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Shahir NM, Wang JR, Wolber EA, Schaner MS, Frank DN, Ir D, Robertson CE, Chaumont N, Sadiq TS, Koruda MJ, Rahbar R, Nix BD, Newberry RD, Sartor RB, Sheikh SZ, Furey TS. Crohn's Disease Differentially Affects Region-Specific Composition and Aerotolerance Profiles of Mucosally Adherent Bacteria. Inflamm Bowel Dis 2020; 26:1843-1855. [PMID: 32469069 PMCID: PMC7676424 DOI: 10.1093/ibd/izaa103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND The intestinal microbiota play a key role in the onset, progression, and recurrence of Crohn disease (CD). Most microbiome studies assay fecal material, which does not provide region-specific information on mucosally adherent bacteria that directly interact with host systems. Changes in luminal oxygen have been proposed as a contributor to CD dybiosis. METHODS The authors generated 16S rRNA data using colonic and ileal mucosal bacteria from patients with CD and without inflammatory bowel disease. We developed profiles reflecting bacterial abundance within defined aerotolerance categories. Bacterial diversity, composition, and aerotolerance profiles were compared across intestinal regions and disease phenotypes. RESULTS Bacterial diversity decreased in CD in both the ileum and the colon. Aerotolerance profiles significantly differed between intestinal segments in patients without inflammatory bowel disease, although both were dominated by obligate anaerobes, as expected. In CD, high relative levels of obligate anaerobes were maintained in the colon and increased in the ileum. Relative abundances of similar and distinct taxa were altered in colon and ileum. Notably, several obligate anaerobes, such as Bacteroides fragilis, dramatically increased in CD in one or both intestinal segments, although specific increasing taxa varied across patients. Increased abundance of taxa from the Proteobacteria phylum was found only in the ileum. Bacterial diversity was significantly reduced in resected tissues of patients who developed postoperative disease recurrence across 2 independent cohorts, with common lower abundance of bacteria from the Bacteroides, Streptococcus, and Blautia genera. CONCLUSIONS Mucosally adherent bacteria in the colon and ileum show distinct alterations in CD that provide additional insights not revealed in fecal material.
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Affiliation(s)
- Nur M Shahir
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina (UNC) at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Center for Gastrointestinal Biology and Disease, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeremy R Wang
- Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - E Ashley Wolber
- Department of Medicine, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Matthew S Schaner
- Department of Medicine, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Daniel N Frank
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Diana Ir
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Charles E Robertson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Nicole Chaumont
- Department of Surgery, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Timothy S Sadiq
- Department of Surgery, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark J Koruda
- Department of Surgery, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Reza Rahbar
- Department of Surgery, REX Healthcare of Wakefield, Wakefield, North Carolina, USA
| | - B Darren Nix
- Division of Gastroenterology, John T. Milliken Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - Rodney D Newberry
- Division of Gastroenterology, John T. Milliken Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, USA
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Medicine, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shehzad Z Sheikh
- Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Center for Gastrointestinal Biology and Disease, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Medicine, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Terrence S Furey
- Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Center for Gastrointestinal Biology and Disease, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Lineberger Comprehensive Cancer Center, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Biology, UNC at Chapel Hill, Chapel Hill, North Carolina, USA,Address correspondence to: Terrence S. Furey, PhD, Departments of Genetics and Biology, University of North Carolina at Chapel Hill, 5022 Genetic Medicine Building, 120 Mason Farm Road, Chapel Hill, NC 27599 ()
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Keith BP, Barrow JB, Toyonaga T, Kazgan N, O'Connor MH, Shah ND, Schaner MS, Wolber EA, Trad OK, Gipson GR, Pitman WA, Kanke M, Saxena SJ, Chaumont N, Sadiq TS, Koruda MJ, Cotney PA, Allbritton N, Trembath DG, Sylvester F, Furey TS, Sethupathy P, Sheikh SZ. Colonic epithelial miR-31 associates with the development of Crohn's phenotypes. JCI Insight 2018; 3:122788. [PMID: 30282822 DOI: 10.1172/jci.insight.122788] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/21/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Crohn's disease (CD) is highly heterogeneous, due in large part to variability in cellular processes that underlie the natural history of CD, thereby confounding effective therapy. There is a critical need to advance understanding of the cellular mechanisms that drive CD heterogeneity. METHODS We performed small RNA sequencing of adult colon tissue from CD and NIBD controls. Colonic epithelial cells and immune cells were isolated from colonic tissues, and microRNA-31 (miR-31) expression was measured. miR-31 expression was measured in colonoid cultures generated from controls and patients with CD. We performed small RNA-sequencing of formalin-fixed paraffin-embedded colon and ileum biopsies from treatment-naive pediatric patients with CD and controls and collected data on disease features and outcomes. RESULTS Small RNA-sequencing and microRNA profiling in the colon revealed 2 distinct molecular subtypes, each with different clinical associations. Notably, we found that miR-31 expression was a driver of these 2 subtypes and, further, that miR-31 expression was particularly pronounced in epithelial cells. Colonoids revealed that miR-31 expression differences are preserved in this ex vivo system. In adult patients, low colonic miR-31 expression levels at the time of surgery were associated with worse disease outcome as measured by need for an end ileostomy and recurrence of disease in the neoterminal ileum. In pediatric patients, lower miR-31 expression at the time of diagnosis was associated with future development of fibrostenotic ileal CD requiring surgeryCONCLUSIONS. These findings represent an important step forward in designing more effective clinical trials and developing personalized CD therapies. FUNDING This work was supported by CCF Career Development Award (SZS), R01-ES024983 from NIEHS (SZS and TSF), 1R01DK104828-01A1 from NIDDK (SZS and TSF), P01-DK094779-01A1 from NIDDK (SZS), P30-DK034987 from NIDDK (SZS), 1-16-ACE-47 ADA Pathway Award (PS), UNC Nutrition Obesity Research Center Pilot & Feasibility Grant P30DK056350 (PS), CCF PRO-KIIDS NETWORK (SZS and PS), UNC CGIBD T32 Training Grant from NIDDK (JBB), T32 Training Grant (5T32GM007092-42) from NIGMS (MH), and SHARE from the Helmsley Trust (SZS). The UNC Translational Pathology Laboratory is supported, in part, by grants from the National Cancer Institute (3P30CA016086) and the UNC University Cancer Research Fund (UCRF) (PS).
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Affiliation(s)
- Benjamin P Keith
- Curriculum in Bioinformatics and Computational Biology.,Center for Gastrointestinal Biology and Disease, and
| | | | | | - Nevzat Kazgan
- Center for Gastrointestinal Biology and Disease, and
| | - Michelle Hoffner O'Connor
- Center for Gastrointestinal Biology and Disease, and.,Curriculum in Genetics and Molecular Biology, University of North Carolina (UNC) at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Neil D Shah
- Center for Gastrointestinal Biology and Disease, and
| | | | | | - Omar K Trad
- Center for Gastrointestinal Biology and Disease, and
| | - Greg R Gipson
- Center for Gastrointestinal Biology and Disease, and
| | - Wendy A Pitman
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Matthew Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | | | | | | | | | - Paul A Cotney
- Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nancy Allbritton
- Joint Department of Biomedical Engineering, UNC, Chapel Hill, North Carolina, USA, and North Carolina State University, Raleigh, North Carolina, USA
| | | | | | - Terrence S Furey
- Curriculum in Bioinformatics and Computational Biology.,Center for Gastrointestinal Biology and Disease, and.,Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA.,Lineberger Comprehensive Cancer Center, and.,Department of Biology, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Shehzad Z Sheikh
- Center for Gastrointestinal Biology and Disease, and.,Curriculum in Genetics and Molecular Biology, University of North Carolina (UNC) at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Genetics, UNC at Chapel Hill, Chapel Hill, North Carolina, USA
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Weiser M, Simon JM, Kochar B, Tovar A, Israel JW, Robinson A, Gipson GR, Schaner MS, Herfarth HH, Sartor RB, McGovern DP, Rahbar R, Sadiq TS, Koruda MJ, Furey TS, Sheikh SZ. Molecular classification of Crohn's disease reveals two clinically relevant subtypes. Gut 2018; 67:36-42. [PMID: 27742763 PMCID: PMC5426990 DOI: 10.1136/gutjnl-2016-312518] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/09/2016] [Accepted: 09/18/2016] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The clinical presentation and course of Crohn's disease (CD) is highly variable. We sought to better understand the cellular and molecular mechanisms that guide this heterogeneity, and characterise the cellular processes associated with disease phenotypes. DESIGN We examined both gene expression and gene regulation (chromatin accessibility) in non-inflamed colon tissue from a cohort of adult patients with CD and control patients. To support the generality of our findings, we analysed previously published expression data from a large cohort of treatment-naïve paediatric CD and control ileum. RESULTS We found that adult patients with CD clearly segregated into two classes based on colon tissue gene expression-one that largely resembled the normal colon and one where certain genes showed expression patterns normally specific to the ileum. These classes were supported by changes in gene regulatory profiles observed at the level of chromatin accessibility, reflective of a fundamental shift in underlying molecular phenotypes. Furthermore, gene expression from the ilea of a treatment-naïve cohort of paediatric patients with CD could be similarly subdivided into colon-like and ileum-like classes. Finally, expression patterns within these CD subclasses highlight large-scale differences in the immune response and aspects of cellular metabolism, and were associated with multiple clinical phenotypes describing disease behaviour, including rectal disease and need for colectomy. CONCLUSIONS Our results strongly suggest that these molecular signatures define two clinically relevant forms of CD irrespective of tissue sampling location, patient age or treatment status.
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Affiliation(s)
- Matthew Weiser
- Department of Genetics, University of North Carolina at Chapel Hill,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill
| | - Jeremy M. Simon
- Department of Genetics, University of North Carolina at Chapel Hill
| | - Bharati Kochar
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill,Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill
| | - Adelaide Tovar
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill
| | | | - Adam Robinson
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill
| | - Gregory R. Gipson
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill
| | - Matthew S. Schaner
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill
| | - Hans H. Herfarth
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill
| | - R. Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill
| | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Reza Rahbar
- Department of Surgery, University of North Carolina at Chapel Hill
| | - Timothy S. Sadiq
- Department of Surgery, University of North Carolina at Chapel Hill
| | - Mark J. Koruda
- Department of Surgery, University of North Carolina at Chapel Hill
| | - Terrence S. Furey
- Department of Genetics, University of North Carolina at Chapel Hill,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill,Department of Biology, University of North Carolina at Chapel Hill
| | - Shehzad Z. Sheikh
- Department of Genetics, University of North Carolina at Chapel Hill,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill,Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill
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