs10265554
rs10265554
7
68051712
G
0.6152
<1.0E−5
0.09114
STAG3L4 |
fwd/T
550
783

AUTS2

all
rs199862238
imm_1_153447856
1
155181232
A
2.516
<1.0E−5
0.01493
MTX1
fwd/
551
784

all
rs1579609
imm_6_138299141
6
138257448
G
0.7814
<1.0E−5
0.4073
TNFAIP3 |
fwd/B
552
785

PERP

all
rs9402929
imm_6_138302337
6
138260644
G
0.7827
<1.0E−5
0.4074
TNFAIP3 |
fwd/B
553
786

PERP

all
rs2854725
rs2854725
2
21237786
C
1.385
<1.0E−5
0.1089
APOB
rev/B
554
787

all
rs1579610
imm_6_138299199
6
138257506
C
0.7846
<1.0E−5
0.4077
TNFAIP3 |
fwd/T
555
788

PERP

all
rs12645719
rs126457
4
168576098
A
1.265
<1.0E−5
0.3568
SPOCK3 |
fwd/B
556
789

ANXA10

B2a + B2b vs Ctrl L1

L1
rs525850
imm_61_28020485
6
127978792
A
1.639
<1.0E−5
0.4759
C6orf58 |
fwd/B
409
642

C6orf190

L1
rs4325270
rs4325270
10
60515468
T
0.6173
<1.0E−5
0.4591
LOC728640 |
fwd/
414
647

BICC1

L1
rs658795
imm_6_128029073
6
127987380
A
1.631
<1.0E−5
0.4631
C6orf58 |
rev/B
425
658

C6orf190

L1
rs476148
imm_6_128029246
6
127987553
A
1.607
<1.0E−5
0.487
C6orf58 |
rev/B
426
659

C6orf190

L1
rs570462
imm_6_128027316
6
127985623
G
1.607
<1.0E−5
0.4871
C6orf58 |
rev/T
427
660

C6orf190

L1
rs568675
imm_6_128027478
6
127985785
G
1.607
<1.0E−5
0.4871
C6orf58 |
rev/B
428
661

C6orf190

L1
rs474188
imm_6_128029476
6
127987783
C
1.607
<1.0E−5
0.487
C6orf58 |
rev/
429
662

C6orf190

L1
rs17758350
rs17758350
8
71411688
A
1.976
<1.0E−5
0.09848
NCOA2 |
fwd/
459
692

LOC100130862

L1
rs9480689
rs9480689
6
107024432
G
1.941
<1.0E−5
0.1226
RTN4IP1
fwd/T
474
707

L1
rs4917389
rs4917389
10
105194476
A
0.4625
<1.0E−5
0.1473
PDCD11
fwd/B
557
790

L1
rs6568591
rs6568591
6
109992884
G
1.574
<1.0E−5
0.2874
C6orf199
fwd/B
558
791

L1
rs6925886
rs6925886
6
109878515
A
1.572
<1.0E−5
0.2877
FLJ42177 |
fwd/T
559
792

C6orf199

B2a + B2b vs Ctrl L3

L3
rs11749180
rs11749180
5
40745746
A
1.563
<1.0E−5
0.14
TTC33
fwd/T
394
627

L3
rs116714418
rs1062731
22
28248840
A
0.6567
<1.0E−5
0.223
PITPNB
fwd/B
410
643

L3
rs634641
rs634641
11
69386588
G
3.284
<1.0E−5
0.0385
MYEOV |
fwd/
417
650

CCND1

L3
rs12669698
1kg_7_37404494
7
37437969
G
1.495
<1.0E−5
0.1407
LOC646942 |
fwd/B
420
653

ELMO1

L3
rs1070444
rs1070444
5
40839644
A
1.556
<1.0E−5
0.1343
RPL37 |
rev/B
430
663

CARD6

L3
rs66863235
imm_3_49968323
3
49993319
G
0.7162
<1.0E−5
0.4611
RBM6
fwd/
431
664

L3
rs2080566
rs2080566
2
206806379
A
1.32
<1.0E−5
0.332
NRP2 |
fwd/B
432
665

FLJ20309

L3
rs768755
imm_6_138303642
6
13826149
T
0.7561
<1.0E−5
0.4307
TNFAIP3 |
fwd/
433
666

PERP

L3
rs6962616
rs6962616
7
68060815
A
0.4465
<1.0E−5
0.08535
STAG3L4 |
fwd/B
475
708

AUTS2

L3
rs10265554
rs10265554
7
68051712
G
0.5317
<1.0E−5
0.09114
STAG3L4 |
fwd/T
496
729

AUTS2

L3
rs1493871
rs1493871
16
17882019
G
1.521
<1.0E−5
0.1169
XYLT1 |
rev/T
501
734

LOC728222

L3
rs840709
rs840709
11
4951958
G
1.36
<1.0E−5
0.2803
OR51G1 |
fwd/B
560
793

OR51A4

B2a vs B1

all
rs11052804
imm_12_9786609
12
9895342
A
1.951
<1.0E−5
0.04818
CLECL1 |
fwd/B
434
667

CD69

all
rs4332037
rs4332037
7
1950809
A
0.6438
<1.0E−5
0.1849
MAD1L1
fwd/B
460
693

all
rs79665096
imm_10_61734528
10
62064522
A
3.977
<1.0E−5
0.01858
ANK3
rev/
561
794

B2a vs B1 L1

L1
rs17697480
rs17697480
16
87101424
G
3.563
<1.0E−5
0.1392
LOC729979 |
fwd/
461
694

LOC730018

L1
rs9480689
rs9480689
6
107024432
G
3.295
<1.0E−5
0.1226
RTN4IP1
fwd/T
476
709

B2a vs B1 L2

L2
rs3736502
imm_4_152284647
4
152065197
A
10.59
<1.0E−5
0.03985
SH3D19
fwd/B
435
668

L2
rs6074737
rs6074737
20
14420556
A
3.745
<1.0E−5
0.4654
FLRT3 |
fwd/T
462
695

MACROD2

L2
rs904910
rs904910
1
16200163
G
3.6
<1.0E−5
0.3161
SPEN
fwd/T
477
710

L2
rs12972487
seq-rs12972487
19
55817537
A
4.896
<1.0E−5
0.0998
BRSK1
fwd/B
490
723

L2
rs445417
rs445417
20
14433643
A
3.556
<1.0E−5
0.4828
FLRT3 |
fwd/T
497
730

MACROD2

L2
rs12973169
seq-rs12973169
19
55817676
A
4.186
<1.0E−5
0.1002
BRSK1
fwd/T
562
795

B2a vs B1 L3

L3
rs7416358
rs7416358
1
168653857
G
0.6406
<1.0E−5
0.328
XCL1 |
fwd/B
405
638

DPT

L3
rs635624
rs635624
8
109197799
C
1.525
<1.0E−5
0.4876
RSPO2 |
rev/
463
696

EIF3E

L3
rs684093
rs684093
8
109199355
G
1.556
<1.0E−5
0.4779
RSPO2 |
rev/
563
796

EIF3E

L3
rs6879067
1kg_5_159872373
5
159939795
A
1.743
<1.0E−5
0.1964
PTTG1 |
fwd/
564
797

ATP10B

B2a vs B3

all
12-54819630-
12-54819630-
12
56533363
I
0.5306
<1.0E−5
0.3705
FAM62A
fwd/
395
628

G-INSERTION
G-INSERTION

all
rs7987649
rs7987649
13
28894415
G
1.754
<1.0E−5
0.3199
FLT1
fwd/T
436
669

all
rs177665
rs177665
7
90102196
C
0.5591
<1.0E−5
0.4917
LOC100129289
rev/
478
711

all
rs11171747
imm_12_54804675
12
56518408
C
0.5458
<1.0E−5
0.3825
ZC3H10 |
fwd/B
565
798

FAM62A

all
rs112668709
imm_12_54907064
12
56620797
A
0.5224
<1.0E−5
0.4204
OBFC2B
fwd/B
566
799

all
rs7960225
imm_12_54851078
12
56564811
A
0.5863
<1.0E−5
0.3565
SMARCC2
fwd/T
567
800

B2a vs B3 L1

L1
rs10775375
rs10775375
17
13544722
A
0.2558
<1.0E−5
0.2867
HS3ST3A1 |
fwd/T
568
801

CDRT15P

B2a vs B3 L3

L3
rs7096293
rs7096293
10
4241547
C
0.5439
<1.0E−5
0.3764
LOC727894 |
fwd/T
569
802

LOC728544

B2a vs Ctrl

all
rs1070444
rs1070444
5
40839644
A
1.536
<1.0E−5
0.1343
RPL37 |
rev/B
396
629

CARD6

all
rs10912583
imm_1_171547622
1
173280999
A
0.7262
<1.0E−5
0.3939
TNFSF4 |
fwd/B
406
639

LOC730070

all
rs1179180
rs11749180
5
40745746
A
1.488
<1.0E−5
0.14
TTC33
fwd/T
437
670

all
rs12914919
rs12914919
15
33693686
G
1.852
<1.0E−5
0.0649
RYR3
fwd/B
491
724

all
rs2854725
rs2854725
2
21237786
C
1.478
<1.0E−5
0.1089
APOB
rev/B
498
731

all
rs772926
imm_12_54726515
12
56440248
A
4.071
<1.0E−5
0.01006
RPS26 |
fwd/B
570
803

ERBB3

B2a vs Ctrl L1

L1
rs658795
imm_6_128029073
6
127987380
A
1.746
<1.0E−5
0.4631
C6orf58 |
rev/B
415
648

C6orf190

L1
rs9480689
rs9480689
6
107024432
G
2.228
<1.0E−5
0.1226
RTN4IP1
fwd/T
464
697

L1
rs71472147
imm_11_2175557
11
2218981
A
2.046
<1.0E−5
0.1223
TH |
fwd/
479
712

ASCL2

L1
rs72939578
1kg_6_111633302
6
111526609
A
4.254
<1.0E−5
0.01356
SLC16A10
fwd/B
492
725

L1
rs17758350
rs17758350
8
71411688
A
2.016
<1.0E−5
0.09848
NCOA2 |
fwd/
500
733

LOC100130862

L1
rs144260901
imm_9_34751635
9
34761635
A
5.049
<1.0E−5
0.01902
LOC259308 |
fwd/
502
735

LOC100128556

L1
rs525850
imm_6_128020485
6
127978792
A
1.75
<1.0E−5
0.4759
C6orf58 |
fwd/B
571
804

C6orf190

L1
rs4945759
rs4945759
6
107043751
A
1.896
<1.0E−5
0.1432
RTN4IP1
fwd/T
572
805

L1
rs476148
imm_6_128029246
6
127987553
A
1.735
<1.0E−5
0.487
C6orf58 |
rev/B
573
806

C6orf190

L1
rs570462
imm_6_128027316
6
127985623
G
1.735
<1.0E−5
0.4871
C6orf58 |
rev/T
574
807

C6orf190

L1
rs568675
imm_6_128027478
6
127985785
G
1.735
<1.0E−5
0.4871
C6orf58 |
rev/B
575
808

C6orf190

L1
rs474188
imm_6_128029476
6
127987783
C
1.734
<1.0E−5
0.487
C6orf58 |
rev/
576
809

C6orf190

L1
rs7112535
imm_11_2175558
11
2218982
A
1.974
<1.0E−5
0.1198
TH |
fwd/T
577
810

ASCL2

L1
rs17594783
rs17594783
4
42845691
G
2.306
<1.0E−5
0.04582
ATP8A1 |
fwd/T
578
811

LOC389207

B2a vs Ctrl L2

L2
rs10801129
imm_1_190788214
1
192521591
C
3.292
<1.0E−5
0.2577
RGS21 |
fwd/B
465
698

RGS1

L2
rs6684404
imm_1_190797238
1
192530615
G
3.769
<1.0E−5
0.2728
RGS21 |
fwd/T
579
812

RGS1

L3
rs10912583
imm_1_171547622
1
173280999
A
0.6823
<1.0E−5
0.3939
TNFSF4 |
fwd/B
411
644

LOC730070

B2a vs Ctrl L3

L3
rs7774349
rs7774349
6
137475858
A
0.6782
<1.0E−5
0.4594
IL22RA2
fwd/B
418
651

L3
rs1702870
imm_12_54743443
12
56457176
A
4.873
<1.0E−5
0.0101
RPS26 |
rev/T
480
713

ERBB3

L3
rs2452822
imm_12_54714611
12
56428344
C
5.317
<1.0E−5
0.01389
IKZF4
fwd/
499
732

L3
rs772926
imm_12_54726515
12
56440248
A
4.833
<1.0E−5
0.01006
RPS26 |
fwd/B
580
813

ERBB3

L3
rs1581007
imm_12_54747402
12
56461135
C
5.317
<1.0E−5
0.01324
RPS26 |
rev/
581
814

ERBB3

L3
rs12126248
imm_1_171549389
1
17328276
G
0.6628
<1.0E−5
0.2734
TNFSF4 |
fwd/B
582
815

LOC730070

L3
rs7224733
rs7224733
17
81004770
G
0.632
<1.0E−5
0.2238
B3GNTL1
fwd/T
583
816

L3
rs202138565
12-54741792-
12
56455525
I
5.801
<1.0E−5
0.01346
RPS26 |
fwd/
584
817

CTC-DELETION

ERBB3

L3
rs808896
imm_12_54691421
12
56405154
G
4.849
<1.0E−5
0.01387
SUOX |
fwd/B
585
818

IKZF4

L3
rs1689516
imm_12_54695787
12
56409520
G
4.849
<1.0E−5
0.01373
SUOX |
fwd/T
586
819

IKZF4

L3
rs1619653
imm_12_54712844
12
56426577
A
4.849
<1.0E−5
0.0135
IKZF4
rev/T
587
820

L3
rs705706
imm_12_54722739
12
56436472
A
4.849
<1.0E−5
0.0135
RPS26
fwd/B
588
821

L3
rs772925
imm_12_54726336
12
56440069
A
4.849
<1.0E−5
0.01359
RPS26 |
fwd/B
589
822

ERBB3

L3
rs1689507
imm_12_54726968
12
56440701
G
4.849
<1.0E−5
0.01345
RPS26 |
rev/T
590
823

ERBB3

L3
rs1702875
imm_12_54752220
12
56465953
C
4.849
<1.0E−5
0.01359
RPS26 |
rev/B
591
824

ERBB3

L3
rs7301099
imm_12_54829965
12
56543698
C
4.825
<1.0E−5
0.01251
FAM62A |
fwd/B
592
825

MYL6B

L3
rs773647
imm_12_54855905
12
56569638
G
4.825
<1.0E−5
0.01246
SMARCC2
fwd/
593
826

L3
rs72700983
imm_1_150808526
1
152541902
G
0.6875
<1.0E−5
0.3449
LCE3E |
fwd/T
594
827

LCE3D

B2b vs B1

all
rs17946479
1kg_7_37389853
7
37423328
A
4.244
<1.0E−5
0.01427
LOC646942 |
fwd/
407
640

ELMO1

all
rs4705272
rs4705272
5
148237855
G
0.5885
<1.0E−5
0.2281
ADRB2 |
fwd/
466
69

SH3TC2

9

B2b vs B1 L1

L1
rs936126
rs936126
2
129124335
A
2.636
<1.0E−5
0.4916
HS6ST1 |
fwd/T
467
700

LOC100130768

B2b vs B1 L3

L3
rs6722613
1kg_2_25392861
2
25539357
G
1.603
<1.0E−5
0.4271
DNMT3A
fwd/T
438
671

L3
rs2644621
rs2644621
1
156861243
A
5.772
<1.0E−5
0.1243
NTRK1 |
fwd/T
439
672

PEAR1

L3
rs666478
rs666478
9
27173180
G
1.579
<1.0E−5
0.461
TEK
rev/B
440
673

B2b vs B3

all
rs4733883
rs4733883
8
38437040
A
0.5541
<1.0E−5
0.3315
FLJ43582 |
fwd/T
595
828

RNF5P1

B2b vs B3 L3

L3
rs7143837
rs7143837
14
81640722
T
0.3454
<1.0E−5
0.1032
TSHR |
fwd/
596
829

GTF2A1

L3
rs12249558
rs12249558
10
130446595
G
3.297
<1.0E−5
0.1248
MKI67 |
fwd/T
597
830

LOC728327

B2b vs Ctrl

all
rs634641
rs634641
11
69386588
G
4.081
<1.0E−5
0.0385
MYEOV |
fwd/
397
630

CCND1

all
rs12669698
1kg_7_37404494
7
37437969
G
1.633
<1.0E−5
0.1407
LOC646942 |
fwd/B
441
674

ELMO1

all
rs8097844
rs8097844
18
20186986
G
1.44
<1.0E−5
0.3225
CTAGE1 |
fwd/B
442
675

RBBP8

all
rs8085592
rs8085592
18
20187420
A
1.439
<1.0E−5
0.3227
CTAGE1 |
fwd/B
443
676

RBBP8

all
rs4309500
rs4309500
18
20171748
A
1.437
<1.0E−5
0.3156
CTAGE1 |
fwd/
444
677

RBBP8

all
rs3002685
rs3002685
1
3177480
G
1.523
<1.0E−5
0.2097
PRDM16
fwd/T
598
831

all
rs6962616
rs6962616
7
68060815
A
0.3783
<1.0E−5
0.08535
STAG3L4 |
fwd/B
599
832

AUTS2

all
rs7130717
rs7130717
11
129313340
G
1.563
<1.0E−5
0.4695
BARX2
fwd/
600
833

all
rs646103
rs646103
2
31496984
A
0.6071
<1.0E−5
0.1908
EHD3 |
rev/T
601
834

XDH

B2b vs Ctrl L1

L1
rs2314737
rs2314737
3
182783344
G
2.475
<1.0E−5
0.3036
MCCC1
rev/B
493
726

B2b vs Ctrl L3

L3
rs634641
rs634641
11
69386588
G
4.862
<1.0E−5
0.0385
MYEOV |
fwd/
408
641

CCND1

L3
rs116714418
rs1062731
22
28248840
A
0.5511
<1.0E−5
0.223
PITPNB
fwd/B
445
678

L3
rs3002685
rs3002685
1
3177480
G
1.718
<1.0E−5
0.2097
PRDM16
fwd/T
468
701

L3
rs2455099
rs2455099
1
3181415
A
1.733
<1.0E−5
0.1794
PRDM16
rev/T
602
835

L3
rs8097844
rs8097844
18
20186986
G
1.546
<1.0E−5
0.3225
CTAGE1 |
fwd/B
603
836

RBBP8

L3
rs8085592
rs8085592
18
20187420
A
1.545
<1.0E−5
0.3227
CTAGE1 |
fwd/B
604
837

RBBP8

L3
rs200145
rs200145
6
143343770
G
0.5111
<1.0E−5
0.1847
HIVEP2 |
fwd/B
605
838

AIG1

L3
rs16915033
rs16915033
8
51462627
G
1.823
<1.0E−5
0.1003
SNTG1
fwd/T
606
839

L3
rs41305602
imm_3_50239710
3
50264706
T
3.453
<1.0E−5
0.01202
SLC38A3 |
fwd/
607
840

GNAI2

L3
rs4309500
rs4309500
18
20171748
A
1.525
<1.0E−5
0.3156
CTAGE1 |
fwd/
608
841

RBBP8

L3
rs7233496
rs7233496
18
20185643
A
1.517
<1.0E−5
0.3197
CTAGE1 |
fwd/B
609
842

RBBP8

L3
rs35929393
1kg_6_111635077
6
111528384
A
2.69
<1.0E−5
0.02056
SLC16A10
fwd/
610
843

L3
rs398869
rs398869
20
12893710
G
1.928
<1.0E−5
0.06728
BTBD3 |
rev/T
611
844

SPTLC3

B3 vs B1

all
rs12496281
rs12496281
3
14973320
G
2.544
<1.0E−5
0.07225
FGD5
fwd/T
398
631

all
rs3808240
rs3808240
7
90468989
C
2.283
<1.0E−5
0.08872
PFTK1
fwd/T
412
645

all
rs1352071
imm_2_163065624
2
163357378
G
1.988
<1.0E−5
0.1247
KCNH
rev/B
446
679

7

all
rs10134119
rs10134119
14
59460239
T
1.66
<1.0E−5
0.3622
LOC440181 |
fwd/
481
714

DAAM1

all
rs6499323
rs6499323
16
70624483
G
1.65
<1.0E−5
0.262
SF3B3 |
fwd/T
612
845

C16orf77

all
rs11161618
rs11161618
1
85915402
A
0.5485
<1.0E−5
0.4417
DDAH1
fwd/B
613
846

B3 v B1 L2

L2
rs1890843
rs1890843
1
210836847
G
7.977
<1.0E−5
0.07966
LOC100129235 |
fwd/B
469
702

HHAT

L2
rs11829981
rs11829981
12
27032213
A
16.23
<1.0E−5
0.03272
ITPR2 |
fwd/T
482
715

C12orf11

L2
rs7312159
rs7312159
12
27027742
A
16.23
<1.0E−5
0.03271
ITPR2 |
fwd/B
614
847

C12orf11

B3 vs B1 L3

L3
rs12496281
rs12496281
3
14973320
G
3.021
<1.0E−5
0.07225
FGD5
fwd/T
399
632

L3
rs3808240
rs3808240
7
90468989
C
2.67
<1.0E−5
0.08872
PFTK1
fwd/T
447
680

L3
rs11161618
rs11161618
1
85915402
A
0.4755
<1.0E−5
0.4417
DDAH1
fwd/B
615
848

L3
rs28408641
1kg_18_41136921
18
42882923
A
0.4042
<1.0E−5
0.1641
LOC100131669 |
fwd/T
616
849

SLC14A2

L3
rs12455102
1kg_18_41137957
18
42883959
C
0.4042
<1.0E−5
0.1644
LOC100131669 |
fwd/T
617
850

SLC14A2

L3
rs6801634
rs6801634
3
4354697
A
1.96
<1.0E−5
0.141
SETMAR
fwd/T
618
851

B3 vs Ctrl

all
rs1352071
imm_2_163065624
2
163357378
G
1.832
<1.0E−5
0.1247
KCNH7
rev/B
448
681

all
rs2383184
rs2383184
9
21763566
G
2.397
<1.0E−5
0.06435
IFNE1 |
rev/B
470
703

MTAP

all
rs144260901
imm_9_34751635
9
34761635
A
4.215
<1.0E−5
0.01902
LOC259308 |
fwd/
483
716

LOC100128556

all
rs7037277
rs7037277
9
21772064
G
2.229
<1.0E−5
0.06627
IFNE1 |
fwd/T
619
852

MTAP

all
rs12419184
rs12419184
11
126056308
A
1.803
<1.0E−5
0.1124
CDON |
fwd/B
620
853

RPUSD4

all
rs351758
rs351758
8
28029018
A
0.6242
<1.0E−5
0.4949
ELP3
rev/B
621
854

B3 vs Ctrl L3

L3
rs1352071
imm_2_163065624
2
163357378
G
1.988
<1.0E−5
0.1247
KCNH7
rev/B
449
682

L3
rs6801634
rs6801634
3
4354697
A
1.989
<1.0E−5
0.141
SETMAR
fwd/T
471
704

L3
rs2383184
rs2383184
9
21763566
G
2.623
<1.0E−5
0.06435
IFNE1 |
rev/B
484
717

MTAP

L3
rs2954756
rs2954756
17
15339283
G
2.071
<1.0E−5
0.134
TEKT3 |
fwd/B
494
727

CDRT4

L3
rs12419184
rs12419184
11
126056308
A
1.975
<1.0E−5
0.1124
CDON |
fwd/B
622
855

RPUSD4

L3
rs7037277
rs7037277
9
21772064
G
2.441
<1.0E−5
0.06627
IFNE1 |
fwd/T
623
856

MTAP

L3
rs74950346
imm_16_73786858
16
75229357
A
2.25
<1.0E−5
0.05648
ZFP1 |
fwd/
624
857

CTRB2

Methods
Methods of Detection

Methods disclosed herein for detecting a genotype in a sample from a subject comprise analyzing the genetic material in the sample to detect at least one of a presence, an absence, and a quantity of a nucleic acid sequence encompassing the genotype of interest. In some cases, the nucleic acid sequence comprises DNA. In some instances, the nucleic acid sequence comprises a denatured DNA molecule or fragment thereof. In some instances, the nucleic acid sequence comprises DNA selected from: genomic DNA, viral DNA, mitochondrial DNA, plasmid DNA, amplified DNA, circular DNA, circulating DNA, cell-free DNA, or exosomal DNA. In some instances, the DNA is single-stranded DNA (ssDNA), double-stranded DNA, denaturing double-stranded DNA, synthetic DNA, and combinations thereof. The circular DNA may be cleaved or fragmented. In some instances, the nucleic acid sequence comprises RNA. In some instances, the nucleic acid sequence comprises fragmented RNA. In some instances, the nucleic acid sequence comprises partially degraded RNA. In some instances, the nucleic acid sequence comprises a microRNA or portion thereof. In some instances, the nucleic acid sequence comprises an RNA molecule or a fragmented RNA molecule (RNA fragments) selected from: a microRNA (miRNA), a pre-miRNA, a pri-miRNA, a mRNA, a pre-mRNA, a viral RNA, a viroid RNA, a virusoid RNA, circular RNA (circRNA), a ribosomal RNA (rRNA), a transfer RNA (tRNA), a pre-tRNA, a long non-coding RNA (lncRNA), a small nuclear RNA (snRNA), a circulating RNA, a cell-free RNA, an exosomal RNA, a vector-expressed RNA, an RNA transcript, a synthetic RNA, and combinations thereof.

Nucleic acid-based detection techniques that may be useful for the methods herein include quantitative polymerase chain reaction (qPCR), gel electrophoresis, immunochemistry, in situ hybridization such as fluorescent in situ hybridization (FISH), cytochemistry, and next generation sequencing. In some embodiments, the methods involve TaqMan™ qPCR, which involves a nucleic acid amplification reaction with a specific primer pair, and hybridization of the amplified nucleic acids with a hydrolysable probe specific to a target nucleic acid.

In some instances, the methods involve hybridization and/or amplification assays that include, but are not limited to, Southern or Northern analyses, polymerase chain reaction analyses, and probe arrays. Non-limiting amplification reactions include, but are not limited to, qPCR, self-sustained sequence replication, transcriptional amplification system, Q-Beta Replicase, rolling circle replication, or any other nucleic acid amplification known in the art. As discussed, reference to qPCR herein includes use of TaqMan™ methods. An additional exemplary hybridization assay includes the use of nucleic acid probes conjugated or otherwise immobilized on a bead, multi-well plate, or other substrate, wherein the nucleic acid probes are configured to hybridize with a target nucleic acid sequence of a genotype provided herein. A non-limiting method is one employed in Anal Chem. 2013 February 5; 85(3):1932-9.

In some embodiments, detecting the presence or absence of a genotype comprises sequencing genetic material from the subject. Sequencing can be performed with any appropriate sequencing technology, including but not limited to single-molecule real-time (SMRT) sequencing, Polony sequencing, sequencing by ligation, reversible terminator sequencing, proton detection sequencing, ion semiconductor sequencing, nanopore sequencing, electronic sequencing, pyrosequencing, Maxam-Gilbert sequencing, chain termination (e.g., Sanger) sequencing, +S sequencing, or sequencing by synthesis. Sequencing methods also include next-generation sequencing, e.g., modern sequencing technologies such as Illumina sequencing (e.g., Solexa), Roche 454 sequencing, Ion torrent sequencing, and SOLiD sequencing. In some cases, next-generation sequencing involves high-throughput sequencing methods. Additional sequencing methods available to one of skill in the art may also be employed.

In some instances, a number of nucleotides that are sequenced are at least 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 100, 150, 200, 300, 400, 500, 2000, 4000, 6000, 8000, 10000, 20000, 50000, 100000, or more than 100000 nucleotides. In some instances, the number of nucleotides sequenced is in a range of about 1 to about 100000 nucleotides, about 1 to about 10000 nucleotides, about 1 to about 1000 nucleotides, about 1 to about 500 nucleotides, about 1 to about 300 nucleotides, about 1 to about 200 nucleotides, about 1 to about 100 nucleotides, about 5 to about 100000 nucleotides, about 5 to about 10000 nucleotides, about 5 to about 1000 nucleotides, about 5 to about 500 nucleotides, about 5 to about 300 nucleotides, about 5 to about 200 nucleotides, about 5 to about 100 nucleotides, about 10 to about 100000 nucleotides, about 10 to about 10000 nucleotides, about 10 to about 1000 nucleotides, about 10 to about 500 nucleotides, about 10 to about 300 nucleotides, about 10 to about 200 nucleotides, about 10 to about 100 nucleotides, about 20 to about 100000 nucleotides, about 20 to about 10000 nucleotides, about 20 to about 1000 nucleotides, about 20 to about 500 nucleotides, about 20 to about 300 nucleotides, about 20 to about 200 nucleotides, about 20 to about 100 nucleotides, about 30 to about 100000 nucleotides, about 30 to about 10000 nucleotides, about 30 to about 1000 nucleotides, about 30 to about 500 nucleotides, about 30 to about 300 nucleotides, about 30 to about 200 nucleotides, about 30 to about 100 nucleotides, about 50 to about 100000 nucleotides, about 50 to about 10000 nucleotides, about 50 to about 1000 nucleotides, about 50 to about 500 nucleotides, about 50 to about 300 nucleotides, about 50 to about 200 nucleotides, or about 50 to about 100 nucleotides.

Exemplary probes comprise a nucleic acid sequence of at least 10 contiguous nucleic acids provided in any one of SEQ ID NOS: 1-82, including nucleoposition 26 or 31 within any one of SEQ ID NOS: 1-82, or a reverse complement thereof. In some instances, the probes comprises a nucleic acid at nucleoposition 26 that is, or is a complement to, the allele provided in Table 1 corresponding to the polymorphism being detected. In some embodiments, the exemplary probes comprise at least a portion of a nucleic acid sequence flanking the 3′ end of the risk allele, and at least a portion of a nucleic acid sequence flanking the 5′ end of the risk allele, such as those provided in Table 1.

Examples of molecules that are utilized as probes include, but are not limited to, RNA and DNA. In some embodiments, the term “probe” with regards to nucleic acids, refers to any molecule that is capable of selectively binding to a specifically intended target nucleic acid sequence. In some instances, probes are specifically designed to be labeled, for example, with a radioactive label, a fluorescent label, an enzyme, a chemiluminescent tag, a colorimetric tag, or other labels or tags that are known in the art. In some instances, the fluorescent label comprises a fluorophore. In some instances, the fluorophore is an aromatic or heteroaromatic compound. In some instances, the fluorophore is a pyrene, anthracene, naphthalene, acridine, stilbene, benzoxaazole, indole, benzindole, oxazole, thiazole, benzothiazole, canine, carbocyanine, salicylate, anthranilate, xanthenes dye, coumarin. Exemplary xanthene dyes include, e.g., fluorescein and rhodamine dyes. Fluorescein and rhodamine dyes include, but are not limited to 6-carboxyfluorescein (FAM), 2′7′-dimethoxy-4′5′-dichloro-6-carboxyfluorescein (JOE), tetrachlorofluorescein (TET), 6-carboxyrhodamine (R6G), N,N,N; N′-tetramethyl-6-carboxyrhodamine (TAMRA), 6-carboxy-X-rhodamine (ROX). Suitable fluorescent probes also include the naphthylamine dyes that have an amino group in the alpha or beta position. For example, naphthylamino compounds include 1-dimethylaminonaphthyl-5-sulfonate, 1-anilino-8-naphthalene sulfonate and 2-p-toluidinyl-6-naphthalene sulfonate, 5-(2′-aminoethyl)aminonaphthalene-1-sulfonic acid (EDANS). Exemplary coumarins include, e.g., 3-phenyl-7-isocyanatocoumarin; acridines, such as 9-isothiocyanatoacridine and acridine orange; N-(p-(2-benzoxazolyl)phenyl) maleimide; cyanines, such as, e.g., indodicarbocyanine 3 (Cy3), indodicarbocyanine 5 (Cy5), indodicarbocyanine 5.5 (Cy5.5), 3-(-carboxy-pentyl)-3′-ethyl-5,5′-dimethyloxacarbocyanine (CyA); 1H, 5H, 11H, 15H-Xantheno[2,3, 4-ij: 5,6, 7-i′j′]diquinolizin-18-ium, 9-[2 (or 4)-[[[6-[2,5-dioxo-1-pyrrolidinyl)oxy]-6-oxohexyl]amino]sulfonyl]-4 (or 2)-sulfophenyl]-2,3, 6,7, 12,13, 16,17-octahydro-inner salt (TR or Texas Red); or BODIPY™ dyes. In some cases, the probe comprises FAM as the dye label.

In some instances, primers and/or probes described herein for detecting a target nucleic acid are used in an amplification reaction. In some instances, the amplification reaction is qPCR. An exemplary qPCR is a method employing a TaqMan™ assay.

In some instances, qPCR comprises using an intercalating dye. Examples of intercalating dyes include SYBR green I, SYBR green II, SYBR gold, ethidium bromide, methylene blue, Pyronin Y, DAPI, acridine orange, Blue View or phycoerythrin. In some instances, the intercalating dye is SYBR.

In some instances, a number of amplification cycles for detecting a target nucleic acid in an amplification assay is about 5 to about 30 cycles. In some instances, the number of amplification cycles for detecting a target nucleic acid is at least about 5 cycles. In some instances, the number of amplification cycles for detecting a target nucleic acid is at most about 30 cycles. In some instances, the number of amplification cycles for detecting a target nucleic acid is about 5 to about 10, about 5 to about 15, about 5 to about 20, about 5 to about 25, about 5 to about 30, about 10 to about 15, about 10 to about 20, about 10 to about 25, about 10 to about 30, about 15 to about 20, about 15 to about 25, about 15 to about 30, about 20 to about 25, about 20 to about 30, or about 25 to about 30 cycles.

In one aspect, the methods provided herein for determining the presence, absence, and/or quantity of a nucleic acid sequence from a particular genotype comprise an amplification reaction such as qPCR. In an exemplary method, genetic material is obtained from a sample of a subject, e.g., a sample of blood or serum. In certain embodiments where nucleic acids are extracted, the nucleic acids are extracted using any technique that does not interfere with subsequent analysis. In certain embodiments, this technique uses alcohol precipitation using ethanol, methanol or isopropyl alcohol. In certain embodiments, this technique uses phenol, chloroform, or any combination thereof. In certain embodiments, this technique uses cesium chloride. In certain embodiments, this technique uses sodium, potassium or ammonium acetate or any other salt commonly used to precipitate DNA. In certain embodiments, this technique utilizes a column or resin based nucleic acid purification scheme such as those commonly sold commercially, one non-limiting example would be the GenElute Bacterial Genomic DNA Kit available from Sigma Aldrich. In certain embodiments, after extraction the nucleic acid is stored in water, Tris buffer, or Tris-EDTA buffer before subsequent analysis. In an exemplary embodiment, the nucleic acid material is extracted in water. In some cases, extraction does not comprise nucleic acid purification.

In the exemplary qPCR assay, the nucleic acid sample is combined with primers and probes specific for a target nucleic acid that may or may not be present in the sample, and a DNA polymerase. An amplification reaction is performed with a thermal cycler that heats and cools the sample for nucleic acid amplification, and illuminates the sample at a specific wavelength to excite a fluorophore on the probe and detect the emitted fluorescence. For TaqMan™ methods, the probe may be a hydrolysable probe comprising a fluorophore and quencher that is hydrolyzed by DNA polymerase when hybridized to a target nucleic acid. In some cases, the presence of a target nucleic acid is determined when the number of amplification cycles to reach a threshold value is less than 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, or 20 cycles.

The target nucleic acid sequence can comprise at least 10 contiguous nucleic acids comprising a polymorphism selected from the group consisting of rs2726797, rs7108993, rs79665096, rs7604404, rs73085878, rs78727269, rs2736352, rs4924935, rs11227112, rs2285043, rs6989059, rs3807552, rs111455641, rs9480689, rs7416358, rs6879067, rs11128532, rs177665, rs11171747, rs10775375, rs6801634, rs1070444, rs116714418, rs6962616, rs7220814, rs4325270, rs768755, rs17758350, rs9480689, rs525850, rs4325270, rs11749180, rs6962616, rs116714418, rs10265554, rs634641, rs1493871, rs12669698, rs4332037, rs17697480, rs9480689, rs6074737, rs904910, rs12972487, rs445417, rs635624, rs7416358, 12-54819630-G-INSERTION, rs177665, rs1070444, rs10912583, rs12914919, rs2854725, rs948068, rs71472147, rs72939578, rs658795, rs17758350, rs144260901, rs10801129, rs1702870, rs10912583, rs2452822, rs7774349, rs4705272, rs117946479, rs936126, rs634641, rs2314737, rs3002685, rs634641, rs12496281, rs10134119, rs3808240, rs1890843, rs11829981, rs12496281, rs2383184, rs144260901, rs6801634, rs2383184, rs2954756, provided in any one of SEQ ID NOS: 1-82. The primers and probes in the assay may include any combination of the primers and probes described herein. As such, a multiplex assay may be performed where combination of polymorphisms is detectable in the assay, the combination comprising at least one polymorphism at a nucleoposition 26 within any one of SEQ ID NOS: 1-82. In some instances, an exemplary probe to detect the polymorphism has a nucleic acid sequence provided in SEQ ID NO: 1, or its reverse complement. In some instances, provided is a probe comprises at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity to any one of SEQ ID NOS: 1-82, or its reverse complement. In some instances, forward and reverse primers are used to amplify the target nucleic acid sequence. Forward and reverse primers may comprise a nucleic acid sequence flanking the allele (“N”) in any one of SEQ ID NOS: 1-82, or a reverse complement thereof. Forward and reverse primers may comprise a nucleic acid sequence flanking the allele (“N”) that is 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity to any one of SEQ ID NOS: 1-82, or a reverse complement thereof.

To practice the methods and systems provided herein, genetic material may be extracted from a sample obtained from a subject, e.g., a sample of blood or serum. In certain embodiments where nucleic acids are extracted, the nucleic acids are extracted using any technique that does not interfere with subsequent analysis. In certain embodiments, this technique uses alcohol precipitation using ethanol, methanol or isopropyl alcohol. In certain embodiments, this technique uses phenol, chloroform, or any combination thereof. In certain embodiments, this technique uses cesium chloride. In certain embodiments, this technique uses sodium, potassium or ammonium acetate or any other salt commonly used to precipitate DNA. In certain embodiments, this technique utilizes a column or resin based nucleic acid purification scheme such as those commonly sold commercially, one non-limiting example would be the GenElute Bacterial Genomic DNA Kit available from Sigma Aldrich. In certain embodiments, after extraction the nucleic acid is stored in water, Tris buffer, or Tris-EDTA buffer before subsequent analysis. In an exemplary embodiment, the nucleic acid material is extracted in water. In some cases, extraction does not comprise nucleic acid purification. In certain embodiments, RNA may be extracted from cells using RNA extraction techniques including, for example, using acid phenol/guanidine isothiocyanate extraction (RNAzol B; Biogenesis), RNeasy RNA preparation kits (Qiagen) or PAXgene (PreAnalytix, Switzerland).

In some embodiments, methods of detecting a presence, absence, or level of a target protein (e.g., biomarker) in the sample obtained from the subject involve detecting protein activity or expression. A target protein may be detected by use of an antibody-based assay, where an antibody specific to the target protein is utilized. In some embodiments, antibody-based detection methods utilize an antibody that binds to any region of target protein. An exemplary method of analysis comprises performing an enzyme-linked immunosorbent assay (ELISA). The ELISA assay may be a sandwich ELISA or a direct ELISA. Another exemplary method of analysis comprises a single molecule array, e.g., Simoa. Other exemplary methods of detection include immunohistochemistry and lateral flow assay. Additional exemplary methods for detecting target protein include, but are not limited to, gel electrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), hyperdiffusion chromatography, and the like, or various immunological methods such as fluid or gel precipitation reactions, immunodiffusion (single or double), immunoelectrophoresis, radioimmunoassay (RIA), immunofluorescent assays, and Western blotting. In some embodiments, antibodies, or antibody fragments, are used in methods such as Western blots or immunofluorescence techniques to detect the expressed proteins. The antibody or protein can be immobilized on a solid support for Western blots and immunofluorescence techniques. Suitable solid phase supports or carriers include any support capable of binding an antigen or an antibody. Exemplary supports or carriers include glass, polystyrene, polypropylene, polyethylene, dextran, nylon, amylases, natural and modified celluloses, polyacrylamides, gabbros, and magnetite.

In some cases, a target protein may be detected by detecting binding between the target protein and a binding partner of the target protein. In some cases, the target protein comprises a protein expressed from a gene selected from the group consisting MAPT, ANK3, C1QTNF6, SSTR3, NAT6, WBSCR16, LOC653375, STK33, IMP5, LOC728191, ODZ3, POLS, ITGA6, MLSTD2, LOC729147, PROK2, RYBP, C14orf145, TSHR, RASGRP3, PDHB, KCTD6, KCNQ1DN, CDKN1C, CSMD1, C5orf30, NUDT12, XKR6, LOC157740, SLC2A13, B4GALNT1, OS9, LOC100130776, CTDSP2, XRCC6BP1, NAALADL1, CDCA5, EGF, MSRA, LOC100132391, PRPSAP2, CYP2R1, CALCA, LOC100129427, DDC, LOC100129060, CACNA2D2, LOC100128485, FLJ40296, LOC100130336, LOC100131830, PVT1, LOC728724, ZNF184, LOC100131289, TNK1, MTX1, TNFAIP3, PERP, STAG3L4, AUTS2, PITPNB, RPL37, CARD6, TTC33. SPOCK3, ANXA10, APOB, LOC728640, BICC1, C6orf58, C6orf190, NCOA2, LOC100130862, PDCD11, C6orf199, FLJ42177, RTN4IP1, LOC64694, ELMO1, RBM6, XYLT1, LOC728222, NRP2, FLJ20309, MYEOV, CCND1, OR51G1, OR51A4, KCNH7, LOC259308, LOC100128556, CDON, RPUSD4, IFNE1, MTAP, ELP3, ZFP1, CTRB2, TEKT3, CDRT4, SETMAR, TNFSF4, LOC730070, RPS26, ERBB3, RYR3, SLC16A10, TH, ASCL2, ATP8A1, LOC389207, RGS21, RGS1, LCE3E, LCE3D, SUOX, IKZF4, FAM62A, MYL6B, SMARCC2, B3GNTL1, IL22RA2, PRDM16, CTAGE1, RBBP8, EHD3, XDH, BARX2, MCCC1, SLC38A3, GNAI2, SNTG1, HIVEP2, AIG1, BTBD3, SPTLC3, RAB3GAP1, ZRANB3, YSK4, DDR2, FLRT3, MACROD2, SPEN, PTTG1, ATP10B, SLC6A11, XCL1, DPT, LOC440181, DAAM1, DDAH1, FGD5, PFTK1, SF3B3, C16orf77, ITPR2, C12orf11, LOC100129235, HHAT, LOC100131669, SLC14A2, CLECL1, CD69, MAD1L1, LOC729979, LOC730018, SH3D19, BRSK1, RSPO2, EIF3E, ADRB2, SH3TC2, HS6ST1, LOC100130768, DNMT3A, NTRK1, PEAR1, TEK, FAM62A, ZC3H10, OBFC2B, LOC100129289, HS3ST3A1, CDRT15P, GTF2A1, FLT, LOC727894. LOC728544, FLJ43582, RNF5P1, MKI67, and LOC728327. Exemplary methods of analysis of protein-protein binding comprise performing an assay in vivo or in vitro, or ex vivo. In some instances, the method of analysis comprises an assay such as a co-immunoprecipitation (co-IP), pull-down, crosslinking protein interaction analysis, labeled transfer protein interaction analysis, or Far-western blot analysis, FRET based assay, including, for example FRET-FLIM, a yeast two-hybrid assay, BiFC, or split luciferase assay.

Disclosed herein are methods of detecting a presence or a level of one or more serological markers in a sample obtained from a subject. In some embodiments, the one or more serological markers comprises anti-Saccharomyces cerevisiae antibody (ASCA), an anti-neutrophil cytoplasmic antibody (ANCA), antibody against E. coli outer membrane porin protein C (anti-OmpC), anti-chitin antibody, pANCA antibody, anti-I2 antibody, and anti-Cbir1 flagellin antibody. In some embodiments, the antibodies comprises immunoglobulin A (IgA), immunoglobulin G (IgG), immunoglobulin E (IgE), or immunoglobulin M (IgM), immunoglobulin D (IgD), or a combination thereof. Any suitable method for detecting a target protein or biomarker disclosed herein may be used to detect a presence, absence, or level of a serological marker. In some embodiments, the presence or the level of the one or more serological markers is detected using an enzyme-linked immunosorbent assay (ELISA), a single molecule array (Simoa), immunohistochemistry, internal transcribed spacer (ITS) sequencing, or any combination thereof. In some embodiments, the ELISA is a fixed leukocyte ELISA. In some embodiments, the ELISA is a fixed neutrophil ELISA. A fixed leukocyte or neutrophil ELISA may be useful for the detection of certain serological markers, such as those described in Saxon et al., A distinct subset of antineutrophil cytoplasmic antibodies is associated with inflammatory bowel disease, J. Allergy Clin. Immuno. 86:2; 202-210 (August 1990). In some embodiments, ELISA units (EU) are used to measure positivity of a presence or level of a serological marker (e.g., seropositivity), which reflects a percentage of a standard or reference value. In some embodiments, the standard comprises pooled sera obtained from well-characterized patient population (e.g., diagnosed with the same disease or condition the subject has, or is suspected of having) reported as being seropositive for the serological marker of interest. In some embodiments, the control or reference value comprises 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 EU. In some instances, a quartile sum scores are calculated using, for example, the methods reported in Landers C J, Cohavy O, Misra R. et al., Selected loss of tolerance evidenced by Crohn's disease-associated immune responses to auto- and microbial antigens. Gastroenterology (2002) 123:689-699.

Methods of Treatment

Disclosed herein are methods of treating a disease or condition, or a symptom of the disease or condition, in a subject, comprising administrating of therapeutic effective amount of one or more therapeutic agents to the subject. In some embodiments, the one or more therapeutic agents is administered to the subject alone (e.g., standalone therapy). In some embodiments, the one or more therapeutic agents is administered in combination with an additional agent. In some embodiments, the therapeutic agent is a first-line therapy for the disease or condition. In some embodiments, the therapeutic agent is a second-line, third-line, or fourth-line therapy, for the disease or condition.

Therapeutic Agent

Disclosed herein, in some embodiments, are therapeutic agents useful for the treatment of a disease or condition, or symptom of the disease or condition, disclosed herein. In some embodiments, the therapeutic agent comprises a modulator of a gene or gene expression product disclosed herein (such as, for e.g., genes containing, or associated with, a genotype disclosed herein). Non-limiting examples of genes affected by, or associated with, a presence of a genotype disclosed herein includes X—C Motif Chemokine Ligand 1 (XCL1), Dermatopontin (DPT), TNF Superfamily Member 4 (TNFSF4), C-Type Lectin Like 1 (CLECL1), CD69 Molecule (CD69), and Fms Related Tyrosine Kinase 1 (FLT1). In some embodiments, the therapeutic agent comprises at least one a modulator of Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 (MAP4K4), Prostaglandin E Receptor 4 (PTGER4), interleukin 18 receptor 1 (IL18R1). 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 3 (PFKFB3), Interleukin 18 Receptor Accessory Protein (IL18RAP), Adenylate Cyclase 7 (ADCY7), B Lymphoid Tyrosine Kinase (BLK), G Protein-Coupled Receptor 65 (GPR65), Sprouty Related EVH1 Domain Containing 2 (SPRED2), Src Kinase Associated Phosphoprotein 2 (SKAP2), CD30 ligand (CD30L), Receptor Interacting Serine/Threonine Kinase 2 (RIPK2), and TNF Ligand Superfamily Member 15 (TL1A).

XCL1/DPT Modulators

Chemokine Ligand 1 (XCL1) (HGNC: 10645 Entrez Gene: 6375 Ensembl: ENSG00000143184 OMIM: 600250 UniProtKB: P479920) is an antimicrobial gene that encodes a member of the chemokine superfamily. XCL1 is thought to be specifically chemotactic for T cells. Dermatopontin (DPT) (HGNC: 3011 Entrez Gene: 1805 Ensembl: ENSG00000143196 OMIM: 125597 UniProtKB: Q07507) is an extracellular matrix protein that is thought to be involved in antimicrobial response, by modifying the behavior of TGF-beta through interaction with decorin.

In some embodiments, the therapeutic agent comprises a modulator, agonist, and/or antagonist of at least one of XCL1 and DPT. In some embodiments, the therapeutic agent is effective to modify expression and/or activity of XCL1 or DPT. Therapeutic agents that modify expression and/or activity of XCL1 or DPT may also be referred to herein as XCL1 or DPT-targeting agents. Alternatively or additionally, compositions, kits and methods disclosed herein may comprise and/or utilize a therapeutic agent or use thereof, wherein the therapeutic agent modifies expression and/or activity of a protein that functions upstream or downstream of a pathway that involves XCL1 or DPT. In some embodiments, the modulator of XCL1 or DPT is effective to increase or activate the activity or expression of XCL1 or DPT in the subject (e.g., agonist or partial agonist). In some embodiments, the modulator of XCL1 or DPT is effective to decrease or reduce the activity or expression of XCL1 or DPT (e.g., antagonist or partial antagonist).

In some embodiments, the XCL1 or DPT modulator is an antibody, an antigen binding fragment, a RNA interfering agent (RNAi), a small interfering RNA (siRNA), a short hairpin RNA (shRNA), a microRNA (miRNA), an antisense oligonucleotide, a peptide, a peptidomimetic, a small molecule, or an aptamer.

In some instances, the therapeutic agent is an antagonist of XCL1 or DPT. In some instances, the antagonist acts as an inverse agonist. In some instances, the therapeutic agent is an allosteric modulator of XCL1 or DPT. In some instances, the therapeutic agent is an agonist of XCL1 or DPT.

In some instances, the subject has a genotype that is associated with, or causes, an increased expression of XCL1 or DPT. In some instances, the subject has a genotype that is associated with, or causes increased activity of XCL1 or DPT. In some instances, the genotype is associated with, or causes and increase expression of XCL1 or DPT. In some instances, the genotype is associated with, or causes an increase activity of XCL1 or DPT. In these instances, it may be suitable to use an XCL1 or DPT antagonist to bring XCL1 or DPT activity back to a normal level, e.g., that of a person without the IBD of the subject.

In some instances, the subject has a genotype that is associated with, or causes decreased expression of XCL1 or DPT. In some instances, the subject has a genotype is associated with, or causes, decreased activity of XCL1 or DPT. In some instances, the genotype is associated with, or causes, a decrease in expression of XCL1 or DPT. In some instances, the genotype is associated with, or causes, decreased activity of XCL1 or DPT. In these instances, it may be suitable to use an XCL1 or DPT agonist to bring XCL1 or DPT activity back to a normal level, e.g., that of a person without the IBD of the subject.

In some instances, the therapeutic agent is a small molecule that binds XCL1 or DPT. In some instances, the small molecule that binds XCL1 or DPT is an XCL1 or DPT agonist. In some instances, the small molecule that binds XCL1 or DPT is an XCL1 or DPT partial agonist. In some instances, the small molecule that binds XCL1 or DPT is an XCL1 or DPT antagonist. In some instances, the small molecule that binds XCL1 or DPT is an XCL1 or DPT partial agonist.

In some embodiments, the modulator of XCL1 comprises an XCL1 polypeptide. In some embodiments, the XCL1 polypeptide comprises a human XCL1 (huXCL1), or a homolog thereof. In some instances the polypeptide is an antagonist, agonist or modulator (e.g., allosteric modulator, orthosteric modulator) of XCL1 or DPT. In some embodiments, the XCL1 polypeptide comprises a recombinant XCL1 polypeptide. In some embodiments, the recombinant huXCL1 protein comprises SEQ ID NO: 858, which is the amino acid sequence of human XCL1 (NCBI Reference Sequence No. NP 002986). In some embodiments, the XCL1 polypeptide comprises a recombinant XCL1 polypeptide. In some embodiments, the huXCL1 comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 858. In some embodiments, the recombinant huXCL1 precursor protein comprises SEQ ID NO: 859, which is the amino acid sequence of human DPT (NCBI Reference Sequence No. NP_001928). In some embodiments, the huXCL1 or DPT comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 859.

In some instances, the XCL1 or DPT polypeptide is truncated. In some instances, the truncation is an N-terminal deletion. In other instances, the truncation is a C-terminal deletion. In additional instances, the truncation comprises both N-terminal and C-terminal deletions. For example, the truncation can be a deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, or more residues from either the N-terminus or the C-terminus, or both termini. In some cases, the XCL1 or DPT polypeptide comprises an N-terminal deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, or more residues. In some cases, the XCL1 or DPT polypeptide comprises an N-terminal deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 residues.

In some embodiments, the XCL1 or DPT polypeptide has an enhanced plasma half-life. In some instances, the plasma half-life comprises at least 30 minutes, 45 minutes, 60 minutes, 75 minutes, or 90 minutes, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 18 hours, 24 hours, 36 hours, 48 hours, 3 days, 4 days, 5 days, 6 days, 7 days, 10 days, 12 days, 14 days, 21 days, 28 days, 30 days, or longer than the plasma half-life of the wild-type XCL1 or DPT protein.

In some embodiments, the XCL1 or DPT polypeptide is a conjugate. In some embodiments, the XCL1 or DPT conjugate comprises an XCL1 or DPT polypeptide comprising at least one amino acid and a conjugating moiety bound to the at least one 1 amino acid. In some embodiments, the at least one amino acid is located proximal to the N-terminus (e.g., proximal to the N-terminal residue). For example, the at least one amino acid is located optionally within the first 10, 20, 30, 40, or 50 residues from the N-terminus. In some cases, the at least one amino acid is located at the N-terminus (i.e., the at least one amino acid is the N-terminal residue of the XCL1 or DPT polypeptide). In other embodiments, the at least one amino acid is located proximal to the C-terminus (e.g., proximal to the C-terminal residue). For example, the at least one amino acid is located optionally within the first 10, 20, 30, 40, or 50 residues from the C-terminus. In some cases, the at least one amino acid is located at the C-terminus (i.e., the at least one amino acid is the C-terminal residue of the XCL1 or DPT polypeptide). In some instances, the XCL1 or DPT conjugate has an enhanced plasma half-life, such as the half-lives described herein. In some embodiments, the XCL1 or DPT conjugate is functionally active (e.g., retains activity). In some embodiments, the XCL1 or DPT conjugate is not functionally active (e.g., devoid of activity). In some embodiments, the conjugating moiety comprises a polymer comprising Polyethylene glycol (PEG).

In some embodiments, the XCL1 or DPT polypeptide is fused with a second polypeptide. In some embodiments, the second polypeptide comprises a polypeptide with a long plasma half-life relative to the plasma half-life of the XCL1 or DPT polypeptide. In some embodiments, the second polypeptide comprises an antibody or antibody fragment. In some embodiments, the antibody or antibody fragment comprises an IgG1, IgG2, IgG4, IgG3, or IgE. In some embodiments, the IgG is an Fc. In some embodiments, the IgG Fc is human. In some instances, the long plasma half-life polypeptide comprises HSA, transferrin, IgA monomer, Retinol-binding protein, Factor H, Factor XIII, C-reactive protein, Factor IX, Fibrinogen, IFN-alpha, Pentameric IgM, IL-2, or Thyroglobulin.

TNFSF4 Modulators

TNF Superfamily Member 4 (TNFSF4) (HGNC: 11892 Entrez Gene: 7124 Ensembl: ENSG00000232810 OMIM: 191160 UniProtKB: P01375) encodes a multifunctional proinflammatory cytokine that belongs to the tumor necrosis factor (TNF) superfamily (TNFL4). TNFSF4 is secreted by macrophages, and is involved in regulation of cell proliferation, differentiation, apoptosis, and lipid metabolism.

In some embodiments, the therapeutic agent comprises a modulator, agonist, and/or antagonist of at least one of TNFL4 or the gene encoding TNFL4 (TNFSF4). In some embodiments, the therapeutic agent is effective to modify expression and/or activity of TNFL4. Therapeutic agents that modify expression and/or activity of TNFL4 may also be referred to herein as TNFL4-targeting agents. Alternatively or additionally, compositions, kits and methods disclosed herein may comprise and/or utilize a therapeutic agent or use thereof, wherein the therapeutic agent modifies expression and/or activity of a protein that functions upstream or downstream of a pathway that involves TNFL4 or the gene encoding TNFL4 (TNFSF4). In some embodiments, the modulator of TNFL4 is effective to increase or activate the activity or expression of TNFL4 in the subject (e.g., agonist or partial agonist). In some embodiments, the modulator of TNFL4 is effective to decrease or reduce the activity or expression of TNFL4 (e.g., antagonist or partial antagonist).

In some embodiments, the TNFL4 modulator is an antibody, an antigen binding fragment, a RNA interfering agent (RNAi), a small interfering RNA (siRNA), a short hairpin RNA (shRNA), a microRNA (miRNA), an antisense oligonucleotide, a peptide, a peptidomimetic, a small molecule, or an aptamer.

In some instances, the therapeutic agent is an antagonist of TNFL4. In some instances, the antagonist acts as an inverse agonist. In some instances, the therapeutic agent is an allosteric modulator of TNFL4. In some instances, the therapeutic agent is an agonist of TNFL4.

In some instances, the subject has a genotype that is associated with, or causes, an increased expression of TNFL4. In some instances, the subject has a genotype that is associated with, or causes increased activity of TNFL4. In some instances, the genotype is associated with, or causes and increase expression of TNFL4. In some instances, the genotype is associated with, or causes an increase activity of TNFL4. In these instances, it may be suitable to use a TNFL4 antagonist to bring TNFL4 activity back to a normal level, e.g., that of a person without the IBD of the subject.

In some instances, the subject has a genotype that is associated with, or causes decreased expression of TNFL4. In some instances, the subject has a genotype is associated with, or causes, decreased activity of TNFL4. In some instances, the genotype is associated with, or causes, a decrease in expression of TNFL4. In some instances, the genotype is associated with, or causes, decreased activity of TNFL4. In these instances, it may be suitable to use a TNFL4 agonist to bring TNFL4 activity back to a normal level, e.g., that of a person without the IBD of the subject.

In some instances, the therapeutic agent is a small molecule drug. By way of non-limiting example, a small molecule drug may be a chemical compound. In some instances, the therapeutic agent is a large molecule drug. Large molecule drugs generally comprise a peptide or nucleic acid. By way of non-limiting example, the large molecule drug may comprise an antibody or antigen binding antibody fragment. In some instances, the therapeutic agent comprises a small molecule and a large molecule. By way of non-limiting example, the therapeutic agent may comprise an antibody-drug conjugate. In some instances, the antibody or antigen-binding fragment is a neutralizing antibody or antigen-binding fragment. In some instances, the antibody is a monoclonal antibody. A non-limiting example of a neutralizing monoclonal antibody against TNFL4 includes oxelumab.

In some instances, the therapeutic agent is a small molecule that binds TNFL4. In some instances, the small molecule that binds TNFL4 is a TNFL4 agonist. In some instances, the small molecule that binds TNFL4 is a TNFL4 partial agonist. In some instances, the small molecule that binds TNFL4 is a TNFL4 antagonist. In some instances, the small molecule that binds TNFL4 is a TNFL4 partial agonist.

In some embodiments, the modulator of TNFL4 comprises a TNFL4 polypeptide. In some embodiments, the TNFL4 polypeptide comprises a human TNFL4 (huTNFSF4), or a homolog thereof. In some instances the polypeptide is an antagonist, agonist or modulator (e.g., allosteric modulator, orthosteric modulator) of TNFL4. In some embodiments, the TNFL4 polypeptide comprises a recombinant TNFL4 polypeptide. In some embodiments, the recombinant huTNFL4 protein comprises SEQ ID NO: 860, which is the amino acid sequence of human TNFL4 (NCBI Reference Sequence No. NP_003317). In some embodiments, the TNFL4 polypeptide comprises a recombinant TNFL4 polypeptide. In some embodiments, the huTNFL4 comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 860. In some embodiments, the recombinant huTNFSF4 precursor protein comprises SEQ ID NO: 861, which is the amino acid sequence of human TNFL4 (NCBI Reference Sequence No. NP_001284491). In some embodiments, the huTNFL4 comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 861.

In some instances, the TNFL4 polypeptide is truncated. In some instances, the truncation is an N-terminal deletion. In other instances, the truncation is a C-terminal deletion. In additional instances, the truncation comprises both N-terminal and C-terminal deletions. For example, the truncation can be a deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, or more residues from either the N-terminus or the C-terminus, or both termini. In some cases, the TNFL4 polypeptide comprises an N-terminal deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, or more residues. In some cases, the TNFL4 polypeptide comprises an N-terminal deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 residues.

In some embodiments, the TNFL4 polypeptide has an enhanced plasma half-life. In some instances, the plasma half-life comprises at least 30 minutes, 45 minutes, 60 minutes, 75 minutes, or 90 minutes, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 18 hours, 24 hours, 36 hours, 48 hours, 3 days, 4 days, 5 days, 6 days, 7 days, 10 days, 12 days, 14 days, 21 days, 28 days, 30 days, or longer than the plasma half-life of the wild-type TNFL4 protein.

In some embodiments, the TNFL4 polypeptide is a conjugate. In some embodiments, the TNFL4 conjugate comprises an TNFL4 polypeptide comprising at least one amino acid and a conjugating moiety bound to the at least one 1 amino acid. In some embodiments, the at least one amino acid is located proximal to the N-terminus (e.g., proximal to the N-terminal residue). For example, the at least one amino acid is located optionally within the first 10, 20, 30, 40, or 50 residues from the N-terminus. In some cases, the at least one amino acid is located at the N-terminus (i.e., the at least one amino acid is the N-terminal residue of the TNFL4 polypeptide). In other embodiments, the at least one amino acid is located proximal to the C-terminus (e.g., proximal to the C-terminal residue). For example, the at least one amino acid is located optionally within the first 10, 20, 30, 40, or 50 residues from the C-terminus. In some cases, the at least one amino acid is located at the C-terminus (i.e., the at least one amino acid is the C-terminal residue of the TNFL4 polypeptide). In some instances, the TNFL4 conjugate has an enhanced plasma half-life, such as the half-lives described herein. In some embodiments, the TNFL4 conjugate is functionally active (e.g., retains activity). In some embodiments, the TNFL4 conjugate is not functionally active (e.g., devoid of activity). In some embodiments, the conjugating moiety comprises a polymer comprising Polyethylene glycol (PEG).

In some embodiments, the TNFL4 polypeptide is fused with a second polypeptide. In some embodiments, the second polypeptide comprises a polypeptide with a long plasma half-life relative to the plasma half-life of the TNFL4 polypeptide. In some embodiments, the second polypeptide comprises an antibody or antibody fragment. In some embodiments, the antibody or antibody fragment comprises an IgG1, IgG2, IgG4, IgG3, or IgE. In some embodiments, the IgG is an Fc. In some embodiments, the IgG Fc is human. In some instances, the long plasma half-life polypeptide comprises HSA, transferrin, IgA monomer, Retinol-binding protein, Factor H, Factor XIII, C-reactive protein, Factor IX, Fibrinogen, IFN-alpha, Pentameric IgM, IL-2, or Thyroglobulin.

CLECL1/CD69 Modulators

C-Type Lectin Like 1 (CLECL1) (HGNC: 24462 Entrez Gene: 160365 Ensembl: ENSG00000184293 OMIM: 607467 UniProtKB: Q8IZS7) encodes a type II transmembrane, C-type lectin-like protein that is highly expressed in B cells. CLECL1 may act as a T-cell costimulatory molecule that enhances interleukin-4 (IL-4) production, and maybe involved in the regulation of the immune response. CD69 Molecule (CD69) (HGNC: 1694 Entrez Gene: 969 Ensembl: ENSG00000110848 OMIM: 107273 UniProtKB: Q07108) encodes a member of the calcium dependent lectin superfamily of type II transmembrane receptors. Expression of the encoded protein is induced upon activation of T lymphocytes, and may play a role in proliferation.

In some embodiments, the therapeutic agent comprises a modulator, agonist, and/or antagonist of at least one of CLECL1 or CD69. In some embodiments, the therapeutic agent is effective to modify expression and/or activity of CLECL1 or CD69. Therapeutic agents that modify expression and/or activity of CLECL1 or CD69 may also be referred to herein as CLECL1 or CD69-targeting agents. Alternatively or additionally, compositions, kits and methods disclosed herein may comprise and/or utilize a therapeutic agent or use thereof, wherein the therapeutic agent modifies expression and/or activity of a protein that functions upstream or downstream of a pathway that involves CLECL1 or CD69 or the gene encoding CLECL1 or CD69. In some embodiments, the modulator of CLECL1 or CD69 is effective to increase or activate the activity or expression of CLECL1 or CD69 in the subject (e.g., agonist or partial agonist). In some embodiments, the modulator of CLECL1 or CD69 is effective to decrease or reduce the activity or expression of CLECL1 or CD69 (e.g., antagonist or partial antagonist).

In some embodiments, the CLECL1 or CD69 modulator is an antibody, an antigen binding fragment, a RNA interfering agent (RNAi), a small interfering RNA (siRNA), a short hairpin RNA (shRNA), a microRNA (miRNA), an antisense oligonucleotide, a peptide, a peptidomimetic, a small molecule, or an aptamer.

In some instances, the therapeutic agent is an antagonist of CLECL1 or CD69. In some instances, the antagonist acts as an inverse agonist. In some instances, the therapeutic agent is an allosteric modulator of CLECL1 or CD69. In some instances, the therapeutic agent is an agonist of CLECL1 or CD69.

In some instances, the subject has a genotype that is associated with, or causes, an increased expression of CLECL1 or CD69. In some instances, the subject has a genotype that is associated with, or causes increased activity of CLECL1 or CD69. In some instances, the genotype is associated with, or causes and increase expression of CLECL1 or CD69. In some instances, the genotype is associated with, or causes an increase activity of CLECL1 or CD69. In these instances, it may be suitable to use a CLECL1 or CD69 antagonist to bring CLECL1 or CD69 activity back to a normal level, e.g., that of a person without the IBD of the subject.

In some instances, the subject has a genotype that is associated with, or causes decreased expression of CLECL1 or CD69. In some instances, the subject has a genotype is associated with, or causes, decreased activity of CLECL1 or CD69. In some instances, the genotype is associated with, or causes, a decrease in expression of CLECL1 or CD69. In some instances, the genotype is associated with, or causes, decreased activity of CLECL1 or CD69. In these instances, it may be suitable to use a CLECL1 or CD69 agonist to bring CLECL1 or CD69 activity back to a normal level, e.g., that of a person without the IBD of the subject.

In some instances, the therapeutic agent is a small molecule that binds CLECL1 or CD69. In some instances, the small molecule that binds CLECL1 or CD69 is a CLECL1 or CD69 agonist. In some instances, the small molecule that binds CLECL1 or CD69 is a CLECL1 or CD69 partial agonist. In some instances, the small molecule that binds CLECL1 or CD69 is a CLECL1 or CD69 antagonist. In some instances, the small molecule that binds CLECL1 or CD69 is a CLECL1 or CD69 partial agonist.

In some embodiments, the modulator of CLECL1 or CD69 comprises a CLECL1 polypeptide. In some embodiments, the CLECL1 polypeptide comprises a human CLECL1 (huCLECL1), or a homolog thereof. In some instances the polypeptide is an antagonist, agonist or modulator (e.g., allosteric modulator, orthosteric modulator) of CLECL1. In some embodiments, the CLECL1 polypeptide comprises a recombinant CLECL1 polypeptide. In some embodiments, the recombinant huCLECL1 protein comprises SEQ ID NO: 862, which is the amino acid sequence of human CLECL1 or CD69 (NCBI Reference Sequence No. NP_001240677). In some embodiments, the CLECL1 polypeptide comprises a recombinant CLECL1 polypeptide. In some embodiments, the huCLECL1 comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 862. In some embodiments, the recombinant huCLECL1 protein comprises SEQ ID NO: 863, which is the amino acid sequence of human CLECL1 (NCBI Reference Sequence No. NP_001240679). In some embodiments, the huCLECL1 comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 863. In some embodiments, the recombinant huCLECL1 protein comprises SEQ ID NO: 864, which is the amino acid sequence of human CLECL. In some embodiments, the huCLECL1 comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 864. In some embodiments, the recombinant huCLECL1 protein comprises SEQ ID NO: 865, which is the amino acid sequence of human CLECL1 (NCBI Reference Sequence No. NP_001254630). In some embodiments, the huCLECL1 comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 865. In some embodiments, the agonist of CLECL1 or CD69 comprises a CD69 polypeptide. In some embodiments, the recombinant huCD69 protein comprises SEQ ID NO: 866, which is the amino acid sequence of human CD69 (NCBI Reference Sequence No. NP_001772). In some embodiments, the huCD69 comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 866.

In some instances, the CLECL1 or CD69 polypeptide is truncated. In some instances, the truncation is an N-terminal deletion. In other instances, the truncation is a C-terminal deletion. In additional instances, the truncation comprises both N-terminal and C-terminal deletions. For example, the truncation can be a deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, or more residues from either the N-terminus or the C-terminus, or both termini. In some cases, the CLECL1 or CD69 polypeptide comprises an N-terminal deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, or more residues. In some cases, the CLECL1 or CD69 polypeptide comprises an N-terminal deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 residues.

In some embodiments, the CLECL1 or CD69 polypeptide has an enhanced plasma half-life. In some instances, the plasma half-life comprises at least 30 minutes, 45 minutes, 60 minutes, 75 minutes, or 90 minutes, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 18 hours, 24 hours, 36 hours, 48 hours, 3 days, 4 days, 5 days, 6 days, 7 days, 10 days, 12 days, 14 days, 21 days, 28 days, 30 days, or longer than the plasma half-life of the wild-type CLECL1 or CD69 protein.

In some embodiments, the CLECL1 or CD69 polypeptide is a conjugate. In some embodiments, the CLECL1 or CD69 conjugate comprises an CLECL1 or CD69 polypeptide comprising at least one amino acid and a conjugating moiety bound to the at least one 1 amino acid. In some embodiments, the at least one amino acid is located proximal to the N-terminus (e.g., proximal to the N-terminal residue). For example, the at least one amino acid is located optionally within the first 10, 20, 30, 40, or 50 residues from the N-terminus. In some cases, the at least one amino acid is located at the N-terminus (i.e., the at least one amino acid is the N-terminal residue of the CLECL1 or CD69 polypeptide). In other embodiments, the at least one amino acid is located proximal to the C-terminus (e.g., proximal to the C-terminal residue). For example, the at least one amino acid is located optionally within the first 10, 20, 30, 40, or 50 residues from the C-terminus. In some cases, the at least one amino acid is located at the C-terminus (i.e., the at least one amino acid is the C-terminal residue of the CLECL1 or CD69 polypeptide). In some instances, the CLECL1 or CD69 conjugate has an enhanced plasma half-life, such as the half-lives described herein. In some embodiments, the CLECL1 or CD69 conjugate is functionally active (e.g., retains activity). In some embodiments, the CLECL1 or CD69 conjugate is not functionally active (e.g., devoid of activity). In some embodiments, the conjugating moiety comprises a polymer comprising Polyethylene glycol (PEG).

In some embodiments, the CLECL1 or CD69 polypeptide is fused with a second polypeptide. In some embodiments, the second polypeptide comprises a polypeptide with a long plasma half-life relative to the plasma half-life of the CLECL1 or CD69 polypeptide. In some embodiments, the second polypeptide comprises an antibody or antibody fragment. In some embodiments, the antibody or antibody fragment comprises an IgG1, IgG2, IgG4, IgG3, or IgE. In some embodiments, the IgG is an Fc. In some embodiments, the IgG Fc is human. In some instances, the long plasma half-life polypeptide comprises HSA, transferrin, IgA monomer, Retinol-binding protein, Factor H, Factor XIII, C-reactive protein, Factor IX, Fibrinogen, IFN-alpha, Pentameric IgM, IL-2, or Thyroglobulin.

VEGFR1 Modulators

Fms Related Tyrosine Kinase 1 (FLT1) (HGNC: 3763 Entrez Gene: 2321 Ensembl: ENSG00000102755 OMIM: 165070 UniProtKB: P17948) encodes a member of the vascular endothelial growth factor receptor (VEGFR) family called vascular endothelial growth factor receptor 1 (VEGFR1). In some embodiments, the therapeutic agent comprises a modulator, agonist, and/or antagonist of at least one of VEGFR1. In some embodiments, the modulator of VEGFR is an antagonist of VEGFR. Non-limiting example of antagonist of VEGFR1 include ABT-869, Axitinib, IMC-1C11, Lenvatinib, N-(4-chlorophenyl)-2-[(pyridin-4-ylmethyl)amino]benzamide, Nintedanib, OSI-930, Pazopanib, Regorafenib, Sorafenib, Sunitinib, TG100801, Vatalanib, Motesanib, and Vandetanib.

In some embodiments, the therapeutic agent is effective to modify expression and/or activity of VEGFR1. Therapeutic agents that modify expression and/or activity of VEGFR1 may also be referred to herein as VEGFR1-targeting agents. Alternatively or additionally, compositions, kits and methods disclosed herein may comprise and/or utilize a therapeutic agent or use thereof, wherein the therapeutic agent modifies expression and/or activity of a protein that functions upstream or downstream of a pathway that involves VEGFR1 or the gene encoding VEGFR1 (FLT1). In some embodiments, the modulator of VEGFR1 is effective to increase or activate the activity or expression of VEGFR1 in the subject (e.g., agonist or partial agonist). In some embodiments, the modulator of VEGFR1 is effective to decrease or reduce the activity or expression of VEGFR1 (e.g., antagonist or partial antagonist). In some instances, the therapeutic agent is an allosteric modulator of VEGFR1.

In some embodiments, the VEGFR1 modulator is an antibody, an antigen binding fragment, a RNA interfering agent (RNAi), a small interfering RNA (siRNA), a short hairpin RNA (shRNA), a microRNA (miRNA), an antisense oligonucleotide, a peptide, a peptidomimetic, a small molecule, or an aptamer.

In some instances, the subject has a genotype that is associated with, or causes, an increased expression of VEGFR1. In some instances, the subject has a genotype that is associated with, or causes increased activity of VEGFR1. In some instances, the genotype is associated with, or causes and increase expression of VEGFR1. In some instances, the genotype is associated with, or causes an increase activity of VEGFR1. In these instances, it may be suitable to use a VEGFR1 antagonist to bring VEGFR1 activity back to a normal level, e.g., that of a person without the IBD of the subject.

In some instances, the subject has a genotype that is associated with, or causes decreased expression of VEGFR1. In some instances, the subject has a genotype is associated with, or causes, decreased activity of VEGFR1. In some instances, the genotype is associated with, or causes, a decrease in expression of VEGFR1. In some instances, the genotype is associated with, or causes, decreased activity of VEGFR1. In these instances, it may be suitable to use a VEGFR1 agonist to bring VEGFR1 activity back to a normal level, e.g., that of a person without the IBD of the subject.

In some instances, the therapeutic agent is a small molecule that binds VEGFR1. In some instances, the small molecule that binds VEGFR1 is a VEGFR1 agonist. In some instances, the small molecule that binds VEGFR1 is a VEGFR1 partial agonist. In some instances, the small molecule that binds VEGFR1 is a VEGFR1 antagonist. In some instances, the small molecule that binds VEGFR1 is a VEGFR1 partial agonist.

In some embodiments, the therapeutic agent comprises a VEGFR1 polypeptide. In some embodiments, the VEGFR1 polypeptide comprises a human VEGFR1 (huVEGFR1), or a homolog thereof. In some instances the polypeptide is an antagonist, agonist or modulator (e.g., allosteric modulator, orthosteric modulator) of VEGFR1. In some embodiments, the VEGFR1 polypeptide comprises a recombinant VEGFR1 polypeptide. In some embodiments, the recombinant huVEGFR1 protein comprises SEQ ID NO: 867), which is the amino acid sequence of human VEGFR1 (NCBI Reference Sequence No. NP_002010). In some embodiments, the VEGFR1 polypeptide comprises a recombinant VEGFR1 polypeptide. In some embodiments, the huVEGFR1 comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 867.

In some embodiments, the recombinant huVEGFR1 protein comprises SEQ ID NO: 868, which is the amino acid sequence of human VEGFR1 (NCBI Reference Sequence No. NP_001153392). In some embodiments, the huVEGFR1 comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 868.

In some embodiments, the recombinant huVEGFR1 protein comprises SEQ ID NO: 869, which is the amino acid sequence of human VEGFR1 (NCBI Reference Sequence No. NP_001153502). In some embodiments, the huVEGFR1 comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 869.

In some embodiments, the recombinant huVEGFR1 protein comprises SEQ ID NO: 870, which is the amino acid sequence of human VEGFR1 (NCBI Reference Sequence No. NP_001153503). In some embodiments, the huVEGFR1 comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 870.

In some instances, the VEGFR1 polypeptide is truncated. In some instances, the truncation is an N-terminal deletion. In other instances, the truncation is a C-terminal deletion. In additional instances, the truncation comprises both N-terminal and C-terminal deletions. For example, the truncation can be a deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, or more residues from either the N-terminus or the C-terminus, or both termini. In some cases, the VEGFR1 polypeptide comprises an N-terminal deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, or more residues. In some cases, the VEGFR1 polypeptide comprises an N-terminal deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 residues.

In some embodiments, the VEGFR1 polypeptide has an enhanced plasma half-life. In some instances, the plasma half-life comprises at least 30 minutes, 45 minutes, 60 minutes, 75 minutes, or 90 minutes, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 18 hours, 24 hours, 36 hours, 48 hours, 3 days, 4 days, 5 days, 6 days, 7 days, 10 days, 12 days, 14 days, 21 days, 28 days, 30 days, or longer than the plasma half-life of the wild-type VEGFR1 protein.

In some embodiments, the VEGFR1 polypeptide is a conjugate. In some embodiments, the VEGFR1 conjugate comprises an VEGFR1 polypeptide comprising at least one amino acid and a conjugating moiety bound to the at least one 1 amino acid. In some embodiments, the at least one amino acid is located proximal to the N-terminus (e.g., proximal to the N-terminal residue). For example, the at least one amino acid is located optionally within the first 10, 20, 30, 40, or 50 residues from the N-terminus. In some cases, the at least one amino acid is located at the N-terminus (i.e., the at least one amino acid is the N-terminal residue of the VEGFR1 polypeptide). In other embodiments, the at least one amino acid is located proximal to the C-terminus (e.g., proximal to the C-terminal residue). For example, the at least one amino acid is located optionally within the first 10, 20, 30, 40, or 50 residues from the C-terminus. In some cases, the at least one amino acid is located at the C-terminus (i.e., the at least one amino acid is the C-terminal residue of the VEGFR1 polypeptide). In some instances, the VEGFR1 conjugate has an enhanced plasma half-life, such as the half-lives described herein. In some embodiments, the VEGFR1 conjugate is functionally active (e.g., retains activity). In some embodiments, the VEGFR1 conjugate is not functionally active (e.g., devoid of activity). In some embodiments, the conjugating moiety comprises a polymer comprising Polyethylene glycol (PEG).

In some embodiments, the VEGFR1 polypeptide is fused with a second polypeptide. In some embodiments, the second polypeptide comprises a polypeptide with a long plasma half-life relative to the plasma half-life of the VEGFR1 polypeptide. In some embodiments, the second polypeptide comprises an antibody or antibody fragment. In some embodiments, the antibody or antibody fragment comprises an IgG1, IgG2, IgG4, IgG3, or IgE. In some embodiments, the IgG is an Fc. In some embodiments, the IgG Fc is human. In some instances, the long plasma half-life polypeptide comprises HSA, transferrin, IgA monomer, Retinol-binding protein, Factor H, Factor XIII, C-reactive protein, Factor IX, Fibrinogen, IFN-alpha, Pentameric IgM, IL-2, or Thyroglobulin.

TEK Modulators

TEK Receptor Tyrosine Kinase (TEK) (HGNC: 11724 Entrez Gene: 7010 Ensembl: ENSG00000120156 OMIM: 600221 UniProtKB: Q02763) encodes a receptor that belongs to the protein tyrosine kinase Tie2 family, Angiopoietin-1 receptor (TIE2). In some embodiments, the therapeutic agent comprises a modulator, agonist, and/or antagonist of at least one of TIE2. In some embodiments, the therapeutic agent is effective to modify expression and/or activity of TIE2. Therapeutic agents that modify expression and/or activity of TIE2 may also be referred to herein as TIE2-targeting agents. Alternatively or additionally, compositions, kits and methods disclosed herein may comprise and/or utilize a therapeutic agent or use thereof, wherein the therapeutic agent modifies expression and/or activity of a protein that functions upstream or downstream of a pathway that involves TIE2 or the gene encoding TIE2 (TEK). In some embodiments, the modulator of TIE2 is effective to increase or activate the activity or expression of TIE2 in the subject (e.g., agonist or partial agonist). In some embodiments, the modulator of TIE2 is effective to decrease or reduce the activity or expression of TIE2 (e.g., antagonist or partial antagonist). In some instances, the therapeutic agent is an allosteric modulator of TIE2.

In some embodiments, the TIE2 modulator is an antibody, an antigen binding fragment, a RNA interfering agent (RNAi), a small interfering RNA (siRNA), a short hairpin RNA (shRNA), a microRNA (miRNA), an antisense oligonucleotide, a peptide, a peptidomimetic, a small molecule, or an aptamer.

In some instances, the subject has a genotype that is associated with, or causes, an increased expression of TIE2. In some instances, the subject has a genotype that is associated with, or causes increased activity of TIE2. In some instances, the genotype is associated with, or causes and increase expression of TIE2. In some instances, the genotype is associated with, or causes an increase activity of TIE2. In these instances, it may be suitable to use a TIE2 antagonist to bring TIE2 activity back to a normal level, e.g., that of a person without the IBD of the subject.

In some instances, the subject has a genotype that is associated with, or causes decreased expression of TIE2. In some instances, the subject has a genotype is associated with, or causes, decreased activity of TIE2. In some instances, the genotype is associated with, or causes, a decrease in expression of TIE2. In some instances, the genotype is associated with, or causes, decreased activity of TIE2. In these instances, it may be suitable to use a TIE2 agonist to bring TIE2 activity back to a normal level, e.g., that of a person without the IBD of the subject.

In some instances, the therapeutic agent is a small molecule that binds TIE2. In some instances, the small molecule that binds TIE2 is a TIE2 agonist. In some instances, the small molecule that binds TIE2 is a TIE2 partial agonist. In some instances, the small molecule that binds TIE2 is a TIE2 antagonist. In some instances, the small molecule that binds TIE2 is a TIE2 partial agonist.

In some embodiments, the therapeutic agent comprises a TIE2 polypeptide. In some embodiments, the TIE2 polypeptide comprises a human TIE2 (huTIE2), or a homolog thereof. In some instances the polypeptide is an antagonist, agonist or modulator (e.g., allosteric modulator, orthosteric modulator) of TIE2.

In some embodiments, the TIE2 polypeptide comprises a recombinant TIE2 polypeptide. In some embodiments, the recombinant huTIE2 protein comprises SEQ ID NO: 871, which is the amino acid sequence of human TIE2 (NCBI Reference Sequence No. NP_000450). In some embodiments, the huTIE2 comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 871.

In some embodiments, the recombinant huTIE2 protein comprises SEQ ID NO: 872, which is the amino acid sequence of human TIE2 (NCBI Reference Sequence No. NP_005251619). In some embodiments, the huTIE2 comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 872.

In some embodiments, the recombinant huTIE2 protein comprises SEQ ID NO: 873, which is the amino acid sequence of human TIE2 (NCBI Reference Sequence No. NP_01277007). In some embodiments, the huTIE2 comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 873.

In some instances, the TIE2 polypeptide is truncated. In some instances, the truncation is an N-terminal deletion. In other instances, the truncation is a C-terminal deletion. In additional instances, the truncation comprises both N-terminal and C-terminal deletions. For example, the truncation can be a deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, or more residues from either the N-terminus or the C-terminus, or both termini. In some cases, the TIE2 polypeptide comprises an N-terminal deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, or more residues. In some cases, the TIE2 polypeptide comprises an N-terminal deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 residues.

In some embodiments, the TIE2 polypeptide has an enhanced plasma half-life. In some instances, the plasma half-life comprises at least 30 minutes, 45 minutes, 60 minutes, 75 minutes, or 90 minutes, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 18 hours, 24 hours, 36 hours, 48 hours, 3 days, 4 days, 5 days, 6 days, 7 days, 10 days, 12 days, 14 days, 21 days, 28 days, 30 days, or longer than the plasma half-life of the wild-type TIE2 protein.

In some embodiments, the TIE2 polypeptide is a conjugate. In some embodiments, the TIE2 conjugate comprises an TIE2 polypeptide comprising at least one amino acid and a conjugating moiety bound to the at least one 1 amino acid. In some embodiments, the at least one amino acid is located proximal to the N-terminus (e.g., proximal to the N-terminal residue). For example, the at least one amino acid is located optionally within the first 10, 20, 30, 40, or 50 residues from the N-terminus. In some cases, the at least one amino acid is located at the N-terminus (i.e., the at least one amino acid is the N-terminal residue of the TIE2 polypeptide). In other embodiments, the at least one amino acid is located proximal to the C-terminus (e.g., proximal to the C-terminal residue). For example, the at least one amino acid is located optionally within the first 10, 20, 30, 40, or 50 residues from the C-terminus. In some cases, the at least one amino acid is located at the C-terminus (i.e., the at least one amino acid is the C-terminal residue of the TIE2 polypeptide). In some instances, the TIE2 conjugate has an enhanced plasma half-life, such as the half-lives described herein. In some embodiments, the TIE2 conjugate is functionally active (e.g., retains activity). In some embodiments, the TIE2 conjugate is not functionally active (e.g., devoid of activity). In some embodiments, the conjugating moiety comprises a polymer comprising Polyethylene glycol (PEG).

In some embodiments, the TIE2 polypeptide is fused with a second polypeptide. In some embodiments, the second polypeptide comprises a polypeptide with a long plasma half-life relative to the plasma half-life of the TIE2 polypeptide. In some embodiments, the second polypeptide comprises an antibody or antibody fragment. In some embodiments, the antibody or antibody fragment comprises an IgG1, IgG2, IgG4, IgG3, or IgE. In some embodiments, the IgG is an Fc. In some embodiments, the IgG Fc is human. In some instances, the long plasma half-life polypeptide comprises HSA, transferrin, IgA monomer, Retinol-binding protein, Factor H, Factor XIII, C-reactive protein, Factor IX, Fibrinogen, IFN-alpha, Pentameric IgM, IL-2, or Thyroglobulin.

KCNH7 Modulators

Potassium Voltage-Gated Channel Subfamily H Member 7 (KCNH7) (HGNC: 18863 Entrez Gene: 90134 Ensembl: ENSG00000184611 OMIM: 608169 UniProtKB: Q9NS40) encodes a member of the potassium channel, voltage-gated, subfamily H (KCNH7). In some embodiments, the therapeutic agent comprises a modulator, agonist, and/or antagonist of at least one of KCNH7. A non-limiting example of a modulator of KCNH7 is Dalfampridine. In some embodiments, the therapeutic agent is effective to modify expression and/or activity of KCNH7. Therapeutic agents that modify expression and/or activity of KCNH7 may also be referred to herein as KCNH7-targeting agents. Alternatively or additionally, compositions, kits and methods disclosed herein may comprise and/or utilize a therapeutic agent or use thereof, wherein the therapeutic agent modifies expression and/or activity of a protein that functions upstream or downstream of a pathway that involves KCNH7 or the gene encoding KCNH7. In some embodiments, the modulator of KCNH7 is effective to increase or activate the activity or expression of KCNH7 in the subject (e.g., agonist or partial agonist). In some embodiments, the modulator of KCNH7 is effective to decrease or reduce the activity or expression of KCNH7 (e.g., antagonist or partial antagonist). In some instances, the therapeutic agent is an allosteric modulator of KCNH7.

In some embodiments, the KCNH7 modulator is an antibody, an antigen binding fragment, a RNA interfering agent (RNAi), a small interfering RNA (siRNA), a short hairpin RNA (shRNA), a microRNA (miRNA), an antisense oligonucleotide, a peptide, a peptidomimetic, a small molecule, or an aptamer.

In some instances, the subject has a genotype that is associated with, or causes, an increased expression of KCNH7. In some instances, the subject has a genotype that is associated with, or causes increased activity of KCNH7. In some instances, the genotype is associated with, or causes and increase expression of KCNH7. In some instances, the genotype is associated with, or causes an increase activity of KCNH7. In these instances, it may be suitable to use a KCNH7 antagonist to bring KCNH7 activity back to a normal level, e.g., that of a person without the IBD of the subject.

In some instances, the subject has a genotype that is associated with, or causes decreased expression of KCNH7. In some instances, the subject has a genotype is associated with, or causes, decreased activity of KCNH7. In some instances, the genotype is associated with, or causes, a decrease in expression of KCNH7. In some instances, the genotype is associated with, or causes, decreased activity of KCNH7. In these instances, it may be suitable to use a KCNH7 agonist to bring KCNH7 activity back to a normal level, e.g., that of a person without the IBD of the subject.

In some instances, the therapeutic agent is a small molecule that binds KCNH7. In some instances, the small molecule that binds KCNH7 is a KCNH7 agonist. In some instances, the small molecule that binds KCNH7 is a KCNH7 partial agonist. In some instances, the small molecule that binds KCNH7 is a KCNH7 antagonist. In some instances, the small molecule that binds KCNH7 is a KCNH7 partial agonist.

In some embodiments, the therapeutic agent comprises a KCNH7 polypeptide. In some embodiments, the KCNH7 polypeptide comprises a human KCNH7 (huKCNH7), or a homolog thereof. In some instances the polypeptide is an antagonist, agonist or modulator (e.g., allosteric modulator, orthosteric modulator) of KCNH7. In some embodiments, the KCNH7 polypeptide comprises a recombinant KCNH7 polypeptide. In some embodiments, the recombinant huKCNH7 protein comprises SEQ ID NO: 874, which is the amino acid sequence of human KCNH7 (NCBI Reference Sequence No. NP_150375). In some embodiments, the KCNH7 polypeptide comprises a recombinant KCNH7 polypeptide. In some embodiments, the huKCNH7 comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 874.

In some embodiments, the recombinant huKCNH7 protein comprises SEQ ID NO: 875, which is the amino acid sequence of human KCNH7 (NCBI Reference Sequence No. NP_775185). In some embodiments, the huKCNH7 comprises an amino acid sequence about 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, or 90% homologous to SEQ ID NO: 875.

In some instances, the KCNH7 polypeptide is truncated. In some instances, the truncation is an N-terminal deletion. In other instances, the truncation is a C-terminal deletion. In additional instances, the truncation comprises both N-terminal and C-terminal deletions. For example, the truncation can be a deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, or more residues from either the N-terminus or the C-terminus, or both termini. In some cases, the KCNH7 polypeptide comprises an N-terminal deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, or more residues. In some cases, the KCNH7 polypeptide comprises an N-terminal deletion of at least or about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 residues.

In some embodiments, the KCNH7 polypeptide has an enhanced plasma half-life. In some instances, the plasma half-life comprises at least 30 minutes, 45 minutes, 60 minutes, 75 minutes, or 90 minutes, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 18 hours, 24 hours, 36 hours, 48 hours, 3 days, 4 days, 5 days, 6 days, 7 days, 10 days, 12 days, 14 days, 21 days, 28 days, 30 days, or longer than the plasma half-life of the wild-type KCNH7 protein.

In some embodiments, the KCNH7 polypeptide is a conjugate. In some embodiments, the KCNH7 conjugate comprises an KCNH7 polypeptide comprising at least one amino acid and a conjugating moiety bound to the at least one 1 amino acid. In some embodiments, the at least one amino acid is located proximal to the N-terminus (e.g., proximal to the N-terminal residue). For example, the at least one amino acid is located optionally within the first 10, 20, 30, 40, or 50 residues from the N-terminus. In some cases, the at least one amino acid is located at the N-terminus (i.e., the at least one amino acid is the N-terminal residue of the KCNH7 polypeptide). In other embodiments, the at least one amino acid is located proximal to the C-terminus (e.g., proximal to the C-terminal residue). For example, the at least one amino acid is located optionally within the first 10, 20, 30, 40, or 50 residues from the C-terminus. In some cases, the at least one amino acid is located at the C-terminus (i.e., the at least one amino acid is the C-terminal residue of the KCNH7 polypeptide). In some instances, the KCNH7 conjugate has an enhanced plasma half-life, such as the half-lives described herein. In some embodiments, the KCNH7 conjugate is functionally active (e.g., retains activity). In some embodiments, the KCNH7 conjugate is not functionally active (e.g., devoid of activity). In some embodiments, the conjugating moiety comprises a polymer comprising Polyethylene glycol (PEG).

In some embodiments, the KCNH7 polypeptide is fused with a second polypeptide. In some embodiments, the second polypeptide comprises a polypeptide with a long plasma half-life relative to the plasma half-life of the KCNH7 polypeptide. In some embodiments, the second polypeptide comprises an antibody or antibody fragment. In some embodiments, the antibody or antibody fragment comprises an IgG1, IgG2, IgG4, IgG3, or IgE. In some embodiments, the IgG is an Fc. In some embodiments, the IgG Fc is human. In some instances, the long plasma half-life polypeptide comprises HSA, transferrin, IgA monomer, Retinol-binding protein, Factor H, Factor XIII, C-reactive protein, Factor IX, Fibrinogen, IFN-alpha, Pentameric IgM, IL-2, or Thyroglobulin.

CD30L Modulators

In some embodiments, the therapeutic agent is a modulator of CD30 ligand (CD30L). In some embodiments, the modulator of CD30L is an agonist or an antagonist of CD30L. In some instances, the antagonist of CD30L is an inhibitor of CD30L. In some embodiments, an inhibitor of CD30L specifically binds directly or indirectly to CD30L, CD30, or a molecule that interferes directly or indirectly with binding between CD30L and CD30. In some embodiments, as used herein, an inhibitor of CD30L comprises an agent that modulates at least one functional activity of CD30L, such as binding to CD30. Non-limiting examples of inhibitors of CD30L include agents that specifically bind to CD30L, including a polypeptide such as an anti-CD30L antibody or antigen binding fragment thereof, and a nucleic acid, e.g., an antisense construct, siRNA, and ribozyme. An antisense construct includes an expression plasmid that when transcribed in the cell produces RNA complementary to a portion of mRNA encoding CD30L, and an oligonucleotide that inhibits protein expression by hybridizing with the CD30L mRNA. In some embodiments the inhibitor of CD30L comprises a non-polypeptide or non-nucleic acid portion as an active agent that binds to and inhibits CD30L activity.

In some embodiments, an inhibitor of CD30L is a polypeptide that binds to CD30L and/or CD30. In some cases, the polypeptide is a CD30 polypeptide or a portion thereof, wherein the portion retains the ability to bind to CD30L. A portion of a CD30 polypeptide includes at least about 10, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids that have at least about 85%, 90%, or 95% identity to human CD30 having SEQ ID NO: 94, or SEQ ID NO: 95, or a sequence of any CD30 protein-coding isoform (for e.g., P28908). For example, an inhibitor of CD30L comprises a CD30 polypeptide that comprises all or part of the extracellular region of human CD30. In some embodiments, the CD30 polypeptide comprises amino acids 19-390 of SEQ ID NO: 18 or a binding fragment thereof, having at least about 85%, 90%, or 95% sequence identity to CD30. In some embodiments, the CD30 polypeptide is a homologue of mammalian CD30, e.g., the CD30 polypeptide inhibitor of CD30L is a viral CD30 polypeptide or fragment thereof. As a non-limiting example, the viral CD30 polypeptide comprises viral CD30 from a poxvirus, such as ectromelia virus or cowpox virus.

In a non-limiting example, the inhibitor is an anti-CD30L antibody or an anti-CD30 antibody. As used herein, an antibody includes an antigen-binding fragment of a full length antibody, e.g., a Fab or scFv. In some embodiments, the antibody binds to the extracellular domain of CD30L. In some embodiments, an anti-CD30L antibody comprises a heavy chain comprising three complementarity-determining regions: HCDR1, HCDR2, and HCDR3; and a light chain comprising three complementarity-determining regions: LCDR1, LCDR2, and LCDR3. In some embodiments, the anti-CD30L antibody comprises a HCDR1 comprising SEQ ID NO: 100, a HCDR2 comprising SEQ ID NO: 101, a HCDR3 comprising SEQ ID NO: 102, a LCDR1 comprising SEQ ID NO: 103, a LCDR2 comprising SEQ ID NO: 104, and a LCDR3 comprising SEQ ID NO: 105.

In some embodiments, the anti-CD30L antibody comprises a HCDR1 comprising SEQ ID NO: 106, a HCDR2 comprising SEQ ID NO: 107, a HCDR3 comprising SEQ ID NO: 108, a LCDR1 comprising SEQ ID NO: 109, a LCDR2 comprising SEQ ID NO: 110, and a LCDR3 comprising SEQ ID NO: 111.

In some embodiments, the anti-CD30L antibody comprises a HCDR1 comprising SEQ ID NO: 112, a HCDR2 comprising SEQ ID NO: 113, a HCDR3 comprising SEQ ID NO: 114, a LCDR1 comprising SEQ ID NO: 115, a LCDR2 comprising SEQ ID NO: 116, and a LCDR3 comprising SEQ ID NO: 117.

In some embodiments, the anti-CD30L antibody comprises a HCDR1 comprising SEQ ID NO: 118, a HCDR2 comprising SEQ ID NO: 119, a HCDR3 comprising SEQ ID NO: 120, a LCDR1 comprising SEQ ID NO: 121, a LCDR2 comprising SEQ ID NO: 122, and a LCDR3 comprising SEQ ID NO: 123.

In some embodiments, the anti-CD30L antibody comprises a HCDR1 comprising SEQ ID NO: 124, a HCDR2 comprising SEQ ID NO: 125, a HCDR3 comprising SEQ ID NO: 126, a LCDR1 comprising SEQ ID NO: 127, a LCDR2 comprising SEQ ID NO: 128, and a LCDR3 comprising SEQ ID NO: 129.

In some embodiments, the anti-CD30L antibody comprises a HCDR1 comprising SEQ ID NO: 130, a HCDR2 comprising SEQ ID NO: 131, a HCDR3 comprising SEQ ID NO: 132, a LCDR1 comprising SEQ ID NO: 133, a LCDR2 comprising SEQ ID NO: 134, and a LCDR3 comprising SEQ ID NO: 135.

In some cases, the anti-CD30L antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 136 and a light chain (LC) variable domain comprising SEQ ID NO: 137. In some cases, the anti-CD30L antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 138 and a light chain (LC) variable domain comprising SEQ ID NO: 139. In some cases, the anti-CD30L antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 140 and a light chain (LC) variable domain comprising SEQ ID NO: 141. In some cases, the anti-CD30L antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 142 and a light chain (LC) variable domain comprising SEQ ID NO: 143. In some cases, the anti-CD30L antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 144 and a light chain (LC) variable domain comprising SEQ ID NO: 145. In some cases, the anti-CD30L antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 146 and a light chain (LC) variable domain comprising SEQ ID NO: 154. In some cases, the anti-CD30L antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 147 and a light chain (LC) variable domain comprising SEQ ID NO: 154. In some cases, the anti-CD30L antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 148 and a light chain (LC) variable domain comprising SEQ ID NO: 154. In some cases, the anti-CD30L antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 149 and a light chain (LC) variable domain comprising SEQ ID NO: 154. In some cases, the anti-CD30L antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 150 and a light chain (LC) variable domain comprising SEQ ID NO: 154. In some cases, the anti-CD30L antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 151 and a light chain (LC) variable domain comprising SEQ ID NO: 154. In some cases, the anti-CD30L antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 152 and a light chain (LC) variable domain comprising SEQ ID NO: 154. In some cases, the anti-CD30L antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 153 and a light chain (LC) variable domain comprising SEQ ID NO: 154.

In some embodiments, the anti-CD30 antibody comprises a heavy chain variable region comprising SEQ ID NO: 96 and a light chain variable region comprising SEQ ID NO: 97. Non-limiting examples of anti-CD30 antibodies include MDX-60, Ber-H2, SGN-30 (cAC10), Ki-4.dgA, HRS-3/A9, AFM13, and H22xKi-4.

In some embodiments, the anti-CD30 antibody comprises an antibody drug conjugate. As a non-limiting example, the antibody drug conjugate is brentuximab, an anti-CD30 antibody conjugated to monomethyl auristatin E.

RIPK2 Modulators

Disclosed herein, in some embodiments, are therapeutic agents useful for the treatment of a disease or condition, or symptom of the disease or condition, disclosed herein. Disclosed herein, in some embodiments, are modulators of RIPK2 activity or expression that are useful for the treatment of an inflammatory, fibrotic, and/or fibrostenotic disease or condition. In some embodiments, the inflammatory disease comprises inflammatory bowel disease (IBD), Crohn's disease (CD), and/or ulcerative colitis (UC). In some embodiments, a modulator of RIPK2 activity or expression comprises an antagonist or a partial antagonist of RIPK2. In some embodiments, the RIPK2 antagonist or partial antagonist comprises an antibody or antigen-binding fragment, or a small molecule.

In some embodiments, the RIPK2 antagonist or partial antagonist comprises a type I RIPK2 inhibitor effective to bind to the ATP binding pocket of an active conformation of the RIPK2 kinase domain. In some embodiments, the RIPK2 antagonist or partial antagonist comprises a type PA RIPK2 inhibitor effective to bind to the ATP binding pocket of an inactive conformation of the RIPK2 kinase domain without displacing the RIPK2 kinase activation segment. In some embodiments, the RIPK2 antagonist or partial antagonist comprises a type II RIPK2 inhibitor effective to displace a RIPK2 kinase activation segment. In some embodiments, the RIPK2 antagonist or partial antagonist comprises a type III RIPK2 inhibitor effective to bind an allosteric site of RIPK2 located in the cleft between the small and large lobes adjacent to the ATP binding pocket. In some embodiments, the RIPK2 antagonist or partial antagonist comprises a type IV RIPK2 inhibitor effective to bind an allosteric site of RIPK2 located outside of the cleft and the phosphoacceptor region. In some embodiments, the RIPK2 antagonist or partial antagonist comprises a type V RIPK2 inhibitor effective to span two regions of the RIPK2 kinase domain. In some embodiments, the RIPK2 antagonist or partial antagonist comprises a type VI RIPK2 inhibitor effective to form a covalent adduct with RIPK2. In some embodiments, the RIPK2 antagonist or partial antagonist comprises a RIPK2 inhibitor effective to inhibit RIPK2 ubiquitination. In some embodiments, the RIPK2 antagonist or partial antagonist comprises a RIPK2 inhibitor effective to inhibit RIPK2 autophosphorylation. In some embodiments, the RIPK2 antagonist or partial antagonist comprises a RIPK2 inhibitor effective to block NOD-dependent tumor necrosis factor production without affecting lipopolysaccharide-dependent pathways. In some embodiments, the RIPK2 antagonist or partial antagonist comprises ponatinib, sorafenib, regorafenib, gefitinib, or erlotinib. In some embodiments, the RIPK2 antagonist or partial antagonist comprises GSK2983559, GSK583, Inhibitor 7, Biaryl Urea, CSR35, CSLP37, CSLP43, RIPK2 inhibitor 1, CS6, PP2, WEHI-345, SB203580, OD36, OD38, RIPK2-IN-8, RIPK2-IN-1, or RIPK2-IN-2, or any combination thereof.

Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (I) or a pharmaceutically acceptable salt or isotopic variant thereof:

embedded image

- wherein
- Ring A is C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, or 6- to 10-membered aryl;
- X is N or CR⁴;
- R¹and R²are independently —H, halogen, —OH, —OR⁵, —CN, —N(R⁶)₂, —NR⁶C(O)R⁵, —C(O)OR⁵, —C(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_3-8cycloalkyl, —C_1-6alkyl-OH, —C_1-6alkyl-OR⁵, —C_1-6alkyl-N(R⁶)₂, —O—C_1-6alkyl, —O—C_1-6alkyl-OH, —O—C_1-6alkyl-OR⁵, —O—C_1-6alkyl-N(R⁶)₂, or —S(═O)₂R⁵;
- each R³is independently —H, halogen, —NO₂, —CN, —OH, —OR⁵, —SR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷;
- R⁴is —H, halogen, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl, wherein the alkyl, haloalkyl, cycloalkyl, phenyl, heteroaryl, and heterocycloalkyl are optionally substituted;
- each R⁵is independently —H, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl;
- each R⁶is independently —H, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, or C_2-9heteroaryl; or two R⁶substituents are taken together with the nitrogen atom to which they are attached to form a 5- or 6-membered heterocycle; and
- R⁷is —H, halogen, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl; and
- n is 0, 1, 2, 3, 4, or 5.

In some embodiments of a compound of Formula (I), Ring A is C_3-8cycloalkyl, C_2-9-heterocycloalkyl, C_2-9heteroaryl, or 6- to 10-membered aryl. In some embodiments of a compound of Formula (I), Ring A is C_3-7heteroaryl or 6-membered aryl. In some embodiments of a compound of Formula (I), Ring A is pyrrazolyl. In some embodiments of a compound of Formula (I), Ring A is C₇heteroaryl. In some embodiments of a compound of Formula (I), Ring A is phenyl.

In some embodiments, for a compound of Formula (I), X is N or CR⁴. In some embodiments, for a compound of Formula (I), X is N or CH. In some embodiments, for a compound of Formula (I), X is N. In some embodiments, for a compound of Formula (I), X is CH.

In some embodiments, for a compound of Formula (I), R¹is —H, halogen, —OH, —CN, —N(R⁶)₂, —NR⁶C(O)R⁵, —C(O)OR⁵, —C(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_3-8cycloalkyl, —C_1-6alkyl-OH, —C_1-6alkyl-OR⁵, —C_1-6alkyl-N(R⁶)₂, —O—C_1-6alkyl, —O—C_1-6alkyl-OH, —O—C_1-6alkyl-N(R⁶)₂, or —S(═O)₂R⁵. In some embodiments, for a compound of Formula (I), R¹is C_1-6alkyl, C_2-6alkenyl, —C_1-6alkyl-OH, —C_1-6alkyl-OR⁵, —C_1-6alkyl-N(R⁶)₂, —O—C_1-6alkyl, —O—C_1-6alkyl-OH, —O—C_1-6alkyl-OR⁵, —O—C_1-6alkyl-N(R⁶)₂, or —S(═O)₂R⁵. In some embodiments, for a compound of Formula (I), R¹is —O—C_1-6alkyl, —O—C_1-6alkyl-N(R⁶)₂, or —S(═O)₂R⁵. In some embodiments, for a compound of Formula (I), R¹is —O—C_1-6alkyl. In some embodiments, for a compound of Formula (I), R¹is —OCH₃. In some embodiments, for a compound of Formula (I), R¹is —O—C_1-6alkyl-OR⁵. In some embodiments, for a compound of Formula (I), R¹is —OCH₂CH₂OCH₃. In some embodiments, for a compound of Formula (I), R¹is —O—C_1-6alkyl-N(R⁶)₂. In some embodiments, for a compound of Formula (I), R¹is —OCH₂CH₂CH₂morpholine. In some embodiments, for a compound of Formula (I), R¹is —S(═O)₂R⁵. In some embodiments, for a compound of Formula (I), R¹is —S(═O)₂tert-butyl.

In some embodiments, for a compound of Formula (I), R²is —H, halogen, —OH, —CN, —N(R⁶)₂, —NR⁶C(O)R⁵, —C(O)OR⁵, —C(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_3-8cycloalkyl, —C_1-6alkyl-OH, —C_1-6alkyl-N(R⁶)₂, —O—C_1-6alkyl, —O—C_1-6alkyl-OH, —O—C_1-6alkyl-OR⁵, —O—C_1-6alkyl-N(R⁶)₂, or —S(═O)₂R⁵. In some embodiments, for a compound of Formula (I), R²is —H, —O—C_1-6alkyl, —O—C_1-6alkyl-OR⁵, or —O—C_1-6alkyl-OH. In some embodiments, for a compound of Formula (I), R²is —H. In some embodiments, for a compound of Formula (I), R²is —O—C_1-6alkyl. In some embodiments, for a compound of Formula (I), R²is —OCH₃. In some embodiments, for a compound of Formula (I), R²is —O—C_1-6alkyl-OR⁵. In some embodiments, for a compound of Formula (I), R²is —OCH₂CH₂OCH₃. In some embodiments, for a compound of Formula (I), R²is —O—C_1-6alkyl-OH. In some embodiments, for a compound of Formula (I), R²is —OCH₂CH₂OH.

In some embodiments, for a compound of Formula (I), R³is —H, halogen, —NO₂, —CN, —OH, —OR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (I), R³is —H, halogen, C_1-6alkyl, C_2-6alkynyl, or —O-phenyl. In some embodiments, for a compound of Formula (I), R³is —H. In some embodiments, for a compound of Formula (I), R³is —Cl. In some embodiments, for a compound of Formula (I), R³is —F. In some embodiments, for a compound of Formula (I), R³is —CH₃. In some embodiments, for a compound of Formula (I), R³is —CCH. In some embodiments, for a compound of Formula (I), R³is —O-phenyl.

In some embodiments, for a compound of Formula (I), n is 0, 1, 2, or 3. In some embodiments, for a compound of Formula (I), n is 1, 2, or 3. In some embodiments, for a compound of Formula (I), n is 1 or 2. In some embodiments, for a compound of Formula (I), n is 0. In some embodiments, for a compound of Formula (I), n is 1. In some embodiments, for a compound of Formula (I), n is 2. In some embodiments, for a compound of Formula (I), n is 3.

Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (Ia) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein;

each R³is independently —H, halogen, —C≡CH, or —O-aryl; and

each R⁵is independently C_1-6alkyl, —C_1-6alkyl-O—C_1-6alkyl, or —C_1-6alkyl-heterocycloalkyl.

Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (Ia) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein;

each R³is independently —H, —Cl, —F, —C≡CH, or —O-phenyl; and

each R⁵is independently —CH₃, —CH₂CH₂OCH₃, or —CH₂CH₂CH₂morpholine.

Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (Ib) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein;

Ring A is C_3-7heteroaryl;

X is N or CH;

R²is —H, —OC_1-6alkyl, or —O—C_1-6alkyl-OH;

each R³is independently —H, —C_1-6alkyl, or halogen; and

n is 0, 1, or 2.

Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (Ib) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein;

Ring A is C_3-7heteroaryl;

X is N or CH;

R²is —H, —OCH₃, or —OCH₂CH₂OH;

each R³is independently —H, —CH₃, or —F; and

n is 0, 1, or 2.

In some embodiments a compound of Formula (I) or a pharmaceutically acceptable salt or isotopic variant thereof has the structure of:

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Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (II) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein

- Rings A and B are independently C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, or 6- to 10-membered aryl;
- X¹, X², and X³are independently N or CR⁴;
- Y¹and Y²are independently a bond, —O—, —S—, —C(R⁵)₂, —NR⁶—, —NR⁶C(O)—, —C(O)NR⁶—, or —NR⁶C(O)NR⁶—;
- each R¹and R²is independently —H, halogen, —NO₂, —CN, —OH, —OR⁵, —SR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —SCH₂C(O)OR⁵, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷;
- each R⁴is independently —H, halogen, —N(R⁶)₂, —NO₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl, wherein the alkyl, haloalkyl, cycloalkyl, phenyl, heteroaryl, and heterocycloalkyl are optionally substituted;
- each R⁵is independently —H, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl;
- each R⁶is independently —H, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, or C_2-9heteroaryl; or two R⁶are taken together with the nitrogen atom to which they are attached to form a 5- or 6-membered heterocycle; and
- R⁷is —H, halogen, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl; and m and n are each independently 0, 1, 2, 3, 4, or 5.

In some embodiments, for a compound of Formula (II), Rings A and B are independently C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, or 6- to 10-membered aryl. In some embodiments, for a compound of Formula (II), Rings A and B are independently C_2-9heteroaryl or 6- to 10-membered aryl. In some embodiments, for a compound of Formula (II), Ring A is phenyl. In some embodiments, for a compound of Formula (II), Ring A is pyridyl. In some embodiments, for a compound of Formula (II), Ring A is furanyl. In some embodiments, for a compound of Formula (II), Ring B is phenyl. In some embodiments, for a compound of Formula (II), Ring B is pyrrazolyl. In some embodiments, for a compound of Formula (II), Ring B is pyridyl. In some embodiments, for a compound of Formula (II), Ring B is isoxazolyl. In some embodiments, for a compound of Formula (II), Ring A is phenyl and Ring B is pyrrazolyl. In some embodiments, for a compound of Formula (II), Ring A is phenyl and Ring B is phenyl. In some embodiments, for a compound of Formula (II), Ring A is phenyl and Ring B is pyridyl. In some embodiments, for a compound of Formula (II), Ring A is pyridyl and Ring B is phenyl. In some embodiments, for a compound of Formula (II), Ring A is pyridyl and Ring B is isoxazolyl. In some embodiments, for a compound of Formula (II), Ring A is isoxazolyl and Ring B is pyridyl. In some embodiments, for a compound of Formula (II), Ring A is furanyl and Ring B is phenyl.

In some embodiments, for a compound of Formula (II), X¹, X², and X³are independently N or CR⁴. In some embodiments, for a compound of Formula (II), X¹is CH. In some embodiments, for a compound of Formula (II), X¹is CF. In some embodiments, for a compound of Formula (II), X¹is CCH₃. In some embodiments, for a compound of Formula (II), X¹is CNH₂. In some embodiments, for a compound of Formula (II), X¹is N. In some embodiments, for a compound of Formula (II), X²is CH. In some embodiments, for a compound of Formula (II), X²is CF. In some embodiments, for a compound of Formula (II), X²is N. In some embodiments, for a compound of Formula (II), X²is C—N-methylpyrazine. In some embodiments, for a compound of Formula (II), X³is CH. In some embodiments, for a compound of Formula (II), X³is N. In some embodiments, for a compound of Formula (II), X¹is CF and X²and X³are CH. In some embodiments, for a compound of Formula (II), X²is CF and X¹and X³are CH. In some embodiments, for a compound of Formula (II), X¹, X², and X³are CH. In some embodiments, for a compound of Formula (II), X¹is CCH₃and X²and X³are CH. In some embodiments, for a compound of Formula (II), X¹is CNH₂, X²is N, and X³is CH. In some embodiments, for a compound of Formula (II), X²is C—N-methylpyrazine and X¹and X³are N.

In some embodiments, for a compound of Formula (II), Y¹and Y²are independently a bond, —O—, —S—, —NR⁶—, —NR⁶C(O)—, —C(O)NR⁶—, or —NR⁶C(O)NR⁶—. In some embodiments, for a compound of Formula (II), Y¹is —NR⁶C(O)—. In some embodiments, for a compound of Formula (II), Y¹is —O—. In some embodiments, for a compound of Formula (II), Y¹is —NR⁶C(O)NR⁶—. In some embodiments, for a compound of Formula (II), Y¹is a bond. In some embodiments, for a compound of Formula (II), Y¹is —NR⁶—. In some embodiments, for a compound of Formula (II), Y²is —NR⁶C(O)—. In some embodiments, for a compound of Formula (II), Y²is —O—. In some embodiments, for a compound of Formula (II), Y²is —NR⁶C(O)NR⁶—. In some embodiments, for a compound of Formula (II), Y²is a bond. In some embodiments, for a compound of Formula (II), Y¹is —S—. In some embodiments, for a compound of Formula (II), Y¹and Y²are —NHC(O)—. In some embodiments, for a compound of Formula (II), Y¹is —O— and Y²is —NHC(O)NH—. In some embodiments, for a compound of Formula (II), Y¹is —NHC(O)NH— and Y²is —O—. In some embodiments, for a compound of Formula (II), Y¹and Y²are bonds. In some embodiments, for a compound of Formula (II), Y¹is —NH— and Y²is —S—.

In some embodiments, for a compound of Formula (II), R¹is —H, halogen, —NO₂, —CN, —OH, —OR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (II), R¹is —Cl. In some embodiments, for a compound of Formula (II), R¹is —F. In some embodiments, for a compound of Formula (II), R¹is —C(O)NHCH₃. In some embodiments, for a compound of Formula (II), R¹is 2-methylpyrrazolyl. In some embodiments, for a compound of Formula (II), R¹is N-methylimidazolyl. In some embodiments, for a compound of Formula (II), R¹is tert-butyl. In some embodiments, for a compound of Formula (II), R¹is —NHC(O)cyclopropyl. In some embodiments, for a compound of Formula (II), R¹is —SCH₂C(O)OH. In some embodiments, for a compound of Formula (II), R¹is —OCH₃. In some embodiments, for a compound of Formula (II), R¹is —NHS(═O)₂CH₂CH₂CH₃.

In some embodiments, for a compound of Formula (II), R²is —H, halogen, —NO₂, —CN, —OH, —OR⁵, —SR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (II), R²is —Cl. In some embodiments, for a compound of Formula (II), R²is —F. In some embodiments, for a compound of Formula (II), R²is —C(O)NHCH₃. In some embodiments, for a compound of Formula (II), R¹is 2-methylpyrrazolyl. In some embodiments, for a compound of Formula (II), R¹is N-methylimidazolyl. In some embodiments, for a compound of Formula (II), R²is —CH₂-(2-iso-propylimidazole). In some embodiments, for a compound of Formula (II), R²is tert-butyl. In some embodiments, for a compound of Formula (II), R²is —CH₃. In some embodiments, for a compound of Formula (II), R²is —C(O)NHCH₃. In some embodiments, for a compound of Formula (II), R²is pyrazinyl.

In some embodiments, for a compound of Formula (II), m is 1 or 2. In some embodiments, for a compound of Formula (II), m is 1. In some embodiments, for a compound of Formula (II), m is 2. In some embodiments, for a compound of Formula (II), n is 1 or 2. In some embodiments, for a compound of Formula (II), n is 1. In some embodiments, for a compound of Formula (II), n is 2.

Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (IIa) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein

Ring A is phenyl or isoxazolyl;

each R¹is independently C_1-6alkyl, halogen, —C_1-6fluoroalkyl, or —S—C_1-6alkyl-C(O)OH;

R²is —H or —C(O)NHCH₃;

R⁴is —H or halogen; and

m is 1 or 2.

Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (IIa) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein

Ring A is phenyl or isoxazolyl;

each R¹is independently tert-butyl, —Cl, —F, —CF₃, or —SCH₂C(O)OH;

R²is —H or —C(O)NHCH₃;

R⁴is —H or halogen; and

m is 1 or 2.

Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (IIb) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein

R¹is halogen or —OR⁵.

In some embodiments a compound of Formula (II) or a pharmaceutically acceptable salt or isotopic variant thereof has the structure of:

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Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (III) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein

- X is N or CR⁴;
- Y is a bond, —O—, —S—, —C(R⁵)₂, —NR⁶—, —NR⁶C(O)—, —C(O)NR⁶—, or —NR⁶C(O)NR⁶—; R¹is —H, halogen, —OH, —CN, —N(R⁶)₂, —NR⁶C(O)R⁵, —C(O)OR⁵, —C(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_3-8cycloalkyl, —C_1-6alkyl-OH, —C_1-6alkyl-OR⁵, —C_1-6alkyl-N(R⁶)₂, —O—C_1-6alkyl, —O—C_1-6alkyl-OH, —O—C_1-6alkyl-OR⁵, —O—C_1-6alkyl-N(R⁶)₂, or —S(═O)₂R⁵;
- R²and R³are independently —H, halogen, —NO₂, —CN, —OH, —OR⁵, —SR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷; or
  - R²and R³are taken together with the atoms to which they are attached to form an optionally substituted C_3-8cycloalkyl; and
- R⁴is hydrogen, halogen, —N(R⁶)₂, —NO₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl, wherein the alkyl, haloalkyl, cycloalkyl, phenyl, heteroaryl, and heterocycloalkyl are optionally substituted;
- R⁵is —H, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl;
- each R⁶is independently —H, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, or C_2-9heteroaryl; or
  - two R⁶substituents are taken together with the nitrogen atom to which they are attached to form a 5- or 6-membered heterocycle; and
- R⁷is —H, halogen, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl.

In some embodiments, for a compound of Formula (III), X is N or CR⁴. In some embodiments, for a compound of Formula (III), X is N and CH. In some embodiments, for a compound of Formula (III), X is N. In some embodiments, for a compound of Formula (III), X is CH.

In some embodiments, for a compound of Formula (III), Y is a bond, —O—, —S—, —C(R⁵)₂, —NR⁶—, —NR⁶C(O)—, —C(O)NR⁶—, or —NR⁶C(O)NR⁶—. In some embodiments, for a compound of Formula (III), Y is —NR⁶C(O)— or —C(O)NR⁶—. In some embodiments, for a compound of Formula (III), Y is —NHC(O)—. In some embodiments, for a compound of Formula (III), Y is —C(O)NH—.

In some embodiments, for a compound of Formula (III), R¹is —H, halogen, —OH, —CN, —N(R⁶)₂, —NR⁶C(O)R⁵, —C(O)OR⁵, —C(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_3-8cycloalkyl, —C_1-6alkyl-OH, —C_1-6alkyl-OR⁵, —C_1-6alkyl-N(R⁶)₂, —O—C_1-6alkyl, —O—C_1-6alkyl-OH, —O—C_1-6alkyl-OR⁵, —O—C_1-6alkyl-N(R⁶)₂, or —S(═O)₂R⁵. In some embodiments, for a compound of Formula (III), R¹is —H, halogen, —OH, —CN, —N(R⁶)₂, C_1-6alkyl, C_2-6alkynyl, or C_3-8cycloalkyl. In some embodiments, for a compound of Formula (III), R¹is C_1-6alkyl. In some embodiments, for a compound of Formula (III), R¹is —CH₃. In some embodiments, for a compound of Formula (III), R¹is tert-butyl.

In some embodiments, for a compound of Formula (III), R²is —H, halogen, —NO₂, —CN, —OH, —OR⁵, —SR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷, or R²and R³are taken together with the atoms to which they are attached to form an optionally substituted C_3-8cycloalkyl. In some embodiments, for a compound of Formula (III), R²is —H, halogen, —NO₂, —CN, —OH, —OR⁵, C_1-6alkyl, C_1-6haloalkyl, C_1-6heteroalkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, or 6- to 10-membered aryl, or R²and R³are taken together with the atoms to which they are attached to form an optionally substituted C_3-8cycloalkyl. In some embodiments, for a compound of Formula (III), R²is C_1-6alkyl, C_1-6haloalkyl, or C_3-8cycloalkyl, or R²and R³are taken together with the atoms to which they are attached to form an optionally substituted C_3-8cycloalkyl. In some embodiments, for a compound of Formula (III), R²is —CH₃, —CF₃, or cyclopropyl, or R²and R³are taken together with the atoms to which they are attached to form an optionally substituted C_3-8cycloalkyl. In some embodiments, for a compound of Formula (III), R²is —CH₃, —CF₃, or cyclopropyl. In some embodiments, for a compound of Formula (III), R²is —CH₃. In some embodiments, for a compound of Formula (III), R²is —CF₃. In some embodiments, for a compound of Formula (III), R²is cyclopropyl. In some embodiments, for a compound of Formula (III), R²and R³are taken together with the atoms to which they are attached to form a C₅cycloalkyl. In some embodiments, for a compound of Formula (III), R²and R³are taken together with the atoms to which they are attached to form a C₅cycloalkyl substituted with an N-methylpiperazine.

In some embodiments, for a compound of Formula (III), R³is —H, halogen, —NO₂, —CN, —OH, —OR⁵, —SR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷, or R²and R³are taken together with the atoms to which they are attached to form an optionally substituted C_3-8cycloalkyl. In some embodiments, for a compound of Formula (III), R³is —H, halogen, —CN, —OR⁵, —N(R⁶)₂, —S(═O)₂R⁵, —C(O)R⁵, —C(O)OR⁵, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_1-6heteroalkyl, C_2-9heterocycloalkyl, or C_2-9heteroaryl, wherein each alkyl, heteroalkyl, heterocycloalkyl, and heteroaryl is optionally substituted with one or more R⁷, or R²and R³are taken together with the atoms to which they are attached to form an optionally substituted C_3-8cycloalkyl. In some embodiments, for a compound of Formula (III), R³is C_1-6alkyl substituted with C_2-9heterocycloalkyl. In some embodiments, for a compound of Formula (III), R³is CH₂—N-methylpiperazine. In some embodiments, for a compound of Formula (III), R²and R³are taken together with the atoms to which they are attached to form a C₅cycloalkyl. In some embodiments, for a compound of Formula (III), R²and R³are taken together with the atoms to which they are attached to form a C₅cycloalkyl substituted with an N-methylpiperazine.

Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (III) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein

R¹is C_1-6alkyl.

In some embodiments a compound of Formula (III) or a pharmaceutically acceptable salt or isotopic variant thereof has the structure of:

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Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (IV) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein

- Ring A is C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, or 6- to 10-membered aryl;
- Y is a bond, —O—, —S—, —C(R⁵)₂—, —NR⁶—, —NR⁶C(O)—, —C(O)NR⁶—, or —NR⁶C(O)NR⁶—; R¹is —H, halogen, —OH, —CN, —N(R⁶)₂, —NR⁶C(O)R⁵, —C(O)OR⁵, —C(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_3-8cycloalkyl, —C_1-6alkyl-OH, —C_1-6alkyl-OR⁵, —C_1-6alkyl-N(R⁶)₂, —O—C_1-6alkyl, —O—C_1-6alkyl-OH, —O—C_1-6alkyl-OR⁵, —O—C_1-6alkyl-N(R⁶)₂, or —S(═O)₂R⁵;
- R²is —H, halogen, —NO₂, —CN, —OH, —OR⁵, —SR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷;
- R⁵is —H, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl;
- each R⁶is independently —H, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, or C_2-9heteroaryl; or two R⁶substituents are taken together with the nitrogen atom to which they are attached to form a 5- or 6-membered heterocycle;
- R⁷is —H, halogen, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl; and
- n is 0, 1, 2, 3, 4, or 5.

In some embodiments, for a compound of Formula (IV), Ring A is C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, or 6- to 10-membered aryl. In some embodiments, for a compound of Formula (IV), Ring A is 6- to 10-membered aryl. In some embodiments, for a compound of Formula (IV), Ring A is phenyl. In some embodiments, for a compound of Formula (IV), Ring A is naphthyl.

In some embodiments, for a compound of Formula (IV), Y is a bond, —O—, —S—, —C(R⁵)₂—, —NR⁶—, —NR⁶C(O)—, —C(O)NR⁶—, or —NR⁶C(O)NR⁶—. In some embodiments, for a compound of Formula (IV), Y is a bond or —C(R⁵)₂—. In some embodiments, for a compound of Formula (IV), Y is a bond. In some embodiments, for a compound of Formula (IV), Y is —CH₂—.

In some embodiments, for a compound of Formula (IV), R¹is —H, halogen, —OH, —CN, —N(R⁶)₂, —NR⁶C(O)R⁵, —C(O)OR⁵, —C(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_3-8cycloalkyl, —C_1-6alkyl-OH, —C_1-6alkyl-OR⁵, —C_1-6alkyl-N(R⁶)₂, —O—C_1-6alkyl, —O—C_1-6alkyl-OH, —O—C_1-6alkyl-OR⁵, —O—C_1-6alkyl-N(R⁶)₂, or —S(═O)₂R⁵. In some embodiments, for a compound of Formula (IV), R¹is —H, halogen, or C_1-6alkyl. In some embodiments, for a compound of Formula (IV), R¹is —H, —Cl, or CH₃. In some embodiments, for a compound of Formula (IV), R¹is —H. In some embodiments, for a compound of Formula (IV), R¹is —Cl. In some embodiments, for a compound of Formula (IV), R¹is —CH₃.

In some embodiments, for a compound of Formula (IV), R²is —H, halogen, —NO₂, —CN, —OH, —OR⁵, —SR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (IV), R²is —H or —NR⁶C(O)R⁵. In some embodiments, for a compound of Formula (IV), R²is —H or —NR⁶C(O)C_2-9heteroaryl. In some embodiments, for a compound of Formula (IV), R²is —H. In some embodiments, for a compound of Formula (IV), R²is —NHC(O)pyridyl.

In some embodiments, for a compound of Formula (IV), n is 1, 2, or 3. In some embodiments, for a compound of Formula (IV), n is 1 or 2. In some embodiments, for a compound of Formula (IV), n is 1. In some embodiments, for a compound of Formula (IV), n is 2. In some embodiments, for a compound of Formula (IV), n is 3.

Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (IVa) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein

R¹is halogen or C_1-6alkyl.

Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (IVb) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein Y is a bond or —C_1-3alkyl-.

Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (IVb) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein

Y is a bond or —CH₂—.

In some embodiments a compound of Formula (IV) or a pharmaceutically acceptable salt or isotopic variant thereof has the structure of:

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Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (V) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein

- X¹and X²are independently N or CR⁴;
- Y is S, O, or NR¹;
- R¹is —H, —S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —C(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, or 6- to 10-membered aryl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷;
- R²is —H, halogen, —NO₂, —CN, —OH, —OR⁵, —SR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷; or
  - R¹and R²are taken together with the atoms to which they are attached to form an optionally substituted C_3-8heterocycloalkyl; and
- R³and R⁴are independently —H, halogen, —NO₂, —CN, —OH, —OR⁵, —SR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷;
- R⁵is —H, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl;
- each R⁶is independently —H, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, or C_2-9heteroaryl; or
  - two R⁶substituents are taken together with the nitrogen atom to which they are attached to form a 5- or 6-membered heterocycle; and
- R⁷is —H, halogen, —S(═O)CH₃, —N(R⁶)₂, —C(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl.

In some embodiments, for a compound of Formula (V), X¹and X²are independently N or CR⁴. In some embodiments, for a compound of Formula (V), X¹is N. In some embodiments, for a compound of Formula (V), X¹is CR⁴. In some embodiments, for a compound of Formula (V), X²is N. In some embodiments, for a compound of Formula (V), X²is CR⁴. In some embodiments, for a compound of Formula (V), X¹is N and X²is CR⁴. In some embodiments, for a compound of Formula (V), X¹is CR⁴and X²is N.

In some embodiments, for a compound of Formula (V), Y is S, O, or NR¹. In some embodiments, for a compound of Formula (V), Y is S. In some embodiments, for a compound of Formula (V), Y is NH. In some embodiments, for a compound of Formula (V), Y is NR¹.

In some embodiments, for a compound of Formula (V), R¹is —H, —S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —C(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, or 6- to 10-membered aryl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (V), R¹is —H, C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, or 6- to 10-membered aryl, wherein each cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (V), R¹is aryl optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (V), R¹is 2,4-dichlorophenyl.

In some embodiments, for a compound of Formula (V), R²is —H, halogen, —NO₂, —CN, —OH, —OR⁵, —SR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷, or R¹and R²are taken together with the atoms to which they are attached to form an optionally substituted C_3-8heterocycloalkyl. In some embodiments, for a compound of Formula (V), R²is —H, halogen, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —C(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷, or R¹and R²are taken together with the atoms to which they are attached to form an optionally substituted C_3-8heterocycloalkyl. In some embodiments, for a compound of Formula (V), R²is —C(O)N(R⁶)₂or 6-membered aryl optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (V), R²is 4-fluorophenyl. In some embodiments, for a compound of Formula (V), R²is 4-chlorophenyl. In some embodiments, for a compound of Formula (V), R²is 2-methylpyridinyl. In some embodiments, for a compound of Formula (V), R²is —C(O)NH-(2-methyl-6-chlorophenyl). In some embodiments, for a compound of Formula (V), R¹and R²are taken together with the atoms to which they are attached to form an optionally substituted C_3-8heterocycloalkyl. In some embodiments, for a compound of Formula (V), R¹and R²are taken together with the atoms to which they are attached to form a C₅heterocycloalkyl.

In some embodiments, for a compound of Formula (V), R³is —H, halogen, —NO₂, —CN, —OH, —OR⁵, —SR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (V), R³is —H, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (V), R³is —H or C_2-9heteroaryl optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (V), R³is H. In some embodiments, for a compound of Formula (V), R³is C_2-9heteroaryl optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (V), R³is optionally substituted pyridinyl. In some embodiments, for a compound of Formula (V), R³is optionally substituted quinolinyl. In some embodiments, for a compound of Formula (V), R³is optionally substituted [1,2,4]triazolopyridinyl.

In some embodiments, for a compound of Formula (V), R⁴is —H, halogen, —NO₂, —CN, —OH, —OR⁵, —SR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (V), R⁴is —H, —N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (V), R⁴is —N(R⁶)₂, C_1-6alkyl, C_2-9heteroaryl, or 6- to 10-membered aryl, wherein each aryl and heteroaryl is optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (V), R⁴is optionally substituted phenyl. In some embodiments, for a compound of Formula (V), R⁴is optionally substituted pyridyl. In some embodiments, for a compound of Formula (V), R⁴is —NHpyrimidine. In some embodiments, for a compound of Formula (V), R⁴is —CH₂phenyl. In some embodiments, for a compound of Formula (V), R⁴is CH₂NHphenyl.

In some embodiments a compound of Formula (V) or a pharmaceutically acceptable salt or isotopic variant thereof has the structure of:

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Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (VI) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein

- X¹and X²are independently N or C;
- X³is N or CR⁴;
- Y is a bond, —O—, —S—, —C(R⁵)₂, —NR⁶—, —NR⁶C(O)—, —C(O)NR⁶—, or —NR⁶C(O)NR⁶—;
- R is —H, halogen, —NO₂, —CN, —OH, —OR⁵, —SR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷;
- R⁴is —H, halogen, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl, wherein the alkyl, haloalkyl, cycloalkyl, phenyl, heteroaryl, and heterocycloalkyl are optionally substituted;
- R⁵is —H, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl;
- each R⁶is independently —H, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, or C_2-9heteroaryl; or two R⁶are taken together with the nitrogen atom to which they are attached to form a 5- or 6-membered heterocycle; and
- R⁷is —H, halogen, —S(═O)CH₃, —N(R⁶)₂, —C(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl.

In some embodiments, for a compound of Formula (VII), X¹and X²are independently N or C. In some embodiments, for a compound of Formula (VII), X¹is N. In some embodiments, for a compound of Formula (VII), X¹is C. In some embodiments, for a compound of Formula (VII), X²is N. In some embodiments, for a compound of Formula (VII), X²is C. In some embodiments, for a compound of Formula (VII), X¹is N and X²is C. In some embodiments, for a compound of Formula (VII), X¹is C and X²is N.

In some embodiments, for a compound of Formula (VII), X³is N or CR⁴. In some embodiments, for a compound of Formula (VII), X³is N or CH. In some embodiments, for a compound of Formula (VII), X³is N. In some embodiments, for a compound of Formula (VII), X³is CH.

In some embodiments, for a compound of Formula (VI), Y is a bond, —O—, —S—, —C(R⁵)₂, —NR⁶—, —NR⁶C(O)—, —C(O)NR⁶—, or —NR⁶C(O)NR⁶—. In some embodiments, for a compound of Formula (VI), Y is —O— or —NR⁶—. In some embodiments, for a compound of Formula (VI), Y is —O— or —NH—. In some embodiments, for a compound of Formula (VI), Y is —O—. In some embodiments, for a compound of Formula (VI), Y is —NH—.

In some embodiments, for a compound of Formula (VI), R is —H, halogen, —NO₂, —CN, —OH, —OR⁵, —SR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (VI), R is —H, halogen, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_1-6heteroalkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (VI), R is —H or halogen. In some embodiments, for a compound of Formula (VI), R is —H. In some embodiments, for a compound of Formula (VI), R is —Cl.

In some embodiments a compound of Formula (VI) or a pharmaceutically acceptable salt or isotopic variant thereof has the structure of:

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Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (VII) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein

- X¹and X²are independently N or C;
- X³is N or CR⁴;
- Y is a bond, —O—, —S—, —C(R⁵)₂, —NR⁶—, —NR⁶C(O)—, —C(O)NR⁶—, or —NR⁶C(O)NR⁶—;
- R¹and R²are independently —H, halogen, —OH, —CN, —N(R⁶)₂, —NR⁶C(O)R⁵, —C(O)OR⁵, —C(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_3-8cycloalkyl, —C_1-6alkyl-OH, —C_1-6alkyl-OR⁵, —C_1-6alkyl-N(R⁶)₂, —O—C_1-6alkyl, —O—C_1-6alkyl-OH, —O—C_1-6alkyl-OR⁵, —O—C_1-6alkyl-N(R⁶)₂, or —S(═O)₂R⁵;
- R³is —H, halogen, —NO₂, —CN, —OH, —OR⁵, —SR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷;
- R⁴is —H, halogen, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl, wherein the alkyl, haloalkyl, cycloalkyl, phenyl, heteroaryl, and heterocycloalkyl are optionally substituted;
- R⁵is —H, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl;
- each R⁶is independently —H, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, or C_2-9heteroaryl; or two R⁶substituents are taken together with the nitrogen atom to which they are attached to form a 5- or 6-membered heterocycle;
- R⁷is —H, halogen, —S(═O)CH₃, —N(R⁶)₂, —C(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, C_3-8cycloalkyl, —C_1-6alkyl-C_3-8cycloalkyl, phenyl, —C_1-6alkyl-phenyl, C_2-9heterocycloalkyl, —C_1-6alkyl-C_2-9heterocycloalkyl, C_2-9heteroaryl, or —C_1-6alkyl-C_2-9heteroaryl; and
- n is 0, 1, 2, 3, 4, or 5.

In some embodiments, for a compound of Formula (VII), Y is a bond, —O—, —S—, —C(R⁵)₂, —NR⁶—, —NR⁶C(O)—, —C(O)NR⁶—, or —NR⁶C(O)NR⁶—. In some embodiments, for a compound of Formula (VII), Y is a bond, —NR⁶C(O)—, or —C(O)NR⁶—. In some embodiments, for a compound of Formula (VII), Y is a bond, —NHC(O)—, or —C(O)NH—. In some embodiments, for a compound of Formula (VII), Y is a bond. In some embodiments, for a compound of Formula (VII), Y is —NHC(O)—. In some embodiments, for a compound of Formula (VII), Y is —C(O)NH—.

In some embodiments, for a compound of Formula (VII), R¹is —H, halogen, —OH, —CN, —N(R⁶)₂, —NR⁶C(O)R⁵, —C(O)OR⁵, —C(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_3-8cycloalkyl, —C_1-6alkyl-OH, —C_1-6alkyl-OR⁵, —C_1-6alkyl-N(R⁶)₂, —O—C_1-6alkyl, —O—C_1-6alkyl-OR⁵, —O—C_1-6alkyl-N(R⁶)₂, or —S(═O)₂R⁵. In some embodiments, for a compound of Formula (VII), R¹is —H, halogen, —N(R⁶)₂, —NR⁶C(O)R⁵, C_1-6alkyl, C_3-8cycloalkyl, —C_1-6alkyl-OR⁵, —C_1-6alkyl-N(R⁶)₂, —O—C_1-6alkyl-N(R⁶)₂, or —S(═O)₂R⁵. In some embodiments, for a compound of Formula (VII), R¹is —H or —S(═O)₂R⁵. In some embodiments, for a compound of Formula (VII), R¹is —H. In some embodiments, for a compound of Formula (VII), R¹is —S(═O)₂iso-propyl. In some embodiments, for a compound of Formula (VII), R¹is —S(═O)₂tert-butyl.

In some embodiments, for a compound of Formula (VII), R²is —H, halogen, —OH, —CN, —N(R⁶)₂, —NR⁶C(O)R⁵, —C(O)OR⁵, —C(O)N(R⁶)₂, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_3-8cycloalkyl, —C_1-6alkyl-OH, —C_1-6alkyl-N(R⁶)₂, —O—C_1-6alkyl, —O—C_1-6alkyl-OH, —O—C_1-6alkyl-OR⁵, —O—C_1-6alkyl-N(R⁶)₂, or —S(═O)₂R⁵. In some embodiments, for a compound of Formula (VII), R²is —H, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_3-8cycloalkyl, —O—C_1-6alkyl-OH, or —O—C_1-6alkyl-OR⁵. In some embodiments, for a compound of Formula (VII), R²is —H or —O—C_1-6alkyl. In some embodiments, for a compound of Formula (VII), R²is —H. In some embodiments, for a compound of Formula (VII), R²is —OCH₃. In some embodiments, for a compound of Formula (VII), R²is —OCH₂CH₃.

In some embodiments, for a compound of Formula (VII), R³is —H, halogen, —NO₂, —CN, —OH, —OR⁵, —N(R⁶)₂, —S(O)R⁵, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —C(O)R⁵, —C(O)OR⁵, —OC(O)R⁵, —C(O)N(R⁶)₂, —OC(O)N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-6haloalkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, 6- to 10-membered aryl, or —O-phenyl, wherein each alkyl, haloalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (VII), R³is —H, halogen, —N(R⁶)₂, —S(═O)₂R⁵, —NR⁶S(═O)₂R⁵, —S(═O)₂N(R⁶)₂, —NR⁶C(O)N(R⁶)₂, —NR⁶C(O)R⁵, —NR⁶C(O)OR⁵, C_1-6alkyl, C_1-6heteroalkyl, —O—C_1-6alkyl, C_3-8cycloalkyl, C_2-9heterocycloalkyl, C_2-9heteroaryl, or 6- to 10-membered aryl, wherein each alkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, aryl, and heteroaryl is optionally substituted with one or more R⁷. In some embodiments, for a compound of Formula (VII), R³is —H, halogen, —N(R⁶)₂, or C_1-6alkyl. In some embodiments, for a compound of Formula (VII), R³is —H. In some embodiments, for a compound of Formula (VII), R³is —Cl. In some embodiments, for a compound of Formula (VII), R³is —F. In some embodiments, for a compound of Formula (VII), R³is —CH₃.

In some embodiments a compound of Formula (VII) or a pharmaceutically acceptable salt or isotopic variant thereof has the structure of:

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Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (VIII) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein:

HET is

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- X is N and Y is CH; or
  - X is CH and Y is N;
- R¹is —H, or —F;
- R²is C_1-3alkyl, —Cl, or —F;
- R³and R⁴are each independently —H; —OR⁵; —O—C_1-6alkyl-O—C_1-3alkyl; —O—C_3-6cycloalkyl; —C(O)R⁵, C_1-6alkyl optionally substituted with one to three —OH, —F, C_3-8heterocycloalkyl optionally substituted with oxo, C_3-6cycloalkyl, —C(O)OR⁵, —O—C_1-6alkyl, aryl, —N(R⁵)(R⁶), —CN, or —C(O)N(R⁵)(R⁶); C_3-6cycloalkyl optionally substituted with one to three —OH, one to three —F, C_1-6alkyl, C_1-6alkyl-OC_1-6alkyl, C_1-6alkyl-OH, —CF₃, —CN, —OC_3-6cycloalkyl, —C(O)OH, —C(O)OR⁵, C_3-6cycloalkyl, 5-6 membered heteroaryl, C_3-6heterocycloalkyl, N(R⁵)(R⁶), or —C(O)N(R⁵)(R⁶); —C(O)OR⁵; —C(O)N(R⁵)(R⁶); —S(═O)₂N(R⁵)(R⁶); —S(O)_n—R⁵; a 4-10 membered monocyclic, bicyclic, or spirocyclic heterocyclyl group containing nitrogen, sulfur, or oxygen and optionally substituted with one to three —N(R⁵)(R⁶), halogen, —C_1-6alkyl, —O—C_1-6alkyl, or —C_1-6haloalkyl; aryl; —N(R⁵)(R⁶); or halogen;
- R⁵and R⁶are each independently —H; —C_1-6alkyl-C_3-8heterocycloalkyl; a 4-6 membered heterocycloalkyl wherein the heterocycloalkyl ring is optionally substituted with one to three C_1-6alkyl, —OC_1-6alkyl, —C_1-6haloalkyl, C_1-6cycloalkyl, halogen, acyl, heterocycloalkyl, heterocycloalkyl-C_1-6alkyl, heterocycloalkyl-O—C_1-6alkyl, heterocycloalkyl-OH, heterocycloalkyl-C(O)CH₃, heterocycloalkyl-C(O)OC_1-3alkyl, —C_1-6alkyl-heterocycloalkyl, —C_1-6alkyl-heterocycloalkyl-C_1-6alkyl, —C_1-6alkyl-OH, —C_1-6alkyl-O—C_1-6alkyl, C_3-6cycloalkyl, —C_1-6alkyl-cycloalkyl, C_3-6cycloalkyl-C_1-6alkyl, C_3-6cycloalkyl-O—C_1-6alkyl, or C_3-6cycloalkyl-O—C_1-6alkyl-OH; acyl; C_3-6cycloalkyl-C(O)—C_1-3alkyl; —C(O)—C_1-3alkyl-O—CH₃; —C(O)—C_1-3alkyl; —C(O)—C_3-6cycloalkyl; —C(O)—NH—C_1-3alkyl; —C(O)—NH—C_1-3alkyl; —C(O)—NH—C_3-6cycloalkyl optionally monosubstituted or disubstituted with —C_1-3alkyl-OH, —C(O)—NH—C_3-6heterocyclyl, —C(O)-aryl, —C(O)— heteroaryl, or —S(O)_n—C_1-3alkyl; and C_1-6alkyl optionally substituted with —OH, O—C_1-3alkyl, C_3-6cycloalkyl, heterocyclyl, aryl, —NH—C_1-3alkyl, or —N—(C_1-3alkyl)₂; or
  - R⁵and R⁶together with the nitrogen atom to which they are attached form a 5-6 membered heterocyclic ring optionally substituted with methyl; and
- n is 0, 1, or 2.

In some embodiments, for a compound of Formula (VIII), HET is

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X is N, Y is CH, and n is 1 or 2. In some embodiments, for a compound of Formula (VIII), HET is

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X is N, Y is CH, R²is —CH₃or —Cl, R⁴is H, and n is 2. In some embodiments, for a compound of Formula (VIII), HET is

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X is N, Y is CH, R²is —CH₃or —Cl, and n is 2. In some embodiments, for a compound of Formula (VIII), HET is

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In some embodiments, for a compound of Formula (VIII), HET is

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X is CH, Y is N, R²is —CH₃or —Cl, and n is 2. In some embodiments, for a compound of Formula (VIII), HET is

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X is CH, Y is N, R²is —CH₃or —Cl, R⁴is —H, and n is 2. In some embodiments, for a compound of Formula (VIII), HET is

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X is CH, Y is N, R²is —CH₃or —Cl, R⁴is —H, and n is 2.

In some embodiments, for a compound of Formula (VIII), HET is

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X is N, Y is CH, R¹is —F, and R²is —CH₃. In some embodiments, for a compound of Formula (VIII), HET is

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X is N, Y is CH, le is —F, and R²is —CH₃. In some embodiments, for a compound of Formula (VIII), HET is

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X is N, Y is CH, R¹is —F, and R²is —CH₃.

In some embodiments, for a compound of Formula (VIII), HET is

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X is N, Y is CH, R²is —CH₃or —Cl, R⁴is H, and n is 2. In some embodiments, for a compound of Formula (VIII), HET is

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X is N, and Y is CH. In some embodiments, for a compound of Formula (VIII), HET is

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X is CH, and Y is N. In some embodiments, for a compound of Formula (VIII), HET is

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X is CH, and Y is N.

In some embodiments, for a compound of Formula (VIII), HET is

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X is N, Y is CH, R²is —CH₃or —Cl, R⁴is H, and n is 2.

In some embodiments, a compound of Formula (VIII), or a pharmaceutically acceptable salt or isotopic variant thereof, has the structure of:

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Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (IX), or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein

- R is —H; or
- R is

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- available ring position;
- A and D are independently N or CH;
- E is N, CH, or CR;
- B and C are independently N, CH, or C—Cl;
- R¹is H; or
- R¹is C—Cl, C—F, C—OCH₃, C—C(CH₃)₃, or C—OH at one available ring position; and
- X—Y are C═C or

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wherein R²is —H, C_1-6alkyl, C_1-6alkyl-OH, C_1-6alkyl-OC_1-6alkyl, or C_1-6alkyl-aryl.

In some embodiments, for a compound of Formula (IX), R²is methyl, ethyl, isobutyl, 2-hydroxyethyl, 2-methoxyethyl, benzyl, or phenethyl. In some embodiments, for a compound of Formula (IX), R²is methyl. In some embodiments, for a compound of Formula (IX), R²is ethyl. In some embodiments, for a compound of Formula (IX), R²is isobutyl. In some embodiments, for a compound of Formula (IX), R²is 2-hydroxyethyl. In some embodiments, for a compound of Formula (IX), R²is 2-methoxyethyl. In some embodiments, for a compound of Formula (IX), R²is benzyl. In some embodiments, for a compound of Formula (IX), R²is phenethyl.

In some embodiments, a compound of Formula (IX), or a pharmaceutically acceptable salt and isotopic variant thereof, has the structure of:

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Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (IXa) or a pharmaceutically acceptable salt and isotopic variant thereof:

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wherein

- R is —H,

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- R¹is C_1-6alkyl or 6- to 10-membered aryl;
- A and D are independently N or CH;
- E is N, CH, or CR;
- B and C are independently N, CH, or C—Cl;
- R³is H; or
- R³is C—Cl, C—F, C—OCH₃, C—C(CH₃)₃, or C—OH at one available ring position; and
- X—Y are C═C or

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wherein R²is —H, C_1-6alkyl, C_1-6alkyl-OH, C_1-6alkyl-OC_1-6alkyl, or C_1-6alkyl-aryl.

In some embodiments, for a compound of Formula (IXa), R¹is methyl, ethyl, or propyl. In some embodiments, for a compound of Formula (IXa), R¹is methyl. In some embodiments, for a compound of Formula (IXa), R¹is ethyl. In some embodiments, for a compound of Formula (IXa), R¹is propyl.

In some embodiments, for a compound of Formula (IXa), R²is methyl, ethyl, isobutyl, 2-hydroxyethyl, 2-methoxyethyl, benzyl, or phenethyl. In some embodiments, for a compound of Formula (IXa), R²is methyl. In some embodiments, for a compound of Formula (IXa), R²is ethyl. In some embodiments, for a compound of Formula (IXa), R²is isobutyl. In some embodiments, for a compound of Formula (IXa), R²is 2-hydroxyethyl. In some embodiments, for a compound of Formula (IXa), R²is 2-methoxyethyl. In some embodiments, for a compound of Formula (IXa), R²is benzyl. In some embodiments, for a compound of Formula (IXa), R²is phenethyl.

Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (X), or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein

- Cy is C_3-8cycloalkyl, C_2-9heterocycloalkyl, 6- to 10-membered aryl, or C_2-9heteroaryl;
- Y is absent, —CR^bR^b—, —O—, —NR^b—, or —S(O)_n—;
- R¹is C_3-8cycloalkyl, C_2-9heterocycloalkyl, 6- to 10-membered aryl, or C_2-9heteroaryl, each of which is optionally substituted with one to three R^a;
- R³is —H, C_2-9heterocycloalkyl, or C_2-9heteroaryl, wherein the heterocycloalkyl and heteroaryl are optionally substituted with one to three —F, —Cl, —Br, I, —CN, —NO₂, —OR^b, C_1-4alkyl, —C_1-3alkyl-OR^b, —C_1-3alkyl-NR^bR^b, C_1-4haloalkyl, C_1-4haloalkoxy, C_3-8cycloalkyl, —NR^bR^b, —C(O)NR^bR^b, —NR^bC(O)NR^bR^b, —S(O)_nNR^bR^b, C(O)OR^b, —OC(O)OR^b, —S(O)_nR^b, —NR^bS(O)_nR^b, —C(S)OR^b, —OC(S)R^b, —NR^bC(O)R^b, —C(S)NR^bR^b, —NR^bC(S)R^b, —NR^bC(O)OR^b, —OC(O)NR^bR^b, —NR^bC(S)OR^b, —OC(S)NR^bR^b, —NRC(S)NR^bR^b, —C(S)R^b, or —C(O)R^b;
- each R⁴is independently halogen, —CN, —NR^bR^b, —OR^b, C_1-4alkyl, —C_1-3alkyl-OR^b, —C_1-3alkyl-NR^bR^b, C_1-4haloalkyl, or C_1-4haloalkoxy;
  - each R^ais independently —F, —Cl, —Br, I, —CN, OR^b, C_1-4alkyl, C_2-6alkenyl, C_2-6alkynyl, C_1-4haloalkyl, C_1-4haloalkoxy, —C_1-3alkyl-OR^b, or —C_1-3alkyl-NR^bR^b;
  - each R^bis independently —H or C_1-4alkyl;
- x is 0, 1, 2, 3, or 4;
- each m is independently 0, 1, 2, or 3; and
- each n is independently 0, 1, or 2.

Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (Xa) or a pharmaceutically acceptable salt or isotopic variant thereof:

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Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (Xb) or a pharmaceutically acceptable salt or isotopic variant thereof:

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In some embodiments, for a compound of Formula (X), R¹is optionally substituted phenyl, optionally substituted cyclopentyl, optionally substituted cyclohexyl, optionally substituted thienyl, optionally substituted pyridinyl, optionally substituted thiazolyl, optionally substituted pyrrolyl, optionally substituted imidazolyl, optionally substituted furanyl, optionally substituted oxazolyl, optionally substituted isoxazolyl, optionally substituted pyrazolyl, optionally substituted isothiazolyl, optionally substituted pyrimidinyl, optionally substituted pyrazinyl, optionally substituted pyridazinyl, optionally substituted oxadiazolyl, optionally substituted tetrahydropyranyl, optionally substituted triazolyl, or optionally substituted thiadiazolyl. In some embodiments, for a compound of Formula (X), R¹is optionally substituted phenyl, optionally substituted cyclopentyl, optionally substituted thienyl, or optionally substituted tetrahydropyranyl. In some embodiments, for a compound of Formula (X), R¹is optionally substituted phenyl. In some embodiments, for a compound of Formula (X), R¹is optionally substituted cyclopentyl. In some embodiments, for a compound of Formula (X), R¹is optionally substituted thienyl. In some embodiments, for a compound of Formula (X), R¹is optionally substituted tetrahydropyranyl.

In some embodiments, for a compound of Formula (X), R³is optionally substituted monocyclic heterocycloalkyl or optionally substituted monocyclic heteroaryl. In some embodiments, for a compound of Formula (X), R³is optionally substituted monocyclic heterocycloalkyl. In some embodiments, for a compound of Formula (X), R³is optionally substituted monocyclic heterocycloaryl.

In some embodiments, for a compound of Formula (X), m is 0 to 3. In some embodiments, for a compound of Formula (X), m is 0. In some embodiments, for a compound of Formula (X), m is 1. In some embodiments, for a compound of Formula (X), m is 2. In some embodiments, for a compound of Formula (X), m is 3.

In some embodiments, for a compound of Formula (X), R³is optionally substituted azetidinyl, optionally substituted morpholinyl, optionally substituted piperazinyl, optionally substituted piperidinyl, optionally substituted tetrahydropyranyl, optionally substituted pyrrolidinyl, optionally substituted thiomorpholinyl, optionally substituted tetrahydrofuryanyl, optionally substituted homomorpholinyl, optionally substituted homopiperazinyl, optionally substituted thiomorpholine dioxide, or optionally substituted thienomorpholine oxide. In some embodiments, for a compound of Formula (X), R³is optionally substituted morpholinyl, optionally substituted piperazinyl, optionally substituted piperidinyl, or optionally substituted thiomorpholinyl. In some embodiments, for a compound of Formula (X), R³is optionally substituted morpholinyl. In some embodiments, for a compound of Formula (X), R³is optionally substituted piperazinyl. In some embodiments, for a compound of Formula (X), R³is optionally substituted piperidinyl. In some embodiments, for a compound of Formula (X), R³is optionally substituted thiomorpholinyl.

Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (Xc) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein

R⁵is C_1-4alkyl or —C_1-3alkyl-OR^b.

Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (Xd) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein:

Y is absent or —CH₂—; and

Y is attached to the meta or para position of the phenyl ring.

Disclosed herein, in some embodiments, are antagonists or partial antagonists of RIPK2 having a structure of Formula (Xe) or a pharmaceutically acceptable salt or isotopic variant thereof:

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wherein

R⁵is —H, C_1-4alkyl, or —C_1-3alkyl-OR^b;

Y is absent or —CH₂—; and

Y is attached to the meta or para position of the phenyl ring.

In some embodiments, for a compound of Formula (X), R¹is

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In some embodiments, for a compound of Formula (X), R¹is

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wherein each R^ais independently —F, —Cl, or —CH₃.

TL1A Modulators

In some embodiments, the therapeutic agent comprises a modulator of Tumor Necrosis Factor Ligand 1A (TL1A) (UniProtKB: 095150). In some embodiments, the modulator of TL1A is an antagonist of TL1A. In some embodiments the therapeutic agent comprises an inhibitor of TL1A expression or activity. In some cases, the inhibitor of TL1A expression or activity is effective to inhibit TL1A-DR3 binding. In some embodiments, the inhibitor of TL1A expression or activity comprises an allosteric modulator of TL1A. An allosteric modulator of TL1A may indirectly influence the effects TL1A on DR3, or TR6/DcR3 on TL1A or DR3. The inhibitor of TL1A expression or activity may be a direct inhibitor or indirect inhibitor. Non-limiting examples of an inhibitor of TL1A expression include RNA to protein TL1A translation inhibitors, antisense oligonucleotides targeting the TNFSF15 mRNA (such as miRNAs, or siRNA), epigenetic editing (such as targeting the DNA-binding domain of TNFSF15, or post-translational modifications of histone tails and/or DNA molecules). Non-limiting examples of an inhibitor of TL1A activity include antagonists to the TL1A receptors, (DR3 and TR6/DcR3), antagonists to TL1A antigen, and antagonists to gene expression products involved in TL1A mediated disease. Antagonists as disclosed herein, may include, but are not limited to, an anti-TL1A antibody, an anti-TL1A-binding antibody fragment, or a small molecule. The small molecule may be a small molecule that binds to TL1A or DR3. The anti-TL1A antibody may be monoclonal or polyclonal. The anti-TL1A antibody may be humanized or chimeric. The anti-TL1A antibody may be a fusion protein. The anti-TL1A antibody may be a blocking anti-TL1A antibody. A blocking antibody blocks binding between two proteins, e.g., a ligand and its receptor. Therefore, a TL1A blocking antibody includes an antibody that prevents binding of TL1A to DR3 or TR6/DcR3 receptors. In a non-limiting example, the TL1A blocking antibody binds to DR3. In another example, the TL1A blocking antibody binds to DcR3. In some cases, the TL1A antibody is an anti-TL1A antibody that specifically binds to TL1A.

The anti-TL1A antibody may comprise one or more of the antibody sequences of Table 2. The anti-DR3 antibody may comprise an amino acid sequence that is at least 85% identical to any one of SEQ ID NOS: 358-370 and an amino acid sequence that is at least 85% identical to any one of SEQ ID NOS: 371-375. The anti-DR3 antibody may comprise an amino acid sequence comprising the HCDR1, HCDR2, HCDR3 domains of any one of SEQ ID NOS: 358-370 and the LCDR1, LCDR2, and LCDR3 domains of any one of SEQ ID NOS: 371-375.

In some embodiments, an anti-TL1A antibody comprises a heavy chain comprising three complementarity-determining regions: HCDR1, HCDR2, and HCDR3; and a light chain comprising three complementarity-determining regions: LCDR1, LCDR2, and LCDR3. In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 209, a HCDR2 comprising SEQ ID NO: 210, a HCDR3 comprising SEQ ID NO: 211, a LCDR1 comprising SEQ ID NO: 212, a LCDR2 comprising SEQ ID NO: 213, and a LCDR3 comprising SEQ ID NO: 214. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 215 and a light chain (LC) variable domain comprising SEQ ID NO: 216.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 217, a HCDR2 comprising SEQ ID NO: 218, a HCDR3 comprising SEQ ID NO: 219, a LCDR1 comprising SEQ ID NO: 220, a LCDR2 comprising SEQ ID NO: 221, and a LCDR3 comprising SEQ ID NO: 222. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 223 and a light chain (LC) variable domain comprising SEQ ID NO: 224.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 225, a HCDR2 comprising SEQ ID NO: 226, a HCDR3 comprising SEQ ID NO: 227, a LCDR1 comprising SEQ ID NO: 228, a LCDR2 comprising SEQ ID NO: 229, and a LCDR3 comprising SEQ ID NO: 230. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 231 and a light chain (LC) variable domain comprising SEQ ID NO: 232.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 233, a HCDR2 comprising SEQ ID NO: 234, a HCDR3 comprising SEQ ID NO: 235, a LCDR1 comprising SEQ ID NO: 239, a LCDR2 comprising SEQ ID NO: 240, and a LCDR3 comprising SEQ ID NO: 241. In some cases, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 2000136, a HCDR2 comprising SEQ ID NO: 237, a HCDR3 comprising SEQ ID NO: 238, a LCDR1 comprising SEQ ID NO: 239, a LCDR2 comprising SEQ ID NO: 240, and a LCDR3 comprising SEQ ID NO: 241. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 242 and a light chain (LC) variable domain comprising SEQ ID NO: 243. In some cases, the anti-TL1A antibody comprises a heavy chain comprising SEQ ID NO: 244. In some cases, the anti-TL1A antibody comprises a light chain comprising SEQ ID NO: 245.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 246, a HCDR2 comprising SEQ ID NO: 247, a HCDR3 comprising SEQ ID NO: 248, a LCDR1 comprising SEQ ID NO: 249, a LCDR2 comprising SEQ ID NO: 250, and a LCDR3 comprising SEQ ID NO: 251. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 252 and a light chain (LC) variable domain comprising SEQ ID NO: 253.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 254, a HCDR2 comprising SEQ ID NO: 255, a HCDR3 comprising SEQ ID NO: 256, a LCDR1 comprising SEQ ID NO: 257, a LCDR2 comprising SEQ ID NO: 258, and a LCDR3 comprising SEQ ID NO: 259. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 260 and a light chain (LC) variable domain comprising SEQ ID NO: 261.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 262, a HCDR2 comprising SEQ ID NO: 264, a HCDR3 comprising SEQ ID NO: 265, a LCDR1 comprising SEQ ID NO: 267, a LCDR2 comprising SEQ ID NO: 269, and a LCDR3 comprising SEQ ID NO: 270. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 271 and a light chain (LC) variable domain comprising SEQ ID NO: 275. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 271 and a light chain (LC) variable domain comprising SEQ ID NO: 276. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 271 and a light chain (LC) variable domain comprising SEQ ID NO: 277. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 271 and a light chain (LC) variable domain comprising SEQ ID NO: 278.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 262, a HCDR2 comprising SEQ ID NO: 264, a HCDR3 comprising SEQ ID NO: 265, a LCDR1 comprising SEQ ID NO: 268, a LCDR2 comprising SEQ ID NO: 269, and a LCDR3 comprising SEQ ID NO: 270. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 271 and a light chain (LC) variable domain comprising SEQ ID NO: 279. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 271 and a light chain (LC) variable domain comprising SEQ ID NO: 280. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 271 and a light chain (LC) variable domain comprising SEQ ID NO: 281. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 271 and a light chain (LC) variable domain comprising SEQ ID NO: 282.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 262, a HCDR2 comprising SEQ ID NO: 264, a HCDR3 comprising SEQ ID NO: 265, a LCDR1 comprising SEQ ID NO: 267, a LCDR2 comprising SEQ ID NO: 269, and a LCDR3 comprising SEQ ID NO: 270. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 272 and a light chain (LC) variable domain comprising SEQ ID NO: 275. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 272 and a light chain (LC) variable domain comprising SEQ ID NO: 276. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 272 and a light chain (LC) variable domain comprising SEQ ID NO: 277. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 272 and a light chain (LC) variable domain comprising SEQ ID NO: 278.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 262, a HCDR2 comprising SEQ ID NO: 264, a HCDR3 comprising SEQ ID NO: 265, a LCDR1 comprising SEQ ID NO: 268, a LCDR2 comprising SEQ ID NO: 269, and a LCDR3 comprising SEQ ID NO: 270. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 272 and a light chain (LC) variable domain comprising SEQ ID NO: 279. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 272 and a light chain (LC) variable domain comprising SEQ ID NO: 280. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 272 and a light chain (LC) variable domain comprising SEQ ID NO: 281. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 272 and a light chain (LC) variable domain comprising SEQ ID NO: 282.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 263, a HCDR2 comprising SEQ ID NO: 264, a HCDR3 comprising SEQ ID NO: 266, a LCDR1 comprising SEQ ID NO: 267, a LCDR2 comprising SEQ ID NO: 269, and a LCDR3 comprising SEQ ID NO: 270. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 273 and a light chain (LC) variable domain comprising SEQ ID NO: 275. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 273 and a light chain (LC) variable domain comprising SEQ ID NO: 276. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 273 and a light chain (LC) variable domain comprising SEQ ID NO: 277. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 273 and a light chain (LC) variable domain comprising SEQ ID NO: 278. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 273 and a light chain (LC) variable domain comprising SEQ ID NO: 279. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 273 and a light chain (LC) variable domain comprising SEQ ID NO: 280. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 273 and a light chain (LC) variable domain comprising SEQ ID NO: 281. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 273 and a light chain (LC) variable domain comprising SEQ ID NO: 282.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 263, a HCDR2 comprising SEQ ID NO: 264, a HCDR3 comprising SEQ ID NO: 266, a LCDR1 comprising SEQ ID NO: 268, a LCDR2 comprising SEQ ID NO: 269, and a LCDR3 comprising SEQ ID NO: 270. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 274 and a light chain (LC) variable domain comprising SEQ ID NO: 279. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 274 and a light chain (LC) variable domain comprising SEQ ID NO: 280. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 274 and a light chain (LC) variable domain comprising SEQ ID NO: 281. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 274 and a light chain (LC) variable domain comprising SEQ ID NO: 282. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 274 and a light chain (LC) variable domain comprising SEQ ID NO: 275. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 274 and a light chain (LC) variable domain comprising SEQ ID NO: 276. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 274 and a light chain (LC) variable domain comprising SEQ ID NO: 277. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 274 and a light chain (LC) variable domain comprising SEQ ID NO: 278.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 283, a HCDR2 comprising SEQ ID NO: 284, a HCDR3 comprising SEQ ID NO: 285, a LCDR1 comprising SEQ ID NO: 286, a LCDR2 comprising SEQ ID NO: 287, and a LCDR3 comprising SEQ ID NO: 288. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 289 and a light chain (LC) variable domain comprising SEQ ID NO: 294. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 289 and a light chain (LC) variable domain comprising SEQ ID NO: 295. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 289 and a light chain (LC) variable domain comprising SEQ ID NO: 296. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 289 and a light chain (LC) variable domain comprising SEQ ID NO: 297. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 290 and a light chain (LC) variable domain comprising SEQ ID NO: 294. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 290 and a light chain (LC) variable domain comprising SEQ ID NO: 295. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 290 and a light chain (LC) variable domain comprising SEQ ID NO: 296. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 290 and a light chain (LC) variable domain comprising SEQ ID NO: 297. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 291 and a light chain (LC) variable domain comprising SEQ ID NO: 294. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 291 and a light chain (LC) variable domain comprising SEQ ID NO: 295. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 291 and a light chain (LC) variable domain comprising SEQ ID NO: 296. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 291 and a light chain (LC) variable domain comprising SEQ ID NO: 297. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 292 and a light chain (LC) variable domain comprising SEQ ID NO: 294. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 292 and a light chain (LC) variable domain comprising SEQ ID NO: 295. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 292 and a light chain (LC) variable domain comprising SEQ ID NO: 296. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 292 and a light chain (LC) variable domain comprising SEQ ID NO: 297. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 293 and a light chain (LC) variable domain comprising SEQ ID NO: 294. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 293 and a light chain (LC) variable domain comprising SEQ ID NO: 295. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 293 and a light chain (LC) variable domain comprising SEQ ID NO: 296. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 293 and a light chain (LC) variable domain comprising SEQ ID NO: 297.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 298, a HCDR2 comprising SEQ ID NO: 299, a HCDR3 comprising SEQ ID NO: 300, a LCDR1 comprising SEQ ID NO: 301, a LCDR2 comprising SEQ ID NO: 302, and a LCDR3 comprising SEQ ID NO: 303. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 304 and a light chain (LC) variable domain comprising SEQ ID NO: 305. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 306 and a light chain (LC) variable domain comprising SEQ ID NO: 307. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 308 and a light chain (LC) variable domain comprising SEQ ID NO: 309. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 310 and a light chain (LC) variable domain comprising SEQ ID NO: 311. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 312 and a light chain (LC) variable domain comprising SEQ ID NO: 313. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 314 and a light chain (LC) variable domain comprising SEQ ID NO: 315. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 316 and a light chain (LC) variable domain comprising SEQ ID NO: 317. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 318 and a light chain (LC) variable domain comprising SEQ ID NO: 319. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 320 and a light chain (LC) variable domain comprising SEQ ID NO: 321. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 322 and a light chain (LC) variable domain comprising SEQ ID NO: 323. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 324 and a light chain (LC) variable domain comprising SEQ ID NO: 325. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 326 and a light chain (LC) variable domain comprising SEQ ID NO: 327.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 328, a HCDR2 comprising SEQ ID NO: 329, a HCDR3 comprising SEQ ID NO: 330, a LCDR1 comprising SEQ ID NO: 331, a LCDR2 comprising SEQ ID NO: 332, and a LCDR3 comprising SEQ ID NO: 333. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 334 and a light chain (LC) variable domain comprising SEQ ID NO: 335.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 336, a HCDR2 comprising SEQ ID NO: 337, a HCDR3 comprising SEQ ID NO: 338, a LCDR1 comprising SEQ ID NO: 339, a LCDR2 comprising SEQ ID NO: 340, and a LCDR3 comprising SEQ ID NO: 341. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 342 and a light chain (LC) variable domain comprising SEQ ID NO: 343.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 346, a HCDR2 comprising SEQ ID NO: 347, a HCDR3 comprising SEQ ID NO: 348, a LCDR1 comprising SEQ ID NO: 349, a LCDR2 comprising SEQ ID NO: 350, and a LCDR3 comprising SEQ ID NO: 351. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 344 and a light chain (LC) variable domain comprising SEQ ID NO: 345. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 352 and a light chain (LC) variable domain comprising SEQ ID NO: 353. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 354 and a light chain (LC) variable domain comprising SEQ ID NO: 355. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 356 and a light chain (LC) variable domain comprising SEQ ID NO: 357.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 376, a HCDR2 comprising SEQ ID NO: 377, a HCDR3 comprising SEQ ID NO: 378, a LCDR1 comprising SEQ ID NO: 379, a LCDR2 comprising SEQ ID NO: 380, and a LCDR3 comprising SEQ ID NO: 381. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 382 and a light chain (LC) variable domain comprising SEQ ID NO: 383.

In some embodiments, the anti-TL1A antibody comprises a HCDR1 comprising SEQ ID NO: 384, a HCDR2 comprising SEQ ID NO: 385, a HCDR3 comprising SEQ ID NO: 386, a LCDR1 comprising SEQ ID NO: 387, a LCDR2 comprising SEQ ID NO: 388, and a LCDR3 comprising SEQ ID NO: 399. In some cases, the anti-TL1A antibody comprises a heavy chain (HC) variable domain comprising SEQ ID NO: 390 and a light chain (LC) variable domain comprising SEQ ID NO: 391.

In some embodiments, the anti-TL1A antibody comprises one or more of A101-A177 of Table 17. In some embodiments, the anti-TL1A antibody is A100. In some embodiments, the anti-TL1A antibody is A101. In some embodiments, the anti-TL1A antibody is A102. In some embodiments, the anti-TL1A antibody is A103. In some embodiments, the anti-TL1A antibody is A104. In some embodiments, the anti-TL1A antibody is A105. In some embodiments, the anti-TL1A antibody is A106. In some embodiments, the anti-TL1A antibody is A107. In some embodiments, the anti-TL1A antibody is A108. In some embodiments, the anti-TL1A antibody is A109. In some embodiments, the anti-TL1A antibody is A110. In some embodiments, the anti-TL1A antibody is A111. In some embodiments, the anti-TL1A antibody is A112. In some embodiments, the anti-TL1A antibody is A113. In some embodiments, the anti-TL1A antibody is A114. In some embodiments, the anti-TL1A antibody is A115. In some embodiments, the anti-TL1A antibody is A116. In some embodiments, the anti-TL1A antibody is A117. In some embodiments, the anti-TL1A antibody is A118. In some embodiments, the anti-TL1A antibody is A119. In some embodiments, the anti-TL1A antibody is A120. In some embodiments, the anti-TL1A antibody is A121. In some embodiments, the anti-TL1A antibody is A122. In some embodiments, the anti-TL1A antibody is A123. In some embodiments, the anti-TL1A antibody is A124. In some embodiments, the anti-TL1A antibody is A125. In some embodiments, the anti-TL1A antibody is A126. In some embodiments, the anti-TL1A antibody is A127. In some embodiments, the anti-TL1A antibody is A128. In some embodiments, the anti-TL1A antibody is A129. In some embodiments, the anti-TL1A antibody is A130. In some embodiments, the anti-TL1A antibody is A131. In some embodiments, the anti-TL1A antibody is A132. In some embodiments, the anti-TL1A antibody is A133. In some embodiments, the anti-TL1A antibody is A134. In some embodiments, the anti-TL1A antibody is A135. In some embodiments, the anti-TL1A antibody is A136. In some embodiments, the anti-TL1A antibody is A137. In some embodiments, the anti-TL1A antibody is A138. In some embodiments, the anti-TL1A antibody is A139. In some embodiments, the anti-TL1A antibody is A140. In some embodiments, the anti-TL1A antibody is A141. In some embodiments, the anti-TL1A antibody is A142. In some embodiments, the anti-TL1A antibody is A143. In some embodiments, the anti-TL1A antibody is A144. In some embodiments, the anti-TL1A antibody is A145. In some embodiments, the anti-TL1A antibody is A146. In some embodiments, the anti-TL1A antibody is A147. In some embodiments, the anti-TL1A antibody is A148. In some embodiments, the anti-TL1A antibody is A149. In some embodiments, the anti-TL1A antibody is A150. In some embodiments, the anti-TL1A antibody is A151. In some embodiments, the anti-TL1A antibody is A152. In some embodiments, the anti-TL1A antibody is A153. In some embodiments, the anti-TL1A antibody is A154. In some embodiments, the anti-TL1A antibody is A155. In some embodiments, the anti-TL1A antibody is A156. In some embodiments, the anti-TL1A antibody is A157. In some embodiments, the anti-TL1A antibody is A158. In some embodiments, the anti-TL1A antibody is A159. In some embodiments, the anti-TL1A antibody is A160. In some embodiments, the anti-TL1A antibody is A161. In some embodiments, the anti-TL1A antibody is A162. In some embodiments, the anti-TL1A antibody is A163. In some embodiments, the anti-TL1A antibody is A164. In some embodiments, the anti-TL1A antibody is A165. In some embodiments, the anti-TL1A antibody is A166. In some embodiments, the anti-TL1A antibody is A167. In some embodiments, the anti-TL1A antibody is A168. In some embodiments, the anti-TL1A antibody is A169. In some embodiments, the anti-TL1A antibody is A170. In some embodiments, the anti-TL1A antibody is A171. In some embodiments, the anti-TL1A antibody is A172. In some embodiments, the anti-TL1A antibody is A173. In some embodiments, the anti-TL1A antibody is A174. In some embodiments, the anti-TL1A antibody is A175. In some embodiments, the anti-TL1A antibody is A176. In some embodiments, the anti-TL1A antibody is A177.

In some embodiments, the anti-DR3 is A178. In some embodiments, the anti-DR3 is A179. In some embodiments, the anti-DR3 is A180. In some embodiments, the anti-DR3 is A181. In some embodiments, the anti-DR3 is A182. In some embodiments, the anti-DR3 is A183. In some embodiments, the anti-DR3 is A184. In some embodiments, the anti-DR3 is A185. In some embodiments, the anti-DR3 is A186. In some embodiments, the anti-DR3 is A187. In some embodiments, the anti-DR3 is A188. In some embodiments, the anti-DR3 is A189. In some embodiments, the anti-DR3 is A190. In some embodiments, the anti-DR3 is A191. In some embodiments, the anti-DR3 is A192. In some embodiments, the anti-DR3 is A193. In some embodiments, the anti-DR3 is A194. In some embodiments, the anti-DR3 is A195. In some embodiments, the anti-DR3 is A196. In some embodiments, the anti-DR3 is A197. In some embodiments, the anti-DR3 is A198. In some embodiments, the anti-DR3 is A199. In some embodiments, the anti-DR3 is A200. In some embodiments, the anti-DR3 is A201. In some embodiments, the anti-DR3 is A202. In some embodiments, the anti-DR3 is A203. In some embodiments, the anti-DR3 is A204. In some embodiments, the anti-DR3 is A205. In some embodiments, the anti-DR3 is A206. In some embodiments, the anti-DR3 is A207. In some embodiments, the anti-DR3 is A208. In some embodiments, the anti-DR3 is A209. In some embodiments, the anti-DR3 is A210. In some embodiments, the anti-DR3 is A211. In some embodiments, the anti-DR3 is A212. In some embodiments, the anti-DR3 is A213. In some embodiments, the anti-DR3 is A214. In some embodiments, the anti-DR3 is A215. In some embodiments, the anti-DR3 is A216. In some embodiments, the anti-DR3 is A217. In some embodiments, the anti-DR3 is A218. In some embodiments, the anti-DR3 is A219. In some embodiments, the anti-DR3 is A220. In some embodiments, the anti-DR3 is A221. In some embodiments, the anti-DR3 is A222. In some embodiments, the anti-DR3 is A223. In some embodiments, the anti-DR3 is A224. In some embodiments, the anti-DR3 is A225. In some embodiments, the anti-DR3 is A226. In some embodiments, the anti-DR3 is A227. In some embodiments, the anti-DR3 is A228. In some embodiments, the anti-DR3 is A229. In some embodiments, the anti-DR3 is A230. In some embodiments, the anti-DR3 is A231. In some embodiments, the anti-DR3 is A232. In some embodiments, the anti-DR3 is A233. In some embodiments, the anti-DR3 is A234. In some embodiments, the anti-DR3 is A235. In some embodiments, the anti-DR3 is A236. In some embodiments, the anti-DR3 is A237. In some embodiments, the anti-DR3 is A238. In some embodiments, the anti-DR3 is A239. In some embodiments, the anti-DR3 is A240. In some embodiments, the anti-DR3 is A241. In some embodiments, the anti-DR3 is A242.

TABLE 2

Non-Limiting Examples of anti-TL1A and anti-DR3 Antibodies

HC
LC

Variable
Variable

Domain
Domain

Antibody
(SEQ ID
(SEQ ID

Name
NO)
NO)

A100
215
216

A101
223
224

A102
231
232

A103
242
243

A104
252
253

A105
260
261

A106
271
275

A107
271
276

A108
271
277

A109
271
278

A110
271
279

A111
271
280

A112
271
281

A113
271
282

A114
272
275

A115
272
276

A116
272
277

A117
272
278

A118
272
279

A119
272
280

A120
272
281

A121
272
282

A122
273
275

A123
273
276

A124
273
277

Modulators of Certain Pathways

In some embodiments, the therapeutic agent is capable of modulating an expression of a gene, or an activity or an expression of a gene expression product expressed from the gene involved in a pathway implicated in the pathology or pathogenesis of a disease or condition disclosed herein. In some instances, the pathway comprises the Janus Kinase (JAK)/Signal Transducer and Transcription Activator (STAT) pathway. Non-limiting genes involved in the JAK/STAT pathway include Interferon Regulatory Factor 1 (IRF1), Klotho Beta (KLB), Mitogen-Activated Protein Kinase Kinase 1 (MAP2K1), Nuclear Receptor Subfamily 3 Group C Member 1 (NR3C1), Protein Kinase C Beta (PRKCB), Protein Kinase C Epsilon (PRKCE), Protein Kinase C Gamma (PRKCG), Protein Kinase C Eta (PRKCH), Protein Kinase C Theta (PRKCQ), Prolactin Receptor (PRLR), Protein Tyrosine Phosphatase, Non-Receptor Type 11 (PTPN11), Signal Transducer And Activator Of Transcription 1 (STAT1), Signal Transducer And Activator Of Transcription 5A (STAT5A), and Signal Transducer And Activator Of Transcription 5B (STAT5B).

In some instances, the pathway comprises the genes or gene expression products expressed from gens involved in autophagy pathways. Non-limiting examples of genes involved in autophagy include Autophagy Related 10 (ATG10), Autophagy Related 16 Like 1 (ATG16L1), Autophagy Related 4A Cysteine Peptidase (ATG4A), Autophagy Related 4C Cysteine Peptidase (ATG4C), Cathepsin H (CTSH), Sequestosome 1 (SQSTM1), Unc-51 Like Autophagy Activating Kinase 1 (ULK1), and WD Repeat And FYVE Domain Containing 3 (WDFY3).

Further provided are therapeutic agents capable of modulating an expression of a gene, or an activity or an expression of a gene expression product expressed from the gene that is involved implicated in inflammatory bowel disease (IBD) pathogenesis. In some embodiments, the gene is selected from the group consisting of Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 (MAP4K4), Prostaglandin E Receptor 4 (PTGER4), Interleukin 18 Receptor 1 (IL18R1), Interleukin 18 Receptor Accessory Protein (IL18RAP), Adenylate Cyclase 7 (ADCY7), B Lymphoid Tyrosine Kinase (BLK), G Protein-Coupled Receptor 65 (GPR65), Sprouty Related EVH1 Domain Containing 2 (SPRED2), and Src Kinase Associated Phosphoprotein 2 (SKAP2). The amino acid sequence for IL18R1 is provided in SEQ ID NOS: 83-84. The amino acid sequence for IL18RAP is provided in SEQ ID NOS: 85-89. The amino acid sequence for GPR65 is provided in SEQ ID NO: 90. The amino acid sequence for SPRED2 is provided in SEQ ID NO: 91. The amino acid sequence for SKAP2 is provided in SEQ ID NOS: 92-93.

Non-limiting examples of MAP4K4 modulators include GNE-220 and PF-6260933. Non-limiting examples of PTGER4 modulators include grapiprant (CJ-023,423), ONO-AE3-208, GW627368X, AH23848, ONO-AE2-227, ONO-AE1-734, AGN205203, rivenprost (ONO-4819), CJ-023,423, and BGC20-1531. Exemplary modulators of PFKFB3 include, but are not limited to 3-(3-pyridinyl)-1-(4-pyridinyl)-2-propen-1-one (3P0), 1-(4-pyridinyl)-3-(2-quinolinyl)-2-propen-1-one (PFK15), 5-triazolo-2-arylpyridazinone, 125 1-(3-pyridinyl)-3-(2-quinolinyl)-2-propen-1-one (PQP), 126 5, 6, 7, 8-tetrahydroxy-2-(4-hydroxyphenyl) chrome-4-one (N4A), and 7, 8-dihydroxy-3-(4-hydroxyphenyl) chromen-4-one (YN1). Non-limiting modulators of ADCY7 include forskolin and colforsin daropate. Non-limiting examples of GPR65 modulators include BTB09089 (3-[(2,4-dichlorophenyl)methylsulfanyl]-1,6-dimethylpyridazino[4,5-e][1,3,4]thiadiazin-5-one), and ZINC62678696.

The therapeutic agent targeting the above genes or gene expression products may be an antibody or antigen binding fragment thereof. The therapeutic agent may be a small molecule. The therapeutic agent may be a peptide or a protein. The therapeutic agent may be an agonist, or partial agonist. The therapeutic agent may be an allosteric modulator, such as a positive allosteric modulator (PAM). The therapeutic agent may be an antagonist, or partial antagonist. The therapeutic agent may be an inverse agonist. The therapeutic agent may be a negative allosteric modulator (NAM).

In some embodiments, the therapeutic agent comprises an agonist of Janus Kinase 1 (JAK1). Non-limiting examples of JAK1 inhibitors include Ruxolitinib (INCB018424), S-Ruxolitinib (INCB018424), Baricitinib (LY3009104, INCB028050), Filgotinib (GLPG0634), Momelotinib (CYT387), Cerdulatinib (PRT062070, PRT2070), LY2784544, NVP-BSK805, 2HCl, Tofacitinib (CP-690550, Tasocitinib), XL019, Pacritinib (SB1518), or ZM 39923 HCl.

Dosages and Routes of Administration

In general, methods disclosed herein comprise administering a therapeutic agent by oral administration. However, in some instances, methods comprise administering a therapeutic agent by intraperitoneal injection. In some instances, methods comprise administering a therapeutic agent in the form of an anal suppository. In some instances, methods comprise administering a therapeutic agent by intravenous (“i.v.”) administration. It is conceivable that one may also administer therapeutic agents disclosed herein by other routes, such as subcutaneous injection, intramuscular injection, intradermal injection, transdermal injection percutaneous administration, intranasal administration, intralymphatic injection, rectal administration intragastric administration, or any other suitable parenteral administration. In some embodiments, routes for local delivery closer to site of injury or inflammation are preferred over systemic routes. Routes, dosage, time points, and duration of administrating therapeutics may be adjusted. In some embodiments, administration of therapeutics is prior to, or after, onset of either, or both, acute and chronic symptoms of the disease or condition.

An effective dose and dosage of therapeutics to prevent or treat the disease or condition disclosed herein is defined by an observed beneficial response related to the disease or condition, or symptom of the disease or condition. Beneficial response comprises preventing, alleviating, arresting, or curing the disease or condition, or symptom of the disease or condition (e.g., reduced instances of diarrhea, rectal bleeding, weight loss, and size or number of intestinal lesions or strictures, reduced fibrosis or fibrogenesis, reduced fibrostenosis, reduced inflammation). In some embodiments, the beneficial response may be measured by detecting a measurable improvement in the presence, level, or activity, of biomarkers, transcriptomic risk profile, or intestinal microbiome in the subject. An “improvement,” as used herein refers to shift in the presence, level, or activity towards a presence, level, or activity, observed in normal individuals (e.g. individuals who do not suffer from the disease or condition). In instances wherein the therapeutic agent is not therapeutically effective or is not providing a sufficient alleviation of the disease or condition, or symptom of the disease or condition, then the dosage amount and/or route of administration may be changed, or an additional agent may be administered to the subject, along with the therapeutic agent. In some embodiments, as a patient is started on a regimen of a therapeutic agent, the patient is also weaned off (e.g., step-wise decrease in dose) a second treatment regimen.

Suitable dose and dosage administrated to a subject is determined by factors including, but no limited to, the particular therapeutic agent, disease condition and its severity, the identity (e.g., weight, sex, age) of the subject in need of treatment, and can be determined according to the particular circumstances surrounding the case, including, e.g., the specific agent being administered, the route of administration, the condition being treated, and the subject or host being treated. In general, however, doses employed for adult human treatment are typically in the range of 0.01 mg-5000 mg per day. In one aspect, doses employed for adult human treatment are from about 1 mg to about 1000 mg per day. In one embodiment, the desired dose is conveniently presented in a single dose or in divided doses administered simultaneously (or over a short period of time) or at appropriate intervals, for example as two, three, four or more sub-doses per day. Non-limiting examples of effective dosages of for oral delivery of a therapeutic agent include between about 0.1 mg/kg and about 100 mg/kg of body weight per day, and preferably between about 0.5 mg/kg and about 50 mg/kg of body weight per day. In other instances, the oral delivery dosage of effective amount is about 1 mg/kg and about 10 mg/kg of body weight per day of active material. Non-limiting examples of effective dosages for intravenous administration of the therapeutic agent include at a rate between about 0.01 to 100 pmol/kg body weight/min. In some embodiments, the daily dosage or the amount of active in the dosage form are lower or higher than the ranges indicated herein, based on a number of variables in regard to an individual treatment regime. In various embodiments, the daily and unit dosages are altered depending on a number of variables including, but not limited to, the activity of the therapeutic agent used, the disease or condition to be treated, the mode of administration, the requirements of the individual subject, the severity of the disease or condition being treated, and the judgment of the practitioner.

In some embodiments, the administration of the therapeutic agent is hourly, once every 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16 hours, 17 hours, 18 hours, 19 hours, 20 hours, 21 hours 22 hours, 23 hours, 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, 15 days, 1 month, 2 months, 3 months, 4 months, 5 months, 6 months, 7 months, 8 months, 9 months, 10 months, 11 months, 1 year, 2 years, 3 years, 4 years, or 5 years, or 10 years. The effective dosage ranges may be adjusted based on subject's response to the treatment. Some routes of administration will require higher concentrations of effective amount of therapeutics than other routes.

In certain embodiments wherein the patient's condition does not improve, upon the doctor's discretion the administration of therapeutic agent is administered chronically, that is, for an extended period of time, including throughout the duration of the patient's life in order to ameliorate or otherwise control or limit the symptoms of the patient's disease or condition. In certain embodiments wherein a patient's status does improve, the dose of therapeutic agent being administered may be temporarily reduced or temporarily suspended for a certain length of time (i.e., a “drug holiday”). In specific embodiments, the length of the drug holiday is between 2 days and 1 year, including by way of example only, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 10 days, 12 days, 15 days, 20 days, 28 days, or more than 28 days. The dose reduction during a drug holiday is, by way of example only, by 10%-100%, including by way of example only 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, and 100%. In certain embodiments, the dose of drug being administered may be temporarily reduced or temporarily suspended for a certain length of time (i.e., a “drug diversion”). In specific embodiments, the length of the drug diversion is between 2 days and 1 year, including by way of example only, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 10 days, 12 days, 15 days, 20 days, 28 days, or more than 28 days. The dose reduction during a drug diversion is, by way of example only, by 10%-100%, including by way of example only 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, and 100%. After a suitable length of time, the normal dosing schedule is optionally reinstated.

In some embodiments, once improvement of the patient's conditions has occurred, a maintenance dose is administered if necessary. Subsequently, in specific embodiments, the dosage or the frequency of administration, or both, is reduced, as a function of the symptoms, to a level at which the improved disease, disorder or condition is retained. In certain embodiments, however, the patient requires intermittent treatment on a long-term basis upon any recurrence of symptoms.

Toxicity and therapeutic efficacy of such therapeutic regimens are determined by standard pharmaceutical procedures in cell cultures or experimental animals, including, but not limited to, the determination of the LD50 and the ED50. The dose ratio between the toxic and therapeutic effects is the therapeutic index and it is expressed as the ratio between LD50 and ED50. In certain embodiments, the data obtained from cell culture assays and animal studies are used in formulating the therapeutically effective daily dosage range and/or the therapeutically effective unit dosage amount for use in mammals, including humans. In some embodiments, the daily dosage amount of the therapeutic agent described herein lies within a range of circulating concentrations that include the ED50 with minimal toxicity. In certain embodiments, the daily dosage range and/or the unit dosage amount varies within this range depending upon the dosage form employed and the route of administration utilized.

Additional Therapeutic Agent

A therapeutic agent may be used alone or in combination with an additional therapeutic agent. In some cases, an “additional therapeutic agent” as used herein is administered alone. The therapeutic agents may be administered together or sequentially. The combination therapies may be administered within the same day, or may be administered one or more days, weeks, months, or years apart. In some cases, a therapeutic agent provided herein is administered if the subject is determined to be non-responsive to a first line of therapy, e.g., such as TNF inhibitor. Such determination may be made by treatment with the first line therapy and monitoring of disease state and/or diagnostic determination that the subject would be non-responsive to the first line therapy.

In some embodiments, the additional therapeutic agent comprises an anti-TNF therapy, e.g., an anti-TNFα therapy. In some embodiments, the additional therapeutic agent comprises a second-line treatment to an anti-TNF therapy. In some embodiments, the additional therapeutic agent comprises an immunosuppressant, or a class of drugs that suppress, or reduce, the strength of the immune system. In some embodiments, the immunosuppressant is an antibody. Non-limiting examples of immunosuppressant therapeutic agents include STELARA® (ustekinumab) azathioprine (AZA), 6-mercaptopurine (6-MP), methotrexate, cyclosporin A. (CsA).

In some embodiments, the additional therapeutic agent comprises a selective anti-inflammatory drug, or a class of drugs that specifically target pro-inflammatory molecules in the body. In some embodiments, the anti-inflammatory drug comprises an antibody. In some embodiments, the anti-inflammatory drug comprises a small molecule. Non-limiting examples of anti-inflammatory drugs include ENTYVIO (vedolizumab), corticosteroids, aminosalicylates, mesalamine, balsalazide (Colazal) and olsalazine (Dipentum).

In some embodiments, the additional therapeutic agent comprises a stem cell therapy. The stem cell therapy may be embryonic or somatic stem cells. The stem cells may be isolated from a donor (allogeneic) or isolated from the subject (autologous). The stem cells may be expanded adipose-derived stem cells (eASCs), hematopoietic stem cells (HSCs), mesenchymal stem (stromal) cells (MSCs), or induced pluripotent stem cells (iPSCs) derived from the cells of the subject. In some embodiments, the therapeutic agent comprises Cx601/Alofisel® (darvadstrocel).

In some embodiments, the additional therapeutic agent comprises a small molecule. The small molecule may be used to treat inflammatory diseases or conditions, or fibrostenonic or fibrotic disease. Non-limiting examples of small molecules include Otezla® (apremilast), alicaforsen, or ozanimod (RPC-1063).

The additional therapeutic agent may comprise an antimycotic agent. In some instances, the antimycotic agent comprises an active agent that inhibits growth of a fungus. In some instances, the antimycotic agent comprises an active agent that kills a fungus. In some embodiments, the antimycotic agent comprises polyene, an azole, an echinocandin, an flucytosine, an allylamine, a tolnaftate, or griseofulvin, or a combination thereof. In other embodiments, the azole comprises triazole, imidazole, clotrimazole, ketoconazole, itraconazole, terconazole, oxiconazole, miconazole, econazole, tioconazole, voriconazole, fluconazole, isavuconazole, itraconazole, pramiconazole, ravuconazole, or posaconazole. In some other embodiments, the polyene comprises amphotericin B, nystatin, or natamycin. In yet other embodiments, the echinocandin comprises caspofungin, anidulafungin, or micafungin. In various other embodiments, the allylamine comprises naftifine or terbinafine.

Pharmaceutical Composition

A pharmaceutical composition, as used herein, refers to a mixture of a therapeutic agent, with other chemical components (i.e. pharmaceutically acceptable inactive ingredients), such as carriers, excipients, binders, filling agents, suspending agents, flavoring agents, sweetening agents, disintegrating agents, dispersing agents, surfactants, lubricants, colorants, diluents, solubilizers, moistening agents, plasticizers, stabilizers, penetration enhancers, wetting agents, anti-foaming agents, antioxidants, preservatives, or one or more combination thereof. Optionally, the compositions include two or more therapeutic agent (e.g., one or more therapeutic agents and one or more additional agents) as discussed herein. In practicing the methods of treatment or use provided herein, therapeutically effective amounts of therapeutic agents described herein are administered in a pharmaceutical composition to a mammal having a disease, disorder, or condition to be treated, e.g., an inflammatory disease, fibrostenotic disease, and/or fibrotic disease. In some embodiments, the mammal is a human. A therapeutically effective amount can vary widely depending on the severity of the disease, the age and relative health of the subject, the potency of the therapeutic agent used and other factors. The therapeutic agents can be used singly or in combination with one or more therapeutic agents as components of mixtures.

The pharmaceutical formulations described herein are administered to a subject by appropriate administration routes, including but not limited to, intravenous, intraarterial, oral, parenteral, buccal, topical, transdermal, rectal, intramuscular, subcutaneous, intraosseous, transmucosal, inhalation, or intraperitoneal administration routes. The pharmaceutical formulations described herein include, but are not limited to, aqueous liquid dispersions, self-emulsifying dispersions, solid solutions, liposomal dispersions, aerosols, solid dosage forms, powders, immediate release formulations, controlled release formulations, fast melt formulations, tablets, capsules, pills, delayed release formulations, extended release formulations, pulsatile release formulations, multiparticulate formulations, and mixed immediate and controlled release formulations.

Pharmaceutical compositions including a therapeutic agent are manufactured in a conventional manner, such as, by way of example only, by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or compression processes.

The pharmaceutical compositions may include at least a therapeutic agent as an active ingredient in free-acid or free-base form, or in a pharmaceutically acceptable salt form. In addition, the methods and pharmaceutical compositions described herein include the use of N-oxides (if appropriate), crystalline forms, amorphous phases, as well as active metabolites of these compounds having the same type of activity. In some embodiments, therapeutic agents exist in unsolvated form or in solvated forms with pharmaceutically acceptable solvents such as water, ethanol, and the like. The solvated forms of the therapeutic agents are also considered to be disclosed herein.

In some embodiments, a therapeutic agent exists as a tautomer. All tautomers are included within the scope of the agents presented herein. As such, it is to be understood that a therapeutic agent or a salt thereof may exhibit the phenomenon of tautomerism whereby two chemical compounds that are capable of facile interconversion by exchanging a hydrogen atom between two atoms, to either of which it forms a covalent bond. Since the tautomeric compounds exist in mobile equilibrium with each other they may be regarded as different isomeric forms of the same compound.

In some embodiments, a therapeutic agent exists as an enantiomer, diastereomer, or other stereoisomeric form. The agents disclosed herein include all enantiomeric, diastereomeric, and epimeric forms as well as mixtures thereof.

In some embodiments, therapeutic agents described herein may be prepared as prodrugs. A “prodrug” refers to an agent that is converted into the parent drug in vivo. Prodrugs are often useful because, in some situations, they may be easier to administer than the parent drug. They may, for instance, be bioavailable by oral administration whereas the parent is not. The prodrug may also have improved solubility in pharmaceutical compositions over the parent drug. An example, without limitation, of a prodrug would be a therapeutic agent described herein, which is administered as an ester (the “prodrug”) to facilitate transmittal across a cell membrane where water solubility is detrimental to mobility but which then is metabolically hydrolyzed to the carboxylic acid, the active entity, once inside the cell where water-solubility is beneficial. A further example of a prodrug might be a short peptide (polyaminoacid) bonded to an acid group where the peptide is metabolized to reveal the active moiety. In certain embodiments, upon in vivo administration, a prodrug is chemically converted to the biologically, pharmaceutically or therapeutically active form of the therapeutic agent. In certain embodiments, a prodrug is enzymatically metabolized by one or more steps or processes to the biologically, pharmaceutically or therapeutically active form of the therapeutic agent.

Prodrug forms of the therapeutic agents, wherein the prodrug is metabolized in vivo to produce an agent as set forth herein are included within the scope of the claims. Prodrug forms of the herein described therapeutic agents, wherein the prodrug is metabolized in vivo to produce an agent as set forth herein are included within the scope of the claims. In some cases, some of the therapeutic agents described herein may be a prodrug for another derivative or active compound. In some embodiments described herein, hydrazones are metabolized in vivo to produce a therapeutic agent.

In certain embodiments, compositions provided herein include one or more preservatives to inhibit microbial activity. Suitable preservatives include mercury-containing substances such as merfen and thiomersal; stabilized chlorine dioxide; and quaternary ammonium compounds such as benzalkonium chloride, cetyltrimethylammonium bromide and cetylpyridinium chloride.

In some embodiments, formulations described herein benefit from antioxidants, metal chelating agents, thiol containing compounds and other general stabilizing agents. Examples of such stabilizing agents, include, but are not limited to: (a) about 0.5% to about 2% w/v glycerol, (b) about 0.1% to about 1% w/v methionine, (c) about 0.1% to about 2% w/v monothioglycerol, (d) about 1 mM to about 10 mM EDTA, (e) about 0.01% to about 2% w/v ascorbic acid, (f) 0.003% to about 0.02% w/v polysorbate 80, (g) 0.001% to about 0.05% w/v. polysorbate 20, (h) arginine, (i) heparin, (j) dextran sulfate, (k) cyclodextrins, (l) pentosan polysulfate and other heparinoids, (m) divalent cations such as magnesium and zinc; or (n) combinations thereof.

The pharmaceutical compositions described herein are formulated into any suitable dosage form, including but not limited to, aqueous oral dispersions, liquids, gels, syrups, elixirs, slurries, suspensions, solid oral dosage forms, aerosols, controlled release formulations, fast melt formulations, effervescent formulations, lyophilized formulations, tablets, powders, pills, dragees, capsules, delayed release formulations, extended release formulations, pulsatile release formulations, multiparticulate formulations, and mixed immediate release and controlled release formulations. In one aspect, a therapeutic agent as discussed herein, e.g., therapeutic agent is formulated into a pharmaceutical composition suitable for intramuscular, subcutaneous, or intravenous injection. In one aspect, formulations suitable for intramuscular, subcutaneous, or intravenous injection include physiologically acceptable sterile aqueous or non-aqueous solutions, dispersions, suspensions or emulsions, and sterile powders for reconstitution into sterile injectable solutions or dispersions. Examples of suitable aqueous and non-aqueous carriers, diluents, solvents, or vehicles include water, ethanol, polyols (propyleneglycol, polyethylene-glycol, glycerol, cremophor and the like), suitable mixtures thereof, vegetable oils (such as olive oil) and injectable organic esters such as ethyl oleate. Proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants. In some embodiments, formulations suitable for subcutaneous injection also contain additives such as preserving, wetting, emulsifying, and dispensing agents. Prevention of the growth of microorganisms can be ensured by various antibacterial and antifungal agents, such as parabens, chlorobutanol, phenol, sorbic acid, and the like. In some cases it is desirable to include isotonic agents, such as sugars, sodium chloride, and the like. Prolonged absorption of the injectable pharmaceutical form can be brought about by the use of agents delaying absorption, such as aluminum monostearate and gelatin.

For intravenous injections or drips or infusions, a therapeutic agent described herein is formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hank's solution, Ringer's solution, or physiological saline buffer. For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art. For other parenteral injections, appropriate formulations include aqueous or nonaqueous solutions, preferably with physiologically compatible buffers or excipients. Such excipients are known.

Parenteral injections may involve bolus injection or continuous infusion. Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multi dose containers, with an added preservative. The pharmaceutical composition described herein may be in a form suitable for parenteral injection as a sterile suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents. In one aspect, the active ingredient is in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.

For administration by inhalation, a therapeutic agent is formulated for use as an aerosol, a mist or a powder. Pharmaceutical compositions described herein are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebuliser, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol, the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, such as, by way of example only, gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the therapeutic agent described herein and a suitable powder base such as lactose or starch.

Representative intranasal formulations are described in, for example, U.S. Pat. Nos. 4,476,116, 5,116,817 and 6,391,452. Formulations that include a therapeutic agent are prepared as solutions in saline, employing benzyl alcohol or other suitable preservatives, fluorocarbons, and/or other solubilizing or dispersing agents known in the art. See, for example, Ansel, H. C. et al., Pharmaceutical Dosage Forms and Drug Delivery Systems, Sixth Ed. (1995). Preferably these compositions and formulations are prepared with suitable nontoxic pharmaceutically acceptable ingredients. These ingredients are known to those skilled in the preparation of nasal dosage forms and some of these can be found in REMINGTON: THE SCIENCE AND PRACTICE OF PHARMACY, 21st edition, 2005. The choice of suitable carriers is dependent upon the exact nature of the nasal dosage form desired, e.g., solutions, suspensions, ointments, or gels. Nasal dosage forms generally contain large amounts of water in addition to the active ingredient. Minor amounts of other ingredients such as pH adjusters, emulsifiers or dispersing agents, preservatives, surfactants, gelling agents, or buffering and other stabilizing and solubilizing agents are optionally present. Preferably, the nasal dosage form should be isotonic with nasal secretions.

Pharmaceutical preparations for oral use are obtained by mixing one or more solid excipient with one or more of the therapeutic agents described herein, optionally grinding the resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients include, for example, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methylcellulose, microcrystalline cellulose, hydroxypropylmethylcellulose, sodium carboxymethylcellulose; or others such as: polyvinylpyrrolidone (PVP or povidone) or calcium phosphate. If desired, disintegrating agents are added, such as the cross linked croscarmellose sodium, polyvinylpyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate. In some embodiments, dyestuffs or pigments are added to the tablets or dragee coatings for identification or to characterize different combinations of active therapeutic agent doses.

In some embodiments, pharmaceutical formulations of a therapeutic agent are in the form of a capsules, including push fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. The push fit capsules contain the active ingredients in admixture with filler such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers. In soft capsules, the active therapeutic agent is dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols. In some embodiments, stabilizers are added. A capsule may be prepared, for example, by placing the bulk blend of the formulation of the therapeutic agent inside of a capsule. In some embodiments, the formulations (non-aqueous suspensions and solutions) are placed in a soft gelatin capsule. In other embodiments, the formulations are placed in standard gelatin capsules or non-gelatin capsules such as capsules comprising HPMC. In other embodiments, the formulation is placed in a sprinkle capsule, wherein the capsule is swallowed whole or the capsule is opened and the contents sprinkled on food prior to eating.

All formulations for oral administration are in dosages suitable for such administration. In one aspect, solid oral dosage forms are prepared by mixing a therapeutic agent with one or more of the following: antioxidants, flavoring agents, and carrier materials such as binders, suspending agents, disintegration agents, filling agents, surfactants, solubilizers, stabilizers, lubricants, wetting agents, and diluents. In some embodiments, the solid dosage forms disclosed herein are in the form of a tablet, (including a suspension tablet, a fast-melt tablet, a bite-disintegration tablet, a rapid-disintegration tablet, an effervescent tablet, or a caplet), a pill, a powder, a capsule, solid dispersion, solid solution, bioerodible dosage form, controlled release formulations, pulsatile release dosage forms, multiparticulate dosage forms, beads, pellets, granules. In other embodiments, the pharmaceutical formulation is in the form of a powder. Compressed tablets are solid dosage forms prepared by compacting the bulk blend of the formulations described above. In various embodiments, tablets will include one or more flavoring agents. In other embodiments, the tablets will include a film surrounding the final compressed tablet. In some embodiments, the film coating can provide a delayed release of a therapeutic agent from the formulation. In other embodiments, the film coating aids in patient compliance (e.g., Opadry® coatings or sugar coating). Film coatings including Opadry® typically range from about 1% to about 3% of the tablet weight. In some embodiments, solid dosage forms, e.g., tablets, effervescent tablets, and capsules, are prepared by mixing particles of a therapeutic agent with one or more pharmaceutical excipients to form a bulk blend composition. The bulk blend is readily subdivided into equally effective unit dosage forms, such as tablets, pills, and capsules. In some embodiments, the individual unit dosages include film coatings. These formulations are manufactured by conventional formulation techniques.

In another aspect, dosage forms include microencapsulated formulations. In some embodiments, one or more other compatible materials are present in the microencapsulation material. Exemplary materials include, but are not limited to, pH modifiers, erosion facilitators, anti-foaming agents, antioxidants, flavoring agents, and carrier materials such as binders, suspending agents, disintegration agents, filling agents, surfactants, solubilizers, stabilizers, lubricants, wetting agents, and diluents. Exemplary useful microencapsulation materials include, but are not limited to, hydroxypropyl cellulose ethers (HPC) such as Klucel® or Nisso HPC, low-substituted hydroxypropyl cellulose ethers (L-HPC), hydroxypropyl methyl cellulose ethers (HPMC) such as Seppifilm-LC, Pharmacoat®, Metolose SR, Methocel®-E, Opadry YS, PrimaFlo, Benecel MP824, and Benecel MP843, methylcellulose polymers such as Methocel®-A, hydroxypropylmethylcellulose acetate stearate Aqoat (HF-LS, HF-LG, HF-MS) and Metolose®, Ethylcelluloses (EC) and mixtures thereof such as E461, Ethocel®, Aqualon®-EC, Surelease®, Polyvinyl alcohol (PVA) such as Opadry AMB, hydroxyethylcelluloses such as Natrosol®, carboxymethylcelluloses and salts of carboxymethylcelluloses (CMC) such as Aqualon®-CMC, polyvinyl alcohol and polyethylene glycol co-polymers such as Kollicoat monoglycerides (Myverol), triglycerides (KLX), polyethylene glycols, modified food starch, acrylic polymers and mixtures of acrylic polymers with cellulose ethers such as Eudragit® EPO, Eudragit® L30D-55, Eudragit® FS 30D Eudragit® L100-55, Eudragit® L100, Eudragit® S100, Eudragit® RD100, Eudragit® E100, Eudragit® L12.5, Eudragit® S12.5, Eudragit® NE30D, and Eudragit® NE 40D, cellulose acetate phthalate, sepifilms such as mixtures of HPMC and stearic acid, cyclodextrins, and mixtures of these materials.

Liquid formulation dosage forms for oral administration are optionally aqueous suspensions selected from the group including, but not limited to, pharmaceutically acceptable aqueous oral dispersions, emulsions, solutions, elixirs, gels, and syrups. See, e.g., Singh et al., Encyclopedia of Pharmaceutical Technology, 2nd Ed., pp. 754-757 (2002). In addition to therapeutic agent the liquid dosage forms optionally include additives, such as: (a) disintegrating agents; (b) dispersing agents; (c) wetting agents; (d) at least one preservative, (e) viscosity enhancing agents, (f) at least one sweetening agent, and (g) at least one flavoring agent. In some embodiments, the aqueous dispersions further includes a crystal-forming inhibitor.

In some embodiments, the pharmaceutical formulations described herein are self-emulsifying drug delivery systems (SEDDS). Emulsions are dispersions of one immiscible phase in another, usually in the form of droplets. Generally, emulsions are created by vigorous mechanical dispersion. SEDDS, as opposed to emulsions or microemulsions, spontaneously form emulsions when added to an excess of water without any external mechanical dispersion or agitation. An advantage of SEDDS is that only gentle mixing is required to distribute the droplets throughout the solution. Additionally, water or the aqueous phase is optionally added just prior to administration, which ensures stability of an unstable or hydrophobic active ingredient. Thus, the SEDDS provides an effective delivery system for oral and parenteral delivery of hydrophobic active ingredients. In some embodiments, SEDDS provides improvements in the bioavailability of hydrophobic active ingredients. Methods of producing self-emulsifying dosage forms include, but are not limited to, for example, U.S. Pat. Nos. 5,858,401, 6,667,048, and 6,960,563.

Buccal formulations that include a therapeutic agent are administered using a variety of formulations known in the art. For example, such formulations include, but are not limited to, U.S. Pat. Nos. 4,229,447, 4,596,795, 4,755,386, and 5,739,136. In addition, the buccal dosage forms described herein can further include a bioerodible (hydrolysable) polymeric carrier that also serves to adhere the dosage form to the buccal mucosa. For buccal or sublingual administration, the compositions may take the form of tablets, lozenges, or gels formulated in a conventional manner.

For intravenous injections, a therapeutic agent is optionally formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hank's solution, Ringer's solution, or physiological saline buffer. For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. For other parenteral injections, appropriate formulations include aqueous or nonaqueous solutions, preferably with physiologically compatible buffers or excipients.

Parenteral injections optionally involve bolus injection or continuous infusion. Formulations for injection are optionally presented in unit dosage form, e.g., in ampoules or in multi dose containers, with an added preservative. In some embodiments, a pharmaceutical composition described herein is in a form suitable for parenteral injection as a sterile suspensions, solutions or emulsions in oily or aqueous vehicles, and contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Pharmaceutical formulations for parenteral administration include aqueous solutions of an agent that modulates the activity of a carotid body in water soluble form. Additionally, suspensions of an agent that modulates the activity of a carotid body are optionally prepared as appropriate, e.g., oily injection suspensions.

Conventional formulation techniques include, e.g., one or a combination of methods: (1) dry mixing, (2) direct compression, (3) milling, (4) dry or non-aqueous granulation, (5) wet granulation, or (6) fusion. Other methods include, e.g., spray drying, pan coating, melt granulation, granulation, fluidized bed spray drying or coating (e.g., wurster coating), tangential coating, top spraying, tableting, extruding and the like.

Suitable carriers for use in the solid dosage forms described herein include, but are not limited to, acacia, gelatin, colloidal silicon dioxide, calcium glycerophosphate, calcium lactate, maltodextrin, glycerine, magnesium silicate, sodium caseinate, soy lecithin, sodium chloride, tricalcium phosphate, dipotassium phosphate, sodium stearoyl lactylate, carrageenan, monoglyceride, diglyceride, pregelatinized starch, hydroxypropylmethylcellulose, hydroxypropylmethylcellulose acetate stearate, sucrose, microcrystalline cellulose, lactose, mannitol and the like.

Suitable filling agents for use in the solid dosage forms described herein include, but are not limited to, lactose, calcium carbonate, calcium phosphate, dibasic calcium phosphate, calcium sulfate, microcrystalline cellulose, cellulose powder, dextrose, dextrates, dextran, starches, pregelatinized starch, hydroxypropylmethycellulose (HPMC), hydroxypropylmethycellulose phthalate, hydroxypropylmethylcellulose acetate stearate (HPMCAS), sucrose, xylitol, lactitol, mannitol, sorbitol, sodium chloride, polyethylene glycol, and the like.

Suitable disintegrants for use in the solid dosage forms described herein include, but are not limited to, natural starch such as corn starch or potato starch, a pregelatinized starch, or sodium starch glycolate, a cellulose such as methylcrystalline cellulose, methylcellulose, microcrystalline cellulose, croscarmellose, or a cross-linked cellulose, such as cross-linked sodium carboxymethylcellulose, cross-linked carboxymethylcellulose, or cross-linked croscarmellose, a cross-linked starch such as sodium starch glycolate, a cross-linked polymer such as crospovidone, a cross-linked polyvinylpyrrolidone, alginate such as alginic acid or a salt of alginic acid such as sodium alginate, a gum such as agar, guar, locust bean, Karaya, pectin, or tragacanth, sodium starch glycolate, bentonite, sodium lauryl sulfate, sodium lauryl sulfate in combination starch, and the like.

Binders impart cohesiveness to solid oral dosage form formulations: for powder filled capsule formulation, they aid in plug formation that can be filled into soft or hard shell capsules and for tablet formulation, they ensure the tablet remaining intact after compression and help assure blend uniformity prior to a compression or fill step. Materials suitable for use as binders in the solid dosage forms described herein include, but are not limited to, carboxymethylcellulose, methylcellulose, hydroxypropylmethylcellulose, hydroxypropylmethylcellulose acetate stearate, hydroxyethylcellulose, hydroxypropylcellulose, ethylcellulose, and microcrystalline cellulose, microcrystalline dextrose, amylose, magnesium aluminum silicate, polysaccharide acids, bentonites, gelatin, polyvinylpyrrolidone/vinyl acetate copolymer, crospovidone, povidone, starch, pregelatinized starch, tragacanth, dextrin, a sugar, such as sucrose, glucose, dextrose, molasses, mannitol, sorbitol, xylitol, lactose, a natural or synthetic gum such as acacia, tragacanth, ghatti gum, mucilage of isapol husks, starch, polyvinylpyrrolidone, larch arabogalactan, polyethylene glycol, waxes, sodium alginate, and the like.

In general, binder levels of 20-70% are used in powder-filled gelatin capsule formulations. Binder usage level in tablet formulations varies whether direct compression, wet granulation, roller compaction, or usage of other excipients such as fillers which itself can act as moderate binder. Binder levels of up to 70% in tablet formulations is common.

Suitable lubricants or glidants for use in the solid dosage forms described herein include, but are not limited to, stearic acid, calcium hydroxide, talc, corn starch, sodium stearyl fumerate, alkali-metal and alkaline earth metal salts, such as aluminum, calcium, magnesium, zinc, stearic acid, sodium stearates, magnesium stearate, zinc stearate, waxes, Stearowet®, boric acid, sodium benzoate, sodium acetate, sodium chloride, leucine, a polyethylene glycol or a methoxypolyethylene glycol such as Carbowax™, PEG 4000, PEG 5000, PEG 6000, propylene glycol, sodium oleate, glyceryl behenate, glyceryl palmitostearate, glyceryl benzoate, magnesium or sodium lauryl sulfate, and the like.

Suitable diluents for use in the solid dosage forms described herein include, but are not limited to, sugars (including lactose, sucrose, and dextrose), polysaccharides (including dextrates and maltodextrin), polyols (including mannitol, xylitol, and sorbitol), cyclodextrins and the like.

Suitable wetting agents for use in the solid dosage forms described herein include, for example, oleic acid, glyceryl monostearate, sorbitan monooleate, sorbitan monolaurate, triethanolamine oleate, polyoxyethylene sorbitan monooleate, polyoxyethylene sorbitan monolaurate, quaternary ammonium compounds (e.g., Polyquat 100), sodium oleate, sodium lauryl sulfate, magnesium stearate, sodium docusate, triacetin, vitamin E TPGS and the like.

Suitable surfactants for use in the solid dosage forms described herein include, for example, sodium lauryl sulfate, sorbitan monooleate, polyoxyethylene sorbitan monooleate, polysorbates, polaxomers, bile salts, glyceryl monostearate, copolymers of ethylene oxide and propylene oxide, e.g., Pluronic® (BASF), and the like.

Suitable suspending agents for use in the solid dosage forms described here include, but are not limited to, polyvinylpyrrolidone, e.g., polyvinylpyrrolidone K12, polyvinylpyrrolidone K17, polyvinylpyrrolidone K25, or polyvinylpyrrolidone K30, polyethylene glycol, e.g., the polyethylene glycol can have a molecular weight of about 300 to about 6000, or about 3350 to about 4000, or about 7000 to about 5400, vinyl pyrrolidone/vinyl acetate copolymer (S630), sodium carboxymethylcellulose, methylcellulose, hydroxy-propylmethylcellulose, polysorbate-80, hydroxyethylcellulose, sodium alginate, gums, such as, e.g., gum tragacanth and gum acacia, guar gum, xanthans, including xanthan gum, sugars, cellulosics, such as, e.g., sodium carboxymethylcellulose, methylcellulose, sodium carboxymethylcellulose, hydroxypropylmethylcellulose, hydroxyethylcellulose, polysorbate-80, sodium alginate, polyethoxylated sorbitan monolaurate, polyethoxylated sorbitan monolaurate, povidone and the like.

Suitable antioxidants for use in the solid dosage forms described herein include, for example, e.g., butylated hydroxytoluene (BHT), sodium ascorbate, and tocopherol.

It should be appreciated that there is considerable overlap between additives used in the solid dosage forms described herein. Thus, the above-listed additives should be taken as merely exemplary, and not limiting, of the types of additives that can be included in solid dosage forms of the pharmaceutical compositions described herein. The amounts of such additives can be readily determined by one skilled in the art, according to the particular properties desired.

In various embodiments, the particles of a therapeutic agents and one or more excipients are dry blended and compressed into a mass, such as a tablet, having a hardness sufficient to provide a pharmaceutical composition that substantially disintegrates within less than about 30 minutes, less than about 35 minutes, less than about 40 minutes, less than about 45 minutes, less than about 50 minutes, less than about 55 minutes, or less than about 60 minutes, after oral administration, thereby releasing the formulation into the gastrointestinal fluid.

In other embodiments, a powder including a therapeutic agent is formulated to include one or more pharmaceutical excipients and flavors. Such a powder is prepared, for example, by mixing the therapeutic agent and optional pharmaceutical excipients to form a bulk blend composition. Additional embodiments also include a suspending agent and/or a wetting agent. This bulk blend is uniformly subdivided into unit dosage packaging or multi-dosage packaging units.

In still other embodiments, effervescent powders are also prepared. Effervescent salts have been used to disperse medicines in water for oral administration.

In some embodiments, the pharmaceutical dosage forms are formulated to provide a controlled release of a therapeutic agent. Controlled release refers to the release of the therapeutic agent from a dosage form in which it is incorporated according to a desired profile over an extended period of time. Controlled release profiles include, for example, sustained release, prolonged release, pulsatile release, and delayed release profiles. In contrast to immediate release compositions, controlled release compositions allow delivery of an agent to a subject over an extended period of time according to a predetermined profile. Such release rates can provide therapeutically effective levels of agent for an extended period of time and thereby provide a longer period of pharmacologic response while minimizing side effects as compared to conventional rapid release dosage forms. Such longer periods of response provide for many inherent benefits that are not achieved with the corresponding short acting, immediate release preparations.

In some embodiments, the solid dosage forms described herein are formulated as enteric coated delayed release oral dosage forms, i.e., as an oral dosage form of a pharmaceutical composition as described herein which utilizes an enteric coating to affect release in the small intestine or large intestine. In one aspect, the enteric coated dosage form is a compressed or molded or extruded tablet/mold (coated or uncoated) containing granules, powder, pellets, beads or particles of the active ingredient and/or other composition components, which are themselves coated or uncoated. In one aspect, the enteric coated oral dosage form is in the form of a capsule containing pellets, beads or granules, which include a therapeutic agent that are coated or uncoated.

Any coatings should be applied to a sufficient thickness such that the entire coating does not dissolve in the gastrointestinal fluids at pH below about 5, but does dissolve at pH about 5 and above. Coatings are typically selected from any of the following: Shellac—this coating dissolves in media of pH>7; Acrylic polymers—examples of suitable acrylic polymers include methacrylic acid copolymers and ammonium methacrylate copolymers. The Eudragit series E, L, S, RL, RS and NE (Rohm Pharma) are available as solubilized in organic solvent, aqueous dispersion, or dry powders. The Eudragit series RL, NE, and RS are insoluble in the gastrointestinal tract but are permeable and are used primarily for colonic targeting. The Eudragit series E dissolve in the stomach. The Eudragit series L, L-30D and S are insoluble in stomach and dissolve in the intestine; Poly Vinyl Acetate Phthalate (PVAP)—PVAP dissolves in pH>5, and it is much less permeable to water vapor and gastric fluids. Conventional coating techniques such as spray or pan coating are employed to apply coatings. The coating thickness must be sufficient to ensure that the oral dosage form remains intact until the desired site of topical delivery in the intestinal tract is reached.

In other embodiments, the formulations described herein are delivered using a pulsatile dosage form. A pulsatile dosage form is capable of providing one or more immediate release pulses at predetermined time points after a controlled lag time or at specific sites. Exemplary pulsatile dosage forms and methods of their manufacture are disclosed in U.S. Pat. Nos. 5,011,692, 5,017,381, 5,229,135, 5,840,329 and 5,837,284. In one embodiment, the pulsatile dosage form includes at least two groups of particles, (i.e. multiparticulate) each containing the formulation described herein. The first group of particles provides a substantially immediate dose of a therapeutic agent upon ingestion by a mammal. The first group of particles can be either uncoated or include a coating and/or sealant. In one aspect, the second group of particles comprises coated particles. The coating on the second group of particles provides a delay of from about 2 hours to about 7 hours following ingestion before release of the second dose. Suitable coatings for pharmaceutical compositions are described herein or known in the art.

In some embodiments, pharmaceutical formulations are provided that include particles of a therapeutic agent and at least one dispersing agent or suspending agent for oral administration to a subject. The formulations may be a powder and/or granules for suspension, and upon admixture with water, a substantially uniform suspension is obtained.

In some embodiments, particles formulated for controlled release are incorporated in a gel or a patch or a wound dressing.

In one aspect, liquid formulation dosage forms for oral administration and/or for topical administration as a wash are in the form of aqueous suspensions selected from the group including, but not limited to, pharmaceutically acceptable aqueous oral dispersions, emulsions, solutions, elixirs, gels, and syrups. See, e.g., Singh et al., Encyclopedia of Pharmaceutical Technology, 2nd Ed., pp. 754-757 (2002). In addition to the particles of a therapeutic agent, the liquid dosage forms include additives, such as: (a) disintegrating agents; (b) dispersing agents; (c) wetting agents; (d) at least one preservative, (e) viscosity enhancing agents, (f) at least one sweetening agent, and (g) at least one flavoring agent. In some embodiments, the aqueous dispersions can further include a crystalline inhibitor.

In some embodiments, the liquid formulations also include inert diluents commonly used in the art, such as water or other solvents, solubilizing agents, and emulsifiers. Exemplary emulsifiers are ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propyleneglycol, 1,3-butyleneglycol, dimethylformamide, sodium lauryl sulfate, sodium doccusate, cholesterol, cholesterol esters, taurocholic acid, phosphotidylcholine, oils, such as cottonseed oil, groundnut oil, corn germ oil, olive oil, castor oil, and sesame oil, glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols, fatty acid esters of sorbitan, or mixtures of these substances, and the like.

Furthermore, pharmaceutical compositions optionally include one or more pH adjusting agents or buffering agents, including acids such as acetic, boric, citric, lactic, phosphoric and hydrochloric acids; bases such as sodium hydroxide, sodium phosphate, sodium borate, sodium citrate, sodium acetate, sodium lactate and tris-hydroxymethylaminomethane; and buffers such as citrate/dextrose, sodium bicarbonate and ammonium chloride. Such acids, bases and buffers are included in an amount required to maintain pH of the composition in an acceptable range.

Additionally, pharmaceutical compositions optionally include one or more salts in an amount required to bring osmolality of the composition into an acceptable range. Such salts include those having sodium, potassium or ammonium cations and chloride, citrate, ascorbate, borate, phosphate, bicarbonate, sulfate, thiosulfate or bisulfite anions; suitable salts include sodium chloride, potassium chloride, sodium thiosulfate, sodium bisulfite and ammonium sulfate.

Other pharmaceutical compositions optionally include one or more preservatives to inhibit microbial activity. Suitable preservatives include mercury-containing substances such as merfen and thiomersal; stabilized chlorine dioxide; and quaternary ammonium compounds such as benzalkonium chloride, cetyltrimethylammonium bromide and cetylpyridinium chloride.

In one embodiment, the aqueous suspensions and dispersions described herein remain in a homogenous state, as defined in The USP Pharmacists' Pharmacopeia (2005 edition, chapter 905), for at least 4 hours. In one embodiment, an aqueous suspension is re-suspended into a homogenous suspension by physical agitation lasting less than 1 minute. In still another embodiment, no agitation is necessary to maintain a homogeneous aqueous dispersion.

Examples of disintegrating agents for use in the aqueous suspensions and dispersions include, but are not limited to, a starch, e.g., a natural starch such as corn starch or potato starch, a pregelatinized starch, or sodium starch glycolate; a cellulose such as methylcrystalline cellulose, methylcellulose, croscarmellose, or a cross-linked cellulose, such as cross-linked sodium carboxymethylcellulose, cross-linked carboxymethylcellulose, or cross-linked croscarmellose; a cross-linked starch such as sodium starch glycolate; a cross-linked polymer such as crospovidone; a cross-linked polyvinylpyrrolidone; alginate such as alginic acid or a salt of alginic acid such as sodium alginate; a gum such as agar, guar, locust bean, Karaya, pectin, or tragacanth; sodium starch glycolate; bentonite; a natural sponge; a surfactant; a resin such as a cation-exchange resin; citrus pulp; sodium lauryl sulfate; sodium lauryl sulfate in combination starch; and the like.

In some embodiments, the dispersing agents suitable for the aqueous suspensions and dispersions described herein include, for example, hydrophilic polymers, electrolytes, Tween® 60 or 80, PEG, polyvinylpyrrolidone, and the carbohydrate-based dispersing agents such as, for example, hydroxypropylcellulose and hydroxypropyl cellulose ethers, hydroxypropyl methylcellulose and hydroxypropyl methylcellulose ethers, carboxymethylcellulose sodium, methylcellulose, hydroxyethylcellulose, hydroxypropylmethyl-cellulose phthalate, hydroxypropylmethyl-cellulose acetate stearate, noncrystalline cellulose, magnesium aluminum silicate, triethanolamine, polyvinyl alcohol (PVA), polyvinylpyrrolidone/vinyl acetate copolymer, 4-(1,1,3,3-tetramethylbutyl)-phenol polymer with ethylene oxide and formaldehyde (also known as tyloxapol), poloxamers; and poloxamines. In other embodiments, the dispersing agent is selected from a group not comprising one of the following agents: hydrophilic polymers; electrolytes; Tween® 60 or 80; PEG; polyvinylpyrrolidone (PVP); hydroxypropylcellulose and hydroxypropyl cellulose ethers; hydroxypropyl methylcellulose and hydroxypropyl methylcellulose ethers; carboxymethylcellulose sodium; methylcellulose; hydroxyethylcellulose; hydroxypropylmethyl-cellulose phthalate; hydroxypropylmethyl-cellulose acetate stearate; non-crystalline cellulose; magnesium aluminum silicate; triethanolamine; polyvinyl alcohol (PVA); 4-(1,1,3,3-tetramethylbutyl)-phenol polymer with ethylene oxide and formaldehyde; poloxamers; or poloxamines.

Wetting agents suitable for the aqueous suspensions and dispersions described herein include, but are not limited to, cetyl alcohol, glycerol monostearate, polyoxyethylene sorbitan fatty acid esters (e.g., the commercially available Tweens® such as e.g., Tween 20® and Tween 80®, and polyethylene glycols, oleic acid, glyceryl monostearate, sorbitan monooleate, sorbitan monolaurate, triethanolamine oleate, polyoxyethylene sorbitan monooleate, polyoxyethylene sorbitan monolaurate, sodium oleate, sodium lauryl sulfate, sodium docusate, triacetin, vitamin E TPGS, sodium taurocholate, simethicone, phosphotidylcholine and the like.

Suitable preservatives for the aqueous suspensions or dispersions described herein include, for example, potassium sorbate, parabens (e.g., methylparaben and propylparaben), benzoic acid and its salts, other esters of parahydroxybenzoic acid such as butylparaben, alcohols such as ethyl alcohol or benzyl alcohol, phenolic compounds such as phenol, or quaternary compounds such as benzalkonium chloride. Preservatives, as used herein, are incorporated into the dosage form at a concentration sufficient to inhibit microbial growth.

Suitable viscosity enhancing agents for the aqueous suspensions or dispersions described herein include, but are not limited to, methyl cellulose, xanthan gum, carboxymethyl cellulose, hydroxypropyl cellulose, hydroxypropylmethyl cellulose, Plasdon® S-630, carbomer, polyvinyl alcohol, alginates, acacia, chitosans and combinations thereof. The concentration of the viscosity enhancing agent will depend upon the agent selected and the viscosity desired.

Examples of sweetening agents suitable for the aqueous suspensions or dispersions described herein include, for example, acacia syrup, acesulfame K, alitame, aspartame, chocolate, cinnamon, citrus, cocoa, cyclamate, dextrose, fructose, ginger, glycyrrhetinate, glycyrrhiza (licorice) syrup, monoammonium glyrrhizinate (MagnaSweet®), malitol, mannitol, menthol, neohesperidine DC, neotame, Prosweet® Powder, saccharin, sorbitol, stevia, sucralose, sucrose, sodium saccharin, saccharin, aspartame, acesulfame potassium, mannitol, sucralose, tagatose, thaumatin, vanilla, xylitol, or any combination thereof.

In some embodiments, a therapeutic agent is prepared as transdermal dosage form. In some embodiments, the transdermal formulations described herein include at least three components: (1) a therapeutic agent; (2) a penetration enhancer; and (3) an optional aqueous adjuvant. In some embodiments the transdermal formulations include additional components such as, but not limited to, gelling agents, creams and ointment bases, and the like. In some embodiments, the transdermal formulation is presented as a patch or a wound dressing. In some embodiments, the transdermal formulation further include a woven or non-woven backing material to enhance absorption and prevent the removal of the transdermal formulation from the skin. In other embodiments, the transdermal formulations described herein can maintain a saturated or supersaturated state to promote diffusion into the skin.

In one aspect, formulations suitable for transdermal administration of a therapeutic agent described herein employ transdermal delivery devices and transdermal delivery patches and can be lipophilic emulsions or buffered, aqueous solutions, dissolved and/or dispersed in a polymer or an adhesive. In one aspect, such patches are constructed for continuous, pulsatile, or on demand delivery of pharmaceutical agents. Still further, transdermal delivery of the therapeutic agents described herein can be accomplished by means of iontophoretic patches and the like. In one aspect, transdermal patches provide controlled delivery of a therapeutic agent. In one aspect, transdermal devices are in the form of a bandage comprising a backing member, a reservoir containing the therapeutic agent optionally with carriers, optionally a rate controlling barrier to deliver the therapeutic agent to the skin of the host at a controlled and predetermined rate over a prolonged period of time, and means to secure the device to the skin.

In further embodiments, topical formulations include gel formulations (e.g., gel patches which adhere to the skin). In some of such embodiments, a gel composition includes any polymer that forms a gel upon contact with the body (e.g., gel formulations comprising hyaluronic acid, pluronic polymers, poly(lactic-co-glycolic acid (PLGA)-based polymers or the like). In some forms of the compositions, the formulation comprises a low-melting wax such as, but not limited to, a mixture of fatty acid glycerides, optionally in combination with cocoa butter which is first melted. Optionally, the formulations further comprise a moisturizing agent.

In certain embodiments, delivery systems for pharmaceutical therapeutic agents may be employed, such as, for example, liposomes and emulsions. In certain embodiments, compositions provided herein can also include an mucoadhesive polymer, selected from among, for example, carboxymethylcellulose, carbomer (acrylic acid polymer), poly(methylmethacrylate), polyacrylamide, polycarbophil, acrylic acid/butyl acrylate copolymer, sodium alginate and dextran.

In some embodiments, a therapeutic agent described herein may be administered topically and can be formulated into a variety of topically administrable compositions, such as solutions, suspensions, lotions, gels, pastes, medicated sticks, balms, creams or ointments. Such pharmaceutical therapeutic agents can contain solubilizers, stabilizers, tonicity enhancing agents, buffers and preservatives.

Numbered Embodiments

Disclosed herein, in some embodiments, are the following:

- 1. A method of identifying a risk of developing a disease or condition in a subject, the method comprising:
  - a. providing a sample obtained from a subject;
  - b. analyzing the sample to detect a presence or the absence of a genotype in the sample; and
  - c. identifying a risk of developing a disease or condition in the subject, provided the presence of the genotype is detected in the sample obtained from the subject.
- 2. The method of embodiment 1, wherein the disease or condition is selected from the group consisting of Crohn's disease (CD), ulcerative colitis (UC), and inflammatory bowel disease (IBD).
- 3. The method of embodiment 2, wherein, the CD is a severe form of CD characterized by a subclinical phenotype selected from the group consisting of stricturing disease, internal penetrating disease, and stricturing and internal penetrating disease.
- 4. The method of embodiments 1-3, wherein the subject is human.
- 5. The method of embodiment 1, further comprising:
  - a. treating or preventing the disease or condition in the subject comprising administering to the subject a therapeutically effective amount of a therapeutic agent.
- 6. The method of embodiment 5, further comprising treating or preventing the disease or condition in the subject comprising administering to the subject a therapeutically effective amount of an additional therapeutic agent.
- 7. The method of embodiment 5, further comprising prescribing to the subject a therapeutically effective amount of at least one of a therapeutic agent and an additional therapeutic agent.
- 8. The method of embodiments 5-7, wherein the therapeutic agent is a modulator of a gene or gene expression product expressed from the gene involved in prolactin signaling.
- 9. The method of embodiment 8, wherein the gene is selected from the group consisting of Interferon Regulatory Factor 1 (IRF1), Klotho Beta (KLB), Mitogen-Activated Protein Kinase Kinase 1 (MAP2K1), Nuclear Receptor Subfamily 3 Group C Member 1 (NR3C1), Protein Kinase C Beta (PRKCB), Protein Kinase C Epsilon (PRKCE), Protein Kinase C Gamma (PRKCG), Protein Kinase C Eta (PRKCH), Protein Kinase C Theta (PRKCQ), Prolactin Receptor (PRLR), Protein Tyrosine Phosphatase, Non-Receptor Type 11 (PTPN11), Signal Transducer And Activator Of Transcription 1 (STAT1), Signal Transducer And Activator Of Transcription 5A (STAT5A), and Signal Transducer And Activator Of Transcription 5B (STAT5B).
- 10. The method of embodiments 5-7, wherein the therapeutic agent is a modulator of a gene or gene expression product expressed from the gene involved in autophagy.
- 11. The method of embodiment 10, wherein the gene is selected from the group consisting of Autophagy Related 10 (ATG10), Autophagy Related 16 Like 1 (ATG16L1), Autophagy Related 4A Cysteine Peptidase (ATG4A), Autophagy Related 4C Cysteine Peptidase (ATG4C), Cathepsin H (CTSH), Sequestosome 1 (SQSTM1), Unc-51 Like Autophagy Activating Kinase 1 (ULK1), and WD Repeat And FYVE Domain Containing 3 (WDFY3).
- 12. The method of embodiments 5-7, wherein the therapeutic agent is a modulator of Janus Kinase 1 (JAK1).
- 13. The method of embodiments 5-7, wherein the therapeutic agent is a modulator of Tumor Necrosis Factor Ligand 1A (TL1A).
- 14. The method of embodiments 1-13, wherein the genotype comprises a polymorphism provided in Table 1, or a polymorphism in linkage disequilibrium (LD) therewith.
- 15. The method of embodiment 14, wherein LD is defined by an r²value of at least about 0.70, 0.75, 0.80, 0.85, 0.90, 0.95, 0.96, 0.97, 0.98, 0.99, or 1.0.
- 16. The method of embodiment 15, wherein the LD is defined by r²value of between 0.85-0.90, 0.90-0.95, and 0.95-1.0.
- 17. The method of embodiments 14-16, wherein genotype comprises at least 2, 3, 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, or more polymorphisms provided in Table 1.
- 18. The method of embodiments 1-17, wherein analyzing the sample to detect the presence or the absence of a genotype in the sample of step (b) comprises:
  - a. contacting a nucleic acid sequence that is capable of hybridizing to the genotype to the sample; and
  - b. detecting binding between the nucleic acid sequence and the genotype.
- 19. The method of embodiment 18, wherein the nucleic acid comprises a detectable moiety.
- 20. The method of embodiments 1-19, wherein analyzing the sample to detect the presence or the absence of a genotype in the sample of step (b) comprises sequencing genetic information in the sample obtained from the subject.
- 21. The method of embodiments 1-20, further comprising:
  - a. analyzing the sample to detect a presence of a serological marker in the sample; and
  - b. identifying the risk of developing the disease or condition in the subject, provided the presence of the serological marker is detected in the sample obtained from the subject.
- 22. The method of embodiment 21, wherein analyzing the sample to detect a presence of the serological marker in the sample of step (a) comprises:
  - a. contacting an antibody or antigen-binding fragment that is capable of binding to at least part of the serological marker or antigen thereof to the sample; and
  - b. detecting binding between the antibody or antigen-binding fragment and the serological marker or antigen thereof.
- 23. The method of embodiment 22, wherein analyzing the sample to detect a presence of the serological marker in the sample of step (a) comprises using an enzyme-linked immunosorbent assay (ELISA).
- 24. The method of embodiments 21-23, wherein the serological marker is selected from the group consisting of anti-Saccharomyces cerevisiae antibody (ASCA), an anti-neutrophil cytoplasmic antibody (ANCA), anti-Escherichia coli outer membrane porin protein C (anti-OmpC) antibody, anti-I2 antibody, and anti-Cbir1 flagellin antibody.
- 25. A method of characterizing a subtype of a disease or condition, the method comprising:
  - a. analyzing a sample obtained from a subject with a disease or a condition to detect a presence or an absence of a genotype in the sample; and
  - b. characterizing the disease or the condition as a severe form of the disease or the condition, provided the presence of the genotype is detected in the sample obtained from the subject.
- 26. The method of embodiment 25, wherein the disease or condition is selected from the group consisting of Crohn's disease (CD), ulcerative colitis (UC), and inflammatory bowel disease (IBD).
- 27. The method of embodiment 25-26, wherein subtype is selected from the group consisting of stricturing disease, internal penetrating disease, and stricturing and internal penetrating disease.
- 28. The method of embodiments 25-27, wherein the subject is human.
- 29. The method of embodiment 25, further comprising treating the disease or condition in the subject comprising administering to the subject a therapeutically effective amount of a therapeutic agent.
- 30. The method of embodiment 25, further comprising treating the disease or condition in the subject comprising administering to the subject a therapeutically effective amount of an additional therapeutic agent.
- 31. The method of embodiment 25, further comprising prescribing to the subject a therapeutically effective amount of at least one of a therapeutic agent and an additional therapeutic agent.
- 32. The method of embodiment 29-31, wherein the therapeutic agent is a modulator of a gene or gene expression product expressed from the gene involved in prolactin signaling.
- 33. The method of embodiment 32, wherein the gene is selected from the group consisting of Interferon Regulatory Factor 1 (IRF1), Klotho Beta (KLB), Mitogen-Activated Protein Kinase Kinase 1 (MAP2K1), Nuclear Receptor Subfamily 3 Group C Member 1 (NR3C1), Protein Kinase C Beta (PRKCB), Protein Kinase C Epsilon (PRKCE), Protein Kinase C Gamma (PRKCG), Protein Kinase C Eta (PRKCH), Protein Kinase C Theta (PRKCQ), Prolactin Receptor (PRLR), Protein Tyrosine Phosphatase, Non-Receptor Type 11 (PTPN11), Signal Transducer And Activator Of Transcription 1 (STAT1), Signal Transducer And Activator Of Transcription 5A (STAT5A), and Signal Transducer And Activator Of Transcription 5B (STAT5B).
- 34. The method of embodiments 29-31, wherein the therapeutic agent is a modulator of a gene or gene expression product expressed from the gene involved in autophagy.
- 35. The method of embodiment 34, wherein the gene is selected from the group consisting of Autophagy Related 10 (ATG10), Autophagy Related 16 Like 1 (ATG16L1), Autophagy Related 4A Cysteine Peptidase (ATG4A), Autophagy Related 4C Cysteine Peptidase (ATG4C), Cathepsin H (CTSH), Sequestosome 1 (SQSTM1), Unc-51 Like Autophagy Activating Kinase 1 (ULK1), and WD Repeat And FYVE Domain Containing 3 (WDFY3).
- 36. The method of embodiments 29-31, wherein the therapeutic agent is a modulator of Janus Kinase 1 (JAK1).
- 37. The method of embodiments 29-31, wherein the therapeutic agent is a modulator of Tumor Necrosis Factor Ligand 1A (TL1A).
- 38. The method of embodiments 25-37, wherein the genotype comprises a polymorphism provided in Table 1, or a polymorphism in linkage disequilibrium (LD) therewith.
- 39. The method of embodiments 38, wherein LD is defined by an r²value of at least about 0.70, 0.75, 0.80, 0.85, 0.90, 0.95, 0.96, 0.97, 0.98, 0.99, or 1.0.
- 40. The method of embodiment 38, wherein the LD is defined by r²value of between 0.85-0.90, 0.90-0.95, and 0.95-1.0.
- 41. The method of embodiments 25-40, wherein genotype comprises at least 2, 3, 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, or more polymorphisms provided in Table 1.
- 42. The method of embodiments 25-41, wherein analyzing the sample to detect the presence or the absence of a genotype in the sample of step (b) comprises:
  - a. contacting a nucleic acid sequence that is capable of hybridizing to the genotype to the sample; and
  - b. detecting binding between the nucleic acid sequence and the genotype.
- 43. The method of embodiment 42, wherein the nucleic acid comprises a detectable moiety.
- 44. The method of embodiments 45-43, wherein analyzing the sample to detect the presence or the absence of a genotype in the sample of step (b) comprises sequencing genetic information in the sample obtained from the subject.
- 45. The method of embodiments 25-44, further comprising:
  - a. analyzing the sample to detect a presence of a serological marker in the sample; and
  - b. identifying the risk of developing the disease or condition in the subject, provided the presence of the serological marker is detected in the sample obtained from the subject.
- 46. The method of embodiment 45, wherein analyzing the sample to detect a presence of the serological marker in the sample of step (a) comprises:
  - a. contacting an antibody or antigen-binding fragment that is capable of binding to at least part of the serological marker or antigen thereof to the sample; and
  - b. detecting binding between the antibody or antigen-binding fragment and the serological marker or antigen thereof.
- 47. The method of embodiment 46, wherein analyzing the sample to detect a presence of the serological marker in the sample of step (a) comprises using an enzyme-linked immunosorbent assay (ELISA).
- 48. The method of embodiments 45-47, wherein the serological marker is selected from the group consisting of anti-Saccharomyces cerevisiae antibody (ASCA), an anti-neutrophil cytoplasmic antibody (ANCA), anti-Escherichia coli outer membrane porin protein C (anti-OmpC) antibody, anti-I2 antibody, and anti-Cbir1 flagellin antibody.
- 49. The method of embodiment 38-48, wherein the polymorphism is selected from the group consisting of rs2726797, rs7108993, rs79665096, rs7604404, rs73085878, rs78727269, rs2736352, rs4924935, rs11227112, rs2285043, rs6989059, rs3807552, rs111455641, rs9480689, rs7416358, rs6879067, rs11128532, rs177665, rs11171747, rs10775375, rs6801634, rs1070444, rs116714418, rs6962616, rs7220814, rs4325270, rs768755, rs17758350, rs9480689, rs525850, rs4325270, rs11749180, rs6962616, rs116714418, rs10265554, rs634641, rs1493871, rs12669698, rs4332037, rs17697480, rs9480689, rs6074737, rs904910, rs12972487, rs445417, rs635624, rs7416358, 12-54819630-G-INSERTION, rs177665, rs1070444, rs10912583, rs12914919, rs2854725, rs948068, rs71472147, rs72939578, rs658795, rs17758350, rs144260901, rs10801129, rs1702870, rs10912583, rs2452822, rs7774349, rs4705272, rs117946479, rs936126, rs634641, rs2314737, rs3002685, rs634641, rs12496281, rs10134119, rs3808240, rs1890843, rs11829981, rs12496281, rs2383184, rs144260901, rs6801634, rs2383184, rs2954756, and a polymorphism in LD therewith.
- 50. The method of the previous embodiments, wherein the polymorphism is selected from the group consisting of rs2726797, rs7108993, rs79665096, rs7604404, and any combination thereof
- 51. The method of the previous embodiments, wherein the polymorphism is selected from the group consisting rs73085878, rs78727269, rs2736352, rs4924935, rs11227112, rs2285043, rs6989059, rs3807552, and any combination thereof.
- 52. The method of the previous embodiments, wherein the polymorphism is selected from the group consisting rs111455641, rs9480689, and any combination thereof.
- 53. The method of the previous embodiments, wherein the polymorphism is selected from the group consisting rs7416358, rs6879067, rs11128532, and any combination thereof
- 54. The method of the previous embodiments, wherein the polymorphism is selected from the group consisting rs177665, rs11171747, and any combination thereof
- 55. The method of the previous embodiments, wherein the polymorphism is rs10775375.
- 56. The method of the previous embodiments, wherein the polymorphism is rs6801634.
- 57. The method of the previous embodiments, wherein the polymorphism is selected from the group consisting rs1070444, rs116714418, rs6962616, rs7220814, rs4325270, rs768755, and any combination thereof
- 58. The method of the previous embodiments, wherein the polymorphism is selected from the group consisting rs17758350, rs9480689, rs525850, rs4325270, and any combination thereof
- 59. The method of the previous embodiments, wherein the polymorphism is selected from the group consisting rs11749180, rs6962616, rs116714418, rs10265554, rs634641, rs1493871, rs12669698, and any combination thereof
- 60. The method of the previous embodiments, wherein the polymorphism is rs4332037.
- 61. The method of the previous embodiments, wherein the polymorphism is selected from the group consisting rs17697480, rs9480689, and any combination thereof
- 62. The method of the previous embodiments, wherein the polymorphism is selected from the group consisting rs6074737, rs904910, rs12972487, rs445417, and any combination thereof
- 63. The method of the previous embodiments, wherein the polymorphism is selected from the group consisting rs635624, rs7416358, and any combination thereof
- 64. The method of the previous embodiments, wherein the polymorphism is selected from the group consisting 12-54819630-G-INSERTION, rs177665, and any combination thereof
- 65. The method of the previous embodiments, wherein the polymorphism is selected from the group consisting rs1070444, rs10912583, rs12914919, rs2854725, and any combination thereof
- 66. The method of the previous embodiments, wherein the polymorphism is selected from the group consisting rs948068, rs71472147, rs72939578, rs658795, rs17758350, rs144260901, and any combination thereof.
- 67. The method of the previous embodiments, wherein the polymorphism is selected from the group consisting rs10801129, rs1702870, rs10912583, rs2452822, rs7774349, and any combination thereof.
- 68. The method of the previous embodiments, wherein the polymorphism is selected from the group consisting rs4705272, rs117946479, and any combination thereof.
- 69. The method of embodiment 49-68, wherein the polymorphism at rs2726797 comprises a C allele at nucleoposition 26 within SEQ ID NO: 1.
- 70. The method of embodiment 49-68, wherein the polymorphism at rs7108993 comprises a C allele at nucleoposition 26 within SEQ ID NO: 2.
- 71. The method of embodiment 49-68, wherein the polymorphism at rs79665096 comprises an A allele at nucleoposition 26 within SEQ ID NO: 3.
- 72. The method of embodiment 49-68, wherein the polymorphism at rs7604404 comprises an A allele at nucleoposition 26 within SEQ ID NO: 4.
- 73. The method of embodiment 49-68, wherein the polymorphism at rs73085878 comprises an A allele at nucleoposition 26 within SEQ ID NO: 5.
- 74. The method of embodiment 49-68, wherein the polymorphism at rs78727269 comprises an A allele at nucleoposition 26 within SEQ ID NO: 6.
- 75. The method of embodiment 49-68, wherein the polymorphism at rs2736352 comprises an A allele at nucleoposition 26 within SEQ ID NO: 7.
- 76. The method of embodiment 49-68, wherein the polymorphism at rs4924935 comprises a G allele at nucleoposition 26 within SEQ ID NO: 8.
- 77. The method of embodiment 49-68, wherein the polymorphism at rs11227112 comprises a G allele at nucleoposition 26 within SEQ ID NO: 9.
- 78. The method of embodiment 49-68, wherein the polymorphism at rs2285043 comprises an A allele at nucleoposition 26 within SEQ ID NO: 10.
- 79. The method of embodiment 49-68, wherein the polymorphism at rs6989059 comprises an A allele at nucleoposition 26 within SEQ ID NO: 11.
- 80. The method of embodiment 49-68, wherein the polymorphism at rs3807552 comprises an A allele at nucleoposition 26 within SEQ ID NO: 12.
- 81. The method of embodiment 49-68, wherein the polymorphism at rs111455641 comprises a G allele at nucleoposition 26 within SEQ ID NO: 13.
- 82. The method of embodiment 49-68, wherein the polymorphism at rs9480689 comprises a G allele at nucleoposition 26 within SEQ ID NO: 14.
- 83. The method of embodiment 49-68, wherein the polymorphism at rs7416358 comprises a G allele at nucleoposition 26 within SEQ ID NO: 15.
- 84. The method of embodiment 49-68, wherein the polymorphism at rs6879067 comprises an A allele at nucleoposition 26 within SEQ ID NO: 16.
- 85. The method of embodiment 49-68, wherein the polymorphism at rs11128532 comprises an A allele at nucleoposition 26 within SEQ ID NO: 17.
- 86. The method of embodiment 49-68, wherein the polymorphism at rs177665 comprises a C allele at nucleoposition 26 within SEQ ID NO: 18.
- 87. The method of embodiment 49-68, wherein the polymorphism at rs11171747 comprises a C allele at nucleoposition 26 within SEQ ID NO: 19.
- 88. The method of embodiment 49-68, wherein the polymorphism at rs10775375 comprises an A allele at nucleoposition 26 within SEQ ID NO: 20.
- 89. The method of embodiment 49-68, wherein the polymorphism at rs6801634 comprises an A allele at nucleoposition 26 within SEQ ID NO: 21.
- 90. The method of embodiment 49-68, wherein the polymorphism at rs1070444 comprises an A allele at nucleoposition 26 within SEQ ID NO: 22.
- 91. The method of embodiment 49-68, wherein the polymorphism at rs116714418 comprises an A allele at nucleoposition 26 within SEQ ID NO: 23.
- 92. The method of embodiment 49-68, wherein the polymorphism at rs6962616 comprises an A allele at nucleoposition 26 within SEQ ID NO: 24.
- 93. The method of embodiment 49-68, wherein the polymorphism at rs7220814 comprises a G allele at nucleoposition 26 within SEQ ID NO: 25.
- 94. The method of embodiment 49-68, wherein the polymorphism at rs4325270 comprises a T allele at nucleoposition 26 within SEQ ID NO: 26.
- 95. The method of embodiment 49-68, wherein the polymorphism at rs768755 comprises a T allele at nucleoposition 26 within SEQ ID NO: 27.
- 96. The method of embodiment 49-68, wherein the polymorphism at rs17758350 comprises an A allele at nucleoposition 31 within SEQ ID NO: 28.
- 97. The method of embodiment 49-68, wherein the polymorphism at rs9480689 comprises a G allele at nucleoposition 26 within SEQ ID NO: 29.
- 98. The method of embodiment 49-68, wherein the polymorphism at rs525850 comprises an A allele at nucleoposition 26 within SEQ ID NO: 30.
- 99. The method of embodiment 49-68, wherein the polymorphism at rs4325270 comprises a T allele at nucleoposition 26 within SEQ ID NO: 31.
- 100. The method of embodiment 49-68, wherein the polymorphism at rs11749180 comprises an A allele at nucleoposition 26 within SEQ ID NO: 32.
- 101. The method of embodiment 49-68, wherein the polymorphism at rs6962616 comprises an A allele at nucleoposition 26 within SEQ ID NO: 33.
- 102. The method of embodiment 49-68, wherein the polymorphism at rs116714418 comprises an A allele at nucleoposition 26 within SEQ ID NO: 34.
- 103. The method of embodiment 49-68, wherein the polymorphism at rs10265554 comprises a G allele at nucleoposition 26 within SEQ ID NO: 35.
- 104. The method of embodiment 49-68, wherein the polymorphism at rs634641 comprises a G allele at nucleoposition 26 within SEQ ID NO: 36.
- 105. The method of embodiment 49-68, wherein the polymorphism at rs1493871 comprises a G allele at nucleoposition 26 within SEQ ID NO: 37.
- 106. The method of embodiment 49-68, wherein the polymorphism at rs12669698 comprises a G allele at nucleoposition 26 within SEQ ID NO: 38.
- 107. The method of embodiment 49-68, wherein the polymorphism at rs4332037 comprises an A allele at nucleoposition 26 within SEQ ID NO: 39.
- 108. The method of embodiment 49-68, wherein the polymorphism at rs17697480 comprises a G allele at nucleoposition 26 within SEQ ID NO: 40.
- 109. The method of embodiment 49-68, wherein the polymorphism at rs9480689 comprises a G allele at nucleoposition 26 within SEQ ID NO: 41.
- 110. The method of embodiment 49-68, wherein the polymorphism at rs6074737 comprises an A allele at nucleoposition 26 within SEQ ID NO: 42.
- 111. The method of embodiment 49-68, wherein the polymorphism at rs904910 comprises a G allele at nucleoposition 26 within SEQ ID NO: 43.
- 112. The method of embodiment 49-68, wherein the polymorphism at rs12972487 comprises an A allele at nucleoposition 26 within SEQ ID NO: 44.
- 113. The method of embodiment 49-68, wherein the polymorphism at rs445417 comprises an A allele at nucleoposition 26 within SEQ ID NO: 45.
- 114. The method of embodiment 49-68, wherein the polymorphism at rs635624 comprises a C allele at nucleoposition 26 within SEQ ID NO: 46.
- 115. The method of embodiment 49-68, wherein the polymorphism at rs7416358 comprises a G allele at nucleoposition 26 within SEQ ID NO: 47.
- 116. The method of embodiment 49-68, wherein the polymorphism at 12-54819630-G-INSERTION comprises an insertion of a G at nucleoposition 26 within SEQ ID NO: 48.
- 117. The method of embodiment 49-68, wherein the polymorphism at rs177665 comprises a C allele at nucleoposition 26 within SEQ ID NO: 49.
- 118. The method of embodiment 49-68, wherein the polymorphism at rs1070444 comprises an A allele at nucleoposition 26 within SEQ ID NO: 50.
- 119. The method of embodiment 49-68, wherein the polymorphism at rs10912583 comprises an A allele at nucleoposition 26 within SEQ ID NO: 51.
- 120. The method of embodiment 49-68, wherein the polymorphism at rs12914919 comprises a G allele at nucleoposition 26 within SEQ ID NO: 52.
- 121. The method of embodiment 49-68, wherein the polymorphism at rs2854725 comprises a C allele at nucleoposition 26 within SEQ ID NO: 53.
- 122. The method of embodiment 49-68, wherein the polymorphism at rs9480689 comprises a G allele at nucleoposition 26 within SEQ ID NO: 54.
- 123. The method of embodiment 49-68, wherein the polymorphism at rs71472147 comprises an A allele at nucleoposition 26 within SEQ ID NO: 55.
- 124. The method of embodiment 49-68, wherein the polymorphism at rs72939578 comprises an A allele at nucleoposition 31 within SEQ ID NO: 56.
- 125. The method of embodiment 49-68, wherein the polymorphism at rs658795 comprises an A allele at nucleoposition 26 within SEQ ID NO: 57.
- 126. The method of embodiment 49-68, wherein the polymorphism at rs17758350 comprises an A allele at nucleoposition 31 within SEQ ID NO: 58.
- 127. The method of embodiment 49-68, wherein the polymorphism at rs144260901 comprises an A allele at nucleoposition 31 within SEQ ID NO: 59.
- 128. The method of embodiment 49-68, wherein the polymorphism at rs10801129 comprises a C allele at nucleoposition 26 within SEQ ID NO: 60.
- 129. The method of embodiment 49-68, wherein the polymorphism at rs1702870 comprises an A allele at nucleoposition 26 within SEQ ID NO: 61.
- 130. The method of embodiment 49-68, wherein the polymorphism at rs10912583 comprises an A allele at nucleoposition 26 within SEQ ID NO: 62.
- 131. The method of embodiment 49-68, wherein the polymorphism at rs2452822 comprises a C allele at nucleoposition 31 within SEQ ID NO: 63.
- 132. The method of embodiment 49-68, wherein the polymorphism at rs7774349 comprises an A allele at nucleoposition 26 within SEQ ID NO: 64.
- 133. The method of embodiment 49-68, wherein the polymorphism at rs4705272 comprises a G allele at nucleoposition 26 within SEQ ID NO: 65.
- 134. The method of embodiment 49-68, wherein the polymorphism at rs117946479 comprises an A allele at nucleoposition 31 within SEQ ID NO: 66.
- 135. The method of embodiment 49-68, wherein the polymorphism at rs936126 comprises an A allele at nucleoposition 26 within SEQ ID NO: 67.
- 136. The method of embodiment 49-68, wherein the polymorphism at rs634641 comprises a G allele at nucleoposition 26 within SEQ ID NO: 68.
- 137. The method of embodiment 49-68, wherein the polymorphism at rs2314737 comprises a G allele at nucleoposition 26 within SEQ ID NO: 69.
- 138. The method of embodiment 49-68, wherein the polymorphism at rs3002685 comprises a G allele at nucleoposition 26 within SEQ ID NO: 70.
- 139. The method of embodiment 49-68, wherein the polymorphism at rs634641 comprises a G allele at nucleoposition 26 within SEQ ID NO: 71.
- 140. The method of embodiment 49-68, wherein the polymorphism at rs12496281 comprises a G allele at nucleoposition 26 within SEQ ID NO: 72.
- 141. The method of embodiment 49-68, wherein the polymorphism at rs10134119 comprises a T allele at nucleoposition 26 within SEQ ID NO: 73.
- 142. The method of embodiment 49-68, wherein the polymorphism at rs3808240 comprises a C allele at nucleoposition 26 within SEQ ID NO: 74.
- 143. The method of embodiment 49-68, wherein the polymorphism at rs1890843 comprises a G allele at nucleoposition 26 within SEQ ID NO: 75.
- 144. The method of embodiment 49-68, wherein the polymorphism at rs11829981 comprises an A allele at nucleoposition 26 within SEQ ID NO: 76.
- 145. The method of embodiment 49-68, wherein the polymorphism at rs12496281 comprises a G allele at nucleoposition 26 within SEQ ID NO: 77.
- 146. The method of embodiment 49-68, wherein the polymorphism at rs2383184 comprises a G allele at nucleoposition 26 within SEQ ID NO: 78.
- 147. The method of embodiment 49-68, wherein the polymorphism at rs144260901 comprises an A allele at nucleoposition 31 within SEQ ID NO: 79.
- 148. The method of embodiment 49-68, wherein the polymorphism at rs6801634 comprises an A allele at nucleoposition 26 within SEQ ID NO: 80.
- 149. The method of embodiment 49-68, wherein the polymorphism at rs2383184 comprises a G allele at nucleoposition 26 within SEQ ID NO: 81.
- 150. The method of embodiment 49-68, wherein the polymorphism at rs2954756 comprises a G allele at nucleoposition 26 within SEQ ID NO: 82.
- 151. The method of any previous embodiment, wherein the therapeutic agent is a modulator of a gene or gene expression product expressed from the gene, the gene selected from group consisting of X—C Motif Chemokine Ligand 1 (XCL1), Dermatopontin (DPT), TNF Superfamily Member 4 (TNFSF4), C-Type Lectin Like 1 (CLECL1), CD69 Molecule (CD69), Fms Related Tyrosine Kinase 1 (FLT1), Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 (MAP4K4), Prostaglandin E Receptor 4 (PTGER4), interleukin 18 receptor 1 (IL18R1). 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 3 (PFKFB3), Interleukin 18 Receptor Accessory Protein (IL18RAP), Adenylate Cyclase 7 (ADCY7), B Lymphoid Tyrosine Kinase (BLK), G Protein-Coupled Receptor 65 (GPR65), Sprouty Related EVH1 Domain Containing 2 (SPRED2), Src Kinase Associated Phosphoprotein 2 (SKAP2), CD30 ligand (CD30L), Receptor Interacting Serine/Threonine Kinase 2 (RIPK2), and TNF Ligand Superfamily Member 15 (TL1A), an a combination thereof.
- 152. The method of any previous embodiment, wherein the modulator of the gene or gene expression product is selected from the group consisting of an antibody or antigen-binding fragment thereof, a small molecule, or a peptide.
- 153. The method of any previous embodiment, wherein the modulator of the gene or gene expression product is an agonist or a partial agonist.
- 154. The method of any previous embodiment, wherein the modulator of the gene or gene expression product is an antagonist or a partial antagonist. In some embodiments, the modulator of the gene or gene expression product is an allosteric modulator.

Kits and Compositions
Compositions

Disclosed herein, in some embodiments, are compositions useful for the detection of a genotype or biomarker in a sample obtained from a subject according to the methods described herein. Aspects disclosed herein provide compositions comprises a polynucleotide sequence comprising at least 10 but less than 50 contiguous nucleotides of any one of SEQ ID NOS: 1-82, or reverse complements thereof, wherein the contiguous polynucleotide sequence comprises a detectable molecule. In some embodiments, the polynucleotide sequence comprises the nucleobase at position 26 or 31 in any one of SEQ ID NOS: 1-82. In various embodiments, the detectable molecule comprises a fluorophore. In other embodiments, the polynucleotide sequences further comprise a quencher.

Also disclosed herein are compositions comprising an antibody or antigen-binding fragment that specifically binds to a serological marker described herein, or antigen thereof, wherein the antibody or antigen-binding fragment comprises a detectable molecule. In various embodiments, the antibody comprises a monoclonal antibody, a chimeric antibody, a CDR-grafted antibody, a Fab, a Fab′, a F(ab′)2, a Fv, a disulfide linked Fv, a scFv, a single domain antibody, a diabody, a multispecific antibody, a dual specific antibody, an anti-idiotypic antibody, or a bispecific antibody. In some embodiments, the antibody or antigen-binding fragment comprises an IgG antibody, an IgM antibody, and/or an IgE antibody. In some embodiments, the detectable molecule comprises a fluorophore. In some embodiments, the antibody or antigen-binding fragment is conjugated to a paramagnetic particle (e.g., bead).

Kits

Disclosed herein, in some embodiments, are kits useful for to detect the genotypes and/or biomarkers disclosed herein. In some embodiments, the kits disclosed herein may be used to diagnose and/or treat a disease or condition in a subject; or select a patient for treatment and/or monitor a treatment disclosed herein. In some embodiments, the kit comprises the compositions described herein, which can be used to perform the methods described herein. Kits comprise an assemblage of materials or components, including at least one of the compositions. Thus, in some embodiments the kit contains a composition including of the pharmaceutical composition, for the treatment of IBD. In other embodiments, the kits contains all of the components necessary and/or sufficient to perform an assay for detecting and measuring IBD markers, including all controls, directions for performing assays, and any necessary software for analysis and presentation of results.

In some instances, the kits described herein comprise components for detecting the presence, absence, and/or quantity of a target nucleic acid and/or protein described herein. In some embodiments, the kit further comprises components for detecting the presence, absence, and/or quantity of a serological marker described herein. In some embodiments, the kit comprises the compositions (e.g., primers, probes, antibodies) described herein. The disclosure provides kits suitable for assays such as enzyme-linked immunosorbent assay (ELISA), single-molecular array (Simoa), PCR, and qPCR. The exact nature of the components configured in the kit depends on its intended purpose.

In some embodiments, the kits described herein are configured for the purpose of treating and/or characterizing a disease or condition (e.g., Crohn's disease), or subclinical phenotype thereof (e.g., stricturing, penetrating, or stricturing and penetrating disease phenotypes) in a subject. In some embodiments, the kit is configured particularly for the purpose of treating mammalian subjects. In some embodiments, the kit is configured particularly for the purpose of treating human subjects. In further embodiments, the kit is configured for veterinary applications, treating subjects such as, but not limited to, farm animals, domestic animals, and laboratory animals. In some embodiments, the kit is configured to select a subject for a therapeutic agent, such as those disclosed herein. In some embodiments, the kit is configured to select a subject for treatment with a therapeutic agent disclosed herein.

Instructions for use may be included in the kit. Optionally, the kit also contains other useful components, such as, diluents, buffers, pharmaceutically acceptable carriers, syringes, catheters, applicators, pipetting or measuring tools, bandaging materials or other useful paraphernalia. The materials or components assembled in the kit can be provided to the practitioner stored in any convenient and suitable ways that preserve their operability and utility. For example the components can be in dissolved, dehydrated, or lyophilized form; they can be provided at room, refrigerated or frozen temperatures. The components are typically contained in suitable packaging material(s). As employed herein, the phrase “packaging material” refers to one or more physical structures used to house the contents of the kit, such as compositions and the like. The packaging material is constructed by well-known methods, preferably to provide a sterile, contaminant-free environment. The packaging materials employed in the kit are those customarily utilized in gene expression assays and in the administration of treatments. As used herein, the term “package” refers to a suitable solid matrix or material such as glass, plastic, paper, foil, and the like, capable of holding the individual kit components. Thus, for example, a package can be a glass vial or prefilled syringes used to contain suitable quantities of the pharmaceutical composition. The packaging material has an external label which indicates the contents and/or purpose of the kit and its components.

Systems

Disclosed herein, in some embodiments, is a system for detecting a particular genotype described herein in a subject. The system is configured to implement the methods described in this disclosure, including, but not limited to, detecting the presence of a particular CD subtype to determine whether the subject is suitable for treatment with a particular therapy.

In some embodiments, disclosed herein is a system for detecting at least one polymorphism provided in Table 1 in a subject, comprising: (a) a computer processing device, optionally connected to a computer network; and (b) a software module executed by the computer processing device to analyze a target nucleic acid sequence of a at least one polymorphism provided in Table 1 in a sample from a subject. In some instances, the system comprises a central processing unit (CPU), memory (e.g., random access memory, flash memory), electronic storage unit, computer program, communication interface to communicate with one or more other systems, and any combination thereof. In some instances, the system is coupled to a computer network, for example, the Internet, intranet, and/or extranet that is in communication with the Internet, a telecommunication, or data network. In some embodiments, the system comprises a storage unit to store data and information regarding any aspect of the methods described in this disclosure. Various aspects of the system are a product or article or manufacture.

One feature of a computer program includes a sequence of instructions, executable in the digital processing device's CPU, written to perform a specified task. In some embodiments, computer readable instructions are implemented as program modules, such as functions, features, Application Programming Interfaces (APIs), data structures, and the like, that perform particular tasks or implement particular abstract data types. In light of the disclosure provided herein, those of skill in the art will recognize that a computer program may be written in various versions of various languages.

The functionality of the computer readable instructions are combined or distributed as desired in various environments. In some instances, a computer program comprises one sequence of instructions or a plurality of sequences of instructions. A computer program may be provided from one location. A computer program may be provided from a plurality of locations. In some embodiment, a computer program includes one or more software modules. In some embodiments, a computer program includes, in part or in whole, one or more web applications, one or more mobile applications, one or more standalone applications, one or more web browser plug-ins, extensions, add-ins, or add-ons, or combinations thereof.

Web Application

In some embodiments, a computer program includes a web application. In light of the disclosure provided herein, those of skill in the art will recognize that a web application may utilize one or more software frameworks and one or more database systems. A web application, for example, is created upon a software framework such as Microsoft® .NET or Ruby on Rails (RoR). A web application, in some instances, utilizes one or more database systems including, by way of non-limiting examples, relational, non-relational, feature oriented, associative, and XML database systems. Suitable relational database systems include, by way of non-limiting examples, Microsoft® SQL Server, mySQL™, and Oracle®. Those of skill in the art will also recognize that a web application may be written in one or more versions of one or more languages. In some embodiments, a web application is written in one or more markup languages, presentation definition languages, client-side scripting languages, server-side coding languages, database query languages, or combinations thereof. In some embodiments, a web application is written to some extent in a markup language such as Hypertext Markup Language (HTML), Extensible Hypertext Markup Language (XHTML), or eXtensible Markup Language (XML). In some embodiments, a web application is written to some extent in a presentation definition language such as Cascading Style Sheets (CSS). In some embodiments, a web application is written to some extent in a client-side scripting language such as Asynchronous Javascript and XML (AJAX), Flash® Actionscript, Javascript, or Silverlight®. In some embodiments, a web application is written to some extent in a server-side coding language such as Active Server Pages (ASP), ColdFusion®, Perl, Java™, JavaServer Pages (JSP), Hypertext Preprocessor (PHP), Python™, Ruby, Tcl, Smalltalk, WebDNA®, or Groovy. In some embodiments, a web application is written to some extent in a database query language such as Structured Query Language (SQL). A web application may integrate enterprise server products such as IBM® Lotus Domino®. A web application may include a media player element. A media player element may utilize one or more of many suitable multimedia technologies including, by way of non-limiting examples, Adobe® Flash®, HTML 5, Apple® QuickTime®, Microsoft® Silverlight®, Java™, and Unity®.

Mobile Application

In some instances, a computer program includes a mobile application provided to a mobile digital processing device. The mobile application may be provided to a mobile digital processing device at the time it is manufactured. The mobile application may be provided to a mobile digital processing device via the computer network described herein.

A mobile application is created by techniques known to those of skill in the art using hardware, languages, and development environments known to the art. Those of skill in the art will recognize that mobile applications may be written in several languages. Suitable programming languages include, by way of non-limiting examples, C, C++, C#, Featureive-C, Java™, Javascript, Pascal, Feature Pascal, Python™, Ruby, VB.NET, WML, and XHTML/HTML with or without CSS, or combinations thereof.

Suitable mobile application development environments are available from several sources. Commercially available development environments include, by way of non-limiting examples, AirplaySDK, alcheMo, Appceleratort, Celsius, Bedrock, Flash Lite, .NET Compact Framework, Rhomobile, and WorkLight Mobile Platform. Other development environments may be available without cost including, by way of non-limiting examples, Lazarus, MobiFlex, MoSync, and Phonegap. Also, mobile device manufacturers distribute software developer kits including, by way of non-limiting examples, iPhone and iPad (iOS) SDK, Android™ SDK, BlackBerry R SDK, BREW SDK, Palm® OS SDK, Symbian SDK, webOS SDK, and Windows® Mobile SDK.

Those of skill in the art will recognize that several commercial forums are available for distribution of mobile applications including, by way of non-limiting examples, Apple® App Store, Android™ Market, BlackBerry R App World, App Store for Palm devices, App Catalog for webOS, Windows® Marketplace for Mobile, Ovi Store for Nokia® devices, Samsung® Apps, and Nintendo® DSi Shop.

Standalone Application

In some embodiments, a computer program includes a standalone application, which is a program that may be run as an independent computer process, not an add-on to an existing process, e.g., not a plug-in. Those of skill in the art will recognize that standalone applications are sometimes compiled. In some instances, a compiler is a computer program(s) that transforms source code written in a programming language into binary feature code such as assembly language or machine code. Suitable compiled programming languages include, by way of non-limiting examples, C, C++, Featureive-C, COBOL, Delphi, Eiffel, Java™, Lisp, Python™, Visual Basic, and VB .NET, or combinations thereof. Compilation may be often performed, at least in part, to create an executable program. In some instances, a computer program includes one or more executable complied applications.

Web Browser Plug-in

A computer program, in some aspects, includes a web browser plug-in. In computing, a plug-in, in some instances, is one or more software components that add specific functionality to a larger software application. Makers of software applications may support plug-ins to enable third-party developers to create abilities which extend an application, to support easily adding new features, and to reduce the size of an application. When supported, plug-ins enable customizing the functionality of a software application. For example, plug-ins are commonly used in web browsers to play video, generate interactivity, scan for viruses, and display particular file types. Those of skill in the art will be familiar with several web browser plug-ins including, Adobe® Flash® Player, Microsoft® Silverlight®, and Apple® QuickTime®. The toolbar may comprise one or more web browser extensions, add-ins, or add-ons. The toolbar may comprise one or more explorer bars, tool bands, or desk bands.

In view of the disclosure provided herein, those of skill in the art will recognize that several plug-in frameworks are available that enable development of plug-ins in various programming languages, including, by way of non-limiting examples, C++, Delphi, Java™, PHP, Python™, and VB .NET, or combinations thereof.

In some embodiments, Web browsers (also called Internet browsers) are software applications, designed for use with network-connected digital processing devices, for retrieving, presenting, and traversing information resources on the World Wide Web. Suitable web browsers include, by way of non-limiting examples, Microsoft® Internet Explorer®, Mozilla® Firefox®, Google® Chrome, Apple® Safari®, Opera Software® Opera®, and KDE Konqueror. The web browser, in some instances, is a mobile web browser. Mobile web browsers (also called mircrobrowsers, mini-browsers, and wireless browsers) may be designed for use on mobile digital processing devices including, by way of non-limiting examples, handheld computers, tablet computers, netbook computers, subnotebook computers, smartphones, music players, personal digital assistants (PDAs), and handheld video game systems. Suitable mobile web browsers include, by way of non-limiting examples, Google® Android® browser, RIM BlackBerry® Browser, Apple® Safari®, Palm® Blazer, Palm® WebOS® Browser, Mozilla® Firefox® for mobile, Microsoft® Internet Explorer® Mobile, Amazon® Kindle® Basic Web, Nokia® Browser, Opera Software® Opera® Mobile, and Sony® PSP™ browser.

Software Modules

The medium, method, and system disclosed herein comprise one or more softwares, servers, and database modules, or use of the same. In view of the disclosure provided herein, software modules may be created by techniques known to those of skill in the art using machines, software, and languages known to the art. The software modules disclosed herein may be implemented in a multitude of ways. In some embodiments, a software module comprises a file, a section of code, a programming feature, a programming structure, or combinations thereof. A software module may comprise a plurality of files, a plurality of sections of code, a plurality of programming features, a plurality of programming structures, or combinations thereof. By way of non-limiting examples, the one or more software modules comprise a web application, a mobile application, and/or a standalone application. Software modules may be in one computer program or application. Software modules may be in more than one computer program or application. Software modules may be hosted on one machine. Software modules may be hosted on more than one machine. Software modules may be hosted on cloud computing platforms. Software modules may be hosted on one or more machines in one location. Software modules may be hosted on one or more machines in more than one location.

Databases

The medium, method, and system disclosed herein comprise one or more databases, or use of the same. In view of the disclosure provided herein, those of skill in the art will recognize that many databases are suitable for storage and retrieval of geologic profile, operator activities, division of interest, and/or contact information of royalty owners. Suitable databases include, by way of non-limiting examples, relational databases, non-relational databases, feature oriented databases, feature databases, entity-relationship model databases, associative databases, and XML databases. In some embodiments, a database is internet-based. In some embodiments, a database is web-based. In some embodiments, a database is cloud computing-based. A database may be based on one or more local computer storage devices.

Data Transmission

The subject matter described herein, including methods for detecting a particular CD subtype, are configured to be performed in one or more facilities at one or more locations. Facility locations are not limited by country and include any country or territory. In some instances, one or more steps are performed in a different country than another step of the method. In some instances, one or more steps for obtaining a sample are performed in a different country than one or more steps for detecting the presence or absence of a particular CD subtype from a sample. In some embodiments, one or more method steps involving a computer system are performed in a different country than another step of the methods provided herein. In some embodiments, data processing and analyses are performed in a different country or location than one or more steps of the methods described herein. In some embodiments, one or more articles, products, or data are transferred from one or more of the facilities to one or more different facilities for analysis or further analysis. An article includes, but is not limited to, one or more components obtained from a subject, e.g., processed cellular material. Processed cellular material includes, but is not limited to, cDNA reverse transcribed from RNA, amplified RNA, amplified cDNA, sequenced DNA, isolated and/or purified RNA, isolated and/or purified DNA, and isolated and/or purified polypeptide. Data includes, but is not limited to, information regarding the stratification of a subject, and any data produced by the methods disclosed herein. In some embodiments of the methods and systems described herein, the analysis is performed and a subsequent data transmission step will convey or transmit the results of the analysis.

In some embodiments, any step of any method described herein is performed by a software program or module on a computer. In additional or further embodiments, data from any step of any method described herein is transferred to and from facilities located within the same or different countries, including analysis performed in one facility in a particular location and the data shipped to another location or directly to an individual in the same or a different country. In additional or further embodiments, data from any step of any method described herein is transferred to and/or received from a facility located within the same or different countries, including analysis of a data input, such as genetic or processed cellular material, performed in one facility in a particular location and corresponding data transmitted to another location, or directly to an individual, such as data related to the diagnosis, prognosis, responsiveness to therapy, or the like, in the same or different location or country.

Business Methods Utilizing a Computer

The methods described herein may utilize one or more computers. The computer may be used for managing customer and sample information such as sample or customer tracking, database management, analyzing molecular profiling data, analyzing cytological data, storing data, billing, marketing, reporting results, storing results, or a combination thereof. The computer may include a monitor or other graphical interface for displaying data, results, billing information, marketing information (e.g. demographics), customer information, or sample information. The computer may also include means for data or information input. The computer may include a processing unit and fixed or removable media or a combination thereof. The computer may be accessed by a user in physical proximity to the computer, for example via a keyboard and/or mouse, or by a user that does not necessarily have access to the physical computer through a communication medium such as a modem, an internet connection, a telephone connection, or a wired or wireless communication signal carrier wave. In some cases, the computer may be connected to a server or other communication device for relaying information from a user to the computer or from the computer to a user. In some cases, the user may store data or information obtained from the computer through a communication medium on media, such as removable media. It is envisioned that data relating to the methods can be transmitted over such networks or connections for reception and/or review by a party. The receiving party can be but is not limited to an individual, a health care provider or a health care manager. In one embodiment, a computer-readable medium includes a medium suitable for transmission of a result of an analysis of a biological sample, such as exosome bio-signatures. The medium can include a result regarding an exosome bio-signature of a subject, wherein such a result is derived using the methods described herein.

The entity obtaining a report regarding a risk of developing a severe form of Crohn's disease may enter sample information into a database for the purpose of one or more of the following: inventory tracking, assay result tracking, order tracking, customer management, customer service, billing, and sales. Sample information may include, but is not limited to: customer name, unique customer identification, customer associated medical professional, indicated assay or assays, assay results, adequacy status, indicated adequacy tests, medical history of the individual, preliminary diagnosis, suspected diagnosis, sample history, insurance provider, medical provider, third party testing center or any information suitable for storage in a database. Sample history may include but is not limited to: age of the sample, type of sample, method of acquisition, method of storage, or method of transport.

The database may be accessible by a customer, medical professional, insurance provider, or other third party. Database access may take the form of electronic communication such as a computer or telephone. The database may be accessed through an intermediary such as a customer service representative, business representative, consultant, independent testing center, or medical professional. The availability or degree of database access or sample information, such as assay results, may change upon payment of a fee for products and services rendered or to be rendered. The degree of database access or sample information may be restricted to comply with generally accepted or legal requirements for patient or customer confidentiality.

Further Embodiments

Disclosed herein, in some embodiments, are the following:

1. A computer system for evaluating a sample from a subject, the system comprising:
- a. a central computing environment;
- b. an input device operatively connected to said central computing environment, wherein said input device is configured to receive a presence or absence of a genotype that correlates with a disease state in the sample;
- c. a trained algorithm executed by said central computing environment, wherein the trained algorithm is configured to use the presence or absence of the genotype to classify said sample as a disease or normal sample; and
- d. an output device operatively connected to said central computing environment, wherein said output device is configured to provide information on the classification to a user.
2. The computer system of embodiment 1, wherein the disease state comprises at least one of Crohn's disease (CD), ulcerative colitis (UC), and inflammatory bowel disease (IBD).
3. The computer system of embodiment 1 or embodiment 2, wherein the disease state is a severe form of CD characterized by a subclinical phenotype selected from the group consisting of stricturing disease, internal penetrating disease, and stricturing and internal penetrating disease.
4. The computer system of any previous embodiment, wherein the sample comprises whole blood, plasma, serum, or tissue.
5. The computer system of any previous embodiment, wherein the genotype comprises at least one polymorphism at a nucleoposition 26 or 31 within any one of SEQ ID NOS: 1-82, a polymorphism in linkage disequilibrium (LD) therewith, and any combination thereof.
6. The computer system of embodiment 5, where LD is defined by an r²value of at least 0.80, 0.85, 0.90, 0.95, or 1.0.
7. The computer system of any previous embodiment, wherein the genotype is associated with a risk that a subject has, or will develop, the disease state by a P value of at most about 1.0×10⁻⁵.
8. The computer system of any previous embodiment, wherein said output device provides a report summarizing said information on said classification.
9. The computer system of any previous embodiment, wherein said report comprises a recommendation for treatment of said disease state.
10. The computer system of embodiment 13, wherein the treatment comprises administration of therapeutic agent.
11. The computer system of embodiment 14, wherein the therapeutic agent is a modulator of a gene or gene expression product expressed from the gene involved in prolactin signaling.
12. The computer system of embodiment 11, wherein the gene is selected from the group consisting of Interferon Regulatory Factor 1 (IRF1), Klotho Beta (KLB), Mitogen-Activated Protein Kinase Kinase 1 (MAP2K1), Nuclear Receptor Subfamily 3 Group C Member 1 (NR3C1), Protein Kinase C Beta (PRKCB), Protein Kinase C Epsilon (PRKCE), Protein Kinase C Gamma (PRKCG), Protein Kinase C Eta (PRKCH), Protein Kinase C Theta (PRKCQ), Prolactin Receptor (PRLR), Protein Tyrosine Phosphatase, Non-Receptor Type 11 (PTPN11), Signal Transducer And Activator Of Transcription 1 (STAT1), Signal Transducer And Activator Of Transcription 5A (STAT5A), and Signal Transducer And Activator Of Transcription 5B (STAT5B).
13. The method of embodiments 10, wherein the therapeutic agent is a modulator of a gene or gene expression product expressed from the gene involved in autophagy.
14. The method of embodiment 13, wherein the gene is selected from the group consisting of Autophagy Related 10 (ATG10), Autophagy Related 16 Like 1 (ATG16L1), Autophagy Related 4A Cysteine Peptidase (ATG4A), Autophagy Related 4C Cysteine Peptidase (ATG4C), Cathepsin H (CTSH), Sequestosome 1 (SQSTM1), Unc-51 Like Autophagy Activating Kinase 1 (ULK1), and WD Repeat And FYVE Domain Containing 3 (WDFY3).
15. The method of embodiment 10, wherein the therapeutic agent is a modulator of Janus Kinase 1 (JAK1).
16. The method of embodiment 10, wherein the therapeutic agent is a modulator of a gene or gene expression product expressed from the gene, the gene selected from group consisting of X—C Motif Chemokine Ligand 1 (XCL1), Dermatopontin (DPT), TNF Superfamily Member 4 (TNFSF4), C-Type Lectin Like 1 (CLECL1), CD69 Molecule (CD69), Fms Related Tyrosine Kinase 1 (FLT1), Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 (MAP4K4), Prostaglandin E Receptor 4 (PTGER4), interleukin 18 receptor 1 (IL18R1). 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 3 (PFKFB3), Interleukin 18 Receptor Accessory Protein (IL18RAP), Adenylate Cyclase 7 (ADCY7), B Lymphoid Tyrosine Kinase (BLK), G Protein-Coupled Receptor 65 (GPR65), Sprouty Related EVH1 Domain Containing 2 (SPRED2), Src Kinase Associated Phosphoprotein 2 (SKAP2), CD30 ligand (CD30L), Receptor Interacting Serine/Threonine Kinase 2 (RIPK2), and TNF Ligand Superfamily Member 15 (TL1A), an a combination thereof.
17. The method of embodiment 1-16, further wherein the inputting device is further configured to receive a presence or absence of a serological marker that correlates with the disease state in the sample.
18. The method of embodiment 17, wherein the trained algorithm is further configured to use the presence or absence of the serological marker to classify said sample as the disease or normal sample; and
19. The method of embodiments 17-18, wherein the serological marker is selected from the group consisting of anti-Saccharomyces cerevisiae antibody (ASCA), an anti-neutrophil cytoplasmic antibody (ANCA), anti-Escherichia coli outer membrane porin protein C (anti-OmpC) antibody, anti-I2 antibody, and anti-Cbir1 flagellin antibody.
20. Use of a composition comprising one or more binding agents for generating a report that classifies a sample from as subject as disease or non-disease of a disease state, wherein the one or more binding agents specifically bind to a polymorphism at a nucleoposition 26 or 31 within any one of SEQ ID NOS: 1-82, its compliment, a polymorphism in linkage disequilibrium (LD) therewith, and any combination thereof.
21. The use of embodiment 20, wherein generating the report further comprises:
- a. providing the sample from the subject;
- b. assaying the sample from the subject for detecting the presence of the one or more polymorphisms in one or more genes;
- c. generating the report based on the result of step (b); and
- d. determining whether said subject has or is likely to have the disease based on the results of step (b).
22. The use of embodiment 20 or 21, wherein the disease state is selected from the group consisting of inflammatory bowel disease (IBD), Crohn's disease (CD), and ulcerative colitis (UC).
23. The use of embodiment 22, wherein the CD is a severe form of CD characterized by a subclinical phenotype selected from the group consisting of stricturing disease, internal penetrating disease, and stricturing and internal penetrating disease.
24. The use of any of embodiments 20-23, wherein the sample comprises whole blood, plasma, serum, or tissue.
25. The use of embodiment 21-24, wherein assaying the sample from the subject for detecting the presence of the one or more polymorphisms of step (b) comprises:
- a. contacting the sample with the one or more binding agents that specifically bind to the one or more polymorphisms; and
- b. determining whether the sample specifically binds to said one or more binding agents, wherein binding of the sample to the one or more binding agents indicates the presence of the polymorphism in the subject.
26. The use of embodiment 20-24, wherein assaying the sample from the subject for detecting the presence of the one or more polymorphisms of step (b) comprises sequencing of the sample.
27. The use of embodiment 20-26, wherein the one or more binding agents specifically bind to a serological marker or antigen thereof.
28. The use of embodiments 27, wherein the serological marker is selected from the group consisting of anti-Saccharomyces cerevisiae antibody (ASCA), an anti-neutrophil cytoplasmic antibody (ANCA), anti-Escherichia coli outer membrane porin protein C (anti-OmpC) antibody, anti-I2 antibody, and anti-Cbir1 flagellin antibody.
29. The use of embodiments 27-28, wherein generating the report further comprises:
- a. providing the sample from the subject;
- b. assaying the sample from the subject for detecting the presence of the serological marker;
- c. generating the report based on the result of step (b); and
- d. determining whether said subject has or is likely to have the disease based on the results of step (b).
30. The use of embodiment 29, wherein assaying the sample from the subject for detecting the presence of the serological marker of step (b) comprises:
- a. contacting the sample with the one or more binding agents that specifically bind to the serological marker; and
- b. determining whether the sample specifically binds to said one or more binding agents, wherein binding of the sample to the one or more binding agents indicates the presence of the of the serological marker in the subject.
31. The use of embodiment 20, wherein the polymorphism is selected from the group consisting of rs2726797, rs7108993, rs79665096, rs7604404, rs73085878, rs78727269, rs2736352, rs4924935, rs11227112, rs2285043, rs6989059, rs3807552, rs111455641, rs9480689, rs7416358, rs6879067, rs11128532, rs177665, rs11171747, rs10775375, rs6801634, rs1070444, rs116714418, rs6962616, rs7220814, rs4325270, rs768755, rs17758350, rs9480689, rs525850, rs4325270, rs11749180, rs6962616, rs116714418, rs10265554, rs634641, rs1493871, rs12669698, rs4332037, rs17697480, rs9480689, rs6074737, rs904910, rs12972487, rs445417, rs635624, rs7416358, 12-54819630-G-INSERTION, rs177665, rs1070444, rs10912583, rs12914919, rs2854725, rs948068, rs71472147, rs72939578, rs658795, rs17758350, rs144260901, rs10801129, rs1702870, rs10912583, rs2452822, rs7774349, rs4705272, rs117946479, rs936126, rs634641, rs2314737, rs3002685, rs634641, rs12496281, rs10134119, rs3808240, rs1890843, rs11829981, rs12496281, rs2383184, rs144260901, rs6801634, rs2383184, rs2954756, and a polymorphism in LD therewith.
32. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting of rs2726797, rs7108993, rs79665096, rs7604404, and any combination thereof.
33. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs73085878, rs78727269, rs2736352, rs4924935, rs11227112, rs2285043, rs6989059, rs3807552, and any combination thereof
34. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs111455641, rs9480689, and any combination thereof.
35. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs7416358, rs6879067, rs11128532, and any combination thereof
36. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs177665, rs11171747, and any combination thereof.
37. The use of the previous embodiments, wherein the polymorphism is rs10775375.
38. The use of the previous embodiments, wherein the polymorphism is rs6801634.
39. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs1070444, rs116714418, rs6962616, rs7220814, rs4325270, rs768755, and any combination thereof.
40. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs17758350, rs9480689, rs525850, rs4325270, and any combination thereof
41. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs11749180, rs6962616, rs116714418, rs10265554, rs634641, rs1493871, rs12669698, and any combination thereof.
42. The use of the previous embodiments, wherein the polymorphism is rs4332037.
43. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs17697480, rs9480689, and any combination thereof.
44. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs6074737, rs904910, rs12972487, rs445417, and any combination thereof
45. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs635624, rs7416358, and any combination thereof
46. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting 12-54819630-G-INSERTION, rs177665, and any combination thereof.
47. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs1070444, rs10912583, rs12914919, rs2854725, and any combination thereof
48. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs948068, rs71472147, rs72939578, rs658795, rs17758350, rs144260901, and any combination thereof.
49. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs10801129, rs1702870, rs10912583, rs2452822, rs7774349, and any combination thereof
50. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs4705272, rs117946479, and any combination thereof.
51. The use of the previous embodiments, wherein the polymorphism is rs936126.
52. The use of the previous embodiments, wherein the polymorphism is rs634641.
53. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs2314737, rs3002685, rs634641, and any combination thereof.
54. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs12496281, rs10134119, rs3808240, and any combination thereof.
55. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs1890843, rs11829981, and any combination thereof.
56. The use of the previous embodiments, wherein the polymorphism is rs12496281.
57. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs2383184, rs144260901, and any combination thereof.
58. The use of the previous embodiments, wherein the polymorphism is selected from the group consisting rs6801634, rs2383184, rs2954756, and any combination thereof.
59. The use of embodiment 31-58, wherein the polymorphism at rs2726797 comprises a C allele at nucleoposition 26 within SEQ ID NO: 1.
60. The use of embodiment 31-58, wherein the polymorphism at rs7108993 comprises a C allele at nucleoposition 26 within SEQ ID NO: 2.
61. The use of embodiment 31-58, wherein the polymorphism at rs79665096 comprises an A allele at nucleoposition 26 within SEQ ID NO: 3.
62. The use of embodiment 31-58, wherein the polymorphism at rs7604404 comprises an A allele at nucleoposition 26 within SEQ ID NO: 4.
63. The use of embodiment 31-58, wherein the polymorphism at rs73085878 comprises an A allele at nucleoposition 26 within SEQ ID NO: 5.
64. The use of embodiment 31-58, wherein the polymorphism at rs78727269 comprises an A allele at nucleoposition 26 within SEQ ID NO: 6.
65. The use of embodiment 31-58, wherein the polymorphism at rs2736352 comprises an A allele at nucleoposition 26 within SEQ ID NO: 7.
66. The use of embodiment 31-58, wherein the polymorphism at rs4924935 comprises a G allele at nucleoposition 26 within SEQ ID NO: 8.
67. The use of embodiment 31-58, wherein the polymorphism at rs11227112 comprises a G allele at nucleoposition 26 within SEQ ID NO: 9.
68. The use of embodiment 31-58, wherein the polymorphism at rs2285043 comprises an A allele at nucleoposition 26 within SEQ ID NO: 10.
69. The use of embodiment 31-58, wherein the polymorphism at rs6989059 comprises an A allele at nucleoposition 26 within SEQ ID NO: 11.
70. The use of embodiment 31-58, wherein the polymorphism at rs3807552 comprises an A allele at nucleoposition 26 within SEQ ID NO: 12.
71. The use of embodiment 31-58, wherein the polymorphism at rs111455641 comprises a G allele at nucleoposition 26 within SEQ ID NO: 13.
72. The use of embodiment 31-58, wherein the polymorphism at rs9480689 comprises a G allele at nucleoposition 26 within SEQ ID NO: 14.
73. The use of embodiment 31-58, wherein the polymorphism at rs7416358 comprises a G allele at nucleoposition 26 within SEQ ID NO: 15.
74. The use of embodiment 31-58, wherein the polymorphism at rs6879067 comprises an A allele at nucleoposition 26 within SEQ ID NO: 16.
75. The use of embodiment 31-58, wherein the polymorphism at rs11128532 comprises an A allele at nucleoposition 26 within SEQ ID NO: 17.
76. The use of embodiment 31-58, wherein the polymorphism at rs177665 comprises a C allele at nucleoposition 26 within SEQ ID NO: 18.
77. The use of embodiment 31-58, wherein the polymorphism at rs11171747 comprises a C allele at nucleoposition 26 within SEQ ID NO: 19.
78. The use of embodiment 31-58, wherein the polymorphism at rs10775375 comprises an A allele at nucleoposition 26 within SEQ ID NO: 20.
79. The use of embodiment 31-58, wherein the polymorphism at rs6801634 comprises an A allele at nucleoposition 26 within SEQ ID NO: 21.
80. The use of embodiment 31-58, wherein the polymorphism at rs1070444 comprises an A allele at nucleoposition 26 within SEQ ID NO: 22.
81. The use of embodiment 31-58, wherein the polymorphism at rs116714418 comprises an A allele at nucleoposition 26 within SEQ ID NO: 23.
82. The use of embodiment 31-58, wherein the polymorphism at rs6962616 comprises an A allele at nucleoposition 26 within SEQ ID NO: 24.
83. The use of embodiment 31-58, wherein the polymorphism at rs7220814 comprises a G allele at nucleoposition 26 within SEQ ID NO: 25.
84. The use of embodiment 31-58, wherein the polymorphism at rs4325270 comprises a T allele at nucleoposition 26 within SEQ ID NO: 26.
85. The use of embodiment 31-58, wherein the polymorphism at rs768755 comprises a T allele at nucleoposition 26 within SEQ ID NO: 27.
86. The use of embodiment 31-58, wherein the polymorphism at rs17758350 comprises an A allele at nucleoposition 31 within SEQ ID NO: 28.
87. The use of embodiment 31-58, wherein the polymorphism at rs9480689 comprises a G allele at nucleoposition 26 within SEQ ID NO: 29.
88. The use of embodiment 31-58, wherein the polymorphism at rs525850 comprises an A allele at nucleoposition 26 within SEQ ID NO: 30.
89. The use of embodiment 31-58, wherein the polymorphism at rs4325270 comprises a T allele at nucleoposition 26 within SEQ ID NO: 31.
90. The use of embodiment 31-58, wherein the polymorphism at rs11749180 comprises an A allele at nucleoposition 26 within SEQ ID NO: 32.
91. wherein the polymorphism at rs6962616 comprises an A allele at nucleoposition 26 within SEQ ID NO: 33.
92. The use of embodiment 31-58, wherein the polymorphism at rs116714418 comprises an A allele at nucleoposition 26 within SEQ ID NO: 34.
93. The use of embodiment 31-58, wherein the polymorphism at rs10265554 comprises a G allele at nucleoposition 26 within SEQ ID NO: 35.
94. The use of embodiment 31-58, wherein the polymorphism at rs634641 comprises a G allele at nucleoposition 26 within SEQ ID NO: 36.
95. The use of embodiment 31-58, wherein the polymorphism at rs1493871 comprises a G allele at nucleoposition 26 within SEQ ID NO: 37.
96. The use of embodiment 31-58, wherein the polymorphism at rs12669698 comprises a G allele at nucleoposition 26 within SEQ ID NO: 38.
97. The use of embodiment 31-58, wherein the polymorphism at rs4332037 comprises an A allele at nucleoposition 26 within SEQ ID NO: 39.
98. The use of embodiment 31-58, wherein the polymorphism at rs17697480 comprises a G allele at nucleoposition 26 within SEQ ID NO: 40.
99. The use of embodiment 31-58, wherein the polymorphism at rs9480689 comprises a G allele at nucleoposition 26 within SEQ ID NO: 41.
100. The use of embodiment 31-58, wherein the polymorphism at rs6074737 comprises an A allele at nucleoposition 26 within SEQ ID NO: 42.
101. The use of embodiment 31-58, wherein the polymorphism at rs904910 comprises a G allele at nucleoposition 26 within SEQ ID NO: 43.
102. The use of embodiment 31-58, wherein the polymorphism at rs12972487 comprises an A allele at nucleoposition 26 within SEQ ID NO: 44.
103. The use of embodiment 31-58, wherein the polymorphism at rs445417 comprises an A allele at nucleoposition 26 within SEQ ID NO: 45.
104. The use of embodiment 31-58, wherein the polymorphism at rs635624 comprises a C allele at nucleoposition 26 within SEQ ID NO: 46.
105. The use of embodiment 31-58, wherein the polymorphism at rs7416358 comprises a G allele at nucleoposition 26 within SEQ ID NO: 47.
106. The use of embodiment 31-58, wherein the polymorphism at 12-54819630-G-INSERTION comprises an insertion of a G at nucleoposition 26 within SEQ ID NO: 48.
107. The use of embodiment 31-58, wherein the polymorphism at rs177665 comprises a C allele at nucleoposition 26 within SEQ ID NO: 49.
108. The use of embodiment 31-58, wherein the polymorphism at rs1070444 comprises an A allele at nucleoposition 26 within SEQ ID NO: 50.
109. The use of embodiment 31-58, wherein the polymorphism at rs10912583 comprises an A allele at nucleoposition 26 within SEQ ID NO: 51.
110. The use of embodiment 31-58, wherein the polymorphism at rs12914919 comprises a G allele at nucleoposition 26 within SEQ ID NO: 52.
111. The use of embodiment 31-58, wherein the polymorphism at rs2854725 comprises a C allele at nucleoposition 26 within SEQ ID NO: 53.
112. The use of embodiment 31-58, wherein the polymorphism at rs9480689 comprises a G allele at nucleoposition 26 within SEQ ID NO: 54.
113. The use of embodiment 31-58, wherein the polymorphism at rs71472147 comprises an A allele at nucleoposition 26 within SEQ ID NO: 55.
114. The use of embodiment 31-58, wherein the polymorphism at rs72939578 comprises an A allele at nucleoposition 31 within SEQ ID NO: 56.
115. The use of embodiment 31-58, wherein the polymorphism at rs658795 comprises an A allele at nucleoposition 26 within SEQ ID NO: 57.
116. The use of embodiment 31-58, wherein the polymorphism at rs17758350 comprises an A allele at nucleoposition 31 within SEQ ID NO: 58.
117. The use of embodiment 31-58, wherein the polymorphism at rs144260901 comprises an A allele at nucleoposition 31 within SEQ ID NO: 59.
118. The use of embodiment 31-58, wherein the polymorphism at rs10801129 comprises a C allele at nucleoposition 26 within SEQ ID NO: 60.
119. The use of embodiment 31-58, wherein the polymorphism at rs1702870 comprises an A allele at nucleoposition 26 within SEQ ID NO: 61.
120. The use of embodiment 31-58, wherein the polymorphism at rs10912583 comprises an A allele at nucleoposition 26 within SEQ ID NO: 62.
121. The use of embodiment 31-58, wherein the polymorphism at rs2452822 comprises a C allele at nucleoposition 31 within SEQ ID NO: 63.
122. The use of embodiment 31-58, wherein the polymorphism at rs7774349 comprises an A allele at nucleoposition 26 within SEQ ID NO: 64.
123. The use of embodiment 31-58, wherein the polymorphism at rs4705272 comprises a G allele at nucleoposition 26 within SEQ ID NO: 65.
124. The use of embodiment 31-58, wherein the polymorphism at rs117946479 comprises an A allele at nucleoposition 31 within SEQ ID NO: 66.
125. The use of embodiment 31-58, wherein the polymorphism at rs936126 comprises an A allele at nucleoposition 26 within SEQ ID NO: 67.
126. The use of embodiment 31-58, wherein the polymorphism at rs634641 comprises a G allele at nucleoposition 26 within SEQ ID NO: 68.
127. The use of embodiment 31-58, wherein the polymorphism at rs2314737 comprises a G allele at nucleoposition 26 within SEQ ID NO: 69.
128. The use of embodiment 31-58, wherein the polymorphism at rs3002685 comprises a G allele at nucleoposition 26 within SEQ ID NO: 70.
129. The use of embodiment 31-58, wherein the polymorphism at rs634641 comprises a G allele at nucleoposition 26 within SEQ ID NO: 71.
130. The use of embodiment 31-58, wherein the polymorphism at rs12496281 comprises a G allele at nucleoposition 26 within SEQ ID NO: 72.
131. The use of embodiment 31-58, wherein the polymorphism at rs10134119 comprises a T allele at nucleoposition 26 within SEQ ID NO: 73.
132. The use of embodiment 31-58, wherein the polymorphism at rs3808240 comprises a C allele at nucleoposition 26 within SEQ ID NO: 74.
133. The use of embodiment 31-58, wherein the polymorphism at rs1890843 comprises a G allele at nucleoposition 26 within SEQ ID NO: 75.
134. The use of embodiment 31-58, wherein the polymorphism at rs11829981 comprises an A allele at nucleoposition 26 within SEQ ID NO: 76.
135. The use of embodiment 31-58, wherein the polymorphism at rs12496281 comprises a G allele at nucleoposition 26 within SEQ ID NO: 77.
136. The use of embodiment 31-58, wherein the polymorphism at rs2383184 comprises a G allele at nucleoposition 26 within SEQ ID NO: 78.
137. The use of embodiment 31-58, wherein the polymorphism at rs144260901 comprises an A allele at nucleoposition 31 within SEQ ID NO: 79.
138. The use of embodiment 31-58, wherein the polymorphism at rs6801634 comprises an A allele at nucleoposition 26 within SEQ ID NO: 80.
139. The use of embodiment 31-58, wherein the polymorphism at rs2383184 comprises a G allele at nucleoposition 26 within SEQ ID NO: 81.
140. The use of embodiment 31-58, wherein the polymorphism at rs2954756 comprises a G allele at nucleoposition 26 within SEQ ID NO: 82.

EXAMPLES

The following examples are not intended to limit the scope of the claims to the invention, but are rather intended to be exemplary of certain embodiments. Any variations in the exemplified methods which occur to the skilled artisan are intended to fall within the scope of the present invention.

Example 1. Genotypic, Clinical, and Serological Associations with Severe CD

Identification of Genotypes Associated with Severe CD

1919 Caucasian patients with Crohn's disease (CD) were recruited at Inflammatory Bowel Disease Centers. The patient cohorts recruited are described in Table 3. A modified Montreal classification was used: non-stricturing/non-penetrating (B1): stricturing (B2a), stricturing and penetrating (B2b), and isolated internal penetrating (B3). Disease location was defined by the Montreal classification: ileal (L1), colonic (L2), ileocolonic (L3). The diagnosis of each patient was based on standard endoscopic, histologic, and radiographic features.

TABLE 3

Demographic Data of Study Cohort

B1
B2a
B2b
B3

(n = 928)
(n = 522)
(n = 336)
(n = 203)

Average Age, years (SD)
40.71
47.54
45.20
42.89

(17.88)
(16.69)
(15.14)
(15.36)

Male (%)
51.72
51.34
54.76
54.68

Average Age of Diagnosis, years (SD)
25.99
26.50
23.55
23.82

(16.07)
(14.36)
(11.58)
(11.82)

Mean Disease Duration, years (SD)
14.51
21.01
21.66
19.04

(9.72)
(12.27)
(12.52)
(11.54)

Disease Location (%)

Ileal (L1)
13.78
27.20
24.15
14.87

Colonic (L2)
25.69
7.60
2.79
11.28

Ileocolonic (L3)
60.53
65.20
73.07
73.85

Family History of IBD (%)
69.10
67.40
66.98
68.75

Early Steroid Use, <1
30.00
47.58
45.35
33.81

year of diagnosis (%)

Perianal involvement (%)
27.97
39.73
29.25
35.43

Blood samples were collected from patients at the time of enrollment. Blood samples were also collected from individuals without CD. Genotyping was performed at Cedars-Sinai Medical Center using Illumina ImmunoChip on all samples collected. Case-control univariate analyses comparing stricturing (B2a), stricturing and penetrating (B2b), and isolated internal penetrating (B3) to non-stricturing/non-penetrating B1 at various disease locations were performed. Markers/SNPs were excluded from analysis if: there were deviations in Hardy-Weinberg Equilibrium in controls with p≤1.0E-5; genotyping rate <95%; missingness in SNPs>2% and minor allele frequency <1%. Related individuals (Pi-hat scores >0.25) were identified using identity-by-descent and excluded from analysis (PLINK). Admixture was used to generate ethnicity proportion estimations for all individuals. Only subjects identified by admixture as Caucasian (proportion <0.75) were included in the analysis. Table 1 provides polymorphisms significantly associated with subclinical phenotypes of severe CD.

Disease Location is Associated with Severe Crohn's Disease

Severe Crohn's disease (CD) is characterized by a need to undergo surgical treatment. In addition, patients with severe CD typically experience a faster progression to a first surgery, and in some cases, a second surgery. Such surgical treatments include, but are not limited to stricture plasty and small bowel resection or removal. Disease location is associated with CD patient outcomes. For example, CD patients with stricturing disease in the ileum, as compared to the colon, statistically have poorer outcomes (e.g., faster progression to surgery) and a poorer quality of life. The predictive power of the PRS to identify CD patients who are at risk of developing severe forms of CD inform treatment regimens for these individuals that may include earlier interventions that are aggressive to prevent the onset of stricturing or penetrating disease.

To determine whether disease location (e.g., ileum (L1), ileocolonic region (L2), colon (L3)) is associated with a greater risk of developing severe CD, three polygenic risk score (PRS) were calculated for the subjects in the study cohort (Table 3) for inflammatory bowel disease (IBD), ulcerative colitis (UC) and CD. The PRS scores were calculated using the methods in Cleynen I, Boucher G, Jostins L, et al. Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study. Lancet. 2016; 387(10014):156-167, involving known IBD, CD, and UC loci weighted for effect sizes. A linear regression between the PRS score versus the number of stricture-related surgeries in the patient cohort and incidences of stricturing (B2a) and stricturing and penetrating (B2b), were performed. The PRS was calculated, and results are summarized in Table 4.

TABLE 4

Linear Regression: Polygenic Risk Score

v. Number of Stricture-Related Surgeries

Ileal (L1)
Colonic (L2)
Ileocolonic (L3)

Variable
Beta
P
Beta
P
Beta
P

IBD PRS
0.07
0.21
0.30
0.05
0.06
0.24

UC PRS
0.06
0.32
−0.32
0.04
−0.04
0.45

CD PRS
0.08
0.20
0.34
0.03
0.10
0.05

The CD PRS was associated with stricturing (p=0.012, OR 1.20). The CD PRS was associated with need for stricture-related surgeries (p=0.0117, OR 1.28) in L3. The CD PRS was also associated with number of stricture-related surgeries in L2 (p=0.0264, beta (b): 0.34) and L3 (p=0.0475, b: 0.102) locations. In L2, UC PRS was protective of stricturing (p=0.0184, OR 0.662) and number of stricture-related surgeries (p=0.045, b: −0.318). These findings suggest that CD patients with a high CD PRS may benefit from an earlier and more aggressive treatment regiment, than CD patients with a high UC PRS.

Identifying Serological Markers Associated with Severe CD

The blood samples collected from the patient cohort from Table 3 were processed to isolate the blood plasma. Serological marker levels were measured using an enzyme-linked immunosorbent assay (ELISA) in the plasma using monoclonal antibodies specific to the serological marker or antigen thereof. Antibodies against Saccharomyces cerevisiae antibody, neutrophil cytoplasmic antibody (ANCA), antibodies against E. coli outer membrane porin protein C (anti-OmpC), antibodies against I2, and antibodies against Cbir1 flagellin antibody were used. Quartile sum scores (QSS) were calculated for the serologies using methods provided in Landers C J, Cohavy O, Misra R. et al., Selected loss of tolerance evidenced by Crohn's disease-associated immune responses to auto- and microbial antigens. Gastroenterology (2002) 123689-699. A logistic regression analysis was performed to look at an association between stricturing disease (B2a)/stricturing and penetrating (B2b) and quartile sum score. The results are provided in Table 5.

TABLE 5

Serology Association with Stricturing Disease by Disease Location

Ileal (L1)
Colonic (L2)
Ileocolonic (L3)

Variable
p
OR [95% CI]
p
OR [95% CI]
p
OR [95% CI]

ANCA
0.6384
0.73 [0.36-1.58]
0.3865
0.75 [4.23-1.30]
0.0009
0.56 [0.41-0.77]

Seropositivity

Anti-Cbir
0.2808
1.47 [0.91-2.40]
0.0688
1.84 [1.04-3.24]
0.0037
1.53 [1.17-2.01]

Seropositivity

Anti-I2
0.0207
2.97 [1.44-6.61]
0.1755
1.65 [0.88-3.11]
1.08E−06
2.34 [1.69-3.25]

Seropositivity

Anti-Ompc
0.0168
3.49 [1.64-8.62]
0.1216
1.73 [0.937-3.17]
0.0002
1.88 [1.38-2.58]

Seropositivity

ASCA
0.02071
2.005 [1.22-3.31]
0.0128
2.44 [1.36-4.38]
5.81E−13
2.89 [2.19-3.82]

Seropositivity

Quartile Sum
0.0007
1.17 [1.072-1.29]
0.0025
1.15 [1.052-1.27]
2.48E−16
1.22 [1.16-1.28]

Score

Stricturing was associated with ASCA seropositivity in L1 and L3 (p<0.001, OR 1.97-3.2). Stricturing was also associated with ASCA in L2 (p=0.0027, OR 2.44). Higher QSS (p<0.01, OR 1.15-1.22) was associated with stricturing in all three locations. In L3, ANCA seropositivity was associated with B1 (p=2.76E-5, OR 0.52). ASCA seropositivity (p=1.5E-5, OR 2.47) and elevated QSS (p=1.6E-6, OR 1.19) were associated with B3 behavior in L3. In L2, stricturing was associated with perianal disease (p<0.006, OR 3.78). Without wishing to be bound my any particular theory, these findings suggest that certain serological markers can be used as predictors of severe forms of CD characterized by stricturing or penetrating disease phenotypes in various disease locations. For example, ASCA may be used to predict stricturing disease in the ileal region of the intestine, which is associated with poorer patient outcomes and quality of life. Such a patient may benefit from an earlier and more aggressive treatment strategy.

Logistic Regression Analysis: Stricturing Disease v. Multiple Variables

Multiple logistic regression analyses were performed, looking at the association between stricturing disease (B2a)/stricturing and penetrating (B2b) and multiple variables in Table 6. Family history of IBD did not have a statistically significant association with stricturing disease in any disease locations. Similarly, CD patients with high UC PRS have a lower probability of developing colonic stricturing and ileocolonic stricturing, as compared with ileal stricturing. In contrast, perianal involvement was associated with stricturing in colonic CD. The term “perianal involvement” refers to perianal disease, which is disease that affects the tissue around of the anus or the rectum of a patient that has been diagnosed using standard endoscopic, histologic, and radiographic features. “PRS” means polygenic risk score. “OR” refers to the odds ratio. “CI” refers to the confidence interval.

TABLE 6

Summary of Clinical and Genetic Associations with Stricturing CD by Disease Location

Ileal (L1)
Colonic (L2)
Ileocolonic (L3)

Variable
p
OR [95% CI]
p
OR [95% CI]
p
OR [95% CI]

Early
0.9900
7.6e7 [0-NA]
0.9920
1.13e8 [0-NA]
0.2983
1.79 [0.643-5.44]

Steroid Use

Family History
0.8328
0.90 [0.57-1.44]
0.3865
0.74 [0.41-1.30]
0.0833
1.33 [1.01-1.77]

of IBD

Perianal
0.9496
0.96 [0.48-2.05]
0.0017
3.78 [1.86-7.85]
0.2040
1.27 [0.91-1.80]

Involvement

PRS for
0.8749
0.97 [0.75-1.25]
0.2245
1.23 [0.923-1.66]
0.4343
1.06 [0.925-1.21]

all IBD

PRS for
0.8328
0.94 [0.74-1.19]
0.0184
0.662 [0.49-0.875]
0.0058
0.82 [0.72-0.94]

Ulcerative colitis

PRS for
0.8328
0.954 [0.753-1.21]
0.0688
1.38 [1.03-1.87]
0.0176
1.20 [1.04-1.38]

Crohn's disease

Example 2. Pathway Enrichment Analysis

To determine which molecular pathways play a role in severe CD, a pathway analysis tool (Ingenuity Pathway Analysis) was used on polymorphisms detected in Example 1 (P<0.05), positive for an association with stricturing (B2a), stricturing and penetrating (B2b), or isolated internal penetrating (B3), was performed. Enriched pathways included Prolactin Signaling (p=1.86E-3) and Autophagy (p=2.20E-3), which are both involved in CD and Janus Kinase 2 (JAK2)/Signal Transducer and Transcription Activator (STAT) activation. Table 7 provides the results from this study.

TABLE 7

Pathway Enrichment Analysis

Top Canonical Pathways
P Value

T Helper Cell Differentiation
6.40E−05

Th1 and Th2 Activation Pathway
1.81E−03

Prolactin Signaling
1.86E−03

Autophagy
2.20E−03

Protein Kinase A Signaling
2.97E−03

Crosstalk between Dendritic
3.18E−03

Cells and Natural Killer Cells

GP6 Signaling Pathway
3.99E−03

Th1 Pathway
4.70E−03

Th2 Pathway
4.82E−03

Sonic Hedgehog Signaling
5.59E−03

Genes involved in the enriched Prolactin Signaling include IRF1, KLB, MAP2K1, NR3C1, PRKCB, PRKCE, PRKCG, PRKCH, PRKCQ, PRLR, PTPN11, STAT1, STAT5A, and STAT5B. Genes involved in the enriched Autophagy include ATG10, ATG16L1, ATG4A, ATG4C, CTSH, SQSTM1, ULK1, WDFY3. Without being bound by any particular theory, these findings suggestion that a therapeutic strategy targeting the genes, or gene expression products expressed from these genes may be appropriate for patients selected using genotypes associated with B2a, B2b, and B3.

Example 3. Treating Severe Crohn's Disease

An inflammatory disease is treated in a subject, by first, determining a genotype comprising a polymorphism selected from Table 1, or selected from the group consisting of rs7416358G, rs1070444A, rs11749180A, 12-54819630-G-INSERTION, rs12496281G, rs11171747C, rs116714418A, rs111455641G, rs9480689G, rs6879067A, rs11128532A, rs177665C, rs10775375A, rs6801634A, rs6962616A, rs7220814G, rs4325270T, rs768755T, rs17758350A, rs9480689G, rs525850A, rs4325270T, rs6962616A, rs10265554G, rs634641G, rs1493871G, rs12669698G, rs4332037A, rs17697480G, rs9480689G, rs6074737A, rs904910G, rs12972487A, rs445417A, rs63562C, rs7416358G, rs177665C, rs1070444A, rs10912583A, rs12914919G, rs2854725C, rs9480689G, rs71472147A, rs72939578A, rs658795A, rs17758350A, rs144260901A, rs10801129C, rs1702870A, rs10912583A, rs2452822C, rs7774349A, rs4705272G, rs117946479A, rs936126A, rs634641G, rs2314737G, rs3002685G, rs634641G, rs10134119T, rs3808240C, rs1890843G, and rs11829981A. Optionally, the subject is, or is susceptible to be, non-responsive to certain therapies such as anti-TNF, steroids, or immunomodulators, such as those disclosed herein. A sample of whole blood is obtained from the subject. An assay is performed on the sample obtained from the subject to detect a presence or absence of the genotype by Illumina ImmunoArray or polymerase chain reaction (PCR) under standard hybridization conditions. In addition, or alternatively, a sample of intestinal tissue is obtained from the subject. In addition, or alternatively, a sample of blood plasma is obtained from the subject. An assay is performed on the sample obtained from the subject to detect a presence of a serological marker selected from the group consisting of ASCA, ANCA, anti-OmpC antibody, anti-I2 antibody, or anti-Cbir1 antibody by ELISA accordingly to manufacture instructions.

The subject is determined to have, or be at risk for developing, a severe form of Crohn's disease if the genotype and/or the serological marker is detected in the sample obtained from the subject. A therapeutically effective amount of an a therapeutic agent disclosed herein is administered to the subject, provided the subject is determined to have the genotype and/or serological marker.

Example 4. Phase 1A Clinical Trial

A phase 1 clinical trial is performed to evaluate the safety, tolerability, pharmacokinetics and pharmacodynamics of an therapeutic agent in subjects with Crohn's disease having a genotype comprising at least one polymorphism selected from the group consisting of rs7416358G, rs1070444A, rs11749180A, 12-54819630-G-INSERTION, rs12496281G, rs11171747C, rs116714418A, rs111455641G, rs9480689G, rs6879067A, rs11128532A, rs177665C, rs10775375A, rs6801634A, rs6962616A, rs7220814G, rs4325270T, rs768755T, rs17758350A, rs9480689G, rs525850A, rs4325270T, rs6962616A, rs10265554G, rs634641G, rs1493871G, rs12669698G, rs4332037A, rs17697480G, rs9480689G, rs6074737A, rs904910G, rs12972487A, rs445417A, rs63562C, rs7416358G, rs177665C, rs1070444A, rs10912583A, rs12914919G, rs2854725C, rs9480689G, rs71472147A, rs72939578A, rs658795A, rs17758350A, rs144260901A, rs10801129C, rs1702870A, rs10912583A, rs2452822C, rs7774349A, rs4705272G, rs117946479A, rs936126A, rs634641G, rs2314737G, rs3002685G, rs634641G, rs10134119T, rs3808240C, rs1890843G, and rs11829981A.

Single ascending dose (SAD) arms: Subjects in each group (subjects are grouped based on the presence or absence of the genotype) receive either a single dose of the antibody or a placebo. Exemplary doses are 1, 3, 10, 30, 100, 300, 600 and 800 mg of antibody. Safety monitoring and PK assessments are performed for a predetermined time. Based on evaluation of the PK data, and if the antibody is deemed to be well tolerated, dose escalation occurs, either within the same groups or a further group of healthy subjects. Dose escalation continues until the maximum dose has been attained unless predefined maximum exposure is reached or intolerable side effects become apparent.

Multiple ascending dose (MAD) arms: Subjects in each group (subjects are grouped based on the presence or absence of the genotype) receive multiple doses of the antibody or a placebo. The dose levels and dosing intervals are selected as those that are predicted to be safe from the SAD data. Dose levels and dosing frequency are chosen to achieve therapeutic drug levels within the systemic circulation that are maintained at steady state for several days to allow appropriate safety parameters to be monitored. Samples are collected and analyzed to determination PK profiles.

Inclusion Criteria: Subjects of non-childbearing potential between the ages of 18 and 55 years having obstructive Crohn's disease. Female subjects of non-childbearing potential must meet at least one of the following criteria: (1) achieved postmenopausal status, defined as: cessation of regular menses for at least 12 consecutive months with no alternative pathological or physiological cause; and have a serum follicle stimulating hormone (FSH) level within the laboratory's reference range for postmenopausal females; (2) have undergone a documented hysterectomy and/or bilateral oophorectomy; (3) have medically confirmed ovarian failure. All other female subjects (including females with tubal ligations and females that do not have a documented hysterectomy, bilateral oophorectomy and/or ovarian failure) will be considered to be of childbearing potential. Body Mass Index (BMI) of 17.5 to 30.5 kg/m2; and a total body weight >50 kg (110 lbs). Evidence of a personally signed and dated informed consent document indicating that the subject (or a legal representative) has been informed of all pertinent aspects of the study.

Two groups of subjects are selected: subjects having the genotype, and subjects lacking the genotype.

Exclusion Criteria: Evidence or history of clinically significant hematological, renal, endocrine, pulmonary, gastrointestinal, cardiovascular, hepatic, psychiatric, neurologic, or allergic disease (including drug allergies, but excluding untreated, asymptomatic, seasonal allergies at time of dosing) or than Crohn's disease. Subjects with a history of or current positive results for any of the following serological tests: Hepatitis B surface antigen (HBsAg), Hepatitis B core antibody (HBcAb), anti-Hepatitis C antibody (HCV Ab) or human immunodeficiency virus (HIV). Subjects with a history of allergic or anaphylactic reaction to a therapeutic drug. Treatment with an investigational drug within 30 days (or as determined by the local requirement, whichever is longer) or 5 half-lives or 180 days for biologics preceding the first dose of study medication. Pregnant females; breastfeeding females; and females of childbearing potential.

Primary Outcome Measures: Incidence of dose limiting or intolerability treatment related adverse events (AEs) [Time Frame: 12 weeks]. Incidence, severity and causal relationship of treatment emergent AEs (TEAEs) and withdrawals due to treatment emergent adverse events [Time Frame: 12 weeks]. Incidence and magnitude of abnormal laboratory findings [Time Frame: 12 weeks]. Abnormal and clinically relevant changes in vital signs, blood pressure (BP) and electrocardiogram (ECG) parameters [Time Frame: 12 weeks].

Secondary Outcome Measures:

Single Ascending Dose: Maximum Observed Plasma Concentration (Cmax) [Time Frame: 12 weeks]. Single Ascending Dose: Time to Reach Maximum Observed Plasma Concentration (Tmax) [Time Frame: 12 weeks]. Single Ascending Dose: Area under the plasma concentration-time profile from time zero to 14 days (AUC14 days) [Time Frame: 12 weeks]. Single Ascending Dose: Area under the plasma concentration-time profile from time zero extrapolated to infinite time (AUCinf) [Time Frame: 12 weeks]. Single Ascending Dose: Area under the plasma concentration-time profile from time zero to the time of last quantifiable concentration (AUClast) [Time Frame: 12 weeks]. Single Ascending Dose: Dose normalized maximum plasma concentration (Cmax[dn]) [Time Frame: 12 weeks]. Single Ascending Dose: Dose normalized area under the plasma concentration-time profile from time zero extrapolated to infinite time (AUCinf[dn]) [Time Frame: 12 weeks]. Single Ascending Dose: Dose normalized area under the plasma concentration-time profile from time zero to the time of last quantifiable concentration (AUClast[dn]) [Time Frame: 12 weeks]. Single Ascending Dose: Plasma Decay Half-Life (t½) [Time Frame: 12 weeks]. Plasma decay half-life is the time measured for the plasma concentration to decrease by one half. Single Ascending Dose: Mean residence time (MRT) [Time Frame: 12 weeks]. Single Ascending Dose: Volume of Distribution at Steady State (Vss) [Time Frame: 6 weeks]. Volume of distribution is defined as the theoretical volume in which the total amount of drug would need to be uniformly distributed to produce the desired blood concentration of a drug. Steady state volume of distribution (Vss) is the apparent volume of distribution at steady-state. Single Ascending Dose: Systemic Clearance (CL) [Time Frame: 6]. CL is a quantitative measure of the rate at which a drug substance is removed from the body.

Multiple Ascending Dose First Dose: Maximum Observed Plasma Concentration (Cmax) [Time Frame: 12 weeks]. Multiple Ascending Dose First Dose: Time to Reach Maximum Observed Plasma Concentration (Tmax) [Time Frame: 12 weeks]. Multiple Ascending Dose First Dose: Area under the plasma concentration-time profile from time zero to time τ, the dosing interval where τ=2 weeks (AUC′) [Time Frame: 12 weeks]. Multiple Ascending Dose First Dose: Dose normalized maximum plasma concentration (Cmax[dn]) [Time Frame: 12 weeks]. Multiple Ascending Dose First Dose: Dose normalized Area under the plasma concentration-time profile from time zero to time τ, the dosing interval where τ=2 weeks (AUCτ [dn]) [Time Frame: 12 weeks]. Plasma Decay Half-Life (t½) [Time Frame: 12 weeks]. Plasma decay half-life is the time measured for the plasma concentration to decrease by one half. Multiple Ascending Dose First Dose: Mean residence time (MRT) [Time Frame: 12 weeks]. Apparent Volume of Distribution (Vz/F) [Time Frame: 12 weeks]. Volume of distribution is defined as the theoretical volume in which the total amount of drug would need to be uniformly distributed to produce the desired plasma concentration of a drug. Apparent volume of distribution after oral dose (Vz/F) is influenced by the fraction absorbed. Multiple Ascending Dose First Dose: Volume of Distribution at Steady State (Vss) [Time Frame: 12 weeks]. Volume of distribution is defined as the theoretical volume in which the total amount of drug would need to be uniformly distributed to produce the desired blood concentration of a drug. Steady state volume of distribution (Vss) is the apparent volume of distribution at steady-state. Multiple Ascending Dose First Dose: Apparent Oral Clearance (CL/F) [Time Frame: 12 weeks]. Clearance of a drug is a measure of the rate at which a drug is metabolized or eliminated by normal biological processes. Clearance obtained after oral dose (apparent oral clearance) is influenced by the fraction of the dose absorbed. Clearance is estimated from population pharmacokinetic (PK) modeling. Drug clearance is a quantitative measure of the rate at which a drug substance is removed from the blood. Multiple Ascending Dose First Dose: Systemic Clearance (CL) [Time Frame: 12 weeks]. CL is a quantitative measure of the rate at which a drug substance is removed from the body.

Multiple Ascending Dose Multiple Dose: Maximum Observed Plasma Concentration (Cmax) [Time Frame: 12 weeks]. Multiple Ascending Dose Multiple Dose: Time to Reach Maximum Observed Plasma Concentration (Tmax) [Time Frame: 12 weeks]. Multiple Ascending Dose Multiple Dose: Area under the plasma concentration-time profile from time zero to time τ, the dosing interval where τ=2 weeks (AUCτ) [Time Frame: 12 weeks]. Multiple Ascending Dose Multiple Dose: Dose normalized maximum plasma concentration (Cmax[dn]) [Time Frame: 12 weeks]. Multiple Ascending Dose Multiple Dose: Dose normalized Area under the plasma concentration-time profile from time zero to time τ, the dosing interval where τ=2 weeks (AUCτ [dn]) [Time Frame: 12 weeks]. Multiple Ascending Dose Multiple Dose: Plasma Decay Half-Life (t½) [Time Frame: 12 weeks]. Plasma decay half-life is the time measured for the plasma concentration to decrease by one half. Multiple Ascending Dose Multiple Dose: Apparent Volume of Distribution (Vz/F) [Time Frame: 12 weeks]. Volume of distribution is defined as the theoretical volume in which the total amount of drug would need to be uniformly distributed to produce the desired plasma concentration of a drug. Apparent volume of distribution after oral dose (Vz/F) is influenced by the fraction absorbed. Multiple Ascending Dose Multiple Dose: Volume of Distribution at Steady State (Vss) [Time Frame: 12 weeks]. Volume of distribution is defined as the theoretical volume in which the total amount of drug would need to be uniformly distributed to produce the desired blood concentration of a drug. Steady state volume of distribution (Vss) is the apparent volume of distribution at steady-state.

Multiple Ascending Dose Multiple Dose: Apparent Oral Clearance (CL/F) [Time Frame: 12 weeks]. Clearance of a drug is a measure of the rate at which a drug is metabolized or eliminated by normal biological processes. Clearance obtained after oral dose (apparent oral clearance) is influenced by the fraction of the dose absorbed. Clearance was estimated from population pharmacokinetic (PK) modeling. Drug clearance is a quantitative measure of the rate at which a drug substance is removed from the blood. Multiple Ascending Dose Multiple Dose: Systemic Clearance (CL) [Time Frame: 12 weeks]. CL is a quantitative measure of the rate at which a drug substance is removed from the body. Multiple Ascending Dose Multiple Dose: Minimum Observed Plasma Trough Concentration (Cmin) [Time Frame: 12 weeks]. Multiple Ascending Dose Multiple Dose: Average concentration at steady state (Cav) [Time Frame: 12 weeks]. Multiple Ascending Dose Multiple Dose: Observed accumulation ratio (Rac) [Time Frame: 12 weeks]. Multiple Ascending Dose Multiple Dose: Peak to trough fluctuation (PTF) [Time Frame: 12 weeks]. Multiple Ascending Dose Additional Parameter: estimate of bioavailability (F) for subcutaneous administration at the corresponding intravenous dose [Time Frame: 12 weeks]. Immunogenicity for both Single Ascending Dose and Multiple Ascending Dose: Development of anti-drug antibodies (ADA) [Time Frame: 12 weeks].

Example 5: Phase 1B Clinical Trial

A phase 1b open label clinical trial is performed to evaluate efficacy of an therapeutic agent on CD patients having a genotype comprising at least one polymorphism selected from the group consisting of rs7416358G, rs1070444A, rs11749180A, 12-54819630-G-INSERTION, rs12496281G, rs11171747C, rs116714418A, rs111455641G, rs9480689G, rs6879067A, rs11128532A, rs177665C, rs10775375A, rs6801634A, rs6962616A, rs7220814G, rs4325270T, rs768755T, rs17758350A, rs9480689G, rs525850A, rs4325270T, rs6962616A, rs10265554G, rs634641G, rs1493871G, rs12669698G, rs4332037A, rs17697480G, rs9480689G, rs6074737A, rs904910G, rs12972487A, rs445417A, rs63562C, rs7416358G, rs177665C, rs1070444A, rs10912583A, rs12914919G, rs2854725C, rs9480689G, rs71472147A, rs72939578A, rs658795A, rs17758350A, rs144260901A, rs10801129C, rs1702870A, rs10912583A, rs2452822C, rs7774349A, rs4705272G, rs117946479A, rs936126A, rs634641G, rs2314737G, rs3002685G, rs634641G, rs10134119T, rs3808240C, rs1890843G, and rs11829981A. Arms: 10 patients positive for rs911605A are administered the antibody. 5-10 patients negative for the genotype are administered the antibody. Patients are monitored in real-time. Central ready of endoscopy and biopsy is employed, with readers blinded to point of time of treatment and endpoints.

Inclusion Criteria: Two groups of subjects are selected: subjects having the genotype, and subjects lacking the genotype.

Primary Outcome Measures: Simple Endoscopic Score for Crohn's Disease (SESCD), Crohn's Disease Activity Index (CDAI), and Patient Reported Outcome (PRO). If the genotype positive group shows 50% reduction from baseline, a Phase 2a clinical trial is performed.

Inclusion Criteria: PRO entry criteria: Abdominal pain score of 2 or more and/or stool frequency score of 4 or more. Primary outcome would be pain core of 0 or 1 and stool frequency score of 3 or less with no worsening from baseline. Endoscopy entry criteria: SESCD ileum only entry at score of 4 and 6 if colon is involved. Primary endoscopic outcome is 40-50% delta of mean SESCD.

Example 6: Phase 2A Clinical Trial

A phase 2a clinical trial is performed to evaluate efficacy of an therapeutic agent on CD patients having a genotype comprising at least one polymorphism selected from the group consisting of rs7416358G, rs1070444A, rs11749180A, 12-54819630-G-INSERTION, rs12496281G, rs11171747C, rs116714418A, rs111455641G, rs9480689G, rs6879067A, rs11128532A, rs177665C, rs10775375A, rs6801634A, rs6962616A, rs7220814G, rs4325270T, rs768755T, rs17758350A, rs9480689G, rs525850A, rs4325270T, rs6962616A, rs10265554G, rs634641G, rs1493871G, rs12669698G, rs4332037A, rs17697480G, rs9480689G, rs6074737A, rs904910G, rs12972487A, rs445417A, rs63562C, rs7416358G, rs177665C, rs1070444A, rs10912583A, rs12914919G, rs2854725C, rs9480689G, rs71472147A, rs72939578A, rs658795A, rs17758350A, rs144260901A, rs10801129C, rs1702870A, rs10912583A, rs2452822C, rs7774349A, rs4705272G, rs117946479A, rs936126A, rs634641G, rs2314737G, rs3002685G, rs634641G, rs10134119T, rs3808240C, rs1890843G, and rs11829981A.

Arms: 40 patients per arm (antibody and placebo arms) are treated with antibody or placebo for 12 weeks. An interim analysis is performed after 20 patients from each group are treated at the highest dose to look for a 40-50% delta between placebo and treated group in primary outcome (50% reduction from baseline in SESCD, CDAI, and PRO).

Primary Outcome Measures: Simple Endoscopic Score for Crohn's Disease (SESCD), Crohn's Disease Activity Index (CDAI), and Patient Reported Outcome (PRO).

While preferred embodiments have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will occur to those skilled in the art without departing from the scope of this application. Various alternatives to the embodiments described herein may be employed in practicing the scope of this application.

While preferred embodiments of the present examples have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the disclosure. It should be understood that various alternatives to the embodiments of the disclosure described herein may be employed in practicing the disclosure. It is intended that the following claims define the scope of the disclosure and that methods and structures within the scope of these claims and their equivalents be covered thereby.

METHODS AND SYSTEMS FOR CHARACTERIZING SEVERE CROHN'S DISEASE

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