WO2014186750A2 - Variants of tnfsf15 and dcr3 associated with crohn's disease - Google Patents

Variants of tnfsf15 and dcr3 associated with crohn's disease Download PDF

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WO2014186750A2
WO2014186750A2 PCT/US2014/038468 US2014038468W WO2014186750A2 WO 2014186750 A2 WO2014186750 A2 WO 2014186750A2 US 2014038468 W US2014038468 W US 2014038468W WO 2014186750 A2 WO2014186750 A2 WO 2014186750A2
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seq
tnfsf15
variants
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dcr3
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WO2014186750A3 (en
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Dermot P. Mcgovern
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Cedars Sinai Medical Center
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Cedars Sinai Medical Center
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Priority to KR1020237020524A priority Critical patent/KR20230093538A/ko
Priority to EP18201967.9A priority patent/EP3498867B1/en
Priority to CN201480038133.6A priority patent/CN105358713B/zh
Priority to EP21193676.0A priority patent/EP3988673A3/en
Priority to EP14797214.5A priority patent/EP2997165A4/en
Priority to KR1020257028341A priority patent/KR20250130857A/ko
Priority to US14/890,712 priority patent/US20160090629A1/en
Priority to KR1020157034355A priority patent/KR102295125B1/ko
Priority to JP2016514143A priority patent/JP6482533B2/ja
Application filed by Cedars Sinai Medical Center filed Critical Cedars Sinai Medical Center
Priority to KR1020217026836A priority patent/KR20210107176A/ko
Publication of WO2014186750A2 publication Critical patent/WO2014186750A2/en
Publication of WO2014186750A3 publication Critical patent/WO2014186750A3/en
Anticipated expiration legal-status Critical
Priority to US15/946,632 priority patent/US20180230543A1/en
Priority to US17/392,098 priority patent/US12281359B2/en
Priority to US19/084,586 priority patent/US20250243548A1/en
Ceased legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/04—Drugs for disorders of the alimentary tract or the digestive system for ulcers, gastritis or reflux esophagitis, e.g. antacids, inhibitors of acid secretion, mucosal protectants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P29/00—Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/06—Immunosuppressants, e.g. drugs for graft rejection
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
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    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2875—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the NGF/TNF superfamily, e.g. CD70, CD95L, CD153, CD154
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/112—Disease subtyping, staging or classification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/118—Prognosis of disease development
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/172—Haplotypes

Definitions

  • the claimed invention relates to prognosis, diagnosis and treatment of inflammatory bowel disease and related conditions, including methods and compositions for medical therapies.
  • IBD Inflammatory bowel disease
  • CD Crohn's disease
  • TL1A may drive intestinal inflammation through enhancing Thl, Th2 and Thl7 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.
  • TNFSF15 TNF superfamily member
  • DcR3 a known IBD susceptibility gene
  • FIG. 1 depicts, in accordance with embodiments herein, principal component analysis (PC1/PC2).
  • Figure 2 depicts, in accordance with embodiments herein, pACTs of TNFSF15 region in NJ (Non- Jewish) and A J (Ashkenazi Jewish) CD.
  • FIG. 3 depicts, in accordance with embodiments herein, pACTs of DcR3
  • TNFRSF6B (TNFRSF6B) region in NJ and AJ CD.
  • Figure 4 depicts, in accordance with embodiments herein, linkage disequilibrium maps (r 2 ) of the associated TNFSF15 SNPs in NJ and SK.
  • 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 DcPv3genetic loci.
  • 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.
  • the variants are SEQ ID NO. 3 and/or SEQ ID NO.13. In other embodiments, the variant is SEQ ID NO. 22.
  • the subject is non-Jewish Caucasian, Ashkenazi, South Korean and/or Puerto Rican.
  • the subject is South Korean and the variant are SEQ ID NO. 3, SEQ ID NO.13 and/or SEQ ID NO. 22.
  • the variant is a risk variant.
  • the variant is a protective variant.
  • the protective variant quantifies a reduced risk in the subject for structuring, CD, small bowel involvement and/or need for surgical intervention.
  • 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.
  • variants are SEQ ID NO. 3 and/or SEQ ID NO.13.
  • variant is SEQ ID NO. 22.
  • subject is non-Jewish Caucasian, Ashkenazi, South Korean and/or Puerto Rican.
  • subject is South Korean and the variant are SEQ ID NO. 3, SEQ ID NO.13 and/or SEQ ID NO. 22.
  • 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.
  • 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.
  • TLIA 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, TLIA, is elevated in the intestinal mucosa of IBD patients.
  • TNFSF15 haplotypes are associated with susceptibility in non- Jewish Caucasian CD and UC.
  • TNFSF15 haplotype B is not only associated with risk, but also with severity in Jewish CD patients.
  • monocytes from Jewish patients carrying the risk haplotype B express higher levels of TLIA in response to FcyR stimulation.
  • TLIA signals via death domain receptor 3 (DR3) and several studies implicate the TL1A/DR3 signaling pathway in mucosal inflammation.
  • DR3 death domain receptor 3
  • TLIA neutrophil-induced TLlA-antibody ameliorates inflammation in DSS and Gai2-/- T cell transfer chronic colitis models.
  • Constitutive TLIA expression in mice leads to mild spontaneous ileitis and increased collagen deposition.
  • TLIA modulates the adaptive immune response in the T-helper (Th)-l effector arm, as shown by TLIA enhanced interferon (IFN)-y production from peripheral and mucosal T-cells.
  • TLIA is a TNF superfamily member.
  • TNFSF15 SNPs are associated with IBD
  • TNFSF15 ha lotype B has increased TL1A expression with a higher risk of small bowel surgery
  • constitutive Til a expression in mice confers worsened murine ileo-cecal inflammation and intestinal fibrostenosis.
  • TL1A can enhance Thl, Th2, and Thl7 effector cell function
  • TL1A activated T-helper effector pathway induces intestinal inflammation and fibrosis.
  • 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.
  • 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 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.
  • 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.
  • the variants are SEQ ID NO. 3 and/or SEQ ID NO.13. In other embodiments, the variant is SEQ ID NO. 22.
  • the subject is non-Jewish Caucasian, Ashkenazi, South Korean and/or Puerto Rican.
  • the subject is South Korean and the variant are SEQ ID NO. 3, SEQ ID NO.13 and/or SEQ ID NO. 22.
  • the variant is a risk variant.
  • the variant is a protective variant.
  • the protective variant quantifies a reduced risk in the subject for structuring, CD, small bowel involvement and/or need for surgical intervention.
  • 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.
  • variants are SEQ ID NO. 3 and/or SEQ ID NO.13.
  • variant is SEQ ID NO. 22.
  • subject is non-Jewish Caucasian, Ashkenazi, South Korean and/or Puerto Rican.
  • subject is South Korean and the variant are SEQ ID NO. 3, SEQ ID NO.13 and/or SEQ ID NO. 22.
  • 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.
  • 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.
  • 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.
  • the one or more risk variants are at the TNFSF15 and/or DcR3 genetic loci.
  • the one or more risk variants are described in Tables 2 and 3 herein.
  • the subject is Caucasian, Puerto Spainn, or South Korean.
  • the subject is Non-Caucasian.
  • 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.
  • the one or more risk variants are at the TNFSF15 and/or DcR3 genetic loci.
  • the one or more risk variants are described in Tables 2 and 3 herein.
  • the subject is Caucasian, Puerto Spainn, or South Korean.
  • the subject is Non-Caucasian.
  • 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.
  • the one or more risk variants are at the TNFSF15 and/or DcR3 genetic loci.
  • the one or more risk variants are described in Tables 2 and 3 herein.
  • the subject is Caucasian, Puerto Spainn, or South Korean.
  • the subject is Non- Caucasian.
  • 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.
  • the one or more risk variants are at the TNFSF15 and/or DcR3 genetic loci.
  • the one or more risk variants are described in Tables 2 and 3 herein.
  • the subject is Caucasian, Puerto Spainn, or South Korean.
  • the subject is Non-Caucasian.
  • 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.
  • the one or more risk variants are at the TNFSF15 and/or DcR3 genetic loci.
  • the one or more risk variants are described in Tables 2 and 3 herein.
  • the subject is Caucasian, Puerto Spainn, or South Korean.
  • the subject is Non-Caucasian.
  • 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.
  • the one or more risk variants are at the TNFSF15 and/or DcR3 genetic loci.
  • the one or more risk variants are described in Tables 2 and 3 herein.
  • the subject is Caucasian, Puerto Spainn, or South Korean.
  • the subject is Non-Caucasian.
  • 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.
  • 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
  • TNFSF15-150 0.58% 0.07% 2.24% 2.03% 8.50% 5.11% 52.6% 34.4%
  • TNFSF15-120 70.2% 65.1% 75.2% 77.7% 77.8% 77.0% 71.5% 51.3%
  • the 'rare' and 'common' variants can each be tagged by a single SNP (SNP160 & SNP164 respectively) in both NJ and SK.
  • SNP160 & SNP164 SNP160 & SNP164 respectively
  • 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. (Fig2, 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.
  • 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.

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Priority Applications (13)

Application Number Priority Date Filing Date Title
JP2016514143A JP6482533B2 (ja) 2013-05-17 2014-05-16 クローン病に関連するｔｎｆｓｆ１５及びｄｃｒ３の変異体
CN201480038133.6A CN105358713B (zh) 2013-05-17 2014-05-16 与克罗恩病相关的tnfsf15和dcr3的变体
EP21193676.0A EP3988673A3 (en) 2013-05-17 2014-05-16 Variants of tnfsf15 and dcr3 associated with crohn's disease
EP14797214.5A EP2997165A4 (en) 2013-05-17 2014-05-16 Variants of tnfsf15 and dcr3 associated with crohn's disease
KR1020257028341A KR20250130857A (ko) 2013-05-17 2014-05-16 크론병과 연관된 tnfsf15와 dcr3의 변이체
US14/890,712 US20160090629A1 (en) 2013-05-17 2014-05-16 Variants of tnfsf15 and dcr3 associated with crohn's disease
KR1020157034355A KR102295125B1 (ko) 2013-05-17 2014-05-16 크론병과 연관된 tnfsf15와 dcr3의 변이체
KR1020237020524A KR20230093538A (ko) 2013-05-17 2014-05-16 크론병과 연관된 tnfsf15와 dcr3의 변이체
KR1020217026836A KR20210107176A (ko) 2013-05-17 2014-05-16 크론병과 연관된 tnfsf15와 dcr3의 변이체
EP18201967.9A EP3498867B1 (en) 2013-05-17 2014-05-16 Variants of tnfsf15 and dcr3 associated with crohn's disease
US15/946,632 US20180230543A1 (en) 2013-05-17 2018-04-05 Variants of tnfsf15 and dcr3 associated with crohn's disease
US17/392,098 US12281359B2 (en) 2013-05-17 2021-08-02 Variants of TNFSF15 and DCR3 associated with Crohn's disease
US19/084,586 US20250243548A1 (en) 2013-05-17 2025-03-19 Variants of tnfsf15 and dcr3 associated with crohn's disease

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Cited By (11)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2017035017A1 (en) * 2015-08-21 2017-03-02 The Children's Hospital Of Philadelphia Methods of treating autoimmune conditions in patients with genetic variations in dcr3 or in a dcr3 network gene
CN109476698A (zh) * 2016-05-20 2019-03-15 西达-赛奈医疗中心 基于基因的炎性肠病诊断
US10316083B2 (en) 2013-07-19 2019-06-11 Cedars-Sinai Medical Center Signature of TL1A (TNFSF15) signaling pathway
WO2020051580A1 (en) * 2018-09-07 2020-03-12 The Children's Hospital Of Philadelphia Compositions and methods for the diagnosis and treatment of lymphatic system disorders
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US11136386B2 (en) 2019-05-14 2021-10-05 Prometheus Biosciences, Inc. Methods of treating Crohn's disease or ulcerative colitis by administering inhibitors of tumor necrosis factor-like cytokine 1A (TL1A)
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