3951
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Brant SR, Okou DT, Simpson CL, Cutler DJ, Haritunians T, Bradfield JP, Chopra P, Prince J, Begum F, Kumar A, Huang C, Venkateswaran S, Datta LW, Wei Z, Thomas K, Herrinton LJ, Klapproth JMA, Quiros AJ, Seminerio J, Liu Z, Alexander JS, Baldassano RN, Dudley-Brown S, Cross RK, Dassopoulos T, Denson LA, Dhere TA, Dryden GW, Hanson JS, Hou JK, Hussain SZ, Hyams JS, Isaacs KL, Kader H, Kappelman MD, Katz J, Kellermayer R, Kirschner BS, Kuemmerle JF, Kwon JH, Lazarev M, Li E, Mack D, Mannon P, Moulton DE, Newberry RD, Osuntokun BO, Patel AS, Saeed SA, Targan SR, Valentine JF, Wang MH, Zonca M, Rioux JD, Duerr RH, Silverberg MS, Cho JH, Hakonarson H, Zwick ME, McGovern DP, Kugathasan S. Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease. Gastroenterology 2017; 152:206-217.e2. [PMID: 27693347 PMCID: PMC5164948 DOI: 10.1053/j.gastro.2016.09.032] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/14/2016] [Accepted: 09/17/2016] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS The inflammatory bowel diseases (IBD) ulcerative colitis (UC) and Crohn's disease (CD) cause significant morbidity and are increasing in prevalence among all populations, including African Americans. More than 200 susceptibility loci have been identified in populations of predominantly European ancestry, but few loci have been associated with IBD in other ethnicities. METHODS We performed 2 high-density, genome-wide scans comprising 2345 cases of African Americans with IBD (1646 with CD, 583 with UC, and 116 inflammatory bowel disease unclassified) and 5002 individuals without IBD (controls, identified from the Health Retirement Study and Kaiser Permanente database). Single-nucleotide polymorphisms (SNPs) associated at P < 5.0 × 10-8 in meta-analysis with a nominal evidence (P < .05) in each scan were considered to have genome-wide significance. RESULTS We detected SNPs at HLA-DRB1, and African-specific SNPs at ZNF649 and LSAMP, with associations of genome-wide significance for UC. We detected SNPs at USP25 with associations of genome-wide significance for IBD. No associations of genome-wide significance were detected for CD. In addition, 9 genes previously associated with IBD contained SNPs with significant evidence for replication (P < 1.6 × 10-6): ADCY3, CXCR6, HLA-DRB1 to HLA-DQA1 (genome-wide significance on conditioning), IL12B,PTGER4, and TNC for IBD; IL23R, PTGER4, and SNX20 (in strong linkage disequilibrium with NOD2) for CD; and KCNQ2 (near TNFRSF6B) for UC. Several of these genes, such as TNC (near TNFSF15), CXCR6, and genes associated with IBD at the HLA locus, contained SNPs with unique association patterns with African-specific alleles. CONCLUSIONS We performed a genome-wide association study of African Americans with IBD and identified loci associated with UC in only this population; we also replicated IBD, CD, and UC loci identified in European populations. The detection of variants associated with IBD risk in only people of African descent demonstrates the importance of studying the genetics of IBD and other complex diseases in populations beyond those of European ancestry.
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Affiliation(s)
- Steven R. Brant
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns
Hopkins University School of Medicine, Baltimore, MD, 21231, USA,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health,
Baltimore, MD, 21205, USA
| | - David T. Okou
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Claire L. Simpson
- Department of Genetics, Genomics and Informatics, University of Tennessee
Health Science Center, Memphis, TN, 38163, USA,Computational and Statistical Genomics Branch, National Human Genome
Research Institute, National Institutes of Health, Baltimore, MD 21224, USA
| | - David J. Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta,
GA, 30322, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research
Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Jonathan P. Bradfield
- Center for Applied Genomics, Abramson Research Center, The Children's
Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta,
GA, 30322, USA
| | - Jarod Prince
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Ferdouse Begum
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health,
Baltimore, MD, 21205, USA
| | - Archana Kumar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Chengrui Huang
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health,
Baltimore, MD, 21205, USA
| | - Suresh Venkateswaran
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Lisa W. Datta
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns
Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Zhi Wei
- Center for Applied Genomics, Abramson Research Center, The Children's
Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kelly Thomas
- Center for Applied Genomics, Abramson Research Center, The Children's
Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | | | | | - Antonio J. Quiros
- Department of Pediatrics, MUSC Pediatric Center for Inflammatory Bowel
Disorders, Summerville, SC, 29485, USA
| | - Jenifer Seminerio
- Department of Gastroenterology, MUSC Digestive Disease Center, Charleston,
SC, 29486, USA
| | - Zhenqiu Liu
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research
Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Jonathan S. Alexander
- Department of Molecular and Cellular Physiology, Louisiana State University
Health Sciences Center, Shreveport, LA, 71130, USA
| | - Robert N. Baldassano
- Department of Pediatrics, Children's Hospital of Philadelphia,
Philadelphia, PA, 19104, USA
| | - Sharon Dudley-Brown
- Department of Medicine, Johns Hopkins University Schools of Medicine &
Nursing, Baltimore, MD, 21287, USA
| | - Raymond K. Cross
- Department of Medicine, University of Maryland School of Medicine,
Baltimore, MD, 21201, USA
| | | | - Lee A. Denson
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati
Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Tanvi A. Dhere
- Department of Medicine, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Gerald W. Dryden
- Department of Medicine, University of Louisville, Louisville, KY, 40202,
USA
| | - John S. Hanson
- Charlotte Gastroenterology and Hepatology, Charlotte, NC, 28207, USA
| | - Jason K. Hou
- Department of Medicine, Baylor College of Medicine; VA HSR&D Center for
Innovations in Quality Effectiveness and Safety; Michael E. DeBakey VA Medical Center,
Houston, TX, 77030, USA
| | - Sunny Z. Hussain
- Department of Pediatrics, Willis-Knighton Physician Network, Shreveport,
LA, 71118, USA
| | | | - Kim L. Isaacs
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel
Hill, NC, 27514, USA
| | - Howard Kader
- Department of Pediatrics, University of Maryland School of Medicine,
Baltimore, MD, 21201, USA
| | - Michael D. Kappelman
- Department of Pediatrics, University of North Carolina at Chapel Hill,
Chapel Hill, NC, 27514, USA
| | - Jeffry Katz
- Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas
Children's Hospital, Houston, TX, 77030, USA
| | - Barbara S. Kirschner
- Department of Pediatrics, University of Chicago Comer Children's
Hospital, Chicago, IL, 60637, USA
| | - John F. Kuemmerle
- Medicine and Physiology and Biophysics, Medical College of Virginia Campus
of Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - John H. Kwon
- Department of Internal Medicine, University of Texas Southwestern Medical
Center, Dallas, TX, 75390, USA
| | - Mark Lazarev
- Department of Medicine, Johns Hopkins University School of Medicine,
Baltimore, MD, 21205, USA
| | - Ellen Li
- Department of Medicine, Stony Brook University School of Medicine, Stony
Brook, NY, 11794, USA
| | - David Mack
- Department of Pediatrics, University of Ottawa and Children’s
Hospital of Eastern Ontario, Ottawa, Ontario, K1H 8L1, Canada
| | - Peter Mannon
- Department of Medicine, University of Alabama at Birmingham, Birmingham,
AL, 35294, USA
| | | | - Rodney D. Newberry
- Department of Internal Medicine, Washington University School of Medicine,
St. Louis, MO, 63110, USA
| | - Bankole O. Osuntokun
- Department of Pediatrics, Cook Children's Medical Center, Fort Worth,
TX, 76104, USA
| | - Ashish S. Patel
- Department of Pediatrics, University of Texas Southwestern Medical Center,
Dallas, TX, 75390, USA
| | - Shehzad A. Saeed
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati
Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Stephan R. Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research
Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | | | - Ming-Hsi Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic Florida,
Jacksonville, FL, 32224, USA
| | - Martin Zonca
- Department of Internal Medicine, Henry Ford Health System, Detroit, MI,
48202, USA
| | - John D. Rioux
- Department of Medicine, Université de Montréal and the
Montreal Heart Institute Research Center, Montreal, Quebec, H1T 1C8, Canada
| | - Richard H. Duerr
- Department of Medicine and Clinical and Translational Science Institute,
School of Medicine; and Department of Human Genetics, Graduate School of Public Health;
University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mark S. Silverberg
- Department of Medicine, Zane Cohen Centre for Digestive Diseases, Mount
Sinai Hospital, University of Toronto, Toronto, Toronto, Ontario, M5G1X5, Canada
| | - Judy H. Cho
- Medicine and Genetics, Icahn School of Medicine at Mount Sinai, Charles
Bronfman Institute for Personalized Medicine, New York, NY, 10029, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's
Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Michael E. Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta,
GA, 30322, USA
| | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research
Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia; Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia.
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3952
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Cohain A, Divaraniya AA, Zhu K, Scarpa JR, Kasarskis A, Zhu J, Chang R, Dudley JT, Schadt EE. EXPLORING THE REPRODUCIBILITY OF PROBABILISTIC CAUSAL MOLECULAR NETWORK MODELS. Pac Symp Biocomput 2017; 22:120-131. [PMID: 27896968 PMCID: PMC5161348 DOI: 10.1142/9789813207813_0013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Network reconstruction algorithms are increasingly being employed in biomedical and life sciences research to integrate large-scale, high-dimensional data informing on living systems. One particular class of probabilistic causal networks being applied to model the complexity and causal structure of biological data is Bayesian networks (BNs). BNs provide an elegant mathematical framework for not only inferring causal relationships among many different molecular and higher order phenotypes, but also for incorporating highly diverse priors that provide an efficient path for incorporating existing knowledge. While significant methodological developments have broadly enabled the application of BNs to generate and validate meaningful biological hypotheses, the reproducibility of BNs in this context has not been systematically explored. In this study, we aim to determine the criteria for generating reproducible BNs in the context of transcription-based regulatory networks. We utilize two unique tissues from independent datasets, whole blood from the GTEx Consortium and liver from the Stockholm-Tartu Atherosclerosis Reverse Network Engineering Team (STARNET) study. We evaluated the reproducibility of the BNs by creating networks on data subsampled at different levels from each cohort and comparing these networks to the BNs constructed using the complete data. To help validate our results, we used simulated networks at varying sample sizes. Our study indicates that reproducibility of BNs in biological research is an issue worthy of further consideration, especially in light of the many publications that now employ findings from such constructs without appropriate attention paid to reproducibility. We find that while edge-to-edge reproducibility is strongly dependent on sample size, identification of more highly connected key driver nodes in BNs can be carried out with high confidence across a range of sample sizes.
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Affiliation(s)
- Ariella Cohain
- Icahn Institute and Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1498, New York, NY, 10029, USA*Co-first Authors
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3953
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Zhou M, He J, Shen Y, Zhang C, Wang J, Chen Y. New Frontiers in Genetics, Gut Microbiota, and Immunity: A Rosetta Stone for the Pathogenesis of Inflammatory Bowel Disease. Biomed Res Int 2017; 2017:8201672. [PMID: 28831399 PMCID: PMC5558637 DOI: 10.1155/2017/8201672] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/03/2017] [Accepted: 07/03/2017] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel disease (IBD), which encompasses ulcerative colitis (UC) and Crohn's disease (CD), is a complicated, uncontrolled, and multifactorial disorder characterized by chronic, relapsing, or progressive inflammatory conditions that may involve the entire gastrointestinal tract. The protracted nature has imposed enormous economic burdens on patients with IBD, and the treatment is far from optimal due to the currently limited comprehension of IBD pathogenesis. In spite of the exact etiology still remaining an enigma, four identified components, including personal genetic susceptibility, external environment, internal gut microbiota, and the host immune response, are responsible for IBD pathogenesis, and compelling evidence has suggested that IBD may be triggered by aberrant and continuing immune responses to gut microbiota in genetically susceptibility individuals. The past decade has witnessed the flourishing of research on genetics, gut microbiota, and immunity in patients with IBD. Therefore, in this review, we will comprehensively exhibit a series of novel findings and update the major advances regarding these three fields. Undoubtedly, these novel findings have opened a new horizon and shed bright light on the causality research of IBD.
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Affiliation(s)
- Mingxia Zhou
- 1Department of Gastroenterology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Jing He
- 2Department of General Surgery, Huashan Hospital of Fudan University, Shanghai 200040, China
| | - Yujie Shen
- 1Department of Gastroenterology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Cong Zhang
- 1Department of Gastroenterology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Jiazheng Wang
- 1Department of Gastroenterology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Yingwei Chen
- 1Department of Gastroenterology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
- 3Shanghai Institute for Pediatric Research, Shanghai 200092, China
- 4Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai 200092, China
- *Yingwei Chen:
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3954
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Li T, Wernersson R, Hansen RB, Horn H, Mercer J, Slodkowicz G, Workman CT, Rigina O, Rapacki K, Stærfeldt HH, Brunak S, Jensen TS, Lage K. A scored human protein-protein interaction network to catalyze genomic interpretation. Nat Methods 2017; 14:61-64. [PMID: 27892958 PMCID: PMC5839635 DOI: 10.1038/nmeth.4083] [Citation(s) in RCA: 369] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 10/20/2016] [Indexed: 02/07/2023]
Abstract
Genome-scale human protein-protein interaction networks are critical to understanding cell biology and interpreting genomic data, but challenging to produce experimentally. Through data integration and quality control, we provide a scored human protein-protein interaction network (InWeb_InBioMap, or InWeb_IM) with severalfold more interactions (>500,000) and better functional biological relevance than comparable resources. We illustrate that InWeb_InBioMap enables functional interpretation of >4,700 cancer genomes and genes involved in autism.
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Affiliation(s)
- Taibo Li
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rasmus Wernersson
- Intomics A/S, Lyngby, Denmark
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | | | - Heiko Horn
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Johnathan Mercer
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Greg Slodkowicz
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Christopher T Workman
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Olga Rigina
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Kristoffer Rapacki
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Hans H Stærfeldt
- Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Kasper Lage
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Institute for Biological Psychiatry, Mental Health Center Sct. Hans, University of Copenhagen, Roskilde, Denmark
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3955
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Lotem J, Levanon D, Negreanu V, Bauer O, Hantisteanu S, Dicken J, Groner Y. Runx3 in Immunity, Inflammation and Cancer. Adv Exp Med Biol 2017; 962:369-93. [PMID: 28299669 DOI: 10.1007/978-981-10-3233-2_23] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In this chapter we summarize the pros and cons of the notion that Runx3 is a major tumor suppressor gene (TSG). Inactivation of TSGs in normal cells provides a viability/growth advantage that contributes cell-autonomously to cancer. More than a decade ago it was suggested that RUNX3 is involved in gastric cancer development, a postulate extended later to other epithelial cancers portraying RUNX3 as a major TSG. However, evidence that Runx3 is not expressed in normal gastric and other epithelia has challenged the RUNX3-TSG paradigm. In contrast, RUNX3 is overexpressed in a significant fraction of tumor cells in various human epithelial cancers and its overexpression in pancreatic cancer cells promotes their migration, anchorage-independent growth and metastatic potential. Moreover, recent high-throughput quantitative genome-wide studies on thousands of human samples of various tumors and new investigations of the role of Runx3 in mouse cancer models have unequivocally demonstrated that RUNX3 is not a bona fide cell-autonomous TSG. Importantly, accumulating data demonstrated that RUNX3 functions in control of immunity and inflammation, thereby indirectly influencing epithelial tumor development.
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3956
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Affiliation(s)
- Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
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3957
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Fogel O, Richard-miceli C, Tost J. Epigenetic Changes in Chronic Inflammatory Diseases. Chromatin Remodelling and Immunity. Elsevier; 2017. pp. 139-89. [DOI: 10.1016/bs.apcsb.2016.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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3958
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Xia Q, Wang M, Yang X, Li X, Zhang X, Xu S, Shuai Z, Xu J, Fan D, Ding C, Pan F. Autophagy-related IRGM genes confer susceptibility to ankylosing spondylitis in a Chinese female population: a case-control study. Genes Immun 2017; 18:42-7. [PMID: 28031552 DOI: 10.1038/gene.2016.48] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/15/2016] [Accepted: 11/08/2016] [Indexed: 12/16/2022]
Abstract
It is known that ankylosing spondylitis (AS) and inflammatory bowel disease (IBD) shared a common genetic component. The gist of current study is to assess the role of IBD-associated autophagy gene IRGM on AS susceptibility in a Chinese Han population. A total of 1270 unrelated subjects (643 AS and 627 controls) were enrolled. Two tag single-nucleotide polymorphisms (SNPs) (rs10065172 and rs4958846) were selected and were genotyped by iMLDR Assay technology. Genotypes and haplotype analysis were conducted by using SPSS 16.0 and haploview 4.2 software. Among two tag SNPs of IRGM, no correlation was observed between rs10065172 and AS susceptibility. For rs4958846, genotype and allelic frequencies were marginally discrepant between female cases and controls before, not after, Bonferroni correction (P=0.049; P=0.031). Logistic regression analysis revealed that carriers with CT+TT or CT genotype had a significantly decreased risk for developing AS among female subjects when compared with CC genotype (OR=0.514, 95% CI=0.301-0.876, P=0.014; OR=0.518, 95% CI=0.297-0.902, P=0.020, respectively). Additionally, a risk haplotype rs4958846C-rs10065172C (OR=2.093, 95% CI=1.301-3.368) and a protective haplotype rs4958846T-rs10065172C (OR=0.652, 95% CI=0.441-0.964) were also identified to be associated with female AS. IBD-associated IRGM gene is also associated with AS susceptibility in the Chinese female population, indicating that autophagy pathway may involve in AS genetic predisposition.
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3959
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Guo MH, Nandakumar SK, Ulirsch JC, Zekavat SM, Buenrostro JD, Natarajan P, Salem RM, Chiarle R, Mitt M, Kals M, Pärn K, Fischer K, Milani L, Mägi R, Palta P, Gabriel SB, Metspalu A, Lander ES, Kathiresan S, Hirschhorn JN, Esko T, Sankaran VG. Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms. Proc Natl Acad Sci U S A 2017; 114:E327-36. [PMID: 28031487 DOI: 10.1073/pnas.1619052114] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Genetic variants affecting hematopoiesis can influence commonly measured blood cell traits. To identify factors that affect hematopoiesis, we performed association studies for blood cell traits in the population-based Estonian Biobank using high-coverage whole-genome sequencing (WGS) in 2,284 samples and SNP genotyping in an additional 14,904 samples. Using up to 7,134 samples with available phenotype data, our analyses identified 17 associations across 14 blood cell traits. Integration of WGS-based fine-mapping and complementary epigenomic datasets provided evidence for causal mechanisms at several loci, including at a previously undiscovered basophil count-associated locus near the master hematopoietic transcription factor CEBPA The fine-mapped variant at this basophil count association near CEBPA overlapped an enhancer active in common myeloid progenitors and influenced its activity. In situ perturbation of this enhancer by CRISPR/Cas9 mutagenesis in hematopoietic stem and progenitor cells demonstrated that it is necessary for and specifically regulates CEBPA expression during basophil differentiation. We additionally identified basophil count-associated variation at another more pleiotropic myeloid enhancer near GATA2, highlighting regulatory mechanisms for ordered expression of master hematopoietic regulators during lineage specification. Our study illustrates how population-based genetic studies can provide key insights into poorly understood cell differentiation processes of considerable physiologic relevance.
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3960
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Ostrowski J, Paziewska A, Lazowska I, Ambrozkiewicz F, Goryca K, Kulecka M, Rawa T, Karczmarski J, Dabrowska M, Zeber-Lubecka N. Genetic architecture differences between pediatric and adult-onset inflammatory bowel diseases in the Polish population. Sci Rep. 2016;6:39831. [PMID: 28008999 PMCID: PMC5180213 DOI: 10.1038/srep39831] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/29/2016] [Indexed: 12/15/2022] Open
Abstract
Most inflammatory bowel diseases (IBDs) are classic complex disorders represented by common alleles. Here we aimed to define the genetic architecture of pediatric and adult-onset IBDs for the Polish population. A total of 1495 patients were recruited, including 761 patients with Crohn’s disease (CD; 424 pediatric), 734 patients with ulcerative colitis (UC; 390 pediatric), and 934 healthy controls. Allelotyping employed a pooled-DNA genome-wide association study (GWAS) and was validated by individual genotyping. Whole exome sequencing (WES) was performed on 44 IBD patients diagnosed before 6 years of age, 45 patients diagnosed after 40 years of age, and 18 healthy controls. Altogether, out of 88 selected SNPs, 31 SNPs were replicated for association with IBD. A novel BRD2 (rs1049526) association reached significance of P = 5.2 × 10−11 and odds ratio (OR) = 2.43. Twenty SNPs were shared between pediatric and adult patients; 1 and 7 were unique to adult-onset and pediatric-onset IBD, respectively. WES identified numerous rare and potentially deleterious variants in IBD-associated or innate immunity-associated genes. Deleterious alleles in both groups were over-represented among rare variants in affected children. Our GWAS revealed differences in the polygenic architecture of pediatric- and adult-onset IBD. A significant accumulation of rare and deleterious variants in affected children suggests a contribution by yet unexplained genetic components.
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3961
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Abstract
Fungi are ubiquitous in our environment, and a healthy immune system is essential to maintain adequate protection from fungal infections. When this protection breaks down, superficial and invasive fungal infections cause diseases that range from irritating to life-threatening. Millions of people worldwide develop invasive infections during their lives, and mortality for these infections often exceeds 50%. Nevertheless, we are normally colonized with many of the same disease-causing fungi (e.g., on the skin or in the gut). Recent research is dramatically expanding our understanding of the mechanisms by which our immune systems interact with these organisms in health and disease. In this review, we discuss what is currently known about where and how the immune system interacts with common fungi.
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Affiliation(s)
- Matthew L Wheeler
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048; , ,
| | - Jose J Limon
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048; , ,
| | - David M Underhill
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California 90048; , , .,Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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3962
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Jung ES, Park HJ, Kong KA, Choi JH, Cheon JH. Association study between OCTN1 functional haplotypes and Crohn's disease in a Korean population. Korean J Physiol Pharmacol 2016; 21:11-17. [PMID: 28066136 PMCID: PMC5214902 DOI: 10.4196/kjpp.2017.21.1.11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/10/2016] [Accepted: 07/14/2016] [Indexed: 12/19/2022]
Abstract
Crohn's disease (CD) is a chronic inflammatory bowel disease with multifactorial causes including environmental and genetic factors. Several studies have demonstrated that the organic cation/carnitine transporter 1 (OCTN1) non-synonymous variant L503F is associated with susceptibility to CD. However, it was reported that L503F is absent in Asian populations. Previously, we identified and functionally characterized genetic variants of the OCTN1 promoter region in Koreans. In that study, four variants demonstrated significant changes in promoter activity. In the present study, we determined whether four functional variants of the OCTN1 promoter play a role in the susceptibility to or clinical course of CD in Koreans. To examine it, the frequencies of the four variants of the OCTN1 promoter were determined by genotyping using DNA samples from 194 patients with CD and 287 healthy controls. Then, associations between genetic variants and the susceptibility to CD or clinical course of CD were evaluated. We found that susceptibility to CD was not associated with OCTN1 functional promoter variants or haplotypes showing altered promoter activities in in vitro assays. However, OCTN1 functional promoter haplotypes showing decreased promoter activities were significantly associated with a penetrating behavior in CD patients (HR=2.428, p=0.009). Our results suggest that the OCTN1 functional promoter haplotypes can influence the CD phenotype, although these might not be associated with susceptibility to this disease.
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Affiliation(s)
- Eun Suk Jung
- Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea.; Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Hyo Jin Park
- Department of Pharmacology, Tissue Injury Defense Research Center, School of Medicine, Ewha Womans University, Seoul 07985, Korea
| | - Kyoung Ae Kong
- Clinical Trial Center, Ewha Womans University Medical Center, Seoul 07985, Korea
| | - Ji Ha Choi
- Department of Pharmacology, Tissue Injury Defense Research Center, School of Medicine, Ewha Womans University, Seoul 07985, Korea
| | - Jae Hee Cheon
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, Korea
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3963
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Abstract
There is consensus that inflammatory bowel diseases (IBDs) are the result of
“dysregulated” immune reactivity towards commensal microorganisms
in the intestine. This gut microbiome is clearly altered in IBD, but its primary
or secondary role is still debated. The focus has shifted from adaptive to
innate immunity, with its multitude of receptor molecules (Toll-like and NOD
receptors) and antibacterial effector molecules (defensins, cathelicidin, and
others). The latter appear to be at least partly deficient at different
intestinal locations. Host genetics also support the notion that
microbe–host interaction at the mucosa is the prime site of pathogenesis.
In contrast, even the latest therapeutic antibodies are directed against
secondary targets like cytokines and integrins identified decades ago. These
so-called “biologicals” have disappointing long-term results, with
the majority of patients not achieving remission in the long run. A promising
approach is the development of novel drugs like defensin-derived molecules that
substitute for the missing endogenous antibacterials.
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Affiliation(s)
- Eduard F Stange
- Department of Internal Medicine I, Medical University of Tübingen, Tübingen, Germany
| | - Jan Wehkamp
- Department of Internal Medicine I, Medical University of Tübingen, Tübingen, Germany
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3964
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Kagawa R, Fujiki R, Tsumura M, Sakata S, Nishimura S, Itan Y, Kong XF, Kato Z, Ohnishi H, Hirata O, Saito S, Ikeda M, El Baghdadi J, Bousfiha A, Fujiwara K, Oleastro M, Yancoski J, Perez L, Danielian S, Ailal F, Takada H, Hara T, Puel A, Boisson-Dupuis S, Bustamante J, Casanova JL, Ohara O, Okada S, Kobayashi M. Alanine-scanning mutagenesis of human signal transducer and activator of transcription 1 to estimate loss- or gain-of-function variants. J Allergy Clin Immunol 2016; 140:232-241. [PMID: 28011069 DOI: 10.1016/j.jaci.2016.09.035] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 08/29/2016] [Accepted: 09/23/2016] [Indexed: 11/17/2022]
Abstract
BACKGROUND Germline heterozygous mutations in human signal transducer and activator of transcription 1 (STAT1) can cause loss of function (LOF), as in patients with Mendelian susceptibility to mycobacterial diseases, or gain of function (GOF), as in patients with chronic mucocutaneous candidiasis. LOF and GOF mutations are equally rare and can affect the same domains of STAT1, especially the coiled-coil domain (CCD) and DNA-binding domain (DBD). Moreover, 6% of patients with chronic mucocutaneous candidiasis with a GOF STAT1 mutation have mycobacterial disease, obscuring the functional significance of the identified STAT1 mutations. Current computational approaches, such as combined annotation-dependent depletion, do not distinguish LOF and GOF variants. OBJECTIVE We estimated variations in the CCD/DBD of STAT1. METHODS We mutagenized 342 individual wild-type amino acids in the CCD/DBD (45.6% of full-length STAT1) to alanine and tested the mutants for STAT1 transcriptional activity. RESULTS Of these 342 mutants, 201 were neutral, 30 were LOF, and 111 were GOF mutations in a luciferase assay. This assay system correctly estimated all previously reported LOF mutations (100%) and slightly fewer GOF mutations (78.1%) in the CCD/DBD of STAT1. We found that GOF alanine mutants occurred at the interface of the antiparallel STAT1 dimer, suggesting that they destabilize this dimer. This assay also precisely predicted the effect of 2 hypomorphic and dominant negative mutations, E157K and G250E, in the CCD of STAT1 that we found in 2 unrelated patients with Mendelian susceptibility to mycobacterial diseases. CONCLUSION The systematic alanine-scanning assay is a useful tool to estimate the GOF or LOF status and the effect of heterozygous missense mutations in STAT1 identified in patients with severe infectious diseases, including mycobacterial and fungal diseases.
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Affiliation(s)
- Reiko Kagawa
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Ryoji Fujiki
- Department of Technology Development, Kazusa DNA Research Institute, Chiba, Japan
| | - Miyuki Tsumura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Sonoko Sakata
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Shiho Nishimura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Yuval Itan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Xiao-Fei Kong
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Zenichiro Kato
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan; Structural Medicine, United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Hidenori Ohnishi
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Osamu Hirata
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Satoshi Saito
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
| | - Maiko Ikeda
- Department of Pediatrics, Okazaki City Hospital, Aichi, Japan
| | | | - Aziz Bousfiha
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy, Hassan II University of Casablanca, Casablanca, Morocco; Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Averroes University Hospital, Casablanca, Morocco
| | - Kaori Fujiwara
- Department of Pediatrics, National Hospital Organization Fukuyama Medical Center, Hiroshima, Japan
| | - Matias Oleastro
- Department of Immunology, "Juan Pedro Garrahan" National Hospital of Pediatrics, Buenos Aires, Argentina
| | - Judith Yancoski
- Department of Immunology, "Juan Pedro Garrahan" National Hospital of Pediatrics, Buenos Aires, Argentina
| | - Laura Perez
- Department of Immunology, "Juan Pedro Garrahan" National Hospital of Pediatrics, Buenos Aires, Argentina
| | - Silvia Danielian
- Department of Immunology, "Juan Pedro Garrahan" National Hospital of Pediatrics, Buenos Aires, Argentina
| | - Fatima Ailal
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy, Hassan II University of Casablanca, Casablanca, Morocco; Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Averroes University Hospital, Casablanca, Morocco
| | - Hidetoshi Takada
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Toshiro Hara
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; Paris Descartes University, Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; Paris Descartes University, Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Jacinta Bustamante
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; Paris Descartes University, Sorbonne Paris Cité, Imagine Institute, Paris, France; Center for the Study of Primary Immunodeficiencies, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France; Paris Descartes University, Sorbonne Paris Cité, Imagine Institute, Paris, France; Pediatric Hematology-Immunology Unit, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, Paris, France; Howard Hughes Medical Institute, New York, NY
| | - Osamu Ohara
- Department of Technology Development, Kazusa DNA Research Institute, Chiba, Japan; Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan; St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY.
| | - Masao Kobayashi
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima, Japan
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3965
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Yang L, Wang L, Wang X, Xian CJ, Lu H. A Possible Role of Intestinal Microbiota in the Pathogenesis of Ankylosing Spondylitis. Int J Mol Sci 2016; 17:ijms17122126. [PMID: 27999312 PMCID: PMC5187926 DOI: 10.3390/ijms17122126] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/09/2016] [Accepted: 12/14/2016] [Indexed: 12/12/2022] Open
Abstract
Ankylosing spondylitis (AS) is a chronic inflammatory disease primarily affecting the sacroiliac joints and the spine, for which the pathogenesis is thought to be a result of the combination of host genetic factors and environmental triggers. However, the precise factors that determine one’s susceptibility to AS remain to be unraveled. With 100 trillion bacteria residing in the mammalian gut having established a symbiotic relation with their host influencing many aspects of host metabolism, physiology, and immunity, a growing body of evidence suggests that intestinal microbiota may play an important role in AS. Several mechanisms have been suggested to explain the potential role of the microbiome in the etiology of AS, such as alterations of intestinal permeability, stimulation of immune responses, and molecular mimicry. In this review, the existing evidence for the involvement of the microbiome in AS pathogenesis was discussed and the potential of intestinal microbiome-targeting strategies in the prevention and treatment of AS was evaluated.
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Affiliation(s)
- Lianjun Yang
- Academy of Orthopedics of Guangdong Province, Orthopaedic Hospital of Guangdong Province, Department of Orthopedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China.
| | - Liping Wang
- Academy of Orthopedics of Guangdong Province, Orthopaedic Hospital of Guangdong Province, Department of Orthopedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China.
- Sansom Institute for Health Research and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide SA5001, Australia.
| | - Xin Wang
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane QLD4059, Australia.
| | - Cory J Xian
- Academy of Orthopedics of Guangdong Province, Orthopaedic Hospital of Guangdong Province, Department of Orthopedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China.
- Sansom Institute for Health Research and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide SA5001, Australia.
| | - Hai Lu
- Academy of Orthopedics of Guangdong Province, Orthopaedic Hospital of Guangdong Province, Department of Orthopedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, China.
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3966
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Nédélec Y, Sanz J, Baharian G, Szpiech ZA, Pacis A, Dumaine A, Grenier JC, Freiman A, Sams AJ, Hebert S, Pagé Sabourin A, Luca F, Blekhman R, Hernandez RD, Pique-Regi R, Tung J, Yotova V, Barreiro LB. Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens. Cell 2016; 167:657-669.e21. [PMID: 27768889 DOI: 10.1016/j.cell.2016.09.025] [Citation(s) in RCA: 294] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 07/28/2016] [Accepted: 09/15/2016] [Indexed: 12/31/2022]
Abstract
Individuals from different populations vary considerably in their susceptibility to immune-related diseases. To understand how genetic variation and natural selection contribute to these differences, we tested for the effects of African versus European ancestry on the transcriptional response of primary macrophages to live bacterial pathogens. A total of 9.3% of macrophage-expressed genes show ancestry-associated differences in the gene regulatory response to infection, and African ancestry specifically predicts a stronger inflammatory response and reduced intracellular bacterial growth. A large proportion of these differences are under genetic control: for 804 genes, more than 75% of ancestry effects on the immune response can be explained by a single cis- or trans-acting expression quantitative trait locus (eQTL). Finally, we show that genetic effects on the immune response are strongly enriched for recent, population-specific signatures of adaptation. Together, our results demonstrate how historical selective events continue to shape human phenotypic diversity today, including for traits that are key to controlling infection.
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3967
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Assadi G, Vesterlund L, Bonfiglio F, Mazzurana L, Cordeddu L, Schepis D, Mjösberg J, Ruhrmann S, Fabbri A, Vukojevic V, Percipalle P, Salomons FA, Laurencikiene J, Törkvist L, Halfvarson J, D’Amato M. Functional Analyses of the Crohn's Disease Risk Gene LACC1. PLoS One 2016; 11:e0168276. [PMID: 27959965 PMCID: PMC5154582 DOI: 10.1371/journal.pone.0168276] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/28/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Genetic variation in the Laccase (multicopper oxidoreductase) domain-containing 1 (LACC1) gene has been shown to affect the risk of Crohn's disease, leprosy and, more recently, ulcerative colitis and juvenile idiopathic arthritis. LACC1 function appears to promote fatty-acid oxidation, with concomitant inflammasome activation, reactive oxygen species production, and anti-bacterial responses in macrophages. We sought to contribute to elucidating LACC1 biological function by extensive characterization of its expression in human tissues and cells, and through preliminary analyses of the regulatory mechanisms driving such expression. METHODS We implemented Western blot, quantitative real-time PCR, immunofluorescence microscopy, and flow cytometry analyses to investigate fatty acid metabolism-immune nexus (FAMIN; the LACC1 encoded protein) expression in subcellular compartments, cell lines and relevant human tissues. Gene-set enrichment analyses were performed to initially investigate modulatory mechanisms of LACC1 expression. A small-interference RNA knockdown in vitro model system was used to study the effect of FAMIN depletion on peroxisome function. RESULTS FAMIN expression was detected in macrophage-differentiated THP-1 cells and several human tissues, being highest in neutrophils, monocytes/macrophages, myeloid and plasmacytoid dendritic cells among peripheral blood cells. Subcellular co-localization was exclusively confined to peroxisomes, with some additional positivity for organelle endomembrane structures. LACC1 co-expression signatures were enriched for genes involved in peroxisome proliferator-activated receptors (PPAR) signaling pathways, and PPAR ligands downregulated FAMIN expression in in vitro model systems. CONCLUSION FAMIN is a peroxisome-associated protein with primary role(s) in macrophages and other immune cells, where its metabolic functions may be modulated by PPAR signaling events. However, the precise molecular mechanisms through which FAMIN exerts its biological effects in immune cells remain to be elucidated.
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Affiliation(s)
- Ghazaleh Assadi
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Liselotte Vesterlund
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Ferdinando Bonfiglio
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Luca Mazzurana
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Lina Cordeddu
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Danika Schepis
- Rheumatology unit, Department of Medicine Solna, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Jenny Mjösberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Sabrina Ruhrmann
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Alessia Fabbri
- Department of Therapeutic Research and Medicines Evaluation, Istituto Superiore di Sanità, Rome, Italy
| | - Vladana Vukojevic
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Piergiorgio Percipalle
- Biology Program, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Florian A. Salomons
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jurga Laurencikiene
- Lipid laboratory, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Leif Törkvist
- Gastrocentrum, Karolinska University Hospital, Stockholm, Sweden
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Mauro D’Amato
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- BioDonostia Health Research Institute, San Sebastian and IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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3968
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Feenstra B, Bager P, Liu X, Hjalgrim H, Nohr EA, Hougaard DM, Geller F, Melbye M. Genome-wide association study identifies variants in HORMAD2 associated with tonsillectomy. J Med Genet 2016; 54:358-364. [PMID: 27941131 DOI: 10.1136/jmedgenet-2016-104304] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 11/03/2022]
Abstract
BACKGROUND Inflammation of the tonsils is a normal response to infection, but some individuals experience recurrent, severe tonsillitis and massive hypertrophy of the tonsils in which case surgical removal of the tonsils may be considered. OBJECTIVE To identify common genetic variants associated with tonsillectomy. METHODS We used tonsillectomy information from Danish health registers and carried out a genome-wide association study comprising 1464 patients and 12 019 controls of Northwestern European ancestry, with replication in an independent sample set of 1575 patients and 1367 controls. RESULTS The variant rs2412971, intronic in HORMAD2 at chromosome 22q12.2, was robustly associated with tonsillectomy (OR=1.22; p=1.48×10-9) and is highly correlated with SNPs previously found to be associated with IgA nephropathy, Crohn's disease (CD) and early onset inflammatory bowel disease (IBD). The risk allele for tonsillectomy corresponded to increased risk of IgA nephropathy and decreased risk of CD and IBD. We further performed lookup analyses of the top SNP for outcomes related to tonsillectomy in the combined discovery and replication sample and found that rs2412971 was associated with acute tonsillitis (OR=1.19; p=7.82×10-4), chronic disease of the tonsils (OR=1.19; p=2.32×10-6) and appendectomy (OR=1.18; p=1.13×10-3). CONCLUSIONS We identified and replicated a genetic association at 22q12.2 with tonsillectomy. Further functional investigation is required to illuminate whether the molecular mechanisms underlying the genetic association involve general lymphoid hyper-reaction throughout the mucosa-associated lymphoid tissue system.
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Affiliation(s)
- Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Peter Bager
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Xueping Liu
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Henrik Hjalgrim
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.,Department of Haematology, Rigshospitalet, Copenhagen, Denmark
| | - Ellen A Nohr
- Research Unit of Gynaecology & Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - David M Hougaard
- Danish Centre for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
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3969
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Zhang HJZ, Yang H, Hu YS, Wang X, Wu QF. Progress in epigenetic research of ulcerative colitis. Shijie Huaren Xiaohua Zazhi 2016; 24:4584-4588. [DOI: 10.11569/wcjd.v24.i34.4584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ulcerative colitis (UC) is a nonspecific chronic disease that may relapse again and again and be associated with the risk of cancer. At present, the precise pathogenesis and etiology of UC are unclear. Research suggests that epigenetic modifications can mediate the mutual influence between susceptibility genes for ulcerative colitis and the internal and external environment of the body, and thus play an important part in the initial and sustainable development of UC. Regulation of expression of related genes by epigenetic modifications is closely linked to colonic mucosa immunity and defense in UC patients. In this paper, we will summarize the epigenetic mechanisms that may influence the pathogenesis of UC and discuss the role of epigenetic modifications in the pathogenesis of this disease.
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3970
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Khalili H, Malik S, Ananthakrishnan AN, Garber JJ, Higuchi LM, Joshi A, Peloquin J, Richter JM, Stewart KO, Curhan GC, Awasthi A, Yajnik V, Chan AT. Identification and Characterization of a Novel Association between Dietary Potassium and Risk of Crohn's Disease and Ulcerative Colitis. Front Immunol 2016; 7:554. [PMID: 28003811 PMCID: PMC5141241 DOI: 10.3389/fimmu.2016.00554] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 11/18/2016] [Indexed: 12/19/2022] Open
Abstract
Background Recent animal studies have identified that dietary salt intake may modify the risk and progression of autoimmune disorders through modulation of the IL-23/TH17 pathway, which is critical in the pathogenesis of ulcerative colitis (UC) and Crohn’s disease (CD). Methods We conducted a prospective study of U.S. women enrolled in the Nurses’ Health Study (NHS) and NHSII who provided detailed and validated information on diet and lifestyle beginning in 1984 in NHS and 1991 in NHSII. We confirmed incident cases of UC and CD reported through 2010 in NHS and 2011 in NHSII. We used Cox proportional hazards models to calculate hazard ratios and 95% confidence intervals. In a case–control study nested within these cohorts, we evaluated the interaction between single nucleotide polymorphisms (SNPs) in genes involved in TH17 pathway and dietary potassium on risk of CD and UC. In a cohort of healthy volunteers, we also assessed the effect of supplemental potassium on development of naïve and memory T cells, differentiated with TGFβ1 or TH17 conditions. Results Among a total of 194,711 women over a follow-up of 3,220,247 person-years, we documented 273 cases of CD and 335 cases of UC. Dietary intake of potassium (Ptrend = 0.005) but not sodium (Ptrend = 0.44) was inversely associated with risk of CD. Although, both dietary potassium and sodium were not significantly associated with risk of UC, there was a suggestion of an inverse association with dietary potassium (Ptrend = 0.08). The association of potassium with risk of CD and UC appeared to be modified by loci involved in the TH17 pathway that have previously been associated with susceptibility to CD, particularly SNP rs7657746 (IL21) (Pinteraction = 0.004 and 0.01, respectively). In vitro, potassium enhanced the expression of Foxp3 in both naïve and memory CD4+ T cells via activating Smad2/3 and inhibiting Smad7 in TH17 cells. Conclusion Dietary potassium is inversely associated with risk of CD with both in vitro and gene–environment interaction data suggesting a potential role for potassium in regulating immune tolerance through its effect on Tregs and TH17 pathway.
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Affiliation(s)
- Hamed Khalili
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Sakshi Malik
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster , Faridabad , India
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - John J Garber
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School , Boston, MA , USA
| | - Leslie M Higuchi
- Division of Gastroenterology and Nutrition, Boston Children's Hospital, Harvard Medical School , Boston, MA , USA
| | - Amit Joshi
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Joanna Peloquin
- Division of Gastroenterology and Hepatology, Johns Hopkins School of Medicine , Baltimore, MD , USA
| | - James M Richter
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School , Boston, MA , USA
| | - Kathleen O Stewart
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School , Boston, MA , USA
| | - Gary C Curhan
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School , Boston, MA , USA
| | - Amit Awasthi
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster , Faridabad , India
| | - Vijay Yajnik
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School , Boston, MA , USA
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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3971
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Lévy R, Okada S, Béziat V, Moriya K, Liu C, Chai LY, Migaud M, Hauck F, Al Ali A, Cyrus C, Vatte C, Patiroglu T, Unal E, Ferneiny M, Hyakuna N, Nepesov S, Oleastro M, Ikinciogullari A, Dogu F, Asano T, Ohara O, Yun L, Della Mina E, Bronnimann D, Itan Y, Gothe F, Bustamante J, Boisson-Dupuis S, Tahuil N, Aytekin C, Salhi A, Al Muhsen S, Kobayashi M, Toubiana J, Abel L, Li X, Camcioglu Y, Celmeli F, Klein C, AlKhater SA, Casanova JL, Puel A. Genetic, immunological, and clinical features of patients with bacterial and fungal infections due to inherited IL-17RA deficiency. Proc Natl Acad Sci U S A 2016; 113:E8277-85. [PMID: 27930337 DOI: 10.1073/pnas.1618300114] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Chronic mucocutaneous candidiasis (CMC) is defined as recurrent or persistent infection of the skin, nails, and/or mucosae with commensal Candida species. The first genetic etiology of isolated CMC-autosomal recessive (AR) IL-17 receptor A (IL-17RA) deficiency-was reported in 2011, in a single patient. We report here 21 patients with complete AR IL-17RA deficiency, including this first patient. Each patient is homozygous for 1 of 12 different IL-17RA alleles, 8 of which create a premature stop codon upstream from the transmembrane domain and have been predicted and/or shown to prevent expression of the receptor on the surface of circulating leukocytes and dermal fibroblasts. Three other mutant alleles create a premature stop codon downstream from the transmembrane domain, one of which encodes a surface-expressed receptor. Finally, the only known missense allele (p.D387N) also encodes a surface-expressed receptor. All of the alleles tested abolish cellular responses to IL-17A and -17F homodimers and heterodimers in fibroblasts and to IL-17E/IL-25 in leukocytes. The patients are currently aged from 2 to 35 y and originate from 12 unrelated kindreds. All had their first CMC episode by 6 mo of age. Fourteen patients presented various forms of staphylococcal skin disease. Eight were also prone to various bacterial infections of the respiratory tract. Human IL-17RA is, thus, essential for mucocutaneous immunity to Candida and Staphylococcus, but otherwise largely redundant. A diagnosis of AR IL-17RA deficiency should be considered in children or adults with CMC, cutaneous staphylococcal disease, or both, even if IL-17RA is detected on the cell surface.
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3972
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Bonder MJ, Luijk R, Zhernakova DV, Moed M, Deelen P, Vermaat M, van Iterson M, van Dijk F, van Galen M, Bot J, Slieker RC, Jhamai PM, Verbiest M, Suchiman HED, Verkerk M, van der Breggen R, van Rooij J, Lakenberg N, Arindrarto W, Kielbasa SM, Jonkers I, van 't Hof P, Nooren I, Beekman M, Deelen J, van Heemst D, Zhernakova A, Tigchelaar EF, Swertz MA, Hofman A, Uitterlinden AG, Pool R, van Dongen J, Hottenga JJ, Stehouwer CDA, van der Kallen CJH, Schalkwijk CG, van den Berg LH, van Zwet EW, Mei H, Li Y, Lemire M, Hudson TJ, Slagboom PE, Wijmenga C, Veldink JH, van Greevenbroek MMJ, van Duijn CM, Boomsma DI, Isaacs A, Jansen R, van Meurs JBJ, 't Hoen PAC, Franke L, Heijmans BT. Disease variants alter transcription factor levels and methylation of their binding sites. Nat Genet 2016; 49:131-138. [PMID: 27918535 DOI: 10.1038/ng.3721] [Citation(s) in RCA: 289] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 10/18/2016] [Indexed: 12/15/2022]
Abstract
Most disease-associated genetic variants are noncoding, making it challenging to design experiments to understand their functional consequences. Identification of expression quantitative trait loci (eQTLs) has been a powerful approach to infer the downstream effects of disease-associated variants, but most of these variants remain unexplained. The analysis of DNA methylation, a key component of the epigenome, offers highly complementary data on the regulatory potential of genomic regions. Here we show that disease-associated variants have widespread effects on DNA methylation in trans that likely reflect differential occupancy of trans binding sites by cis-regulated transcription factors. Using multiple omics data sets from 3,841 Dutch individuals, we identified 1,907 established trait-associated SNPs that affect the methylation levels of 10,141 different CpG sites in trans (false discovery rate (FDR) < 0.05). These included SNPs that affect both the expression of a nearby transcription factor (such as NFKB1, CTCF and NKX2-3) and methylation of its respective binding site across the genome. Trans methylation QTLs effectively expose the downstream effects of disease-associated variants.
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Affiliation(s)
- Marc Jan Bonder
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - René Luijk
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Daria V Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Matthijs Moed
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Patrick Deelen
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Martijn Vermaat
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Maarten van Iterson
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Freerk van Dijk
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Michiel van Galen
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Jan Bot
- SURFsara, Amsterdam, the Netherlands
| | - Roderick C Slieker
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - P Mila Jhamai
- Department of Internal Medicine, ErasmusMC, Rotterdam, the Netherlands
| | - Michael Verbiest
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - H Eka D Suchiman
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Marijn Verkerk
- Department of Internal Medicine, ErasmusMC, Rotterdam, the Netherlands
| | - Ruud van der Breggen
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jeroen van Rooij
- Department of Internal Medicine, ErasmusMC, Rotterdam, the Netherlands
| | - Nico Lakenberg
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Wibowo Arindrarto
- Medical Statistics Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Szymon M Kielbasa
- Sequence Analysis Support Core, Leiden University Medical Center, Leiden, the Netherlands
| | - Iris Jonkers
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Peter van 't Hof
- Sequence Analysis Support Core, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Marian Beekman
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Joris Deelen
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Diana van Heemst
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Ettje F Tigchelaar
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Morris A Swertz
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Albert Hofman
- Department of Epidemiology, ErasmusMC, Rotterdam, the Netherlands
| | | | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Neuroscience Campus Amsterdam, Amsterdam, the Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Neuroscience Campus Amsterdam, Amsterdam, the Netherlands
| | - Jouke J Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Neuroscience Campus Amsterdam, Amsterdam, the Netherlands
| | - Coen D A Stehouwer
- Department of Internal Medicine, Maastricht University Medical Center, Maastricht, the Netherlands.,School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center, Maastricht, the Netherlands
| | - Carla J H van der Kallen
- Department of Internal Medicine, Maastricht University Medical Center, Maastricht, the Netherlands.,School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center, Maastricht, the Netherlands
| | - Casper G Schalkwijk
- Department of Internal Medicine, Maastricht University Medical Center, Maastricht, the Netherlands.,School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center, Maastricht, the Netherlands
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Erik W van Zwet
- Medical Statistics Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Hailiang Mei
- Sequence Analysis Support Core, Leiden University Medical Center, Leiden, the Netherlands
| | - Yang Li
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - P Eline Slagboom
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Marleen M J van Greevenbroek
- Department of Internal Medicine, Maastricht University Medical Center, Maastricht, the Netherlands.,School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center, Maastricht, the Netherlands
| | - Cornelia M van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, ErasmusMC, Rotterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Neuroscience Campus Amsterdam, Amsterdam, the Netherlands
| | - Aaron Isaacs
- School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center, Maastricht, the Netherlands.,Genetic Epidemiology Unit, Department of Epidemiology, ErasmusMC, Rotterdam, the Netherlands.,Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, the Netherlands
| | - Rick Jansen
- Department of Psychiatry, VU University Medical Center, Neuroscience Campus Amsterdam, Amsterdam, the Netherlands
| | | | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
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3973
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Okada S, Puel A, Casanova JL, Kobayashi M. Chronic mucocutaneous candidiasis disease associated with inborn errors of IL-17 immunity. Clin Transl Immunology 2016; 5:e114. [PMID: 28090315 PMCID: PMC5192062 DOI: 10.1038/cti.2016.71] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/31/2016] [Accepted: 11/02/2016] [Indexed: 12/13/2022] Open
Abstract
Chronic mucocutaneous candidiasis (CMC) is characterized by recurrent or persistent infections affecting the nails, skin and oral and genital mucosae caused by Candida spp., mainly Candida albicans. CMC is an infectious phenotype in patients with inherited or acquired T-cell deficiency. Patients with autosomal-dominant (AD) hyper IgE syndrome (HIES), AD signal transducer and activator of transcription 1 (STAT1) gain-of-function, autosomal-recessive (AR) deficiencies in interleukin (IL)-12 receptor β1 (IL-12Rβ1), IL-12p40, caspase recruitment domain-containing protein 9 (CARD9) or retinoic acid-related orphan receptor γT (RORγT) or AR autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED) develop CMC as a major infectious phenotype that is categorized as Syndromic CMC. In contrast, CMC disease (CMCD) is typically defined as CMC in patients in the absence of any other prominent clinical signs. This definition is not strict; thus, CMCD is currently used to refer to patients presenting with CMC as the main clinical phenotype. The etiology of CMCD is not related to genes that cause severe combined immunodeficiency or combined immunodeficiency, nor to genes responsible for Syndromic CMC. Four genetic etiologies, AR IL-17 receptor A, IL-17 receptor C and ACT1 deficiencies, and AD IL-17F deficiency, are reported to underlie CMCD. Each of these gene defects directly has an impact on IL-17 signaling, suggesting their nonredundant role in host mucosal immunity to Candida. Here, we review current knowledge focusing on IL-17 signaling and the genetic etiologies responsible for, and associated with, CMC.
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Affiliation(s)
- Satoshi Okada
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences , Hiroshima, Japan
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Necker Medical School, Paris, France; Paris Descartes University, Sorbonne Paris Cité, Institut Imagine, Paris, France; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Necker Medical School, Paris, France; Paris Descartes University, Sorbonne Paris Cité, Institut Imagine, Paris, France; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY, USA; Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Paris, France; Howard Hughes Medical Institute, New York, NY, USA
| | - Masao Kobayashi
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences , Hiroshima, Japan
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3974
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Palone F, Vitali R, Cucchiara S, Mennini M, Armuzzi A, Pugliese D, DʼIncà R, Barberio B, Stronati L. Fecal HMGB1 Reveals Microscopic Inflammation in Adult and Pediatric Patients with Inflammatory Bowel Disease in Clinical and Endoscopic Remission. Inflamm Bowel Dis 2016; 22:2886-93. [PMID: 27755215 DOI: 10.1097/MIB.0000000000000938] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Fecal high mobility group box 1 (HMGB1) has been suggested to be a novel noninvasive biomarker of gut inflammation. We aimed to assess the reliability of fecal HMGB1, compared with fecal calprotectin (FC), in detecting intestinal inflammation in pediatric and adult patients with inflammatory bowel disease (IBD) and to evaluate the accuracy of HMGB1 in identifying patients with IBD in clinical and endoscopic remission who still have histologic features of inflammation. METHODS Stool samples from 85 children with IBD (49 Crohn's disease [CD] and 36 ulcerative colitis [UC] and 119 adults [57 Crohn's disease and 62 ulcerative colitis]) were analyzed for the study. Age-matched healthy subjects were used as controls. Fecal HMGB1 and fecal calprotectin were detected through western blot and ELISA, respectively. RESULTS Fecal HMGB1 expression was significantly increased in pediatric and adult patients with Crohn's disease and ulcerative colitis and strongly correlated with the disease severity. Fecal calprotectin and HMGB1 significantly correlated in pediatric (r: 0.60, P < 0.001) and adult (r: 0.72, P < 0.001) IBD patients. Moreover, in patients with clinical and endoscopic remission only fecal HMGB1 showed a strong match with the degree of histological scores of inflammation (CGHAS/IGHAS for Crohn's disease and Geboes Score for ulcerative colitis). CONCLUSIONS Fecal HMGB1 is confirmed to be a reliable biomarker of intestinal inflammation; indeed, it significantly correlates with fecal calprotectin in pediatric and adult IBD patients. Moreover, only fecal HMGB1 identifies histologic inflammation in subjects with IBD in clinical and endoscopic remission.
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3975
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3976
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Rico Y, Ethier DM, Davy CM, Sayers J, Weir RD, Swanson BJ, Nocera JJ, Kyle CJ. Spatial patterns of immunogenetic and neutral variation underscore the conservation value of small, isolated American badger populations. Evol Appl 2016; 9:1271-1284. [PMID: 27877205 PMCID: PMC5108218 DOI: 10.1111/eva.12410] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/14/2016] [Indexed: 12/29/2022] Open
Abstract
Small and isolated populations often exhibit low genetic diversity due to drift and inbreeding, but may simultaneously harbour adaptive variation. We investigate spatial distributions of immunogenetic variation in American badger subspecies (Taxidea taxus), as a proxy for evaluating their evolutionary potential across the northern extent of the species' range. We compared genetic structure of 20 microsatellites and the major histocompatibility complex (MHC DRB exon 2) to evaluate whether small, isolated populations show low adaptive polymorphism relative to large and well-connected populations. Our results suggest that gene flow plays a prominent role in shaping MHC polymorphism across large spatial scales, while the interplay between gene flow and selection was stronger towards the northern peripheries. The similarity of MHC alleles within subspecies relative to their neutral genetic differentiation suggests that adaptive divergence among subspecies can be maintained despite ongoing gene flow along subspecies boundaries. Neutral genetic diversity was low in small relative to large populations, but MHC diversity within individuals was high in small populations. Despite reduced neutral genetic variation, small and isolated populations harbour functional variation that likely contribute to the species evolutionary potential at the northern range. Our findings suggest that conservation approaches should focus on managing adaptive variation across the species range rather than protecting subspecies per se.
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Affiliation(s)
- Yessica Rico
- Forensic Science DepartmentTrent UniversityPeterboroughONCanada
- Natural Resources DNA Profiling and Forensics CentreTrent UniversityPeterboroughONCanada
- Present address: CONACYTInstituto de Ecología A.C.Centro Regional del BajíoAvenida Lázaro Cárdenas 253PátzcuaroMichoacán61600México
| | - Danielle M. Ethier
- Ontario Badger ProjectGuelphONCanada
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Christina M. Davy
- Forensic Science DepartmentTrent UniversityPeterboroughONCanada
- Natural Resources DNA Profiling and Forensics CentreTrent UniversityPeterboroughONCanada
| | | | - Richard D. Weir
- Ecosystems Protection & Sustainability BranchMinistry of EnvironmentVictoriaBCCanada
| | | | - Joseph J. Nocera
- Wildlife Research and Monitoring SectionMinistry of Natural Resources & ForestryPeterboroughONCanada
| | - Christopher J. Kyle
- Forensic Science DepartmentTrent UniversityPeterboroughONCanada
- Natural Resources DNA Profiling and Forensics CentreTrent UniversityPeterboroughONCanada
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3977
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Keerthy D, Youk A, Srinath AI, Malas N, Bujoreanu S, Bousvaros A, Keljo D, DeMaso DR, Szigethy EM. Effect of Psychotherapy on Health Care Utilization in Children With Inflammatory Bowel Disease and Depression. J Pediatr Gastroenterol Nutr 2016; 63:658-64. [PMID: 27035372 DOI: 10.1097/MPG.0000000000001207] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Pediatric patients with inflammatory bowel disease (IBD) are at an increased risk of developing depression compared with community controls. Depression often negatively influences illness behaviors such as resource utilization. We sought to investigate the effects of treating depression on utilization of medical resources in depressed pediatric patients with IBD by comparing rates of health care utilization 1 year before and after psychotherapy. METHOD Two hundred seventeen subjects ages 9 to 17 years with IBD and depression received 3 months of psychotherapy for depression as part of a multicenter randomized controlled trial. Of these 217 subjects, 70 had utilization data available 1 year prior and 1 year after receiving 3 months of psychotherapy. Primary outcomes included frequency of hospitalizations, inpatient hospital days, outpatient gastrointestinal visits, and number of emergency room visits, radiological examinations, and endoscopies. Within subject analyses were completed comparing health care utilization 12 months before psychotherapy compared with the 12 months after the conclusion of psychotherapy. RESULTS Fifty-one and 19 patients had CD and UC, respectively. A total of 55.7% of patients had major depression and 44.3% had minor depression. Overall, all study measures of health care utilization were significantly reduced after psychotherapy (P < 0.01)-including gastrointestinal-related (mean values) hospitalization frequency, inpatient days, outpatient visit, emergency room visits, radiological examinations, and endoscopies. CONCLUSIONS Psychotherapy for comorbid depression in pediatric patients with IBD is associated with decreased GI-related health care utilization. The present study highlights the importance of screening for depression in a pediatric population with IBD, and that psychotherapy may be a reasonable adjunctive treatment for pediatric patients with IBD and comorbid depression.
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3978
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Yang SK, Hong M, Oh H, Low HQ, Jung S, Ahn S, Kim Y, Baek J, Lee CH, Kim E, Kim KM, Ye BD, Kim KJ, Park SH, Lee HS, Lee I, Shin HD, Han B, McGovern DPB, Liu J, Song K. Identification of Loci at 1q21 and 16q23 That Affect Susceptibility to Inflammatory Bowel Disease in Koreans. Gastroenterology 2016; 151:1096-1099.e4. [PMID: 27569725 DOI: 10.1053/j.gastro.2016.08.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 08/17/2016] [Accepted: 08/18/2016] [Indexed: 12/02/2022]
Abstract
Recent genome-wide association studies have identified more than 200 regions that affect susceptibility to inflammatory bowel disease (IBD). However, identified common variants account for only a fraction of IBD heritability and largely have been identified in populations of European ancestry. We performed a genome-wide association study of susceptibility loci in Korean individuals, comprising a total of 1505 IBD patients and 4041 controls. We identified 2 new susceptibility loci for IBD at genome-wide significance: rs3766920 near PYGO2-SHC1 at 1q21 and rs16953946 in CDYL2 at 16q23. In addition, we confirmed associations, in Koreans, with 28 established IBD loci (P < 2.16 × 10-4). Our findings support the complementary value of genetic studies in different populations.
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Affiliation(s)
- Suk-Kyun Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Myunghee Hong
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyunjung Oh
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Hui-Qi Low
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Seonjoo Ahn
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Youngjin Kim
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Jiwon Baek
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Cue Hyunkyu Lee
- Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul, Korea; Asan Institute for Life Sciences, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | - Eunji Kim
- Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul, Korea; Asan Institute for Life Sciences, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea; Department of Chemistry, Seoul National University, Seoul, Korea
| | - Kyung Mo Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyung-Jo Kim
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sang Hyoung Park
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Ho-Su Lee
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Inchul Lee
- Department of Pathology, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | | | - Buhm Han
- Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul, Korea; Asan Institute for Life Sciences, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | - Dermot P B McGovern
- The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jianjun Liu
- Human Genetics Group, Genome Institute of Singapore, Singapore
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea.
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3979
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Prosberg M, Bendtsen F, Vind I, Petersen AM, Gluud LL. The association between the gut microbiota and the inflammatory bowel disease activity: a systematic review and meta-analysis. Scand J Gastroenterol 2016; 51:1407-1415. [PMID: 27687331 DOI: 10.1080/00365521.2016.1216587] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND The pathogenesis of inflammatory bowel diseases (IBD) involves complex interactions between the microbiome and the immune system. We evaluated the association between the gut microbiota and disease activity in IBD patients. METHODS Systematic review of clinical studies based on a published protocol. Included patients had ulcerative colitis (UC) or Crohn's disease (CD) classified as active or in remission. We selected bacteria assessed in at least three studies identified through electronic and manual searches (November 2015). Bias control was evaluated with the Newcastle Ottawa scale (NOS). Results of random-effects meta-analyses were presented as mean differences (MD). RESULTS Three prospective and seven cross-sectional studies (NOS score 6-8) were included. Five studies included patients with CD (231 patients) and eight included patients with UC (392 patients). Compared to patients in remission, patients with active IBD had lower abundance of Clostridium coccoides (MD = -0.49, 95% CI: -0.79 to -0.19), Clostridium leptum (MD = -0.44, 95% CI: -0.74 to -0.14), Faecalibacterium prausnitzii (MD = -0.81, 95% CI: -1.23 to -0.39) and Bifidobacterium (MD = -0.37, 95% CI: -0.56 to -0.17). Subgroup analyses showed a difference in all four bacteria between patients with UC classified as active or in remission. Patients with active CD had fewer C. leptum, F. prausnitzii and Bifidobacterium, but not C. coccoides. CONCLUSION This systematic review suggests that dysbiosis may be involved in the activity of IBD and that there may be differences between patients with CD and UC.
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Affiliation(s)
- Michelle Prosberg
- a Department of Gastroenterology , Hvidovre Hospital, Copenhagen University , Hvidovre , Denmark
| | - Flemming Bendtsen
- a Department of Gastroenterology , Hvidovre Hospital, Copenhagen University , Hvidovre , Denmark
| | - Ida Vind
- a Department of Gastroenterology , Hvidovre Hospital, Copenhagen University , Hvidovre , Denmark
| | - Andreas M Petersen
- a Department of Gastroenterology , Hvidovre Hospital, Copenhagen University , Hvidovre , Denmark.,b Department of Clinical Microbiology , Hvidovre Hospital, Copenhagen University , Hvidovre , Denmark
| | - Lise L Gluud
- a Department of Gastroenterology , Hvidovre Hospital, Copenhagen University , Hvidovre , Denmark
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3980
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Abstract
Endoscopic examination of the gastrointestinal tract (GIT) for diagnostics and therapy in children has evolved markedly over the last 20 or so years and is now usually undertaken by paediatric endoscopists. Updated diagnostic and management guidelines for common disorders including coeliac disease, gastro-oesophageal reflux disease, eosinophilic oesophagitis and inflammatory bowel disease highlight the central role of endoscopy. Therapeutic endoscopic approaches are also now widely available and further broaden the referral spectrum to include treatment of GIT bleeding, gastrostomy insertion, dilation of strictures and polypectomy. Lastly, the advent of newer technologies allows the examination of hitherto inaccessible areas of the GIT such as the mid-small bowel by wireless capsule video-endoscopy and enteroscopy. We summarise recent current practice and clinical guidelines, focussing on the key indications for referrals that are likely to require endoscopic assessment.
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Affiliation(s)
- D Belsha
- Centre for Paediatric Gastroenterology, Sheffield Children's Hospital, Sheffield, UK
| | - R Bremner
- Centre for Paediatric Gastroenterology, Birmingham Children's Hospital, Birmingham, UK
| | - M Thomson
- Centre for Paediatric Gastroenterology, Sheffield Children's Hospital, Sheffield, UK
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3981
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Kalla R, Kennedy NA, Ventham NT, Boyapati RK, Adams AT, Nimmo ER, Visconti MR, Drummond H, Ho GT, Pattenden RJ, Wilson DC, Satsangi J. Serum Calprotectin: A Novel Diagnostic and Prognostic Marker in Inflammatory Bowel Diseases. Am J Gastroenterol 2016; 111:1796-1805. [PMID: 27596694 DOI: 10.1038/ajg.2016.342] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 07/01/2016] [Indexed: 12/11/2022]
Abstract
OBJECTIVES There is an unmet need for novel blood-based biomarkers that offer timely and accurate diagnostic and prognostic testing in inflammatory bowel diseases (IBD). We aimed to investigate the diagnostic and prognostic utility of serum calprotectin (SC) in IBD. METHODS A total of 171 patients (n=96 IBD, n=75 non-IBD) were prospectively recruited. A multi-biomarker model was derived using multivariable logistic regression analysis. Cox proportional hazards model was derived to assess the contribution of each variable to disease outcomes. RESULTS SC correlated strongly with current biomarkers, including fecal calprotectin (FC) (n=50, ρ=0.50, P=1.6 × 10-4). SC was the strongest individual predictor of IBD diagnosis (odds ratio (OR): 9.37 (95% confidence interval (CI): 2.82-34.68), P=4.00 × 10-4) compared with other markers (C-reactive protein (CRP): OR 8.52 (95% CI: 2.75-28.63), P=2.80 × 10-4); albumin: OR 6.12 (95% CI: 1.82-22.16), P=0.004). In a subset of 50 patients with paired SC and FC, the area under receiver operating characteristic discriminating IBD from controls was better for FC than for SC (0.99, (95% CI 0.87-1.00) and 0.87 (95% CI:0.78-0.97), respectively; P=0.01). At follow-up (median 342 days; interquartile range: 88-563), SC predicted treatment escalation and/or surgery in IBD (hazard ratio (HR) 2.7, 95% CI: 1.1-4.9), in particular Crohn's disease (CD) (HR 4.2, 95% CI 1.2-15.3). A model incorporating SC and either CRP or albumin has a positive likelihood ratio of 24.14 for IBD. At 1 year, our prognostic model can predict treatment escalation in IBD in 65% of cases (95% CI: 43-79%) and 80% (95% CI: 31-94%) in CD if ≥2 blood marker criteria are met. CONCLUSIONS A diagnostic and prognostic model that combines SC and other blood-based biomarkers accurately predicts the inflammatory burden in IBD and has the potential to predict disease and its outcomes. Our data warrant further detailed exploration and validation in large multicenter cohorts.
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Affiliation(s)
- Rahul Kalla
- Gastrointestinal Unit, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - Nicholas A Kennedy
- Gastrointestinal Unit, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - Nicholas T Ventham
- Gastrointestinal Unit, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - Ray K Boyapati
- Gastrointestinal Unit, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Alex T Adams
- Gastrointestinal Unit, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - Elaine R Nimmo
- Gastrointestinal Unit, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - Micaela R Visconti
- Metabolic Bone Unit, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - Hazel Drummond
- Gastrointestinal Unit, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
| | - Gwo-Tzer Ho
- Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Rebecca J Pattenden
- Department of Clinical Chemistry, Western General Hospital, NHS Lothian, Edinburgh, UK
| | - David C Wilson
- Child Life and Health, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Jack Satsangi
- Gastrointestinal Unit, Centre for Molecular Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, UK
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3982
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Huang C, De Ravin SS, Paul AR, Heller T, Ho N, Wu Datta L, Zerbe CS, Marciano BE, Kuhns DB, Kader HA, Holland SM, Malech HL, Brant SR; NIDDK IBD Genetics Consortium. Genetic Risk for Inflammatory Bowel Disease Is a Determinant of Crohn's Disease Development in Chronic Granulomatous Disease. Inflamm Bowel Dis 2016; 22:2794-801. [PMID: 27861181 DOI: 10.1097/MIB.0000000000000966] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Approximately, one-third to one-half of children with chronic granulomatous disease (CGD) develop gastrointestinal inflammation characteristic of idiopathic inflammatory bowel disease (IBD), usually Crohn's disease. We hypothesized that the overall IBD genetic risk, determined by IBD genetic risk score (GRS), might in part determine IBD development in CGD. METHODS We reviewed medical records to establish IBD diagnoses in CGD subjects seen at NIAID. IBD risk single nucleotide polymorphism genotypes were determined using the Immunochip, and GRS were estimated by Mangrove. RESULTS Among 157 white patients with CGD, 55 were confirmed, 78 excluded, and 24 were uncertain for IBD. Two hundred one established, independent European IBD risk single nucleotide polymorphisms passed quality control. After sample quality control and removing non-IBD CGD patients with perianal disease, mean GRS for 40 unrelated patients with CGD-IBD was higher than 53 CGD non-IBD patients (in log2-scale 0.08 ± 1.62 versus -0.67 ± 1.64, P = 0.026) but lower than 239 IBD Genetics Consortium (IBDGC) young-onset Crohn's disease cases (0.76 ± 1.60, P = 0.025). GRS for non-IBD CGD was similar to 609 IBDGC controls (-0.69 ± 1.60, P = 0.95). Seven established IBD single nucleotide polymorphisms were nominally significant among CGD-IBD versus CGD non-IBD, including those near LACC1 (P = 0.005), CXCL14 (P = 0.007), and TNFSF15 (P = 0.016). CONCLUSIONS The weight of the common IBD risk alleles are significant determinants of IBD in CGD. However, IBD risk gene burden among CGD children with IBD is significantly lower than that in nonsyndromic pediatric Crohn's disease, congruent with the concept that defective superoxide production in CGD is also a major IBD risk factor. Individual IBD genes might interact with the CGD defect to cause IBD in CGD.
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3983
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Coskun M, Vermeire S, Nielsen OH. Novel Targeted Therapies for Inflammatory Bowel Disease. Trends Pharmacol Sci 2016; 38:127-142. [PMID: 27916280 DOI: 10.1016/j.tips.2016.10.014] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/21/2016] [Accepted: 10/26/2016] [Indexed: 02/07/2023]
Abstract
Our growing understanding of the immunopathogenesis of inflammatory bowel disease (IBD) has opened new avenues for developing targeted therapies. These advances in treatment options targeting different mechanisms of action offer new hope for personalized management. In this review we highlight emerging novel and easily administered therapeutics that may be viable candidates for the management of IBD, such as antibodies against interleukin 6 (IL-6) and IL-12/23, small molecules including Janus kinase inhibitors, antisense oligonucleotide against SMAD7 mRNA, and inhibitors of leukocyte trafficking to intestinal sites of inflammation (e.g., sphingosine 1-phosphate receptor modulators). We also provide an update on the current status in clinical development of these new classes of therapeutics.
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Affiliation(s)
- Mehmet Coskun
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Denmark
| | - Severine Vermeire
- Department of Gastroenterology, University Hospital Gasthuisberg, Leuven, Belgium
| | - Ole Haagen Nielsen
- Department of Gastroenterology, Medical Section, Herlev Hospital, University of Copenhagen, Denmark.
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3984
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Bearoff F, Del Rio R, Case LK, Dragon JA, Nguyen-Vu T, Lin CY, Blankenhorn EP, Teuscher C, Krementsov DN. Natural genetic variation profoundly regulates gene expression in immune cells and dictates susceptibility to CNS autoimmunity. Genes Immun 2016; 17:386-395. [PMID: 27653816 PMCID: PMC5133152 DOI: 10.1038/gene.2016.37] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/15/2016] [Accepted: 08/18/2016] [Indexed: 02/08/2023]
Abstract
Regulation of gene expression in immune cells is known to be under genetic control, and likely contributes to susceptibility to autoimmune diseases such as multiple sclerosis (MS). How this occurs in concert across multiple immune cell types is poorly understood. Using a mouse model that harnesses the genetic diversity of wild-derived mice, more accurately reflecting genetically diverse human populations, we provide an extensive characterization of the genetic regulation of gene expression in five different naive immune cell types relevant to MS. The immune cell transcriptome is shown to be under profound genetic control, exhibiting diverse patterns: global, cell-specific and sex-specific. Bioinformatic analysis of the genetically controlled transcript networks reveals reduced cell type specificity and inflammatory activity in wild-derived PWD/PhJ mice, compared with the conventional laboratory strain C57BL/6J. Additionally, candidate MS-GWAS (genome-wide association study candidate genes for MS susceptibility) genes were significantly enriched among transcripts overrepresented in C57BL/6J cells compared with PWD. These expression level differences correlate with robust differences in susceptibility to experimental autoimmune encephalomyelitis, the principal model of MS, and skewing of the encephalitogenic T-cell responses. Taken together, our results provide functional insights into the genetic regulation of the immune transcriptome, and shed light on how this in turn contributes to susceptibility to autoimmune disease.
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Affiliation(s)
- F Bearoff
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - R Del Rio
- Department of Medicine, University of Vermont, Burlington, VT, USA
| | - L K Case
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - J A Dragon
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA
| | - T Nguyen-Vu
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - C-Y Lin
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - E P Blankenhorn
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - C Teuscher
- Department of Medicine, University of Vermont, Burlington, VT, USA
- Department of Pathology, University of Vermont, Burlington, VT, USA
| | - D N Krementsov
- Department of Medicine, University of Vermont, Burlington, VT, USA
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3985
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Barber GE, Yajnik V, Khalili H, Giallourakis C, Garber J, Xavier R, Ananthakrishnan AN. Genetic Markers Predict Primary Non-Response and Durable Response To Anti-TNF Biologic Therapies in Crohn's Disease. Am J Gastroenterol 2016; 111:1816-1822. [PMID: 27596696 PMCID: PMC5143156 DOI: 10.1038/ajg.2016.408] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/03/2016] [Indexed: 12/11/2022]
Abstract
OBJECTIVES One-fifth of patients with Crohn's disease (CD) are primary non-responders to anti-tumor necrosis factor (anti-TNF) therapy, and an estimated 10-15% will fail therapy annually. Little is known about the genetics of response to anti-TNF therapy. The aim of our study was to identify genetic factors associated with primary non-response (PNR) and loss of response to anti-TNFs in CD. METHODS From a prospective registry, we characterized the response of 427 CD patients to their first anti-TNF therapy. Patients were designated as achieving primary response, durable response, and non-durable response based on clinical, endoscopic, and radiologic criteria. Genotyping was performed on the Illumina Immunochip. Separate genetic scores based on presence of predictive genetic alleles were calculated for PNR and durable response and performance of clinical and genetics models were compared. RESULTS From 359 patients, 36 were adjudged to have PNR (10%), 200 had durable response, and 74 had non-durable response. PNRs had longer disease duration and were more likely to be smokers. Fifteen risk alleles were associated with PNR. Patients with PNR had a significantly higher genetic risk score (GRS) (P =8 × 10-12). A combined clinical-genetic model more accurately predicted PNR when compared with a clinical only model (0.93 vs. 0.70, P <0.001). Sixteen distinct single nucleotide polymorphisms predicted durable response with a higher GRS (P =7 × 10-13). The GRSs for PNR and durable response were not mutually correlated, suggesting distinct mechanisms. CONCLUSIONS Genetic risk alleles can predict primary non-response and durable response to anti-TNF therapy in CD.
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Affiliation(s)
- Grant E Barber
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School
| | - Vijay Yajnik
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School
| | - Hamed Khalili
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School
| | - Cosmas Giallourakis
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School
| | - John Garber
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School
| | - Ramnik Xavier
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School
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3986
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Mancini I, Ricaño-Ponce I, Pappalardo E, Cairo A, Gorski MM, Casoli G, Ferrari B, Alberti M, Mikovic D, Noris M, Wijmenga C, Peyvandi F. Immunochip analysis identifies novel susceptibility loci in the human leukocyte antigen region for acquired thrombotic thrombocytopenic purpura. J Thromb Haemost 2016; 14:2356-2367. [PMID: 27762046 DOI: 10.1111/jth.13548] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/28/2016] [Indexed: 12/11/2022]
Abstract
Essentials Genetic predisposition to acquired thrombotic thrombocytopenic purpura (aTTP) is mainly unknown. Genetic risk factors for aTTP were studied by Immunochip analysis and replication study. Human leukocyte antigen (HLA) variant rs6903608 conferred a 2.5-fold higher risk of developing aTTP. rs6903608 and HLA-DQB1*05:03 may explain most of the HLA association signal in aTTP. Click to hear Dr Cataland's presentation on acquired thrombotic thrombocytopenic purpura SUMMARY: Background Acquired thrombotic thrombocytopenic purpura (TTP) is a rare, life-threatening thrombotic microangiopathy associated with the development of autoantibodies against the von Willebrand factor-cleaving protease ADAMTS-13. Similarly to what has been found for other autoimmune disorders, there is evidence of a genetic contribution, including the association of the human leukocyte antigen (HLA) class II complex with disease risk. Objective To identify novel genetic risk factors in acquired TTP. Patients/Methods We undertook a case-control genetic association study in 190 European-origin TTP patients and 1255 Italian healthy controls by using the Illumina Immunochip. Replication analysis in 88 Italian cases and 456 controls was performed with single-nucleotide polymorphism (SNP) TaqMan assays. Results and conclusion We identified one common variant (rs6903608) located within the HLA class II locus that was independently associated with acquired TTP at genome-wide significance and conferred a 2.6-fold increased risk of developing a TTP episode (95% confidence interval [CI] 2.02-3.27, P = 1.64 × 10-14 ). We also found five non-HLA variants mapping to chromosomes 2, 6, 8 and X that were suggestively associated with the disease: rs9490550, rs115265285, rs5927472, rs7823314, and rs1334768 (nominal P-values ranging from 1.59 × 10-5 to 7.60 × 10-5 ). Replication analysis confirmed the association of HLA variant rs6903608 with acquired TTP (pooled P = 3.95 × 10-19 ). Imputation of classic HLA genes followed by stepwise conditional analysis revealed that the combination of rs6903608 and HLA-DQB1*05:03 may explain most of the HLA association signal in acquired TTP. Our results refined the association of the HLA class II locus with acquired TTP, confirming its importance in the etiology of this autoimmune disease.
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Affiliation(s)
- I Mancini
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, and Fondazione Luigi Villa, Milan, Italy
| | - I Ricaño-Ponce
- Genetics Department, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - E Pappalardo
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, and Fondazione Luigi Villa, Milan, Italy
| | - A Cairo
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - M M Gorski
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, and Fondazione Luigi Villa, Milan, Italy
| | - G Casoli
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - B Ferrari
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - M Alberti
- IRCCS - Istituto di Ricerche Farmacologiche 'Mario Negri', Clinical Research Center for Rare Diseases, Aldo e Cele Daccò, Bergamo, Italy
| | - D Mikovic
- Hemostasis Department and Hemophilia Center, Blood Transfusion Institute of Serbia, Belgrade, Serbia
| | - M Noris
- IRCCS - Istituto di Ricerche Farmacologiche 'Mario Negri', Clinical Research Center for Rare Diseases, Aldo e Cele Daccò, Bergamo, Italy
| | - C Wijmenga
- Genetics Department, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - F Peyvandi
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, and Fondazione Luigi Villa, Milan, Italy
- Angelo Bianchi Bonomi Hemophilia and Thrombosis Center, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
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3987
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Sarmento OF, Svingen PA, Xiong Y, Sun Z, Bamidele AO, Mathison AJ, Smyrk TC, Nair AA, Gonzalez MM, Sagstetter MR, Baheti S, McGovern DPB, Friton JJ, Papadakis KA, Gautam G, Xavier RJ, Urrutia RA, Faubion WA. The Role of the Histone Methyltransferase Enhancer of Zeste Homolog 2 (EZH2) in the Pathobiological Mechanisms Underlying Inflammatory Bowel Disease (IBD). J Biol Chem 2016; 292:706-722. [PMID: 27909059 DOI: 10.1074/jbc.m116.749663] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 11/21/2016] [Indexed: 12/14/2022] Open
Abstract
Regulatory T (Treg) cells expressing the transcription factor FOXP3 play a pivotal role in maintaining immunologic self-tolerance. We and others have shown previously that EZH2 is recruited to the FOXP3 promoter and its targets in Treg cells. To further address the role for EZH2 in Treg cellular function, we have now generated mice that lack EZH2 specifically in Treg cells (EZH2Δ/ΔFOXP3+). We find that EZH2 deficiency in FOXP3+ T cells results in lethal multiorgan autoimmunity. We further demonstrate that EZH2Δ/ΔFOXP3+ T cells lack a regulatory phenotype in vitro and secrete proinflammatory cytokines. Of special interest, EZH2Δ/ΔFOXP3+ mice develop spontaneous inflammatory bowel disease. Guided by these results, we assessed the FOXP3 and EZH2 gene networks by RNA sequencing in isolated intestinal CD4+ T cells from patients with Crohn's disease. Gene network analysis demonstrates that these CD4+ T cells display a Th1/Th17-like phenotype with an enrichment of gene targets shared by FOXP3 and EZH2. Combined, these results suggest that the inflammatory milieu found in Crohn's disease could lead to or result from deregulation of FOXP3/EZH2-enforced T cell gene networks contributing to the underlying intestinal inflammation.
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Affiliation(s)
- Olga F Sarmento
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - Phyllis A Svingen
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - Yuning Xiong
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - Zhifu Sun
- Division of Biomedical Statistics and Informatics, and
| | - Adebowale O Bamidele
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - Angela J Mathison
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - Thomas C Smyrk
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota 55905
| | - Asha A Nair
- Division of Biomedical Statistics and Informatics, and
| | - Michelle M Gonzalez
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - Mary R Sagstetter
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | | | - Dermot P B McGovern
- the F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Hospital, Los Angeles, California 90048
| | - Jessica J Friton
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - Konstantinos A Papadakis
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - Goel Gautam
- the Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, and.,the Center for Computational and Integrative Biology, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Ramnik J Xavier
- the Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, and.,the Center for Computational and Integrative Biology, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Raul A Urrutia
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine
| | - William A Faubion
- From the Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine,
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3988
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Lichtenstein GR, McGovern DPB. Using Markers in IBD to Predict Disease and Treatment Outcomes: Rationale and a Review of Current Status. ACTA ACUST UNITED AC 2016. [DOI: 10.1038/ajgsup.2016.17] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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3989
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Buijck M, Berkhout DJ, de Groot EF, Benninga MA, van der Schee MP, Kneepkens CM, de Boer NK, de Meij TG. Sniffing Out Paediatric Gastrointestinal Diseases: The Potential of Volatile Organic Compounds as Biomarkers for Disease. J Pediatr Gastroenterol Nutr 2016; 63:585-91. [PMID: 27875502 DOI: 10.1097/MPG.0000000000001250] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The diagnostic work-up and follow-up of paediatric functional gastrointestinal disorders and organic conditions usually includes invasive tests, carrying a high burden on patients. There is a place, therefore, for novel, noninvasive disease-specific biomarkers. Volatile organic compounds (VOCs), originating from (patho)physiological metabolic processes in the human body, are excreted as waste products through all conceivable bodily excrements. The spectrum of VOCs harbours a magnificent source of information, with the potential to serve as noninvasive diagnostic biomarkers and to monitor disease activity. VOC analysis has been studied in children and infants with a variety of gastrointestinal diseases, including inflammatory bowel disease, liver diseases, irritable bowel syndrome, necrotizing enterocolitis and infectious diarrhoea. Most of these studies, although limited in sample size, show that patients can be discriminated from controls based on their VOC profiles, underscoring the potential of VOC analysis in diagnosis and follow-up. Currently, however, the application of VOC analysis in clinical practice is limited; substantial challenges, including methodological, biological, and analytical problems, still need to be met. In this review we provide an overview of the available literature on the potential of VOCs as biomarkers for paediatric gastrointestinal diseases. We discuss the available techniques to analyse VOCs and provide topics for VOC-related research, which need to be addressed before VOC diagnostics can be implemented in daily clinical practice.
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3990
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Abstract
The completion of the human genome project in 2003 represented a major scientific landmark, ushering in a new era with hopes and expectations of fresh insights into disease mechanisms and treatments. In inflammatory bowel disease (IBD), many important discoveries soon followed, notably the identification of >200 genetic susceptibility loci and characterization of the gut microbiome. As "big data", driven by advances in technology, becomes increasingly available and affordable, individuals with IBD and clinicians alike yearn for tangible outcomes from the promise of "precision medicine"-precise diagnosis, monitoring, and treatment. Here, we provide a commentary on the prospects and challenges of precision medicine and biomarkers in IBD. We focus on the three key areas where precision IBD will have the most impact: (1) disease susceptibility, activity, and behavior; (2) prediction of drug response and adverse effects; and (3) identification of subphenotypic mechanisms to facilitate drug discovery and selection of new treatments in IBD.
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Affiliation(s)
- Ray K Boyapati
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK.,Department of Gastroenterology, Monash Health, Clayton, Victoria, Australia
| | - Rahul Kalla
- Gastrointestinal Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Jack Satsangi
- Gastrointestinal Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Gwo-Tzer Ho
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK.,Gastrointestinal Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Edinburgh, UK
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3991
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Ley D, Duhamel A, Behal H, Vasseur F, Sarter H, Michaud L, Gower-Rousseau C, Turck D. Growth Pattern in Paediatric Crohn Disease Is Related to Inflammatory Status. J Pediatr Gastroenterol Nutr 2016; 63:637-43. [PMID: 26925610 DOI: 10.1097/MPG.0000000000001177] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVES The respective role of disease activity and steroid therapy in growth impairment in paediatric-onset Crohn disease (CD) is still debated. Our aim was to investigate whether the growth pattern of children with CD was correlated with the inflammatory status during the disease course, regardless the cumulative duration of steroid therapy. METHODS One hundred and seven patients with a diagnosis of CD <17 years, followed during ≥2 years and for whom ≥2 height measures were available during follow-up, were identified between 1998 and 2010. Height, C-reactive protein (CRP), orosomucoid, and steroid therapy duration were collected at each visit. The relationship between the evolution of growth velocity and inflammatory status during follow-up was investigated using a linear mixed model with random coefficients. RESULTS Median age at diagnosis was 11.7 years (Q1-Q3: 9.8-13.5). Mean height for age (H/A) z score was 0.14 ± 1.29 at diagnosis and 0.05 ± 1.23 among the 75 patients who had reached their final height at maximal follow-up (median: 4.9 years; Q1-Q3: 3.8-6.4). Growth failure (H/A z score <-2) was present in 7 (8%) patients at diagnosis and 5 (5%) at maximal follow-up. Growth velocity was negatively correlated with the evolution of CRP (P < 0.0001) and orosomucoid (P < 0.0001) during follow-up. After adjustment for the cumulative duration of steroid therapy, these 2 correlations remained significant (CRP: P = 0.0008; orosomucoid: P < 0.0001). CONCLUSIONS Children with CD with uncontrolled inflammatory status have a lower growth velocity. The inflammatory status should be kept as close to normal as possible in paediatric-onset patients with CD to optimize their growth pattern.
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3992
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Dunn KA, Moore-Connors J, MacIntyre B, Stadnyk AW, Thomas NA, Noble A, Mahdi G, Rashid M, Otley AR, Bielawski JP, Van Limbergen J. Early Changes in Microbial Community Structure Are Associated with Sustained Remission After Nutritional Treatment of Pediatric Crohn's Disease. Inflamm Bowel Dis 2016; 22:2853-62. [PMID: 27805918 DOI: 10.1097/MIB.0000000000000956] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Clinical remission achieved by exclusive enteral nutrition (EEN) is associated with marked microbiome changes. In this prospective study of exclusive enteral nutrition, we employ a hierarchical model of microbial community structure to distinguish between pediatric Crohn's disease patients who achieved sustained remission (SR) and those who relapsed early (non-SR), after restarting a normal diet. METHODS Fecal samples were obtained from 10 patients (age 10-16) and from 5 healthy controls (age 9-14). The microbiota was assessed via 16S rRNA sequencing. In addition to standard measures of microbial biodiversity, we employed Bayesian methods to characterize the hierarchical community structure. Community structure between patients who sustained remission (wPCDAI <12.5) up to their 24-week follow-up (SR) was compared with patients that had not sustained remission (non-SR). RESULTS Microbial diversity was lower in Crohn's disease patients relative to controls and lowest in patients who did not achieve SR. SR patients differed from non-SR patients in terms of the structure and prevalence of their microbial communities. The SR prevalent community contained a number of strains of Akkermansia muciniphila and Bacteroides and was limited in Proteobacteria, whereas the non-SR prevalent community had a large Proteobacteria component. Their communities were so different that a model trained to discriminate SR and non-SR had 80% classification accuracy, already at baseline sampling. CONCLUSIONS Microbial community structure differs between healthy controls, patients who have an enduring response to exclusive enteral nutrition, and those who relapse early on introduction of normal diet. Our novel Bayesian approach to these differences is able to predict sustained remission after exclusive enteral nutrition.
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3993
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Chu J, Vila-Farres X, Inoyama D, Ternei M, Cohen LJ, Gordon EA, Reddy BVB, Charlop-Powers Z, Zebroski HA, Gallardo-Macias R, Jaskowski M, Satish S, Park S, Perlin DS, Freundlich JS, Brady SF. Discovery of MRSA active antibiotics using primary sequence from the human microbiome. Nat Chem Biol 2016; 12:1004-1006. [PMID: 27748750 PMCID: PMC5117632 DOI: 10.1038/nchembio.2207] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 08/11/2016] [Indexed: 01/21/2023]
Abstract
Here we present a natural product discovery approach, whereby structures are bioinformatically predicted from primary sequence and produced by chemical synthesis (synthetic-bioinformatic natural products, syn-BNPs), circumventing the need for bacterial culture and gene expression. When we applied the approach to nonribosomal peptide synthetase gene clusters from human-associated bacteria, we identified the humimycins. These antibiotics inhibit lipid II flippase and potentiate β-lactam activity against methicillin-resistant Staphylococcus aureus in mice, potentially providing a new treatment regimen.
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Affiliation(s)
- John Chu
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Xavier Vila-Farres
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Daigo Inoyama
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
| | - Melinda Ternei
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Louis J. Cohen
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Emma A. Gordon
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Boojala Vijay B. Reddy
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Zachary Charlop-Powers
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
| | - Henry A. Zebroski
- Proteomics Resource Center, The Rockefeller University, New York, New York, USA
| | - Ricardo Gallardo-Macias
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
| | - Mark Jaskowski
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
| | - Shruthi Satish
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
| | - Steven Park
- Public Health Research Institute, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
| | - David S. Perlin
- Public Health Research Institute, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
| | - Joel S. Freundlich
- Department of Pharmacology, Physiology, and Neuroscience, Rutgers University – New Jersey Medical School, Newark, New Jersey, USA
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, New York, USA
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3994
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Krela-Kaźmierczak I, Kaczmarek-Ryś M, Szymczak A, Michalak M, Skrzypczak-Zielińska M, Drwęska-Matelska N, Marcinkowska M, Eder P, Łykowska-Szuber L, Wysocka E, Linke K, Słomski R. Bone Metabolism and the c.-223C > T Polymorphism in the 5'UTR Region of the Osteoprotegerin Gene in Patients with Inflammatory Bowel Disease. Calcif Tissue Int 2016; 99:616-624. [PMID: 27639566 PMCID: PMC5097783 DOI: 10.1007/s00223-016-0192-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/03/2016] [Indexed: 01/02/2023]
Abstract
Osteoporosis is more frequent in inflammatory bowel disease (IBD) patients. A reduction in bone mineral mass in these individuals is caused not only by inflammatory processes in the bowel, because osteoporosis occurs already in very young IBD patients and in newly diagnosed individuals who have not yet undergone any pharmacological treatment. One of individual determinants of the bone turnover parameters is osteoprotegerin (OPG) encoded by the TNFRSF11B gene. The c.-223C > T polymorphism in this gene has been extensively studied in post-menopausal osteoporosis patients. However, no such studies exist for osteoporosis related to IBD. The aim of our study was to determine whether the c.-223C > T (rs2073617) polymorphism in the 5'UTR region of the gene encoding osteoprotegerin is a functional polymorphism which may change the gene expression and resulting OPG levels, and so be associated with osteopenia and osteoporosis, and impaired bone metabolism in Crohn's disease and ulcerative colitis patients. Our study included 198 IBD patients and 41 healthy controls. Lumbar spine and femoral neck bone mineral density, T-score, Z-score as well as OPG, RANKL, vitamin D, calcium and interleukin 4 and 10 concentrations were determined for all study subjects. Genotyping of the TNFRSF11B polymorphic site was performed by restriction fragment length polymorphism technique. Statistical analyses were conducted using Statistica software. Odds ratios, 95 % confidence intervals, and P values were calculated using the HWE calculator. Our results did not allow determining an unequivocal association between the polymorphic variants of the TNFRSF11B 5'UTR region and a susceptibility to osteoporosis in IBD patients. We have shown, however, that the c.-223T allele was twice as more frequent in Crohn's disease (CD) patients than among controls (OR = 1.99, P value = 0.009). Interestingly, average osteoprotegerin levels in CD patients did not significantly differ from those in controls, whereas in ulcerative colitis patients, OPG levels were significantly lower. We have concluded that low OPG levels may be associated with osteoporosis in ulcerative colitis, but it is not correlated with the c.-223C > T polymorphism in the TNFRSF11B gene. In CD patients, in turn, we observed increased RANKL levels. Our observations confirm different pathogeneses of Crohn's disease and ulcerative colitis as well as different molecular backgrounds of osteoporosis associated with these two diseases.
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Affiliation(s)
- Iwona Krela-Kaźmierczak
- Department of Gastroenterology, Human Nutrition and Internal Diseases, Poznań University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznan, Poland.
| | - Marta Kaczmarek-Ryś
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznan, Poland.
| | - Aleksandra Szymczak
- Department of Gastroenterology, Human Nutrition and Internal Diseases, Poznań University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznan, Poland
| | - Michał Michalak
- Department of Computer Science and Statistics, University of Medical Sciences, Poznan, Poland
| | | | - Natalia Drwęska-Matelska
- Department of Biochemistry and Biotechnology, University of Life Sciences in Poznań, Poznan, Poland
| | | | - Piotr Eder
- Department of Gastroenterology, Human Nutrition and Internal Diseases, Poznań University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznan, Poland
| | - Lilianna Łykowska-Szuber
- Department of Gastroenterology, Human Nutrition and Internal Diseases, Poznań University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznan, Poland
| | - Ewa Wysocka
- Department of Laboratory Diagnostics, University of Medical Sciences, Poznan, Poland
| | - Krzysztof Linke
- Department of Gastroenterology, Human Nutrition and Internal Diseases, Poznań University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznan, Poland
| | - Ryszard Słomski
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznan, Poland
- Department of Biochemistry and Biotechnology, University of Life Sciences in Poznań, Poznan, Poland
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3995
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Eriksson D, Bianchi M, Landegren N, Nordin J, Dalin F, Mathioudaki A, Eriksson GN, Hultin-Rosenberg L, Dahlqvist J, Zetterqvist H, Karlsson Å, Hallgren Å, Farias FHG, Murén E, Ahlgren KM, Lobell A, Andersson G, Tandre K, Dahlqvist SR, Söderkvist P, Rönnblom L, Hulting AL, Wahlberg J, Ekwall O, Dahlqvist P, Meadows JRS, Bensing S, Lindblad-Toh K, Kämpe O, Pielberg GR. Extended exome sequencing identifies BACH2 as a novel major risk locus for Addison's disease. J Intern Med 2016; 280:595-608. [PMID: 27807919 DOI: 10.1111/joim.12569] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND Autoimmune disease is one of the leading causes of morbidity and mortality worldwide. In Addison's disease, the adrenal glands are targeted by destructive autoimmunity. Despite being the most common cause of primary adrenal failure, little is known about its aetiology. METHODS To understand the genetic background of Addison's disease, we utilized the extensively characterized patients of the Swedish Addison Registry. We developed an extended exome capture array comprising a selected set of 1853 genes and their potential regulatory elements, for the purpose of sequencing 479 patients with Addison's disease and 1394 controls. RESULTS We identified BACH2 (rs62408233-A, OR = 2.01 (1.71-2.37), P = 1.66 × 10-15 , MAF 0.46/0.29 in cases/controls) as a novel gene associated with Addison's disease development. We also confirmed the previously known associations with the HLA complex. CONCLUSION Whilst BACH2 has been previously reported to associate with organ-specific autoimmune diseases co-inherited with Addison's disease, we have identified BACH2 as a major risk locus in Addison's disease, independent of concomitant autoimmune diseases. Our results may enable future research towards preventive disease treatment.
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Affiliation(s)
- D Eriksson
- Department of Medicine (Solna), Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Endocrinology, Metabolism and Diabetes Karolinska University Hospital, Stockholm, Sweden
| | - M Bianchi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - N Landegren
- Department of Medicine (Solna), Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - J Nordin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - F Dalin
- Department of Medicine (Solna), Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - A Mathioudaki
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - G N Eriksson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - L Hultin-Rosenberg
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - J Dahlqvist
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - H Zetterqvist
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Å Karlsson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Å Hallgren
- Department of Medicine (Solna), Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - F H G Farias
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - E Murén
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - K M Ahlgren
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - A Lobell
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - G Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - K Tandre
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - S R Dahlqvist
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - P Söderkvist
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - L Rönnblom
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - A-L Hulting
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - J Wahlberg
- Department of Endocrinology, Department of Medical and Health Sciences, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - O Ekwall
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - P Dahlqvist
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - J R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - S Bensing
- Department of Endocrinology, Metabolism and Diabetes Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - K Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - O Kämpe
- Department of Medicine (Solna), Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Endocrinology, Metabolism and Diabetes Karolinska University Hospital, Stockholm, Sweden.,Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - G R Pielberg
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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3996
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Abstract
The pathophysiology of Crohn's disease (CD), a chronic inflammatory bowel disease, remains imperfectly elucidated. Consequently, the therapeutic armamentarium remains limited and has not changed the natural history of CD hitherto. Accordingly, physicians need to identify new therapeutic targets to be able to alter the intestinal damage. The most recent hypothesis considered CD as resulting from an abnormal interaction between microbiota and host immune system influenced by genetics and environmental factors. Several experimental and genetic evidence point out intestinal macrophages in CD etiology. An increase of macrophages number and the presence of granulomas are especially observed in the intestinal mucosa of patients with CD. These macrophages could be defective and particularly in responses to infectious agents like CD-associated Escherichia coli. This review focuses on, what is currently known regarding the role of macrophages, macrophages/E. coli interaction, and the impact of CD therapies on macrophages in CD. We also speculate that macrophages modulation could lead to important translational implications in CD with the end goal of promoting gut health.
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3997
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Borghese B, Zondervan K, Abrao M, Chapron C, Vaiman D. Recent insights on the genetics and epigenetics of endometriosis. Clin Genet 2016; 91:254-264. [DOI: 10.1111/cge.12897] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/25/2016] [Accepted: 10/14/2016] [Indexed: 12/21/2022]
Affiliation(s)
- B. Borghese
- Cochin Institute, U1016 INSERM, CNRS 8104; Université Paris Descartes; Paris France
- Department of Gynecology Obstetrics II and Reproductive Medicine, Faculté de Médecine, AP-HP, Groupe Hospitalier Ouest; Centre Hospitalier Universitaire Paris Centre; Paris France
| | - K.T. Zondervan
- Nuffield Department of Obstetrics and Gynaecology, Endometriosis Care Centre; University of Oxford; Oxford UK
| | - M.S. Abrao
- Endometriosis Division, Obstetrics and Gynecology Department; Sao Paulo University; Sao Paulo Brazil
- Reproductive Clinic; Sirio Libanes Hospital; Sao Paulo Brazil
| | - C. Chapron
- Cochin Institute, U1016 INSERM, CNRS 8104; Université Paris Descartes; Paris France
- Department of Gynecology Obstetrics II and Reproductive Medicine, Faculté de Médecine, AP-HP, Groupe Hospitalier Ouest; Centre Hospitalier Universitaire Paris Centre; Paris France
| | - D. Vaiman
- Cochin Institute, U1016 INSERM, CNRS 8104; Université Paris Descartes; Paris France
- Department of Gynecology Obstetrics II and Reproductive Medicine, Faculté de Médecine, AP-HP, Groupe Hospitalier Ouest; Centre Hospitalier Universitaire Paris Centre; Paris France
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3998
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Meddens CA, Harakalova M, van den Dungen NAM, Foroughi Asl H, Hijma HJ, Cuppen EPJG, Björkegren JLM, Asselbergs FW, Nieuwenhuis EES, Mokry M. Systematic analysis of chromatin interactions at disease associated loci links novel candidate genes to inflammatory bowel disease. Genome Biol 2016; 17:247. [PMID: 27903283 PMCID: PMC5131449 DOI: 10.1186/s13059-016-1100-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 11/07/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have revealed many susceptibility loci for complex genetic diseases. For most loci, the causal genes have not been identified. Currently, the identification of candidate genes is predominantly based on genes that localize close to or within identified loci. We have recently shown that 92 of the 163 inflammatory bowel disease (IBD)-loci co-localize with non-coding DNA regulatory elements (DREs). Mutations in DREs can contribute to IBD pathogenesis through dysregulation of gene expression. Consequently, genes that are regulated by these 92 DREs are to be considered as candidate genes. This study uses circular chromosome conformation capture-sequencing (4C-seq) to systematically analyze chromatin-interactions at IBD susceptibility loci that localize to regulatory DNA. RESULTS Using 4C-seq, we identify genomic regions that physically interact with the 92 DRE that were found at IBD susceptibility loci. Since the activity of regulatory elements is cell-type specific, 4C-seq was performed in monocytes, lymphocytes, and intestinal epithelial cells. Altogether, we identified 902 novel IBD candidate genes. These include genes specific for IBD-subtypes and many noteworthy genes including ATG9A and IL10RA. We show that expression of many novel candidate genes is genotype-dependent and that these genes are upregulated during intestinal inflammation in IBD. Furthermore, we identify HNF4α as a potential key upstream regulator of IBD candidate genes. CONCLUSIONS We reveal many novel and relevant IBD candidate genes, pathways, and regulators. Our approach complements classical candidate gene identification, links novel genes to IBD and can be applied to any existing GWAS data.
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Affiliation(s)
- Claartje A. Meddens
- Department of Pediatric Gastroenterology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Huispostnummer KA.03.019.0, Lundlaan 6, P.O. Box 85090, 3508 AB Utrecht, The Netherlands
| | - Magdalena Harakalova
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Hassan Foroughi Asl
- Vascular Biology Unit, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Hemme J. Hijma
- Department of Pediatric Gastroenterology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Huispostnummer KA.03.019.0, Lundlaan 6, P.O. Box 85090, 3508 AB Utrecht, The Netherlands
| | - Edwin P. J. G. Cuppen
- Department of Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
- Hubrecht Institute, Utrecht, The Netherlands
| | - Johan L. M. Björkegren
- Vascular Biology Unit, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Physiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Folkert W. Asselbergs
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
- Durrer Center for Cardiogenetic Research, Utrecht, The Netherlands
- Institute of Cardiovascular Science, University College London, London, UK
| | - Edward E. S. Nieuwenhuis
- Department of Pediatric Gastroenterology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Huispostnummer KA.03.019.0, Lundlaan 6, P.O. Box 85090, 3508 AB Utrecht, The Netherlands
| | - Michal Mokry
- Department of Pediatric Gastroenterology, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Huispostnummer KA.03.019.0, Lundlaan 6, P.O. Box 85090, 3508 AB Utrecht, The Netherlands
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3999
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Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S, Karamanis N, Maguire M, Papa E, Pierleoni A, Pignatelli M, Platt T, Rowland F, Wankar P, Bento AP, Burdett T, Fabregat A, Forbes S, Gaulton A, Gonzalez CY, Hermjakob H, Hersey A, Jupe S, Kafkas Ş, Keays M, Leroy C, Lopez FJ, Magarinos MP, Malone J, McEntyre J, Munoz-Pomer Fuentes A, O'Donovan C, Papatheodorou I, Parkinson H, Palka B, Paschall J, Petryszak R, Pratanwanich N, Sarntivijal S, Saunders G, Sidiropoulos K, Smith T, Sondka Z, Stegle O, Tang YA, Turner E, Vaughan B, Vrousgou O, Watkins X, Martin MJ, Sanseau P, Vamathevan J, Birney E, Barrett J, Dunham I. Open Targets: a platform for therapeutic target identification and validation. Nucleic Acids Res 2016; 45:D985-D994. [PMID: 27899665 PMCID: PMC5210543 DOI: 10.1093/nar/gkw1055] [Citation(s) in RCA: 267] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/19/2016] [Accepted: 11/03/2016] [Indexed: 01/16/2023] Open
Abstract
We have designed and developed a data integration and visualization platform that provides evidence about the association of known and potential drug targets with diseases. The platform is designed to support identification and prioritization of biological targets for follow-up. Each drug target is linked to a disease using integrated genome-wide data from a broad range of data sources. The platform provides either a target-centric workflow to identify diseases that may be associated with a specific target, or a disease-centric workflow to identify targets that may be associated with a specific disease. Users can easily transition between these target- and disease-centric workflows. The Open Targets Validation Platform is accessible at https://www.targetvalidation.org.
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Affiliation(s)
- Gautier Koscielny
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK .,GSK, Medicines Research Center, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Peter An
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Biogen, Cambridge, MA 02142, USA
| | - Denise Carvalho-Silva
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jennifer A Cham
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Luca Fumis
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Rippa Gasparyan
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Biogen, Cambridge, MA 02142, USA
| | - Samiul Hasan
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,GSK, Medicines Research Center, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Nikiforos Karamanis
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Michael Maguire
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Eliseo Papa
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Biogen, Cambridge, MA 02142, USA
| | - Andrea Pierleoni
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Miguel Pignatelli
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Theo Platt
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Biogen, Cambridge, MA 02142, USA
| | - Francis Rowland
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Priyanka Wankar
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Biogen, Cambridge, MA 02142, USA
| | - A Patrícia Bento
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Tony Burdett
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Antonio Fabregat
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Simon Forbes
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Anna Gaulton
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Cristina Yenyxe Gonzalez
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Henning Hermjakob
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,National Center for Protein Research, No. 38, Life Science Park Road, Changping District, 102206 Beijing, China
| | - Anne Hersey
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Steven Jupe
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Şenay Kafkas
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Maria Keays
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Catherine Leroy
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Francisco-Javier Lopez
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Maria Paula Magarinos
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - James Malone
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Johanna McEntyre
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Alfonso Munoz-Pomer Fuentes
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Claire O'Donovan
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Irene Papatheodorou
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Helen Parkinson
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Barbara Palka
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Justin Paschall
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Robert Petryszak
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Naruemon Pratanwanich
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sirarat Sarntivijal
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Gary Saunders
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Konstantinos Sidiropoulos
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Thomas Smith
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Zbyslaw Sondka
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Oliver Stegle
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Y Amy Tang
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Edward Turner
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Brendan Vaughan
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Olga Vrousgou
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Xavier Watkins
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Maria-Jesus Martin
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Philippe Sanseau
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,GSK, Medicines Research Center, Gunnels Wood Road, Stevenage, SG1 2NY, UK
| | - Jessica Vamathevan
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ewan Birney
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Jeffrey Barrett
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ian Dunham
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK .,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
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Lopetuso LR, Petito V, Zinicola T, Graziani C, Gerardi V, Arena V, Caristo ME, Poscia A, Cammarota G, Papa A, Cufino V, Sgambato A, Gasbarrini A, Scaldaferri F. Infliximab does not increase colonic cancer risk associated to murine chronic colitis. World J Gastroenterol 2016; 22:9727-9733. [PMID: 27956796 PMCID: PMC5124977 DOI: 10.3748/wjg.v22.i44.9727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/23/2016] [Accepted: 09/14/2016] [Indexed: 02/06/2023] Open
Abstract
AIM To explore the influence of Infliximab (IFX) on cancer progression in a murine model of colonic cancer associated to chronic colitis.
METHODS AOM/DSS model was induced in C57BL/6 mice. Mice were injected with IFX (5 mg/kg) during each DSS cycle while control mice received saline. Body weight, occult blood test and stool consistency were measured to calculate the disease activity index (DAI). Mice were sacrificed at week 10 and colons were analyzed macroscopically and microscopically for number of cancers and degree of inflammation. MTT assay was performed on CT26 to evaluate the potential IFX role on metabolic activity and proliferation. Cells were incubated with TNF-α or IFX or TNF-α plus IFX, and cell vitality was evaluated after 6, 24 and 48 h. The same setting was used after pre-incubation with TNF-α for 24 h.
RESULTS IFX significantly reduced DAI and body weight loss in mice compared with controls, preserving also colon length at sacrifice. Histological score was also reduced in treated mice. At macroscopic analysis, IFX treated mice showed a lower number of tumor lesions compared to controls. This was confirmed at microscopic analysis, although differences were not statistically significant. In vitro, IFX treated CT26 maintained similar proliferation ability at MTT test, both when exposed to IFX alone and when associated to TNF-α.
CONCLUSION IFX did not increase colonic cancer risk in AOM-DSS model of cancer on chronic colitis nor influence directly the proliferation of murine colon cancer epithelial cells.
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