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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] [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 : THE PREPRINT SERVER FOR HEALTH SCIENCES 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] [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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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: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [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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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: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [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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Aliferi A, Sundaram S, Ballard D, Freire-Aradas A, Phillips C, Lareu MV, Court DS. Combining current knowledge on DNA methylation-based age estimation towards the development of a superior forensic DNA intelligence tool. Forensic Sci Int Genet 2021; 57:102637. [PMID: 34852982 DOI: 10.1016/j.fsigen.2021.102637] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/19/2021] [Accepted: 11/17/2021] [Indexed: 01/09/2023]
Abstract
The estimation of chronological age from biological fluids has been an important quest for forensic scientists worldwide, with recent approaches exploiting the variability of DNA methylation patterns with age in order to develop the next generation of forensic 'DNA intelligence' tools for this application. Drawing from the conclusions of previous work utilising massively parallel sequencing (MPS) for this analysis, this work introduces a DNA methylation-based age estimation method for blood that exhibits the best combination of prediction accuracy and sensitivity reported to date. Statistical evaluation of markers from 51 studies using microarray data from over 4000 individuals, followed by validation using in-house generated MPS data, revealed a final set of 11 markers with the greatest potential for accurate age estimation from minimal DNA material. Utilising an algorithm based on support vector machines, the proposed model achieved an average error (MAE) of 3.3 years, with this level of accuracy retained down to 5 ng of starting DNA input (~ 1 ng PCR input). The accuracy of the model was retained (MAE = 3.8 years) in a separate test set of 88 samples of Spanish origin, while predictions for donors of greater forensic interest (< 55 years of age) displayed even higher accuracy (MAE = 2.6 years). Finally, no sex-related bias was observed for this model, while there were also no signs of variation observed between control and disease-associated populations for schizophrenia, rheumatoid arthritis, frontal temporal dementia and progressive supranuclear palsy in microarray data relating to the 11 markers.
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Affiliation(s)
- Anastasia Aliferi
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Sudha Sundaram
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - David Ballard
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Maria Victoria Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Denise Syndercombe Court
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
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Xu B, Xu Z, Chen Y, Lu N, Shu Z, Tan X. Genetic and epigenetic associations of ANRIL with coronary artery disease and risk factors. BMC Med Genomics 2021; 14:240. [PMID: 34615528 PMCID: PMC8496081 DOI: 10.1186/s12920-021-01094-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 09/30/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Both DNA genotype and methylation of antisense non-coding RNA in the INK4 locus (ANRIL) have been robustly associated with coronary artery disease (CAD), but the interdependent mechanisms of genotype and methylation remain unclear. METHODS Eighteen tag single nucleotide polymorphisms (SNPs) of ANRIL were genotyped in a matched case-control study (cases 503 and controls 503). DNA methylation of ANRIL and the INK4/ARF locus (p14ARF, p15INK4b and p16INK4a) was measured using pyrosequencing in the same set of samples (cases 100 and controls 100). RESULTS Polymorphisms of ANRIL (rs1004638, rs1333048 and rs1333050) were significantly associated with CAD (p < 0.05). The incidence of CAD, multi-vessel disease, and modified Gensini scores demonstrated a strong, direct association with ANRIL gene dosage (p < 0.05). There was no significant association between ANRIL polymorphisms and myocardial infarction/acute coronary syndrome (MI/ACS) (p > 0.05). Methylation levels of ANRIL were similar between the two studied groups (p > 0.05), but were different in the rs1004638 genotype, with AA and AT genotype having a higher level of ANRIL methylation (pos4, p = 0.006; pos8, p = 0.019). Further Spearman analyses indicated that methylation levels of ANRIL were positively associated with systolic blood pressure (pos6, r = 0.248, p = 0.013), diastolic blood pressure (pos3, r = 0.213, p = 0.034; pos6, r = 0.220, p = 0.028), and triglyceride (pos4, r = 0.253, p = 0.013), and negatively associated with high-density lipoprotein cholesterol (pos2, r = - 0.243, p = 0.017). Additionally, we identified 12 transcription factor binding sites (TFBS) within the methylated ANRIL region, and functional annotation indicated these TFBS were associated with basal transcription. Methylation at the INK4/ARF locus was not associated with ANRIL genotype. CONCLUSIONS These results indicate that ANRIL genotype (tag SNPs rs1004638, rs1333048 and rs1333050) mainly affects coronary atherosclerosis, but not MI/ACS. There may be allele-related DNA methylation and allele-related binding of transcription factors within the ANRIL promoter.
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Affiliation(s)
- Bayi Xu
- Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Zhixia Xu
- Department of Medical Service, Second Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Yequn Chen
- Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Nan Lu
- Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Zhouwu Shu
- Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China
| | - Xuerui Tan
- Department of Cardiology, First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong, China.
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The role of epigenetic modifications for the pathogenesis of Crohn's disease. Clin Epigenetics 2021; 13:108. [PMID: 33980294 PMCID: PMC8117638 DOI: 10.1186/s13148-021-01089-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [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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8
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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: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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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Taman H, Fenton CG, Anderssen E, Florholmen J, Paulssen RH. DNA hypo-methylation facilitates anti-inflammatory responses in severe ulcerative colitis. PLoS One 2021; 16:e0248905. [PMID: 33793617 PMCID: PMC8016308 DOI: 10.1371/journal.pone.0248905] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/06/2021] [Indexed: 12/16/2022] Open
Abstract
Severe ulcerative colitis (UC) is a potentially life-threatening disease with a potential colorectal cancer (CRC) risk. The aim of this study was to explore the relationship between transcriptomic and genome-wide DNA methylation profiles in a well-stratified, treatment-naïve severe UC patient population in order to define specific epigenetic changes that could be responsible for the grade of disease severity. Mucosal biopsies from treatment-naïve severe UC patients (n = 8), treatment-naïve mild UC (n = 8), and healthy controls (n = 8) underwent both whole transcriptome RNA-Seq and genome-wide DNA bisulfite- sequencing, and principal component analysis (PCA), cell deconvolutions and diverse statistical methods were applied to obtain a dataset of significantly differentially expressed genes (DEGs) with correlation to DNA methylation for severe UC. DNA hypo-methylation correlated with approximately 80% of all DEGs in severe UC when compared to mild UC. Enriched pathways of annotated hypo-methylated genes revealed neutrophil degranulation, and immuno-regulatory interactions of the lymphoid system. Specifically, hypo-methylated anti-inflammatory genes found for severe UC were IL10, SIGLEC5, CD86, CLMP and members of inflammasomes NLRP3 and NLRC4. Hypo-methylation of anti-inflammatory genes during severe UC implies an interplay between the epithelium and lamina propria in order to mitigate inflammation in the gut. The specifically DNA hypo-methylated genes found for severe UC can potentially be useful biomarkers for determining disease severity and in the development of new targeted treatment strategies for severe UC patients.
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Affiliation(s)
- Hagar Taman
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT- The Arctic University of Norway, Tromsø, Norway
- Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Christopher G. Fenton
- Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Endre Anderssen
- Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Jon Florholmen
- Gastroenterology and Nutrition Research Group, Department of Clinical Medicine, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Ruth H. Paulssen
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT- The Arctic University of Norway, Tromsø, Norway
- Genomics Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT- The Arctic University of Norway, Tromsø, Norway
- * E-mail:
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10
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Nair J, Maheshwari A. Epigenetics in Necrotizing Enterocolitis. Curr Pediatr Rev 2021; 17:172-184. [PMID: 33882811 DOI: 10.2174/1573396317666210421110608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/14/2021] [Accepted: 02/26/2021] [Indexed: 11/22/2022]
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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11
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Smyth LJ, Patterson CC, Swan EJ, Maxwell AP, McKnight AJ. DNA Methylation Associated With Diabetic Kidney Disease in Blood-Derived DNA. Front Cell Dev Biol 2020; 8:561907. [PMID: 33178681 PMCID: PMC7593403 DOI: 10.3389/fcell.2020.561907] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/15/2020] [Indexed: 12/23/2022] Open
Abstract
A subset of individuals with type 1 diabetes will develop diabetic kidney disease (DKD). DKD is heritable and large-scale genome-wide association studies have begun to identify genetic factors that influence DKD. Complementary to genetic factors, we know that a person’s epigenetic profile is also altered with DKD. This study reports analysis of DNA methylation, a major epigenetic feature, evaluating methylome-wide loci for association with DKD. Unique features (n = 485,577; 482,421 CpG probes) were evaluated in blood-derived DNA from carefully phenotyped White European individuals diagnosed with type 1 diabetes with (cases) or without (controls) DKD (n = 677 samples). Explicitly, 150 cases were compared to 100 controls using the 450K array, with subsequent analysis using data previously generated for a further 96 cases and 96 controls on the 27K array, and de novo methylation data generated for replication in 139 cases and 96 controls. Following stringent quality control, raw data were quantile normalized and beta values calculated to reflect the methylation status at each site. The difference in methylation status was evaluated between cases and controls; resultant P-values for array-based data were adjusted for multiple testing. Genes with significantly increased (hypermethylated) and/or decreased (hypomethylated) levels of DNA methylation were considered for biological relevance by functional enrichment analysis using KEGG pathways. Twenty-two loci demonstrated statistically significant fold changes associated with DKD and additional support for these associated loci was sought using independent samples derived from patients recruited with similar inclusion criteria. Markers associated with CCNL1 and ZNF187 genes are supported as differentially regulated loci (P < 10–8), with evidence also presented for AFF3, which has been identified from a meta-analysis and subsequent replication of genome-wide association studies. Further supporting evidence for differential gene expression in CCNL1 and ZNF187 is presented from kidney biopsy and blood-derived RNA in people with and without kidney disease from NephroSeq. Evidence confirming that methylation sites influence the development of DKD may aid risk prediction tools and stimulate research to identify epigenomic therapies which might be clinically useful for this disease.
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Affiliation(s)
- Laura J Smyth
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
| | | | - Elizabeth J Swan
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
| | - Alexander P Maxwell
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom.,Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom
| | - Amy Jayne McKnight
- Centre for Public Health, Queen's University Belfast, Belfast, United Kingdom
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12
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Taber A, Christensen E, Lamy P, Nordentoft I, Prip F, Lindskrog SV, Birkenkamp-Demtröder K, Okholm TLH, Knudsen M, Pedersen JS, Steiniche T, Agerbæk M, Jensen JB, Dyrskjøt L. Molecular correlates of cisplatin-based chemotherapy response in muscle invasive bladder cancer by integrated multi-omics analysis. Nat Commun 2020; 11:4858. [PMID: 32978382 PMCID: PMC7519650 DOI: 10.1038/s41467-020-18640-0] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 09/03/2020] [Indexed: 01/05/2023] Open
Abstract
Overtreatment with cisplatin-based chemotherapy is a major issue in the management of muscle-invasive bladder cancer (MIBC), and currently none of the reported biomarkers for predicting response have been implemented in the clinic. Here we perform a comprehensive multi-omics analysis (genomics, transcriptomics, epigenomics and proteomics) of 300 MIBC patients treated with chemotherapy (neoadjuvant or first-line) to identify molecular changes associated with treatment response. DNA-based associations with response converge on genomic instability driven by a high number of chromosomal alterations, indels, signature 5 mutations and/or BRCA2 mutations. Expression data identifies the basal/squamous gene expression subtype to be associated with poor response. Immune cell infiltration and high PD-1 protein expression are associated with treatment response. Through integration of genomic and transcriptomic data, we demonstrate patient stratification to groups of low and high likelihood of cisplatin-based response. This could pave the way for future patient selection following validation in prospective clinical trials. There are currently only a few biomarkers to predict the response of muscle invasive bladder cancer to therapy. Here, the authors analyse 300 tumors using exome and RNA sequencing and find that tumors with a high degree of genomic instability and a non-basal/squamous gene expression subtype are most likely to respond to treatment.
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Affiliation(s)
- Ann Taber
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Emil Christensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Frederik Prip
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Sia Viborg Lindskrog
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Karin Birkenkamp-Demtröder
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Trine Line Hauge Okholm
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Michael Knudsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Jakob Skou Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Torben Steiniche
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Mads Agerbæk
- Department of Oncology, Aarhus University Hospital, Aarhus, Denmark
| | - Jørgen Bjerggaard Jensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark. .,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
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13
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Hendrickx JO, van Gastel J, Leysen H, Martin B, Maudsley S. High-dimensionality Data Analysis of Pharmacological Systems Associated with Complex Diseases. Pharmacol Rev 2020; 72:191-217. [PMID: 31843941 DOI: 10.1124/pr.119.017921] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
It is widely accepted that molecular reductionist views of highly complex human physiologic activity, e.g., the aging process, as well as therapeutic drug efficacy are largely oversimplifications. Currently some of the most effective appreciation of biologic disease and drug response complexity is achieved using high-dimensionality (H-D) data streams from transcriptomic, proteomic, metabolomics, or epigenomic pipelines. Multiple H-D data sets are now common and freely accessible for complex diseases such as metabolic syndrome, cardiovascular disease, and neurodegenerative conditions such as Alzheimer's disease. Over the last decade our ability to interrogate these high-dimensionality data streams has been profoundly enhanced through the development and implementation of highly effective bioinformatic platforms. Employing these computational approaches to understand the complexity of age-related diseases provides a facile mechanism to then synergize this pathologic appreciation with a similar level of understanding of therapeutic-mediated signaling. For informative pathology and drug-based analytics that are able to generate meaningful therapeutic insight across diverse data streams, novel informatics processes such as latent semantic indexing and topological data analyses will likely be important. Elucidation of H-D molecular disease signatures from diverse data streams will likely generate and refine new therapeutic strategies that will be designed with a cognizance of a realistic appreciation of the complexity of human age-related disease and drug effects. We contend that informatic platforms should be synergistic with more advanced chemical/drug and phenotypic cellular/tissue-based analytical predictive models to assist in either de novo drug prioritization or effective repurposing for the intervention of aging-related diseases. SIGNIFICANCE STATEMENT: All diseases, as well as pharmacological mechanisms, are far more complex than previously thought a decade ago. With the advent of commonplace access to technologies that produce large volumes of high-dimensionality data (e.g., transcriptomics, proteomics, metabolomics), it is now imperative that effective tools to appreciate this highly nuanced data are developed. Being able to appreciate the subtleties of high-dimensionality data will allow molecular pharmacologists to develop the most effective multidimensional therapeutics with effectively engineered efficacy profiles.
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Affiliation(s)
- Jhana O Hendrickx
- Receptor Biology Laboratory, Department of Biomedical Research (J.O.H., J.v.G., H.L., S.M.) and Faculty of Pharmacy, Biomedical and Veterinary Sciences (J.O.H., J.v.G., H.L., B.M., S.M.), University of Antwerp, Antwerp, Belgium
| | - Jaana van Gastel
- Receptor Biology Laboratory, Department of Biomedical Research (J.O.H., J.v.G., H.L., S.M.) and Faculty of Pharmacy, Biomedical and Veterinary Sciences (J.O.H., J.v.G., H.L., B.M., S.M.), University of Antwerp, Antwerp, Belgium
| | - Hanne Leysen
- Receptor Biology Laboratory, Department of Biomedical Research (J.O.H., J.v.G., H.L., S.M.) and Faculty of Pharmacy, Biomedical and Veterinary Sciences (J.O.H., J.v.G., H.L., B.M., S.M.), University of Antwerp, Antwerp, Belgium
| | - Bronwen Martin
- Receptor Biology Laboratory, Department of Biomedical Research (J.O.H., J.v.G., H.L., S.M.) and Faculty of Pharmacy, Biomedical and Veterinary Sciences (J.O.H., J.v.G., H.L., B.M., S.M.), University of Antwerp, Antwerp, Belgium
| | - Stuart Maudsley
- Receptor Biology Laboratory, Department of Biomedical Research (J.O.H., J.v.G., H.L., S.M.) and Faculty of Pharmacy, Biomedical and Veterinary Sciences (J.O.H., J.v.G., H.L., B.M., S.M.), University of Antwerp, Antwerp, Belgium
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14
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Cypris O, Eipel M, Franzen J, Rösseler C, Tharmapalan V, Kuo CC, Vieri M, Nikolić M, Kirschner M, Brümmendorf TH, Zenke M, Lampert A, Beier F, Wagner W. PRDM8 reveals aberrant DNA methylation in aging syndromes and is relevant for hematopoietic and neuronal differentiation. Clin Epigenetics 2020; 12:125. [PMID: 32819411 PMCID: PMC7439574 DOI: 10.1186/s13148-020-00914-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Dyskeratosis congenita (DKC) and idiopathic aplastic anemia (AA) are bone marrow failure syndromes that share characteristics of premature aging with severe telomere attrition. Aging is also reflected by DNA methylation changes, which can be utilized to predict donor age. There is evidence that such epigenetic age predictions are accelerated in premature aging syndromes, but it is yet unclear how this is related to telomere length. DNA methylation analysis may support diagnosis of DKC and AA, which still remains a challenge for these rare diseases. RESULTS In this study, we analyzed blood samples of 70 AA and 18 DKC patients to demonstrate that their epigenetic age predictions are overall increased, albeit not directly correlated with telomere length. Aberrant DNA methylation was observed in the gene PRDM8 in DKC and AA as well as in other diseases with premature aging phenotype, such as Down syndrome and Hutchinson-Gilford-Progeria syndrome. Aberrant DNA methylation patterns were particularly found within subsets of cell populations in DKC and AA samples as measured with barcoded bisulfite amplicon sequencing (BBA-seq). To gain insight into the functional relevance of PRDM8, we used CRISPR/Cas9 technology to generate induced pluripotent stem cells (iPSCs) with heterozygous and homozygous knockout. Loss of PRDM8 impaired hematopoietic and neuronal differentiation of iPSCs, even in the heterozygous knockout clone, but it did not impact on epigenetic age. CONCLUSION Taken together, our results demonstrate that epigenetic aging is accelerated in DKC and AA, independent from telomere attrition. Furthermore, aberrant DNA methylation in PRDM8 provides another biomarker for bone marrow failure syndromes and modulation of this gene in cellular subsets may be related to the hematopoietic and neuronal phenotypes observed in premature aging syndromes.
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Affiliation(s)
- Olivia Cypris
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Monika Eipel
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Corinna Rösseler
- Institute of Physiology, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Vithurithra Tharmapalan
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Chao-Chung Kuo
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Margherita Vieri
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Miloš Nikolić
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
| | - Martin Kirschner
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Tim H. Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Martin Zenke
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
- Institute for Biomedical Engineering – Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
| | - Angelika Lampert
- Institute of Physiology, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty University Hospital Aachen, RWTH Aachen University, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University, Pauwelsstrasse 20, Aachen, Germany
- Institute for Biomedical Engineering – Cell Biology, RWTH Aachen University Medical School, Aachen, Germany
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15
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Marzullo P, Di Renzo L, Pugliese G, De Siena M, Barrea L, Muscogiuri G, Colao A, Savastano S. From obesity through gut microbiota to cardiovascular diseases: a dangerous journey. INTERNATIONAL JOURNAL OF OBESITY SUPPLEMENTS 2020; 10:35-49. [PMID: 32714511 PMCID: PMC7371682 DOI: 10.1038/s41367-020-0017-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The co-existence of humans and gut microbiota started millions of years ago. Until now, a balance gradually developed between gut bacteria and their hosts. It is now recognized that gut microbiota are key to form adequate immune and metabolic functions and, more in general, for the maintenance of good health. Gut microbiota are established before birth under the influence of maternal nutrition and metabolic status, which can impact the future metabolic risk of the offspring in terms of obesity, diabetes, and cardiometabolic disorders during the lifespan. Obesity and diabetes are prone to disrupt the gut microbiota and alter the gut barrier permeability, leading to metabolic endotoxaemia with its detrimental consequences on health. Specific bacterial sequences are now viewed as peculiar signatures of the metabolic syndrome across life stages in each individual, and are linked to pathogenesis of cardiovascular diseases (CVDs) via metabolic products (metabolites) and immune modulation. These mechanisms have been linked, in association with abnormalities in microbial richness and diversity, to an increased risk of developing arterial hypertension, systemic inflammation, nonalcoholic fatty liver disease, coronary artery disease, chronic kidney disease, and heart failure. Emerging strategies for the manipulation of intestinal microbiota represent a promising therapeutic option for the prevention and treatment of CVD especially in individuals prone to CV events.
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Affiliation(s)
- Paolo Marzullo
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
- Division of General Medicine, IRCCS Istituto Auxologico Italiano, 28923 Piancavallo, Verbania Italy
| | - Laura Di Renzo
- Section of Clinical Nutrition and Nutrigenomic, Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00136 Rome, Italy
| | - Gabriella Pugliese
- Unit of Endocrinology, Dipartimento di Medicina Clinica e Chirurgia, Federico II University, 80131 Naples, Italy
| | - Martina De Siena
- Division of Gastroenterology, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, Roma, Italy
- Digestive Endoscopy Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, Roma, Italy
| | - Luigi Barrea
- Unit of Endocrinology, Dipartimento di Medicina Clinica e Chirurgia, Federico II University, 80131 Naples, Italy
| | - Giovanna Muscogiuri
- Unit of Endocrinology, Dipartimento di Medicina Clinica e Chirurgia, Federico II University, 80131 Naples, Italy
| | - Annamaria Colao
- Unit of Endocrinology, Dipartimento di Medicina Clinica e Chirurgia, Federico II University, 80131 Naples, Italy
| | - Silvia Savastano
- Unit of Endocrinology, Dipartimento di Medicina Clinica e Chirurgia, Federico II University, 80131 Naples, Italy
| | - on behalf of Obesity Programs of nutrition, Education, Research and Assessment (OPERA) Group
- Department of Translational Medicine, Università del Piemonte Orientale, 28100 Novara, Italy
- Division of General Medicine, IRCCS Istituto Auxologico Italiano, 28923 Piancavallo, Verbania Italy
- Section of Clinical Nutrition and Nutrigenomic, Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00136 Rome, Italy
- Unit of Endocrinology, Dipartimento di Medicina Clinica e Chirurgia, Federico II University, 80131 Naples, Italy
- Division of Gastroenterology, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, Roma, Italy
- Digestive Endoscopy Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, Roma, Italy
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16
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Han Y, Franzen J, Stiehl T, Gobs M, Kuo CC, Nikolić M, Hapala J, Koop BE, Strathmann K, Ritz-Timme S, Wagner W. New targeted approaches for epigenetic age predictions. BMC Biol 2020; 18:71. [PMID: 32580727 PMCID: PMC7315536 DOI: 10.1186/s12915-020-00807-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/08/2020] [Indexed: 12/16/2022] Open
Abstract
Background Age-associated DNA methylation changes provide a promising biomarker for the aging process. While genome-wide DNA methylation profiles enable robust age-predictors by integration of many age-associated CG dinucleotides (CpGs), there are various alternative approaches for targeted measurements at specific CpGs that better support standardized and cost-effective high-throughput analysis. Results In this study, we utilized 4647 Illumina BeadChip profiles of blood to select CpG sites that facilitate reliable age-predictions based on pyrosequencing. We demonstrate that the precision of DNA methylation measurements can be further increased with droplet digital PCR (ddPCR). In comparison, bisulfite barcoded amplicon sequencing (BBA-seq) gave slightly lower correlation between chronological age and DNA methylation at individual CpGs, while the age-predictions were overall relatively accurate. Furthermore, BBA-seq data revealed that the correlation of methylation levels with age at neighboring CpG sites follows a bell-shaped curve, often associated with a CTCF binding site. We demonstrate that within individual BBA-seq reads the DNA methylation at neighboring CpGs is not coherently modified, but reveals a stochastic pattern. Based on this, we have developed a new approach for epigenetic age predictions based on the binary sequel of methylated and non-methylated sites in individual reads, which reflects heterogeneity in epigenetic aging within a sample. Conclusion Targeted DNA methylation analysis at few age-associated CpGs by pyrosequencing, BBA-seq, and particularly ddPCR enables high precision of epigenetic age-predictions. Furthermore, we demonstrate that the stochastic evolution of age-associated DNA methylation patterns in BBA-seq data enables epigenetic clocks for individual DNA strands.
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Affiliation(s)
- Yang Han
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Julia Franzen
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Thomas Stiehl
- Interdisciplinary Center for Scientific Computing (IWR), Institute of Applied Mathematics, University of Heidelberg, Heidelberg, Germany
| | - Michael Gobs
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Chao-Chung Kuo
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Miloš Nikolić
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Jan Hapala
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | | | - Klaus Strathmann
- Institute for Transfusion Medicine, RWTH Aachen University Medical School, Aachen, Germany
| | - Stefanie Ritz-Timme
- Institute for Legal Medicine, Heinrich Heine University, Düsseldorf, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Pauwelsstraße 20, 52074, Aachen, Germany. .,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany.
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17
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MapReduce-Based Parallel Genetic Algorithm for CpG-Site Selection in Age Prediction. Genes (Basel) 2019; 10:genes10120969. [PMID: 31775313 PMCID: PMC6947642 DOI: 10.3390/genes10120969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/12/2019] [Accepted: 11/15/2019] [Indexed: 11/23/2022] Open
Abstract
Genomic biomarkers such as DNA methylation (DNAm) are employed for age prediction. In recent years, several studies have suggested the association between changes in DNAm and its effect on human age. The high dimensional nature of this type of data significantly increases the execution time of modeling algorithms. To mitigate this problem, we propose a two-stage parallel algorithm for selection of age related CpG-sites. The algorithm first attempts to cluster the data into similar age ranges. In the next stage, a parallel genetic algorithm (PGA), based on the MapReduce paradigm (MR-based PGA), is used for selecting age-related features of each individual age range. In the proposed method, the execution of the algorithm for each age range (data parallel), the evaluation of chromosomes (task parallel) and the calculation of the fitness function (data parallel) are performed using a novel parallel framework. In this paper, we consider 16 different healthy DNAm datasets that are related to the human blood tissue and that contain the relevant age information. These datasets are combined into a single unioned set, which is in turn randomly divided into two sets of train and test data with a ratio of 7:3, respectively. We build a Gradient Boosting Regressor (GBR) model on the selected CpG-sites from the train set. To evaluate the model accuracy, we compared our results with state-of-the-art approaches that used these datasets, and observed that our method performs better on the unseen test dataset with a Mean Absolute Deviation (MAD) of 3.62 years, and a correlation (R2) of 95.96% between age and DNAm. In the train data, the MAD and R2 are 1.27 years and 99.27%, respectively. Finally, we evaluate our method in terms of the effect of parallelization in computation time. The algorithm without parallelization requires 4123 min to complete, whereas the parallelized execution on 3 computing machines having 32 processing cores each, only takes a total of 58 min. This shows that our proposed algorithm is both efficient and scalable.
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18
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Wu X, Chen W, Lin F, Huang Q, Zhong J, Gao H, Song Y, Liang H. DNA methylation profile is a quantitative measure of biological aging in children. Aging (Albany NY) 2019; 11:10031-10051. [PMID: 31756171 PMCID: PMC6914436 DOI: 10.18632/aging.102399] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 10/26/2019] [Indexed: 12/21/2022]
Abstract
DNA methylation changes within the genome can be used to predict human age. However, the existing biological age prediction models based on DNA methylation are predominantly adult-oriented. We established a methylation-based age prediction model for children (9-212 months old) using data from 716 blood samples in 11 DNA methylation datasets. Our elastic net model includes 111 CpG sites, mostly in genes associated with development and aging. The model performed well and exhibited high precision, yielding a 98% correlation between the DNA methylation age and the chronological age, with an error of only 6.7 months. When we used the model to assess age acceleration in children based on their methylation data, we observed the following: first, the aging rate appears to be fastest in mid-childhood, and this acceleration is more pronounced in autistic children; second, lead exposure early in life increases the aging rate in boys, but not in girls; third, short-term recombinant human growth hormone treatment has little effect on the aging rate of children. Our child-specific methylation-based age prediction model can effectively detect epigenetic changes and health imbalances early in life. This may thus be a useful model for future studies of epigenetic interventions for age-related diseases.
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Affiliation(s)
- Xiaohui Wu
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China.,Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China.,Guangdong Province Key Laboratory of Psychiatric Disorders, Guangzhou, Guangdong, China
| | - Weidan Chen
- Department of Cardiovascular Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Fangqin Lin
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Qingsheng Huang
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jiayong Zhong
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Huan Gao
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yanyan Song
- The Guangdong Early Childhood Development Applied Engineering and Technology Research Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong, China
| | - Huiying Liang
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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19
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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: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [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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20
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Whyte JM, Ellis JJ, Brown MA, Kenna TJ. Best practices in DNA methylation: lessons from inflammatory bowel disease, psoriasis and ankylosing spondylitis. Arthritis Res Ther 2019; 21:133. [PMID: 31159831 PMCID: PMC6547594 DOI: 10.1186/s13075-019-1922-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Advances in genomic technology have enabled a greater understanding of the genetics of common immune-mediated diseases such as ankylosing spondylitis (AS), inflammatory bowel disease (IBD) and psoriasis. The substantial overlap in genetically identified pathogenic pathways has been demonstrated between these diseases. However, to date, gene discovery approaches have only mapped a minority of the heritability of these common diseases, and most disease-associated variants have been found to be non-coding, suggesting mechanisms of disease-association through transcriptional regulatory effects. Epigenetics is a major interface between genetic and environmental modifiers of disease and strongly influence transcription. DNA methylation is a well-characterised epigenetic mechanism, and a highly stable epigenetic marker, that is implicated in disease pathogenesis. DNA methylation is an under-investigated area in immune-mediated diseases, and many studies in the field are affected by experimental design limitations, related to study design, technical limitations of the methylation typing methods employed, and statistical issues. This has resulted in both sparsity of investigations into disease-related changes in DNA methylation, a paucity of robust findings, and difficulties comparing studies in the same disease. In this review, we cover the basics of DNA methylation establishment and control, and the methods used to examine it. We examine the current state of DNA methylation studies in AS, IBD and psoriasis; the limitations of previous studies; and the best practices for DNA methylation studies. The purpose of this review is to assist with proper experimental design and consistency of approach in future studies to enable a better understanding of the functional role of DNA methylation in immune-mediated disease.
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Affiliation(s)
- Jessica M Whyte
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Jonathan J Ellis
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia. .,Translational Research Institute, Princess Alexandra Hospital, 37 Kent Street, Woolloongabba, Queensland, 4102, Australia.
| | - Tony J Kenna
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
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21
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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: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [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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22
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Lu YH, Wang BH, Jiang F, Mo XB, Wu LF, He P, Lu X, Deng FY, Lei SF. Multi-omics integrative analysis identified SNP-methylation-mRNA: Interaction in peripheral blood mononuclear cells. J Cell Mol Med 2019; 23:4601-4610. [PMID: 31106970 PMCID: PMC6584519 DOI: 10.1111/jcmm.14315] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 02/18/2019] [Accepted: 03/14/2019] [Indexed: 11/29/2022] Open
Abstract
Genetic variants have potential influence on DNA methylation and thereby regulate mRNA expression. This study aimed to comprehensively reveal the relationships among SNP, methylation and mRNA, and identify methylation-mediated regulation patterns in human peripheral blood mononuclear cells (PBMCs). Based on in-house multi-omics datasets from 43 Chinese Han female subjects, genome-wide association trios were constructed by simultaneously testing the following three association pairs: SNP-methylation, methylation-mRNA and SNP-mRNA. Causal inference test (CIT) was used to identify methylation-mediated genetic effects on mRNA. A total of 64,184 significant cis-methylation quantitative trait loci (meQTLs) were identified (FDR < 0.05). Among the 745 constructed trios, 464 trios formed SNP-methylation-mRNA regulation chains (CIT). Network analysis (Cytoscape 3.3.0) constructed multiple complex regulation networks among SNP, methylation and mRNA (eg a total of 43 SNPs simultaneously connected to cg22517527 and further to PRMT2, DIP2A and YBEY). The regulation chains were supported by the evidence from 4DGenome database, relevant to immune or inflammatory related diseases/traits, and overlapped with previous eQTLs from dbGaP and GTEx. The results provide new insights into the regulation patterns among SNP, DNA methylation and mRNA expression, especially for the methylation-mediated effects, and also increase our understanding of functional mechanisms underlying the established associations.
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Affiliation(s)
- Yi-Hua Lu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Department of Epidemiology and Health Statistics, School of Public Health, Nantong University, Nantong, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
| | - Bing-Hua Wang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
| | - Fei Jiang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
| | - Xing-Bo Mo
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
| | - Long-Fei Wu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
| | - Pei He
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
| | - Xin Lu
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
| | - Fei-Yan Deng
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
| | - Shu-Feng Lei
- Center for Genetic Epidemiology and Genomics, School of Public Health, Medical College of Soochow University, Suzhou, P. R. China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, P. R. China
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23
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Dhingra R, Kwee LC, Diaz-Sanchez D, Devlin RB, Cascio W, Hauser ER, Gregory S, Shah S, Kraus WE, Olden K, Ward-Caviness CK. Evaluating DNA methylation age on the Illumina MethylationEPIC Bead Chip. PLoS One 2019; 14:e0207834. [PMID: 31002714 PMCID: PMC6474589 DOI: 10.1371/journal.pone.0207834] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/29/2019] [Indexed: 01/12/2023] Open
Abstract
DNA methylation age (DNAm age) has become a widely utilized epigenetic biomarker for the aging process. The Horvath method for determining DNAm age is perhaps the most widely utilized and validated DNA methylation age assessment measure. Horvath DNAm age is calculated based on methylation measurements at 353 loci, present on Illumina's 450k and 27k DNA methylation microarrays. With increasing use of the more recently developed Illumina MethylationEPIC (850k) microarray, it is worth revisiting this aging measure to evaluate estimation differences due to array design. Of the requisite 353 loci, 17 are missing from the 850k microarray. Similarly, an alternate, 71 loci DNA methylation age assessment measure created by Hannum et al. is missing 6 requisite loci. Using 17 datasets with 27k, 450k, and/or 850k methylation data, we compared each sample's epigenetic age estimated from all 353 loci required by the Horvath DNAm age calculator, and using only the 336 loci available on the 850k array. In 450k/27k data, removing loci not on the 850k array resulted in underestimation of Horvath's DNAm age. Underestimation of Horvath DNAm age increased from ages 0 to ~20, remaining stable thereafter (mean deviation = -3.46 y, SD = 1.13 for individuals ≥20 years). Underestimation of Horvath's DNAm age by the reduced 450k/27k data was similar to the underestimation observed in the 850k data indicating it is driven by missing probes. In analogous examination of Hannum's DNAm age, the magnitude and direction of epigenetic age misestimation varied with chronological age. In conclusion, inter-array deviations in DNAm age estimations may be largely driven by missing probes between arrays, despite default probe imputation procedures. Though correlations and associations based on Horvath's DNAm age may be unaffected, researchers should exercise caution when interpreting results based on absolute differences in DNAm age or when mixing samples assayed on different arrays.
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Affiliation(s)
- Radhika Dhingra
- National Health and Environmental Effects Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
- Department of Environmental Sciences and Engineering, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC, United States of America
- Institute for Environmental Health Solutions, University of North Carolina, Chapel Hill, NC United States of America
- * E-mail:
| | - Lydia Coulter Kwee
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
| | - David Diaz-Sanchez
- National Health and Environmental Effects Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - Robert B. Devlin
- National Health and Environmental Effects Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - Wayne Cascio
- National Health and Environmental Effects Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - Elizabeth R. Hauser
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, United States of America
- Cooperative Studies Program Epidemiology Center, Durham Veterans Affairs Medical Center, Durham, NC, United States of America
| | - Simon Gregory
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
| | - Svati Shah
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
- Division of Cardiology, Department of Medicine, School of Medicine, Duke University, Durham, NC, United States of America
| | - William E. Kraus
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, United States of America
- Division of Cardiology, Department of Medicine, School of Medicine, Duke University, Durham, NC, United States of America
| | - Kenneth Olden
- National Center for Environmental Assessment, US Environmental Protection Agency, Chapel Hill, NC, United States of America
| | - Cavin K. Ward-Caviness
- National Health and Environmental Effects Laboratory, US Environmental Protection Agency, Chapel Hill, NC, United States of America
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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] [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
| | - Konstantinos N. Lazaridis
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
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25
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Reddavide R, Rotolo O, Caruso MG, Stasi E, Notarnicola M, Miraglia C, Nouvenne A, Meschi T, De' Angelis GL, Di Mario F, Leandro G. The role of diet in the prevention and treatment of Inflammatory Bowel Diseases. ACTA BIO-MEDICA : ATENEI PARMENSIS 2018; 89:60-75. [PMID: 30561397 PMCID: PMC6502201 DOI: 10.23750/abm.v89i9-s.7952] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Indexed: 02/06/2023]
Abstract
Inflammatory bowel diseases (IBD) – Crohn’s disease (CD) and ulcerative colitis (UC) – are chronic conditions characterised by relapsing inflammation of the gastrointestinal tract. They represent an increasing public health concern and an aetiological enigma due to unknown causal factors. The current knowledge on the pathogenesis of IBD is that genetically susceptible individuals develop intolerance to a dysregulated gut microflora (dysbiosis) and chronic inflammation develops as a result of environmental triggers. Among the environmental factors associated with IBD, diet plays an important role in modulating the gut microbiome, and, consequently, it could have a therapeutic impact on the disease course. An overabundance of calories and some macronutrients typical of the Western dietetic pattern increase gut inflammation, whereas several micronutrients characteristic of the Mediterranean Diet have the potential to modulate gut inflammation, according to recent evidence. Immunonutrition has emerged as a new concept putting forward the role of vitamins such as vitamins A, C, E, and D, folic acid, beta carotene and trace elements such as zinc, selenium, manganese and iron. However, when assessed in clinical trials, specific micronutrients showed a limited benefit. Further research is required to evaluate the role of individual food compounds and complex nutritional interventions with the potential to decrease inflammation as a means of prevention and management of IBD. The current dietary recommendations for disease prevention and management are scarce and non evidence-based. This review summarizes the current knowledge on the complex interaction between diet, microbiome and immune-modulation in IBD, with particular focus to the role of the Mediterranean Diet as a tool for prevention and treatment of the disease. (www.actabiomedica.it)
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Affiliation(s)
- Rosa Reddavide
- National Institute of Gastroenterology "S. De Bellis" Research Hospital, Castellana Grotte, Italy.
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Taman H, Fenton CG, Hensel IV, Anderssen E, Florholmen J, Paulssen RH. Genome-wide DNA Methylation in Treatment-naïve Ulcerative Colitis. J Crohns Colitis 2018; 12:1338-1347. [PMID: 30137272 PMCID: PMC6236200 DOI: 10.1093/ecco-jcc/jjy117] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS The aim of this study was to investigate the genome-wide DNA methylation status in treatment-naïve ulcerative colitis [UC], and to explore the relationship between DNA methylation patterns and gene expression levels in tissue biopsies from a well-stratified treatment-naïve UC patient group. METHODS Mucosal biopsies from treatment-naïve patients [n = 10], and a healthy control group [n = 11] underwent genome-wide DNA bisulfite sequencing. Principal component analysis [PCA] and diverse statistical methods were applied to obtain a dataset of differentially methylated genes. DNA methylation annotation was investigated using the UCSC Genome Browser. Gene set enrichments were obtained using the Kyoto Encyclopaedia of Genes and Genomes [KEGG] and PANTHER. RESULTS Of all significantly differentially expressed genes [DEGs], 25% correlated with DNA methylation patterns; 30% of these genes were methylated at CpG sites near their transcription start site [TSS]. Hyper-methylation was observed for genes involved in homeostasis and defence, whereas hypo-methylation was observed for genes playing a role in immune response [i.e. chemokines and interleukins]. Of the differentially DNA methylated genes, 25 were identified as inflammatory bowel disease [IBD] susceptibility genes. Four genes [DEFFA6, REG1B, BTNL3, OLFM4] showed DNA methylation in the absence of known CpG islands. CONCLUSIONS Genome-wide DNA methylation analysis revealed distinctive functional patterns for hyper-and hypo-methylation in treatment-naïve UC. These distinct patterns could be of importance in the development and pathogenesis of UC. Further investigation of DNA methylation patterns may be useful in the development of the targeting of epigenetic processes, and may allow new treatment and target strategies for UC patients.
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Affiliation(s)
- Hagar Taman
- Genomics Support Centre Tromsø [GSCT], Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway
| | - Christopher G Fenton
- Genomics Support Centre Tromsø [GSCT], Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway
| | - Inga V Hensel
- Genomics Support Centre Tromsø [GSCT], Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway,Gastroenterology and Nutrition Research Group, Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway
| | - Endre Anderssen
- Genomics Support Centre Tromsø [GSCT], Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway
| | - Jon Florholmen
- Gastroenterology and Nutrition Research Group, Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway,Department of Gastroenterology, University Hospital of North Norway, Tromsø, Norway
| | - Ruth H Paulssen
- Genomics Support Centre Tromsø [GSCT], Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway,Gastroenterology and Nutrition Research Group, Department of Clinical Medicine, Arctic University of Norway, Tromsø, Norway,Corresponding author: Ruth H. Paulssen, PhD, Department of Clinical Medicine, Gastroenterology and Nutrition Research Group, UiT The Arctic University of Norway, Faculty of Health, Sykehusveien 38, N-9038 Tromsø, Norway/ Tel.: +47 77 64 54 80;
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Xiao FH, Chen XQ, He YH, Kong QP. Accelerated DNA methylation changes in middle-aged men define sexual dimorphism in human lifespans. Clin Epigenetics 2018; 10:133. [PMID: 30373676 PMCID: PMC6206726 DOI: 10.1186/s13148-018-0573-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/21/2018] [Indexed: 12/26/2022] Open
Abstract
Background Accelerated age-associated DNA methylation changes in males may explain the earlier onset of age-related diseases (e.g., cardiovascular disease (CVD)) and thus contribute to sexually dimorphic morbidity and lifespan. However, the details regarding the emergence of this sex-biased methylation pattern remain unclear. Results To address these issues, we collected publicly available peripheral blood methylation datasets detected by Illumina HumanMethylation450 BeadChip platform from four studies that contain age and gender information of samples. We analyzed peripheral blood methylation data screened from 708 subjects of European ancestry. Results revealed a significant methylation change acceleration in middle-aged males (40–50 years old), which was further supported by another cohort containing 2711 subjects with Indian ancestry. Additional analyses suggested that these sexually dimorphic methylation changes were significantly overrepresented in genes associated with CVD, which may impact the potential activation of disease expression. Furthermore, we showed that higher prevalence of drinking and smoking in the males has some contribution to the sex-based methylation patterns during aging. Conclusion Our results indicated that the sex-biased methylation changes occurred in middle-aged men in an acceleration manner and likely contribute to the sexual dimorphism observed in human lifespan by promoting the occurrence of CVD. As drinking and smoking were also found to be associated with this accelerated methylation change in men, it is possible that male lifespan may be prolonged by improving unhealthy lifestyles at or before middle age. Electronic supplementary material The online version of this article (10.1186/s13148-018-0573-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fu-Hui Xiao
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming Key Laboratory of Healthy Aging Study, Kunming, 650223, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China
| | - Xiao-Qiong Chen
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming Key Laboratory of Healthy Aging Study, Kunming, 650223, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China
| | - Yong-Han He
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.,Kunming Key Laboratory of Healthy Aging Study, Kunming, 650223, China.,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China. .,Kunming Key Laboratory of Healthy Aging Study, Kunming, 650223, China. .,KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, 650223, China.
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28
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May S, Owen H, Phesse TJ, Greenow KR, Jones G, Blackwood A, Cook PC, Towers C, Gallimore AM, Williams GT, Stürzl M, Britzen‐Laurent N, Sansom OJ, MacDonald AS, Bird AP, Clarke AR, Parry L. Mbd2 enables tumourigenesis within the intestine while preventing tumour-promoting inflammation. J Pathol 2018; 245:270-282. [PMID: 29603746 PMCID: PMC6032908 DOI: 10.1002/path.5074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 02/22/2018] [Accepted: 03/08/2018] [Indexed: 01/14/2023]
Abstract
Epigenetic regulation plays a key role in the link between inflammation and cancer. Here we examine Mbd2, which mediates epigenetic transcriptional silencing by binding to methylated DNA. In separate studies the Mbd2-/- mouse has been shown (1) to be resistant to intestinal tumourigenesis and (2) to have an enhanced inflammatory/immune response, observations that are inconsistent with the links between inflammation and cancer. To clarify its role in tumourigenesis and inflammation, we used constitutive and conditional models of Mbd2 deletion to explore its epithelial and non-epithelial roles in the intestine. Using a conditional model, we found that suppression of intestinal tumourigenesis is due primarily to the absence of Mbd2 within the epithelia. Next, we demonstrated, using the DSS colitis model, that non-epithelial roles of Mbd2 are key in preventing the transition from acute to tumour-promoting chronic inflammation. Combining models revealed that prior to inflammation the altered Mbd2-/- immune response plays a role in intestinal tumour suppression. However, following inflammation the intestine converts from tumour suppressive to tumour promoting. To summarise, in the intestine the normal function of Mbd2 is exploited by cancer cells to enable tumourigenesis, while in the immune system it plays a key role in preventing tumour-enabling inflammation. Which role is dominant depends on the inflammation status of the intestine. As environmental interactions within the intestine can alter DNA methylation patterns, we propose that Mbd2 plays a key role in determining whether these interactions are anti- or pro-tumourigenic and this makes it a useful new epigenetic model for inflammation-associated carcinogenesis. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Stephanie May
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Heather Owen
- Wellcome Trust Centre for Cell BiologyUniversity of Edinburgh, Michael Swann BuildingEdinburghUK
| | - Toby J Phesse
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Kirsty R Greenow
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Gareth‐Rhys Jones
- Manchester Collaborative Centre for Inflammation ResearchManchesterUK
| | - Adam Blackwood
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Peter C Cook
- Manchester Collaborative Centre for Inflammation ResearchManchesterUK
| | - Christopher Towers
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Awen M Gallimore
- Cardiff Institute of Infection and Immunity, Henry Wellcome BuildingCardiffUK
| | - Geraint T Williams
- Institute of Cancer and GeneticsCardiff University School of MedicineCardiffUK
| | - Michael Stürzl
- Division of Molecular and Experimental Surgery, Department of SurgeryFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg and Universitätsklinikum ErlangenErlangenGermany
| | - Nathalie Britzen‐Laurent
- Division of Molecular and Experimental Surgery, Department of SurgeryFriedrich‐Alexander‐Universität (FAU) Erlangen‐Nürnberg and Universitätsklinikum ErlangenErlangenGermany
| | | | | | - Adrian P Bird
- Wellcome Trust Centre for Cell BiologyUniversity of Edinburgh, Michael Swann BuildingEdinburghUK
| | - Alan R Clarke
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
| | - Lee Parry
- European Cancer Stem Cell Research InstituteCardiff University, School of BiosciencesCardiffUK
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Kennedy EM, Goehring GN, Nichols MH, Robins C, Mehta D, Klengel T, Eskin E, Smith AK, Conneely KN. An integrated -omics analysis of the epigenetic landscape of gene expression in human blood cells. BMC Genomics 2018; 19:476. [PMID: 29914364 PMCID: PMC6006777 DOI: 10.1186/s12864-018-4842-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/30/2018] [Indexed: 01/06/2023] Open
Abstract
Background Gene expression can be influenced by DNA methylation 1) distally, at regulatory elements such as enhancers, as well as 2) proximally, at promoters. Our current understanding of the influence of distal DNA methylation changes on gene expression patterns is incomplete. Here, we characterize genome-wide methylation and expression patterns for ~ 13 k genes to explore how DNA methylation interacts with gene expression, throughout the genome. Results We used a linear mixed model framework to assess the correlation of DNA methylation at ~ 400 k CpGs with gene expression changes at ~ 13 k transcripts in two independent datasets from human blood cells. Among CpGs at which methylation significantly associates with transcription (eCpGs), > 50% are distal (> 50 kb) or trans (different chromosome) to the correlated gene. Many eCpG-transcript pairs are consistent between studies and ~ 90% of neighboring eCpGs associate with the same gene, within studies. We find that enhancers (P < 5e-18) and microRNA genes (P = 9e-3) are overrepresented among trans eCpGs, and insulators and long intergenic non-coding RNAs are enriched among cis and distal eCpGs. Intragenic-eCpG-transcript correlations are negative in 60–70% of occurrences and are enriched for annotated gene promoters and enhancers (P < 0.002), highlighting the importance of intragenic regulation. Gene Ontology analysis indicates that trans eCpGs are enriched for transcription factor genes and chromatin modifiers, suggesting that some trans eCpGs represent the influence of gene networks and higher-order transcriptional control. Conclusions This work sheds new light on the interplay between epigenetic changes and gene expression, and provides useful data for mining biologically-relevant results from epigenome-wide association studies. Electronic supplementary material The online version of this article (10.1186/s12864-018-4842-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth M Kennedy
- Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA. .,Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
| | - George N Goehring
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael H Nichols
- Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA.,Department of Biology, Emory University, Atlanta, GA, USA
| | - Chloe Robins
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.,Population Biology, Ecology and Evolution Program, Emory University, Atlanta, GA, USA
| | - Divya Mehta
- School of Psychology and Counseling, Faculty of Health, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Australia
| | - Torsten Klengel
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, CA, USA
| | - Alicia K Smith
- Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA.,Department of Gynecology and Obstetrics, Emory University School of Medicine, Atlanta, GA, USA.,Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Karen N Conneely
- Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA.,Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
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30
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Chiba H, Kakuta Y, Kinouchi Y, Kawai Y, Watanabe K, Nagao M, Naito T, Onodera M, Moroi R, Kuroha M, Kanazawa Y, Kimura T, Shiga H, Endo K, Negoro K, Nagasaki M, Unno M, Shimosegawa T. Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease. PLoS One 2018; 13:e0194036. [PMID: 29547621 PMCID: PMC5856270 DOI: 10.1371/journal.pone.0194036] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 02/25/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) has an unknown etiology; however, accumulating evidence suggests that IBD is a multifactorial disease influenced by a combination of genetic and environmental factors. The influence of genetic variants on DNA methylation in cis and cis effects on expression have been demonstrated. We hypothesized that IBD susceptibility single-nucleotide polymorphisms (SNPs) regulate susceptibility gene expressions in cis by regulating DNA methylation around SNPs. For this, we determined cis-regulated allele-specific DNA methylation (ASM) around IBD susceptibility genes in CD4+ effector/memory T cells (Tem) in lamina propria mononuclear cells (LPMCs) in patients with IBD and examined the association between the ASM SNP genotype and neighboring susceptibility gene expressions. METHODS CD4+ effector/memory T cells (Tem) were isolated from LPMCs in 15 Japanese IBD patients (ten Crohn's disease [CD] and five ulcerative colitis [UC] patients). ASM analysis was performed by methylation-sensitive SNP array analysis. We defined ASM as a changing average relative allele score ([Formula: see text]) >0.1 after digestion by methylation-sensitive restriction enzymes. Among SNPs showing [Formula: see text] >0.1, we extracted the probes located on tag-SNPs of 200 IBD susceptibility loci and around IBD susceptibility genes as candidate ASM SNPs. To validate ASM, bisulfite-pyrosequencing was performed. Transcriptome analysis was examined in 11 IBD patients (seven CD and four UC patients). The relation between rs36221701 genotype and neighboring gene expressions were analyzed. RESULTS We extracted six candidate ASM SNPs around IBD susceptibility genes. The top of [Formula: see text] (0.23) was rs1130368 located on HLA-DQB1. ASM around rs36221701 ([Formula: see text] = 0.14) located near SMAD3 was validated using bisulfite pyrosequencing. The SMAD3 expression was significantly associated with the rs36221701 genotype (p = 0.016). CONCLUSIONS We confirmed the existence of cis-regulated ASM around IBD susceptibility genes and the association between ASM SNP (rs36221701) genotype and SMAD3 expression, a susceptibility gene for IBD. These results give us supporting evidence that DNA methylation mediates genetic effects on disease susceptibility.
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Affiliation(s)
- Hirofumi Chiba
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoichi Kakuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshitaka Kinouchi
- Institute for Excellence in Higher Education, Tohoku University, Sendai, Japan
| | - Yosuke Kawai
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kazuhiro Watanabe
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Munenori Nagao
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takeo Naito
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Motoyuki Onodera
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Rintaro Moroi
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masatake Kuroha
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshitake Kanazawa
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomoya Kimura
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hisashi Shiga
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Katsuya Endo
- Division of Gastroenterology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Kenichi Negoro
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masao Nagasaki
- Institute for Excellence in Higher Education, Tohoku University, Sendai, Japan
| | - Michiaki Unno
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tooru Shimosegawa
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
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31
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Weidner CI, Lin Q, Birkhofer C, Gerstenmaier U, Kaifie A, Kirschner M, Bruns H, Balabanov S, Trummer A, Stockklausner C, Höchsmann B, Schrezenmeier H, Wlodarski M, Panse J, Brümmendorf TH, Beier F, Wagner W. DNA methylation in PRDM8 is indicative for dyskeratosis congenita. Oncotarget 2017; 7:10765-72. [PMID: 26909595 PMCID: PMC4905437 DOI: 10.18632/oncotarget.7458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 02/09/2016] [Indexed: 02/06/2023] Open
Abstract
Dyskeratosis congenita (DKC) is associated with impaired telomere maintenance and with clinical features of premature aging. In this study, we analysed global DNA methylation (DNAm) profiles of DKC patients. Age-associated DNAm changes were not generally accelerated in DKC, but there were significant differences to DNAm patterns of healthy controls, particularly in CpG sites related to an internal promoter region of PR domain containing 8 (PRDM8). Notably, the same genomic region was also hypermethylated in aplastic anemia (AA) – another bone marrow failure syndrome. Site-specific analysis of DNAm level in PRDM8 with pyrosequencing and MassARRAY validated aberrant hypermethylation in 11 DKC patients and 27 AA patients. Telomere length, measured by flow-FISH, did not directly correlate with DNAm in PRDM8. Therefore the two methods may be complementary to also identify patients with still normal telomere length. In conclusion, blood of DKC patients reveals aberrant DNAm patterns, albeit age-associated DNAm patterns are not generally accelerated. Aberrant hypermethylation is particularly observed in PRDM8 and this may support identification and classification of bone marrow failure syndromes.
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Affiliation(s)
- Carola I Weidner
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Aachen, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
| | - Qiong Lin
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Aachen, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
| | | | | | - Andrea Kaifie
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical Faculty, Aachen, Germany
| | - Martin Kirschner
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical Faculty, Aachen, Germany
| | - Heiko Bruns
- Department of Internal Medicine 5-Hematology/Oncology, University Hospital Erlangen, Erlangen, Germany
| | - Stefan Balabanov
- Division of Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Arne Trummer
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Clemens Stockklausner
- Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Britta Höchsmann
- Institute of Transfusion Medicine, University of Ulm, Ulm, Germany.,Institute of Clinical Transfusion Medicine and Immunogenetics, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen and University Hospital Ulm, Ulm, Germany
| | - Hubert Schrezenmeier
- Institute of Transfusion Medicine, University of Ulm, Ulm, Germany.,Institute of Clinical Transfusion Medicine and Immunogenetics, German Red Cross Blood Transfusion Service Baden-Württemberg-Hessen and University Hospital Ulm, Ulm, Germany
| | - Marcin Wlodarski
- Department of Pediatrics, Hematology and Oncology, University of Freiburg, Freiburg, Germany
| | - Jens Panse
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical Faculty, Aachen, Germany
| | - Tim H Brümmendorf
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical Faculty, Aachen, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, RWTH Aachen University Medical Faculty, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Aachen, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
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32
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Frobel J, Božić T, Lenz M, Uciechowski P, Han Y, Herwartz R, Strathmann K, Isfort S, Panse J, Esser A, Birkhofer C, Gerstenmaier U, Kraus T, Rink L, Koschmieder S, Wagner W. Leukocyte Counts Based on DNA Methylation at Individual Cytosines. Clin Chem 2017; 64:566-575. [PMID: 29118064 DOI: 10.1373/clinchem.2017.279935] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/17/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND White blood cell counts are routinely measured with automated hematology analyzers, by flow cytometry, or by manual counting. Here, we introduce an alternative approach based on DNA methylation (DNAm) at individual CG dinucleotides (CpGs). METHODS We identified candidate CpGs that were nonmethylated in specific leukocyte subsets. DNAm levels (ranging from 0% to 100%) were analyzed by pyrosequencing and implemented into deconvolution algorithms to determine the relative composition of leukocytes. For absolute quantification of cell numbers, samples were supplemented with a nonmethylated reference DNA. RESULTS Conventional blood counts correlated with DNAm at individual CpGs for granulocytes (r = -0.91), lymphocytes (r = -0.91), monocytes (r = -0.74), natural killer (NK) cells (r = -0.30), T cells (r = -0.73), CD4+ T cells (r = -0.41), CD8+ T cells (r = -0.88), and B cells (r = -0.66). Combination of these DNAm measurements into the "Epi-Blood-Count" provided similar precision as conventional methods in various independent validation sets. The method was also applicable to blood samples that were stored at 4 °C for 7 days or at -20 °C for 3 months. Furthermore, absolute cell numbers could be determined in frozen blood samples upon addition of a reference DNA, and the results correlated with measurements of automated analyzers in fresh aliquots (r = 0.84). CONCLUSIONS White blood cell counts can be reliably determined by site-specific DNAm analysis. This approach is applicable to very small blood volumes and frozen samples, and it allows for more standardized and cost-effective analysis in clinical application.
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Affiliation(s)
- Joana Frobel
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Tanja Božić
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Michael Lenz
- Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany.,Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany.,Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, the Netherlands
| | - Peter Uciechowski
- Institute of Immunology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Yang Han
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany.,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
| | - Reinhild Herwartz
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Klaus Strathmann
- Institute for Transfusion Medicine, University Hospital Aachen, Aachen, Germany
| | - Susanne Isfort
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Jens Panse
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - André Esser
- Institute for Occupational and Social Medicine, RWTH Aachen University, Aachen, Germany
| | | | | | - Thomas Kraus
- Institute for Occupational and Social Medicine, RWTH Aachen University, Aachen, Germany
| | - Lothar Rink
- Institute of Immunology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany; .,Institute for Biomedical Engineering - Cell Biology, University Hospital of RWTH Aachen, Aachen, Germany
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Palmieri O, Mazza T, Castellana S, Panza A, Latiano T, Corritore G, Andriulli A, Latiano A. Inflammatory Bowel Disease Meets Systems Biology: A Multi-Omics Challenge and Frontier. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 20:692-698. [PMID: 27930092 DOI: 10.1089/omi.2016.0147] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The inflammatory bowel disease (IBD) is a systemic disease that is characterized by the inflammation of the gastrointestinal tract. It includes ulcerative colitis and the Crohn's disease. Presently, IBD is one of the most investigated common complex human disorders, although its causes remain unclear. Multi-omics mechanisms involving genomic, transcriptomic, proteomic, and epigenomic variations, not to forget the miRNome, together with environmental contributions, result in an impairment of the immune system in persons with IBD. Such interactions at multiple levels of biology and in concert with the environment constitute the actual engine of this complex disease, demanding a multifactorial and multi-omics perspective to better understand the root causes of IBD. This expert analysis reviews and examines the latest literature and underscores, from the perspective of systems biology, the value of multi-omics technologies as opportunities to unravel the "IBD integrome." We anticipate that multi-omics research will accelerate the new discoveries and insights on IBD in the near future. It shall also pave the way for early diagnosis and help clinicians and families with IBD to forecast and make informed decisions about the prognosis and, possibly, personalized therapeutics in the future.
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Affiliation(s)
- Orazio Palmieri
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Tommaso Mazza
- 2 Laboratory of Bioinformatics, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Stefano Castellana
- 2 Laboratory of Bioinformatics, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Anna Panza
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Tiziana Latiano
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Giuseppe Corritore
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Angelo Andriulli
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
| | - Anna Latiano
- 1 Division of Gastroenterology, IRCCS "Casa Sollievo della Sofferenza" Hospital , San Giovanni Rotondo, Italy
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Recent Advances in the Etiopathogenesis of Inflammatory Bowel Disease: The Role of Omics. Mol Diagn Ther 2017; 22:11-23. [DOI: 10.1007/s40291-017-0298-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Aleksandrova K, Romero-Mosquera B, Hernandez V. Diet, Gut Microbiome and Epigenetics: Emerging Links with Inflammatory Bowel Diseases and Prospects for Management and Prevention. Nutrients 2017; 9:nu9090962. [PMID: 28867793 PMCID: PMC5622722 DOI: 10.3390/nu9090962] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/15/2017] [Accepted: 08/25/2017] [Indexed: 12/17/2022] Open
Abstract
Inflammatory bowel diseases (IBD) represent a growing public health concern due to increasing incidence worldwide. The current notion on the pathogenesis of IBD is that genetically susceptible individuals develop intolerance to dysregulated gut microflora (dysbiosis) and chronic inflammation develops as a result of environmental triggers. Among the environmental factors associated with IBD, diet plays an important role in modulating the gut microbiome, influencing epigenetic changes, and, therefore, could be applied as a therapeutic tool to improve the disease course. Nevertheless, the current dietary recommendations for disease prevention and management are scarce and have weak evidence. This review summarises the current knowledge on the complex interactions between diet, microbiome and epigenetics in IBD. Whereas an overabundance of calories and some macronutrients increase gut inflammation, several micronutrients have the potential to modulate it. Immunonutrition has emerged as a new concept putting forward the importance of vitamins such as vitamins A, C, E, and D, folic acid, beta carotene and trace elements such as zinc, selenium, manganese and iron. However, when assessed in clinical trials, specific micronutrients exerted a limited benefit. Beyond nutrients, an anti-inflammatory dietary pattern as a complex intervention approach has become popular in recent years. Hence, exclusive enteral nutrition in paediatric Crohn’s disease is the only nutritional intervention currently recommended as a first-line therapy. Other nutritional interventions or specific diets including the Specific Carbohydrate Diet (SCD), the low fermentable oligosaccharides, disaccharides, monosaccharides, and polyol (FODMAP) diet and, most recently, the Mediterranean diet have shown strong anti-inflammatory properties and show promise for improving disease symptoms. More work is required to evaluate the role of individual food compounds and complex nutritional interventions with the potential to decrease inflammation as a means of prevention and management of IBD.
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Affiliation(s)
- Krasimira Aleksandrova
- Nutrition, Immunity and Metabolism Start-up Lab, Department of Epidemiology, German Institute of Human Nutrition Potsdam-Rehbrücke, Arthur-Scheunert Allee 114-116, 14558 Nuthetal, Germany.
| | - Beatriz Romero-Mosquera
- Department of Gastroenterology, Instituto Investigación Sanitaria Galicia Sur, Estrutura Organizativa de Xestión Integrada de Vigo, 36312 Vigo, Spain.
| | - Vicent Hernandez
- Department of Gastroenterology, Instituto Investigación Sanitaria Galicia Sur, Estrutura Organizativa de Xestión Integrada de Vigo, 36312 Vigo, Spain.
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Generali E, Ceribelli A, Stazi MA, Selmi C. Lessons learned from twins in autoimmune and chronic inflammatory diseases. J Autoimmun 2017; 83:51-61. [PMID: 28431796 DOI: 10.1016/j.jaut.2017.04.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 04/10/2017] [Indexed: 12/16/2022]
Abstract
Autoimmunity and chronic inflammation recognize numerous shared factors and, as a result, the resulting diseases frequently coexist in the same patients or respond to the same treatments. Among the convenient truths of autoimmune and chronic inflammatory diseases, there is now agreement that these are complex conditions in which the individual genetic predisposition provides a rate of heritability. The concordance rates in monozygotic and dizygotic twins allows to estimate the weight of the environment in determining disease susceptibility, despite recent data supporting that only a minority of immune markers depend on hereditary factors. Concordance rates in monozygotic and dizygotic twins should be evaluated over an observation period to minimize the risk of false negatives and this is well represented by type I diabetes mellitus. Further, concordance rates in monozygotic twins should be compared to those in dizygotic twins, which share 50% of their genes, as in regular siblings, but also young-age environmental factors. Twin studies have been extensively performed in several autoimmune conditions and cumulatively suggest that some diseases, i.e. celiac disease and psoriasis, are highly genetically determined, while rheumatoid arthritis or systemic sclerosis have a limited role for genetics. These observations are necessary to interpret data gathered by genome-wide association studies of polymorphisms and DNA methylation in MZ twins. New high-throughput technological platforms are awaited to provide new insights into the mechanisms of disease discordance in twins beyond strong associations such as those with HLA alleles.
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Affiliation(s)
- Elena Generali
- Division of Rheumatology and Clinical Immunology, Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Angela Ceribelli
- Division of Rheumatology and Clinical Immunology, Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Maria Antonietta Stazi
- Italian Twin Registry, Centre for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Rome, Italy
| | - Carlo Selmi
- Division of Rheumatology and Clinical Immunology, Humanitas Research Hospital, Rozzano, Milan, Italy; BIOMETRA Department, University of Milan, Milan, Italy.
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Abstract
The human epigenome may link environmental exposures and commensal microbiota changes to host pathology in respect to the developmental origins of inflammatory bowel diseases (ulcerative colitis [UC] and Crohn's disease [more appropriately Crohn disease, CD]). Genetic predisposition - prenatal, perinatal and pediatric environmental influences - microbiome aberration (dysbiosis) and immune dysregulation appear to be important elements in disease development, progression and maintenance. The prevalence of combined genetic and epigenetic susceptibility toward UC and CD is calculated herein to be as high as 2%, and approximately 1% for UC and CD in highly developed countries, respectively. This review emphasizes the significant challenges for epigenetic research in inflammatory bowel diseases. Overcoming these challenges, however, could reveal unique opportunities for disease prevention, treatment and possible cure.
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Affiliation(s)
- Richard Kellermayer
- Section of Pediatric Gastroenterology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, USDA/ARS Children's Nutrition Research Center, Houston, TX 77030, USA
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38
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Epigenetic Changes in Chronic Inflammatory Diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 106:139-189. [DOI: 10.1016/bs.apcsb.2016.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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39
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Lin Q, Weidner CI, Costa IG, Marioni RE, Ferreira MRP, Deary IJ, Wagner W. DNA methylation levels at individual age-associated CpG sites can be indicative for life expectancy. Aging (Albany NY) 2016; 8:394-401. [PMID: 26928272 PMCID: PMC4789590 DOI: 10.18632/aging.100908] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
DNA-methylation (DNAm) levels at age-associated CpG sites can be combined into epigenetic aging signatures to estimate donor age. It has been demonstrated that the difference between such epigenetic age-predictions and chronological age is indicative for of all-cause mortality in later life. In this study, we tested alternative epigenetic signatures and followed the hypothesis that even individual age-associated CpG sites might be indicative for life-expectancy. Using a 99-CpG aging model, a five-year higher age-prediction was associated with 11% greater mortality risk in DNAm profiles of the Lothian Birth Cohort 1921 study. However, models based on three CpGs, or even individual CpGs, generally revealed very high offsets in age-predictions if applied to independent microarray datasets. On the other hand, we demonstrate that DNAm levels at several individual age-associated CpGs seem to be associated with life expectancy - e.g., at CpGs associated with the genesPDE4C and CLCN6. Our results support the notion that small aging signatures should rather be analysed by more quantitative methods, such as site-specific pyrosequencing, as the precision of age-predictions is rather low on independent microarray datasets. Nevertheless, the results hold the perspective that simple epigenetic biomarkers, based on few or individual age-associated CpGs, could assist the estimation of biological age.
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Affiliation(s)
- Qiong Lin
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
| | - Carola I Weidner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
| | - Ivan G Costa
- Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany.,Interdisciplinary Centre for Clinical Research (IZKF), RWTH University Medical School, Aachen, Germany
| | - Riccardo E Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK.,Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.,Queensland Brain Institute, The University of Queensland, Brisbane 4072, QLD, Australia
| | - Marcelo R P Ferreira
- Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany.,Interdisciplinary Centre for Clinical Research (IZKF), RWTH University Medical School, Aachen, Germany.,Department of Statistics, Centre for Natural and Exact Sciences, Federal University of Paraiba, CEP 58051-900, João Pessoa, Brazil
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK.,Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH University Medical School, Aachen, Germany.,Institute for Biomedical Technology - Cell Biology, RWTH University Medical School, Aachen, Germany
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40
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Ventham NT, Kennedy NA, Adams AT, Kalla R, Heath S, O'Leary KR, Drummond H, Wilson DC, Gut IG, Nimmo ER, Satsangi J. Integrative epigenome-wide analysis demonstrates that DNA methylation may mediate genetic risk in inflammatory bowel disease. Nat Commun 2016; 7:13507. [PMID: 27886173 PMCID: PMC5133631 DOI: 10.1038/ncomms13507] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 10/11/2016] [Indexed: 02/06/2023] Open
Abstract
Epigenetic alterations may provide important insights into gene-environment interaction in inflammatory bowel disease (IBD). Here we observe epigenome-wide DNA methylation differences in 240 newly-diagnosed IBD cases and 190 controls. These include 439 differentially methylated positions (DMPs) and 5 differentially methylated regions (DMRs), which we study in detail using whole genome bisulphite sequencing. We replicate the top DMP (RPS6KA2) and DMRs (VMP1, ITGB2 and TXK) in an independent cohort. Using paired genetic and epigenetic data, we delineate methylation quantitative trait loci; VMP1/microRNA-21 methylation associates with two polymorphisms in linkage disequilibrium with a known IBD susceptibility variant. Separated cell data shows that IBD-associated hypermethylation within the TXK promoter region negatively correlates with gene expression in whole-blood and CD8+ T cells, but not other cell types. Thus, site-specific DNA methylation changes in IBD relate to underlying genotype and associate with cell-specific alteration in gene expression.
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Affiliation(s)
- N. T. Ventham
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 6XU, UK
| | - N. A. Kennedy
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 6XU, UK
| | - A. T. Adams
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 6XU, UK
| | - R. Kalla
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 6XU, UK
| | - S. Heath
- CNAG-CRG, Centro Nacional de Análisis Genómico, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - K. R. O'Leary
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 6XU, UK
| | - H. Drummond
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 6XU, UK
| | - D. C. Wilson
- Department of Child Life and Health, University of Edinburgh, Edinburgh EH9 1UW, UK
| | - I. G. Gut
- CNAG-CRG, Centro Nacional de Análisis Genómico, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain
- Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - E. R. Nimmo
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 6XU, UK
| | - J. Satsangi
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 6XU, UK
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41
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Gabbani T, Deiana S, Annese AL, Lunardi S, Annese V. The genetic burden of inflammatory bowel diseases: implications for the clinic? Expert Rev Gastroenterol Hepatol 2016; 10:1109-1117. [PMID: 27258545 DOI: 10.1080/17474124.2016.1196131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Inflammatory bowel diseases (IBD), which include Crohn's disease (CD) and ulcerative colitis (UC), are characterized by chronic intestinal inflammation. Their etiology is multifactorial, with complex interactions between genetic and environmental factors, which are still largely unclear. Areas covered: The influence of genetics is clearly demonstrated by important epidemiological data, including familial aggregation and concordance in twins. In 2001, the first genetic susceptibility gene for IBD, the NOD2 gene, was identified. Currently, thanks to genetic wide association studies, over 200 susceptibility genetic markers are know. Expert commentary: However, clinically highly relevant gene associations are still very limited and the usefulness of these information in the current clinical strategies for treatment and surveillance of IBD is weak. Nevertheless, the recent identification of some genetic risk variants has clarified some newbiological pathways of these diseases thus paving the way for the discoveries in the near future of new targeted therapies.
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Affiliation(s)
- Tommaso Gabbani
- a Division of Gastroenterology , AOU Careggi University Hospital , Florence , Italy
| | - Simona Deiana
- a Division of Gastroenterology , AOU Careggi University Hospital , Florence , Italy
| | - Antonio Luca Annese
- a Division of Gastroenterology , AOU Careggi University Hospital , Florence , Italy
| | - Sarah Lunardi
- b Division of Internal Medicine 4 , AOU Careggi University Hospital , Florence , Italy
| | - Vito Annese
- a Division of Gastroenterology , AOU Careggi University Hospital , Florence , Italy
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42
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Li Yim AYF, Duijvis NW, Zhao J, de Jonge WJ, D'Haens GRAM, Mannens MMAM, Mul ANPM, Te Velde AA, Henneman P. Peripheral blood methylation profiling of female Crohn's disease patients. Clin Epigenetics 2016; 8:65. [PMID: 27279921 PMCID: PMC4897922 DOI: 10.1186/s13148-016-0230-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/22/2016] [Indexed: 01/17/2023] Open
Abstract
Background Crohn’s disease (CD) is a chronic inflammatory disorder belonging to the inflammatory bowel diseases (IBD). CD affects distinct parts of the gastrointestinal tract, leading to symptoms including diarrhea, fever, abdominal pain, weight loss, and anemia. The aim of this study was to assess whether the DNA methylome of peripheral blood cells can be associated with CD in women. Methods Samples were obtained from 18 female patients with histologically confirmed ileal or ileocolic CD and 25 healthy age- and gender-matched controls (mean age and standard deviation: 30.5 ± 6.5 years for both groups). Genome-wide DNA methylation was determined using the Illumina HumanMethylation 450k BeadChip. Results Our analysis implicated 4287 differentially methylated positions (DMPs; corrected p < 0.05) that are associated to 2715 unique genes. Gene ontology enrichment analysis revealed significant enrichment of our DMPs in immune response processes and inflammatory pathways. Of the 4287 DMPs, 32 DMPs were located on chromosome X with several hits for MIR223 and PABPC5. Comparison with previously performed (epi)genome-wide studies revealed that we replicated 33 IBD-associated genes. In addition to DMPs, we found eight differentially methylated regions (DMRs). Conclusions CD patients display a characteristic DNA methylation landscape, with the differentially methylated genes being implicated in immune response. Additionally, DMPs were found on chromosome X suggesting X-linked manifestations of CD that could be associated with female-specific symptoms. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0230-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew Y F Li Yim
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Academic Medical Center Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.,Epinova Discovery Performance Unit, GlaxoSmithKline, Stevenage, UK
| | - Nicolette W Duijvis
- Tytgat Institute for Liver & Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands
| | - Jing Zhao
- Tytgat Institute for Liver & Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands
| | - Wouter J de Jonge
- Tytgat Institute for Liver & Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands
| | - Geert R A M D'Haens
- Department of Gastroenterology, Academic Medical Center, Amsterdam, The Netherlands
| | - Marcel M A M Mannens
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Academic Medical Center Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Adri N P M Mul
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Academic Medical Center Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Anje A Te Velde
- Tytgat Institute for Liver & Intestinal Research, Academic Medical Center, Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Academic Medical Center Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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43
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Bai AHC, Wu WKK, Xu L, Wong SH, Go MY, Chan AWH, Harbord M, Zhang S, Chen M, Wu JCY, Chan MWY, Chan MTV, Chan FKL, Sung JJY, Yu J, Cheng ASL, Ng SC. Dysregulated Lysine Acetyltransferase 2B Promotes Inflammatory Bowel Disease Pathogenesis Through Transcriptional Repression of Interleukin-10. J Crohns Colitis 2016; 10:726-34. [PMID: 26802082 DOI: 10.1093/ecco-jcc/jjw020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 12/15/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS Accumulating evidence supports epigenetic modifications in mediating intestinal immunity in inflammatory bowel disease [IBD] pathogenesis. This study aimed to identify key dysregulated epigenetic modulators and the molecular downstream pathways in IBD. METHODS Expression of 116 well-defined epigenetic modulators was profiled and validated in 96 intestinal tissues from patients with Crohn's disease [CD], ulcerative colitis [UC], and healthy controls using quantitative reverse transcriptase polymerase chain reaction [QRT-PCR], western blot, and immunohistochemistry. Dysregulation of histone modifications and IBD-related cytokines were examined by chromatin immunoprecipitation, luciferase activity, and gene expression analyses in normal colonic epithelial cell line, NCM460, upon small-molecule inhibition or RNA interference, followed by validation in primary colonic tissues. RESULTS Targeted expression profiling uncovered seven differentially expressed epigenetic modulators, of which the down-regulation of lysine acetyltransferase 2B [KAT2B] mRNA and protein was the most significant and was consequently validated in inflamed CD and UC compared with healthy colonic tissues. KAT2B protein localised abundantly in nuclei of normal colonic epithelium but diminished in paired inflamed CD and UC tissues. Pharmacological inhibition of KAT2B by anacardic acid in NCM460 cells reduced the levels of histone H4 lysine 5 acetylation [H4K5ac] and interleukin-10 [IL-10] in a dose-dependent manner. Knockdown of KAT2B reduced the IL-10 promoter occupancy of KAT2B and H4K5ac, resulting in transcriptional silencing. IL-10 level was also diminished in inflamed IBD tissues. CONCLUSIONS Our findings demonstrated a novel epigenetic mechanism of IL-10 dysregulation in IBD. Down-regulation of KAT2B may disrupt the innate and adaptive inflammatory responses due to the suppression of this crucial anti-inflammatory cytokine.
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Affiliation(s)
- Alfa H C Bai
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, Chinese University of Hong Kong, Hong Kong SAR Department of Medicine and Therapeutics and Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR
| | - William K K Wu
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, Chinese University of Hong Kong, Hong Kong SAR Department of Anaesthesia and Intensive Care, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong SAR
| | - Liangliang Xu
- School of Biomedical Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong SAR
| | - Sunny H Wong
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, Chinese University of Hong Kong, Hong Kong SAR Department of Medicine and Therapeutics and Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR
| | - Minnie Y Go
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, Chinese University of Hong Kong, Hong Kong SAR Department of Medicine and Therapeutics and Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR
| | - Anthony W H Chan
- Department of Anatomical and Cellular Pathology, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong SAR
| | - Marcus Harbord
- Chelsea and Westminster Hospital, Imperial College London, London, UK
| | - Shenghong Zhang
- Division of Gastroenterology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Minhu Chen
- Division of Gastroenterology, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Justin C Y Wu
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, Chinese University of Hong Kong, Hong Kong SAR Department of Medicine and Therapeutics and Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR
| | - Michael W Y Chan
- Department of Life Science, National Chung Cheng University, Minxiong, Taiwan
| | - Matthew T V Chan
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong SAR
| | - Francis K L Chan
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, Chinese University of Hong Kong, Hong Kong SAR Department of Medicine and Therapeutics and Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR
| | - Joseph J Y Sung
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, Chinese University of Hong Kong, Hong Kong SAR Department of Medicine and Therapeutics and Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR
| | - Jun Yu
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, Chinese University of Hong Kong, Hong Kong SAR Department of Medicine and Therapeutics and Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR
| | - Alfred S L Cheng
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, Chinese University of Hong Kong, Hong Kong SAR School of Biomedical Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong SAR
| | - Siew C Ng
- Institute of Digestive Disease and State Key Laboratory of Digestive Disease, Chinese University of Hong Kong, Hong Kong SAR Department of Medicine and Therapeutics and Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR
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Microbiome-Epigenome Interactions and the Environmental Origins of Inflammatory Bowel Diseases. J Pediatr Gastroenterol Nutr 2016; 62:208-19. [PMID: 26308318 PMCID: PMC4724338 DOI: 10.1097/mpg.0000000000000950] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The incidence of pediatric inflammatory bowel disease (IBD), which includes Crohn disease and ulcerative colitis, has risen alarmingly in the Western and developing world in recent decades. Epidemiologic (including monozygotic twin and migrant) studies highlight the substantial role of environment and nutrition in IBD etiology. Here we review the literature supporting the developmental and environmental origins hypothesis of IBD. We also provide a detailed exploration of how the human microbiome and epigenome (primarily through DNA methylation) may be important elements in the developmental origins of IBD in both children and adults.
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45
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Houseman EA, Kim S, Kelsey KT, Wiencke JK. DNA Methylation in Whole Blood: Uses and Challenges. Curr Environ Health Rep 2016; 2:145-54. [PMID: 26231364 DOI: 10.1007/s40572-015-0050-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Due to its convenience, the blood is commonly used in epigenomic studies, but its heterogeneous nature leads to interpretation difficulties, given the now widely recognized potential for confounding by cell composition effects. Many recent publications have reported significant associations between DNA methylation and a variety of health conditions or exposures. In this review, we summarize many of these recent publications, highlighting the findings in the context of potential cell composition effects, particularly findings that are indicative of immune response or inflammation. While there is substantial evidence for confounding by cell composition, there is nevertheless also evidence for differential DNA methylation suggestive of processes that are not cell mediated. We conclude that important biological insights still may be gained from studying DNA methylation in whole blood, either by investigating the cell composition effects themselves or processes that demonstrate associations even after adjusting for cell composition effects.
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Affiliation(s)
- E Andres Houseman
- School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA,
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Aslani S, Mahmoudi M, Karami J, Jamshidi AR, Malekshahi Z, Nicknam MH. Epigenetic alterations underlying autoimmune diseases. Autoimmunity 2016; 49:69-83. [DOI: 10.3109/08916934.2015.1134511] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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47
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McDermott E, Ryan EJ, Tosetto M, Gibson D, Burrage J, Keegan D, Byrne K, Crowe E, Sexton G, Malone K, Harris RA, Kellermayer R, Mill J, Cullen G, Doherty GA, Mulcahy H, Murphy TM. DNA Methylation Profiling in Inflammatory Bowel Disease Provides New Insights into Disease Pathogenesis. J Crohns Colitis 2016; 10:77-86. [PMID: 26419460 PMCID: PMC5013897 DOI: 10.1093/ecco-jcc/jjv176] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/15/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Inflammatory bowel diseases (IBDs) are heterogeneous disorders with complex aetiology. Quantitative genetic studies suggest that only a small proportion of the disease variance observed in IBD is accounted for by genetic variation, indicating a potential role for differential epigenetic regulation in disease aetiology. The aim of this study was to assess genome-wide DNA methylation changes specifically associated with ulcerative colitis (UC), Crohn's disease (CD) and IBD activity. METHODS DNA methylation was quantified in peripheral blood mononuclear cells (PBMCs) from 149 IBD cases (61 UC, 88 CD) and 39 controls using the Infinium HumanMethylation450 BeadChip. Technical and functional validation was performed using pyrosequencing and the real-time polymerase chain reaction. Cross-tissue replication of the top differentially methylated positions (DMPs) was tested in colonic mucosa tissue samples obtained from paediatric IBD cases and controls. RESULTS A total of 3196 probes were differentially methylated between CD cases and controls, while 1481 probes were differentially methylated between UC cases and controls. There was considerable (45%) overlap between UC and CD DMPs. The top-ranked IBD-associated PBMC differentially methylated region (promoter region of TRIM39-RPP2) was also significantly hypomethylated in colonic mucosa from paediatric UC patients. In addition, we confirmed TRAF6 hypermethylation using pyrosequencing and found reduced TRAF6 gene expression in PBMCs of IBD patients. CONCLUSIONS Our data provide new insights into differential epigenetic regulation of genes and molecular pathways, which may contribute to the pathogenesis and activity of IBD.
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Affiliation(s)
- Edel McDermott
- Centre for Colorectal Disease, St Vincent’s University Hospital, Dublin, Ireland,School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - Elizabeth J. Ryan
- Centre for Colorectal Disease, St Vincent’s University Hospital, Dublin, Ireland,School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - Miriam Tosetto
- Centre for Colorectal Disease, St Vincent’s University Hospital, Dublin, Ireland
| | - David Gibson
- Centre for Colorectal Disease, St Vincent’s University Hospital, Dublin, Ireland,School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter, Exeter, Devon, UK
| | - Denise Keegan
- Centre for Colorectal Disease, St Vincent’s University Hospital, Dublin, Ireland
| | - Kathryn Byrne
- Centre for Colorectal Disease, St Vincent’s University Hospital, Dublin, Ireland
| | - Eimear Crowe
- School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland,Department of Psychiatry, Psychotherapy & Mental Health Research, St Vincent’s University Hospital, Dublin, Ireland
| | - Gillian Sexton
- Centre for Colorectal Disease, St Vincent’s University Hospital, Dublin, Ireland
| | - Kevin Malone
- School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland,Department of Psychiatry, Psychotherapy & Mental Health Research, St Vincent’s University Hospital, Dublin, Ireland
| | - R. Alan Harris
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Richard Kellermayer
- Department of Pediatrics, Baylor College of Medicine, USDA/ARS Children’s Nutrition Research Center, Texas Children’s Hospital, Houston, TX, USA
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, Devon, UK,MRC Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, UK
| | - Garret Cullen
- Centre for Colorectal Disease, St Vincent’s University Hospital, Dublin, Ireland,School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - Glen A. Doherty
- Centre for Colorectal Disease, St Vincent’s University Hospital, Dublin, Ireland,School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland
| | - Hugh Mulcahy
- Centre for Colorectal Disease, St Vincent’s University Hospital, Dublin, Ireland,School of Medicine and Medical Sciences, University College Dublin, Dublin, Ireland,*These author’s contributed equally to this work
| | - Therese M. Murphy
- University of Exeter Medical School, University of Exeter, Exeter, Devon, UK,*These author’s contributed equally to this work
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Tigchelaar EF, Zhernakova A, Dekens JAM, Hermes G, Baranska A, Mujagic Z, Swertz MA, Muñoz AM, Deelen P, Cénit MC, Franke L, Scholtens S, Stolk RP, Wijmenga C, Feskens EJM. Cohort profile: LifeLines DEEP, a prospective, general population cohort study in the northern Netherlands: study design and baseline characteristics. BMJ Open 2015; 5:e006772. [PMID: 26319774 PMCID: PMC4554905 DOI: 10.1136/bmjopen-2014-006772] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
PURPOSE There is a critical need for population-based prospective cohort studies because they follow individuals before the onset of disease, allowing for studies that can identify biomarkers and disease-modifying effects, and thereby contributing to systems epidemiology. PARTICIPANTS This paper describes the design and baseline characteristics of an intensively examined subpopulation of the LifeLines cohort in the Netherlands. In this unique subcohort, LifeLines DEEP, we included 1539 participants aged 18 years and older. FINDINGS TO DATE We collected additional blood (n = 1387), exhaled air (n = 1425) and faecal samples (n = 1248), and elicited responses to gastrointestinal health questionnaires (n = 1176) for analysis of the genome, epigenome, transcriptome, microbiome, metabolome and other biological levels. Here, we provide an overview of the different data layers in LifeLines DEEP and present baseline characteristics of the study population including food intake and quality of life. We also describe how the LifeLines DEEP cohort allows for the detailed investigation of genetic, genomic and metabolic variation for a wide range of phenotypic outcomes. Finally, we examine the determinants of gastrointestinal health, an area of particular interest to us that can be addressed by LifeLines DEEP. FUTURE PLANS We have established a cohort of which multiple data levels allow for the integrative analysis of populations for translation of this information into biomarkers for disease, and which will offer new insights into disease mechanisms and prevention.
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Affiliation(s)
- Ettje F Tigchelaar
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Top Institute Food and Nutrition, Wageningen, The Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Top Institute Food and Nutrition, Wageningen, The Netherlands
| | - Jackie A M Dekens
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Top Institute Food and Nutrition, Wageningen, The Netherlands
| | - Gerben Hermes
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Agnieszka Baranska
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Department of Toxicology, Nutrition and Toxicology Research (NUTRIM), Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Zlatan Mujagic
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Morris A Swertz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
| | - Angélica M Muñoz
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Research Group in Food and Human Nutrition, University of Antioquia, Medellín, Colombia
| | - Patrick Deelen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, The Netherlands
| | - Maria C Cénit
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Salome Scholtens
- LifeLines Cohort Study, Groningen, The Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ronald P Stolk
- LifeLines Cohort Study, Groningen, The Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Top Institute Food and Nutrition, Wageningen, The Netherlands
| | - Edith J M Feskens
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- Division of Human Nutrition, Section Nutrition and Epidemiology, Wageningen University, Wageningen, The Netherlands
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Swan EJ, Maxwell AP, McKnight AJ. Distinct methylation patterns in genes that affect mitochondrial function are associated with kidney disease in blood-derived DNA from individuals with Type 1 diabetes. Diabet Med 2015; 32:1110-5. [PMID: 25850930 DOI: 10.1111/dme.12775] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/02/2015] [Indexed: 12/18/2022]
Abstract
AIMS Epigenetic modifications, such as DNA methylation, can influence the risk of developing kidney disease. We studied methylation profiles in genes related to mitochondrial function to assess whether differences in these epigenetic features were associated with diabetic kidney disease in people with Type 1 diabetes. METHODS A case-control association study was undertaken (n = 196 individuals with diabetic kidney disease vs. n = 246 individuals without renal disease). Participants were White and diagnosed with Type 1 diabetes before 31 years of age. Genes that encode mitochondrial proteins (n = 780) were downloaded from mitoproteome.org. DNA methylation profiles from blood-derived DNA were generated using the Illumina Infinium HumanMethylation450 (262 samples) and Illumina Infinium HumanMethylation27 (192 samples) arrays. Beta values (β) were calculated and quality control was conducted, including evaluating blind duplicate DNA samples. RESULTS Fifty-four Cytosine-phosphate-Guanine probes across 51 unique genes were significantly associated (P ≤ 10(-8) ) with diabetic kidney disease across both the 450K and the 27K methylation arrays. A subanalysis, employing the 450K array, identified 755 Cytosine-phosphate-Guanine probes in 374 genes that were significantly associated (P ≤ 10(-8) ) with end-stage renal disease. Forty-six of the top-ranked variants for diabetic kidney disease were also identified as being differentially methylated in individuals with end-stage renal disease. The largest change in methylation (Δβ = 0.2) was observed for cg03169527 in the TAMM41 gene, chromosome 3p25.2. Three genes, PMPCB, TSFM and AUH, were observed with differential methylation at multiple Cytosine-phosphate-Guanine sites each (P < 10(-12) ). CONCLUSIONS Differential methylation in genes that influence mitochondrial function are associated with kidney disease in individuals with Type 1 diabetes.
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Affiliation(s)
- E J Swan
- Centre for Public Health, Queen's University of Belfast
| | - A P Maxwell
- Centre for Public Health, Queen's University of Belfast
- Regional Nephrology Unit, Belfast City Hospital, Belfast, UK
| | - A J McKnight
- Centre for Public Health, Queen's University of Belfast
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50
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Lévesque ML, Casey KF, Szyf M, Ismaylova E, Ly V, Verner MP, Suderman M, Brendgen M, Vitaro F, Dionne G, Boivin M, Tremblay RE, Booij L. Genome-wide DNA methylation variability in adolescent monozygotic twins followed since birth. Epigenetics 2015; 9:1410-21. [PMID: 25437055 DOI: 10.4161/15592294.2014.970060] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
DNA methylation patterns are characterized by highly conserved developmental programs, but allow for divergent gene expression resulting from stochastic epigenetic drift or divergent environments. Genome-wide methylation studies in monozygotic (MZ) twins are providing insight into the extent of epigenetic variation that occurs, irrespective of genotype. However, little is known about the variability of DNA methylation patterns in adolescence, a period involving significant and rapid physical, emotional, social, and neurodevelopmental change. Here, we assessed genome-wide DNA methylation using the 450 K Illumina BeadChip in a sample of 37 MZ twin pairs followed longitudinally since birth to investigate: 1) the extent of variation in DNA methylation in identical genetic backgrounds in adolescence and; 2) whether these variations are randomly distributed or enriched in particular functional pathways. We also assessed stability of DNA methylation over 3-6 months to distinguish stable trait-like and variable state-like genes. A pathway analysis found high within-pair variability in genes associated with development, cellular mechanisms, tissue and cell morphology, and various disorders. Test-retest analyses performed in a sub-sample of 8 twin pairs demonstrated enrichment in gene pathways involved in organismal development, cellular growth and proliferation, cell signaling, and particular disorders. The variability found in functional gene pathways may plausibly underlie phenotypic differences in this adolescent MZ twin sample. Furthermore, we assessed stability of methylation over 3-6 months and found that some genes were stable while others were unstable, suggesting that the methylome remains dynamic in adolescence and that dynamic sites tend to be organized in certain gene pathways.
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