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Henry C, Bassignani A, Berland M, Langella O, Sokol H, Juste C. Modern Metaproteomics: A Unique Tool to Characterize the Active Microbiome in Health and Diseases, and Pave the Road towards New Biomarkers—Example of Crohn’s Disease and Ulcerative Colitis Flare-Ups. Cells 2022; 11:cells11081340. [PMID: 35456018 PMCID: PMC9028112 DOI: 10.3390/cells11081340] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/06/2022] [Accepted: 04/11/2022] [Indexed: 11/16/2022] Open
Abstract
Thanks to the latest developments in mass spectrometry, software and standards, metaproteomics is emerging as the vital complement of metagenomics, to make headway in understanding the actual functioning of living and active microbial communities. Modern metaproteomics offers new possibilities in the area of clinical diagnosis. This is illustrated here, for the still highly challenging diagnosis of intestinal bowel diseases (IBDs). Using bottom-up proteomics, we analyzed the gut metaproteomes of the same twenty faecal specimens processed either fresh or after a two-month freezing period. We focused on metaproteomes of microbial cell envelopes since it is an outstanding way of capturing host and host–microbe interaction signals. The protein profiles of pairs of fresh and frozen-thawed samples were closely related, making feasible deferred analysis in a distant diagnosis centre. The taxonomic and functional landscape of microbes in diverse IBD phenotypes—active ulcerative colitis, or active Crohn’s disease either with ileo-colonic or exclusive colonic localization—differed from each other and from the controls. Based on their specific peptides, we could identify proteins that were either strictly overrepresented or underrepresented in all samples of one clinical group compared to all samples of another group, paving the road for promising additional diagnostic tool for IBDs.
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Affiliation(s)
- Céline Henry
- PAPPSO, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.H.); (A.B.)
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
| | - Ariane Bassignani
- PAPPSO, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France; (C.H.); (A.B.)
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
- MGP, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
| | - Magali Berland
- MGP, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
| | - Olivier Langella
- PAPPSO, GQE-Le Moulon, AgroParisTech, CNRS, INRAE, Université Paris-Saclay, 91190 Gif-sur-Yvette, France;
| | - Harry Sokol
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
- Gastroenterology Department, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Sorbonne Université, 75012 Paris, France
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, Service de Gastro-Entérologie et Nutrition, Hôpital Saint-Antoine, Direction de la Recherche Clinique et de l’Innovation (DRCI) de l’AP-HP, CEDEX 12, 75571 Paris, France
| | - Catherine Juste
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France;
- Correspondence: ; Tel.: +33-67-72-82-035
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Polygenic inheritance, GWAS, polygenic risk scores, and the search for functional variants. Proc Natl Acad Sci U S A 2020; 117:18924-18933. [PMID: 32753378 DOI: 10.1073/pnas.2005634117] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The reconciliation between Mendelian inheritance of discrete traits and the genetically based correlation between relatives for quantitative traits was Fisher's infinitesimal model of a large number of genetic variants, each with very small effects, whose causal effects could not be individually identified. The development of genome-wide genetic association studies (GWAS) raised the hope that it would be possible to identify single polymorphic variants with identifiable functional effects on complex traits. It soon became clear that, with larger and larger GWAS on more and more complex traits, most of the significant associations had such small effects, that identifying their individual functional effects was essentially hopeless. Polygenic risk scores that provide an overall estimate of the genetic propensity to a trait at the individual level have been developed using GWAS data. These provide useful identification of groups of individuals with substantially increased risks, which can lead to recommendations of medical treatments or behavioral modifications to reduce risks. However, each such claim will require extensive investigation to justify its practical application. The challenge now is to use limited genetic association studies to find individually identifiable variants of significant functional effect that can help to understand the molecular basis of complex diseases and traits, and so lead to improved disease prevention and treatment. This can best be achieved by 1) the study of rare variants, often chosen by careful candidate assessment, and 2) the careful choice of phenotypes, often extremes of a quantitative variable, or traits with relatively high heritability.
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Kim TO, Park DI, Han YK, Kang K, Park SG, Park HR, Yi JM. Genome-Wide Analysis of the DNA Methylation Profile Identifies the Fragile Histidine Triad ( FHIT) Gene as a New Promising Biomarker of Crohn's Disease. J Clin Med 2020; 9:jcm9051338. [PMID: 32375395 PMCID: PMC7291297 DOI: 10.3390/jcm9051338] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 12/26/2022] Open
Abstract
Inflammatory bowel disease is known to be associated with a genetic predisposition involving multiple genes; however, there is growing evidence that abnormal interactions with environmental factors, particularly epigenetic factors, can also significantly contribute to the development of inflammatory bowel disease (IBD). Although many genome-wide association studies have been performed to identify the genetic changes underlying the pathogenesis of Crohn’s disease, the role of epigenetic alterations based on molecular complications arising from Crohn’s disease (CD) is poorly understood. We employed an unbiased approach to define DNA methylation alterations in colonoscopy samples from patients with CD using the HumanMethylation450K BeadChip platform. Technical and functional validation was performed by methylation-specific PCR (MSP) and bisulfite sequencing of a validation set of 207 patients with CD samples. Immunohistochemistry (IHC) analysis was performed in the representative sample sets. DNA methylation profile in CD revealed that 135 probes (24 hypermethylated and 111 hypomethylated probes) were differentially methylated. We validated the methylation levels of 19 genes that showed hypermethylation in patients with CD compared with normal controls. We uniquely identified that the fragile histidine triad (FHIT) gene was hypermethylated in a disease-specific manner and its protein level was downregulated in patients with CD. Pathway analysis of the hypermethylated candidates further suggested putative molecular interactions relevant to IBD pathology. Our data provide information on the biological and clinical implications of DNA hypermethylated genes in CD, identifying FHIT methylation as a promising new biomarker for CD. Further study of the role of FHIT in IBD pathogenesis may lead to the development of new therapeutic targets.
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Affiliation(s)
- Tae-Oh Kim
- Department of Internal Medicine, Inje University, Haeundae Paik Hospital, Busan 48108, Korea;
| | - Dong-Il Park
- Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea;
| | - Yu Kyeong Han
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan 47392, Korea; (Y.K.H.); (S.-G.P.)
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan 31116, Korea;
| | - Sae-Gwang Park
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan 47392, Korea; (Y.K.H.); (S.-G.P.)
| | - Hae Ryoun Park
- Department of Oral Pathology, School of Dentistry, Pusan National University, Yangsan, Gyeongsangnam do 50612, Korea;
| | - Joo Mi Yi
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan 47392, Korea; (Y.K.H.); (S.-G.P.)
- Correspondence: ; Tel.: +82-51-890-6734
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Coufal S, Galanova N, Bajer L, Gajdarova Z, Schierova D, Jiraskova Zakostelska Z, Kostovcikova K, Jackova Z, Stehlikova Z, Drastich P, Tlaskalova-Hogenova H, Kverka M. Inflammatory Bowel Disease Types Differ in Markers of Inflammation, Gut Barrier and in Specific Anti-Bacterial Response. Cells 2019; 8:cells8070719. [PMID: 31337064 PMCID: PMC6678638 DOI: 10.3390/cells8070719] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/06/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
Crohn’s disease (CD), ulcerative colitis (UC) and inflammatory bowel disease (IBD) associated with primary sclerosing cholangitis (PSC-IBD), share three major pathogenetic mechanisms of inflammatory bowel disease (IBD)-gut dysbiosis, gut barrier failure and immune system dysregulation. While clinical differences among them are well known, the underlying mechanisms are less explored. To gain an insight into the IBD pathogenesis and to find a specific biomarker pattern for each of them, we used protein array, ELISA and flow cytometry to analyze serum biomarkers and specific anti-microbial B and T cell responses to the gut commensals. We found that decrease in matrix metalloproteinase (MMP)-9 and increase in MMP-14 are the strongest factors discriminating IBD patients from healthy subjects and that PSC-IBD patients have higher levels of Mannan-binding lectin, tissue inhibitor of metalloproteinases 1 (TIMP-1), CD14 and osteoprotegerin than patients with UC. Moreover, we found that low transforming growth factor-β1 (TGF-β1) is associated with disease relapse and low osteoprotegerin with anti-tumor necrosis factor-alpha (TNF-α) therapy. Patients with CD have significantly decreased antibody and increased T cell response mainly to genera Eubacterium, Faecalibacterium and Bacteroides. These results stress the importance of the gut barrier function and immune response to commensal bacteria and point at the specific differences in pathogenesis of PSC-IBD, UC and CD.
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Affiliation(s)
- Stepan Coufal
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Natalie Galanova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Lukas Bajer
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
- Institute for Clinical and Experimental Medicine, Videnska 1958/9, 140 21 Prague, Czech Republic
| | - Zuzana Gajdarova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Dagmar Schierova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | | | - Klara Kostovcikova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Zuzana Jackova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Zuzana Stehlikova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Pavel Drastich
- Institute for Clinical and Experimental Medicine, Videnska 1958/9, 140 21 Prague, Czech Republic
| | - Helena Tlaskalova-Hogenova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Miloslav Kverka
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic.
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic.
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The gut mycobiota: insights into analysis, environmental interactions and role in gastrointestinal diseases. Nat Rev Gastroenterol Hepatol 2019; 16:331-345. [PMID: 30824884 DOI: 10.1038/s41575-019-0121-2] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The gut microbiota is a dense and diverse ecosystem that is involved in many physiological functions as well as in disease pathogenesis. It is dominated by bacteria, which have been extensively studied in the past 15 years; however, other microorganisms, such as fungi, phages, archaea and protists, are also present in the gut microbiota. Exploration of the fungal component, namely, the mycobiota, is at an early stage, and several specific technical challenges are associated with mycobiota analysis. The number of fungi in the lower gastrointestinal tract is far lower than that of bacteria, but fungal cells are much larger and much more complex than bacterial cells. In addition, a role of the mycobiota in disease, notably in IBD, is indicated by both descriptive data in humans and mechanistic data in mice. Interactions between bacteria and fungi within the gut, their functional roles and their interplay with the host and its immune system are fascinating areas that researchers are just beginning to investigate. In this Review, we discuss the newest data on the gut mycobiota and explore both the technical aspects of its study and its role in health and gastrointestinal diseases.
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Cunningham KE, Novak EA, Vincent G, Siow VS, Griffith BD, Ranganathan S, Rosengart MR, Piganelli JD, Mollen KP. Calcium/calmodulin-dependent protein kinase IV (CaMKIV) activation contributes to the pathogenesis of experimental colitis via inhibition of intestinal epithelial cell proliferation. FASEB J 2018; 33:1330-1346. [PMID: 30113881 DOI: 10.1096/fj.201800535r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The incidence and prevalence of inflammatory bowel disease (IBD) are increasing worldwide. IBD is known to be multifactorial, but inflammatory signaling within the intestinal epithelium and a subsequent failure of the intestinal epithelial barrier have been shown to play essential roles in disease pathogenesis. CaMKIV is a multifunctional protein kinase associated with inflammation and cell cycle regulation. CaMKIV has been extensively studied in autoimmune diseases, but a role in idiopathic intestinal inflammation has not been described. In this study, active CaMKIV was highly expressed within the intestinal epithelium of humans with ulcerative colitis and wild-type (WT) mice with experimental induced colitis. Clinical disease severity directly correlates with CaMKIV activation, as does expression of proinflammatory cytokines and histologic features of colitis. In WT mice, CaMKIV activation is associated with increases in expression of 2 cell cycle proarrest signals: p53 and p21. Cell cycle arrest inhibits proliferation of the intestinal epithelium and ultimately results in compromised intestinal epithelial barrier integrity, further perpetuating intestinal inflammation during experimental colitis. Using a CaMKIV null mutant mouse, we demonstrate that a loss of CaMKIV protects against murine DSS colitis. Small molecules targeting CaMKIV activation may provide therapeutic benefit for patients with IBD.-Cunningham, K. E., Novak, E. A., Vincent, G., Siow, V. S., Griffith, B. D., Ranganathan, S., Rosengart, M. R., Piganelli, J. D., Mollen, K. P. Calcium/calmodulin-dependent protein kinase IV (CaMKIV) activation contributes to the pathogenesis of experimental colitis via inhibition of intestinal epithelial cell proliferation.
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Affiliation(s)
- Kellie E Cunningham
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Elizabeth A Novak
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Division of Pediatric Surgery, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center (UPMC), Pittsburgh, Pennsylvania, USA
| | - Garret Vincent
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Division of Pediatric Surgery, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center (UPMC), Pittsburgh, Pennsylvania, USA
| | - Vei Shaun Siow
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Brian D Griffith
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Sarangarajan Ranganathan
- Department of Pathology, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center (UPMC), Pittsburgh, Pennsylvania, USA
| | - Matthew R Rosengart
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jon D Piganelli
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kevin P Mollen
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Division of Pediatric Surgery, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center (UPMC), Pittsburgh, Pennsylvania, USA
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Gu P, Kapur A, Li D, Haritunians T, Vasiliauskas E, Shih DQ, Targan SR, Spiegel BM, McGovern DP, Black JT, Melmed GY. Serological, genetic and clinical associations with increased health-care resource utilization in inflammatory bowel disease. J Dig Dis 2018; 19:15-23. [PMID: 29251413 PMCID: PMC6023617 DOI: 10.1111/1751-2980.12566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 12/05/2017] [Accepted: 12/12/2017] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Inflammatory bowel diseases (IBD) are associated with significant morbidity and economic burden. The variable course of IBD creates a need for predictors of clinical outcomes and health resource utilization (HRU) to guide treatment decisions. We aimed to identify clinical, serological or genetic markers associated with inpatient resource utilization in patients with ulcerative colitis (UC) and Crohn's disease (CD). METHODS Patients with IBD with available genetic and serological data who had at least one emergency department visit or hospitalization in a 3-year period were included. The primary outcome measure was HRU, as measured by the All Patient Refined Diagnosis Related Group classification system. Univariate and multivariate linear and logistic regression models were used to identify the associations with HRU. RESULTS Altogether 858 (562 CD and 296 UC) patients were included. Anti-CBir1 seropositivity (P = 0.002, effect size [ES]: 0.762, 95% confidence interval [CI] 0.512-1.012) and low socioeconomic status (P = 0.005, ES: 1.620 [95% CI 1.091-2.149]) were independently associated with a high HRU. CD diagnosis (P = 0.006, ES: -0.701 [95% CI -0.959 to -0.443]) was independently associated with a low inpatient HRU. CONCLUSION In patients with IBD who required at least one emergency department visit or hospitalization, anti-CBir1 antibody status may be a useful biomarker of HRU when formulating management strategies to reduce disease complications and resource utilization.
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Affiliation(s)
- Phillip Gu
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Anshika Kapur
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Dalin Li
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Talin Haritunians
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Eric Vasiliauskas
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - David Q. Shih
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Stephan R. Targan
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Brennan M.R. Spiegel
- Center for Outcomes Research and Education, Cedars-Sinai Health System, Los Angeles, CA
| | - Dermot P.B. McGovern
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Jeanne T. Black
- Resource & Outcomes Management Department, Cedars-Sinai Health System, Los Angeles, CA
| | - Gil Y. Melmed
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
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Brooks PT, Brakel KA, Bell JA, Bejcek CE, Gilpin T, Brudvig JM, Mansfield LS. Transplanted human fecal microbiota enhanced Guillain Barré syndrome autoantibody responses after Campylobacter jejuni infection in C57BL/6 mice. MICROBIOME 2017; 5:92. [PMID: 28789710 PMCID: PMC5547673 DOI: 10.1186/s40168-017-0284-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/05/2017] [Indexed: 05/10/2023]
Abstract
BACKGROUND Campylobacter jejuni is the leading antecedent infection to the autoimmune neuropathy Guillain-Barré syndrome (GBS), which is accompanied by an autoimmune anti-ganglioside antibody attack on peripheral nerves. Previously, we showed that contrasting immune responses mediate C. jejuni induced colitis and autoimmunity in interleukin-10 (IL-10)-deficient mice, dependent upon the infecting strain. Strains from colitis patients elicited T helper 1 (TH1)-dependent inflammatory responses while strains from GBS patients elicited TH2-dependent autoantibody production. Both syndromes were exacerbated by antibiotic depletion of the microbiota, but other factors controlling susceptibility to GBS are unknown. METHODS Using 16S rRNA gene high-throughput sequencing, we examined whether structure of the gut microbial community alters host (1) gastrointestinal inflammation or (2) anti-ganglioside antibody responses after infection with C. jejuni strains from colitis or GBS patients. We compared these responses in C57BL/6 mice with either (1) stable human gut microbiota (Humicrobiota) transplants or (2) conventional mouse microbiota (Convmicrobiota). RESULTS Inoculating germ-free C57BL/6 wild-type (WT) mice with a mixed human fecal slurry provided a murine model that stably passed its microbiota over >20 generations. Mice were housed in specific pathogen-free (SPF) facilities, while extra precautions of having caretakers wear sterile garb along with limited access ensured that no mouse pathogens were acquired. Humicrobiota conferred many changes upon the WT model in contrast to previous results, which showed only colonization with no disease after C. jejuni challenge. When compared to Convmicrobiota mice for susceptibility to C. jejuni enteric or GBS patient strains, infected Humicrobiota mice had (1) 10-100 fold increases in C. jejuni colonization of both strains, (2) pathologic change in draining lymph nodes but only mild changes in colon or cecal lamina propria, (3) significantly lower Th1/Th17-dependent anti-C. jejuni responses, (4) significantly higher IL-4 responses at 5 but not 7 weeks post infection (PI), (5) significantly higher Th2-dependent anti-C. jejuni responses, and (6) significantly elevated anti-ganglioside autoantibodies after C. jejuni infection. These responses in Humicrobiota mice were correlated with a dominant Bacteroidetes and Firmicutes microbiota. CONCLUSIONS These data demonstrate that Humicrobiota altered host-pathogen interactions in infected mice, increasing colonization and Th-2 and autoimmune responses in a C. jejuni strain-dependent manner. Thus, microbiota composition is another factor controlling susceptibility to GBS.
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Affiliation(s)
- Phillip T Brooks
- Comparative Enteric Diseases Laboratory, Michigan State University, East Lansing, MI, USA
- Comparative Medicine and Integrative Biology, Michigan State University, East Lansing, MI, USA
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, USA
| | - Kelsey A Brakel
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Julia A Bell
- Comparative Enteric Diseases Laboratory, Michigan State University, East Lansing, MI, USA
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Christopher E Bejcek
- Comparative Enteric Diseases Laboratory, Michigan State University, East Lansing, MI, USA
| | - Trey Gilpin
- Comparative Enteric Diseases Laboratory, Michigan State University, East Lansing, MI, USA
| | - Jean M Brudvig
- Comparative Enteric Diseases Laboratory, Michigan State University, East Lansing, MI, USA
- Comparative Medicine and Integrative Biology, Michigan State University, East Lansing, MI, USA
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Linda S Mansfield
- Comparative Enteric Diseases Laboratory, Michigan State University, East Lansing, MI, USA.
- Comparative Medicine and Integrative Biology, Michigan State University, East Lansing, MI, USA.
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI, USA.
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA.
- Department of Microbiology and Molecular Genetics, Michigan State University, 181 Food Safety Building; 1129 Farm Lane, East Lansing, MI, 48824, USA.
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Kim J, Lee HS, Park SH, Yang SK, Ye BD, Yang DH, Kim KJ, Byeon JS, Yoon YS, Yu CS, Kim J. Pathologic features of colorectal carcinomas associated with Crohn’s disease in Korean population. Pathol Res Pract 2017; 213:250-255. [DOI: 10.1016/j.prp.2016.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 02/07/2023]
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Common NOD2/CARD15 and TLR4 Polymorphisms Are Associated with Crohn's Disease Phenotypes in Southeastern Brazilians. Dig Dis Sci 2016; 61:2636-47. [PMID: 27107867 DOI: 10.1007/s10620-016-4172-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 04/15/2016] [Indexed: 02/07/2023]
Abstract
AIM To investigate whether variants in NOD2/CARD15 and TLR4 are associated with CD and ulcerative colitis (UC) in a genetically admixed population of Rio de Janeiro, where IBD has continued to rise. METHODS We recruited 67 consecutive patients with CD, 61 patients with UC, and 86 healthy and ethnically matched individuals as controls. DNA was extracted from buccal brush samples and genotyped by PCR with restriction enzymes for G908R and L1007finsC NOD2/CARD15 single-nucleotide polymorphisms (SNPs) and for T399I and D299G TLR4 SNPs. Clinical data were registered for subsequent analysis with multivariate models. RESULTS NOD2/CARD15 G908R and L1007finsC SNPs were found in one and three patients, respectively, with CD. NOD2/CARD15 G908R and L1007finsC SNPs were not found in any patients with UC, but were found in three and three controls, respectively. With regard to the TLR4 gene, no significant difference was detected among the groups. Overall, none of the SNPs investigated determined a differential risk for a specific diagnosis. Genotype-phenotype associations were found in only CD, where L1007finsC was associated with colonic localization; however, TLR4 T399I SNP was associated with male gender, and D299G SNP was associated with colonic involvement, chronic corticosteroid use, and the need for anti-TNF-alpha therapy. CONCLUSION Variants of NOD2/CARD15 and TLR4 do not confer susceptibility to IBD, but appear to determine CD phenotypes in this southeastern Brazilian population.
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Sifuentes-Dominguez L, Patel AS. Genetics and Therapeutics in Pediatric Ulcerative Colitis: the Past, Present and Future. F1000Res 2016; 5. [PMID: 26973787 PMCID: PMC4776672 DOI: 10.12688/f1000research.7440.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/22/2016] [Indexed: 12/19/2022] Open
Abstract
Ulcerative colitis (UC) is a relapsing and remitting disease with significant phenotypic and genotypic variability. Though more common in adults, UC is being increasingly diagnosed in childhood. The subsequent lifelong course of disease results in challenges for the patient and physician. Currently, there is no medical cure for UC. Even though surgical removal of the colon can be curative, complications including infertility in females make colectomy an option often considered only when the disease presents with life-threatening complications or when medical management fails. One of the greatest challenges the clinician faces in the care of patients with UC is the inability to predict at diagnosis which patient is going to respond to a specific therapy or will eventually require surgery. This therapeutic conundrum frames the discussion to follow, specifically the concept of individualized or personalized treatment strategies based on genetic risk factors. As we move to therapeutics, we will elucidate traditional approaches and discuss known and novel agents. As we look to the future, we can expect increasing integrated approaches using several scientific disciplines to inform how genetic interactions shape and mold the pathogenesis and therapeutics of UC.
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Affiliation(s)
| | - Ashish S Patel
- Children's Health, UT Southwestern Medical Center, Dallas, Texas, USA
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Lobert VH, Mouradov D, Heath JK. Focusing the Spotlight on the Zebrafish Intestine to Illuminate Mechanisms of Colorectal Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:411-37. [PMID: 27165364 DOI: 10.1007/978-3-319-30654-4_18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Colorectal cancer, encompassing colon and rectal cancer, arises from the epithelial lining of the large bowel. It is most prevalent in Westernised societies and is increasing in frequency as the world becomes more industrialised. Unfortunately, metastatic colorectal cancer is not cured by chemotherapy and the annual number of deaths caused by colorectal cancer, currently 700,000, is expected to rise. Our understanding of the contribution that genetic mutations make to colorectal cancer, although incomplete, is reasonably well advanced. However, it has only recently become widely appreciated that in addition to the ongoing accumulation of genetic mutations, chronic inflammation also plays a critical role in the initiation and progression of this disease. While a robust and tractable genetic model of colorectal cancer in zebrafish, suitable for pre-clinical studies, is not yet available, the identification of genes required for the rapid proliferation of zebrafish intestinal epithelial cells during development has highlighted a number of essential genes that could be targeted to disable colorectal cancer cells. Moreover, appreciation of the utility of zebrafish to study intestinal inflammation is on the rise. In particular, zebrafish provide unique opportunities to investigate the impact of genetic and environmental factors on the integrity of intestinal epithelial barrier function. With currently available tools, the interplay between epigenetic regulators, intestinal injury, microbiota composition and innate immune cell mobilisation can be analysed in exquisite detail. This provides excellent opportunities to define critical events that could potentially be targeted therapeutically. Further into the future, the use of zebrafish larvae as hosts for xenografts of human colorectal cancer tissue, while still in its infancy, holds great promise that zebrafish could one day provide a practical, preclinical personalized medicine platform for the rapid assessment of the metastatic potential and drug-sensitivity of patient-derived cancers.
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Affiliation(s)
- Viola H Lobert
- Development and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.,Department of Biochemistry, Institute for Cancer Research, Oslo University Hospital, Montebello, N-0379, Oslo, Norway
| | - Dmitri Mouradov
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Joan K Heath
- Development and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
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13
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Cheng Y, Zhu Y, Huang X, Zhang W, Han Z, Liu S. Association between TLR2 and TLR4 Gene Polymorphisms and the Susceptibility to Inflammatory Bowel Disease: A Meta-Analysis. PLoS One 2015; 10:e0126803. [PMID: 26023918 PMCID: PMC4449210 DOI: 10.1371/journal.pone.0126803] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 04/08/2015] [Indexed: 12/18/2022] Open
Abstract
Background The associations between toll-like receptor 2 (TLR2) and toll-like receptor 4(TLR4) polymorphisms and inflammatory bowel disease (IBD) susceptibility remain controversial. A meta-analysis was performed to assess these associations. Methods A systematic search was performed to identify all relevant studies relating TLR2 and TLR4 polymorphisms and IBD susceptibility. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated. Subgroup analyses were performed by ethnicity and publication quality. Results Thirty-eight eligible studies, assessing 10970 cases and 7061 controls were included. No TLR2 Arg677Trp polymorphism was found. No significant association was observed between TLR2 Arg753Gln polymorphism and Crohn’s disease (CD) or ulcerative colitis (UC) in all genetic models. Interestingly, TLR4 Asp299Gly polymorphism was significantly associated with increased risk of CD and UC in all genetic models, except for the additive one in CD. In addition, a statistically significant association between TLR4 Asp299Gly polymorphism and IBD was observed among high quality studies evaluating Caucasians, but not Asians. Associations between TLR4 Thr399Ile polymorphisms and CD risk were found only in the allele and dominant models. The TLR4 Thr399Ile polymorphism was associated with UC risk in pooled results as well as subgroup analysis of high quality publications assessing Caucasians, in allele and dominant models. Conclusions The meta-analysis provides evidence that TLR2 Arg753Gln is not associated with CD and UC susceptibility in Asians; TLR4 Asp299Gly is associated with CD and UC susceptibility in Caucasians, but not Asians. TLR4 Thr399Ile may be associated with IBD susceptibility in Caucasians only. Additional well-powered studies of Asp299Gly and other TLR4 variants are warranted.
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Affiliation(s)
- Yang Cheng
- First clinical college, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Yun Zhu
- Liver Tumor Center, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Xiuping Huang
- First clinical college, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Wei Zhang
- First clinical college, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Zelong Han
- First clinical college, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Side Liu
- Department of Digestion, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
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Taher L, Narlikar L, Ovcharenko I. Identification and computational analysis of gene regulatory elements. Cold Spring Harb Protoc 2015; 2015:pdb.top083642. [PMID: 25561628 PMCID: PMC5885252 DOI: 10.1101/pdb.top083642] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Over the last two decades, advances in experimental and computational technologies have greatly facilitated genomic research. Next-generation sequencing technologies have made de novo sequencing of large genomes affordable, and powerful computational approaches have enabled accurate annotations of genomic DNA sequences. Charting functional regions in genomes must account for not only the coding sequences, but also noncoding RNAs, repetitive elements, chromatin states, epigenetic modifications, and gene regulatory elements. A mix of comparative genomics, high-throughput biological experiments, and machine learning approaches has played a major role in this truly global effort. Here we describe some of these approaches and provide an account of our current understanding of the complex landscape of the human genome. We also present overviews of different publicly available, large-scale experimental data sets and computational tools, which we hope will prove beneficial for researchers working with large and complex genomes.
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Affiliation(s)
- Leila Taher
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, 18051 Rostock, Germany
| | - Leelavati Narlikar
- Chemical Engineering and Process Development Division, National Chemical Laboratory, CSIR, Pune 411008, India
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894
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15
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Peprah E, Xu H, Tekola-Ayele F, Royal CD. Genome-wide association studies in Africans and African Americans: expanding the framework of the genomics of human traits and disease. Public Health Genomics 2014; 18:40-51. [PMID: 25427668 DOI: 10.1159/000367962] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 08/29/2014] [Indexed: 01/11/2023] Open
Abstract
Genomic research is one of the tools for elucidating the pathogenesis of diseases of global health relevance and paving the research dimension to clinical and public health translation. Recent advances in genomic research and technologies have increased our understanding of human diseases, genes associated with these disorders, and the relevant mechanisms. Genome-wide association studies (GWAS) have proliferated since the first studies were published several years ago and have become an important tool in helping researchers comprehend human variation and the role genetic variants play in disease. However, the need to expand the diversity of populations in GWAS has become increasingly apparent as new knowledge is gained about genetic variation. Inclusion of diverse populations in genomic studies is critical to a more complete understanding of human variation and elucidation of the underpinnings of complex diseases. In this review, we summarize the available data on GWAS in recent African ancestry populations within the western hemisphere (i.e. African Americans and peoples of the Caribbean) and continental African populations. Furthermore, we highlight ways in which genomic studies in populations of recent African ancestry have led to advances in the areas of malaria, HIV, prostate cancer, and other diseases. Finally, we discuss the advantages of conducting GWAS in recent African ancestry populations in the context of addressing existing and emerging global health conditions.
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16
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Juste C, Kreil DP, Beauvallet C, Guillot A, Vaca S, Carapito C, Mondot S, Sykacek P, Sokol H, Blon F, Lepercq P, Levenez F, Valot B, Carré W, Loux V, Pons N, David O, Schaeffer B, Lepage P, Martin P, Monnet V, Seksik P, Beaugerie L, Ehrlich SD, Gibrat JF, Van Dorsselaer A, Doré J. Bacterial protein signals are associated with Crohn's disease. Gut 2014; 63:1566-77. [PMID: 24436141 PMCID: PMC4173658 DOI: 10.1136/gutjnl-2012-303786] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE No Crohn's disease (CD) molecular maker has advanced to clinical use, and independent lines of evidence support a central role of the gut microbial community in CD. Here we explore the feasibility of extracting bacterial protein signals relevant to CD, by interrogating myriads of intestinal bacterial proteomes from a small number of patients and healthy controls. DESIGN We first developed and validated a workflow-including extraction of microbial communities, two-dimensional difference gel electrophoresis (2D-DIGE), and LC-MS/MS-to discover protein signals from CD-associated gut microbial communities. Then we used selected reaction monitoring (SRM) to confirm a set of candidates. In parallel, we used 16S rRNA gene sequencing for an integrated analysis of gut ecosystem structure and functions. RESULTS Our 2D-DIGE-based discovery approach revealed an imbalance of intestinal bacterial functions in CD. Many proteins, largely derived from Bacteroides species, were over-represented, while under-represented proteins were mostly from Firmicutes and some Prevotella members. Most overabundant proteins could be confirmed using SRM. They correspond to functions allowing opportunistic pathogens to colonise the mucus layers, breach the host barriers and invade the mucosae, which could still be aggravated by decreased host-derived pancreatic zymogen granule membrane protein GP2 in CD patients. Moreover, although the abundance of most protein groups reflected that of related bacterial populations, we found a specific independent regulation of bacteria-derived cell envelope proteins. CONCLUSIONS This study provides the first evidence that quantifiable bacterial protein signals are associated with CD, which can have a profound impact on future molecular diagnosis.
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Affiliation(s)
| | - David P Kreil
- Chair of Bioinformatics, Boku University Vienna, Vienna, Austria,Department of Life Sciences, University of Warwick, Warwickshire, UK
| | | | - Alain Guillot
- Plate-forme d'Analyse Protéomique de Paris Sud-Ouest (PAPPSO), INRA, Gif-sur-Yvette, France
| | - Sebastian Vaca
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, Strasbourg, France
| | | | - Peter Sykacek
- Chair of Bioinformatics, Boku University Vienna, Vienna, Austria
| | - Harry Sokol
- UMR1319 Micalis, INRA, Jouy-en-Josas, France,Gastroenterology and Nutrition Unit, Hôpital Saint-Antoine, AP-HP, Paris, France
| | | | | | | | - Benoît Valot
- Plate-forme d'Analyse Protéomique de Paris Sud-Ouest (PAPPSO), INRA, Gif-sur-Yvette, France
| | - Wilfrid Carré
- UR1077, Mathématique Informatique et Génome (MIG), INRA, Jouy-en-Josas, France
| | - Valentin Loux
- UR1077, Mathématique Informatique et Génome (MIG), INRA, Jouy-en-Josas, France
| | | | - Olivier David
- UR341, Mathématiques et Informatique Appliquées (MIA), INRA, Jouy-en-Josas, France
| | - Brigitte Schaeffer
- UR341, Mathématiques et Informatique Appliquées (MIA), INRA, Jouy-en-Josas, France
| | | | - Patrice Martin
- UMR1313 GABI, Iso Cell Express (ICE), INRA, Jouy-en-Josas, France
| | | | - Philippe Seksik
- Gastroenterology and Nutrition Unit, Hôpital Saint-Antoine, AP-HP, Paris, France
| | - Laurent Beaugerie
- Gastroenterology and Nutrition Unit, Hôpital Saint-Antoine, AP-HP, Paris, France
| | | | | | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, Strasbourg, France
| | - Joël Doré
- UMR1319 Micalis, INRA, Jouy-en-Josas, France
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Strisciuglio C, Auricchio R, Martinelli M, Staiano A, Giugliano FP, Andreozzi M, De Rosa M, Giannetti E, Gianfrani C, Izzo P, Troncone R, Miele E. Autophagy genes variants and paediatric Crohn's disease phenotype: a single-centre experience. Dig Liver Dis 2014; 46:512-7. [PMID: 24656308 DOI: 10.1016/j.dld.2014.02.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 02/10/2014] [Accepted: 02/18/2014] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Little evidence demonstrating the correlation between several single nucleotide polymorphisms and a specific phenotype of Crohn's disease has been reported in children. We investigated the relationship between autophagy genes variants and clinical features in our children with Crohn's disease. METHODS Genotyping for ATG16L1, NOD2/CARD15, and IRGM1 was performed in 80 consecutive patients with Crohn's disease (median age: 11 years; range: 0.7-17.9 years). Crohn's disease location and behaviour were classified using the Paris classification. Additional data were collected from clinical records on patients' demographics, age at symptom onset and diagnosis, extraintestinal manifestations, therapy, clinical relapses, and need of surgical intervention. RESULTS Patients homozygous for the risk allele ATG16L1 (T300A) showed a trend towards switching to a stricturing phenotype during the course of disease compared to children either homozygous for the wild-type allele or heterozygous for the ATG16L1 single nucleotide polymorphism (p=0.01). Homozygosity for the ATG16L1 risk allele was associated with a major recurrence of clinical relapses and earlier introduction of immunosuppressants (p=0.006 and p=0.04, respectively). Heterozygosity for the NOD2 rs2066847 allele was associated with major ileal involvement (p=0.01). CONCLUSION In patients carrying the T300A variant, Crohn's disease follows a more aggressive clinical course.
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Affiliation(s)
- Caterina Strisciuglio
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples "Federico II", Italy
| | - Renata Auricchio
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples "Federico II", Italy
| | - Massimo Martinelli
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples "Federico II", Italy
| | - Annamaria Staiano
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples "Federico II", Italy.
| | - Francesca Paola Giugliano
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples "Federico II", Italy
| | - Marialuisa Andreozzi
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples "Federico II", Italy
| | - Marina De Rosa
- Department of Molecular Medicine and Medical Biotechnology and CEINGE, University of Naples "Federico II", Italy
| | - Eleonora Giannetti
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples "Federico II", Italy
| | - Carmela Gianfrani
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples "Federico II", Italy; Institute of Protein Biochemistry-CNR, Naples, Italy
| | - Paola Izzo
- Department of Molecular Medicine and Medical Biotechnology and CEINGE, University of Naples "Federico II", Italy
| | - Riccardo Troncone
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples "Federico II", Italy
| | - Erasmo Miele
- Department of Translational Medical Sciences, Section of Pediatrics, University of Naples "Federico II", Italy
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18
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Murugan D, Albert MH, Langemeier J, Bohne J, Puchalka J, Järvinen PM, Hauck F, Klenk AK, Prell C, Schatz S, Diestelhorst J, Sciskala B, Kohistani N, Belohradsky BH, Müller S, Kirchner T, Walter MR, Bufler P, Muise AM, Snapper SB, Koletzko S, Klein C, Kotlarz D. Very early onset inflammatory bowel disease associated with aberrant trafficking of IL-10R1 and cure by T cell replete haploidentical bone marrow transplantation. J Clin Immunol 2014; 34:331-9. [PMID: 24519095 DOI: 10.1007/s10875-014-9992-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 01/20/2014] [Indexed: 12/19/2022]
Abstract
PURPOSE Loss-of-function mutations in IL10 and IL10R cause very early onset inflammatory bowel disease (VEO-IBD). Here, we investigated the molecular pathomechanism of a novel intronic IL10RA mutation and describe a new therapeutic approach of T cell replete haploidentical hematopoietic stem cell transplantation (HSCT). METHODS Clinical data were collected by chart review. Genotypes of IL10 and IL10R genes were determined by Sanger sequencing. Expression and function of mutated IL-10R1 were assessed by quantitative PCR, Western blot analysis, enzyme-linked immunosorbent assays, confocal microscopy, and flow cytometry. RESULTS We identified a novel homozygous point mutation in intron 3 of the IL10RA (c.368-10C > G) in three related children with VEO-IBD. Bioinformatical analysis predicted an additional 3' splice site created by the mutation. Quantitative PCR analysis showed normal mRNA expression of mutated IL10RA. Sequencing of the patient's cDNA revealed an insertion of the last nine nucleotides of intron 3 as a result of aberrant splicing. Structure-based modeling suggested misfolding of mutated IL-10R1. Western blot analysis demonstrated a different N-linked glycosylation pattern of mutated protein. Immunofluorescence and FACS analysis revealed impaired expression of mutated IL-10R1 at the plasma membrane. In the absence of HLA-identical donors, T cell replete haploidentical HSCT was successfully performed in two patients. CONCLUSIONS Our findings expand the spectrum of IL10R mutations in VEO-IBD and emphasize the need for genetic diagnosis of mutations in conserved non-coding sequences of candidate genes. Transplantation of haploidentical stem cells represents a curative therapy in IL-10R-deficient patients, but may be complicated by non-engraftment.
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Affiliation(s)
- Dhaarini Murugan
- Dr. von Hauner Children's Hospital, Ludwig Maximilians University, Munich, Germany
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19
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Decreased lymphatic vessel density is associated with postoperative endoscopic recurrence in Crohn's disease. Inflamm Bowel Dis 2013; 19:2084-90. [PMID: 23851640 DOI: 10.1097/mib.0b013e3182971cec] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
BACKGROUND Increased lymphatic vessel (LV) density has been found in uninflamed intestinal wall of patients with Crohn's disease (CD). The goal of the study was to search for an association between LV density in the proximal ileal resection margin at the time of surgery and endoscopic recurrence. METHODS Ileocolonic resection specimens were obtained from 28 CD patients and 10 control subjects. The ileal proximal uninflamed section was used for the histological quantification of LV using immunohistochemistry with D2-40 antibody in the mucosa and submucosa. Quantification of LV was performed in 8 consecutive fields and was blinded to recurrence score. Patients were divided into 2 groups based on the presence (Rutgeerts score, i3/i4) (R+) or absence (Rutgeerts score, i0/i1) (R-) of endoscopic recurrence 1 year after the surgery. All patients were free of immunomodulators or biologics between surgery and postoperative endoscopy. RESULTS Median LV density was lower in control subjects than in CD patients in the mucosa (4.5%; interquartile range [IQR], 3.6-5.3 versus 5.9%; IQR, 4.2-8.5; P = 0.04) and submucosa (2.4%; IQR, 1.9-3.6 versus 5.7%; IQR, 4.3-6.9; P < 0.01). R- patients had a higher LV density in the proximal resection margin at surgery than R+ patients, both in the mucosa (8.5%; IQR, 6.5-10.3 versus 4.4%; IQR, 3.1-6.1; P < 0.01) and in the submucosa (6.3%; IQR, 5.5-9.3 versus 5.3%; IQR, 3.4-5.9; P = 0.03). Mucosal LV density greater than 7% predicted the absence of endoscopic recurrence at 1 year, with a sensitivity of 81% and a specificity of 75%. CONCLUSIONS Decreased LV density is associated with high risk of endoscopic recurrence after surgery. Therapies that improve lymphatic flow in the gut may reduce the incidence of endoscopic recurrence.
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Michail S, Bultron G, Depaolo RW. Genetic variants associated with Crohn's disease. APPLICATION OF CLINICAL GENETICS 2013; 6:25-32. [PMID: 23935379 PMCID: PMC3735034 DOI: 10.2147/tacg.s33966] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Crohn’s disease is an immune-related disorder characterized by inflammation of the gastrointestinal mucosa, which can occur in any area throughout the digestive tract. This life-long disease commonly presents with abdominal pain, diarrhea, vomiting, and weight loss. While the exact etiology of this disease is largely unknown, it is thought to arise from an interaction between microbial, immunological, and environmental factors in a genetically susceptible host, whereby the immune system attacks the intestine as it cross reacts against gut microbial antigens. The study of genetic variants associated with Crohn’s disease has shed light on our understanding of disease pathophysiology. A large number of genetic variants identified in Crohn’s disease are related to genes targeting microbial recognition and bacterial wall sensing, the most common being NOD2/CARD15 gene. This review will discuss the recent advance in our knowledge of genetic variants of this disease and how they influence the disease course and prognosis.
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Affiliation(s)
- Sonia Michail
- The University of Southern California, Children's Hospital of Los Angeles, Los Angeles, CA, USA
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21
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Saxena R, Saleheen D, Been LF, Garavito ML, Braun T, Bjonnes A, Young R, Ho WK, Rasheed A, Frossard P, Sim X, Hassanali N, Radha V, Chidambaram M, Liju S, Rees SD, Ng DPK, Wong TY, Yamauchi T, Hara K, Tanaka Y, Hirose H, McCarthy MI, Morris AP, Basit A, Barnett AH, Katulanda P, Matthews D, Mohan V, Wander GS, Singh JR, Mehra NK, Ralhan S, Kamboh MI, Mulvihill JJ, Maegawa H, Tobe K, Maeda S, Cho YS, Tai ES, Kelly MA, Chambers JC, Kooner JS, Kadowaki T, Deloukas P, Rader DJ, Danesh J, Sanghera DK. Genome-wide association study identifies a novel locus contributing to type 2 diabetes susceptibility in Sikhs of Punjabi origin from India. Diabetes 2013; 62:1746-55. [PMID: 23300278 PMCID: PMC3636649 DOI: 10.2337/db12-1077] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We performed a genome-wide association study (GWAS) and a multistage meta-analysis of type 2 diabetes (T2D) in Punjabi Sikhs from India. Our discovery GWAS in 1,616 individuals (842 case subjects) was followed by in silico replication of the top 513 independent single nucleotide polymorphisms (SNPs) (P < 10⁻³) in Punjabi Sikhs (n = 2,819; 801 case subjects). We further replicated 66 SNPs (P < 10⁻⁴) through genotyping in a Punjabi Sikh sample (n = 2,894; 1,711 case subjects). On combined meta-analysis in Sikh populations (n = 7,329; 3,354 case subjects), we identified a novel locus in association with T2D at 13q12 represented by a directly genotyped intronic SNP (rs9552911, P = 1.82 × 10⁻⁸) in the SGCG gene. Next, we undertook in silico replication (stage 2b) of the top 513 signals (P < 10⁻³) in 29,157 non-Sikh South Asians (10,971 case subjects) and de novo genotyping of up to 31 top signals (P < 10⁻⁴) in 10,817 South Asians (5,157 case subjects) (stage 3b). In combined South Asian meta-analysis, we observed six suggestive associations (P < 10⁻⁵ to < 10⁻⁷), including SNPs at HMG1L1/CTCFL, PLXNA4, SCAP, and chr5p11. Further evaluation of 31 top SNPs in 33,707 East Asians (16,746 case subjects) (stage 3c) and 47,117 Europeans (8,130 case subjects) (stage 3d), and joint meta-analysis of 128,127 individuals (44,358 case subjects) from 27 multiethnic studies, did not reveal any additional loci nor was there any evidence of replication for the new variant. Our findings provide new evidence on the presence of a population-specific signal in relation to T2D, which may provide additional insights into T2D pathogenesis.
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Affiliation(s)
- Richa Saxena
- Center for Human Genetic Research and Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Danish Saleheen
- Center for Non-Communicable Diseases, Karachi, Pakistan
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, U.K
- Departments of Biostatistics and Epidemiology and Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Latonya F. Been
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Martha L. Garavito
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Timothy Braun
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Andrew Bjonnes
- Center for Human Genetic Research and Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Robin Young
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, U.K
| | - Weang Kee Ho
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, U.K
| | - Asif Rasheed
- Center for Non-Communicable Diseases, Karachi, Pakistan
| | | | - Xueling Sim
- Center for Statistical Genetics and Department of Statistics, University of Michigan, Ann Arbor, Michigan
- Centre for Molecular Epidemiology, National University of Singapore, Singapore
| | - Neelam Hassanali
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, U.K
| | | | | | - Samuel Liju
- Madras Diabetes Research Foundation, Chennai, India
| | - Simon D. Rees
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
- Diabetes Centre, Heart of England National Health Service Foundation Trust, Birmingham, U.K
| | - Daniel Peng-Keat Ng
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
- Department of Ophthalmology, National University of Singapore, Singapore
- Centre for Eye Research Australia, University of Melbourne, Melbourne, Australia
| | - Toshimasa Yamauchi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuo Hara
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Integrated Molecular Science on Metabolic Diseases, 22nd Century Medical and Research Center, The University of Tokyo, Tokyo, Japan
| | - Yasushi Tanaka
- Department of Internal Medicine, Division of Metabolism and Endocrinology, St. Marianna University School of Medicine, Kanagawa, Japan
| | - Hiroshi Hirose
- Health Center, Keio University School of Medicine, Tokyo, Japan
| | - Mark I. McCarthy
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, U.K
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
- Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Oxford, U.K
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, U.K
| | | | | | | | - Abdul Basit
- Baqai Institute of Diabetology and Endocrinology, Karachi, Pakistan
| | - Anthony H. Barnett
- Diabetes Centre, Heart of England National Health Service Foundation Trust, Birmingham, U.K
| | - Prasad Katulanda
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, U.K
- Diabetes Research Unit, Department of Clinical Medicine, University of Colombo, Colombo, Sri Lanka
| | - David Matthews
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, U.K
| | - Viswanathan Mohan
- Madras Diabetes Research Foundation, Chennai, India
- Dr. Mohan's Diabetes Specialities Centre, Chennai, India
| | - Gurpreet S. Wander
- Hero Dayanand Medical College and Heart Institute, Ludhiana, Punjab, India
| | - Jai Rup Singh
- Central University of Punjab, Bathinda, Punjab, India
| | - Narinder K. Mehra
- All India Institute of Medical Sciences and Research, New Delhi, India
| | - Sarju Ralhan
- Hero Dayanand Medical College and Heart Institute, Ludhiana, Punjab, India
| | - M. Ilyas Kamboh
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - John J. Mulvihill
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Hiroshi Maegawa
- Department of Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Kazuyuki Tobe
- First Department of Internal Medicine, University of Toyama, Toyama, Japan
| | - Shiro Maeda
- Laboratory for Endocrinology and Metabolism, RIKEN Center for Genomic Medicine, Kanagawa, Japan
| | - Yoon S. Cho
- Department of Biomedical Science, Hallym University, Chuncheon, Gangwon-do 200-702, Republic of Korea
| | - E. Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Duke-NUS Graduate Medical School Singapore, Singapore
| | - M. Ann Kelly
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, U.K
- Diabetes Centre, Heart of England National Health Service Foundation Trust, Birmingham, U.K
| | - John C. Chambers
- Ealing Hospital National Health Service Trust, Middlesex, U.K
- Imperial College Healthcare National Health Service Trust, London, U.K
- Epidemiology and Biostatistics, Imperial College London, London, U.K
| | - Jaspal S. Kooner
- Ealing Hospital National Health Service Trust, Middlesex, U.K
- Imperial College Healthcare National Health Service Trust, London, U.K
- National Heart and Lung Institute, Imperial College London, Hammersmith Hospital, London, U.K
| | - Takashi Kadowaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | | | - Daniel J. Rader
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - John Danesh
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, U.K
| | - Dharambir K. Sanghera
- Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
- Corresponding author: Dharambir K. Sanghera,
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22
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Wojtal KA, Wolfram L, Frey-Wagner I, Lang S, Scharl M, Vavricka SR, Rogler G. The effects of vitamin A on cells of innate immunity in vitro. Toxicol In Vitro 2013; 27:1525-32. [PMID: 23562973 DOI: 10.1016/j.tiv.2013.03.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 03/05/2013] [Accepted: 03/18/2013] [Indexed: 12/13/2022]
Abstract
Retinoid treatment is suggested to promote development of inflammatory bowel disease, although preclinical studies are not supportive. We evaluated the effect of retinoids on cytokine response in in vitro-differentiated human dendritic cells (ivDCs) and macrophages (ivMACs) derived from healthy human donors and in cultured human THP-1 cells. Effect on human intestinal epithelial cell integrity was also assessed. Each cell type was incubated (±lipopolysaccharide [LPS]) with all-trans retinoic acid (ATRA), 13-cis-RA (isotretinoin) and 4-oxo-13-cis-RA. Cytokine analysis was performed by array analysis. Cultured human endothelial colorectal adenocarcinoma (Caco-2) cells were incubated with these retinoids and media analyzed for leakage by spectrofluorometric analysis. ATRA consistently and significantly inhibited LPS-induced release of the pro-inflammatory cytokines tumor necrosis factor, interleukin (IL)-6, macrophage inflammatory protein (MIP)-1α and MIP-1β. All retinoids tested stimulated release of the anti-inflammatory cytokines granulocyte-macrophage colony-stimulating factor and IL-10, and also monocyte chemotactic protein-1, vascular endothelial growth factor and eotaxin-1. Incubation with retinoids did not significantly alter the permeability of Caco-2 monolayers. Pre-treatment of each cell type with retinoids promoted an anti-inflammatory cytokine profile with only minimal effect on intestinal epithelial cell permeability; consistent with in vivo studies.
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Affiliation(s)
- Kacper A Wojtal
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University-Hospital of Zürich, Switzerland
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23
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Willson TA, Jurickova I, Collins M, Denson LA. Deletion of intestinal epithelial cell STAT3 promotes T-lymphocyte STAT3 activation and chronic colitis following acute dextran sodium sulfate injury in mice. Inflamm Bowel Dis 2013; 19:512-25. [PMID: 23429443 PMCID: PMC4330009 DOI: 10.1097/mib.0b013e31828028ad] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Intestinal epithelial cell (IEC) STAT3 is required for wound healing following acute dextran sodium sulfate (DSS) injury. We hypothesized that loss of IEC STAT3 would promote the development of chronic colitis following acute DSS injury. METHODS Colitis was induced in IEC-specific STAT3-deficient mice (STAT3)[INCREMENT]IEC and littermate controls (STAT3 Flx/Flx) with 4% DSS for 7 days, followed by water consumption for 21 days. Epithelial and immune mediators and severity of colitis were determined. RESULTS Survival, colon length, and histologic injury were significantly worse at day 28 in STAT3[INCREMENT]IEC mice. IEC proliferation and apoptosis did not vary by genotype at day 14 or day 28. The colonic lamina propria frequency of pSTAT3* cells was increased at day 28 and correlated with histologic injury in STAT3 [INCREMENT]IEC mice. The frequency of colonic F480* pSTAT3* macrophages and CD3* pSTAT3* T lymphocytes were increased in STAT3[INCREMENT]IEC mice as compared with STAT3 Flx/Flx controls. In STAT3[INCREMENT]IEC mice, colonic expression of STAT3 target genes Reg3β and Reg3γ, which mediate epithelial restitution, were significantly decreased, whereas expression of interleukin (IL)-17a, IFNγ, CXCL2, CXCL10, and CCL2 were significantly increased and correlated with the increase in histologic severity at day 28(P < 0.05). IL-17a expression also correlated with the increased lamina propria frequency of CD3* pSTAT3* T lymphocytes. CONCLUSIONS Loss of intestinal epithelial STAT3 leads to more severe chronic inflammation following acute injury, which is not accounted for by a sustained defect in epithelial proliferation or apoptosis 7 or 21 days after 1 cycle of DSS but rather defective REG3 expression and expansion of pSTAT3* lymphocytes and IL-17A expression.
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Affiliation(s)
- Tara A. Willson
- Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH,Cancer and Cell Biology Program, the University of Cincinnati College of Medicine, Cincinnati, OH
| | - Ingrid Jurickova
- Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Margaret Collins
- Pathology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Lee A. Denson
- Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH,Cancer and Cell Biology Program, the University of Cincinnati College of Medicine, Cincinnati, OH,to whom correspondence should be addressed: MLC 2010, 3333 Burnet Avenue, Cincinnati, OH 45229, Tel: 513-636-7575, Fax: 513-636-5581,
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24
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Oehlers SH, Flores MV, Hall CJ, Okuda KS, Sison JO, Crosier KE, Crosier PS. Chemically induced intestinal damage models in zebrafish larvae. Zebrafish 2013; 10:184-93. [PMID: 23448252 DOI: 10.1089/zeb.2012.0824] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Several intestinal damage models have been developed using zebrafish, with the aim of recapitulating aspects of human inflammatory bowel disease (IBD). These experimentally induced inflammation models have utilized immersion exposure to an array of colitogenic agents (including live bacteria, bacterial products, and chemicals) to induce varying severity of inflammation. This technical report describes methods used to generate two chemically induced intestinal damage models using either dextran sodium sulfate (DSS) or trinitrobenzene sulfonic acid (TNBS). Methods to monitor intestinal damage and inflammatory processes, and chemical-genetic methods to manipulate the host response to injury are also described.
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Affiliation(s)
- Stefan H Oehlers
- Department of Molecular Medicine and Pathology, School of Medical Sciences, The University of Auckland, Auckland, New Zealand
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25
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Elding H, Lau W, Swallow D, Maniatis N. Refinement in localization and identification of gene regions associated with Crohn disease. Am J Hum Genet 2013; 92:107-13. [PMID: 23246291 PMCID: PMC3542460 DOI: 10.1016/j.ajhg.2012.11.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 08/03/2012] [Accepted: 11/05/2012] [Indexed: 12/13/2022] Open
Abstract
The risk of Crohn disease (CD) has a large genetic component. A recent meta-analysis of 6 genome-wide association studies reported 71 chromosomal intervals but does not account for all of the known genetic contribution. Here, we refine localization of the previously reported intervals and also identify additional CD susceptibility genes using a mapping approach that localizes causal variants based on genetic maps in linkage disequilibrium units (LDU maps). Using 2 of the 6 cohorts, 66 of the 71 previously reported loci are confirmed and more precise location estimates for these intervals are given. We identify 78 additional gene regions that pass genome-wide significance, providing strong evidence for 144 genes. Additionally, 56 nominally significant signals, but with more stringent and precise colocalization, are identified. In total, we provide evidence for 200 gene regions confirming that CD is truly multifactorial and complex in nature. Many identified genes have functions that are compatible with involvement in immune/inflammatory processes and seem to have a large effect in individuals with extra ileal as well as ileal inflammation. The precise locations and the evidence that some genes reflect phenotypic subgroups will help identify functional variants and will lead to greater insight of CD etiology.
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Affiliation(s)
- Heather Elding
- Research Department of Genetics Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Winston Lau
- Research Department of Genetics Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Dallas M. Swallow
- Research Department of Genetics Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Nikolas Maniatis
- Research Department of Genetics Evolution & Environment, University College London, Gower Street, London WC1E 6BT, UK
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26
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Pathway-based genetic analysis of preterm birth. Genomics 2013; 101:163-70. [PMID: 23298525 DOI: 10.1016/j.ygeno.2012.12.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 12/17/2012] [Accepted: 12/25/2012] [Indexed: 01/06/2023]
Abstract
Preterm birth in the United States is now 12%. Multiple genes, gene networks, and variants have been associated with this disease. Using a custom database for preterm birth (dbPTB) with a refined set of genes extensively curated from literature and biological databases, we analyzed GWAS of preterm birth for complete genotype data on nearly 2000 preterm and term mothers. We used both the curated genes and a genome-wide approach to carry out a pathway-based analysis. There were 19 significant pathways, which withstood FDR correction for multiple testing that were identified using both the curated genes and the genome-wide approach. The analysis based on the curated genes was more significant than genome-wide in 15 out of 19 pathways. This approach demonstrates the use of a validated set of genes, in the analysis of otherwise unsuccessful GWAS data, to identify gene-gene interactions in a way that enhances statistical power and discovery.
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27
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Goodhand JR, Wahed M, Mawdsley JE, Farmer AD, Aziz Q, Rampton DS. Mood disorders in inflammatory bowel disease: relation to diagnosis, disease activity, perceived stress, and other factors. Inflamm Bowel Dis 2012; 18:2301-9. [PMID: 22359369 DOI: 10.1002/ibd.22916] [Citation(s) in RCA: 161] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 01/23/2012] [Indexed: 12/14/2022]
Abstract
BACKGROUND Anxiety and depression are common in patients with inflammatory bowel disease (IBD); however, the factors associated with mood disorders in patients with ulcerative colitis (UC) and Crohn's disease (CD) are poorly defined. METHODS In all, 103 patients with UC, 101 with CD, and 124 healthy controls completed the Hospital Anxiety and Depression Scale (HADS). Disease activity was defined both from symptom scores and in UC endoscopically, and in CD by fecal calprotectin and/or serum C-reactive protein. Multivariate regression analyses were used to identify factors associated with anxiety and depression. RESULTS In both UC and CD, anxiety (HADS-A) and depression (HADS-D) scores were higher than in controls (HADS-A: 8.5 ± 4.1 [mean ± SD], 8.6 ± 3.9, 3.2 ± 1.8, P < 0.001; and HADS-D: 4.1 ± 3.3, 4.7 ± 3.3, 1.7 ± 1.4, P < 0.001, respectively). There were no differences in the prevalence of mild, moderate, and severe anxiety and depression in UC and CD. In UC, anxiety scores were associated with perceived stress and a new diagnosis of IBD; depression was associated with stress, inpatient status, and active disease. In CD, anxiety was associated with perceived stress, abdominal pain, and lower socioeconomic status, and depression with perceived stress and increasing age. CONCLUSIONS Anxiety and depression are common in IBD. Perceived stress is associated with mood disturbances in both UC and CD, but the other associated factors differ in the two diseases. Gastroenterologists should look for mood disorders in IBD and consider stress management and psychotherapy in affected patients.
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Affiliation(s)
- J R Goodhand
- Centre for Digestive Diseases, Blizard Institute of Cell and Molecular Science, Barts and London School of Medicine and Dentistry, London, UK
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28
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Genomic modulators of the immune response. Trends Genet 2012; 29:74-83. [PMID: 23122694 PMCID: PMC3605582 DOI: 10.1016/j.tig.2012.10.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 09/30/2012] [Accepted: 10/05/2012] [Indexed: 12/11/2022]
Abstract
Our understanding of immunity has historically been informed by studying heritable mutations in both the adaptive and innate immune responses, including primary immunodeficiency and autoimmune diseases. Recent advances achieved through the application of genomic and epigenomic approaches are reshaping the study of immune dysfunction and opening up new avenues for therapeutic interventions. Moreover, applying genomic techniques to resolve functionally important genetic variation between individuals is providing new insights into immune function in health. This review describes progress in the study of rare variants and primary immunodeficiency diseases arising from whole-exome sequencing (WES), and discusses the application, success, and challenges of applying genome-wide association studies (GWAS) to disorders of immune function and how they may inform more rational use of therapeutics. In addition, the application of expression quantitative-trait mapping to immune phenotypes, progress in understanding MHC disease associations, and insights into epigenetic mechanisms at the interface of immunity and the environment are reviewed.
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29
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Folci M, Meda F, Gershwin ME, Selmi C. Cutting-edge issues in primary biliary cirrhosis. Clin Rev Allergy Immunol 2012; 42:342-54. [PMID: 21243445 DOI: 10.1007/s12016-011-8253-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Several crucial issues remain open in our understanding of primary biliary cirrhosis (PBC), an autoimmune liver disease targeting the small- and medium-sized intrahepatic bile ducts. These issues include the high tissue specificity of the autoimmune injury despite the nontraditional autoantigens found in all mitochondria recognized by PBC-associated autoantibodies, the causes of the commonly observed pruritus, and the disease etiology per se. In all these fields, there has been recent interest secondary to the use of large-scale efforts (such as genome-wide association studies) that were previously considered poorly feasible in a rare disease such as PBC as well as other intuitions. Accordingly, there are now fascinating theories to explain the onset and severity of pruritus due to elevated autotaxin levels, the peculiar apoptotic features of bile duct cells to explain the tissue specificity, and genomic and epigenetic associations contributing to disease susceptibility. We have arbitrarily chosen these four aspects as the most promising in the PBC recent literature and will provide herein a discussion of the recent data and their potential implications.
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Affiliation(s)
- Marco Folci
- Division of Internal Medicine, IRCCS Istituto Clinico Humanitas, via A. Manzoni 56, Rozzano, 20089, Milan, Italy
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30
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Bye H, Prescott NJ, Lewis CM, Matejcic M, Moodley L, Robertson B, Rensburg CV, Parker MI, Mathew CG. Distinct genetic association at the PLCE1 locus with oesophageal squamous cell carcinoma in the South African population. Carcinogenesis 2012; 33:2155-61. [PMID: 22865593 DOI: 10.1093/carcin/bgs262] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Oesophageal squamous cell carcinoma (OSCC) has a high prevalence in the Black and Mixed Ancestry populations of South Africa. Recently, three genome-wide association studies in Chinese populations identified five new OSCC susceptibility loci, including variants at PLCE1, C20orf54, PDE4D, RUNX1 and UNC5CL, but their contribution to disease risk in other populations is unknown. In this study, we report testing variants from these five loci for association with OSCC in the South African Black (407 cases and 849 controls) and Mixed Ancestry (257 cases and 860 controls) populations. The RUNX1 variant rs2014300, which reduced risk in the Chinese population, was associated with an increased risk of OSCC in the Mixed Ancestry population [odds ratio (OR) = 1.33, 95% confidence interval (CI) = 1.09-1.63, P = 0.0055], and none of the five loci were associated in the Black population. Since PLCE1 variants increased the risk of OSCC in all three Chinese studies, this gene was investigated further by sequencing in 46 Black South Africans. This revealed 48 variants, 10 of which resulted in amino acid substitutions, and much lower linkage disequilibrium across the PLCE1 locus than in the Chinese population. We genotyped five PLCE1 variants in cases and controls, and found association of Arg548Leu (rs17417407) with a reduced risk of OSCC (OR = 0.74, 95% CI = 0.60-0.93, P = 0.008) in the Black population. These findings indicate several differences in the genetic contribution to OSCC between the South African and Chinese populations that may be related to differences in their genetic architecture.
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Affiliation(s)
- Hannah Bye
- Department of Medical and Molecular Genetics, King's College London, King's Health Partners, Guy's Hospital, London, United Kingdom
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31
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Kotlarz D, Beier R, Murugan D, Diestelhorst J, Jensen O, Boztug K, Pfeifer D, Kreipe H, Pfister ED, Baumann U, Puchalka J, Bohne J, Egritas O, Dalgic B, Kolho KL, Sauerbrey A, Buderus S, Güngör T, Enninger A, Koda YKL, Guariso G, Weiss B, Corbacioglu S, Socha P, Uslu N, Metin A, Wahbeh GT, Husain K, Ramadan D, Al-Herz W, Grimbacher B, Sauer M, Sykora KW, Koletzko S, Klein C. Loss of interleukin-10 signaling and infantile inflammatory bowel disease: implications for diagnosis and therapy. Gastroenterology 2012; 143:347-55. [PMID: 22549091 DOI: 10.1053/j.gastro.2012.04.045] [Citation(s) in RCA: 327] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 04/06/2012] [Accepted: 04/18/2012] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS Homozygous loss of function mutations in interleukin-10 (IL10) and interleukin-10 receptors (IL10R) cause severe infantile (very early onset) inflammatory bowel disease (IBD). Allogeneic hematopoietic stem cell transplantation (HSCT) was reported to induce sustained remission in 1 patient with IL-10R deficiency. We investigated heterogeneity among patients with very early onset IBD, its mechanisms, and the use of allogeneic HSCT to treat this disorder. METHODS We analyzed 66 patients with early onset IBD (younger than 5 years of age) for mutations in the genes encoding IL-10, IL-10R1, and IL-10R2. IL-10R deficiency was confirmed by functional assays on patients' peripheral blood mononuclear cells (immunoblot and enzyme-linked immunosorbent assay analyses). We assessed the therapeutic effects of standardized allogeneic HSCT. RESULTS Using a candidate gene sequencing approach, we identified 16 patients with IL-10 or IL-10R deficiency: 3 patients had mutations in IL-10, 5 had mutations in IL-10R1, and 8 had mutations in IL-10R2. Refractory colitis became manifest in all patients within the first 3 months of life and was associated with perianal disease (16 of 16 patients). Extraintestinal symptoms included folliculitis (11 of 16) and arthritis (4 of 16). Allogeneic HSCT was performed in 5 patients and induced sustained clinical remission with a median follow-up time of 2 years. In vitro experiments confirmed reconstitution of IL-10R-mediated signaling in all patients who received the transplant. CONCLUSIONS We identified loss of function mutations in IL-10 and IL-10R in patients with very early onset IBD. These findings indicate that infantile IBD patients with perianal disease should be screened for IL-10 and IL-10R deficiency and that allogeneic HSCT can induce remission in those with IL-10R deficiency.
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Affiliation(s)
- Daniel Kotlarz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
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Saito M, Katsuno T, Nakagawa T, Sato T, Noguchi Y, Sazuka S, Saito K, Arai M, Yokote K, Yokosuka O. Intestinal epithelial cells with impaired autophagy lose their adhesive capacity in the presence of TNF-α. Dig Dis Sci 2012; 57:2022-30. [PMID: 22466076 DOI: 10.1007/s10620-012-2133-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 03/02/2012] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND OBJECTIVES Genome-wide association studies have revealed a link between autophagy-related (ATG) genes and susceptibility to Crohn's disease. This suggests underlying involvement of autophagy impairment in the pathogenesis of Crohn's disease. This study was performed to investigate the pathophysiological importance of autophagy impairment in intestinal epithelial cells exposed to TNF-α. METHODS Human colonic epithelial cells (HT-29) and rat small intestinal epithelial cells (IEC-18) were used. Formation of phosphatidylethanolamine-conjugated microtubule-associated protein light chain 3 (LC3-II) was monitored as a marker of autophagy. Autophagy was inhibited using 3-methyladenine or short interfering RNA targeting ATG5 and ATG16L1. RESULTS TNF-α treatment elicited a significant dose-dependent increase in LC3-II protein levels, thus autophagy is induced in the presence of TNF-α. Combined autophagy inhibition and TNF-α treatment induced a marked increase in the number of detached cells and a decrease in activated integrin β1 protein levels. Trypan blue staining indicated 70-80 % of the detached cells were alive, suggesting that these cells became detached not because they were killed but because of dysfunction of cellular adhesion. CONCLUSIONS This is the first study indicating that intestinal epithelial cells with impaired autophagy lose their adhesive capacity in the presence of TNF-α. These observations indicate that impairment of autophagy leads to disruption of the intestinal epithelial cell layers in TNF-α-rich environments.
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Affiliation(s)
- Masaya Saito
- Department of Medicine and Clinical Oncology (K1), Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi 260-8670, Japan
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Hollands GJ, Whitwell SCL, Parker RA, Prescott NJ, Forbes A, Sanderson J, Mathew CG, Lewis CM, Watts S, Sutton S, Armstrong D, Kinmonth AL, Prevost AT, Marteau TM. Effect of communicating DNA based risk assessments for Crohn's disease on smoking cessation: randomised controlled trial. BMJ 2012; 345:e4708. [PMID: 22822007 PMCID: PMC3401124 DOI: 10.1136/bmj.e4708] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE To test the hypothesis that communicating risk of developing Crohn's disease based on genotype and that stopping smoking can reduce this risk, motivates behaviour change among smokers at familial risk. DESIGN Parallel group, cluster randomised controlled trial. SETTING Families with Crohn's disease in the United Kingdom. PARTICIPANTS 497 smokers (mean age 42.6 (SD 14.4) years) who were first degree relatives of probands with Crohn's disease, with outcomes assessed on 209/251 (based on DNA analysis) and 217/246 (standard risk assessment). INTERVENTION Communication of risk assessment for Crohn's disease by postal booklet based on family history of the disease and smoking status alone, or with additional DNA analysis for the NOD2 genotype. Participants were then telephoned by a National Health Service Stop Smoking counsellor to review the booklet and deliver brief standard smoking cessation intervention. Calls were tape recorded and a random subsample selected to assess fidelity to the clinical protocol. MAIN OUTCOME MEASURE The primary outcome was smoking cessation for 24 hours or longer, assessed at six months. RESULTS The proportion of participants stopping smoking for 24 hours or longer did not differ between arms: 35% (73/209) in the DNA arm versus 36% (78/217) in the non-DNA arm (difference -1%, 95% confidence interval -10% to 8%, P=0.83). The proportion making a quit attempt within the DNA arm did not differ between those who were told they had mutations putting them at increased risk (36%), those told they had none (35%), and those in the non-DNA arm (36%). CONCLUSION Among relatives of patients with Crohn's disease, feedback of DNA based risk assessments does not motivate behaviour change to reduce risk any more or less than standard risk assessment. These findings accord with those across a range of populations and behaviours. They do not support the promulgation of commercial DNA based tests nor the search for gene variants that confer increased risk of common complex diseases on the basis that they effectively motivate health related behaviour change. TRIAL REGISTRATION Current Controlled Trials ISRCTN21633644.
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Affiliation(s)
- Gareth J Hollands
- Department of Psychology at Guy's, Section of Health Psychology, King's College London, London SE1 9RT, UK
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STAT3 genotypic variation and cellular STAT3 activation and colon leukocyte recruitment in pediatric Crohn disease. J Pediatr Gastroenterol Nutr 2012; 55:32-43. [PMID: 22197944 PMCID: PMC3996847 DOI: 10.1097/mpg.0b013e318246be78] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Genotypic variation in signal transducer and activator of transcription 3 (STAT3) increases risk for inflammatory bowel disease (IBD), and STAT3-dependent inflammatory networks are induced in the colon in these patients. We hypothesized that STAT3 "A" risk allele carriage would be associated with increased cellular STAT3 activation and colon leukocyte recruitment. METHODS Colonic expression of genes regulating STAT3 signaling and leukocyte recruitment and function was measured in pediatric patients with Crohn disease (CD) stratified by STAT3 genotype. The frequency of colonic pSTAT3* and CXCR2* neutrophils was determined using immunohistochemistry. STAT3 tyrosine phosphorylation (pSTAT3) was measured in circulating leukocytes by flow cytometry, and mechanisms regulating STAT3 activation were tested in IBD Epstein-Barr virus (EBV)-transformed lymphocytes (EBL). RESULTS Colonic expression of interleukin 6 (IL-6), the STAT3 target gene SOCS3, the neutrophil chemoattractants IL-8, CXCL1, and CXCL3, and the neutrophil products S100A8, S100A9, and S100A12 were increased in patients carrying the STAT3 "A" risk allele. The frequency of neutrophils expressing the cognate receptor for IL-8, CXCR2, was increased in colonic biopsies from patients carrying the risk allele, and the frequency of pSTAT3* or CXCR2* neutrophils correlated with histologic severity. The frequency of CD4 lymphocytes and granulocytes expressing pSTAT3 was increased in patients carrying the STAT3 "A" risk allele. EBLs from patients carrying the STAT3 "A" risk allele exhibited increased basal and IL-6-stimulated STAT3 tyrosine phosphorylation, increased transcription of STAT3 and SOCS3 after IL-6 stimulation, and increased membrane localization of the IL-6 receptor, GP130, and Janus-associated kinase 2. CONCLUSIONS The STAT3 "A" risk allele is associated with increased cellular STAT3 activation and upregulation of pathways that promote recruitment of CXCR2* neutrophils to the gut.
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Naidoo N, Pawitan Y, Soong R, Cooper DN, Ku CS. Human genetics and genomics a decade after the release of the draft sequence of the human genome. Hum Genomics 2012; 5:577-622. [PMID: 22155605 PMCID: PMC3525251 DOI: 10.1186/1479-7364-5-6-577] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Substantial progress has been made in human genetics and genomics research over the past ten years since the publication of the draft sequence of the human genome in 2001. Findings emanating directly from the Human Genome Project, together with those from follow-on studies, have had an enormous impact on our understanding of the architecture and function of the human genome. Major developments have been made in cataloguing genetic variation, the International HapMap Project, and with respect to advances in genotyping technologies. These developments are vital for the emergence of genome-wide association studies in the investigation of complex diseases and traits. In parallel, the advent of high-throughput sequencing technologies has ushered in the 'personal genome sequencing' era for both normal and cancer genomes, and made possible large-scale genome sequencing studies such as the 1000 Genomes Project and the International Cancer Genome Consortium. The high-throughput sequencing and sequence-capture technologies are also providing new opportunities to study Mendelian disorders through exome sequencing and whole-genome sequencing. This paper reviews these major developments in human genetics and genomics over the past decade.
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Affiliation(s)
- Nasheen Naidoo
- Centre for Molecular Epidemiology, Department of Epidemiology and Public Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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Abstract
The individual human genome and epigenome are being defined at unprecedented resolution by current advances in sequencing technologies with important implications for human disease. This review uses examples relevant to clinical practice to illustrate the functional consequences of genetic and epigenetic variation. The insights gained from genome-wide association studies are described together with current efforts to understand the role of rare variants in common disease, set in the context of recent successes in Mendelian traits through the application of whole exome sequencing. The application of functional genomics to interrogate the genome and epigenome, build up an integrated picture of the regulatory genomic landscape and inform disease association studies is discussed, together with the role of expression quantitative trait mapping and analysis of allele-specific gene expression.
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Affiliation(s)
- J C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.
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Uzun A, Sharma S, Padbury J. A bioinformatics approach to preterm birth. Am J Reprod Immunol 2012; 67:273-7. [PMID: 22385126 DOI: 10.1111/j.1600-0897.2012.01122.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 02/06/2012] [Indexed: 01/06/2023] Open
Abstract
A vast body of literature has suggested genetic programming of preterm birth. However, there is a complete lack of an organized analysis and stratification of genetic variants that may indeed be involved in the pathogenesis of preterm birth. We developed a novel bioinformatics approach to identify the nominal genetic variants associated with preterm birth. We used semantic data mining to extract all published articles related to preterm birth. Genes identified from public databases and archives of expression arrays were aggregated with genes curated from the literature. Pathway analysis was used to impute genes from pathways identified in the curations. The curated articles and collected genetic information are available in a web-based tool, the database for preterm birth (dbPTB) that forms a unique resource for investigators interested in preterm birth.
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Affiliation(s)
- Alper Uzun
- Department of Pediatrics, Women and Infants Hospital of Rhode Island, Providence, USA
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Xue F, Li S, Luan J, Yuan Z, Luben RN, Khaw KT, Wareham NJ, Loos RJF, Zhao JH. A latent variable partial least squares path modeling approach to regional association and polygenic effect with applications to a human obesity study. PLoS One 2012; 7:e31927. [PMID: 22384102 PMCID: PMC3288051 DOI: 10.1371/journal.pone.0031927] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 01/18/2012] [Indexed: 01/10/2023] Open
Abstract
Genetic association studies are now routinely used to identify single nucleotide polymorphisms (SNPs) linked with human diseases or traits through single SNP-single trait tests. Here we introduced partial least squares path modeling (PLSPM) for association between single or multiple SNPs and a latent trait that can involve single or multiple correlated measurement(s). Furthermore, the framework naturally provides estimators of polygenic effect by appropriately weighting trait-attributing alleles. We conducted computer simulations to assess the performance via multiple SNPs and human obesity-related traits as measured by body mass index (BMI), waist and hip circumferences. Our results showed that the associate statistics had type I error rates close to nominal level and were powerful for a range of effect and sample sizes. When applied to 12 candidate regions in data (N = 2,417) from the European Prospective Investigation of Cancer (EPIC)-Norfolk study, a region in FTO was found to have stronger association (rs7204609∼rs9939881 at the first intron P = 4.29×10(-7)) than single SNP analysis (all with P>10(-4)) and a latent quantitative phenotype was obtained using a subset sample of EPIC-Norfolk (N = 12,559). We believe our method is appropriate for assessment of regional association and polygenic effect on a single or multiple traits.
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Affiliation(s)
- Fuzhong Xue
- Department of Epidemiology and Health Statistics, School of Public Health, Shandong University, Jinan, China
- MRC Epidemiology Unit and Institute of Metabolic Science, Cambridge, United Kingdom
| | - Shengxu Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Jian'an Luan
- MRC Epidemiology Unit and Institute of Metabolic Science, Cambridge, United Kingdom
| | - Zhongshang Yuan
- Department of Epidemiology and Health Statistics, School of Public Health, Shandong University, Jinan, China
| | - Robert N. Luben
- Strangeways Research Laboratory, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas J. Wareham
- MRC Epidemiology Unit and Institute of Metabolic Science, Cambridge, United Kingdom
| | - Ruth J. F. Loos
- MRC Epidemiology Unit and Institute of Metabolic Science, Cambridge, United Kingdom
| | - Jing Hua Zhao
- MRC Epidemiology Unit and Institute of Metabolic Science, Cambridge, United Kingdom
- * E-mail:
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Uzun A, Laliberte A, Parker J, Andrew C, Winterrowd E, Sharma S, Istrail S, Padbury JF. dbPTB: a database for preterm birth. Database (Oxford) 2012; 2012:bar069. [PMID: 22323062 PMCID: PMC3275764 DOI: 10.1093/database/bar069] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 12/28/2011] [Accepted: 12/29/2011] [Indexed: 02/07/2023]
Abstract
Genome-wide association studies (GWAS) query the entire genome in a hypothesis-free, unbiased manner. Since they have the potential for identifying novel genetic variants, they have become a very popular approach to the investigation of complex diseases. Nonetheless, since the success of the GWAS approach varies widely, the identification of genetic variants for complex diseases remains a difficult problem. We developed a novel bioinformatics approach to identify the nominal genetic variants associated with complex diseases. To test the feasibility of our approach, we developed a web-based aggregation tool to organize the genes, genetic variations and pathways involved in preterm birth. We used semantic data mining to extract all published articles related to preterm birth. All articles were reviewed by a team of curators. Genes identified from public databases and archives of expression arrays were aggregated with genes curated from the literature. Pathway analysis was used to impute genes from pathways identified in the curations. The curated articles and collected genetic information form a unique resource for investigators interested in preterm birth. The Database for Preterm Birth exemplifies an approach that is generalizable to other disorders for which there is evidence of significant genetic contributions.
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Affiliation(s)
- Alper Uzun
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI 02905, USA, Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA and Brown Alpert Medical School, Providence, RI 02912, USA
| | - Alyse Laliberte
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI 02905, USA, Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA and Brown Alpert Medical School, Providence, RI 02912, USA
| | - Jeremy Parker
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI 02905, USA, Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA and Brown Alpert Medical School, Providence, RI 02912, USA
| | - Caroline Andrew
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI 02905, USA, Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA and Brown Alpert Medical School, Providence, RI 02912, USA
| | - Emily Winterrowd
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI 02905, USA, Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA and Brown Alpert Medical School, Providence, RI 02912, USA
| | - Surendra Sharma
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI 02905, USA, Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA and Brown Alpert Medical School, Providence, RI 02912, USA
| | - Sorin Istrail
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI 02905, USA, Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA and Brown Alpert Medical School, Providence, RI 02912, USA
| | - James F. Padbury
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI 02905, USA, Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA and Brown Alpert Medical School, Providence, RI 02912, USA
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Boleij A, Tjalsma H. Gut bacteria in health and disease: a survey on the interface between intestinal microbiology and colorectal cancer. Biol Rev Camb Philos Soc 2012; 87:701-30. [PMID: 22296522 DOI: 10.1111/j.1469-185x.2012.00218.x] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A healthy human body contains at least tenfold more bacterial cells than human cells and the most abundant and diverse microbial community resides in the intestinal tract. Intestinal health is not only maintained by the human intestine itself and by dietary factors, but is also largely supported by this resident microbial community. Conversely, however, a large body of evidence supports a relationship between bacteria, bacterial activities and human colorectal cancer. Symbiosis in this multifaceted organ is thus crucial to maintain a healthy balance within the host-diet-microbiota triangle and accordingly, changes in any of these three factors may drive a healthy situation into a state of disease. In this review, the factors that sustain health or drive this complex intestinal system into dysbiosis are discussed. Emphasis is on the role of the intestinal microbiota and related mechanisms that can drive the initiation and progression of sporadic colorectal cancer (CRC). These mechanisms comprise the induction of pro-inflammatory and pro-carcinogenic pathways in epithelial cells as well as the production of (geno)toxins and the conversion of pro-carcinogenic dietary factors into carcinogens. A thorough understanding of these processes will provide leads for future research and may ultimately aid in development of new strategies for CRC diagnosis and prevention.
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Affiliation(s)
- Annemarie Boleij
- Department of Laboratory Medicine, Nijmegen Institute for Infection, Inflammation and Immunity (N4i) & Radboud University Centre for Oncology (RUCO) of the Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, the Netherlands
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Sehgal R, Berg A, Polinski JI, Hegarty JP, Lin Z, McKenna KJ, Stewart DB, Poritz LS, Koltun WA. Mutations in IRGM are associated with more frequent need for surgery in patients with ileocolonic Crohn's disease. Dis Colon Rectum 2012; 55:115-21. [PMID: 22228152 DOI: 10.1097/dcr.0b013e31823ccea8] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND There are no clear criteria for judging the severity of disease in patients with Crohn's disease. Yet classification of patients into low- and high-risk severity groups would benefit both medical and surgical management. At the time of this study, approximately 80 single-nucleotide polymorphisms within 55 genes had been associated with IBD. OBJECTIVE The aim of this study was to identify genetic determinants (single-nucleotide polymorphisms) that could be markers of Crohn's disease severity by the use of frequency of ileocolic surgery as a surrogate for disease severity. DESIGN Sixty-six patients (30 male) with ileocolonic Crohn's disease who previously underwent ileocolectomy were retrospectively studied. The severity of Crohn's disease was quantified by dividing the total number of ileocolectomy procedures by the time between IBD diagnosis and the patient's last clinic visit, the rationale being that more severe disease would be associated with a more frequent need for surgery. Genotyping for the 83 single-nucleotide polymorphisms associated with IBD was done on a customized Illumina Veracode genotyping platform. Three genetic models (general, additive, and dominant) were used to statistically quantify the genetic association of the studied single-nucleotide polymorphisms to the frequency of surgery after adjusting for covariates (age, smoking, family history, disease location, and disease behavior). RESULTS For the entire group the average number of ileocolectomies per patient was 1.7 (range, 1-5) with an average duration of disease of 14.7 years. Single-nucleotide polymorphism rs4958847 in the IRGM gene (immunity-related GTPase family, M) was the most significant single-nucleotide polymorphism in all 3 models tested (p = 0.007) as being associated with ileocolectomy, and it remained significant even after a Benjamini-Hochberg false-discovery correction for multiple observations. Patients carrying the "at-risk" allele for this single-nucleotide polymorphism (n = 20) had an average of 1 surgery every 6.87 ± 1.33 years in comparison with patients carrying the wild-type genotype (n = 46) who averaged 1 surgery in 11.43 ± 1.21 years (p = 0.007, Mann-Whitney U test). CONCLUSIONS : Single-nucleotide polymorphism rs4958847 in the IRGM gene correlated very significantly with frequency of surgery in patients with ileocolonic Crohn's disease. IRGM is a mediator of innate immune responses and is involved in autophagy. The presence of this IRGM SNP may be a marker for disease severity and/or early recurrence after ileocolectomy and may assist in surgical and medical decision making.
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Affiliation(s)
- Rishabh Sehgal
- Division of Colon and Rectal Surgery, Penn State Milton S. Hershey Medical Center, 500 University Drive, Hershey, PA 17033, USA.
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Abstract
Rather than being polygenic, complex disorders probably represent umbrella terms for collections of conditions caused by rare, recent mutations in any of a large number of different genes.
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Affiliation(s)
- Kevin J Mitchell
- Smurfit Institute of Genetics and Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland.
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43
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Tsianos EV, Katsanos KH, Tsianos VE. Role of genetics in the diagnosis and prognosis of Crohn's disease. World J Gastroenterol 2012; 18:105-18. [PMID: 22253516 PMCID: PMC3257437 DOI: 10.3748/wjg.v18.i2.105] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 04/25/2011] [Accepted: 05/02/2011] [Indexed: 02/06/2023] Open
Abstract
Considering epidemiological, genetic and immunological data, we can conclude that the inflammatory bowel diseases are heterogeneous disorders of multifactorial etiology in which hereditability and environment interact to produce the disease. It is probable that patients have a genetic predisposition for the development of the disease coupled with disturbances in immunoregulation. Several genes have been so far related to the diagnosis of Crohn's disease. Those genes are related to innate pattern recognition receptors, to epithelial barrier homeostasis and maintenance of epithelial barrier integrity, to autophagy and to lymphocyte differentiation. So far, the most strong and replicated associations with Crohn's disease have been done with NOD2, IL23R and ATG16L1 genes. Many genes have so far been implicated in prognosis of Crohn's disease and many attempts have been made to classify genetic profiles in Crohn's disease. CARD15 seems not only a susceptibility gene, but also a disease-modifier gene for Crohn's disease. Enriching our understanding on Crohn's disease genetics is important but when combining genetic data with functional data the outcome could be of major importance to clinicians.
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Nakagome S, Mano S, Kozlowski L, Bujnicki JM, Shibata H, Fukumaki Y, Kidd JR, Kidd KK, Kawamura S, Oota H. Crohn's disease risk alleles on the NOD2 locus have been maintained by natural selection on standing variation. Mol Biol Evol 2012; 29:1569-85. [PMID: 22319155 DOI: 10.1093/molbev/mss006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Risk alleles for complex diseases are widely spread throughout human populations. However, little is known about the geographic distribution and frequencies of risk alleles, which may contribute to differences in disease susceptibility and prevalence among populations. Here, we focus on Crohn's disease (CD) as a model for the evolutionary study of complex disease alleles. Recent genome-wide association studies and classical linkage analyses have identified more than 70 susceptible genomic regions for CD in Europeans, but only a few have been confirmed in non-European populations. Our analysis of eight European-specific susceptibility genes using HapMap data shows that at the NOD2 locus the CD-risk alleles are linked with a haplotype specific to CEU at a frequency that is significantly higher compared with the entire genome. We subsequently examined nine global populations and found that the CD-risk alleles spread through hitchhiking with a high-frequency haplotype (H1) exclusive to Europeans. To examine the neutrality of NOD2, we performed phylogenetic network analyses, coalescent simulation, protein structural prediction, characterization of mutation patterns, and estimations of population growth and time to most recent common ancestor (TMRCA). We found that while H1 was significantly prevalent in European populations, the H1 TMRCA predated human migration out of Africa. H1 is likely to have undergone negative selection because 1) the root of H1 genealogy is defined by a preexisting amino acid substitution that causes serious conformational changes to the NOD2 protein, 2) the haplotype has almost become extinct in Africa, and 3) the haplotype has not been affected by the recent European expansion reflected in the other haplotypes. Nevertheless, H1 has survived in European populations, suggesting that the haplotype is advantageous to this group. We propose that several CD-risk alleles, which destabilize and disrupt the NOD2 protein, have been maintained by natural selection on standing variation because the deleterious haplotype of NOD2 is advantageous in diploid individuals due to heterozygote advantage and/or intergenic interactions.
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Affiliation(s)
- Shigeki Nakagome
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwanoha, Kashiwa, Chiba, Japan
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Tsianos EV, Katsanos KH, Tsianos VE. Role of genetics in the diagnosis and prognosis of Crohn's disease. World J Gastroenterol 2011; 17:5246-59. [PMID: 22219593 PMCID: PMC3247688 DOI: 10.3748/wjg.v17.i48.5246] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 06/15/2011] [Accepted: 06/22/2011] [Indexed: 02/06/2023] Open
Abstract
Considering the epidemiological, genetic and immunological data, we can conclude that the inflammatory bowel diseases are heterogeneous disorders of multifactorial etiology in which hereditability and environment interact to produce the disease. It is probable that patients have a genetic predisposition for the development of the disease coupled with disturbances in immunoregulation. Several genes have so far been related to the diagnosis of Crohn's disease. These genes are related to innate pattern recognition receptors, to epithelial barrier homeostasis and maintenance of epithelial barrier integrity, to autophagy and to lymphocyte differentiation. So far, the strongest and most replicated associations with Crohn's disease have been demonstrated with NOD2, IL23R and ATG16L1 genes. Many genes have so far been implicated in the prognosis of Crohn's disease and many attempts have been made for classification of genetic profiles in Crohn's disease. CARD15 seems to be not only a susceptibility gene, but also a disease-modifier gene for Crohn's disease. Enriching our understanding of Crohn's disease genetics is of value, but when combining genetic data with functional data the outcome could be of major importance to clinicians.
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Current concepts on primary open-angle glaucoma genetics: a contribution to disease pathophysiology and future treatment. Eye (Lond) 2011; 26:355-69. [PMID: 22173078 DOI: 10.1038/eye.2011.309] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Glaucoma is a common, complex, heterogenous disease and it constitutes the major cause of irreversible blindness worldwide. Primary open-angle glaucoma (POAG) is the most common type of glaucoma in all populations. Most of the molecular mechanisms leading to POAG development are still unknown. Gene mutations in various populations have been identified by genetic studies and a genetic basis for glaucoma pathogenesis has been established. Linkage analysis and association studies are genetic approaches in the investigation of the genetic basis of POAG. Genome-wide association studies (GWAS) are more powerful compared with linkage analysis in discovering genes of small effect that might contribute to the development of the disease. POAG links to at least 20 genetic loci, but only 2 genes identified in these loci, myocilin and optineurin, are considered as well-established glaucoma-causing genes, whereas the role of other loci, genes, and variants implicated in the development of POAG remains controversial. Gene mutations associated with POAG result in retinal ganglion cell death, which is the common outcome of pathogenetic mechanisms in glaucoma. In future, if the sensitivity and specificity of genotyping increases, it may be possible to screen individuals routinely for disease susceptibility. This review is an update on the latest progress of genetic studies associated with POAG. It emphasizes the correlation of recent achievements in genetics with glaucoma pathophysiology, glaucoma treatment perspectives, and the possibility of future prevention of irreversible visual loss caused by the disease.
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Diaz-Gallo LM, Espino-Paisán L, Fransen K, Gómez-García M, van Sommeren S, Cardeña C, Rodrigo L, Mendoza JL, Taxonera C, Nieto A, Alcain G, Cueto I, López-Nevot MA, Bottini N, Barclay ML, Crusius JB, van Bodegraven AA, Wijmenga C, Ponsioen CY, Gearry RB, Roberts RL, Weersma RK, Urcelay E, Merriman TR, Alizadeh BZ, Martin J. Differential association of two PTPN22 coding variants with Crohn's disease and ulcerative colitis. Inflamm Bowel Dis 2011; 17:2287-94. [PMID: 21287672 DOI: 10.1002/ibd.21630] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 12/08/2010] [Indexed: 12/12/2022]
Abstract
BACKGROUND The PTPN22 gene is an important risk factor for human autoimmunity. The aim of this study was to evaluate for the first time the role of the R263Q PTPN22 polymorphism in ulcerative colitis (UC) and Crohn's disease (CD), and to reevaluate the association of the R620W PTPN22 polymorphism with both diseases. METHODS A total of 1677 UC patients, 1903 CD patients, and 3111 healthy controls from an initial case-control set of Spanish Caucasian ancestry and two independent sample sets of European ancestry (Dutch and New Zealand) were included in the study. Genotyping was performed using TaqMan SNP assays for the R263Q (rs33996649) and R620W (rs2476601) PTPN22 polymorphisms. Meta-analysis was performed on 6977 CD patients, 5695 UC patients, and 9254 controls to test the overall effect of the minor allele of R620W and R263Q polymorphisms. RESULTS The PTPN22 263Q loss-of-function variant showed initial evidence of association with UC in the Spanish cohort (P = 0.026, odds ratio [OR] = 0.61, 95% confidence interval [CI]: 0.39-0.95), which was confirmed in the meta-analysis (P = 0.013 pooled, OR = 0.69, 95% CI: 0.51-0.93). In contrast, the 263Q allele showed no association with CD (P = 0.22 pooled, OR = 1.16, 95% CI: 0.91-1.47). We found in the pooled analysis that the PTPN22 620W gain-of-function variant was associated with reduced risk of CD (P = 7.4E-06 pooled OR = 0.81, 95% CI: 0.75-0.89) but not of UC (P = 0.88 pooled, OR = 0.98, 95% CI: 0.85-1.15). CONCLUSIONS Our data suggest that two autoimmunity-associated polymorphisms of the PTPN22 gene are differentially associated with CD and UC. The R263Q polymorphism only associated with UC, whereas the R620W was significantly associated with only CD.
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Cleynen I, Jüni P, Bekkering GE, Nüesch E, Mendes CT, Schmied S, Wyder S, Kellen E, Villiger PM, Rutgeerts P, Vermeire S, Lottaz D. Genetic evidence supporting the association of protease and protease inhibitor genes with inflammatory bowel disease: a systematic review. PLoS One 2011; 6:e24106. [PMID: 21931648 PMCID: PMC3169567 DOI: 10.1371/journal.pone.0024106] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 08/04/2011] [Indexed: 12/11/2022] Open
Abstract
As part of the European research consortium IBDase, we addressed the role of proteases and protease inhibitors (P/PIs) in inflammatory bowel disease (IBD), characterized by chronic mucosal inflammation of the gastrointestinal tract, which affects 2.2 million people in Europe and 1.4 million people in North America. We systematically reviewed all published genetic studies on populations of European ancestry (67 studies on Crohn's disease [CD] and 37 studies on ulcerative colitis [UC]) to identify critical genomic regions associated with IBD. We developed a computer algorithm to map the 807 P/PI genes with exact genomic locations listed in the MEROPS database of peptidases onto these critical regions and to rank P/PI genes according to the accumulated evidence for their association with CD and UC. 82 P/PI genes (75 coding for proteases and 7 coding for protease inhibitors) were retained for CD based on the accumulated evidence. The cylindromatosis/turban tumor syndrome gene (CYLD) on chromosome 16 ranked highest, followed by acylaminoacyl-peptidase (APEH), dystroglycan (DAG1), macrophage-stimulating protein (MST1) and ubiquitin-specific peptidase 4 (USP4), all located on chromosome 3. For UC, 18 P/PI genes were retained (14 proteases and 4 protease inhibitors), with a considerably lower amount of accumulated evidence. The ranking of P/PI genes as established in this systematic review is currently used to guide validation studies of candidate P/PI genes, and their functional characterization in interdisciplinary mechanistic studies in vitro and in vivo as part of IBDase. The approach used here overcomes some of the problems encountered when subjectively selecting genes for further evaluation and could be applied to any complex disease and gene family.
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Affiliation(s)
- Isabelle Cleynen
- Department of Gastroenterology, Catholic University Leuven, Leuven, Belgium
| | - Peter Jüni
- Clinical Trials Unit Bern, Bern University Hospital, Bern, Switzerland
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | - Eveline Nüesch
- Clinical Trials Unit Bern, Bern University Hospital, Bern, Switzerland
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Camila T. Mendes
- Department of Rheumatology, Clinical Immunology and Allergology, University Hospital of Bern, Bern, Switzerland
| | - Stefanie Schmied
- Clinical Trials Unit Bern, Bern University Hospital, Bern, Switzerland
| | - Stefan Wyder
- Department of Rheumatology, Clinical Immunology and Allergology, University Hospital of Bern, Bern, Switzerland
| | - Eliane Kellen
- Leuven Centre for Cancer Prevention, University Hospital Leuven, Leuven, Belgium
| | - Peter M. Villiger
- Department of Rheumatology, Clinical Immunology and Allergology, University Hospital of Bern, Bern, Switzerland
| | - Paul Rutgeerts
- Department of Gastroenterology, Catholic University Leuven, Leuven, Belgium
| | - Séverine Vermeire
- Department of Gastroenterology, Catholic University Leuven, Leuven, Belgium
| | - Daniel Lottaz
- Department of Rheumatology, Clinical Immunology and Allergology, University Hospital of Bern, Bern, Switzerland
- * E-mail:
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Repnik K, Potočnik U. Haplotype in the IBD5 region is associated with refractory Crohn's disease in Slovenian patients and modulates expression of the SLC22A5 gene. J Gastroenterol 2011; 46:1081-91. [PMID: 21695374 DOI: 10.1007/s00535-011-0426-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Accepted: 05/27/2011] [Indexed: 02/06/2023]
Abstract
BACKGROUND The IBD5 locus (OMIM ID 606348) on chromosome 5 was suggested to be one of the most important genetic factors involved in the pathogenesis of inflammatory bowel diseases (IBDs). However the main contributor from this region is still unknown. METHODS We investigated the possible association of the IBD5 locus with IBD in Slovenian patients and correlation between disease-associated single nucleotide polymorphisms (SNPs) and quantitative gene expression (eQTL) of candidate genes from the IBD5 locus in peripheral blood lymphocytes and colon tissue biopsies from IBD patients. We genotyped SNPs from the IBD5 locus in 312 healthy controls and 632 IBD patients. RESULTS We found statistically significant association of polymorphisms rs1050152 in gene SLC22A4 (p = 0.005, OR = 2.177, 95% CI = 1.270-3.526) and rs2631372 in gene SLC22A5 (p = 0.001, OR = 0.473, 95% CI = 0.307-0.731) and TC haplotype of both polymorphisms (p = 0.006, OR = 1,541, 95% CI = 1.130-2.100) with refractory Crohn's disease (CD) in Slovenian patients who do not respond to standard therapy, including patients who develop fistulas. We found decreased expression of SLC22A4 and SLC22A5 genes in peripheral blood lymphocytes from IBD patients compared to control group and decreased expression of SLC22A5 gene in inflamed tissue biopsies compared to noninflamed colon (p = 0.009). We found lower expression of SLC22A5 gene in IBD patients with disease-susceptible genotypes for both disease-associated SNPs. CONCLUSIONS Our data suggest that SNPs and haplotype in the IBD5 SLC22A4/SLC22A5 region contribute to the development of particularly refractory Crohn's disease in the Slovenian population, and expression studies in blood lymphocytes and colon tissue biopsies and eQTL analysis suggest that SLC22A5 is the main gene in the IBD5 region contributing to the IBD pathogenesis.
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Affiliation(s)
- Katja Repnik
- Center for Human Molecular Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, Slomškov Trg 15, 2000 Maribor, Slovenia
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50
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Barrett M, Chandra SB. A review of major Crohn’s disease susceptibility genes and their role in disease pathogenesis. Genes Genomics 2011. [DOI: 10.1007/s13258-011-0076-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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