VARIANTS OF TNFSF15 AND DCR3 ASSOCIATED WITH CROHN'S DISEASE

Described herein are methods and compositions related to the discovery of associations in TNFSF15 15 and DcR3 genetic loci across in Caucasian, Puerto Rican, and Korean Crohn's Disease, as demonstrated via trans-ethnic fine mapping. The present invention provides methods of quantifying risk and diagnosing susceptibility to Crohn's disease in a subject by determining the presence of one or more risk variants are at the TNFSF15 (or TL1A) and/or DcR3 genetic loci.

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Description
CROSS-REFERENCE

This application is a continuation of U.S. application Ser. No. 14/890,712 filed Nov. 12, 2015 which is U.S. National Stage application of PCT/US14/38468 filed May 16, 2014 which claims the benefit under 35 U.S.C. § 119(e) to U.S. provisional patent application No. 61/824,932, filed May 17, 2013.

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 on Apr. 5, 2018 is named 52388721301_SL.txt and is 6,237 bytes in size.

FIELD OF THE INVENTION

The claimed invention relates to prognosis, diagnosis and treatment of inflammatory bowel disease and related conditions, including methods and compositions for medical therapies.

BACKGROUND

All publications herein are incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference. The following description includes information that may be useful in understanding the present invention. It is not an admission that any of the information provided herein is prior art or relevant to the presently claimed invention, or that any publication specifically or implicitly referenced is prior art.

Inflammatory bowel disease (IBD) such as Crohn's disease (CD) are chronic inflammatory conditions with pathological features such as patchy transmural inflammation and fibrostenosis. Previous studies show that TL1A may drive intestinal inflammation through enhancing Th1, Th2 and Th17 effector function, TL1A appears to also drive fibrogenesis through increased number of fibroblasts and activated fibroblasts and constitutive TL1A expression in mice has been found to confer worsened murine ileo-cecal inflammation, and intestinal fibrostenosis.

SNPs of TL1A (TNFSF15), a TNF superfamily member, have been found to be associated with IBD, and certain TNFSF15 haplotypes have been found to be associated with increased TL1A expression and have a higher risk of small bowel surgery. Decoy Receptor 3 (DcR3), a known IBD susceptibility gene, is a decoy receptor that can neutralize pro-inflammatory ligands including, TL1A (TNFSF15).

BRIEF DESCRIPTION OF THE FIGURES

Exemplary embodiments are illustrated in referenced figures. It is intended that the embodiments and figures disclosed herein are to be considered illustrative rather than restrictive.

FIG. 1 depicts, in accordance with embodiments herein, principal component analysis (PC1/PC2).

FIG. 2 depicts, in accordance with embodiments herein, pACTs of TNFSF15 region in NJ (Non-Jewish) and AJ (Ashkenazi Jewish) CD.

FIG. 3 depicts, in accordance with embodiments herein, pACTs of DcR3 (TNFRSF6B) region in NJ and AJ CD.

FIG. 4 depicts, in accordance with embodiments herein, linkage disequilibrium maps (r2) of the associated TNFSF15 SNPs in NJ and SK.

 SUMMARY OF THE INVENTION

Described herein is an assay for quantifying risk in a subject to Crohn's disease and/or fibrosist, including obtaining a sample from a subject, subjecting the sample to a genotyping assay adapted to determine the presence or absence of one or more variants at the TNFSF15 and/or DcR3 genetic loci, and quantifying risk in a subject to Crohn's disease and/or fibrosis based on the presence of one or more variants at the TNFSF15 and/or DcR3genetic loci. In various embodiments, the variants include one or more variants selected from the group including: SEQ ID NO. 1, SEQ ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO. 6, SEQ ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID NO. 11, SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 15, SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID NO. 19, SEQ ID NO. 20, SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24, SEQ ID NO. 25, and SEQ ID NO. 26. In other embodiments, the variants are SEQ ID NO. 3 and/or SEQ ID NO. 13. In other embodiments, the variant is SEQ ID NO. 22. In other embodiments, the subject is non-Jewish Caucasian, Ashkenazi, South Korean and/or Puerto Rican. In other embodiments, the subject is South Korean and the variant are SEQ ID NO. 3, SEQ ID NO. 13 and/or SEQ ID NO. 22. In other embodiments, the variant is a risk variant. In other embodiments, the variant is a protective variant. In other embodiments, the protective variant quantifies a reduced risk in the subject for structuring, CD, small bowel involvement and/or need for surgical intervention.

Also described herein is a method of diagnosing susceptibility to Crohn's disease and/or fibrosis in a subject, including obtaining a sample from a subject, subjecting the sample to a genotyping assay adapted to determine the presence or absence of one or more variants at the TNFSF15 and/or DcR3 genetic loci, and diagnosing susceptibility to Crohn's disease and/or fibrosis in the subject based on the presence of one or more variants at the TNFSF15 and/or DcR3 genetic loci. In other embodiments, variants consist of one or more variants selected from the group including: SEQ ID NO. 1, SEQ ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO. 6, SEQ ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID NO. 11, SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 15, SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID NO. 19, SEQ ID NO. 20, SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24, SEQ ID NO. 25, and SEQ ID NO. 26. In other embodiments, variants are SEQ ID NO. 3 and/or SEQ ID NO. 13. In other embodiments, variant is SEQ ID NO. 22. In other embodiments, subject is non-Jewish Caucasian, Ashkenazi, South Korean and/or Puerto Rican. In other embodiments, subject is South Korean and the variant are SEQ ID NO. 3, SEQ ID NO. 13 and/or SEQ ID NO. 22.

Also described herein is a method of treating Crohn's disease and/or fibrosis in a subject, including obtaining a sample from the subject, subjecting the sample to a genotyping assay adapted to determine the presence of one or more variants at the TNFSF15 and/or DcR3 genetic loci, and treating the Crohn's disease and/or fibrosis. In one embodiment, the variants consist of one or more variants selected from the group including: SEQ ID NO. 1, SEQ ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO. 6, SEQ ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID NO. 11, SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 15, SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID NO. 19, SEQ ID NO. 20, SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24, SEQ ID NO. 25, and SEQ ID NO. 26.

DESCRIPTION OF THE INVENTION

All references cited herein are incorporated by reference in their entirety as though fully set forth. Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Allen et al., Remington: The Science and Practice of Pharmacy 22nd ed., Pharmaceutical Press (Sep. 15, 2012); Hornyak et al., Introduction to Nanoscience and Nanotechnology, CRC Press (2008); Singleton and Sainsbury, Dictionary of Microbiology and Molecular Biology 3rd ed., revised ed., J. Wiley & Sons (New York, N.Y. 2006); Smith, March's Advanced Organic Chemistry Reactions, Mechanisms and Structure 7th ed., J. Wiley & Sons (New York, N.Y. 2013); Singleton, Dictionary of DNA and Genome Technology 3rd ed., Wiley-Blackwell (Nov. 28, 2012); and Green and Sambrook, Molecular Cloning: A Laboratory Manual 4th ed., Cold Spring Harbor Laboratory Press (Cold Spring Harbor, N.Y. 2012), provide one skilled in the art with a general guide to many of the terms used in the present application. For references on how to prepare antibodies, see Greenfield, Antibodies A Laboratory Manual 2nd ed., Cold Spring Harbor Press (Cold Spring Harbor N.Y., 2013); Köhler and Milstein, Derivation of specific antibody producing tissue culture and tumor lines by cell fusion, Eur. J. Immunol. 1976 July, 6(7):511-9; Queen and Selick, Humanized immunoglobulins, U.S. Pat. No. 5,585,089 (1996 December); and Riechmann et al., Reshaping human antibodies for therapy, Nature 1988 Mar. 24, 332(6162):323-7.

As disclosed herein, the inventors examined the effect of T-helper pathway on TL1A induced colitis, and the effect of T-helper pathway on TL1A induced gut fibrosis. A role for TL1A in gut mucosal inflammation is highlighted by the finding that neutralizing TL1A antibody prevented and treated chronic colitis in mice. However, the contribution of either lymphoid or myeloid derived TL1A to the development of gut inflammation is not fully known. TL1A is the product of the TNFSF15 gene that is expressed by both lymphoid and myeloid derived cells. Variants in the TNFSF15 gene have been found to be associated with IBD. The protein product of TNFSF15, TL1A, is elevated in the intestinal mucosa of IBD patients. Certain TNFSF15 haplotypes are associated with susceptibility in non-Jewish Caucasian CD and UC. In addition, TNFSF15 haplotype B is not only associated with risk, but also with severity in Jewish CD patients. Moreover, monocytes from Jewish patients carrying the risk haplotype B express higher levels of TL1A in response to FcγR stimulation. These results show that CD associated TNFSF15 genetic variations contribute to enhanced induction of TL1A, resulting in severe, chronic mucosal inflammation and that modulation of TL1A may be a potential target for therapeutic development. TL1A signals via death domain receptor 3 (DR3) and several studies implicate the TL1A/DR3 signaling pathway in mucosal inflammation. Neutralizing TL1A-antibody ameliorates inflammation in DSS and Gαi2−/− T cell transfer chronic colitis models. Constitutive TL1A expression in mice leads to mild spontaneous ileitis and increased collagen deposition. TL1A modulates the adaptive immune response in the T-helper (Th)-1 effector arm, as shown by TL1A enhanced interferon (IFN)-γ production from peripheral and mucosal T-cells. TL1A is a TNF superfamily member. Thus, in summary TNFSF15 SNPs are associated with IBD, TNFSF15 haplotype B has increased TL1A expression with a higher risk of small bowel surgery, and constitutive Tl1a expression in mice confers worsened murine ileo-cecal inflammation and intestinal fibrostenosis. While it is known TL1A can enhance Th1, Th2, and Th17 effector cell function, it is poorly understood which TL1A activated T-helper effector pathway induces intestinal inflammation and fibrosis. Thus, a critical scientific question is understanding the effect of T-helper pathway on TL1A induced colitis and effect of T-helper pathway on TL1A induced gut fibrosis.

As disclosed herein, the inventors performed trans-ethnic fine mapping across TNFSF15 and DcR3 in Caucasian, Puerto Rican, and Korean CD. The inventors identified associations with Non Jewish Caucasian (NJ) Crohn's disease (CD) and rare TNFSF15 variants. This association is independent of previously reported common variants. Also, these variants are much more common in the South Korean (SK) population, and also associated with SK CD. DcR3 is significantly associated with NJ CD, a finding replicated in SK and variation at this locus modifies stricturing phenotype.

Described herein is an assay for quantifying risk in a subject to Crohn's disease and/or fibrosist, including obtaining a sample from a subject, subjecting the sample to a genotyping assay adapted to determine the presence or absence of one or more variants at the TNFSF 15 and/or DcR3 genetic loci, and quantifying risk in a subject to Crohn's disease and/or fibrosis based on the presence of one or more variants at the TNFSF15 and/or DcR3genetic loci. In various embodiments, the variants include one or more variants selected from the group including: SEQ ID NO. 1, SEQ ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO. 6, SEQ ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID NO. 11, SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 15, SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID NO. 19, SEQ ID NO. 20, SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24, SEQ ID NO. 25, and SEQ ID NO. 26. In other embodiments, the variants are SEQ ID NO. 3 and/or SEQ ID NO. 13. In other embodiments, the variant is SEQ ID NO. 22. In other embodiments, the subject is non-Jewish Caucasian, Ashkenazi, South Korean and/or Puerto Rican. In other embodiments, the subject is South Korean and the variant are SEQ ID NO. 3, SEQ ID NO. 13 and/or SEQ ID NO. 22. In other embodiments, the variant is a risk variant. In other embodiments, the variant is a protective variant. In other embodiments, the protective variant quantifies a reduced risk in the subject for structuring, CD, small bowel involvement and/or need for surgical intervention.

Also described herein is a method of diagnosing susceptibility to Crohn's disease and/or fibrosis in a subject, including obtaining a sample from a subject, subjecting the sample to a genotyping assay adapted to determine the presence or absence of one or more variants at the TNFSF15 and/or DcR3 genetic loci, and diagnosing susceptibility to Crohn's disease and/or fibrosis in the subject based on the presence of one or more variants at the TNFSF15 and/or DcR3 genetic loci. In other embodiments, variants consist of one or more variants selected from the group including: SEQ ID NO. 1, SEQ ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO. 6, SEQ ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID NO. 11, SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 15, SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID NO. 19, SEQ ID NO. 20, SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24, SEQ ID NO. 25, and SEQ ID NO. 26. In other embodiments, variants are SEQ ID NO. 3 and/or SEQ ID NO. 13. In other embodiments, variant is SEQ ID NO. 22. In other embodiments, subject is non-Jewish Caucasian, Ashkenazi, South Korean and/or Puerto Rican. In other embodiments, subject is South Korean and the variant are SEQ ID NO. 3, SEQ ID NO. 13 and/or SEQ ID NO. 22.

Also described herein is a method of treating Crohn's disease and/or fibrosis in a subject, including obtaining a sample from the subject, subjecting the sample to a genotyping assay adapted to determine the presence of one or more variants at the TNFSF15 and/or DcR3 genetic loci, and treating the Crohn's disease and/or fibrosis. In one embodiment, the variants consist of one or more variants selected from the group including: SEQ ID NO. 1, SEQ ID NO. 2, SEQ ID NO. 3, SEQ ID NO. 4, SEQ ID NO. 5, SEQ ID NO. 6, SEQ ID NO. 7, SEQ ID NO. 8, SEQ ID NO. 9, SEQ ID NO. 10, SEQ ID NO. 11, SEQ ID NO. 12, SEQ ID NO. 13, SEQ ID NO. 14, SEQ ID NO. 15, SEQ ID NO. 16, SEQ ID NO. 17, SEQ ID NO. 18, SEQ ID NO. 19, SEQ ID NO. 20, SEQ ID NO. 21, SEQ ID NO. 22, SEQ ID NO. 23, SEQ ID NO. 24, SEQ ID NO. 25, and SEQ ID NO. 26.

In one embodiment, the present invention provides a method of diagnosing susceptibility to Crohn's disease in a subject by obtaining a sample from the subject, assaying the sample to determine the presence or absence of one or more risk variants in the subject, and diagnosing susceptibility to Crohn's disease based on the presence of one or more risk variants. In another embodiment, the one or more risk variants are at the TNFSF15 and/or DcR3 genetic loci. In another embodiment, the one or more risk variants are described in Tables 2 and 3 herein. In another embodiment, the subject is Caucasian, Puerto Rican, or South Korean. In another embodiment, the subject is Non-Caucasian.

In one embodiment, the present invention provides a method of diagnosing a Crohn's disease subtype in a subject by obtaining a sample from the subject, assaying the sample to determine the presence or absence of one or more risk variants in the subject, and diagnosing the Crohn's disease subtype based on the presence of one or more risk variants. In another embodiment, the one or more risk variants are at the TNFSF15 and/or DcR3 genetic loci. In another embodiment, the one or more risk variants are described in Tables 2 and 3 herein. In another embodiment, the subject is Caucasian, Puerto Rican, or South Korean. In another embodiment, the subject is Non-Caucasian.

In one embodiment, the present invention provides a method of treating Crohn's disease in a subject by determining the presence of one or more one or more risk variants in the subject, and treating the subject. In another embodiment, the one or more risk variants are at the TNFSF15 and/or DcR3 genetic loci. In another embodiment, the one or more risk variants are described in Tables 2 and 3 herein. In another embodiment, the subject is Caucasian, Puerto Rican, or South Korean. In another embodiment, the subject is Non-Caucasian.

In one embodiment, the present invention provides a method of diagnosing susceptibility to fibrosis in a subject by obtaining a sample from the subject, assaying the sample to determine the presence or absence of one or more risk variants in the subject, and diagnosing susceptibility to fibrosis based on the presence of one or more risk variants. In another embodiment, the one or more risk variants are at the TNFSF15 and/or DcR3 genetic loci. In another embodiment, the one or more risk variants are described in Tables 2 and 3 herein. In another embodiment, the subject is Caucasian, Puerto Rican, or South Korean. In another embodiment, the subject is Non-Caucasian.

In one embodiment, the present invention provides a method of diagnosing a fibrosis subtype in a subject by obtaining a sample from the subject, assaying the sample to determine the presence or absence of one or more risk variants in the subject, and diagnosing the fibrosis subtype based on the presence of one or more risk variants. In another embodiment, the one or more risk variants are at the TNFSF15 and/or DcR3 genetic loci. In another embodiment, the one or more risk variants are described in Tables 2 and 3 herein. In another embodiment, the subject is Caucasian, Puerto Rican, or South Korean. In another embodiment, the subject is Non-Caucasian.

In one embodiment, the present invention provides a method of treating fibrosis in a subject by determining the presence of one or more one or more risk variants in the subject, and treating the subject. In another embodiment, the one or more risk variants are at the TNFSF15 and/or DcR3 genetic loci. In another embodiment, the one or more risk variants are described in Tables 2 and 3 herein. In another embodiment, the subject is Caucasian, Puerto Rican, or South Korean. In another embodiment, the subject is Non-Caucasian.

The various methods and techniques described above provide a number of ways to carry out the invention. Of course, it is to be understood that not necessarily all objectives or advantages described may be achieved in accordance with any particular embodiment described herein. Thus, for example, those skilled in the art will recognize that the methods can be performed in a manner that achieves or optimizes one advantage or group of advantages as taught herein without necessarily achieving other objectives or advantages as may be taught or suggested herein. A variety of advantageous and disadvantageous alternatives are mentioned herein. It is to be understood that some preferred embodiments specifically include one, another, or several advantageous features, while others specifically exclude one, another, or several disadvantageous features, while still others specifically mitigate a present disadvantageous feature by inclusion of one, another, or several advantageous features.

Furthermore, the skilled artisan will recognize the applicability of various features from different embodiments. Similarly, the various elements, features and steps discussed above, as well as other known equivalents for each such element, feature or step, can be mixed and matched by one of ordinary skill in this art to perform methods in accordance with principles described herein. Among the various elements, features, and steps some will be specifically included and others specifically excluded in diverse embodiments.

Although the invention has been disclosed in the context of certain embodiments and examples, it will be understood by those skilled in the art that the embodiments of the invention extend beyond the specifically disclosed embodiments to other alternative embodiments and/or uses and modifications and equivalents thereof.

Many variations and alternative elements have been disclosed in embodiments of the present invention. Still further variations and alternate elements will be apparent to one of skill in the art. Among these variations, without limitation, are the selection of constituent modules for the inventive compositions, and the diseases and other clinical conditions that may be diagnosed, prognosed or treated therewith. Various embodiments of the invention can specifically include or exclude any of these variations or elements.

In some embodiments, the numbers expressing quantities of ingredients, properties such as concentration, reaction conditions, and so forth, used to describe and claim certain embodiments of the invention are to be understood as being modified in some instances by the term “about.” Accordingly, in some embodiments, the numerical parameters set forth in the written description and attached claims are approximations that can vary depending upon the desired properties sought to be obtained by a particular embodiment. In some embodiments, the numerical parameters should be construed in light of the number of reported significant digits and by applying ordinary rounding techniques. Notwithstanding that the numerical ranges and parameters setting forth the broad scope of some embodiments of the invention are approximations, the numerical values set forth in the specific examples are reported as precisely as practicable. The numerical values presented in some embodiments of the invention may contain certain errors necessarily resulting from the standard deviation found in their respective testing measurements.

In some embodiments, the terms “a” and “an” and “the” and similar references used in the context of describing a particular embodiment of the invention (especially in the context of certain of the following claims) can be construed to cover both the singular and the plural. The recitation of ranges of values herein is merely intended to serve as a shorthand method of referring individually to each separate value falling within the range. Unless otherwise indicated herein, each individual value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g. “such as”) provided with respect to certain embodiments herein is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention otherwise claimed. No language in the specification should be construed as indicating any non-claimed element essential to the practice of the invention.

Groupings of alternative elements or embodiments of the invention disclosed herein are not to be construed as limitations. Each group member can be referred to and claimed individually or in any combination with other members of the group or other elements found herein. One or more members of a group can be included in, or deleted from, a group for reasons of convenience and/or patentability. When any such inclusion or deletion occurs, the specification is herein deemed to contain the group as modified thus fulfilling the written description of all Markush groups used in the appended claims.

Preferred embodiments of this invention are described herein, including the best mode known to the inventors for carrying out the invention. Variations on those preferred embodiments will become apparent to those of ordinary skill in the art upon reading the foregoing description. It is contemplated that skilled artisans can employ such variations as appropriate, and the invention can be practiced otherwise than specifically described herein. Accordingly, many embodiments of this invention include all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context.

Furthermore, numerous references have been made to patents and printed publications throughout this specification. Each of the above cited references and printed publications are herein individually incorporated by reference in their entirety.

In closing, it is to be understood that the embodiments of the invention disclosed herein are illustrative of the principles of the present invention. Other modifications that can be employed can be within the scope of the invention. Thus, by way of example, but not of limitation, alternative configurations of the present invention can be utilized in accordance with the teachings herein. Accordingly, embodiments of the present invention are not limited to that precisely as shown and described.

EXAMPLES

The following examples are provided to better illustrate the claimed invention and are not to be interpreted as limiting the scope of the invention. To the extent that specific materials are mentioned, it is merely for purposes of illustration and is not intended to limit the invention. One skilled in the art may develop equivalent means or reactants without the exercise of inventive capacity and without departing from the scope of the invention.

Example 1 Methods

The inventors performed trans-ethnic fine mapping across TNFSF15 and DcR3 in Caucasian, Puerto Rican (PR) and South Korean (SK) CD. Immunochip genotyping as performed on the following populations presented in Table 1.

TABLE 1 Study subjects by ethnicity Population CD Control Non-Jewish Caucasian (NJ) 779 4182 Ashkenazi Jewish (AJ) 492 395 Puerto Rican (PR) 300 235 South Korean (SK) 729 469

To measure association of TNFSF15 (416 SNPs) and DcR3 (13 SNPs), logistic regression was applied after controlling for population structure using principal component analysis (PCA) (FIG. 1). The result pACTs function corrects for multiple testing. A value of pACTs<0.05 was considered as statistically significant. Thereafter, population attributable risk (PAR) of the associated TNFSF15-DcR3 pathway SNPs was calculated in each population, the results of which are shown in Tables 2-4.

TABLE 2 SNPs associated with NJ CD. (pACTs <0.05) Odds SNP dbSNP Location A1 A2 CD Control P-Values pACT Ratio Rare variants Allele 1 Frequency TNFSF15-130 rs4979462 INTRON T C 0.64% 0.11% 4.89E−05 7.76E−03 6.62 [SEQ ID NO. 1] TNFSF15-150 rs55768522 INTERGENIC A G 0.58% 0.07% 4.12E−05 6.63E−03 8.95 [SEQ ID NO. 2] TNFSF15-160 rs1322057 INTERGENIC G A 0.83% 0.13% 3.02E−06 5.23E−04 6.97 [SEQ ID NO. 3] TNFSF15-271 rs76779588 INTERGENIC T C 0.64% 0.11% 4.48E−05 7.14E−03 6.70 [SEQ ID NO. 4] Common variants Allele 1 Frequency TNFSF15-90 rs4574921 INTERGENIC T C 77.3% 72.3% 5.31E−05 8.38E−03 1.30 [SEQ ID NO. 5] TNFSF15-106 rs10114470 INTERGENIC C T 72.2% 67.0% 7.98E−05 1.24E−02 1.27 [SEQ ID NO. 6] TNFSF15-110 rs3810936 CODING(SYN) C T 72.1% 67.1% 1.42E−04 2.14E−02 1.26 [SEQ ID NO. 7] TNFSF15-111 rs4246905 INTRON C T 74.9% 69.9% 1.07E−04 1.61E−02 1.28 [SEQ ID NO. 8] TNFSF15-120 rs6478108 INTRON T C 70.2% 65.1% 1.11E−04 1.66E−02 1.26 [SEQ ID NO. 9] TNFSF15-134 rs6478109 INTERGENIC G A 71.0% 66.3% 3.25E−04 4.60E−02 1.24 [SEQ ID NO. 10] TNFSF15-137 rs7848647 INTERGENIC C T 71.2% 66.3% 1.55E−04 2.33E−02 1.26 [SEQ ID NO. 11] TNFSF15-144 rs59418409 INTERGENIC I D 74.3% 69.2% 1.05E−04 1.61E−02 1.27 [SEQ ID NO. 12] TNFSF15-164 rs7869487 INTERGENIC T C 72.8% 67.6% 7.26E−05 1.12E−02 1.28 [SEQ ID NO. 13]

TABLE 3 Association results of DcR3 gene in NJ CD Allele 1 Frequency Odds SNP dbSNP Gene Location A1 A2 CD Control P-Values pACT Ratio DcR3-1 rs6011033 RTEL1 INTRON G A 79.6% 78.0% 1.27E−01 5.90E−01 1.11 [SEQ ID NO. 14] DcR3-2 rs80132799 RTEL1 INTRON C T 93.6% 93.3% 6.93E−01 6.93E−01 1.05 [SEQ ID NO. 15] DcR3-3 rs34412639 RTEL1 INTRON C A 99.6% 99.3% 1.43E−01 5.07E−01 1.88 [SEQ ID NO. 16] DcR3-4 rs2236507 RTEL1 INTRON C G 79.4% 77.3% 5.35E−02 3.23E−01 1.14 [SEQ ID NO. 17] DcR3-5 rs74506932 RTEL1 INTRON T C 1.80% 1.58% 5.28E−01 7.76E−01 1.14 [SEQ ID NO. 18] DcR3-6 rs2738787 TNFRSF6B CODING G A 92.5% 91.7% 3.36E−01 6.54E−01 1.11 [SEQ ID NO. 19] DcR3-7 rs55765053 TNFRSF6B CODING T C 8.09% 7.08% 1.34E−01 5.52E−01 1.17 [SEQ ID NO. 20] DcR3-8 rs1291205 TNFRSF6B CODING C G 78.4% 76.2% 5.02E−02 3.09E−01 1.14 [SEQ ID NO. 21] DcR3-9 rs6062496 TNFRSF6B INTRON A G 59.3% 54.8% 5.83E−04 4.93E−03 1.22 [SEQ ID NO. 22] DcR3-10 rs1291206 TNFRSF6B INTRON G A 78.4% 76.2% 4.88E−02 3.02E−01 1.14 [SEQ ID NO. 23] DcR3-11 rs1291208 ARFRP1 INTRON C T 92.4% 91.7% 3.66E−01 6.87E−01 1.10 [SEQ ID NO. 24] DcR3-12 rs2738788 ARFRP1 INTRON A G 0.19% 0.07% 1.70E−01 4.87E−01 2.67 [SEQ ID NO. 25] DcR3-13 rs2236508 ARFRP1 INTRON G A 78.6% 76.7% 8.49E−02 4.60E−01 1.12 [SEQ ID NO. 26]

TABLE 4A Trans-ethnic allele frequences and results in SNPs associated with NJ-CD NJ AJ PR SK SNP CD Ctrl CD Ctrl CD Ctrl CD Ctrl Rare Variants of TNFSF15 TNFSF15-130 0.64% 0.11% 2.34% 2.28% 14.0% 11.1% 52.7% 34.5% TNFSF15-150 0.58% 0.07% 2.24% 2.03% 8.50% 5.11% 52.6% 34.4% TNFSF15-160 0.83% 0.13% 2.34% 2.78% 10.2% 6.60% 52.7% 34.6% TNFSF15-271 0.64% 0.11% 2.34% 2.15% 8.00% 4.26% 44.9% 31.8% Common Variants of TNFSF15 TNFSF15-90 77.3% 72.3% 77.7% 79.9% 83.2% 81.1% 79.6% 64.7% TNFSF15-106 72.2% 67.0% 73.9% 77.0% 77.5% 77.4% 68.9% 49.9% TNFSF15-110 72.1% 67.1% 74.1% 77.2% 77.3% 77.7% 68.5% 49.8% TNFSF15-111 74.9% 69.9% 77.3% 79.1% 82.3% 79.8% 80.5% 65.9% TNFSF15-120 70.2% 65.1% 75.2% 77.7% 77.8% 77.0% 71.5% 51.3% TNFSF15-134 71.2% 66.3% 78.7% 80.0% 79.5% 76.6% 71.7% 51.8% TNFSF15-137 71.0% 66.3% 78.6% 79.2% 79.3% 77.0% 71.7% 51.8% TNFSF15-144 74.3% 69.2% 81.9% 82.5% 83.3% 79.1% 77.3% 59.1% TNFSF15-164 72.8% 67.6% 80.3% 81.1% 83.0% 79.1% 77.4% 59.1% DeR3 variant DcR3-9 59.3% 54.8% 67.1% 64.3% 60.5% 57.0% 17.6% 14.3%

TABLE 4B Trans-ethnic allele frequences and results in SNPs associated with NJ-CD NJ AJ PR SK SNP CD Ctrl CD Ctrl CD Ctrl CD Ctrl Rare Variants of TNFSF15 TNFSF15-130 4.89E−05 8.70E−01 1.54E−01 6.92E−17 6.62 1.05 1.31 2.10 TNFSF15-150 4.12E−05 7.23E−01 3.10E−02 5.28E−17 8.95 1.13 1.75 2.12 TNFSF15-160 3.02E−06 5.81E−01 3.19E−02 8.66E−17 6.97 0.84 1.67 2.10 TNFSF15-271 4.48E−05 7.99E−01 1.25E−02 3.15E−10 6.70 1.09 2.02 1.76 Common Variants of TNFSF15 TNFSF15-90 5.31E−05 2.92E−01 3.70E−01 5.70E−16 1.30 0.88 1.15 2.26 TNFSF15-106 7.98E−05 1.34E−01 9.96E−01 2.52E−19 1.27 0.84 1.00 2.26 TNFSF15-110 1.42E−04 1.29E−01 8.91E−01 4.03E−19 1.26 0.84 0.98 2.25 TNFSF15-111 1.07E−04 3.90E−01 3.06E−01 5.83E−16 1.28 0.90 1.17 2.30 TNFSF15-120 1.11E−04 2.49E−01 7.65E−01 4.71E−22 1.26 0.88 1.04 2.46 TNFSF15-134 1.55E−04 5.83E−01 2.74E−01 1.69E−21 1.26 0.94 1.17 2.42 TNFSF15-137 3.25E−04 8.34E−01 3.84E−01 1.69E−21 1.24 0.98 1.14 2.42 TNFSF15-144 1.05E−04 8.59E−01 9.14E−02 3.24E−21 1.27 0.98 1.29 2.55 TNFSF15-164 7.26E−05 7.69E−01 1.24E−01 1.98E−21 1.28 0.96 1.26 2.56 DeR3 variant DcR3-9 5.83E−04 1.51E−01 2.49E−01 2.01E−02 1.22 1.16 1.16 1.32

TABLE 5 Conditional analysis of the associated TNFSF15 SNPs in NJ CD and SK CD P-value P-value P-value on SNP P-value on SNP 160 on SNP 164 160&164 SNP NJ SK NJ SK NJ SK NJ SK Rare Variants of TNFSF15 TNFSF15-130 4.89E−05 6.92E−17 8.18E−01 4.82E−01 1.12E−04 9.39E−04 7.83E−01 6.17E−01 TNFSF15-150 4.12E−05 5.28E−17 4.37E−01 2.30E−01 9.92E−05 7.68E−04 4.87E−01 2.73E−01 TNFSF15-160 3.02E−06 8.66E−17 — — 7.83E−06 1.07E−03 — — TNFSF15-271 4.48E−05 3.15E−10 8.11E−01 4.46E−01 1.04E−04 4.38E−02 8.47E−01 5.84E−01 Common Variants of TNFSF15 TNFSF15-90 5.31E−05 5.70E−16 1.07E−04 3.46E−06 1.10E−01 4.34E−01 1.20E−01 4.63E−01 TNFSF15-106 7.98E−05 2.52E−19 1.75E−04 1.87E−06 1.61E−01 7.18E−04 1.87E−01 2.51E−02 TNFSF15-110 1.42E−04 4.03E−19 3.05E−04 2.95E−06 2.42E−01 1.16E−03 2.77E−01 3.78E−02 TNFSF15-111 1.05E−04 5.83E−16 2.09E−04 4.32E−06 2.69E−01 5.35E−01 2.81E−01 5.65E−01 TNFSF15-120 1.11E−04 4.71E−22 2.54E−04 3.38E−08 6.21E−01 1.94E−03 6.91E−01 6.24E−02 TNFSF15-134 3.25E−04 1.69E−21 5.02E−04 1.18E−07 8.35E−01 6.14E−03 7.55E−01 1.49E−01 TNFSF15-137 1.55E−04 1.69E−21 3.38E−04 1.18E−07 5.28E−01 6.14E−03 5.81E−01 1.49E−01 TNFSF15-144 1.07E−04 3.24E−21 2.09E−04 1.99E−08 8.08E−01 7.98E−01 7.88E−01 5.37E−01 TNFSF15-164 7.26E−05 1.98E−21 1.54E−04 1.12E−08 — — — —

TABLE 6 Su results of DcR3 gene in NJ CD CD Risk n Allele Freq Odds SNP Phenotype (+) (−) (+) (−) P-Value Ratio DcR3-9 Surgery 323 248 56.7% 62.9% 3.62E−02 0.77 DcR3-9 Stricturing CD (B2) 229 293 56.1% 63.3% 2.95E−02 0.75 DcR3-9 SB involvement (L1 + L3) 460 98 57.6% 66.3% 2.26E−02 0.68

TABLE 7 G × G interaction analysis with TNFSF15 and DcR3 P-values (SNP × SNP) NJ CD SK CD SNP DcR3-9 TNFSF15_160 0.175 0.607 TNFSF15_164 0.523 0.742

TABLE 8 Population attributable risk of TNFSF15-DcR3 SNPs SNP GENE NJ CD SK CD TNFSF15-160 TNFSF15 1.4% 41.4% TNFSF15-164 TNFSF15 17.0% 70.8% DcR3-9 DcR3 20.5% 9.0% TNFSF15-DcR3 3 SNPs — 32.3% 76.4%

Example 3 TNFSF15 Analysis

As shown by the above results, 4 rare variants and 9 common variants were significantly associated with NJ CD (Table 2). All 13 associations were replicated in SK CD (Table 4), but the rare variants were much more common in the SK population.

Importantly, the ‘rare’ and ‘common’ variants can each be tagged by a single SNP (SNP160 & SNP164 respectively) in both NJ and SK. (Table 5, FIG. 4) The ‘rare’ variants were associated with CD in PR (at higher allele frequency). No association was seen in PR with the common variants. (Table 4). No significant SNP associations were observed in AJ CD. (FIG. 2, Table 4). After correcting for multiple comparisons there were no significant associations with rare or common CD-associated SNPs with clinical subphenotypes in NJ CD.

Example 4 DcR3 Analysis

The above results further indicated that rs6062496 in intron 6 was significantly associated with NJ CD. (FIG. 3, Table 3). The association was confirmed in SK CD, but not in PR and AJ CD. (Table 4). It was further identified that rs6062496 also associated with protection against stricturing CD, small bowel involvement and need for surgery (Table 6).

Example 5 TNFSF15-DcR3 Analysis

The above results further suggest no significant DcR3 and TNFSF15 gene-gene interactions in NJ and SK. (Table 7). The PAR by TNFSF15-DcR3 pathway was 32.3% in NJ CD. (Table 8). The PAR by TNFSF15 variants in SK was the highest seen in either population explaining the dominant effect of this locus in Asian CD (Table 8)

Example 6 Conclusions

Based on the described results, the inventors identified associations with NJ CD and rare TNFSF15 variants. This association is independent of previously reported common variants. These variants are much more common in the SK population, and also associated with SK CD. DcR3 is significantly associated with NJ CD, a finding replicated in SK and variation at this locus modifies stricturing phenotype.

The various methods and techniques described above provide a number of ways to carry out the invention. Of course, it is to be understood that not necessarily all objectives or advantages described may be achieved in accordance with any particular embodiment described herein. Thus, for example, those skilled in the art will recognize that the methods can be performed in a manner that achieves or optimizes one advantage or group of advantages as taught herein without necessarily achieving other objectives or advantages as may be taught or suggested herein. A variety of advantageous and disadvantageous alternatives are mentioned herein. It is to be understood that some preferred embodiments specifically include one, another, or several advantageous features, while others specifically exclude one, another, or several disadvantageous features, while still others specifically mitigate a present disadvantageous feature by inclusion of one, another, or several advantageous features.

Furthermore, the skilled artisan will recognize the applicability of various features from different embodiments. Similarly, the various elements, features and steps discussed above, as well as other known equivalents for each such element, feature or step, can be mixed and matched by one of ordinary skill in this art to perform methods in accordance with principles described herein. Among the various elements, features, and steps some will be specifically included and others specifically excluded in diverse embodiments.

Although the invention has been disclosed in the context of certain embodiments and examples, it will be understood by those skilled in the art that the embodiments of the invention extend beyond the specifically disclosed embodiments to other alternative embodiments and/or uses and modifications and equivalents thereof.

Many variations and alternative elements have been disclosed in embodiments of the present invention. Still further variations and alternate elements will be apparent to one of skill in the art. Among these variations, without limitation, are the methods of prognosis and diagnosis for inflammatory bowel disease related diseases and/or conditions, compositions of generated by the aforementioned techniques, treatment of diseases and/or conditions that relate to the teachings of the invention, techniques and composition and use of solutions used therein, and the particular use of the products created through the teachings of the invention. Various embodiments of the invention can specifically include or exclude any of these variations or elements.

In some embodiments, the numbers expressing quantities of ingredients, properties such as concentration, reaction conditions, and so forth, used to describe and claim certain embodiments of the invention are to be understood as being modified in some instances by the term “about.” Accordingly, in some embodiments, the numerical parameters set forth in the written description and attached claims are approximations that can vary depending upon the desired properties sought to be obtained by a particular embodiment. In some embodiments, the numerical parameters should be construed in light of the number of reported significant digits and by applying ordinary rounding techniques. Notwithstanding that the numerical ranges and parameters setting forth the broad scope of some embodiments of the invention are approximations, the numerical values set forth in the specific examples are reported as precisely as practicable. The numerical values presented in some embodiments of the invention may contain certain errors necessarily resulting from the standard deviation found in their respective testing measurements.

In some embodiments, the terms “a” and “an” and “the” and similar references used in the context of describing a particular embodiment of the invention (especially in the context of certain of the following claims) can be construed to cover both the singular and the plural. The recitation of ranges of values herein is merely intended to serve as a shorthand method of referring individually to each separate value falling within the range. Unless otherwise indicated herein, each individual value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g. “such as”) provided with respect to certain embodiments herein is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention otherwise claimed. No language in the specification should be construed as indicating any non-claimed element essential to the practice of the invention.

Groupings of alternative elements or embodiments of the invention disclosed herein are not to be construed as limitations. Each group member can be referred to and claimed individually or in any combination with other members of the group or other elements found herein. One or more members of a group can be included in, or deleted from, a group for reasons of convenience and/or patentability. When any such inclusion or deletion occurs, the specification is herein deemed to contain the group as modified thus fulfilling the written description of all Markush groups used in the appended claims.

Preferred embodiments of this invention are described herein, including the best mode known to the inventor for carrying out the invention. Variations on those preferred embodiments will become apparent to those of ordinary skill in the art upon reading the foregoing description. It is contemplated that skilled artisans can employ such variations as appropriate, and the invention can be practiced otherwise than specifically described herein. Accordingly, many embodiments of this invention include all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context.

Furthermore, numerous references have been made to patents and printed publications throughout this specification. Each of the above cited references and printed publications are herein individually incorporated by reference in their entirety.

In closing, it is to be understood that the embodiments of the invention disclosed herein are illustrative of the principles of the present invention. Other modifications that can be employed can be within the scope of the invention. Thus, by way of example, but not of limitation, alternative configurations of the present invention can be utilized in accordance with the teachings herein. Accordingly, embodiments of the present invention are not limited to that precisely as shown and described.

Claims

1. A method of treating an inflammatory bowel disease in a subject in need thereof, the method comprising administering to the subject an anti-TL1A antibody, provided that the subject comprises a polymorphism in TNFSF15 at the position “N” within SEQ ID NO: 3, SEQ ID NO: 2, SEQ ID NO: 4, or a combination thereof.

2. The method of claim 1, provided that the inflammatory bowel disease comprises Crohn's disease.

3. The method of claim 1, provided that the subject further comprises a polymorphism in TNFSF15 within rs4979462.

4. The method of claim 1, provided that the subject is of Asian descent.

5. The method of claim 1, provided that the subject further comprises a polymorphism in TNFSF15 within rs7848647, rs6478109, rs59418409, rs7869487, rs6478108, rs10114470, rs3810936, rs4246905, rs4574921, or a combination thereof.

6. The method of claim 1, provided that the subject further comprises a polymorphism in DcR3 within rs6062496, rs1291206, rs1291205, rs2236507, rs2236508, rs6011033, rs55765053, rs34412639, rs2738788, rs2738787, rs1291208, rs74506932, rs80132799, or a combination thereof.

7. A method of treating an inflammatory bowel disease in a subject in need thereof, the method comprising administering to the subject an anti-TL1A antibody, provided that the subject comprises a polymorphism in TNFSF15 at the position “N” within SEQ ID NO: 12.

8. The method of claim 7, provided that the polymorphism is an insertion.

9. The method of claim 7, provided that the inflammatory bowel disease comprises Crohn's disease.

10. The method of claim 7, provided that the subject further comprises a polymorphism in TNFSF15 within rs7848647, rs6478109, rs7869487, rs6478108, rs10114470, rs3810936, rs4246905, rs4574921, or a combination thereof.

11. The method of claim 10, provided that the subject comprises the polymorphism within rs6478109.

12. The method of claim 10, provided that the subject comprises the polymorphism within rs7848647.

13. The method of claim 10, provided that the subject comprises the polymorphism within rs7869487.

14. The method of claim 7, provided that the subject further comprises a polymorphism in TNFSF15 within rs1322057, rs55768522, rs76779588, rs4979462, or a combination thereof.

15. The method of claim 7, provided that the subject further comprises a polymorphism in DcR3 within rs6062496, rs1291206, rs1291205, rs2236507, rs2236508, rs6011033, rs55765053, rs34412639, rs2738788, rs2738787, rs1291208, rs74506932, rs80132799, or a combination thereof.

16. A method of treating an inflammatory bowel disease in a subject in need thereof, the method comprising administering to the subject an anti-TL1A antibody, provided that the subject comprises a polymorphism in DcR3 at the position “N” within SEQ ID NO: 17, SEQ ID NO: 14, SEQ ID NO: 20, SEQ ID NO: 18, or a combination thereof.

17. The method of claim 16, provided that the inflammatory bowel disease comprises Crohn's disease.

18. The method of claim 16, provided that the subject further comprises a polymorphism in DcR3 within rs6062496, rs1291206, rs1291205, rs2236508, rs34412639, rs2738788, rs2738787, rs1291208, rs80132799, or a combination thereof.

19. The method of claim 16, provided that the subject further comprises a polymorphism in TNFSF15 within rs7848647, rs6478109, rs59418409, rs7869487, rs6478108, rs10114470, rs3810936, rs4246905, rs4574921, or a combination thereof.

20. The method of claim 16, provided that the subject further comprises a polymorphism in TNFSF15 within rs1322057, rs55768522, rs76779588, rs4979462, or a combination thereof.

Patent History
Publication number: 20180230543
Type: Application
Filed: Apr 5, 2018
Publication Date: Aug 16, 2018
Inventor: Dermot P. McGovern (Los Angeles, CA)
Application Number: 15/946,632
Classifications
International Classification: C12Q 1/6883 (20060101);