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de Ponthaud C, Abdalla S, Belot MP, Shao X, Penna C, Brouquet A, Bougnères P. Increased CpG methylation at the CDH1 locus in inflamed ileal mucosa of patients with Crohn disease. Clin Epigenetics 2024; 16:28. [PMID: 38355645 PMCID: PMC10865720 DOI: 10.1186/s13148-024-01631-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND E-cadherin, a major actor of cell adhesion in the intestinal barrier, is encoded by the CDH1 gene associated with susceptibility to Crohn Disease (CD) and colorectal cancer. Since epigenetic mechanisms are suspected to contribute to the multifactorial pathogenesis of CD, we studied CpG methylation at the CDH1 locus. The methylation of the CpG island (CGI) and of the 1st enhancer, two critical regulatory positions, was quantified in surgical specimens of inflamed ileal mucosa and in peripheral blood mononuclear cells (PBMC) of 21 CD patients. Sixteen patients operated on for a non-inflammatory bowel disease, although not normal controls, provided a macroscopically normal ileal mucosa and PBMC for comparison. RESULTS In ileal mucosa, 19/21 (90%) CD patients vs 8/16 control patients (50%) (p < 0.01) had a methylated CDH1 promoter CGI. In PBMC, CD patients with methylated CGI were 11/21 (52%) vs 7/16 controls (44%), respectively. Methylation in the 1st enhancer of CDH1 was also higher in the CD group for each of the studied CpGs and for their average value (45 ± 17% in CD patients vs 36 ± 17% in controls; p < 0.001). Again, methylation was comparable in PBMC. Methylation of CGI and 1st enhancer were not correlated in mucosa or PBMC. CONCLUSIONS Methylation of several CpGs at the CDH1 locus was increased in the inflamed ileal mucosa, not in the PBMC, of CD patients, suggesting the association of CDH1 methylation with ileal inflammation. Longitudinal studies will explore if this increased methylation is a risk marker for colorectal cancer.
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Affiliation(s)
- Charles de Ponthaud
- Department of Visceral and Digestive Surgery, Hôpital Bicêtre AP-HP, Paris Saclay University, 94276, Le Kremlin-Bicêtre Cedex, France
- UMR INSERM 1169 and Université Paris Saclay, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France
| | - Solafah Abdalla
- Department of Visceral and Digestive Surgery, Hôpital Bicêtre AP-HP, Paris Saclay University, 94276, Le Kremlin-Bicêtre Cedex, France
- UMR INSERM 1169 and Université Paris Saclay, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France
| | - Marie-Pierre Belot
- Groupe d'Études sur le Diabète, l'Obésité, la Croissance, GETDOC, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France
| | - Xiaojian Shao
- Digital Technologies Research Center, National Research Council Canada, Ottawa, ON, K1A 0R6, Canada
| | - Christophe Penna
- Department of Visceral and Digestive Surgery, Hôpital Bicêtre AP-HP, Paris Saclay University, 94276, Le Kremlin-Bicêtre Cedex, France
| | - Antoine Brouquet
- Department of Visceral and Digestive Surgery, Hôpital Bicêtre AP-HP, Paris Saclay University, 94276, Le Kremlin-Bicêtre Cedex, France
| | - Pierre Bougnères
- UMR INSERM 1169 and Université Paris Saclay, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France.
- Groupe d'Études sur le Diabète, l'Obésité, la Croissance, GETDOC, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France.
- MIRCEN Institute, CEA Paris-Saclay/site de Fontenay-aux-Roses, Bâtiment 56 PC 103, 18 route du Panorama, BP6 92265, Fontenay-aux-Roses Cedex, France.
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Levic DS, Niedzwiecki D, Kandakatla A, Karlovich NS, Juneja A, Park J, Stolarchuk C, Adams S, Willer JR, Schaner MR, Lian G, Beasley C, Marjoram L, Flynn AD, Valentine JF, Onken JE, Sheikh SZ, Davis EE, Evason KJ, Garman KS, Bagnat M. TNF promoter hypomethylation is associated with mucosal inflammation in IBD and anti-TNF response. medRxiv 2024:2024.02.05.24302343. [PMID: 38370739 PMCID: PMC10871362 DOI: 10.1101/2024.02.05.24302343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Background and aims Inflammatory Bowel Diseases (IBD) are chronic inflammatory conditions influenced heavily by environmental factors. DNA methylation is a form of epigenetic regulation linking environmental stimuli to gene expression changes and inflammation. Here, we investigated how DNA methylation of the TNF promoter differs between inflamed and uninflamed mucosa of IBD patients, including anti-TNF responders and non-responders. Methods We obtained mucosal biopsies from 200 participants (133 IBD and 67 controls) and analyzed TNF promoter methylation using bisulfite sequencing, comparing inflamed with uninflamed segments, in addition to paired inflamed/uninflamed samples from individual patients. We conducted similar analyses on purified intestinal epithelial cells from bowel resections. We also compared TNF methylation levels of inflamed and uninflamed mucosa from a separate cohort of 15 anti-TNF responders and 17 non-responders. Finally, we sequenced DNA methyltransferase genes to identify rare variants in IBD patients and functionally tested them using rescue experiments in a zebrafish genetic model of DNA methylation deficiency. Results TNF promoter methylation levels were decreased in inflamed mucosa of IBD patients and correlated with disease severity. Isolated IECs from inflamed tissue showed proportional decreases in TNF methylation. Anti-TNF non-responders showed lower levels of TNF methylation than responders in uninflamed mucosa. Our sequencing analysis revealed two missense variants in DNMT1, one of which had reduced function in vivo. Conclusions Our study reveals an association of TNF promoter hypomethylation with mucosal inflammation, suggesting that IBD patients may be particularly sensitive to inflammatory environmental insults affecting DNA methylation. Together, our analyses indicate that TNF promoter methylation analysis may aid in the characterization of IBD status and evaluation of anti-TNF therapy response.
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Affiliation(s)
- Daniel S. Levic
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Donna Niedzwiecki
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Apoorva Kandakatla
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC, USA
| | - Norah S. Karlovich
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC, USA
| | - Arjun Juneja
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Jieun Park
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Christina Stolarchuk
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC, USA
| | - Shanté Adams
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
| | - Jason R. Willer
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
| | - Matthew R. Schaner
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Grace Lian
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caroline Beasley
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Ann D. Flynn
- Division of Gastroenterology, Hepatology and Nutrition, University of Utah Health, Salt Lake City, Utah
| | - John F. Valentine
- Division of Gastroenterology, Hepatology and Nutrition, University of Utah Health, Salt Lake City, Utah
| | - Jane E. Onken
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC, USA
| | - Shehzad Z. Sheikh
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erica E. Davis
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA
| | - Kimberley J. Evason
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Katherine S. Garman
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC, USA
| | - Michel Bagnat
- Department of Cell Biology, Duke University, Durham, NC, USA
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Yan Ang Q, Plichta D, Kim S, Hyun-A Kim I, Gregory S, Xia Y, Lau H, Xavier R, Ananthakrishnan AN. Differential Impact of Smoking on Methylome and Transcriptome in Crohn's Disease and Ulcerative Colitis. Inflamm Bowel Dis 2023:izad268. [PMID: 38001042 DOI: 10.1093/ibd/izad268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Indexed: 11/26/2023]
Abstract
BACKGROUND Smoking is an environmental factor that differentially impacts Crohn's disease (CD) and ulcerative colitis (UC). The mechanism of impact of smoking on disease risk and clinical outcomes remains to be established. METHODS This study used a prospective cohort of patients with CD or UC. Self-reported smoking status was validated using serum cotinine measurement. We profiled methylation changes in peripheral blood using the Illumina Methylation BeadChip. Transcriptomic profiling was performed on ileal and colonic tissue using an Illumina TruSeq platform. We compared the methylation and transcriptional changes in current, former, and never smokers stratified by disease type. RESULTS Our cohort included 200 patients with CD or UC with methylation profiles and 160 with transcriptomic data. The mean serum cotinine level was higher in current compared with former or never smokers. Epigenetic changes common to both CD and UC included hypomethylation at AHRR. Smoking-associated MGAT3 hypomethylation was associated with severe disease course only in UC, while IER3 hypomethylation was associated with worse course only in CD. Smoking downregulated several inflammatory pathways in UC. Current smoking in CD but not in UC was associated with upregulation of several genes mediating Paneth cell function. Genes with opposite direction of effects in CD and UC include HSD3B2 and GSTA1. CONCLUSIONS Our findings suggest both common and differential effects of cigarette smoking on CD and UC. Paneth cell dysfunction may mediate adverse impact of smoking on CD. Bile acid and oxidative stress pathways may be relevant for the differential effect of smoking on CD and UC.
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Affiliation(s)
| | | | - Sean Kim
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Iris Hyun-A Kim
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Sadie Gregory
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Yan Xia
- Broad Institute, Cambridge, MA, USA
| | - Helena Lau
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Ramnik Xavier
- Broad Institute, Cambridge, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
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Sun Z, Braga-Neto MB, Xiong Y, Bhagwate AV, Gibbons HR, Sagstetter MR, Hamdan FH, Baheti S, Friton J, Nair A, Ye Z, Faubion WA. Hypomethylation and Overexpression of Th17-Associated Genes is a Hallmark of Intestinal CD4+ Lymphocytes in Crohn's Disease. J Crohns Colitis 2023; 17:1847-1857. [PMID: 37280154 PMCID: PMC10673812 DOI: 10.1093/ecco-jcc/jjad093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 04/14/2023] [Accepted: 06/06/2023] [Indexed: 06/08/2023]
Abstract
BACKGROUND The development of Crohn's disease [CD] involves immune cell signalling pathways regulated by epigenetic modifications. Aberrant DNA methylation has been identified in peripheral blood and bulk intestinal tissue from CD patients. However, the DNA methylome of disease-associated intestinal CD4+ lymphocytes has not been evaluated. MATERIALS AND METHODS Genome-wide DNA methylation sequencing was performed from terminal ileum CD4+ cells from 21 CD patients and 12 age- and sex-matched controls. Data were analysed for differentially methylated CpGs [DMCs] and methylated regions [DMRs]. Integration was performed with RNA-sequencing data to evaluate the functional impact of DNA methylation changes on gene expression. DMRs were overlapped with regions of differentially open chromatin [by ATAC-seq] and CCCTC-binding factor [CTCF] binding sites [by ChIP-seq] between peripherally derived Th17 and Treg cells. RESULTS CD4+ cells in CD patients had significantly increased DNA methylation compared to those from the controls. A total of 119 051 DMCs and 8113 DMRs were detected. While hypermethylated genes were mostly related to cell metabolism and homeostasis, hypomethylated genes were significantly enriched within the Th17 signalling pathway. The differentially enriched ATAC regions in Th17 cells [compared to Tregs] were hypomethylated in CD patients, suggesting heightened Th17 activity. There was significant overlap between hypomethylated DNA regions and CTCF-associated binding sites. CONCLUSIONS The methylome of CD patients shows an overall dominant hypermethylation yet hypomethylation is more concentrated in proinflammatory pathways, including Th17 differentiation. Hypomethylation of Th17-related genes associated with areas of open chromatin and CTCF binding sites constitutes a hallmark of CD-associated intestinal CD4+ cells.
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Affiliation(s)
- Zhifu Sun
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Manuel B Braga-Neto
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuning Xiong
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Adytia V Bhagwate
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Hunter R Gibbons
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Mary R Sagstetter
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Feda H Hamdan
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Saurabh Baheti
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jessica Friton
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Asha Nair
- Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenqing Ye
- Greehey Children’s Cancer Research Institute, UT Health Science Center San Antonio, San Antonio, TX 78229, USA
| | - William A Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
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Ahmad S, Sands M, Greenberg E, Tangen L, Huang J, Irudayaraj JMK. Mucosal DNA methylome alteration in Crohn's disease: surgical and non-surgical groups. Front Genet 2023; 14:1244513. [PMID: 38046046 PMCID: PMC10691104 DOI: 10.3389/fgene.2023.1244513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/09/2023] [Indexed: 12/05/2023] Open
Abstract
Crohn's disease (CD) is characterized as a chronic, relapsing, and progressive disorder with a complex etiology involving interactions between host, microbiome, and the external environment. Genome wide association studies (GWAS) suggest several genetic variations in the diseased individuals but that explains only a small proportion of susceptibility to disease conditions. This indicates the possible role of epigenome which links environmental factors to the genetic variation in the disease etiology. The current study is focused on the DNA methylome evolution with disease progression. We performed Reduced Representation Bisulfite Sequencing (RRBS) to analyze differential DNA methylation in the diseased and healthy mucosal tissues of 2 different groups of CD patients: non-surgical and surgical, categorized based on the severity of disease and standard of care needed. Patients in both groups have unique DNA methylation signature compared to the healthy tissue. After removing single nucleotide polymorphisms (SNPs), 1,671 differentially methylated loci were found in the non-surgical and 3,334 in the surgical group of which only 206 were found overlapping in both groups. Furthermore, differential DNA methylation was noted in some of the GWAS associated genes implicated in CD. Also, functional enrichment analysis showed high representation of several key pathways where differential methylations were observed, and these can be implicated in CD pathogenesis. We identified specific DNA methylation patterns in the mucosal DNA of surgical and non-surgical CD patients which indicates evolution of the methylome as the disease progresses from initial to the advance stage. These unique patterns can be used as DNA methylation signatures to identify different stages of the disease.
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Affiliation(s)
- Saeed Ahmad
- Biomedical Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL, United States
- Department of Bioengineering, University of Illinois Urbana-Champaign, Champaign, IL, United States
| | - Mia Sands
- Biomedical Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL, United States
- Department of Bioengineering, University of Illinois Urbana-Champaign, Champaign, IL, United States
| | - Eugene Greenberg
- Digestive Health Institute, Carle Foundation Hospital, Urbana, IL, United States
| | - Lyn Tangen
- Digestive Health Institute, Carle Foundation Hospital, Urbana, IL, United States
| | - Jiacheng Huang
- Biomedical Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL, United States
- Department of Bioengineering, University of Illinois Urbana-Champaign, Champaign, IL, United States
| | - Joseph Maria Kumar Irudayaraj
- Biomedical Research Center, Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL, United States
- Department of Bioengineering, University of Illinois Urbana-Champaign, Champaign, IL, United States
- Carl Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Champaign, IL, United States
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Champaign, IL, United States
- Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Champaign, IL, United States
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Kamal S, Parkash N, Beattie W, Christensen B, Segal JP. Are We Ready to Reclassify Crohn's Disease Using Molecular Classification? J Clin Med 2023; 12:5786. [PMID: 37762727 PMCID: PMC10532006 DOI: 10.3390/jcm12185786] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/21/2023] [Accepted: 09/02/2023] [Indexed: 09/29/2023] Open
Abstract
Crohn's disease (CD) is a type of inflammatory bowel disease. The number of IBD cases worldwide was estimated to be 4.9 million in 2019. CD exhibits heterogeneity in clinical presentation, anatomical involvement, disease behaviour, clinical course and response to treatment. The classical description of CD involves transmural inflammation with skip lesions anywhere along the entire gastrointestinal tract. The complexity and heterogeneity of Crohn's disease is not currently reflected in the conventional classification system. Though the knowledge of Crohn's pathophysiology remains far from understood, the established complex interplay of the omics-genomics, transcriptomics, proteomics, epigenomics, metagenomics, metabolomics, lipidomics and immunophenomics-provides numerous targets for potential molecular markers of disease. Advancing technology has enabled identification of small molecules within these omics, which can be extrapolated to differentiate types of Crohn's disease. The multi-omic future of Crohn's disease is promising, with potential for advancements in understanding of its pathogenesis and implementation of personalised medicine.
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Affiliation(s)
- Shahed Kamal
- Department of Gastroenterology, Northern Hospital, Epping, Melbourne VIC 3076, Australia
| | - Nikita Parkash
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
| | - William Beattie
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
| | - Britt Christensen
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
- Department of Gastroenterology, The University of Melbourne, Parkville, Melbourne VIC 3010, Australia
| | - Jonathan P. Segal
- Department of Gastroenterology, Royal Melbourne Hospital, Parkville, Melbourne VIC 3052, Australia
- Department of Gastroenterology, The University of Melbourne, Parkville, Melbourne VIC 3010, Australia
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Meng G, Monaghan TM, Duggal NA, Tighe P, Peerani F. Microbial-Immune Crosstalk in Elderly-Onset Inflammatory Bowel Disease: Unchartered Territory. J Crohns Colitis 2023; 17:1309-1325. [PMID: 36806917 DOI: 10.1093/ecco-jcc/jjad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Indexed: 02/23/2023]
Abstract
Elderly-onset inflammatory bowel disease [IBD] patients exhibit a distinct natural history compared to younger IBD patients, with unique disease phenotypes, differential responses to therapy, and increased surgical morbidity and mortality. Despite the foreseeable high demand for personalized medicine and specialized IBD care in the elderly, current paradigms of IBD management fail to capture the required nuances of care for elderly-onset IBD patients. Our review postulates the roles of systemic and mucosal immunosenescence, inflammageing and a dysbiotic microbial ecosystem in the pathophysiology of elderly-onset IBD. Ultimately, a better understanding of elderly-onset IBD can lead to improved patient outcomes and the tailoring of future preventative and treatment strategies.
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Affiliation(s)
- Guanmin Meng
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Tanya M Monaghan
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - Niharika A Duggal
- MRC-Arthritis Research UK Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Paddy Tighe
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Farhad Peerani
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
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Ventham NT, Kennedy NA, Kalla R, Adams AT, Noble A, Ennis H, Mowat C, Dunlop MG, Satsangi J. Genome-Wide Methylation Profiling in 229 Patients With Crohn's Disease Requiring Intestinal Resection: Epigenetic Analysis of the Trial of Prevention of Post-operative Crohn's Disease (TOPPIC). Cell Mol Gastroenterol Hepatol 2023; 16:431-450. [PMID: 37331566 PMCID: PMC10372903 DOI: 10.1016/j.jcmgh.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/20/2023]
Abstract
BACKGROUND & AIMS DNA methylation alterations may provide important insights into gene-environment interaction in cancer, aging, and complex diseases, such as inflammatory bowel disease (IBD). We aim first to determine whether the circulating DNA methylome in patients requiring surgery may predict Crohn's disease (CD) recurrence following intestinal resection; and second to compare the circulating methylome seen in patients with established CD with that we had reported in a series of inception cohorts. METHODS TOPPIC was a placebo-controlled, randomized controlled trial of 6-mercaptopurine at 29 UK centers in patients with CD undergoing ileocolic resection between 2008 and 2012. Genomic DNA was extracted from whole blood samples from 229 of the 240 patients taken before intestinal surgery and analyzed using 450KHumanMethylation and Infinium Omni Express Exome arrays (Illumina, San Diego, CA). Coprimary objectives were to determine whether methylation alterations may predict clinical disease recurrence; and to assess whether the epigenetic alterations previously reported in newly diagnosed IBD were present in the patients with CD recruited into the TOPPIC study. Differential methylation and variance analysis was performed comparing patients with and without clinical evidence of recurrence. Secondary analyses included investigation of methylation associations with smoking, genotype (MeQTLs), and chronologic age. Validation of our previously published case-control observation of the methylome was performed using historical control data (CD, n = 123; Control, n = 198). RESULTS CD recurrence in patients following surgery is associated with 5 differentially methylated positions (Holm P < .05), including probes mapping to WHSC1 (P = 4.1 × 10-9, Holm P = .002) and EFNA3 (P = 4.9 × 10-8, Holm P = .02). Five differentially variable positions are demonstrated in the group of patients with evidence of disease recurrence including a probe mapping to MAD1L1 (P = 6.4 × 10-5). DNA methylation clock analyses demonstrated significant age acceleration in CD compared with control subjects (GrimAge + 2 years; 95% confidence interval, 1.2-2.7 years), with some evidence for accelerated aging in patients with CD with disease recurrence following surgery (GrimAge +1.04 years; 95% confidence interval, -0.04 to 2.22). Significant methylation differences between CD cases and control subjects were seen by comparing this cohort in conjunction with previously published control data, including validation of our previously described differentially methylated positions (RPS6KA2 P = 1.2 × 10-19, SBNO2 = 1.2 × 10-11) and regions (TXK [false discovery rate, P = 3.6 × 10-14], WRAP73 [false discovery rate, P = 1.9 × 10-9], VMP1 [false discovery rate, P = 1.7 × 10-7], and ITGB2 [false discovery rate, P = 1.4 × 10-7]). CONCLUSIONS We demonstrate differential methylation and differentially variable methylation in patients developing clinical recurrence within 3 years of surgery. Moreover, we report replication of the CD-associated methylome, previously characterized only in adult and pediatric inception cohorts, in patients with medically refractory disease needing surgery.
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Affiliation(s)
- Nicholas T Ventham
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom.
| | - Nicholas A Kennedy
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Rahul Kalla
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Alex T Adams
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Alexandra Noble
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Holly Ennis
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Craig Mowat
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Malcolm G Dunlop
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
| | - Jack Satsangi
- Centre for Genomic and Experimental Medicine, The University of Edinburgh, Edinburgh, Midlothian, United Kingdom
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9
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Jarmakiewicz-Czaja S, Sokal A, Ferenc K, Motyka E, Helma K, Filip R. The Role of Genetic and Epigenetic Regulation in Intestinal Fibrosis in Inflammatory Bowel Disease: A Descending Process or a Programmed Consequence? Genes (Basel) 2023; 14:1167. [PMID: 37372347 DOI: 10.3390/genes14061167] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Inflammatory bowel diseases (IBDs) are a group of chronic diseases characterized by recurring periods of exacerbation and remission. Fibrosis of the intestine is one of the most common complications of IBD. Based on current analyses, it is evident that genetic factors and mechanisms, as well as epigenetic factors, play a role in the induction and progression of intestinal fibrosis in IBD. Key genetic factors and mechanisms that appear to be significant include NOD2, TGF-β, TLRs, Il23R, and ATG16L1. Deoxyribonucleic acid (DNA) methylation, histone modification, and ribonucleic acid (RNA) interference are the primary epigenetic mechanisms. Genetic and epigenetic mechanisms, which seem to be important in the pathophysiology and progression of IBD, may potentially be used in targeted therapy in the future. Therefore, the aim of this study was to gather and discuss selected mechanisms and genetic factors, as well as epigenetic factors.
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Affiliation(s)
| | - Aneta Sokal
- Institute of Health Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Katarzyna Ferenc
- Institute of Medicine, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Elżbieta Motyka
- Centre for Innovative Research in Medical and Natural Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Kacper Helma
- Institute of Health Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Rafał Filip
- Institute of Medicine, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
- Department of Gastroenterology with IBD, Clinical Hospital No. 2 im. Św. Jadwigi Królowej, 35-301 Rzeszow, Poland
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10
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Venkateswaran S, Somineni HK, Matthews JD, Kilaru V, Hyams JS, Denson LA, Kellamayer R, Gibson G, Cutler DJ, Conneely KN, Smith AK, Kugathasan S. Longitudinal DNA methylation profiling of the rectal mucosa identifies cell-specific signatures of disease status, severity and clinical outcomes in ulcerative colitis cell-specific DNA methylation signatures of UC. Clin Epigenetics 2023; 15:50. [PMID: 36964596 PMCID: PMC10039532 DOI: 10.1186/s13148-023-01462-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 03/07/2023] [Indexed: 03/26/2023] Open
Abstract
BACKGROUND In peripheral blood, DNA methylation (DNAm) patterns in inflammatory bowel disease patients reflect inflammatory status rather than disease status. Here, we examined DNAm in diseased rectal mucosa from ulcerative colitis (UC) patients, focusing on constituent cell types with the goal of identifying therapeutic targets for UC other than the immune system. We profiled DNAm of rectal mucosal biopsies of pediatric UC at diagnosis (n = 211) and non-IBD control (n = 85) patients and performed epigenome-wide association studies (EWAS) of specific cell types to understand DNAm changes in epithelial, immune and fibroblast cells across disease states, course, and clinical outcomes. We also examined longitudinal analysis on follow-up samples (n = 73), and comparisons were made among patients with clinical outcomes including those undergoing colectomy versus those who did not. Additionally, we included RNA-seq from the same subjects to assess the impact of CpG sites on the transcription of nearby genes during the disease course. RESULTS At diagnosis, UC rectal mucosa exhibited a lower proportion of epithelial cells and fibroblasts, and higher proportion of immune cells, in conjunction with variation in the DNAm pattern. While treatment had significant effects on the methylation signature of immune cells, its effects on fibroblasts and epithelial cells were attenuated. Individuals who required colectomy exhibited cell composition and DNAm patterns at follow-up more similar to disease onset than patients who did not require colectomy. Combining these results with gene expression profiles, we identify CpG sites whose methylation patterns are most consistent with a contribution to poor disease outcomes and could thus be potential therapeutic targets. CONCLUSIONS Cell-specific epigenetic changes in the rectal mucosa in UC are associated with disease severity and outcome. Current therapeutics may more effectively target the immune than the epithelial and fibroblast compartments.
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Affiliation(s)
- Suresh Venkateswaran
- Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, 1760 Haygood Drive, W-427, Atlanta, GA, 30322, USA
| | - Hari K Somineni
- Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, 1760 Haygood Drive, W-427, Atlanta, GA, 30322, USA
| | - Jason D Matthews
- Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, 1760 Haygood Drive, W-427, Atlanta, GA, 30322, USA
| | - Varun Kilaru
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children's Medical Center, Hartford, CT, USA
| | - Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Richard Kellamayer
- Section of Pediatric Gastroenterology, Texas Children's Hospital Baylor College of Medicine, Houston, TX, USA
| | - Greg Gibson
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Karen N Conneely
- Department of Human Genetics, Emory University, Atlanta, GA, USA
- Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA
- Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, 1760 Haygood Drive, W-427, Atlanta, GA, 30322, USA.
- Department of Human Genetics, Emory University, Atlanta, GA, USA.
- Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA.
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11
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Joustra V, Hageman IL, Satsangi J, Adams A, Ventham NT, de Jonge WJ, Henneman P, D’Haens GR, Li Yim AYF. Systematic Review and Meta-analysis of Peripheral Blood DNA Methylation Studies in Inflammatory Bowel Disease. J Crohns Colitis 2023; 17:185-198. [PMID: 35998097 PMCID: PMC10024549 DOI: 10.1093/ecco-jcc/jjac119] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND AND AIMS Over the past decade, the DNA methylome has been increasingly studied in peripheral blood of inflammatory bowel disease [IBD] patients. However, a comprehensive summary and meta-analysis of peripheral blood leukocyte [PBL] DNA methylation studies has thus far not been conducted. Here, we systematically reviewed all available literature up to February 2022 and summarized the observations by means of meta-analysis. METHODS We conducted a systematic search and critical appraisal of IBD-associated DNA methylation studies in PBL using the biomarker-based cross-sectional studies [BIOCROSS] tool. Subsequently, we performed meta-analyses on the summary statistics obtained from epigenome-wide association studies [EWAS] that included patients with Crohn's disease [CD], ulcerative colitis [UC] and/or healthy controls [HC]. RESULTS Altogether, we included 15 studies for systematic review. Critical appraisal revealed large methodological and outcome heterogeneity between studies. Summary statistics were obtained from four studies based on a cumulative 552 samples [177 CD, 132 UC and 243 HC]. Consistent differential methylation was identified for 256 differentially methylated probes [DMPs; Bonferroni-adjusted p ≤ 0.05] when comparing CD with HC and 103 when comparing UC with HC. Comparing IBD [CD + UC] with HC resulted in 224 DMPs. Importantly, several of the previously identified DMPs, such as VMP1/TMEM49/MIR21 and RPS6KA2, were consistently differentially methylated across all studies. CONCLUSION Methodological homogenization of IBD epigenetic studies is needed to allow for easier aggregation and independent validation. Nonetheless, we were able to confirm previous observations. Our results can serve as the basis for future IBD epigenetic biomarker research in PBL.
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Affiliation(s)
| | | | - Jack Satsangi
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Alex Adams
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Nicholas T Ventham
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
| | - Wouter J de Jonge
- Amsterdam UMC location University of Amsterdam, Department of Gastroenterology and Hepatology, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, Netherlands
- Amsterdam UMC location University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, Netherlands
| | - Peter Henneman
- Amsterdam UMC location University of Amsterdam, Department of Human Genetics, Genome Diagnostics Laboratory, Amsterdam, Netherlands
- Amsterdam Reproduction & Development, Amsterdam, Netherlands
| | - Geert R D’Haens
- Amsterdam UMC location University of Amsterdam, Department of Gastroenterology and Hepatology, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, Netherlands
| | - Andrew Y F Li Yim
- Corresponding author: Andrew Y. F. Li Yim, Amsterdam UMC location University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, Netherlands.
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12
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Joustra V, Li Yim AYF, Hageman I, Levin E, Adams A, Satsangi J, de Jonge WJ, Henneman P, D'Haens G. Long-term Temporal Stability of Peripheral Blood DNA Methylation Profiles in Patients With Inflammatory Bowel Disease. Cell Mol Gastroenterol Hepatol 2023; 15:869-885. [PMID: 36581079 PMCID: PMC9972576 DOI: 10.1016/j.jcmgh.2022.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/20/2022] [Accepted: 12/20/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND & AIMS There is great current interest in the potential application of DNA methylation alterations in peripheral blood leukocytes (PBLs) as biomarkers of susceptibility, progression, and treatment response in inflammatory bowel disease (IBD). However, the intra-individual stability of PBL methylation in IBD has not been characterized. Here, we studied the long-term stability of all probes located on the Illumina HumanMethylation EPIC BeadChip array. METHODS We followed a cohort of 46 adult patients with IBD (36 Crohn's disease [CD], 10 ulcerative colitis [UC]; median age, 44 years; interquartile range [IQR] 27-56 years; 50% female) that received standard care follow-up at the Amsterdam University Medical Centers. Paired PBL samples were collected at 2 time points with a median of 7 years (range, 2-9 years) in between. Differential methylation and intra-class correlation (ICC) analyses were used to identify time-associated differences and temporally stable CpGs, respectively. RESULTS Around 60% of all EPIC array loci presented poor intra-individual stability (ICC <0.50); 78.114 (≈9%) showed good (ICC, 0.75-0.89), and 41.274 (≈5%) showed excellent (ICC ≥0.90) stability, between both measured time points. Focusing on previously identified consistently differentially methylated positions indicated that 22 CD-, 11 UC-, and 24 IBD-associated loci demonstrated high stability (ICC ≥0.75) over time; of these, we observed a marked stability of CpG loci associated to the HLA genes. CONCLUSIONS Our data provide insight into the long-term stability of the PBL DNA methylome within an IBD context, facilitating the selection of biologically relevant and robust IBD-associated epigenetic biomarkers with increased potential for independent validation. These data also have potential implications in understanding disease pathogenesis.
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Affiliation(s)
- Vincent Joustra
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Andrew Y F Li Yim
- Genome Diagnostics Laboratory, Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Ishtu Hageman
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Evgeni Levin
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands; Horaizon BV, Delft, the Netherlands
| | - Alex Adams
- Oxford University- Hospitals NHS Foundation Trust- John Radcliffe Hospital, Translational Gastroenterology Unit- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Jack Satsangi
- Oxford University- Hospitals NHS Foundation Trust- John Radcliffe Hospital, Translational Gastroenterology Unit- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Wouter J de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Peter Henneman
- Genome Diagnostics Laboratory, Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Geert D'Haens
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.
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Park JM, Kim J, Lee YJ, Bae SU, Lee HW. Inflammatory bowel disease-associated intestinal fibrosis. J Pathol Transl Med 2023; 57:60-66. [PMID: 36623814 PMCID: PMC9846010 DOI: 10.4132/jptm.2022.11.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/02/2022] [Indexed: 01/11/2023] Open
Abstract
Fibrosis is characterized by a proliferation of fibroblasts and excessive extracellular matrix following chronic inflammation, and this replacement of organ tissue with fibrotic tissue causes a loss of function. Inflammatory bowel disease (IBD) is a chronic inflammation of the gastrointestinal tract, and intestinal fibrosis is common in IBD patients, resulting in several complications that require surgery, such as a stricture or penetration. This review describes the pathogenesis and various factors involved in intestinal fibrosis in IBD, including cytokines, growth factors, epithelial-mesenchymal and endothelial-mesenchymal transitions, and gut microbiota. Furthermore, histopathologic findings and scoring systems used for stenosis in IBD are discussed, and differences in the fibrosis patterns of ulcerative colitis and Crohn's disease are compared. Biomarkers and therapeutic agents targeting intestinal fibrosis are briefly mentioned at the end.
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Affiliation(s)
- Ji Min Park
- Department of Pathology, Keimyung University School of Medicine, Daegu,
Korea
| | - Jeongseok Kim
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keimyung University School of Medicine, Daegu,
Korea
| | - Yoo Jin Lee
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keimyung University School of Medicine, Daegu,
Korea
| | - Sung Uk Bae
- Division of Colorectal Surgery, Department of Surgery, Keimyung University School of Medicine, Daegu,
Korea
| | - Hye Won Lee
- Department of Pathology, Keimyung University School of Medicine, Daegu,
Korea
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14
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Fazio A, Bordoni D, Kuiper JWP, Weber-Stiehl S, Stengel ST, Arnold P, Ellinghaus D, Ito G, Tran F, Messner B, Henning A, Bernardes JP, Häsler R, Luzius A, Imm S, Hinrichsen F, Franke A, Huber S, Nikolaus S, Aden K, Schreiber S, Sommer F, Natoli G, Mishra N, Rosenstiel P. DNA methyltransferase 3A controls intestinal epithelial barrier function and regeneration in the colon. Nat Commun 2022; 13:6266. [PMID: 36271073 DOI: 10.1038/s41467-022-33844-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 10/05/2022] [Indexed: 12/25/2022] Open
Abstract
Genetic variants in the DNA methyltransferase 3 A (DNMT3A) locus have been associated with inflammatory bowel disease (IBD). DNMT3A is part of the epigenetic machinery physiologically involved in DNA methylation. We show that DNMT3A plays a critical role in maintaining intestinal homeostasis and gut barrier function. DNMT3A expression is downregulated in intestinal epithelial cells from IBD patients and upon tumor necrosis factor treatment in murine intestinal organoids. Ablation of DNMT3A in Caco-2 cells results in global DNA hypomethylation, which is linked to impaired regenerative capacity, transepithelial resistance and intercellular junction formation. Genetic deletion of Dnmt3a in intestinal epithelial cells (Dnmt3aΔIEC) in mice confirms the phenotype of an altered epithelial ultrastructure with shortened apical-junctional complexes, reduced Goblet cell numbers and increased intestinal permeability in the colon in vivo. Dnmt3aΔIEC mice suffer from increased susceptibility to experimental colitis, characterized by reduced epithelial regeneration. These data demonstrate a critical role for DNMT3A in orchestrating intestinal epithelial homeostasis and response to tissue damage and suggest an involvement of impaired epithelial DNMT3A function in the etiology of IBD.
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Vieujean S, Caron B, Haghnejad V, Jouzeau JY, Netter P, Heba AC, Ndiaye NC, Moulin D, Barreto G, Danese S, Peyrin-Biroulet L. Impact of the Exposome on the Epigenome in Inflammatory Bowel Disease Patients and Animal Models. Int J Mol Sci 2022; 23:7611. [PMID: 35886959 DOI: 10.3390/ijms23147611] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic inflammatory disorders of the gastrointestinal tract that encompass two main phenotypes, namely Crohn’s disease and ulcerative colitis. These conditions occur in genetically predisposed individuals in response to environmental factors. Epigenetics, acting by DNA methylation, post-translational histones modifications or by non-coding RNAs, could explain how the exposome (or all environmental influences over the life course, from conception to death) could influence the gene expression to contribute to intestinal inflammation. We performed a scoping search using Medline to identify all the elements of the exposome that may play a role in intestinal inflammation through epigenetic modifications, as well as the underlying mechanisms. The environmental factors epigenetically influencing the occurrence of intestinal inflammation are the maternal lifestyle (mainly diet, the occurrence of infection during pregnancy and smoking); breastfeeding; microbiota; diet (including a low-fiber diet, high-fat diet and deficiency in micronutrients); smoking habits, vitamin D and drugs (e.g., IBD treatments, antibiotics and probiotics). Influenced by both microbiota and diet, short-chain fatty acids are gut microbiota-derived metabolites resulting from the anaerobic fermentation of non-digestible dietary fibers, playing an epigenetically mediated role in the integrity of the epithelial barrier and in the defense against invading microorganisms. Although the impact of some environmental factors has been identified, the exposome-induced epimutations in IBD remain a largely underexplored field. How these environmental exposures induce epigenetic modifications (in terms of duration, frequency and the timing at which they occur) and how other environmental factors associated with IBD modulate epigenetics deserve to be further investigated.
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Xu HM, Xu J, Yang MF, Liang YJ, Peng QZ, Zhang Y, Tian CM, Nie YQ, Wang LS, Yao J, Li DF. Epigenetic DNA methylation of Zbtb7b regulates the population of double-positive CD4 +CD8 + T cells in ulcerative colitis. J Transl Med 2022; 20:289. [PMID: 35761286 PMCID: PMC9235105 DOI: 10.1186/s12967-022-03477-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/11/2022] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND AND AIMS Ulcerative colitis (UC) is a heterogeneous disorder with complex pathogenesis. Therefore, in the present study, we aimed to assess genome-wide DNA methylation changes associated explicitly with the pathogenesis of UC. METHODS DNA methylation changes were identified by comparing UC tissues with healthy controls (HCs) from the GEO databases. The candidate genes were obtained and verified in clinical samples. Moreover, the underlying molecular mechanism related to Zbtb7b in the pathogenesis of UC was explored using the dextran sodium sulfate (DSS)-induced colitis model. RESULTS Bioinformatic analysis from GEO databases confirmed that Zbtb7b, known as Th-inducing POZ-Kruppel factor (ThPOK), was demethylated in UC tissues. Then, we demonstrated that Zbtb7b was in a hypo-methylation pattern through the DSS-induced colitis model (P = 0.0357), whereas the expression of Zbtb7b at the mRNA and protein levels was significantly up-regulated in the inflamed colonic tissues of UC patients (qRT-PCR, WB, IHC: P < 0.0001, P = 0.0079, P < 0.0001) and DSS-induced colitis model (qRT-PCR, WB, IHC: P < 0.0001, P = 0.0045, P = 0.0004). Moreover, the expression of Zbtb7b was positively associated with the degree of UC activity. Mechanically, over-expression of Zbtb7b might activate the maturation of CD4+T cells (FCM, IF: P = 0.0240, P = 0.0003) and repress the differentiation of double-positive CD4+CD8+T (DP CD4+CD8+T) cells (FCM, IF: P = 0.0247, P = 0.0118), contributing to the production of inflammatory cytokines, such as TNF-α (P = 0.0005, P = 0.0005), IL-17 (P = 0.0014, P = 0.0381), and IFN-γ (P = 0.0016, P = 0.0042), in the serum and colonic tissue of DSS-induced colitis model. CONCLUSIONS Epigenetic DNA hypo-methylation of Zbtb7b activated the maturation of CD4+T cells and repressed the differentiation of DP CD4+CD8+ T cells, resulting in the production of inflammatory cytokines and colonic inflammation in UC. Therefore, Zbtb7b might be a diagnostic and therapeutic biomarker for UC, and hypo-methylation might affect the biological function of Zbtb7b.
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Affiliation(s)
- Hao-Ming Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Yuexiu District, No. 1, Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Jing Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Yuexiu District, No. 1, Panfu Road, Guangzhou, 510180, Guangdong, China
| | - Mei-Feng Yang
- Department of Hematology, Yantian District People's Hospital, Shenzhen, 518020, Guangdong, China
| | - Yu-Jie Liang
- Shenzhen Kangning Hospital, Shenzhen, 518020, Guangdong, China
| | - Quan-Zhou Peng
- Department of Pathology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China
| | - Yuan Zhang
- Department of Medical Administration, Huizhou Institute of Occupational Diseases Control and Prevention, Huizhou, 516000, Guangdong, China
| | - Cheng-Mei Tian
- Department of Emergency, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China
| | - Yu-Qiang Nie
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Yuexiu District, No. 1, Panfu Road, Guangzhou, 510180, Guangdong, China.
| | - Li-Sheng Wang
- Department of Gastroenterology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Luohu District, No. 1017, Dongmen North Road, Shenzhen, 518020, Guangdong, China.
| | - Jun Yao
- Department of Gastroenterology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Luohu District, No. 1017, Dongmen North Road, Shenzhen, 518020, Guangdong, China.
| | - De-Feng Li
- Department of Gastroenterology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Luohu District, No. 1017, Dongmen North Road, Shenzhen, 518020, Guangdong, China.
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Alghoul Z, Yang C, Merlin D. The Current Status of Molecular Biomarkers for Inflammatory Bowel Disease. Biomedicines 2022; 10:1492. [PMID: 35884797 DOI: 10.3390/biomedicines10071492] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 12/12/2022] Open
Abstract
Diagnosis and prognosis of inflammatory bowel disease (IBD)-a chronic inflammation that affects the gastrointestinal tract of patients-are challenging, as most clinical symptoms are not specific to IBD, and are often seen in other inflammatory diseases, such as intestinal infections, drug-induced colitis, and monogenic diseases. To date, there is no gold-standard test for monitoring IBD. Endoscopy and imaging are essential diagnostic tools that provide information about the disease's state, location, and severity. However, the invasive nature and high cost of endoscopy make it unsuitable for frequent monitoring of disease activity in IBD patients, and even when it is possible to replace endoscopy with imaging, high cost remains a concern. Laboratory testing of blood or feces has the advantage of being non-invasive, rapid, cost-effective, and standardizable. Although the specificity and accuracy of laboratory testing alone need to be improved, it is increasingly used to monitor disease activity or to diagnose suspected IBD cases in combination with endoscopy and/or imaging. The literature survey indicates a dearth of summarization of biomarkers for IBD testing. This review introduces currently available non-invasive biomarkers of clinical importance in laboratory testing for IBD, and discusses the trends and challenges in the IBD biomarker studies.
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Nair VS, Heredia M, Samsom J, Huehn J. Impact of gut microenvironment on epigenetic signatures of intestinal T helper cell subsets. Immunol Lett 2022; 246:27-36. [DOI: 10.1016/j.imlet.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/10/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022]
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Xu J, Xu HM, Yang MF, Liang YJ, Peng QZ, Zhang Y, Tian CM, Wang LS, Yao J, Nie YQ, Li DF. New Insights Into the Epigenetic Regulation of Inflammatory Bowel Disease. Front Pharmacol 2022; 13:813659. [PMID: 35173618 PMCID: PMC8841592 DOI: 10.3389/fphar.2022.813659] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/06/2022] [Indexed: 01/10/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the colonic mucosa. Environmental factors, genetics, intestinal microbiota, and the immune system are all involved in the pathophysiology of IBD. Lately, accumulating evidence has shown that abnormal epigenetic changes in DNA methylation, histone markers, and non-coding RNA expression greatly contribute to the development of the entire disease. Epigenetics regulates many functions, such as maintaining the homeostasis of the intestinal epithelium and regulating the immune system of the immune cells. In the present study, we systematically summarized the latest advances in epigenetic modification of IBD and how epigenetics reveals new mechanisms of IBD. Our present review provided new insights into the pathophysiology of IBD. Moreover, exploring the patterns of DNA methylation and histone modification through epigenetics can not only be used as biomarkers of IBD but also as a new target for therapeutic intervention in IBD patients.
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Affiliation(s)
- Jing Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Hao-ming Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Mei-feng Yang
- Department of Hematology, Yantian District People’s Hospital, Shenzhen, China
| | | | - Quan-zhou Peng
- Department of Pathology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Yuan Zhang
- Department of Medical Administration, Huizhou Institute of Occupational Diseases Control and Prevention, Huizhou, China
| | - Cheng-mei Tian
- Department of Emergency, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Li-sheng Wang
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- *Correspondence: De-feng Li, ; Li-sheng Wang, ; Jun Yao, ; Yu-qiang Nie,
| | - Jun Yao
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- *Correspondence: De-feng Li, ; Li-sheng Wang, ; Jun Yao, ; Yu-qiang Nie,
| | - Yu-qiang Nie
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
- *Correspondence: De-feng Li, ; Li-sheng Wang, ; Jun Yao, ; Yu-qiang Nie,
| | - De-feng Li
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- *Correspondence: De-feng Li, ; Li-sheng Wang, ; Jun Yao, ; Yu-qiang Nie,
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20
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Indumathi B, Oruganti SS, Sreenu B, Kutala VK. Association of Promoter Methylation and Expression of Inflammatory Genes IL-6 and TNF-α with the Risk of Coronary Artery Disease in Diabetic and Obese Subjects among Asian Indians. Indian J Clin Biochem 2022; 37:29-39. [PMID: 35125691 PMCID: PMC8799818 DOI: 10.1007/s12291-020-00932-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/01/2020] [Accepted: 10/20/2020] [Indexed: 01/03/2023]
Abstract
The inflammatory cytokines such as interleukin-6 (IL-6) and tumour necrosis factor-alpha (TNF-α) are considered as the most important contributors to the endothelial dysfunction in subjects with type 2 diabetes mellitus (T2DM) and obesity. The hypomethylation of CpG sites in the promoter region of the IL-6 and TNF-α have shown to be associated with the increased expression of IL-6 and TNF-α. However, there are no studies on the methylation and expression of IL-6 and TNF-α with the risk of coronary artery disease (CAD) in subjects with T2DM and obesity in Asian Indians. Hence, the present study was aimed to investigate whether the IL-6, TNF-α promoter methylation and expression in blood leukocyte DNA is associated with the risk of CAD in diabetic and obese subjects in Asian Indians. For this study, we recruited 574 subjects which includes, 207 angiographically confirmed CAD patients, 100 T2DM patients, 82 obese subjects and 185 healthy controls. The methylation status of IL-6 and TNF-α gene loci was determined by methylation specific PCR (MPCR) and gene expression was determined by qPCR. We found significant hypomethylation of IL-6 in CAD and T2DM subjects (OR 1.98 95% CI: 1.32-2.97, p = 0.001, OR: 2.23 95% CI:1.34-3.76, p = 0.001, respectively). Further, a significant increase in the expression of IL-6 in CAD and T2DM subjects (fold change: 26.39 & 14.7, p = 0.0001) compared to the control subjects was observed. A significant increase in the hypomethylation of TNF-α in CAD, T2DM and obese subjects was observed as compared to the control (OR: 2.04 95% CI: 1.36-3.05, p = 0.0005, OR: 1.81 95% CI 1.10-2.96, p = 0.01, and OR: 2.1 95% CI 1.24-3.57, p = 0.007, respectively).We also found an increased expression of TNF-α in CAD, T2DM and obese subjects as compared to controls. In addition, presence of low folate, and hyperhomocysteinemia was observed in the present study, may be the contributing factors for the hypomethylation of IL-6 and TNF-α and oxidative stress. In conclusion, increased expression of IL-6 and TNF-α due to hypomethylation in T2DM and obese individuals may contribute to CAD risk in these subjects. The presence of hyperhomocysteinemia and increased oxidative risk may enhance the CAD risk further.
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Affiliation(s)
- Bobbala Indumathi
- Department of Clinical Pharmacology& Therapeutics, Nizam’s Institute of Medical Sciences, Punjagutta, Hyderabad, India
| | - Sai Satish Oruganti
- Department of Cardiology, Nizam’s Institute of Medical Sciences, Hyderabad, India
| | - Boddupally Sreenu
- Department of Clinical Pharmacology& Therapeutics, Nizam’s Institute of Medical Sciences, Punjagutta, Hyderabad, India
| | - Vijay Kumar Kutala
- Department of Clinical Pharmacology& Therapeutics, Nizam’s Institute of Medical Sciences, Punjagutta, Hyderabad, India
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21
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Feerick CL, McKernan DP. DNA methyltransferase inhibitors increase NOD-like receptor activity and expression in a monocytic cell line. Immunopharmacol Immunotoxicol 2021; 44:99-109. [PMID: 34881658 DOI: 10.1080/08923973.2021.2007264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Background: The intracellular NOD-like receptor (NLR) family of pathogen recognition receptors (PRRa) is involved in initiating the innate immune response of which NOD1 and NOD2 are the best-characterized members. Aberrant expression of NOD1 and NOD2 has been uncovered in a number of chronic inflammatory diseases, such as inflammatory bowel disease and rheumatoid arthritis. However, the mechanism underlying NOD1/NOD2 gene expression regulation is still in its infancy. Epigenetic modifications such as DNA methylation and histone acetylation regulate the expression of genes and alterations in their patterns have been linked to many inflammatory diseases. This study investigated whether epigenetic modifying drugs affect the regulation of NOD1/NOD2 activity and expression. DNA methyltransferase inhibitors have recently been used in the treatment of myelodysplastic syndrome and as combination therapy in cancer but the full extent of their effects has not been quantified.Methods: Pharmacological inhibition of epigenetic enzymes in a human monocytic THP-1 cell line was carried out and NOD1/NOD2 expression and pro-inflammatory responses were quantified.Results: Cells primed with a DNA methyltransferase inhibitor (but not a histone deacetylase [HDAC] inhibitor) were found to be consistently more responsive to NOD1/NOD2 stimulation and had increased basal expression.Conclusion: The novel experimentation carried out here suggests for the first time that NOD1/NOD2 receptor activity and expression in monocytes are possibly regulated directly by DNA methylation.
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Affiliation(s)
- Claire L Feerick
- Pharmacology & Therapeutics, School of Medicine, National University of Ireland, Galway, Ireland
| | - Declan P McKernan
- Pharmacology & Therapeutics, School of Medicine, National University of Ireland, Galway, Ireland
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22
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Fiocchi C, Dragoni G, Iliopoulos D, Katsanos K, Ramirez VH, Suzuki K, Torres J, Scharl M. Results of the Seventh Scientific Workshop of ECCO: Precision Medicine in IBD-What, Why, and How. J Crohns Colitis 2021; 15:1410-1430. [PMID: 33733656 DOI: 10.1093/ecco-jcc/jjab051] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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] [Indexed: 12/13/2022]
Abstract
Many diseases that affect modern humans fall in the category of complex diseases, thus called because they result from a combination of multiple aetiological and pathogenic factors. Regardless of the organ or system affected, complex diseases present major challenges in diagnosis, classification, and management. Current forms of therapy are usually applied in an indiscriminate fashion based on clinical information, but even the most advanced drugs only benefit a limited number of patients and to a variable and unpredictable degree. This 'one measure does not fit all' situation has spurred the notion that therapy for complex disease should be tailored to individual patients or groups of patients, giving rise to the notion of 'precision medicine' [PM]. Inflammatory bowel disease [IBD] is a prototypical complex disease where the need for PM has become increasingly clear. This prompted the European Crohn's and Colitis Organisation to focus the Seventh Scientific Workshop on this emerging theme. The articles in this special issue of the Journal address the various complementary aspects of PM in IBD, including what PM is; why it is needed and how it can be used; how PM can contribute to prediction and prevention of IBD; how IBD PM can aid in prognosis and improve response to therapy; and the challenges and future directions of PM in IBD. This first article of this series is structured on three simple concepts [what, why, and how] and addresses the definition of PM, discusses the rationale for the need of PM in IBD, and outlines the methodology required to implement PM in IBD in a correct and clinically meaningful way.
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Affiliation(s)
- Claudio Fiocchi
- Department of Inflammation & Immunity, Lerner Research Institute, and Department of Gastroenterology, Hepatology & Nutrition, Digestive Disease Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Gabriele Dragoni
- Gastroenterology Research Unit, Department of Experimental and Clinical Biomedical Sciences 'Mario Serio', University of Florence, Florence,Italy.,IBD Referral Center, Gastroenterology Department, Careggi University Hospital, Florence,Italy
| | | | - Konstantinos Katsanos
- Division of Gastroenterology, Department of Internal Medicine, University of Ioannina School of Health Sciences, Ioannina,Greece
| | - Vicent Hernandez Ramirez
- Department of Gastroenterology, Xerencia Xestión Integrada de Vigo, and Research Group in Digestive Diseases, Galicia Sur Health Research Institute [IIS Galicia Sur], SERGAS-UVIGO, Vigo, Spain
| | - Kohei Suzuki
- Division of Digestive and Liver Diseases, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX,USA
| | | | - Joana Torres
- Division of Gastroenterology, Hospital Beatriz Ângelo, Loures, Portugal
| | - Michael Scharl
- Department of Gastroenterology and Hepatology, University Hospital Zürich, Zürich, Switzerland
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23
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Abstract
OBJECTIVES Recent evidence from the fields of microbiology and immunology, as well as a small number of human sepsis studies, suggest that epigenetic regulation may play a central role in the pathogenesis of sepsis. The term "epigenetics" refers to regulatory mechanisms that control gene expression but are not related to changes in DNA sequence. These include DNA methylation, histone modifications, and regulation of transcription via non-coding RNAs. Epigenetic modifications, occurring in response to external stressors, lead to changes in gene expression, and thus lie at the intersection between genetics and the environment. In this review, we examine data from in vitro studies, animal studies, and the existing human sepsis studies in epigenetics to demonstrate that epigenetic mechanisms are likely central to the pathogenesis of sepsis and that epigenetic therapies may have potential in the treatment of sepsis and its associated organ failures. DATA SOURCES Online search of published scientific literature via Pubmed using the term "epigenetics" in combination with the terms "sepsis", "infection", "bacterial infection", "viral infection", "critical illness", "acute respiratory distress syndrome", and "acute lung injury". STUDY SELECTION Articles were chosen for inclusion based on their relevance to sepsis, acute inflammation, sepsis-related immune suppression, and sepsis-related organ failure. Reference lists were reviewed to identify additional relevant articles. DATA EXTRACTION Relevant data was extracted and synthesized for narrative review. DATA SYNTHESIS Epigenetic regulation is a key determinant of gene expression in sepsis. At the onset of infection, host-pathogen interactions often result in epigenetic alterations to host cells that favor pathogen survival. In parallel, the host inflammatory response is characterized by epigenetic modifications in key regulatory genes, including tumor necrosis factor and interleukin-1β. In human sepsis patients, multiple epigenetic modifying enzymes show differential expression in early sepsis, suggesting a role for epigenetics in coordinating the response to infection. In the later stages of sepsis, epigenetic modifications accompany endotoxin tolerance and the immune-suppressed state. In animal models, treatment with epigenetic modifiers can mitigate the effects of sepsis and improve survival as well as reverse sepsis-associated organ injury. CONCLUSIONS Epigenetic modifications are associated with key phases of sepsis, from the host-pathogen interaction, to acute inflammation, to immune suppression. Epigenetic markers show promise in the diagnosis and prognosis of sepsis and epigenetic modifying agents show promise as therapeutic tools in animal models of sepsis. Human studies in the area of epigenetics are sorely lacking and should be a priority for sepsis researchers.
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24
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Hornschuh M, Wirthgen E, Wolfien M, Singh KP, Wolkenhauer O, Däbritz J. The role of epigenetic modifications for the pathogenesis of Crohn's disease. Clin Epigenetics 2021; 13:108. [PMID: 33980294 DOI: 10.1186/s13148-021-01089-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/22/2021] [Indexed: 12/19/2022] Open
Abstract
Epigenetics has become a promising field for finding new biomarkers and improving diagnosis, prognosis, and drug response in inflammatory bowel disease. The number of people suffering from inflammatory bowel diseases, especially Crohn's disease, has increased remarkably. Crohn's disease is assumed to be the result of a complex interplay between genetic susceptibility, environmental factors, and altered intestinal microbiota, leading to dysregulation of the innate and adaptive immune response. While many genetic variants have been identified to be associated with Crohn's disease, less is known about the influence of epigenetics in the pathogenesis of this disease. In this review, we provide an overview of current epigenetic studies in Crohn's disease. In particular, we enable a deeper insight into applied bioanalytical and computational tools, as well as a comprehensive update toward the cell-specific evaluation of DNA methylation and histone modifications.
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25
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Li Y, Wang Z, Wu X, Wang G, Gu G, Ren H, Hong Z, Ren J. Intestinal mucosa-derived DNA methylation signatures in the penetrating intestinal mucosal lesions of Crohn's disease. Sci Rep 2021; 11:9771. [PMID: 33963246 PMCID: PMC8105344 DOI: 10.1038/s41598-021-89087-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/21/2021] [Indexed: 12/11/2022] Open
Abstract
The purpose of this study was to evaluate genome-wide DNA methylation changes in intestinal mucosa tissue of adult patients with Crohn's disease comprehensively. DNA methylation chip was used to analyze abnormal methylation sites among penetrating and non-penetrating intestinal mucosa tissue of Crohn's disease and normal intestinal mucosa tissue of healthy controls. Methylation abnormalities of different locus were verified by pyrosequencing and quantitative polymerase chain reaction. Differential DNA methylation sites were participated in the positive regulation of apoptosis and the positive regulation of IL-8 production and were enriched in signaling pathways related to inflammatory bowel disease and extracellular matrix receptor interaction signaling pathways. Correlation analysis showed that the methylation abnormalities of HLA-DRB1 (r = - 0.62, P < 0.001), MUC1 (r = - 0.45, P = 0.01), YPEL5 (r = - 0.55, P = 0.001) and CBLB (r = - 0.62, P < 0.001) were significantly negatively correlated with their relative expression levels. The degree of methylation abnormality of MUC1 was negatively correlated with the disease activity score of Crohn's disease (r = - 0.50, P = 0.01). Apoptosis, interleukin-8 production and abnormal extracellular matrix might be involved in the mechanism of penetrating intestinal mucosal lesions in Crohn's disease. The degree of abnormal methylation of MUC1 was negatively correlated with the disease activity of Crohn's disease.
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Affiliation(s)
- Yuan Li
- Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Zhiming Wang
- Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China
| | - Xiuwen Wu
- Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China
| | - Gefei Wang
- Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China
| | - Guosheng Gu
- Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China
| | - Huajian Ren
- Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China
| | - Zhiwu Hong
- Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China
| | - Jianan Ren
- Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, China.
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26
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Good M, Chu T, Shaw P, Nolan LS, McClain L, Chamberlain A, Castro C, Gong Q, Cooksey K, Linneman L, DeWitt ON, Finegold DN, Peters DG. Neonatal necrotizing enterocolitis-associated DNA methylation signatures in the colon are evident in stool samples of affected individuals. Epigenomics 2021; 13:829-844. [PMID: 33905263 DOI: 10.2217/epi-2021-0078] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Aim: Neonatal necrotizing enterocolitis (NEC) is a deadly and unpredictable gastrointestinal disease, for which no biomarker exists. We aimed to describe the methylation patterns in stool and colon from infants with NEC. Methods: We performed a high-resolution genome-wide epigenomic analysis using solution-phase hybridization and next-generation sequencing of bisulfite-converted DNA. Results: Our data reveal significant genomic hypermethylation in NEC tissues compared with non-NEC controls. These changes were more pronounced in regions outside CpG islands and gene regulatory elements, suggesting that NEC-specific hypermethylation is not a nonspecific global phenomenon. Conclusions: This study provides evidence of a methylomic signature associated with NEC that is detectable noninvasively and provides a new opportunity for the development of a novel diagnostic method for NEC.
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Affiliation(s)
- Misty Good
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tianjiao Chu
- Departments of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA.,Magee-Women's Research Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Patricia Shaw
- Magee-Women's Research Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Lila S Nolan
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lora McClain
- Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Austin Chamberlain
- Magee-Women's Research Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Carlos Castro
- Magee-Women's Research Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Qingqing Gong
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Krista Cooksey
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Laura Linneman
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Olivia N DeWitt
- Department of Pediatrics, Division of Newborn Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David N Finegold
- Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - David G Peters
- Departments of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA 15213, USA.,Human Genetics, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA.,Magee-Women's Research Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
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27
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Hussey B, Steel RP, Gyimah B, Reynolds JC, Taylor IM, Lindley MR, Mastana S. DNA methylation of tumour necrosis factor (TNF) alpha gene is associated with specific blood fatty acid levels in a gender-specific manner. Mol Genet Genomic Med 2021; 9:e1679. [PMID: 33818919 PMCID: PMC8683629 DOI: 10.1002/mgg3.1679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 03/09/2021] [Accepted: 03/23/2021] [Indexed: 01/22/2023] Open
Abstract
Background Fatty acids, specifically polyunsaturated fatty acids (PUFAs) play an important role in inflammation and its resolution, however, their interaction with the epigenome is relatively unexplored. Here we investigate the relationship between circulating blood fatty acids and the DNA methylation of the cytokine encoding gene tumour necrosis factor (TNF, OMIM 191160). Methods Using a cross‐sectional study approach, we collected blood samples from adults (N=88 (30 males, 58 females); 18–74 years old) for DNA methylation pyrosequencing analysis at four sites in TNF exon 1 and gas‐chromatography mass‐spectrometry analysis of the fatty acid profile of dried blood spots (DBS). Results Methylation levels of TNF exon 1 are significantly correlated with specific fatty acids in a gender‐specific manner. In the males the PUFAs Docosahexaenoic Acid (DHA) and Arachidonic Acid (AA) were positively associated with TNF methylation, as was the saturated fatty acid (SFA) Stearic Acid; in contrast, mono‐unsaturated fatty acids (MUFAs) had a negative association. In the females, omega‐6 PUFA γ‐Linolenic acid (GLA) was negatively correlated with TNF methylation; Adrenic acid and Eicosadienoic Acid were positively correlated with TNF methylation. Conclusion These results suggest that one way that fatty acids interact with the inflammation is through altered methylation profiles of cytokine genes; thus, providing potential therapeutic targets for nutritional and health interventions.
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Affiliation(s)
- Bethan Hussey
- Translational Chemical Biology (TCB) Research Group, Loughborough, University, Loughborough, UK.,School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Richard P Steel
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK.,School of Social Sciences, Nottingham Trent University, Nottingham, UK
| | - Boakye Gyimah
- Translational Chemical Biology (TCB) Research Group, Loughborough, University, Loughborough, UK.,Department of Chemistry, Loughborough University, Loughborough, UK
| | - James C Reynolds
- Translational Chemical Biology (TCB) Research Group, Loughborough, University, Loughborough, UK.,Department of Chemistry, Loughborough University, Loughborough, UK
| | - Ian M Taylor
- School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Martin R Lindley
- Translational Chemical Biology (TCB) Research Group, Loughborough, University, Loughborough, UK.,School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
| | - Sarabjit Mastana
- Translational Chemical Biology (TCB) Research Group, Loughborough, University, Loughborough, UK.,School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK
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28
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Indellicato R, Trinchera M. Epigenetic Regulation of Glycosylation in Cancer and Other Diseases. Int J Mol Sci 2021; 22:ijms22062980. [PMID: 33804149 PMCID: PMC7999748 DOI: 10.3390/ijms22062980] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 12/12/2022] Open
Abstract
In the last few decades, the newly emerging field of epigenetic regulation of glycosylation acquired more importance because it is unraveling physiological and pathological mechanisms related to glycan functions. Glycosylation is a complex process in which proteins and lipids are modified by the attachment of monosaccharides. The main actors in this kind of modification are the glycoenzymes, which are translated from glycosylation-related genes (or glycogenes). The expression of glycogenes is regulated by transcription factors and epigenetic mechanisms (mainly DNA methylation, histone acetylation and noncoding RNAs). This review focuses only on these last ones, in relation to cancer and other diseases, such as inflammatory bowel disease and IgA1 nephropathy. In fact, it is clear that a deeper knowledge in the fine-tuning of glycogenes is essential for acquiring new insights in the glycan field, especially if this could be useful for finding novel and personalized therapeutics.
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Affiliation(s)
- Rossella Indellicato
- Department of Health Sciences, University of Milan, 20142 Milan, Italy
- Correspondence:
| | - Marco Trinchera
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy;
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29
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Giudici F, Cavalli T, Luceri C, Russo E, Zambonin D, Scaringi S, Ficari F, Fazi M, Amedei A, Tonelli F, Malentacchi C. Long-Term Follow-Up, Association between CARD15/NOD2 Polymorphisms, and Clinical Disease Behavior in Crohn's Disease Surgical Patients. Mediators Inflamm 2021; 2021:8854916. [PMID: 33708009 DOI: 10.1155/2021/8854916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/16/2022] Open
Abstract
Background CARD15/NOD2 is the most significant genetic susceptibility in Crohn's disease (CD) even though a relationship between the different polymorphisms and clinical phenotype has not been described yet. The study is aimed at analyzing, in a group of CD patients undergoing surgery, the relationship between CARD15/NOD2 polymorphisms and the clinical CD behavior after a long-term follow-up, in order to identify potential clinical biomarkers of prognosis. Methods 191 surgical CD patients were prospectively characterized both for the main single nucleotide polymorphisms of CARD15/NOD2 and for many other environmental risk factors connected with the severe disease form. After a mean follow-up of 7.3 years, the correlations between clinical features and CD natural history were analyzed. Results CARD15/NOD2 polymorphisms were significantly associated with younger age at diagnosis compared to wild type cases (p < 0.05). Moreover, patients carrying a 3020insC polymorphism presented a larger Δ between diagnosis and surgery (p = 0.0344). Patients carrying an hz881 and a 3020insC exhibited, respectively, a lower rate of responsiveness to azathioprine (p = 0.012), but no difference was found in biologic therapy. Finally, the risk of surgical recurrence was significantly associated, respectively, to age at diagnosis, to familial CD history, to diagnostic delay, to arthritis, and to the presence of perioperative complications. Conclusions 3020insC CARD15 polymorphism is associated with an earlier CD onset, and age at CD diagnosis < 27 years was confirmed to have a detrimental effect on its clinical course. In addition, the familiarity seems to be connected with a more aggressive postoperative course. Finally, for the first time, we have observed a lower rate of responsiveness to azathioprine in patients carrying an hz881 and a 3020insC.
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30
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Li C, Zhu F, Wang S, Wang J, Wu B. Danggui Buxue Decoction Ameliorates Inflammatory Bowel Disease by Improving Inflammation and Rebuilding Intestinal Mucosal Barrier. Evid Based Complement Alternat Med 2021; 2021:8853141. [PMID: 33531923 DOI: 10.1155/2021/8853141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/30/2020] [Accepted: 01/08/2021] [Indexed: 12/19/2022]
Abstract
Objective This study aimed to determine whether Danggui Buxue decoction (DGBX) can improve inflammatory bowel disease (IBD) by regulating immunity and promoting intestinal mucosal repair. Method Dextran sulfate sodium (DSS) was used to induce the IBD model. Drugs (DGBX or saline) were administered to mice, which were randomly divided into three groups (control, model, and experimental groups). Hematoxylin and eosin staining of intestinal tissues was conducted to observe for morphological changes. Changes in cytokines and immune cells in the intestinal tissues were detected by enzyme-linked immunosorbent assay and flow cytometry. Immunofluorescence techniques were used to assess the status of the intestinal mucosal repair. Results This study found that treatment with DGBX can effectively improve the inflammatory state and pathological structure of the IBD model. DGBX not only can significantly change the composition of intestinal mucosal immune cells and promote the regression of inflammation but also significantly increase the proliferation of intestinal epithelial cells and promote the rapid repair of intestinal mucosal barrier injury compared with the model group (p < 0.05). Conclusion Taking these results, DGBX shows promising protective effects on IBD by regulating immunity and promoting intestinal mucosal repair.
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31
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Georgiou AN, Ntritsos G, Papadimitriou N, Dimou N, Evangelou E. Cigarette Smoking, Coffee Consumption, Alcohol Intake, and Risk of Crohn's Disease and Ulcerative Colitis: A Mendelian Randomization Study. Inflamm Bowel Dis 2021; 27:162-168. [PMID: 32628751 DOI: 10.1093/ibd/izaa152] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Crohn's disease (CD) and ulcerative colitis (UC) are widely associated with smoking in epidemiological studies, whereas there are conflicting results for the association between CD and UC for both coffee and alcohol consumption. Herein, we aimed to investigate whether cigarette smoking and alcohol and coffee consumption are causally associated with either CD or UC. METHODS We utilized 540 genome-wide significant single-nucleotide polymorphisms for 3 potentially addictive substances-nicotine, alcohol, and caffeine-to assess the association of smoking, coffee, and alcohol consumption with CD and UC (12,194 CD cases, 12,366 UC cases, and 25,042 controls of European ancestry), using Mendelian randomization analysis. Mendelian randomization estimates were used to evaluate the effect of the exposure factors on CD and UC risk. Sensitivity analysis was employed to test for any directional pleiotropy. RESULTS We found evidence for a positive causal association between the age of smoking initiation and UC risk and between alcohol consumption and CD risk, which disappeared after sensitivity analysis for both associations (P > 0.05). No evidence for a causal association between cigarettes per day, smoking initiation, smoking cessation, and coffee consumption variables and UC or CD was found. CONCLUSIONS We found no clear evidence that either genetically predicted smoking, coffee consumption, or alcohol consumption are causally associated with the risk for CD or UC, although our findings indicate a potential positive association between the age of smoking and UC and between alcohol consumption and CD.
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Affiliation(s)
- Andrea N Georgiou
- Medical School, University of Cyprus, Nicosia, Cyprus
- Clinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, School of Medicine, University of Ioannina, Ioannina, Greece
| | - Georgios Ntritsos
- Clinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, School of Medicine, University of Ioannina, Ioannina, Greece
- Department of Informatics and Telecommunications, School of Informatics and Telecommunications, University of Ioannina, Arta, Greece
| | - Nikos Papadimitriou
- Clinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, School of Medicine, University of Ioannina, Ioannina, Greece
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Niki Dimou
- Clinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, School of Medicine, University of Ioannina, Ioannina, Greece
- Section of Nutrition and Metabolism, International Agency for Research on Cancer, Lyon, France
| | - Evangelos Evangelou
- Clinical and Molecular Epidemiology Unit, Department of Hygiene and Epidemiology, School of Medicine, University of Ioannina, Ioannina, Greece
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
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Alemany-Cosme E, Sáez-González E, Moret I, Mateos B, Iborra M, Nos P, Sandoval J, Beltrán B. Oxidative Stress in the Pathogenesis of Crohn's Disease and the Interconnection with Immunological Response, Microbiota, External Environmental Factors, and Epigenetics. Antioxidants (Basel) 2021; 10:64. [PMID: 33430227 DOI: 10.3390/antiox10010064] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 12/14/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a complex multifactorial disorder in which external and environmental factors have a large influence on its onset and development, especially in genetically susceptible individuals. Crohn’s disease (CD), one of the two types of IBD, is characterized by transmural inflammation, which is most frequently located in the region of the terminal ileum. Oxidative stress, caused by an overabundance of reactive oxygen species, is present locally and systemically in patients with CD and appears to be associated with the well-described imbalanced immune response and dysbiosis in the disease. Oxidative stress could also underlie some of the environmental risk factors proposed for CD. Although the exact etiopathology of CD remains unknown, the key role of oxidative stress in the pathogenesis of CD is extensively recognized. Epigenetics can provide a link between environmental factors and genetics, and numerous epigenetic changes associated with certain environmental risk factors, microbiota, and inflammation are reported in CD. Further attention needs to be focused on whether these epigenetic changes also have a primary role in the pathogenesis of CD, along with oxidative stress.
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Abstract
Epigenetic alterations in our genetic material can lead to heritable changes in the risk, clinical manifestations, course, and outcomes of many diseases. Understanding these epigenetic mechanisms can help in identifying potential therapeutic targets. This is especially important in necrotizing enterocolitis (NEC), where prenatal as well as postnatal factors impact susceptibility to this devastating condition, but our therapeutic options are limited. Developmental factors affecting intestinal structure and function, our immune system, gut microbiome, and postnatal enteral nutrition are all thought to play a prominent role in this disease. In this manuscript, we have reviewed the epigenetic mechanisms involved in NEC. These include key developmental changes in DNA methylation in the immature intestine, the role of long non-coding RNA (lncRNA) in maintaining intestinal barrier function, epigenetic influences of prenatal inflammation on immunological pathways in NEC pathogenesis such as Toll-Like Receptor 4 (TLR4) and epigenetic changes associated with enteral feeding causing upregulation of pro-inflammatory genes. We have assimilated research findings from our own laboratory with an extensive review of the literature utilizing key terms in multiple databases, including PubMed, EMBASE, and Science Direct.
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Affiliation(s)
- Jayasree Nair
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, United States
| | - Akhil Maheshwari
- Department of Pediatrics, Johns Hopkins University, Baltimore, MA, United States
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Samarani S, Dupont-Lucas C, Marcil V, Mack D, Israel D, Deslandres C, Jantchou P, Ahmad A, Amre D. CpG Methylation in TGFβ1 and IL-6 Genes as Surrogate Biomarkers for Diagnosis of IBD in Children. Inflamm Bowel Dis 2020; 26:1572-1578. [PMID: 32407484 DOI: 10.1093/ibd/izaa074] [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] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Diagnostic markers for distinguishing between Crohn disease (CD) and ulcerative colitis (UC) remain elusive. We studied whether methylation marks across the promoters of the transforming growth factor beta 1 (TGFβ1) and interleukin-6 genes have diagnostic utility. METHODS A case-control study was carried out. Cases were treatment-naïve, diagnosed before age 20, and recruited from 3 pediatric gastroenterology clinics across Canada. Control patients did not have inflammatory bowel disease and were recruited from orthopedic clinics within the same hospitals as the gastroenterology clinics. Patient DNA from peripheral blood was processed to identify methylation sites (CpG) across the promoter regions of the TGFβ1 and interleukin-6 genes. After initial nonparametric univariate analyses, multivariate logistic regression models were fit. Models with the best fit (Akaike information criteria) and strongest discriminatory capabilities (area under the curve [AUC]) were identified, and P values were adjusted for multiple comparisons using the false discovery rate method. RESULTS A total of 67 CD, 31 UC, and 43 control patients were included. The age distribution of the 3 groups was similar. Most CD patients had ileocolonic disease (44.8%) and inflammatory disease (88.1%). Most UC patients had extensive (71%) and moderate disease (51.6%). Logistic regression analysis revealed the following: 14 TGFβ1 CpG sites discriminated between CD and control patients (AUC = 0.94), 9 TGFβ1 CpG sites discriminated between UC and control patients (AUC = 0.99), 3 TGFβ1 CpG sites discriminated between CD and UC (AUC = 0.81), and 6 TGFβ1 CpG sites distinguished colonic CD from UC (AUC = 0.91). CONCLUSIONS We found that CpG methylation in the promoter of the TGFβ1 gene has high discriminative power for identifying CD and UC and could serve as an important diagnostic marker.
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Affiliation(s)
- Suzanne Samarani
- Department of Pediatrics, CHU Sainte-Justine, University of Montreal, Montreal, Canada
| | | | - Valerie Marcil
- Department of Pediatrics, CHU Sainte-Justine, University of Montreal, Montreal, Canada
| | - David Mack
- Division of Gastroenterology, Hepatology and Nutrition, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - David Israel
- Division of Gastroenterology & Hepatology, BCCH, Vancouver, British Columbia, Canada
| | - Colette Deslandres
- Department of Pediatrics, CHU Sainte-Justine, University of Montreal, Montreal, Canada
| | - Prevost Jantchou
- Department of Pediatrics, CHU Sainte-Justine, University of Montreal, Montreal, Canada
| | - Ali Ahmad
- Department of Pediatrics, CHU Sainte-Justine, University of Montreal, Montreal, Canada
| | - Devendra Amre
- Department of Pediatrics, CHU Sainte-Justine, University of Montreal, Montreal, Canada
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Gimier E, Chervy M, Agus A, Sivignon A, Billard E, Privat M, Viala S, Minet-Quinard R, Buisson A, Vazeille E, Barnich N, Denizot J. Methyl-donor supplementation prevents intestinal colonization by Adherent-Invasive E. coli in a mouse model of Crohn's disease. Sci Rep 2020; 10:12922. [PMID: 32737335 DOI: 10.1038/s41598-020-69472-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/08/2020] [Indexed: 02/07/2023] Open
Abstract
Deficiencies in methyl-donor molecules (folate, B12 vitamin), DNA methylation alteration and high prevalence of Adherent-Invasive Escherichia coli (AIEC) are frequently observed in Crohn’s disease (CD) patients. AIEC bacteria adhere to the enterocytes through abnormally expressed carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6) glycoprotein on host cells. This work aims at studying the relationship between methyl-donor molecules and AIEC-induced intestinal inflammatory response. CEABAC10 mice, a mouse model of CD, were fed a control or Methyl-donor Supplemented diet (MS diet). CEACAM6 promoter was hypermethylated in intestinal epithelial cells from mice fed an MS diet, which was associated with a significant decrease in CEACAM6 expression. Transcriptomic analysis revealed increased expression of anti-microbial peptides, increase in HSP70 gene family expression and a decreased expression of inflammatory marker Calprotectin upon MS diet, associated to a lower ability of AIEC bacteria to colonize gut mucosa. We observed in a cohort of CD patients that serum folate concentration was inversely correlated to Crohn’s disease endoscopic index of severity and to fecal inflammatory markers. This study demonstrates that methyl-donor supplementation through the diet induces a specific intestinal micro-environment limiting pathobiont colonization of the gut. Clinicians may wish to consider methyl-donor supplementation for methyl-donor deficient CD patients.
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Ronchetti S, Gentili M, Ricci E, Migliorati G, Riccardi C. Glucocorticoid-Induced Leucine Zipper as a Druggable Target in Inflammatory Bowel Diseases. Inflamm Bowel Dis 2020; 26:1017-1025. [PMID: 31961437 DOI: 10.1093/ibd/izz331] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 11/12/2019] [Indexed: 12/11/2022]
Abstract
Inflammatory bowel diseases (IBDs) are chronic inflammatory disorders with a complex pathogenesis, affecting people of all ages. They are characterized by alternating phases of clinical relapse and remission, depending on the fine balance between immune cells and the gut microbiota. The cross talk between cells of the immune system and the gut microbiota can result in either tolerance or inflammation, according to multifactorial triggers, ranging from environmental factors to genetic susceptibility. Glucocorticoid (GC) administration remains the first-line treatment for IBDs, although long-term use is limited by development of serious adverse effects. Recently, new alternative pharmacological therapies have been developed, although these are not always effective in IBD patients. There is a constant demand for effective new drug targets to guarantee total remission and improve the quality of life for IBD patients. The glucocorticoid-induced leucine zipper (GILZ) has been implicated as a promising candidate for this purpose, in view of its powerful anti-inflammatory effects that mimic those of GCs while avoiding their unwanted adverse reactions. Here we present and discuss the latest findings about the involvement of GILZ in IBDs.
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Affiliation(s)
- Simona Ronchetti
- Department of Medicine, Pharmacology Division, University of Perugia, Italy
| | - Marco Gentili
- Department of Medicine, Pharmacology Division, University of Perugia, Italy
| | - Erika Ricci
- Department of Medicine, Pharmacology Division, University of Perugia, Italy
| | | | - Carlo Riccardi
- Department of Medicine, Pharmacology Division, University of Perugia, Italy
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Kerur B, Benchimol EI, Fiedler K, Stahl M, Hyams J, Stephens M, Lu Y, Pfefferkorn M, Alkhouri R, Strople J, Kelsen J, Siebold L, Goyal A, Rosh JR, LeLeiko N, Van Limbergen J, Guerrerio AL, Maltz R, Karam L, Crowley E, Griffiths A, Heyman MB, Deneau M, Benkov K, Noe J, Mouton D, Pappa H, Galanko JA, Snapper S, Muise AM, Kappelman MD. Natural History of Very Early Onset Inflammatory Bowel Disease in North America: A Retrospective Cohort Study. Inflamm Bowel Dis 2020; 27:295-302. [PMID: 32386060 PMCID: PMC8177809 DOI: 10.1093/ibd/izaa080] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 03/22/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND The incidence of very early onset inflammatory bowel disease (VEOIBD) is increasing, yet the phenotype and natural history of VEOIBD are not well described. METHODS We performed a retrospective cohort study of patients diagnosed with VEOIBD (6 years of age and younger) between 2008 and 2013 at 25 North American centers. Eligible patients at each center were randomly selected for chart review. We abstracted data at diagnosis and at 1, 3, and 5 years after diagnosis. We compared the clinical features and outcomes with VEOIBD diagnosed younger than 3 years of age with children diagnosed with VEOIBD at age 3 to 6 years. RESULTS The study population included 269 children (105 [39%] Crohn's disease, 106 [39%] ulcerative colitis, and 58 [22%] IBD unclassified). The median age of diagnosis was 4.2 years (interquartile range 2.9-5.2). Most (94%) Crohn's disease patients had inflammatory disease behavior (B1). Isolated colitis (L2) was the most common disease location (70% of children diagnosed younger than 3 years vs 43% of children diagnosed 3 years and older; P = 0.10). By the end of follow-up, stricturing/penetrating occurred in 7 (6.6%) children. The risk of any bowel surgery in Crohn's disease was 3% by 1 year, 12% by 3 years, and 15% by 5 years and did not differ by age at diagnosis. Most ulcerative colitis patients had pancolitis (57% of children diagnosed younger than 3 years vs 45% of children diagnosed 3 years and older; P = 0.18). The risk of colectomy in ulcerative colitis/IBD unclassified was 0% by 1 year, 3% by 3 years, and 14% by 5 years and did not differ by age of diagnosis. CONCLUSIONS Very early onset inflammatory bowel disease has a distinct phenotype with predominantly colonic involvement and infrequent stricturing/penetrating disease. The cumulative risk of bowel surgery in children with VEOIBD was approximately 14%-15% by 5 years. These data can be used to provide anticipatory guidance in this emerging patient population.
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Affiliation(s)
- Basavaraj Kerur
- University of Massachusetts Medical School (UMMS), Worcester, MA, United States,Address correspondence to: Basavaraj Kerur, MD, University of Massachusetts Medical School, UMass Memorial Medical Center, 55 Lake Avenue North Worcester, MA 01655, USA. E-mail:
| | | | | | - Marisa Stahl
- Children’s Hospital Colorado, Denver, CO, United States
| | - Jeffrey Hyams
- Connecticut Children’s Medical Center, Hartford, CT, United States
| | - Michael Stephens
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
| | - Ying Lu
- Cohen Children’s Medical Center of New York, New York, NY, United States
| | | | | | - Jennifer Strople
- Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, United States
| | - Judith Kelsen
- Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Leah Siebold
- UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Alka Goyal
- Children’s Mercy, Kansas City, MO, United States
| | - Joel R Rosh
- Goryeb Children’s Hospital/Atlantic Health System, Morristown, NJ, United States
| | - Neal LeLeiko
- Hasbro Children’s Hospital, Providence, RI, United States
| | - Johan Van Limbergen
- Amsterdam University Medical Centres, Emma Children’s Hospital, Amsterdam, Netherlands
| | | | - Ross Maltz
- Nationwide Children’s Medical Center, Columbus, OH, United States
| | - Lina Karam
- Texas Children’s Hospital, Houston, TX, United States
| | - Eileen Crowley
- Children’s Hospital, London Health Science Centre, University of Western Ontario, London, Ontario, Canada
| | | | - Melvin B Heyman
- UCSF Benioff Children’s Hospital, San Francisco, CA, United States
| | - Mark Deneau
- University of Utah/Intermountain Primary Children’s Hospital, Salt Lake City, UT, United States
| | - Keith Benkov
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Joshua Noe
- Medical College of Wisconsin, Milwaukee, WI, United States
| | - Dedrick Mouton
- Monroe Carell Jr. Children’s Hospital at Vanderbilt, Nashville, TN, United States
| | - Helen Pappa
- Cardinal Glennon Children’s Hospital, St. Louis, MO, United States
| | - Joseph A Galanko
- University of North Carolina in Chapel Hill, Chapel Hill, NC, United States
| | - Scott Snapper
- Children’s Hospital Boston, Boston, MA, United States
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Kim TO, Park DI, Han YK, Kang K, Park SG, Park HR, Yi JM. Genome-Wide Analysis of the DNA Methylation Profile Identifies the Fragile Histidine Triad ( FHIT) Gene as a New Promising Biomarker of Crohn's Disease. J Clin Med 2020; 9:jcm9051338. [PMID: 32375395 PMCID: PMC7291297 DOI: 10.3390/jcm9051338] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 04/30/2020] [Accepted: 04/30/2020] [Indexed: 12/26/2022] Open
Abstract
Inflammatory bowel disease is known to be associated with a genetic predisposition involving multiple genes; however, there is growing evidence that abnormal interactions with environmental factors, particularly epigenetic factors, can also significantly contribute to the development of inflammatory bowel disease (IBD). Although many genome-wide association studies have been performed to identify the genetic changes underlying the pathogenesis of Crohn’s disease, the role of epigenetic alterations based on molecular complications arising from Crohn’s disease (CD) is poorly understood. We employed an unbiased approach to define DNA methylation alterations in colonoscopy samples from patients with CD using the HumanMethylation450K BeadChip platform. Technical and functional validation was performed by methylation-specific PCR (MSP) and bisulfite sequencing of a validation set of 207 patients with CD samples. Immunohistochemistry (IHC) analysis was performed in the representative sample sets. DNA methylation profile in CD revealed that 135 probes (24 hypermethylated and 111 hypomethylated probes) were differentially methylated. We validated the methylation levels of 19 genes that showed hypermethylation in patients with CD compared with normal controls. We uniquely identified that the fragile histidine triad (FHIT) gene was hypermethylated in a disease-specific manner and its protein level was downregulated in patients with CD. Pathway analysis of the hypermethylated candidates further suggested putative molecular interactions relevant to IBD pathology. Our data provide information on the biological and clinical implications of DNA hypermethylated genes in CD, identifying FHIT methylation as a promising new biomarker for CD. Further study of the role of FHIT in IBD pathogenesis may lead to the development of new therapeutic targets.
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Affiliation(s)
- Tae-Oh Kim
- Department of Internal Medicine, Inje University, Haeundae Paik Hospital, Busan 48108, Korea;
| | - Dong-Il Park
- Department of Internal Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul 03181, Korea;
| | - Yu Kyeong Han
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan 47392, Korea; (Y.K.H.); (S.-G.P.)
| | - Keunsoo Kang
- Department of Microbiology, Dankook University, Cheonan 31116, Korea;
| | - Sae-Gwang Park
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan 47392, Korea; (Y.K.H.); (S.-G.P.)
| | - Hae Ryoun Park
- Department of Oral Pathology, School of Dentistry, Pusan National University, Yangsan, Gyeongsangnam do 50612, Korea;
| | - Joo Mi Yi
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan 47392, Korea; (Y.K.H.); (S.-G.P.)
- Correspondence: ; Tel.: +82-51-890-6734
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Li Yim AY, Duijvis NW, Ghiboub M, Sharp C, Ferrero E, Mannens MM, D’Haens GR, de Jonge WJ, te Velde AA, Henneman P. Whole-Genome DNA Methylation Profiling of CD14+ Monocytes Reveals Disease Status and Activity Differences in Crohn's Disease Patients. J Clin Med 2020; 9:E1055. [PMID: 32276386 PMCID: PMC7230341 DOI: 10.3390/jcm9041055] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
Crohn's disease (CD) is a multifactorial incurable chronic disorder. Current medical treatment seeks to induce and maintain a state of remission. During episodes of inflammation, monocytes infiltrate the inflamed mucosa whereupon they differentiate into macrophages with a pro-inflammatory phenotype. Here, we sought to characterize the circulating monocytes by profiling their DNA methylome and relate it to the level of CD activity. We gathered an all-female age-matched cohort of 16 CD patients and 7 non-CD volunteers. CD patients were further subdivided into 8 CD patients with active disease (CD-active) and 8 CD patients in remission (CD-remissive) as determined by the physician global assessment. We identified 15 and 12 differentially methylated genes (DMGs) when comparing CD with non-CD and CD-active with CD-remissive, respectively. Differential methylation was predominantly found in the promoter regions of inflammatory genes. Comparing our observations with gene expression data on classical (CD14++CD16-), non-classical (CD14+CD16++) and intermediate (CD14++CD16+) monocytes indicated that while 7 DMGs were differentially expressed across the 3 subsets, the remaining DMGs could not immediately be associated with differences in known populations. We conclude that CD activity is associated with differences in DNA methylation at the promoter region of inflammation-associated genes.
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Affiliation(s)
- Andrew Y.F. Li Yim
- Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, Genome Diagnostics Laboratory, Amsterdam Reproduction & Development, 1105 AZ Amsterdam, The Netherlands
- R&D GlaxoSmithKline, Stevenage SG1 2NY, UK; (M.G.); (C.S.); (E.F.)
| | - Nicolette W. Duijvis
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Gastroenterology & Metabolism, 1105 BK Amsterdam, The Netherlands; (N.W.D.); (W.J.d.J.)
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Gastroenterology & Metabolism, 1105 AZ Amsterdam, The Netherlands;
| | - Mohammed Ghiboub
- R&D GlaxoSmithKline, Stevenage SG1 2NY, UK; (M.G.); (C.S.); (E.F.)
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Gastroenterology & Metabolism, 1105 BK Amsterdam, The Netherlands; (N.W.D.); (W.J.d.J.)
| | - Catriona Sharp
- R&D GlaxoSmithKline, Stevenage SG1 2NY, UK; (M.G.); (C.S.); (E.F.)
| | - Enrico Ferrero
- R&D GlaxoSmithKline, Stevenage SG1 2NY, UK; (M.G.); (C.S.); (E.F.)
| | - Marcel M.A.M. Mannens
- Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, Genome Diagnostics Laboratory, Amsterdam Reproduction & Development, 1105 AZ Amsterdam, The Netherlands
| | - Geert R. D’Haens
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Gastroenterology & Metabolism, 1105 AZ Amsterdam, The Netherlands;
| | - Wouter J. de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Gastroenterology & Metabolism, 1105 BK Amsterdam, The Netherlands; (N.W.D.); (W.J.d.J.)
- Department of Surgery, University Clinic of Bonn, 53127 Bonn, Germany
| | - Anje A. te Velde
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam Gastroenterology & Metabolism, 1105 BK Amsterdam, The Netherlands; (N.W.D.); (W.J.d.J.)
| | - Peter Henneman
- Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, Genome Diagnostics Laboratory, Amsterdam Reproduction & Development, 1105 AZ Amsterdam, The Netherlands
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Binnie A, Walsh CJ, Hu P, Dwivedi DJ, Fox-Robichaud A, Liaw PC, Tsang JLY, Batt J, Carrasqueiro G, Gupta S, Marshall JC, Castelo-Branco P, Dos Santos CC. Epigenetic Profiling in Severe Sepsis: A Pilot Study of DNA Methylation Profiles in Critical Illness. Crit Care Med 2020; 48:142-150. [PMID: 31939781 DOI: 10.1097/ccm.0000000000004097] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVES Epigenetic alterations are an important regulator of gene expression in health and disease; however, epigenetic data in sepsis are lacking. To demonstrate proof of concept and estimate effect size, we performed the first epigenome-wide methylation analysis of whole blood DNA samples from a cohort of septic and nonseptic critically ill patients. DESIGN A nested case-control study using genomic DNA isolated from whole blood from septic (n = 66) and nonseptic (n = 68) critically ill patients on "Day 1" of ICU admission. Methylation patterns were identified using Illumina 450K arrays with percent methylation expressed as β values. After quality control, 134 participants and 414,818 autosomal cytosine-phosphate-guanine sites were used for epigenome-wide methylation analyses. SETTING Tertiary care hospitals. SUBJECTS Critically ill septic and nonseptic patients. INTERVENTIONS Observational study. MEASUREMENTS AND MAIN RESULTS A total of 668 differentially methylated regions corresponding to 443 genes were identified. Known sepsis-associated genes included complement component 3; angiopoietin 2; myeloperoxidase; lactoperoxidase; major histocompatibility complex, class I, A; major histocompatibility complex, class II, isotype DR β I; major histocompatibility complex, class I, C; and major histocompatibility complex, class II, isotype DQ β I. When compared with whole blood gene expression data from seven external datasets containing septic and nonseptic patients, 81% of the differentially methylated region-associated genes were differentially expressed in one or more datasets and 31% in three or more datasets. Functional analysis showed enrichment for antigen processing and presentation, methyltransferase activity, cell adhesion, and cell junctions. Analysis by weighted gene coexpression network analysis revealed DNA comethylation modules that were associated with clinical traits including severity of illness, need for vasopressors, and length of stay. CONCLUSIONS DNA methylation marks may provide important causal and potentially biomarker information in critically ill patients with sepsis.
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Affiliation(s)
- Alexandra Binnie
- Department of Critical Care, William Osler Health System, Brampton, ON, Canada
| | - Christopher J Walsh
- Keenan Research Centre for Biomedical Science, St Michael's Hospital, Toronto, ON, Canada
- Institute of Medical Sciences and Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Pingzhao Hu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Dhruva J Dwivedi
- Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada
| | - Alison Fox-Robichaud
- Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Patricia C Liaw
- Thrombosis and Atherosclerosis Research Institute, McMaster University, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Jennifer L Y Tsang
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Niagara Health, St. Catharines, ON, Canada
| | - Jane Batt
- Keenan Research Centre for Biomedical Science, St Michael's Hospital, Toronto, ON, Canada
- Institute of Medical Sciences and Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Gabriela Carrasqueiro
- Centre for Biomedical Research, University of Algarve, Faro, Portugal
- Algarve Biomedical Center, Faro, Portugal
| | - Sahil Gupta
- Keenan Research Centre for Biomedical Science, St Michael's Hospital, Toronto, ON, Canada
- Institute of Medical Sciences and Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - John C Marshall
- Keenan Research Centre for Biomedical Science, St Michael's Hospital, Toronto, ON, Canada
- Institute of Medical Sciences and Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Pedro Castelo-Branco
- Centre for Biomedical Research, University of Algarve, Faro, Portugal
- Algarve Biomedical Center, Faro, Portugal
- Regenerative Medicine Program, Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Portugal
| | - Claudia C Dos Santos
- Keenan Research Centre for Biomedical Science, St Michael's Hospital, Toronto, ON, Canada
- Institute of Medical Sciences and Department of Medicine, University of Toronto, Toronto, ON, Canada
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Yang YX, Shen HH, Cao F, Xie LY, Zhu GL, Sam NB, Wang DG, Pan HF. Therapeutic potential of enhancer of zeste homolog 2 in autoimmune diseases. Expert Opin Ther Targets 2019; 23:1015-1030. [PMID: 31747802 DOI: 10.1080/14728222.2019.1696309] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Introduction: Autoimmune diseases (ADs) are idiopathic and heterogeneous disorders with contentious pathophysiology. Great strides have been made in epigenetics and its involvement in ADs. Zeste homolog 2 (EZH2) has sparked extensive interest because of its pleiotropic roles in distinct pathologic contexts.Areas covered: This review summarizes the epigenetic functions and the biological significance of EZH2 in the etiology of rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), type 1 diabetes (T1D), inflammatory bowel disease (IBD), multiple sclerosis (MS), and systemic sclerosis (SSc). A brief recapitulation of the therapeutic potential of EZH2 targeting is provided.Expert opinion: There are questions marks and controversies surrounding the feasibility and safety of EZH2 targeting; it is recommended in RA and SLE, but queried in T1D, IBD, MS, and SSc. Future work should focus on contrast studies, systematic analyses and preclinical studies with optimizing methodologies. Selective research studies conducted in a stage-dependent manner are necessary because of the relapsing-remitting clinical paradigms.
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Affiliation(s)
- Yue-Xin Yang
- Department of Radiation Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Hui-Hui Shen
- Department of Clinical Medicine, The second School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Fan Cao
- Department of Clinical Medicine, The second School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Liang-Yu Xie
- Department of Clinical Medicine, The second School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Guang-Lin Zhu
- Department of Clinical Medicine, The second School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Napoleon Bellua Sam
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
| | - De-Guang Wang
- Department of Nephrology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Anhui Province Key Laboratory of Major Autoimmune Diseases, Hefei, Anhui, China
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Moret-Tatay I, Cerrillo E, Sáez-González E, Hervás D, Iborra M, Sandoval J, Busó E, Tortosa L, Nos P, Beltrán B. Identification of Epigenetic Methylation Signatures With Clinical Value in Crohn's Disease. Clin Transl Gastroenterol 2019; 10:e00083. [PMID: 31663908 PMCID: PMC6919449 DOI: 10.14309/ctg.0000000000000083] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/16/2019] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION DNA methylation is an epigenetic mechanism that regulates gene expression and represents an important link between genotype, environment, and disease. It is a reversible and inheritable mechanism that could offer treatment targets. We aimed to assess the methylation changes on specific genes previously associated with Crohn's disease (CD) and to study their possible associations with the pathology. METHODS We included 103 participants and grouped them into 2 cohorts (a first [n = 31] and a second validation [n = 72] cohort), with active CD (aCD) and inactive CD (iCD) and healthy participants (CTR). DNA was obtained from the peripheral blood and analyzed by the Agena platform. The selected genes were catalase (CAT), α-defensin 5 (DEFA5), FasR, FasL, tumor necrosis factor (TNF), TNFRSF1A, TNFRSF1B, PPA2, ABCB1, NOD2, PPARγ, and PKCζ. We used the elastic net algorithm and R software. RESULTS We studied 240 CpGs. Sixteen CpGs showed differential methylation profiles among aCD, iCD, and CTR. We selected for validation those with the greatest differences: DEFA5 CpG_11; CpG_13; CAT CpG_31.32; TNF CpG_4, CpG_12; and ABCB1 CpG_21. Our results validated the genes DEFA5 (methylation gain) and TNF (methylation loss) with P values < 0.001. In both cases, the methylation level was maintained and did not change with CD activity (aCD vs iCD). The subanalysis comparison between aCD and iCD showed significant differential methylation profiles in other CpGs: TNF, FAS, ABCB1, CAT, and TNFRS1BF genes. DISCUSSION The methylation status of DEFA5 and TNF genes provides a signature biomarker that characterizes patients with CD and supports the possible implication of the environment and the immune system in CD pathogenesis.
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Affiliation(s)
- Inés Moret-Tatay
- Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
- Biomedical Research Centre, Hepatic and Digestive Diseases Network (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas [CIBEREHD]), Madrid, Spain
| | - Elena Cerrillo
- Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
- Department of Gastroenterology, Hospital La Fe, Valencia, Spain
| | - Esteban Sáez-González
- Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
- Department of Gastroenterology, Hospital La Fe, Valencia, Spain
| | - David Hervás
- Department of Gastroenterology, Hospital La Fe, Valencia, Spain
| | - Marisa Iborra
- Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
- Biomedical Research Centre, Hepatic and Digestive Diseases Network (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas [CIBEREHD]), Madrid, Spain
- Department of Gastroenterology, Hospital La Fe, Valencia, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
| | - Enrique Busó
- Central Unit for Research in Medicine (UCIM),University of Valencia, Valencia, Spain
| | - Luis Tortosa
- Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
- Biomedical Research Centre, Hepatic and Digestive Diseases Network (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas [CIBEREHD]), Madrid, Spain
| | - Pilar Nos
- Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
- Biomedical Research Centre, Hepatic and Digestive Diseases Network (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas [CIBEREHD]), Madrid, Spain
- Department of Gastroenterology, Hospital La Fe, Valencia, Spain
| | - Belén Beltrán
- Inflammatory Bowel Disease Research Group, Health Research Institute La Fe (IIS La Fe), Valencia, Spain
- Biomedical Research Centre, Hepatic and Digestive Diseases Network (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas [CIBEREHD]), Madrid, Spain
- Department of Gastroenterology, Hospital La Fe, Valencia, Spain
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Abstract
PURPOSE OF THE REVIEW This review aims at presenting the most significant data obtained in the field of the genetics of autoinflammatory disorders (AID) over the last past 5 years. RECENT FINDINGS More than 15 genes have been implicated in AID since 2014, unveiling new pathogenic pathways. Recent data have revealed atypical modes of transmission in several inherited AID, such as somatic mosaicism and digenism. First pieces of evidence showing an involvement of epigenetic modifications in the pathogenesis of AID have also been brought to light. Novel genetic data have been obtained on the molecular bases of genetically complex AID. The development of next-generation sequencing in routine clinical practice has led to an explosion in the identification of new AID genes. Advances in the knowledge of AID further blur the limits between monogenic and multifactorial forms of these syndromes, and between autoinflammatory and autoimmune conditions.
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Affiliation(s)
- Isabelle Jéru
- Inserm U938, Saint-Antoine Research Centre, Institute of Cardiometabolism and Nutrition, Sorbonne University, Paris, France. .,Department of Molecular Biology and Genetics, Saint-Antoine University Hospital, Assistance Publique-Hôpitaux de Paris, 184 rue du Faubourg Saint-Antoine, 75571 Cédex 12, Paris, France.
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Mateos B, Palanca-Ballester C, Saez-Gonzalez E, Moret I, Lopez A, Sandoval J. Epigenetics of Inflammatory Bowel Disease: Unraveling Pathogenic Events. Crohn's & Colitis 360 2019. [DOI: 10.1093/crocol/otz017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Epigenetics has emerged as a new and promising field in recent years. Because there exists a need to find new biomarkers and improve diagnosis, prognosis, and drug response for inflammatory bowel diseases, the research on epigenetic biomarkers for molecular diagnostics encourages the translation of this field from the bench to the clinical practice. In this review, we present an overview of the current knowledge and its potential applicability of this emerging field in inflammatory bowel diseases.
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Affiliation(s)
- Beatriz Mateos
- Inflammatory Bowel Disease Research Group, Medical Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
| | - Cora Palanca-Ballester
- Biomarkers and Precision Medicine Unit, Medical Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
| | - Esteban Saez-Gonzalez
- Inflammatory Bowel Disease Research Group, Medical Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
| | - Inés Moret
- Inflammatory Bowel Disease Research Group, Medical Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
- Centro de Investigación Biomédica en Red en el Área temática de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Adrian Lopez
- Biomarkers and Precision Medicine Unit, Medical Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit, Medical Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
- §Epigenomics Core Facility, Medical Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
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Somineni HK, Venkateswaran S, Kilaru V, Marigorta UM, Mo A, Okou DT, Kellermayer R, Mondal K, Cobb D, Walters TD, Griffiths A, Noe JD, Crandall WV, Rosh JR, Mack DR, Heyman MB, Baker SS, Stephens MC, Baldassano RN, Markowitz JF, Dubinsky MC, Cho J, Hyams JS, Denson LA, Gibson G, Cutler DJ, Conneely KN, Smith AK, Kugathasan S. Blood-Derived DNA Methylation Signatures of Crohn's Disease and Severity of Intestinal Inflammation. Gastroenterology 2019; 156:2254-2265.e3. [PMID: 30779925 PMCID: PMC6529254 DOI: 10.1053/j.gastro.2019.01.270] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 12/18/2018] [Accepted: 01/28/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Crohn's disease is a relapsing and remitting inflammatory disorder with a variable clinical course. Although most patients present with an inflammatory phenotype (B1), approximately 20% of patients rapidly progress to complicated disease, which includes stricturing (B2), within 5 years. We analyzed DNA methylation patterns in blood samples of pediatric patients with Crohn's disease at diagnosis and later time points to identify changes that associate with and might contribute to disease development and progression. METHODS We obtained blood samples from 164 pediatric patients (1-17 years old) with Crohn's disease (B1 or B2) who participated in a North American study and were followed for 5 years. Participants without intestinal inflammation or symptoms served as controls (n = 74). DNA methylation patterns were analyzed in samples collected at time of diagnosis and 1-3 years later at approximately 850,000 sites. We used genetic association and the concept of Mendelian randomization to identify changes in DNA methylation patterns that might contribute to the development of or result from Crohn's disease. RESULTS We identified 1189 5'-cytosine-phosphate-guanosine-3' (CpG) sites that were differentially methylated between patients with Crohn's disease (at diagnosis) and controls. Methylation changes at these sites correlated with plasma levels of C-reactive protein. A comparison of methylation profiles of DNA collected at diagnosis of Crohn's disease vs during the follow-up period showed that, during treatment, alterations identified in methylation profiles at the time of diagnosis of Crohn's disease more closely resembled patterns observed in controls, irrespective of disease progression to B2. We identified methylation changes at 3 CpG sites that might contribute to the development of Crohn's disease. Most CpG methylation changes associated with Crohn's disease disappeared with treatment of inflammation and might be a result of Crohn's disease. CONCLUSIONS Methylation patterns observed in blood samples from patients with Crohn's disease accompany acute inflammation; with treatment, these change to resemble methylation patterns observed in patients without intestinal inflammation. These findings indicate that Crohn's disease-associated patterns of DNA methylation observed in blood samples are a result of the inflammatory features of the disease and are less likely to contribute to disease development or progression.
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Affiliation(s)
- Hari K Somineni
- Genetics and Molecular Biology Program, Emory University, Atlanta, Georgia; Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Suresh Venkateswaran
- Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Varun Kilaru
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia
| | - Urko M Marigorta
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, Georgia
| | - Angela Mo
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, Georgia
| | - David T Okou
- Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Kajari Mondal
- Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Dawayland Cobb
- Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia
| | - Thomas D Walters
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Anne Griffiths
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Joshua D Noe
- Department of Pediatric Gastroenterology, Hepatology and Nutrition, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Wallace V Crandall
- Division of Pediatric Gastroenterology, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, Ohio
| | - Joel R Rosh
- Department of Pediatrics, Goryeb Children's Hospital, Morristown, New Jersey
| | - David R Mack
- Department of Pediatrics, Children's Hospital of Eastern Ontario IBD Centre and University of Ottawa, Ottawa, Ontario, Canada
| | - Melvin B Heyman
- Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - Susan S Baker
- Department of Digestive Diseases and Nutrition Center, University at Buffalo, Buffalo, New York
| | - Michael C Stephens
- Department of Pediatric Gastroenterology, Mayo Clinic, Rochester, Minnesota
| | - Robert N Baldassano
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Marla C Dubinsky
- Department of Pediatrics, Mount Sinai Hospital, New York, New York
| | - Judy Cho
- Department of Pediatrics, Mount Sinai Hospital, New York, New York
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children's Medical Center, Hartford, Connecticut
| | - Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Greg Gibson
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, Georgia
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, Georgia
| | - Karen N Conneely
- Genetics and Molecular Biology Program, Emory University, Atlanta, Georgia; Department of Human Genetics, Emory University, Atlanta, Georgia
| | - Alicia K Smith
- Genetics and Molecular Biology Program, Emory University, Atlanta, Georgia; Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, Georgia; Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, Georgia
| | - Subra Kugathasan
- Genetics and Molecular Biology Program, Emory University, Atlanta, Georgia; Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia; Department of Human Genetics, Emory University, Atlanta, Georgia.
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Abstract
Beyond their well-known role in embryonic development of the central and peripheral nervous system, neurotrophins, particularly nerve growth factor and brain-derived neurotrophic factor, exert an essential role in pain production and sensitization. This has mainly been studied within the framework of somatic pain, and even antibodies (tanezumab and fasinumab) have recently been developed for their use in chronic somatic painful conditions, such as osteoarthritis or low back pain. However, data suggest that neurotrophins also exert an important role in the occurrence of visceral pain and visceral sensitization. Visceral pain is a distressing symptom that prompts many consultations and is typically encountered in both 'organic' (generally inflammatory) and 'functional' (displaying no obvious structural changes in routine clinical evaluations) disorders of the gut, such as inflammatory bowel disease and irritable bowel syndrome, respectively. The present review provides a summary of neurotrophins as a molecular family and their role in pain in general and addresses recent investigations of the involvement of nerve growth factor and brain-derived neurotrophic factor in visceral pain, particularly that associated with inflammatory bowel disease and irritable bowel syndrome.
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Zandvakili I, Lazaridis KN. Cell-free DNA testing: future applications in gastroenterology and hepatology. Therap Adv Gastroenterol 2019; 12:1756284819841896. [PMID: 31019553 PMCID: PMC6466469 DOI: 10.1177/1756284819841896] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 03/04/2019] [Indexed: 02/04/2023] Open
Abstract
The application of next-generation sequencing in clinical practice is increasing as accuracy and interpretation have improved and the cost continues to decline rapidly. Cell-free DNA is a unique source for next-generation sequencing that could change routine clinical practice in gastroenterology and hepatology. Testing of cell-free DNA in blood and fecal samples is an easy, rapid, and noninvasive method to assess for premalignant, malignant, metabolic, infectious, inflammatory, and autoimmune gastrointestinal and liver diseases. In this review, we describe cell-free DNA technologies, current applications of cell-free DNA testing, and proposed cell-free DNA targets for gastrointestinal and hepatic diseases, with a specific focus on malignancy. In addition, we provide commentary on how cell-free DNA can be integrated into clinical practice and help guide diagnosis, prognosis, disease management, and therapeutic response.
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Affiliation(s)
- Inuk Zandvakili
- Division of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
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Li Yim AYF, de Bruyn JR, Duijvis NW, Sharp C, Ferrero E, de Jonge WJ, Wildenberg ME, Mannens MMAM, Buskens CJ, D’Haens GR, Henneman P, te Velde AA. A distinct epigenetic profile distinguishes stenotic from non-inflamed fibroblasts in the ileal mucosa of Crohn's disease patients. PLoS One 2018; 13:e0209656. [PMID: 30589872 PMCID: PMC6307755 DOI: 10.1371/journal.pone.0209656] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 12/10/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The chronic remitting and relapsing intestinal inflammation characteristic of Crohn's disease frequently leads to fibrosis and subsequent stenosis of the inflamed region. Approximately a third of all Crohn's disease patients require resection at some stage in their disease course. As the pathogenesis of Crohn's disease associated fibrosis is largely unknown, a strong necessity exists to better understand the pathophysiology thereof. METHODS In this study, we investigated changes of the DNA methylome and transcriptome of ileum-derived fibroblasts associated to the occurrence of Crohn's disease associated fibrosis. Eighteen samples were included in a DNA methylation array and twenty-one samples were used for RNA sequencing. RESULTS Most differentially methylated regions and differentially expressed genes were observed when comparing stenotic with non-inflamed samples. By contrast, few differences were observed when comparing Crohn's disease with non-Crohn's disease, or inflamed with non-inflamed tissue. Integrative methylation and gene expression analyses revealed dysregulation of genes associated to the PRKACA and E2F1 network, which is involved in cell cycle progression, angiogenesis, epithelial to mesenchymal transition, and bile metabolism. CONCLUSION Our research provides evidence that the methylome and the transcriptome are systematically dysregulated in stenosis-associated fibroblasts.
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Affiliation(s)
- Andrew Y. F. Li Yim
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Epigenetics Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom
| | - Jessica R. de Bruyn
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Gastroenterology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Nicolette W. Duijvis
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Catriona Sharp
- Epigenetics Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom
| | - Enrico Ferrero
- Computational Biology, Target Sciences, GlaxoSmithKline, Stevenage, United Kingdom
| | - Wouter J. de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Manon E. Wildenberg
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Marcel M. A. M. Mannens
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Christianne J. Buskens
- Department of Surgery, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Geert R. D’Haens
- Department of Gastroenterology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Peter Henneman
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Anje A. te Velde
- Tytgat Institute for Liver and Intestinal Research, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- * E-mail:
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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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