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Ahmad R, Kumar B, Thapa I, Talmon GA, Salomon J, Ramer-Tait AE, Bastola DK, Dhawan P, Singh AB. Loss of claudin-3 expression increases colitis risk by promoting Gut Dysbiosis. Gut Microbes 2023; 15:2282789. [PMID: 38010872 PMCID: PMC10730149 DOI: 10.1080/19490976.2023.2282789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/08/2023] [Indexed: 11/29/2023] Open
Abstract
Dysregulation of both the gut barrier and microbiota (dysbiosis) promotes susceptibility to and severity of Inflammatory Bowel Diseases (IBD). Leaky gut and dysbiosis often coexist; however, potential interdependence and molecular regulation are not well understood. Robust expression of claudin-3 (CLDN3) characterizes the gut epithelium, and studies have demonstrated a positive association between CLDN3 expression and gut barrier maturity and integrity, including in response to probiotics. However, the exact status and causal role of CLDN3 in IBD and regulation of gut dysbiosis remain unknown. Analysis of mouse and human IBD cohorts helped examine CLDN3 expression in IBD. The causal role was determined by modeling CLDN3 loss of expression during experimental colitis. 16S sequencing and in silico analysis helped examine gut microbiota diversity between Cldn3KO and WT mice and potential host metabolic responses. Fecal microbiota transplant (FMT) studies were performed to assess the role of gut dysbiosis in the increased susceptibility of Cldn3KO mice to colitis. A significant decrease in CLDN3 expression characterized IBD and CLDN3 loss of expression promoted colitis. 16S sequencing analysis suggested gut microbiota changes in Cldn3KO mice that were capable of modulating fatty acid metabolism and oxidative stress response. FMT from naïve Cldn3KO mice promoted colitis susceptibility in recipient germ-free mice (GFM) compared with GFM-receiving microbiota from WT mice. Our data demonstrate a critical role of CLDN3 in maintaining normal gut microbiota and inflammatory responses, which can be harnessed to develop novel therapeutic opportunities for patients with IBD.
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Affiliation(s)
- Rizwan Ahmad
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Balawant Kumar
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ishwor Thapa
- School of Interdisciplinary Informatics, College of Information Science & Technology, University of Nebraska at Omaha, Omaha, NE, USA
| | - Geoffrey A. Talmon
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Jeffrey Salomon
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, USA
| | - Amanda E. Ramer-Tait
- Department of Food Science and Technology and the Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Dhundy K. Bastola
- School of Interdisciplinary Informatics, College of Information Science & Technology, University of Nebraska at Omaha, Omaha, NE, USA
| | - Punita Dhawan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, NE, USA
| | - Amar B. Singh
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
- Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, NE, USA
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Ahmad R, Kumar B, Thapa I, Tamang RL, Yadav SK, Washington MK, Talmon GA, Yu AS, Bastola DK, Dhawan P, Singh AB. Claudin-2 protects against colitis-associated cancer by promoting colitis-associated mucosal healing. J Clin Invest 2023; 133:e170771. [PMID: 37815870 PMCID: PMC10688979 DOI: 10.1172/jci170771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/05/2023] [Indexed: 10/12/2023] Open
Abstract
Patients with inflammatory bowel disease (IBD) are susceptible to colitis-associated cancer (CAC). Chronic inflammation promotes the risk for CAC. In contrast, mucosal healing predicts improved prognosis in IBD and reduced risk of CAC. However, the molecular integration among colitis, mucosal healing, and CAC remains poorly understood. Claudin-2 (CLDN2) expression is upregulated in IBD; however, its role in CAC is not known. The current study was undertaken to examine the role for CLDN2 in CAC. The AOM/DSS-induced CAC model was used with WT and CLDN2-modified mice. High-throughput expression analyses, murine models of colitis/recovery, chronic colitis, ex vivo crypt culture, and pharmacological manipulations were employed in order to increase our mechanistic understanding. The Cldn2KO mice showed significant inhibition of CAC despite severe colitis compared with WT littermates. Cldn2 loss also resulted in impaired recovery from colitis and increased injury when mice were subjected to intestinal injury by other methods. Mechanistic studies demonstrated a possibly novel role of CLDN2 in promotion of mucosal healing downstream of EGFR signaling and by regulation of Survivin expression. An upregulated CLDN2 expression protected from CAC and associated positively with crypt regeneration and Survivin expression in patients with IBD. We demonstrate a potentially novel role of CLDN2 in promotion of mucosal healing in patients with IBD and thus regulation of vulnerability to colitis severity and CAC, which can be exploited for improved clinical management.
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Affiliation(s)
- Rizwan Ahmad
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Balawant Kumar
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Ishwor Thapa
- School of Interdisciplinary Informatics, University of Nebraska Omaha, Omaha, Nebraska, USA
| | - Raju Lama Tamang
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Santosh K. Yadav
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Mary K. Washington
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Geoffrey A. Talmon
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Alan S. Yu
- Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Dhundy K. Bastola
- School of Interdisciplinary Informatics, University of Nebraska Omaha, Omaha, Nebraska, USA
| | - Punita Dhawan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
- VA Nebraska-Western Iowa Health Care System, Omaha, Nebraska, USA
| | - Amar B. Singh
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
- VA Nebraska-Western Iowa Health Care System, Omaha, Nebraska, USA
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Sharygin D, Koniaris LG, Wells C, Zimmers TA, Hamidi T. Role of CD14 in human disease. Immunology 2023; 169:260-270. [PMID: 36840585 PMCID: PMC10591340 DOI: 10.1111/imm.13634] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
The cell surface antigen CD14 is primarily understood to act as a co-receptor for toll-like receptors (TLRs) to activate innate immunity responses to pathogens and tissue injury in macrophages and monocytes. However, roles for CD14 are increasingly being uncovered in disease responses in epithelial and endothelial cells. Consistent with these broader functions, CD14 expression is altered in a variety of non-immune cell types in response to a several of disease states. Moreover, soluble CD14 activated by factors from both pathogens and tissue damage may initiate signalling in a variety of non-immune cells. This review examined the current understanding CD14 in innate immunity as well as its potential functions in nonimmune cells and associated human diseases.
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Affiliation(s)
- Daniel Sharygin
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Chemistry, Massachusetts institute of technology, Cambridge, MA, USA
| | - Leonidas G. Koniaris
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Clark Wells
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Teresa A. Zimmers
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA
- Richard L. Roudebush Veterans Administration Medical Center, Indianapolis, IN, USA
| | - Tewfik Hamidi
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
- Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
- Indiana Center for Musculoskeletal Health, Indiana University School of Medicine, Indianapolis, IN, USA
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Thorne JW, Redden R, Bowdridge SA, Becker GM, Stegemiller MR, Murdoch BM. Genome-Wide Analysis of Sheep Artificially or Naturally Infected with Gastrointestinal Nematodes. Genes (Basel) 2023; 14:1342. [PMID: 37510248 PMCID: PMC10379027 DOI: 10.3390/genes14071342] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
The anthelmintic resistance of gastrointestinal nematodes (GINs) poses a significant threat to sheep worldwide, but genomic selection can serve as an alternative to the use of chemical treatment as a solution for parasitic infection. The objective of this study is to conduct genome-wide association studies (GWASs) to identify single nucleotide polymorphisms (SNPs) in Rambouillet (RA) and Dorper × White Dorper (DWD) lambs associated with the biological response to a GIN infection. All lambs were genotyped with a medium-density genomic panel with 40,598 markers used for analysis. Separate GWASs were conducted using fecal egg counts (FECs) from lambs (<1 year of age) that acquired their artificial infections via an oral inoculation of 10,000 Haemonchus contortus larvae (n = 145) or naturally while grazing on pasture (n = 184). A GWAS was also performed for packed cell volume (PCV) in artificially GIN-challenged lambs. A total of 26 SNPs exceeded significance and 21 SNPs were in or within 20 kb of genes such as SCUBE1, GALNT6, IGF1R, CAPZB and PTK2B. The ontology analysis of candidate genes signifies the importance of immune cell development, mucin production and cellular signaling for coagulation and wound healing following epithelial damage in the abomasal gastric pits via H. contortus during GIN infection in lambs. These results add to a growing body of the literature that promotes the use of genomic selection for increased sheep resistance to GINs.
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Affiliation(s)
- Jacob W Thorne
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID 83844, USA
- Texas A&M AgriLife Research and Extension, San Angelo, TX 76901, USA
| | - Reid Redden
- Texas A&M AgriLife Research and Extension, San Angelo, TX 76901, USA
| | - Scott A Bowdridge
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
| | - Gabrielle M Becker
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Morgan R Stegemiller
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Brenda M Murdoch
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID 83844, USA
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Ilott NE, Neyazi M, Arancibia-Cárcamo CV, Powrie F, Geremia A. Tissue-dependent transcriptional and bacterial associations in primary sclerosing cholangitis-associated inflammatory bowel disease. Wellcome Open Res 2022; 6:199. [DOI: 10.12688/wellcomeopenres.16901.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Background: Patients with primary sclerosing cholangitis (PSC) frequently have co-ocurring ulcerative colitis (UC) and develop colorectal cancer. Colorectal cancer risk in patients with PSC-associated ulcerative colitis (PSC/UC) is elevated relative to patients with ulcerative colitis (UC) alone, reasons for which remain obscure. Understanding the molecular and microbial basis for differences between these two patient groups and how these vary across intestinal sites is important for the development of therapies to prevent colorectal cancer development in at-risk individuals. Methods: We employed ribonucleic acid sequencing (RNA-seq) analysis of biopsy samples across three intestinal tissue locations (ileum, caecum and rectum) in patients with PSC/UC (ileum n = 7, caecum n = 7, rectum n = 7), UC (ileum n = 9, caecum n = 10, rectum n = 10) and healthy controls (ileum n = 11, caecum n = 9, rectum n = 12) to determine tissue-dependent transcriptional alterations in PSC/UC. We also performed 16S ribosomal RNA (rRNA) amplicon sequencing to determine bacterial associations with PSC/UC. Results: Tissue-defining transcriptional signatures revealed that the ileum was enriched for genes involved in lipid and drug metabolism, the caecum for activated immune cells and the rectum for enteric neurogenesis. Transcriptional alterations relative to healthy control samples were largely shared between patients with PSC/UC or UC although were distinct across tissue locations. Nevertheless, we observed reduced expression of gamma-glutamyl transferase 1 (GGT1) specifically in the ileum and caecum of patients with PSC/UC. Analysis of the bacterial component of the microbiome revealed high inter-individual variability of microbiome composition and little evidence for tissue-dependency. We observed a reduction in Parabacteroides relative abundance in the rectum of patients with PSC/UC. Conclusions: The role of gamma-glutamyl transferase in maintaining the redox environment through the glutathione salvage pathway makes our observed alterations a potential pathway to PSC-associated colorectal cancer.
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Chen HM, MacDonald JA. Molecular Network Analyses Implicate Death-Associated Protein Kinase 3 (DAPK3) as a Key Factor in Colitis-Associated Dysplasia Progression. Inflamm Bowel Dis 2022; 28:1485-1496. [PMID: 35604388 PMCID: PMC9527615 DOI: 10.1093/ibd/izac098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Ulcerative colitis (UC) is a progressive disorder that elevates the risk of colon cancer development through a colitis-dysplasia-carcinoma sequence. Gene expression profiling of colitis-associated lesions obtained from patients with varied extents of UC can be mined to define molecular panels associated with colon cancer development. METHODS Differential gene expression profiles of 3 UC clinical subtypes and healthy controls were developed for the GSE47908 microarray data set of healthy controls, left-sided colitis, pancolitis, and colitis-associated dysplasia (CAD) using limma R. RESULTS A gene ontology enrichment analysis of differentially expressed genes (DEGs) revealed a shift in the transcriptome landscape as UC progressed from left-sided colitis to pancolitis to CAD, from being immune-centric to being cytoskeleton-dependent. Hippo signaling (via Yes-associated protein [YAP]) and Ephrin receptor signaling were the top canonical pathways progressively altered in concert with the pathogenic progression of UC. A molecular interaction network analysis of DEGs in left-sided colitis, pancolitis, and CAD revealed 1 pairwise line, or edge, that was topologically important to the network structure. This edge was found to be highly enriched in actin-based processes, and death-associated protein kinase 3 (DAPK3) was a critical member and sole protein kinase member of this network. Death-associated protein kinase 3 is a regulator of actin-cytoskeleton reorganization that controls proliferation and apoptosis. Differential correlation analyses revealed a negative correlation for DAPK3-YAP in healthy controls that flipped to positive in left-sided colitis. With UC progression to CAD, the DAPK3-YAP correlation grew progressively more positive. CONCLUSION In summary, DAPK3 was identified as a candidate gene involved in UC progression to dysplasia.
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Affiliation(s)
- Huey-Miin Chen
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Justin A MacDonald
- Address correspondence to: Justin A. MacDonald, PhD, Department of Biochemistry & Molecular Biology, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6 ()
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Transcription of the Envelope Protein by 1-L Protein–RNA Recognition Code Leads to Genes/Proteins That Are Relevant to the SARS-CoV-2 Life Cycle and Pathogenesis. Curr Issues Mol Biol 2022; 44:791-816. [PMID: 35723340 PMCID: PMC8928949 DOI: 10.3390/cimb44020055] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/21/2022] [Accepted: 02/03/2022] [Indexed: 12/02/2022] Open
Abstract
The theoretical protein–RNA recognition code was used in this study to research the compatibility of the SARS-CoV-2 envelope protein (E) with mRNAs in the human transcriptome. According to a review of the literature, the spectrum of identified genes showed that the virus post-transcriptionally promotes or represses the genes involved in the SARS-CoV-2 life cycle. The identified genes/proteins are also involved in adaptive immunity, in the function of the cilia and wound healing (EMT and MET) in the pulmonary epithelial tissue, in Alzheimer’s and Parkinson’s disease and in type 2 diabetes. For example, the E-protein promotes BHLHE40, which switches off the IL-10 inflammatory “brake” and inhibits antiviral THαβ cells. In the viral cycle, E supports the COPII-SCAP-SREBP-HSP90α transport complex by the lowering of cholesterol in the ER and by the repression of insulin signaling, which explains the positive effect of HSP90 inhibitors in COVID-19 (geldanamycin), and E also supports importin α/β-mediated transport to the nucleus, which explains the positive effect of ivermectin, a blocker of importins α/β. In summary, transcription of the envelope protein by the 1-L protein–RNA recognition code leads to genes/proteins that are relevant to the SARS-CoV-2 life cycle and pathogenesis.
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Lu J, Wang Z, Maimaiti M, Hui W, Abudourexiti A, Gao F. Identification of diagnostic signatures in ulcerative colitis patients via bioinformatic analysis integrated with machine learning. Hum Cell 2022; 35:179-188. [PMID: 34731452 DOI: 10.1007/s13577-021-00641-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/28/2021] [Indexed: 02/07/2023]
Abstract
Ulcerative colitis (UC) is an immune-related disorder with enhanced prevalence globally. Early diagnosis is critical for the effective treatment of UC. However, it still lacks specific diagnostic signatures. The aim of our study was to explore efficient signatures and construct the diagnostic model for UC. Microarray data of GSE87473 and GSE48634, which were obtained from tissue biopsy samples, were downloaded from the Gene Expression Omnibus (GEO), and differently expressed genes (DEGs), GO, and KEGG analyses were performed. We constructed the PPI network via STRING database. The immune infiltration of the samples was evaluated using CIBERSORT methods combined with the LM22 feature matrix. The logistic regression model was constructed, with the expression of selected genes as the predictor variable, and the UC occurrence as the responsive variable. As a result, a total of 126 DEGs between the UC patients and normal counterparts were identified. The GO and KEGG analysis revealed that multiple biological processes, such as antimicrobial humoral immune response mediated by antimicrobial peptide and IL-17 signaling pathway, were enriched. The infiltration of eight immune cell types (B cells naive, Dendritic.cells.activated, Macrophages.M0, Macrophages.M2, Mast.cells.resting, Neutrophils, Plasma.cells, and T.cells.follicular.helper) was significantly different between patients with UC and normal counterparts. The top 50 most significant DEGs were selected for the construction of the PPI network. The average AUC of the logistic regression model in the fivefold cross-validation was 0.8497 in the training set, GSE87473. The AUC of another independent verification set of GSE48634 from the GEO database was 0.7208. In conclusion, we identified potential hub genes, including REG3A, REG1A, DEFA6, REG1B, and DEFA5, which might be significantly associated with UC progression. The logistic regression model based on the five genes could reliably diagnose UC patients.
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Affiliation(s)
- Jiajie Lu
- Xinjiang Medical University, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Zhiyuan Wang
- Department of Gastroenterology, People's Hospital of Xinjiang Uygur Autonomous Region, No. 91, Tianchi Road, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Munila Maimaiti
- Department of Gastroenterology, People's Hospital of Xinjiang Uygur Autonomous Region, No. 91, Tianchi Road, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Wenjia Hui
- Department of Gastroenterology, People's Hospital of Xinjiang Uygur Autonomous Region, No. 91, Tianchi Road, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Adilai Abudourexiti
- Department of Gastroenterology, People's Hospital of Xinjiang Uygur Autonomous Region, No. 91, Tianchi Road, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Feng Gao
- Department of Gastroenterology, People's Hospital of Xinjiang Uygur Autonomous Region, No. 91, Tianchi Road, Urumqi, 830001, Xinjiang Uygur Autonomous Region, China.
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Li D, Tan Y. Dysregulation of alternative splicing is associated with the pathogenesis of ulcerative colitis. Biomed Eng Online 2021; 20:121. [PMID: 34838026 PMCID: PMC8627048 DOI: 10.1186/s12938-021-00959-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/15/2021] [Indexed: 12/21/2022] Open
Abstract
Background Although numerous risk loci for ulcerative colitis (UC) have been identified in the human genome, the pathogenesis of UC remains unclear. Recently, multiple transcriptomic analyses have shown that aberrant gene expression in the colon tissues of UC patients is associated with disease progression. A pioneering study also demonstrated that altered post-transcriptional regulation is involved in the progression of UC. Here, we provide a genome-wide analysis of alternative splicing (AS) signatures in UC patients. We analyzed three datasets containing 74 tissue samples from UC patients and identified over 2000 significant AS events. Results Skipped exon and alternative first exon were the two most significantly altered AS events in UC patients. The immune response-related pathways were remarkably enriched in the UC-related AS events. Genes with significant AS events were more likely to be dysregulated at the expression level. Conclusions We present a genomic landscape of AS events in UC patients based on a combined analysis of two cohorts. Our results indicate that dysregulation of AS may have a pivotal role in determining the pathogenesis of UC. In addition, our study uncovers genes with potential therapeutic implications for UC treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12938-021-00959-4.
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Affiliation(s)
- Daowei Li
- Department of Radiology, The People's Hospital of China Medical University & The People's Hospital of Liaoning Province, No. 33, Wenyi Road, Shenhe District, Shenyang, 110016, China
| | - Yue Tan
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Tiexi District, 39 Huaxiang Road, Shenyang, 110022, China.
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Ilott NE, Neyazi M, Arancibia-Cárcamo CV, Powrie F, Geremia A. Tissue-dependent transcriptional and bacterial associations in primary sclerosing cholangitis-associated inflammatory bowel disease. Wellcome Open Res 2021; 6:199. [DOI: 10.12688/wellcomeopenres.16901.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Primary sclerosing cholangitis (PSC) is a disease of the bile duct and liver. However, patients frequently have co-morbidities including inflammatory bowel disease (IBD) and colorectal cancer. Colorectal cancer risk in patients with PSC-associated ulcerative colitis (PSC/UC) is elevated relative to patients with ulcerative colitis (UC) alone, reasons for which remain obscure. Further, clinical and immunological features, and involved intestinal sites differ between PSC/UC and UC. Understanding the molecular and microbial basis for differences in cancer risk between these two patient groups and how these differ across intestinal sites is important for the development of therapies to prevent colorectal cancer development in at-risk individuals. Methods: We employed ribonucleic acid sequencing (RNA-seq) analysis of biopsy samples across three intestinal tissue locations (ileum, caecum and rectum) in patients with PSC/UC (n = 8), UC (n = 10) and healthy controls (n = 12) to determine tissue-dependent transcriptional alterations in PSC/UC. We also performed 16S ribosomal RNA (rRNA) amplicon sequencing to determine bacterial associations with PSC/UC and host-microbiome associations. Results: Tissue-defining transcriptional signatures revealed that the ileum was enriched for genes involved in lipid and drug metabolism, the caecum for activated immune cells and the rectum for enteric neurogenesis. Transcriptional alterations relative to healthy control samples were largely shared between patients with PSC/UC or UC although were distinct across tissue locations. Nevertheless, we observed reduced expression of gamma-glutamyl transferase 1 (GGT1) specifically in the ileum and caecum of patients with PSC/UC. Analysis of the bacterial component of the microbiome revealed high inter-individual variability of microbiome composition and little evidence for tissue-dependency. We observed a reduction in Parabacteroides relative abundance in the rectum of patients with PSC/UC. Conclusions: The role of gamma-glutamyl transferase in maintaining the redox environment through the glutathione salvage pathway makes our observed alterations a potential pathway to PSC-associated colorectal cancer.
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Du J, Yin J, Du H, Zhang J. Revisiting an Expression Dataset of Discordant Inflammatory Bowel Disease Twin Pairs Using a Mutation Burden Test Reveals CYP2C18 as a Novel Marker. Front Genet 2021; 12:680125. [PMID: 34211502 PMCID: PMC8239360 DOI: 10.3389/fgene.2021.680125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/24/2021] [Indexed: 01/03/2023] Open
Abstract
The aim of this study was to investigate the expression features of discordant inflammatory bowel disease (IBD) twin pairs to identify novel molecular features and markers. We collected an expression dataset of discordant twin pairs with ulcerative colitis and performed integrative analysis to identify the genetic-independent expression features. Through deconvolution of the immune cell populations and tissue expression specificity, we refined the candidate genes for susceptibility to ulcerative colitis. We found that dysregulated immune systems and NOD-related pathways were enriched in the expression network of the discordant IBD twin pairs. Among the identified factors were significantly increased proportions of immune cells, including megakaryocytes, neutrophils, natural killer T cells, and lymphatic endothelial cells. The differentially expressed genes were significantly enriched in a gene set associated with cortical and medullary thymocytes. Finally, by combining these expression features with genetic resources, we identified some candidate genes with potential to serve as novel markers of ulcerative colitis, such as CYP2C18. Ulcerative colitis is a subtype of inflammatory bowel disease and a polygenic disorder. Through integrative analysis, we identified some genes, such as CYP2C18, that are involved in the pathogenesis of IBD as well as some candidate therapeutic targets, such as LOXL2.
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Affiliation(s)
- Juan Du
- Department of Gastroenterology, First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Yin
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Department of Human Genetics, Zhejiang University School of Medicine, Institute of Genetics, Zhejiang University, Hangzhou, China
| | - Haojie Du
- Department of Gastroenterology, First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Jiawei Zhang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Bhatnagar G, Rodriguez-Justo M, Higginson A, Bassett P, Windsor A, Cohen R, Halligan S, Taylor SA. Inflammation and fibrosis in Crohn's disease: location-matched histological correlation of small bowel ultrasound features. Abdom Radiol (NY) 2021; 46:144-155. [PMID: 32564208 PMCID: PMC7864849 DOI: 10.1007/s00261-020-02603-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 05/20/2020] [Accepted: 05/26/2020] [Indexed: 02/06/2023]
Abstract
PURPOSE To evaluate the utility of mural and extramural sonographic features of Crohn's Disease as potential imaging biomarkers of inflammation and fibrosis against whole-mount histological sections. METHODS Twelve Crohn's disease patients (Mean age 35(25-69), 7 males) underwent small bowel ultrasound prior to small bowel resection. Two radiologists in consensus graded multiple parameters including mural, mucosal and submucosal thickness, submucosal/mesenteric echogenicity and clarity and mural Doppler signal in 50 selected bowel cross-sections. Matching with histological sampling sites was facilitated via scanning of the resected specimen. A histopathologist scored acute and chronic inflammation, and fibrosis (using histological scoring systems) following analysis of whole mount block sections. The association between sonographic observations and histopathological scores was examined via univariable and multivariable analysis. RESULTS In univariate analyses, bowel wall thickness (regression co-efficient and 95% CI 0.8 (0.3, 1.3) p = 0.001), mesenteric fat echogenicity (8.7(3.0, 14.5) p = 0.005), submucosal layer thickness (7.4(1.2, 13.5) p = 0.02), submucosal layer clarity (4.4(0.6, 8.2) p = 0.02) and mucosal layer thickness (4.6(1.8, 7.4) p = 0.001) were all significantly associated with acute inflammation. Mesenteric fat echogenicity (674(8.67, 52404) p = 0.009), submucosal layer thickness (79.9(2.16, 2951) p = 0.02) and mucosal layer thickness (13.6(1.54, 121) p = 0.02) were significantly associated with chronic inflammation. Submucosal layer echogenicity (p = 0.03), clarity (25.0(1.76, 356) p = 0.02) and mucosal layer thickness (53.8(3.19, 908) p = 0.006) were significantly associated with fibrosis. In multivariate analyses, wall and mucosal thickness remained significantly associated with acute inflammation (p = 0.02), mesenteric fat echogenicity with chronic inflammation (p = 0.009) and mucosal thickness (p = 0.006) with fibrosis. CONCLUSION Multiple sonographic parameters are associated with histological phenotypes in Crohn's disease although there is overlap between ultrasonic stigmata of acute inflammation, chronic inflammation and fibrosis.
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Affiliation(s)
- Gauraang Bhatnagar
- grid.83440.3b0000000121901201Centre for Medical Imaging, University College London, 2nd Floor Charles Bell House, 43-45 Foley Street, London, W1W 7TS UK
| | - Manuel Rodriguez-Justo
- grid.439749.40000 0004 0612 2754Department of Histology, University College Hospitals, London, UK
| | - Antony Higginson
- grid.415470.30000 0004 0392 0072Department of Radiology, Queen Alexandra Hospital, Portsmouth, UK
| | | | - Alastair Windsor
- grid.439749.40000 0004 0612 2754Department of Colorectal Surgery, University College Hospitals, London, UK
| | - Richard Cohen
- grid.439749.40000 0004 0612 2754Department of Colorectal Surgery, University College Hospitals, London, UK
| | - Steve Halligan
- grid.83440.3b0000000121901201Centre for Medical Imaging, University College London, 2nd Floor Charles Bell House, 43-45 Foley Street, London, W1W 7TS UK
| | - Stuart A. Taylor
- grid.83440.3b0000000121901201Centre for Medical Imaging, University College London, 2nd Floor Charles Bell House, 43-45 Foley Street, London, W1W 7TS UK
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13
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Efthymakis K, Clemente E, Marchioni M, Di Nicola M, Neri M, Sallese M. An Exploratory Gene Expression Study of the Intestinal Mucosa of Patients with Non-Celiac Wheat Sensitivity. Int J Mol Sci 2020; 21:ijms21061969. [PMID: 32183058 PMCID: PMC7139384 DOI: 10.3390/ijms21061969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/06/2020] [Accepted: 03/11/2020] [Indexed: 12/12/2022] Open
Abstract
Non-celiac wheat sensitivity (NCWS) is a recently recognized syndrome triggered by a gluten-containing diet. The pathophysiological mechanisms engaged in NCWS are poorly understood and, in the absence of laboratory markers, the diagnosis relies only on a double-blind protocol of symptoms evaluation during a gluten challenge. We aimed to shed light on the molecular mechanisms governing this disorder and identify biomarkers helpful to the diagnosis. By a genome-wide transcriptomic analysis, we investigated gene expression profiles of the intestinal mucosa of 12 NCWS patients, as well as 7 controls. We identified 300 RNA transcripts whose expression differed between NCWS patients and controls. Only 37% of these transcripts were protein-coding RNA, whereas the remaining were non-coding RNA. Principal component analysis (PCA) and receiver operating characteristic curves showed that these microarray data are potentially useful to set apart NCWS from controls. Literature and network analyses indicated a possible implication/dysregulation of innate immune response, hedgehog pathway, and circadian rhythm in NCWS. This exploratory study indicates that NCWS can be genetically defined and gene expression profiling might be a suitable tool to support the diagnosis. The dysregulated genes suggest that NCWS may result from a deranged immune response. Furthermore, non-coding RNA might play an important role in the pathogenesis of NCWS.
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Affiliation(s)
- Konstantinos Efthymakis
- Department of Medicine and Ageing Sciences, ‘G. d’Annunzio’ University of Chieti–Pescara, 66100 Chieti, Italy;
- Center for Advanced Studies and Technology (CAST), ‘G. d’Annunzio’ University of Chieti-Pescara, 66100 Chieti, Italy;
| | - Emanuela Clemente
- Center for Advanced Studies and Technology (CAST), ‘G. d’Annunzio’ University of Chieti-Pescara, 66100 Chieti, Italy;
- Department of Medical, Oral and Biotechnological Sciences, ‘G. d’Annunzio’ University of Chieti–Pescara, 66100 Chieti, Italy; (M.M.); (M.D.N.)
| | - Michele Marchioni
- Department of Medical, Oral and Biotechnological Sciences, ‘G. d’Annunzio’ University of Chieti–Pescara, 66100 Chieti, Italy; (M.M.); (M.D.N.)
| | - Marta Di Nicola
- Department of Medical, Oral and Biotechnological Sciences, ‘G. d’Annunzio’ University of Chieti–Pescara, 66100 Chieti, Italy; (M.M.); (M.D.N.)
| | - Matteo Neri
- Department of Medicine and Ageing Sciences, ‘G. d’Annunzio’ University of Chieti–Pescara, 66100 Chieti, Italy;
- Center for Advanced Studies and Technology (CAST), ‘G. d’Annunzio’ University of Chieti-Pescara, 66100 Chieti, Italy;
- Correspondence: (M.N.); (M.S.)
| | - Michele Sallese
- Center for Advanced Studies and Technology (CAST), ‘G. d’Annunzio’ University of Chieti-Pescara, 66100 Chieti, Italy;
- Department of Medical, Oral and Biotechnological Sciences, ‘G. d’Annunzio’ University of Chieti–Pescara, 66100 Chieti, Italy; (M.M.); (M.D.N.)
- Correspondence: (M.N.); (M.S.)
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14
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Kaiko GE, Chen F, Lai CW, Chiang IL, Perrigoue J, Stojmirović A, Li K, Muegge BD, Jain U, VanDussen KL, Goggins BJ, Keely S, Weaver J, Foster PS, Lawrence DA, Liu TC, Stappenbeck TS. PAI-1 augments mucosal damage in colitis. Sci Transl Med 2020; 11:11/482/eaat0852. [PMID: 30842312 DOI: 10.1126/scitranslmed.aat0852] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 10/10/2018] [Accepted: 02/12/2019] [Indexed: 12/13/2022]
Abstract
There is a major unmet clinical need to identify pathways in inflammatory bowel disease (IBD) to classify patient disease activity, stratify patients that will benefit from targeted therapies such as anti-tumor necrosis factor (TNF), and identify new therapeutic targets. In this study, we conducted global transcriptome analysis to identify IBD-related pathways using colon biopsies, which highlighted the coagulation gene pathway as one of the most enriched gene sets in patients with IBD. Using this gene-network analysis across 14 independent cohorts and 1800 intestinal biopsies, we found that, among the coagulation pathway genes, plasminogen activator inhibitor-1 (PAI-1) expression was highly enriched in active disease and in patients with IBD who did not respond to anti-TNF biologic therapy and that PAI-1 is a key link between the epithelium and inflammation. Functionally, PAI-1 and its direct target, the fibrinolytic protease tissue plasminogen activator (tPA), played an important role in regulating intestinal inflammation. Intestinal epithelial cells produced tPA, which was protective against chemical and mechanical-mediated colonic injury in mice. In contrast, PAI-1 exacerbated mucosal damage by blocking tPA-mediated cleavage and activation of anti-inflammatory TGF-β, whereas the inhibition of PAI-1 reduced both mucosal damage and inflammation. This study identifies an immune-coagulation gene axis in IBD where elevated PAI-1 may contribute to more aggressive disease.
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Affiliation(s)
- Gerard E Kaiko
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, NSW 2308, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Feidi Chen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chin-Wen Lai
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - I-Ling Chiang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | | | - Katherine Li
- Janssen Research & Development LLC, Spring House, PA 19002, USA
| | - Brian D Muegge
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Umang Jain
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kelli L VanDussen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Bridie J Goggins
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, NSW 2308, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Simon Keely
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, NSW 2308, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Jessica Weaver
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, NSW 2308, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Paul S Foster
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, NSW 2308, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Daniel A Lawrence
- Departments of Pathology and Internal Medicine, Division of Cardiovascular Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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15
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Genome-wide significant regions in 43 Utah high-risk families implicate multiple genes involved in risk for completed suicide. Mol Psychiatry 2020; 25:3077-3090. [PMID: 30353169 PMCID: PMC6478563 DOI: 10.1038/s41380-018-0282-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/31/2018] [Accepted: 09/26/2018] [Indexed: 12/31/2022]
Abstract
Suicide is the 10th leading cause of death in the United States. Although environment has undeniable impact, evidence suggests that genetic factors play a significant role in completed suicide. We linked a resource of ~ 4500 DNA samples from completed suicides obtained from the Utah Medical Examiner to genealogical records and medical records data available on over eight million individuals. This linking has resulted in the identification of high-risk extended families (7-9 generations) with significant familial risk of completed suicide. Familial aggregation across distant relatives minimizes effects of shared environment, provides more genetically homogeneous risk groups, and magnifies genetic risks through familial repetition. We analyzed Illumina PsychArray genotypes from suicide cases in 43 high-risk families, identifying 30 distinct shared genomic segments with genome-wide evidence (p = 2.02E-07-1.30E-18) of segregation with completed suicide. The 207 genes implicated by the shared regions provide a focused set of genes for further study; 18 have been previously associated with suicide risk. Although PsychArray variants do not represent exhaustive variation within the 207 genes, we investigated these for specific segregation within the high-risk families, and for association of variants with predicted functional impact in ~ 1300 additional Utah suicides unrelated to the discovery families. None of the limited PsychArray variants explained the high-risk family segregation; sequencing of these regions will be needed to discover segregating risk variants, which may be rarer or regulatory. However, additional association tests yielded four significant PsychArray variants (SP110, rs181058279; AGBL2, rs76215382; SUCLA2, rs121908538; APH1B, rs745918508), raising the likelihood that these genes confer risk of completed suicide.
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16
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Whyte JM, Ellis JJ, Brown MA, Kenna TJ. Best practices in DNA methylation: lessons from inflammatory bowel disease, psoriasis and ankylosing spondylitis. Arthritis Res Ther 2019; 21:133. [PMID: 31159831 PMCID: PMC6547594 DOI: 10.1186/s13075-019-1922-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Advances in genomic technology have enabled a greater understanding of the genetics of common immune-mediated diseases such as ankylosing spondylitis (AS), inflammatory bowel disease (IBD) and psoriasis. The substantial overlap in genetically identified pathogenic pathways has been demonstrated between these diseases. However, to date, gene discovery approaches have only mapped a minority of the heritability of these common diseases, and most disease-associated variants have been found to be non-coding, suggesting mechanisms of disease-association through transcriptional regulatory effects. Epigenetics is a major interface between genetic and environmental modifiers of disease and strongly influence transcription. DNA methylation is a well-characterised epigenetic mechanism, and a highly stable epigenetic marker, that is implicated in disease pathogenesis. DNA methylation is an under-investigated area in immune-mediated diseases, and many studies in the field are affected by experimental design limitations, related to study design, technical limitations of the methylation typing methods employed, and statistical issues. This has resulted in both sparsity of investigations into disease-related changes in DNA methylation, a paucity of robust findings, and difficulties comparing studies in the same disease. In this review, we cover the basics of DNA methylation establishment and control, and the methods used to examine it. We examine the current state of DNA methylation studies in AS, IBD and psoriasis; the limitations of previous studies; and the best practices for DNA methylation studies. The purpose of this review is to assist with proper experimental design and consistency of approach in future studies to enable a better understanding of the functional role of DNA methylation in immune-mediated disease.
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Affiliation(s)
- Jessica M Whyte
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Jonathan J Ellis
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia. .,Translational Research Institute, Princess Alexandra Hospital, 37 Kent Street, Woolloongabba, Queensland, 4102, Australia.
| | - Tony J Kenna
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
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17
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Low END, Mokhtar NM, Wong Z, Raja Ali RA. Colonic Mucosal Transcriptomic Changes in Patients with Long-Duration Ulcerative Colitis Revealed Colitis-Associated Cancer Pathways. J Crohns Colitis 2019; 13:755-763. [PMID: 30954025 PMCID: PMC6535502 DOI: 10.1093/ecco-jcc/jjz002] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIMS Patients with ulcerative colitis [UC] with long disease duration have a higher risk of developing colitis-associated cancer [CAC] compared with patients with short-duration UC. The aim of this study was to identify transcriptomic differences associated with the duration of UC disease. METHODS We conducted transcriptome profiling on 32 colonic biopsies [11 long-duration UC, ≥20 years; and 21 short-duration UC, ≤5 years] using Affymetrix Human Transcriptome Array 2.0. Differentially expressed genes [fold change > 1.5, p < 0.05] and alternative splicing events [splicing index > 1.5, p < 0.05] were determined using the Transcriptome Analysis Console. KOBAS 3.0 and DAVID 6.8 were used for KEGG and GO analysis. Selected genes from microarray analysis were validated using qPCR. RESULTS There were 640 differentially expressed genes between both groups. The top ten upregulated genes were HMGCS2, UGT2A3 isoforms, B4GALNT2, MEP1B, GUCA2B, ADH1C, OTOP2, SLC9A3, and LYPD8; the top ten downregulated genes were PI3, DUOX2, VNN1, SLC6A14, GREM1, MMP1, CXCL1, TNIP3, TFF1, and LCN2. Among the 123 altered KEGG pathways, the most significant were metabolic pathways; fatty acid degradation; valine, leucine, and isoleucine degradation; the peroxisome proliferator-activated receptor signalling pathway; and bile secretion, which were previously linked with CAC. Analysis showed that 3560 genes exhibited differential alternative splicing between long- and short-duration UC. Among them, 374 were differentially expressed, underscoring the intrinsic relationship between altered gene expression and alternative splicing. CONCLUSIONS Long-duration UC patients have altered gene expressions, pathways, and alternative splicing events as compared with short-duration UC patients, and these could be further validated to improve our understanding of the pathogenesis of CAC.
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Affiliation(s)
- Eden Ngah Den Low
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Norfilza Mohd Mokhtar
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Zhiqin Wong
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Raja Affendi Raja Ali
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia,Corresponding author: Professor Dr Raja Affendi Raja Ali, MD, FRCP, Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latif, Bandar Tun Razak, 56000 Cheras, Kuala Lumpur, Malaysia. Tel: 603-9145-6094; Fax: 603-9145-6679;
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18
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Vinayaga-Pavan M, Frampton M, Pontikos N, Levine AP, Smith PJ, Jonasson JG, Björnsson ES, Segal AW, Smith AM. Elevation in Cell Cycle and Protein Metabolism Gene Transcription in Inactive Colonic Tissue From Icelandic Patients With Ulcerative Colitis. Inflamm Bowel Dis 2019; 25:317-327. [PMID: 30452647 PMCID: PMC6327231 DOI: 10.1093/ibd/izy350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND A combination of genetic and environmental factors is thought to be involved in the pathogenesis of ulcerative colitis (UC). In Iceland, the incidence of UC is one of the highest in the world. The aim of this study was to characterize patients with UC and identify potential germline mutations and pathways that could be associated with UC in this population. METHODS Exome sequencing and genome-wide microarray analysis on macroscopically noninflamed colonic mucosa from patients and controls were performed. Exome sequence data were examined for very rare or novel mutations that were over-represented in the UC cohort. Combined matching of variant analysis and downstream influence on transcriptomic expression in the rectum were analyzed. RESULTS One thousand eight hundred thirty-eight genes were differentially expressed in rectal tissue from UC patients and identified an upregulation in genes associated with cell cycle control and protein processing in the endoplasmic reticulum (ER). Two missense mutations in thiopurine S-methyltransferase (TPMT) with a minor allele frequency of 0.22 in the UC patients compared with a reported 0.062 in the Icelandic population were identified. A predicted damaging mutation in the gene SLC26A3 is potentially associated with increased expression of DUOX2 and DUOXA2 in rectal tissue. CONCLUSIONS Colonic mucosa of UC patients demonstrates evidence of an elevation in genes involving cell proliferation and processing of proteins within the ER. Exome sequencing identified a possible increased prevalence of 2 damaging TPMT variants within the UC population, suggesting screening the UC population before initiation of thiopurine analogue therapy to avoid toxicity associated with these mutations.
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Affiliation(s)
| | | | - Nikolas Pontikos
- UCL Genetics Institute, University College London, London, United Kingdom
| | | | | | - Jon G Jonasson
- Department of Pathology, Landspitali University Hospital Reykjavik, Iceland,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Einar S Björnsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland,Department of Gastroenterology and Hepatology, Landspitali University Hospital, Reykjavik, Iceland
| | | | - Andrew M Smith
- Microbial Diseases, Eastman Dental Institute,Molecular Medicine, Division of Medicine,Address correspondence to: Andrew M. Smith, PhD, Microbial Diseases, Eastman Dental Institute, Rayne Building, 5 University Street, University College London, London WC1E 6JF, United Kingdom ()
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19
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Taman H, Fenton CG, Hensel IV, Anderssen E, Florholmen J, Paulssen RH. Genome-wide DNA Methylation in Treatment-naïve Ulcerative Colitis. J Crohns Colitis 2018; 12:1338-1347. [PMID: 30137272 PMCID: PMC6236200 DOI: 10.1093/ecco-jcc/jjy117] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS The aim of this study was to investigate the genome-wide DNA methylation status in treatment-naïve ulcerative colitis [UC], and to explore the relationship between DNA methylation patterns and gene expression levels in tissue biopsies from a well-stratified treatment-naïve UC patient group. METHODS Mucosal biopsies from treatment-naïve patients [n = 10], and a healthy control group [n = 11] underwent genome-wide DNA bisulfite sequencing. Principal component analysis [PCA] and diverse statistical methods were applied to obtain a dataset of differentially methylated genes. DNA methylation annotation was investigated using the UCSC Genome Browser. Gene set enrichments were obtained using the Kyoto Encyclopaedia of Genes and Genomes [KEGG] and PANTHER. RESULTS Of all significantly differentially expressed genes [DEGs], 25% correlated with DNA methylation patterns; 30% of these genes were methylated at CpG sites near their transcription start site [TSS]. Hyper-methylation was observed for genes involved in homeostasis and defence, whereas hypo-methylation was observed for genes playing a role in immune response [i.e. chemokines and interleukins]. Of the differentially DNA methylated genes, 25 were identified as inflammatory bowel disease [IBD] susceptibility genes. Four genes [DEFFA6, REG1B, BTNL3, OLFM4] showed DNA methylation in the absence of known CpG islands. CONCLUSIONS Genome-wide DNA methylation analysis revealed distinctive functional patterns for hyper-and hypo-methylation in treatment-naïve UC. These distinct patterns could be of importance in the development and pathogenesis of UC. Further investigation of DNA methylation patterns may be useful in the development of the targeting of epigenetic processes, and may allow new treatment and target strategies for UC patients.
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Affiliation(s)
- Hagar Taman
- Genomics Support Centre Tromsø [GSCT], Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway
| | - Christopher G Fenton
- Genomics Support Centre Tromsø [GSCT], Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway
| | - Inga V Hensel
- Genomics Support Centre Tromsø [GSCT], Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway,Gastroenterology and Nutrition Research Group, Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway
| | - Endre Anderssen
- Genomics Support Centre Tromsø [GSCT], Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway
| | - Jon Florholmen
- Gastroenterology and Nutrition Research Group, Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway,Department of Gastroenterology, University Hospital of North Norway, Tromsø, Norway
| | - Ruth H Paulssen
- Genomics Support Centre Tromsø [GSCT], Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway,Gastroenterology and Nutrition Research Group, Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway,Corresponding author: Ruth H. Paulssen, PhD, Department of Clinical Medicine, Gastroenterology and Nutrition Research Group, UiT The Arctic University of Norway, Faculty of Health, Sykehusveien 38, N-9038 Tromsø, Norway/ Tel.: +47 77 64 54 80;
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Molecular Comparison of Adult and Pediatric Ulcerative Colitis Indicates Broad Similarity of Molecular Pathways in Disease Tissue. J Pediatr Gastroenterol Nutr 2018; 67:45-52. [PMID: 29401083 DOI: 10.1097/mpg.0000000000001898] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Efficacy data from adult ulcerative colitis (UC) clinical trials are often extrapolated for pediatric prescribing. Consequently, it is important to understand similarities/differences in pediatric and adult UC. Pediatric UC tends to have more extensive disease at presentation, yet genetic studies have not detected pathways that distinguish the populations, and differences in mucosal gene expression between adult and pediatric UC are not well characterized. METHODS Using colonic microarray data from a phase 3 trial of golimumab in adult UC (87 UC; 21 healthy), the GSE10616 pediatric dataset (10 UC; 11 healthy), and a phase 1B trial of golimumab in pediatric UC (n = 19), UC expression profiles were compared and unique genes were defined as those with significant changes (|FC|>2×, adjusted P < 0.05) in one population, but not the other (|FC| < 1.2×, adjusted P > 0.05). Pathway and upstream regulator analyses were performed. Profiles by disease extent (extensive [pancolitis] vs limited [left-sided] involvement) were compared within each population. RESULTS Pediatric and adult disease profiles overlapped substantially, with ∼50% to 75% overlap, depending on the fold-change cutoff used. Conversely, <10% of the disease profiles were unique to each population. Similar canonical pathways were enriched in both datasets. Predicted upstream regulators were also concordant, including lipopolysaccharide, interleukin-1β, and tumor necrosis factor-α. Expression profiles of extensive UC were indistinguishable from those of patients with limited involvement in each population. CONCLUSIONS The UC gene expression landscape is shared by adults and children, independent of disease extent. This supports extrapolation of efficacy from adults to children in developing new therapies for UC.
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21
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Feng J, Gao Q, Liu Q, Wang F, Lin X, Zhao Q, Liu J, Li J. Integrated strategy of differentially expressed genes associated with ulcerative colitis. Mol Med Rep 2017; 16:7479-7489. [PMID: 28944823 PMCID: PMC5865879 DOI: 10.3892/mmr.2017.7509] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 07/11/2017] [Indexed: 12/23/2022] Open
Abstract
Ulcerative colitis (UC) is a chronic inflammatory bowel disease that is associated with both genetic and environmental factors; however, the underlying pathogenesis of UC remains unclear. The present study aimed to further explore 12 microarray datasets from patients with UC obtained from the Gene Expression Omnibus repository, for potential genetic pathogenesis of UC through a global bioinformatics view, which included identification of differentially expressed genes (DEGs), functional enrichments, protein-protein interactions, transcriptional and post-transcriptional regulation and drug-gene associations. This integrated analysis screened 233 DEGs that were compared between UC and normal control tissue samples; these included 173 upregulated and 60 downregulated DEGs. Subsequently, transcription factors, such as TATA-binding protein 1 (TBP1; hsa_TATAAA_V$TATA_01) and nuclear factor-κB (NF-κB; hsa_V$NFKAPPAB_01) and microRNAs (miRNAs; such as miR-516-3p and miR-23a) were revealed to be associated with 233 DEGs. Notably, further analysis indicated that these DEGs were enriched in certain diseases, including inflammation, fibrosis and immune system diseases, and were also associated with some drugs, including prednisone, collagenase and mycophenolate mofetil, which may provide choice for treatment of UC. In conclusion, this study may provide novel insights into discovering potential molecular targets involved in the pathogenesis and treatment of UC.
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Affiliation(s)
- Juerong Feng
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, Hubei 430071, P.R. China
| | - Qian Gao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, Hubei 430071, P.R. China
| | - Qing Liu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, Hubei 430071, P.R. China
| | - Fan Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, Hubei 430071, P.R. China
| | - Xue Lin
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, Hubei 430071, P.R. China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, Hubei 430071, P.R. China
| | - Jing Liu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, Hubei 430071, P.R. China
| | - Jin Li
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, Hubei 430071, P.R. China
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Epigenetic Changes in Chronic Inflammatory Diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 106:139-189. [DOI: 10.1016/bs.apcsb.2016.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Gould NJ, Davidson KL, Nwokolo CU, Arasaradnam RP. A systematic review of the role of DNA methylation on inflammatory genes in ulcerative colitis. Epigenomics 2016; 8:667-84. [PMID: 27096966 DOI: 10.2217/epi-2016-0006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Ulcerative colitis (UC) is an idiopathic disease of the large intestine with evidence pointing to the role of epigenetic changes. METHODS Searches were performed in three databases (EMBASE, MEDLINE and Web of Science), following PRISMA protocol. DNA methylation was the only epigenetic mechanism affecting genes linked to inflammatory response in UC. RESULTS A total of 25 differentially methylated inflammatory genes were identified. Hypermethylation of miR-1247 significantly correlates (p = 0.0006) with refractory UC while PAR2 hypermethylation correlates (p = 0.007) with corticosteroid dependence. CONCLUSION Evidence points to a step-wise increase in methylation status of the genome between a healthy colon, quiescent UC and when inflamed. Inflammatory genes (which are aberrantly methylated), have also been implicated in cancer development in UC.
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Affiliation(s)
| | | | - Chuka U Nwokolo
- Department of Gastroenterology, University Hospital Coventry & Warwickshire, CV2 2DX, UK
| | - Ramesh P Arasaradnam
- Department of Gastroenterology, University Hospital Coventry & Warwickshire, CV2 2DX, UK.,Clinical Sciences Research Institute, University Hospital Coventry & Warwickshire, CV2 2DX, UK
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Grgurevic L, Christensen GL, Schulz TJ, Vukicevic S. Bone morphogenetic proteins in inflammation, glucose homeostasis and adipose tissue energy metabolism. Cytokine Growth Factor Rev 2015; 27:105-18. [PMID: 26762842 DOI: 10.1016/j.cytogfr.2015.12.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/10/2015] [Accepted: 12/23/2015] [Indexed: 12/13/2022]
Abstract
Bore morphogenetic proteins (BMPs) are members of the transforming growth factor (TGF)-β superfamily, a group of secreted proteins that regulate embryonic development. This review summarizes the effects of BMPs on physiological processes not exclusively linked to the musculoskeletal system. Specifically, we focus on the involvement of BMPs in inflammatory disorders, e.g. fibrosis, inflammatory bowel disease, anchylosing spondylitis, rheumatoid arthritis. Moreover, we discuss the role of BMPs in the context of vascular disorders, and explore the role of these signalling proteins in iron homeostasis (anaemia, hemochromatosis) and oxidative damage. The second and third parts of this review focus on BMPs in the development of metabolic pathologies such as type-2 diabetes mellitus and obesity. The pancreatic beta cells are the sole source of the hormone insulin and BMPs have recently been implicated in pancreas development as well as control of adult glucose homeostasis. Lastly, we review the recently recognized role of BMPs in brown adipose tissue formation and their consequences for energy expenditure and adiposity. In summary, BMPs play a pivotal role in metabolism beyond their role in skeletal homeostasis. However, increased understanding of these pleiotropic functions also highlights the necessity of tissue-specific strategies when harnessing BMP action as a therapeutic target.
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Affiliation(s)
- Lovorka Grgurevic
- University of Zagreb School of Medicine, Center for Translational and Clinical Research, Laboratory for Mineralized Tissues, Zagreb, Croatia
| | | | - Tim J Schulz
- German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany; German Center for Diabetes Research (DZD), München-Neuherberg, Germany.
| | - Slobodan Vukicevic
- University of Zagreb School of Medicine, Center for Translational and Clinical Research, Laboratory for Mineralized Tissues, Zagreb, Croatia.
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Singh T, Levine AP, Smith PJ, Smith AM, Segal AW, Barrett JC. Characterization of expression quantitative trait loci in the human colon. Inflamm Bowel Dis 2015. [PMID: 25569741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
BACKGROUND Many genetic risk loci have been identified for inflammatory bowel disease and colorectal cancer; however, identifying the causal genes for each association signal remains a challenge. Expression quantitative trait loci (eQTL) studies have identified common variants that induce differential gene expression and eQTLs can be cross-referenced with disease association signals for gene prioritization. However, the genetics of gene expression are highly tissue-specific, and further eQTL datasets from primary tissues are needed. METHODS We have conducted an eQTL discovery study using tissue extracted endoscopically from the terminal ileum and 4 colonic locations of non-inflamed bowel from 65 controls and patients with quiescent inflammatory bowel disease. A genome-wide cis-eQTL analysis was performed on >3,600,000 variants and 13,558 expressed probes. RESULTS We identified 1312 independent eQTLs associated with the differential expression of 1222 genes in rectal mucosa. One hundred seventy-one, 211, 168, and 102 independent eQTLs were identified in the sigmoid, descending colon, ascending colon, and terminal ileum, respectively. Twenty-six percent of genes with rectal eQTLs were novel and unique compared with 7 published eQTL datasets. Rectal eQTLs were significantly enriched for genes expressed in the colon. Examining 163 inflammatory bowel disease risk loci identified 11 tag single-nucleotide polymorphisms that were rectal eQTLs. A colorectal cancer locus at 11q23 contained a rectal eQTL for COLCA2, a protein implicated in colon cancer pathogenesis. CONCLUSIONS This study defines a catalog of ileal and colonic eQTLs. Our data reaffirm the tissue specificity of eQTLs and support the notion that identification of functional variants in relevant tissue can be effective in fine-mapping genetic risk loci.
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Affiliation(s)
- Tarjinder Singh
- *Medical Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom; †Division of Medicine, University College London, London, United Kingdom; ‡Department of Gastroenterology, University College London Hospitals NHS Foundation Trust, London, United Kingdom; and §Eastman Dental Institute, University College London, London, United Kingdom
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Abstract
BACKGROUND Many genetic risk loci have been identified for inflammatory bowel disease and colorectal cancer; however, identifying the causal genes for each association signal remains a challenge. Expression quantitative trait loci (eQTL) studies have identified common variants that induce differential gene expression and eQTLs can be cross-referenced with disease association signals for gene prioritization. However, the genetics of gene expression are highly tissue-specific, and further eQTL datasets from primary tissues are needed. METHODS We have conducted an eQTL discovery study using tissue extracted endoscopically from the terminal ileum and 4 colonic locations of non-inflamed bowel from 65 controls and patients with quiescent inflammatory bowel disease. A genome-wide cis-eQTL analysis was performed on >3,600,000 variants and 13,558 expressed probes. RESULTS We identified 1312 independent eQTLs associated with the differential expression of 1222 genes in rectal mucosa. One hundred seventy-one, 211, 168, and 102 independent eQTLs were identified in the sigmoid, descending colon, ascending colon, and terminal ileum, respectively. Twenty-six percent of genes with rectal eQTLs were novel and unique compared with 7 published eQTL datasets. Rectal eQTLs were significantly enriched for genes expressed in the colon. Examining 163 inflammatory bowel disease risk loci identified 11 tag single-nucleotide polymorphisms that were rectal eQTLs. A colorectal cancer locus at 11q23 contained a rectal eQTL for COLCA2, a protein implicated in colon cancer pathogenesis. CONCLUSIONS This study defines a catalog of ileal and colonic eQTLs. Our data reaffirm the tissue specificity of eQTLs and support the notion that identification of functional variants in relevant tissue can be effective in fine-mapping genetic risk loci.
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Lu B, Yu WG, Yan J, Wu GD, Li L. Effect of γ-aminobutyric acid on isolated colonic smooth muscle from rats with experimental ulcerative colitis. Shijie Huaren Xiaohua Zazhi 2014; 22:4907-4914. [DOI: 10.11569/wcjd.v22.i32.4907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To assess the effect of γ-aminobutyric acid (GABA) on isolated colonic smooth muscle from rats with experimental ulcerative colitis (UC).
METHODS: Seventeen Wistar rats were randomly divided into either a normal group (six rats) or a model group (eleven rats). The normal group was given distilled water, while the model group was given distilled water containing 3% dextran sulfate 5000. The body mass of the rats and the character of the stool were observed every day, and the disease active index (DIA) was scored. Nine days later, all the rats were killed to observe the changes of the gross morphology and the pathologic changes of the colon under a microscope by taking tissue specimens from serious lesion sites for HE staining. Meanwhile, colonic smooth muscle was isolated to observe the effect of muscimol, a receptor agonist of the GABA and GABAA, bicuculline, an antagonist of the GABAA, and baclofen, a receptor antagonist of the GABAB on the isolated colonic smooth muscle using isometric tension as an indicator.
RESULTS: After four days of treatment with dextran sulfate 5000, the character of the stool of rats in the model group changed, with 30% of rats showing loose stool and 70% showing diarrhea. After six days, about 40% of rats had obvious bloody stool and an obvious decrease in activity and eating. In rats of the normal group, gross pathological examination revealed that the colon had no adhesion, the mucosa had mild hyperemia but no ulcers; microscopic pathological examination revealed intact tissue structure and regularly arranged glands. In rats of the model group, the number of glands decreased, the tissue structure was disorderly, the mucosa was erosive, bleeding, necrotic, and had large deep ulcers. Compared with the normal group, the DIA (3.83 ± 2.74 vs 1.23 ± 1.62, P < 0.05) and histopathologic score (2.52 ± 1.36 vs 0.41 ± 0.74, P < 0.05) were increased significantly in the model group. Treatment with GABA significantly inhibited the independent contraction activities of the isolated colonic smooth muscle from rats of both the normal and model groups (P < 0.05). Treatment with GABA at 0.01 mmol/L and 100 mmol/L resulted in inhibition rates of 20.00% ± 0.02% and 67.60% ± 0.03%, respectively, for the normal group, and 19.50% ± 0.02% and 64.50% ± 0.05% for the model group. There were no significant differences in the above inhibition rates between the two groups (P > 0.05). Treatment with 0.01 mmol/L bicuculline increased the contractile tension of the isolated colonic smooth muscle of the rats (1.25 g ± 0.03 g vs 0.77 g ± 0.04 g, P < 0.05), but treatment with 0.01 mmol/L muscimol or 0.01 mmol/L baclofen decreased the contractile tension significantly (0.38 g ± 0.03 g vs 0.75 g ± 0.06 g, P < 0.05; 0.45 g ± 0.05 g vs 0.75 g ± 0.04 g, P < 0.05).
CONCLUSION: GABA has inhibitory effects on the contraction of the isolated colonic smooth muscle of rats. There exist GABAA and GABAB in the isolated colonic smooth muscle of rats, and GABA has inhibitory effects on the muscle contraction when acting on GABAA, but has stimulating effects when acting on GABAB.
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