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Christiansen C, Potier L, Martin TC, Villicaña S, Castillo-Fernandez JE, Mangino M, Menni C, Tsai PC, Campbell PJ, Mullin S, Ordoñana JR, Monteagudo O, Sachdev PS, Mather KA, Trollor JN, Pietilainen KH, Ollikainen M, Dalgård C, Kyvik K, Christensen K, van Dongen J, Willemsen G, Boomsma DI, Magnusson PKE, Pedersen NL, Wilson SG, Grundberg E, Spector TD, Bell JT. Enhanced resolution profiling in twins reveals differential methylation signatures of type 2 diabetes with links to its complications. EBioMedicine 2024; 103:105096. [PMID: 38574408 PMCID: PMC11004697 DOI: 10.1016/j.ebiom.2024.105096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 03/18/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Type 2 diabetes (T2D) susceptibility is influenced by genetic and environmental factors. Previous findings suggest DNA methylation as a potential mechanism in T2D pathogenesis and progression. METHODS We profiled DNA methylation in 248 blood samples from participants of European ancestry from 7 twin cohorts using a methylation sequencing platform targeting regulatory genomic regions encompassing 2,048,698 CpG sites. FINDINGS We find and replicate 3 previously unreported T2D differentially methylated CpG positions (T2D-DMPs) at FDR 5% in RGL3, NGB and OTX2, and 20 signals at FDR 25%, of which 14 replicated. Integrating genetic variation and T2D-discordant monozygotic twin analyses, we identify both genetic-based and genetic-independent T2D-DMPs. The signals annotate to genes with established GWAS and EWAS links to T2D and its complications, including blood pressure (RGL3) and eye disease (OTX2). INTERPRETATION The results help to improve our understanding of T2D disease pathogenesis and progression and may provide biomarkers for its complications. FUNDING Funding acknowledgements for each cohort can be found in the Supplementary Note.
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Affiliation(s)
| | - Louis Potier
- APHP, Paris Cité University, INSERM, Paris, France
| | | | | | | | | | | | - Pei-Chien Tsai
- King's College London, UK; Department of Biomedical Sciences, Chang Gung University, Taoyuan City, Taiwan; Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan City, Taiwan
| | - Purdey J Campbell
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Shelby Mullin
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia; School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | | | | | | | | | | | - Kirsi H Pietilainen
- Obesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Finland; HealthyWeightHub, Abdominal Center, Helsinki University Hospital and University of Helsinki, Finland
| | - Miina Ollikainen
- Minerva Foundation Institute for Medical Research, Helsinki, Finland; Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Finland
| | | | | | | | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, the Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, the Netherlands
| | | | | | - Scott G Wilson
- King's College London, UK; Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, WA, Australia; School of Biomedical Sciences, University of Western Australia, Crawley, WA, 6009, Australia
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Li X, Shao X, Kou M, Wang X, Ma H, Grundberg E, Bazzano LA, Smith SR, Bray GA, Sacks FM, Qi L. DNA Methylation at ABCG1 and Long-term Changes in Adiposity and Fat Distribution in Response to Dietary Interventions: The POUNDS Lost Trial. Diabetes Care 2023; 46:2201-2207. [PMID: 37770056 DOI: 10.2337/dc23-0748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/07/2023] [Indexed: 10/03/2023]
Abstract
OBJECTIVE To examine whether participants with different levels of diabetes-related DNA methylation at ABCG1 might respond differently to dietary weight loss interventions with long-term changes in adiposity and body fat distribution. RESEARCH DESIGN AND METHODS The current study included overweight/obese participants from the POUNDS Lost trial. Blood levels of regional DNA methylation at ABCG1 were profiled by high-resolution methylC-capture sequencing at baseline among 673 participants, of whom 598 were followed up at 6 months and 543 at 2 years. Two-year changes in adiposity and computed tomography-measured body fat distribution were calculated. RESULTS Regional DNA methylation at ABCG1 showed significantly different associations with long-term changes in body weight and waist circumference at 6 months and 2 years in dietary interventions varying in protein intake (interaction P < 0.05 for all). Among participants assigned to an average-protein (15%) diet, lower baseline regional DNA methylation at ABCG1 was associated with greater reductions in body weight and waist circumference at 6 months and 2 years, whereas opposite associations were found among those assigned to a high-protein (25%) diet. Similar interaction patterns were also observed for body fat distribution, including visceral adipose tissue, subcutaneous adipose tissue, deep subcutaneous adipose tissue, and total adipose tissue at 6 months and 2 years (interaction P < 0.05 for all). CONCLUSIONS Baseline DNA methylation at ABCG1 interacted with dietary protein intake on long-term decreases in adiposity and body fat distribution. Participants with lower methylation at ABCG1 benefitted more in long-term reductions in body weight, waist circumference, and body fat distribution when consuming an average-protein diet.
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Affiliation(s)
- Xiang Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Minghao Kou
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Xuan Wang
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Hao Ma
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Elin Grundberg
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO
| | - Lydia A Bazzano
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | | | - George A Bray
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA
| | - Frank M Sacks
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
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Rouskas K, Katsareli EA, Amerikanou C, Dimopoulos AC, Glentis S, Kalantzi A, Skoulakis A, Panousis N, Ongen H, Bielser D, Planchon A, Romano L, Harokopos V, Reczko M, Moulos P, Griniatsos I, Diamantis T, Dermitzakis ET, Ragoussis J, Dedoussis G, Dimas AS. Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population. BMC Genomics 2023; 24:442. [PMID: 37543566 PMCID: PMC10403965 DOI: 10.1186/s12864-023-09532-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/25/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND Expression quantitative trait loci (eQTL) studies provide insights into regulatory mechanisms underlying disease risk. Expanding studies of gene regulation to underexplored populations and to medically relevant tissues offers potential to reveal yet unknown regulatory variants and to better understand disease mechanisms. Here, we performed eQTL mapping in subcutaneous (S) and visceral (V) adipose tissue from 106 Greek individuals (Greek Metabolic study, GM) and compared our findings to those from the Genotype-Tissue Expression (GTEx) resource. RESULTS We identified 1,930 and 1,515 eGenes in S and V respectively, over 13% of which are not observed in GTEx adipose tissue, and that do not arise due to different ancestry. We report additional context-specific regulatory effects in genes of clinical interest (e.g. oncogene ST7) and in genes regulating responses to environmental stimuli (e.g. MIR21, SNX33). We suggest that a fraction of the reported differences across populations is due to environmental effects on gene expression, driving context-specific eQTLs, and suggest that environmental effects can determine the penetrance of disease variants thus shaping disease risk. We report that over half of GM eQTLs colocalize with GWAS SNPs and of these colocalizations 41% are not detected in GTEx. We also highlight the clinical relevance of S adipose tissue by revealing that inflammatory processes are upregulated in individuals with obesity, not only in V, but also in S tissue. CONCLUSIONS By focusing on an understudied population, our results provide further candidate genes for investigation regarding their role in adipose tissue biology and their contribution to disease risk and pathogenesis.
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Affiliation(s)
- Konstantinos Rouskas
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
- Institute of Applied Biosciences, Centre for Research & Technology Hellas, Thessaloniki, Greece
| | - Efthymia A Katsareli
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Charalampia Amerikanou
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Alexandros C Dimopoulos
- Institute for Fundamental Biomedical Science, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
- Hellenic Naval Academy, Hatzikyriakou Avenue, Pireaus, Greece
| | - Stavros Glentis
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
- Pediatric Hematology/Oncology Unit (POHemU), First Department of Pediatrics, University of Athens, Aghia Sophia Children's Hospital, Athens, Greece
| | - Alexandra Kalantzi
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | - Anargyros Skoulakis
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | | | - Halit Ongen
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Swiss Institute of Bioinformatics, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva, University of Geneva, Geneva, Switzerland
| | - Deborah Bielser
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Alexandra Planchon
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Luciana Romano
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Vaggelis Harokopos
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | - Martin Reczko
- Institute for Fundamental Biomedical Science, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
| | - Panagiotis Moulos
- Institute for Fundamental Biomedical Science, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece
- Center of New Biotechnologies & Precision Medicine, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis Griniatsos
- First Department of Surgery, National and Kapodistrian University of Athens, Medical School, Laiko Hospital, Athens, Greece
| | - Theodoros Diamantis
- First Department of Surgery, National and Kapodistrian University of Athens, Medical School, Laiko Hospital, Athens, Greece
| | - Emmanouil T Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University Genome Centre, McGill University, Montréal, QC, Canada
- Department of Bioengineering, McGill University, Montréal, QC, Canada
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University, Athens, Greece
| | - Antigone S Dimas
- Institute for Bioinnovation, Biomedical Sciences Research Center 'Alexander Fleming', Vari, Greece.
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Li X, Shao X, Xue Q, Kou M, Champagne CM, Koseva BS, Heianza Y, Grundberg E, Bazzano LA, Bray GA, Sacks FM, Qi L. DNA Methylation Near CPT1A and Changes in Triglyceride-rich Lipoproteins in Response to Weight-loss Diet Interventions. J Clin Endocrinol Metab 2023; 108:e542-e549. [PMID: 36800272 PMCID: PMC10348458 DOI: 10.1210/clinem/dgad086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/18/2023]
Abstract
CONTEXT Carnitine palmitoyltransferase-1A, encoded by the CPT1A gene, plays a key role in the oxidation of long-chain fatty acids in the mitochondria and may be important in triglyceride metabolism. Previous work has shown that high fat intake was negatively associated with CPT1A methylation and positively associated with CPT1A expression. OBJECTIVE We aim to investigate the association of DNA methylation (DNAm) at the CPT1A gene with reductions in triglycerides and triglyceride-rich lipoproteins (TRLs) in response to weight-loss diet interventions. METHODS The current study included 538 White participants, who were randomly assigned to 1 of 4 diets varying in macronutrient components. We defined the regional DNAm at CPT1A as the average methylation level over CpGs within 500 bp of the 3 triglyceride-related DNAm sites. RESULTS Dietary fat intake significantly modified the association between baseline DNAm at CPT1A and 2-year changes in total plasma triglycerides, independent of concurrent weight loss. Among participants assigned to a low-fat diet, a higher regional DNAm level at CPT1A was associated with a greater reduction in total plasma triglycerides at 2 years (P = .01), compared with those assigned to a high-fat diet (P = .64) (P interaction = .018). Further investigation on lipids and apolipoproteins in very low-density lipoprotein (VLDL) revealed similar interaction patterns for 2-year changes in VLDL-triglycerides, VLDL-cholesterol, and VLDL-apolipoprotein B (P interaction = .009, .002, and .016, respectively), but not for VLDL-apoC-III (P interaction = .36). CONCLUSION Participants with a higher regional DNAm level at CPT1A benefit more in long-term improvement in triglycerides, particularly in the TRLs and related apolipoproteins when consuming a low-fat weight-loss diet.
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Affiliation(s)
- Xiang Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Xiaojian Shao
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, Ontario K1C 0R6, Canada
| | - Qiaochu Xue
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Minghao Kou
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Catherine M Champagne
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA 70808, USA
| | - Boryana S Koseva
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Yoriko Heianza
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - Elin Grundberg
- Department of Pediatrics, Genomic Medicine Center, Children's Mercy Kansas City, Kansas City, MO 64108, USA
| | - Lydia A Bazzano
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - George A Bray
- Pennington Biomedical Research Center, Louisiana State University, Baton Rouge, LA 70808, USA
| | - Frank M Sacks
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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5
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Liu L, Ju M, Hu Y, Luan C, Zhang J, Chen K. Genome-wide DNA methylation and transcription analysis in psoriatic epidermis. Epigenomics 2023; 15:209-226. [PMID: 37158398 DOI: 10.2217/epi-2022-0458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Aim: To identify DNA methylation and transcription biomarkers in the psoriatic epidermis. Materials & methods: Gene transcription and DNA methylation datasets of psoriatic epidermal tissue were obtained from the Gene Expression Omnibus. Machine learning algorithm analysis and weighted gene coexpression network analysis were carried out to screen hub genes. Results: Differentially methylated and expressed genes were identified in the psoriatic epidermis. Six hub genes were selected - GZMB, CRIP1, S100A12, ISG15, CRABP2 and VNN1 - whose transcript levels showed a significant correlation with Psoriasis Area and Severity Index scores and immune infiltration. Conclusion: Psoriatic epidermis is primarily in a hypermethylated status. Epidermis-specific hub differentially methylated and expressed genes are potential biomarkers to help judge the condition of psoriasis.
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Affiliation(s)
- Lingxi Liu
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, 210042, China
| | - Mei Ju
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, 210042, China
| | - Yu Hu
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, 210042, China
| | - Chao Luan
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, 210042, China
| | - Jiaan Zhang
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, 210042, China
| | - Kun Chen
- Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, Jiangsu, 210042, China
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Abstract
Graves disease and Hashimoto disease form part of the spectrum of autoimmune thyroid disease (AITD), to which genetic and environmental factors are recognized contributors. Epigenetics provides a potential link between environmental influences, gene expression, and thyroid autoimmunity. DNA methylation (DNAm) is the best studied epigenetic process, and global hypomethylation of leukocyte DNA is reported in several autoimmune disorders. This review summarizes the current understanding of DNAm in AITD. Targeted DNAm studies of blood samples from AITD patients have reported differential DNAm in the promoter regions of several genes implicated in AITD, including TNF, IFNG, IL2RA, IL6, ICAM1, and PTPN22. In many cases, however, the findings await replication and are unsupported by functional studies to support causal roles in AITD pathogenesis. Furthermore, thyroid hormones affect DNAm, and in many studies confounding by reverse causation has not been considered. Recent studies have shown that DNAm patterns in candidate genes including ITGA6, PRKAA2, and DAPK1 differ between AITD patients from regions with different iodine status, providing a potential mechanism for associations between iodine and AITD. Research focus in the field is moving from candidate gene studies to an epigenome-wide approach. Genome-wide methylation studies of AITD patients have demonstrated multiple differentially methylated positions, including some in immunoregulatory genes such as NOTCH1, HLA-DRB1, TNF, and ICAM1. Large, epigenome-wide studies are required to elucidate the pathophysiological role of DNAm in AITD, with the potential to provide novel diagnostic and prognostic biomarkers as well as therapeutic targets.
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Affiliation(s)
- Nicole Lafontaine
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia 6009, Australia
- Medical School, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Scott G Wilson
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - John P Walsh
- Department of Endocrinology & Diabetes, Sir Charles Gairdner Hospital, Nedlands, Western Australia 6009, Australia
- Medical School, University of Western Australia, Crawley, Western Australia 6009, Australia
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Chan D, Oros Klein K, Riera-Escamilla A, Krausz C, O’Flaherty C, Chan P, Robaire B, Trasler JM. Sperm DNA methylome abnormalities occur both pre- and post-treatment in men with Hodgkin disease and testicular cancer. Clin Epigenetics 2023; 15:5. [PMID: 36611168 PMCID: PMC9826600 DOI: 10.1186/s13148-022-01417-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Combination chemotherapy has contributed to increased survival from Hodgkin disease (HD) and testicular cancer (TC). However, questions concerning the quality of spermatozoa after treatment have arisen. While studies have shown evidence of DNA damage and aneuploidy in spermatozoa years following anticancer treatment, the sperm epigenome has received little attention. Our objectives here were to determine the impact of HD and TC, as well as their treatments, on sperm DNA methylation. Semen samples were collected from community controls (CC) and from men undergoing treatment for HD or TC, both before initiation of chemotherapy and at multiple times post-treatment. Sperm DNA methylation was assessed using genome-wide and locus-specific approaches. RESULTS Imprinted gene methylation was not affected in the sperm of HD or TC men, before or after treatment. Prior to treatment, using Illumina HumanMethylation450 BeadChip (450 K) arrays, a subset of 500 probes was able to distinguish sperm samples from TC, HD and CC subjects; differences between groups persisted post-treatment. Comparing altered sperm methylation between HD or TC patients versus CC men, twice as many sites were affected in TC versus HD men; for both groups, the most affected CpGs were hypomethylated. For TC patients, the promoter region of GDF2 contained the largest region of differential methylation. To assess alterations in DNA methylation over time/post-chemotherapy, serial samples from individual patients were compared. With restriction landmark genome scanning and 450 K array analyses, some patients who underwent chemotherapy showed increased alterations in DNA methylation, up to 2 to 3 years post-treatment, when compared to the CC cohort. Similarly, a higher-resolution human sperm-specific assay that includes assessment of environmentally sensitive regions, or "dynamic sites," also demonstrated persistently altered sperm DNA methylation in cancer patients post-treatment and suggested preferential susceptibility of "dynamic" CpG sites. CONCLUSIONS Distinct sperm DNA methylation signatures were present pre-treatment in men with HD and TC and may help explain increases in birth defects reported in recent clinical studies. Epigenetic defects in spermatozoa of some cancer survivors were evident even up to 2 years post-treatment. Abnormalities in the sperm epigenome both pre- and post-chemotherapy may contribute to detrimental effects on future reproductive health.
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Affiliation(s)
- Donovan Chan
- grid.63984.300000 0000 9064 4811Research Institute of the McGill University Health Centre, 1001 Décarie Boul. Block E, Montréal, QC Canada
| | - Kathleen Oros Klein
- grid.414980.00000 0000 9401 2774Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC Canada
| | - Antoni Riera-Escamilla
- grid.7080.f0000 0001 2296 0625Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Catalonia Spain
| | - Csilla Krausz
- grid.7080.f0000 0001 2296 0625Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Catalonia Spain ,grid.8404.80000 0004 1757 2304Department of Biomedical, Experimental and Clinical Sciences Mario Serio, University of Florence, Florence, Italy
| | - Cristian O’Flaherty
- grid.63984.300000 0000 9064 4811Research Institute of the McGill University Health Centre, 1001 Décarie Boul. Block E, Montréal, QC Canada ,grid.14709.3b0000 0004 1936 8649Department of Surgery, McGill University, Montréal, QC Canada ,grid.14709.3b0000 0004 1936 8649Department of Pharmacology and Therapeutics, McGill University, Montréal, QC Canada
| | - Peter Chan
- grid.63984.300000 0000 9064 4811Research Institute of the McGill University Health Centre, 1001 Décarie Boul. Block E, Montréal, QC Canada ,grid.14709.3b0000 0004 1936 8649Department of Urology, McGill University, Montréal, QC Canada
| | - Bernard Robaire
- grid.14709.3b0000 0004 1936 8649Department of Pharmacology and Therapeutics, McGill University, Montréal, QC Canada ,grid.14709.3b0000 0004 1936 8649Department of Obstetrics and Gynecology, McGill University, Montréal, QC Canada
| | - Jacquetta M. Trasler
- grid.63984.300000 0000 9064 4811Research Institute of the McGill University Health Centre, 1001 Décarie Boul. Block E, Montréal, QC Canada ,grid.14709.3b0000 0004 1936 8649Department of Pharmacology and Therapeutics, McGill University, Montréal, QC Canada ,grid.14709.3b0000 0004 1936 8649Departments of Pediatrics and Human Genetics, McGill University, Montréal, QC Canada
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Christiansen C, Tomlinson M, Eliot M, Nilsson E, Costeira R, Xia Y, Villicaña S, Mompeo O, Wells P, Castillo-Fernandez J, Potier L, Vohl MC, Tchernof A, Moustafa JES, Menni C, Steves CJ, Kelsey K, Ling C, Grundberg E, Small KS, Bell JT. Adipose methylome integrative-omic analyses reveal genetic and dietary metabolic health drivers and insulin resistance classifiers. Genome Med 2022; 14:75. [PMID: 35843982 PMCID: PMC9290282 DOI: 10.1186/s13073-022-01077-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 06/21/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND There is considerable evidence for the importance of the DNA methylome in metabolic health, for example, a robust methylation signature has been associated with body mass index (BMI). However, visceral fat (VF) mass accumulation is a greater risk factor for metabolic disease than BMI alone. In this study, we dissect the subcutaneous adipose tissue (SAT) methylome signature relevant to metabolic health by focusing on VF as the major risk factor of metabolic disease. We integrate results with genetic, blood methylation, SAT gene expression, blood metabolomic, dietary intake and metabolic phenotype data to assess and quantify genetic and environmental drivers of the identified signals, as well as their potential functional roles. METHODS Epigenome-wide association analyses were carried out to determine visceral fat mass-associated differentially methylated positions (VF-DMPs) in SAT samples from 538 TwinsUK participants. Validation and replication were performed in 333 individuals from 3 independent cohorts. To assess functional impacts of the VF-DMPs, the association between VF and gene expression was determined at the genes annotated to the VF-DMPs and an association analysis was carried out to determine whether methylation at the VF-DMPs is associated with gene expression. Further epigenetic analyses were carried out to compare methylation levels at the VF-DMPs as the response variables and a range of different metabolic health phenotypes including android:gynoid fat ratio (AGR), lipids, blood metabolomic profiles, insulin resistance, T2D and dietary intake variables. The results from all analyses were integrated to identify signals that exhibit altered SAT function and have strong relevance to metabolic health. RESULTS We identified 1181 CpG positions in 788 genes to be differentially methylated with VF (VF-DMPs) with significant enrichment in the insulin signalling pathway. Follow-up cross-omic analysis of VF-DMPs integrating genetics, gene expression, metabolomics, diet, and metabolic traits highlighted VF-DMPs located in 9 genes with strong relevance to metabolic disease mechanisms, with replication of signals in FASN, SREBF1, TAGLN2, PC and CFAP410. PC methylation showed evidence for mediating effects of diet on VF. FASN DNA methylation exhibited putative causal effects on VF that were also strongly associated with insulin resistance and methylation levels in FASN better classified insulin resistance (AUC=0.91) than BMI or VF alone. CONCLUSIONS Our findings help characterise the adiposity-associated methylation signature of SAT, with insights for metabolic disease risk.
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Affiliation(s)
- Colette Christiansen
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Max Tomlinson
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Melissa Eliot
- Department of Epidemiology, Brown University School of Public Health, Providence, R.I., USA
| | - Emma Nilsson
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Ricardo Costeira
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Yujing Xia
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Olatz Mompeo
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Philippa Wells
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Louis Potier
- Diabetology Department, Bichat Hospital, AP-HP, Université de Paris, Paris, France
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Université Laval, Québec, QC, Canada
| | - Andre Tchernof
- Québec Heart and Lung Institute, Université Laval, Québec, QC, Canada
| | | | - Cristina Menni
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Claire J Steves
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Karl Kelsey
- Department of Epidemiology, Brown University School of Public Health, Providence, R.I., USA
| | - Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Scania University Hospital, Malmö, Sweden
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Kerrin S Small
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
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9
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Chapin N, Fernandez J, Poole J, Delatte B. Anchor-based bisulfite sequencing determines genome-wide DNA methylation. Commun Biol 2022; 5:596. [PMID: 35710818 PMCID: PMC9203462 DOI: 10.1038/s42003-022-03543-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
Whole Genome Bisulfite Sequencing (WGBS) is the current standard for DNA methylation profiling. However, this approach is costly as it requires sequencing coverage over the entire genome. Here we introduce Anchor-Based Bisulfite Sequencing (ABBS). ABBS captures accurate DNA methylation information in Escherichia coli and mammals, while requiring up to 10 times fewer sequencing reads than WGBS. ABBS interrogates the entire genome and is not restricted to the CpG islands assayed by methods like Reduced Representation Bisulfite Sequencing (RRBS). The ABBS protocol is simple and can be performed in a single day. Anchor-Based Bisulfite Sequencing (ABBS) is a sequencing based method that enables analysis of DNA methylation states, based on specific hybridization of bisulfite-refractory methylcytosines with 8-aza-7-deaza-2-deoxyguanosine, incorporated in a primer at the end of 5 random nucleotides.
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Affiliation(s)
- Nathaniel Chapin
- Advanced Research Laboratory, Active Motif, 1914 Palomar Oaks Way STE 150, Carlsbad, CA, 92008, USA
| | - Joseph Fernandez
- Advanced Research Laboratory, Active Motif, 1914 Palomar Oaks Way STE 150, Carlsbad, CA, 92008, USA
| | - Jason Poole
- Advanced Research Laboratory, Active Motif, 1914 Palomar Oaks Way STE 150, Carlsbad, CA, 92008, USA
| | - Benjamin Delatte
- Advanced Research Laboratory, Active Motif, 1914 Palomar Oaks Way STE 150, Carlsbad, CA, 92008, USA.
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10
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Shao X, Le Stunff C, Cheung W, Kwan T, Lathrop M, Pastinen T, Bougnères P. Differentially methylated CpGs in response to growth hormone administration in children with idiopathic short stature. Clin Epigenetics 2022; 14:65. [PMID: 35585611 PMCID: PMC9118695 DOI: 10.1186/s13148-022-01281-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/17/2022] [Indexed: 11/17/2022] Open
Abstract
Background Recombinant human growth hormone (rhGH) has shown a great growth-promoting potential in children with idiopathic short stature (ISS). However, the response to rhGH differs across individuals, largely due to genetic and epigenetic heterogeneity. Since epigenetic marks on the methylome can be dynamically influenced by GH, we performed a comprehensive pharmacoepigenomics analysis of DNA methylation changes associated with long-term rhGH administration in children with ISS.
Results We measured DNA methylation profiles before and after GH treatment (with a duration of ~ 18 months in average) on 47 healthy children using customized methylC-seq capture sequencing. Their changes were compared and associated with changes in plasma IGF1 by adjusting sex, age, treatment duration and estimated blood proportions. We observed a considerable inter-individual heterogeneity of DNA methylation changes responding to GH treatment. We identified 267 response-associated differentially methylated cytosines (DMCs) that were enriched in promoter regions, CpG islands and blood cell-type-specific regulatory elements. Furthermore, the genes associated with these DMCs were enriched in the biology process of “cell development,” “neuron differentiation” and “developmental growth,” and in the TGF-beta signaling pathway, PPAR Alpha pathway, endoderm differentiation pathway, adipocytokine signaling pathway as well as PI3K-Akt signaling pathway, and cAMP signaling pathway. Conclusion Our study provides a first insight in DNA methylation changes associated with rhGH administration, which may help understand mechanisms of epigenetic regulation on GH-responsive genes. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01281-z.
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Affiliation(s)
- Xiaojian Shao
- Digital Technologies Research Center, National Research Council Canada, Ottawa, ON, K1A 0R6, Canada.
| | - Catherine Le Stunff
- UMR INSERM 1195 and Université Paris Saclay, Endocrinologie Pédiatrique, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France
| | - Warren Cheung
- Genomic Medicine Center, Children's Mercy - Kansas City and Children's Mercy Research Institute, Kansas City, MO, 64108, USA
| | - Tony Kwan
- Department of Human Genetics, McGill University and McGill Genome Center, Montreal, QC, H3A 0G1, Canada
| | - Mark Lathrop
- Department of Human Genetics, McGill University and McGill Genome Center, Montreal, QC, H3A 0G1, Canada
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy - Kansas City and Children's Mercy Research Institute, Kansas City, MO, 64108, USA.
| | - Pierre Bougnères
- UMR INSERM 1195 and Université Paris Saclay, Endocrinologie Pédiatrique, Hôpital Bicêtre, 94276, Le Kremlin-Bicêtre Cedex, France.
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11
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Li X, Shao X, Bazzano LA, Xue Q, Koseva BS, Grundberg E, Shai I, Bray GA, Sacks FM, Qi L. Blood DNA methylation at TXNIP and glycemic changes in response to weight-loss diet interventions: the POUNDS lost trial. Int J Obes (Lond). [PMID: 35165382 PMCID: PMC9156542 DOI: 10.1038/s41366-022-01084-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/24/2022] [Accepted: 01/28/2022] [Indexed: 01/01/2023]
Abstract
Background: Methods: Results: Conclusions:
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12
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Tost J. Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns. Advances in Experimental Medicine and Biology 2022; 1389:395-469. [DOI: 10.1007/978-3-031-11454-0_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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13
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Yang E, Guan W, Gong D, Li J, Han C, Zhang J, Wang H, Kang S, Gao X, Li Y, Yu L. Epigenetic silencing of UBXN8 contributes to leukemogenesis in t(8;21) acute myeloid leukemia. Exp Mol Med 2021. [PMID: 34921223 DOI: 10.1038/s12276-021-00695-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/01/2021] [Accepted: 07/02/2021] [Indexed: 11/21/2022] Open
Abstract
The formation of the RUNX1-RUNX1T1 fusion protein, resulting from the t(8;21) translocation, is considered to be one of the initiating events of t(8;21) acute myeloid leukemia (AML). However, the mechanisms of the oncogenic mechanism of RUNX1-RUNX1T1 remain unclear. In this study, we found that RUNX1-RUNX1T1 triggers the heterochromatic silencing of UBXN8 by recognizing the RUNX1-binding sites and recruiting chromatin-remodeling enzymes to the UBXN8 promoter region. Decitabine, a specific inhibitor of DNA methylation, upregulated the expression of UBXN8 in RUNX1-RUNX1T1+ AML cell lines. Overexpression of UBXN8 inhibited the proliferation and colony-forming ability of and promoted cell cycle arrest in t(8;21) AML cell lines. Enhancing UBXN8 levels can significantly inhibit tumor proliferation and promote the differentiation of RUNX1-RUNX1T1+ cells in vivo. In conclusion, our results indicated that epigenetic silencing of UBXN8 via methylation of its promoter region mediated by the RUNX1-RUNX1T1 fusion protein contributes to the leukemogenesis of t(8;21) AML and that UBXN8 targeting may be a potential therapeutic strategy for t(8;21) AML. The protein byproduct of a common chromosomal rearrangement in acute myeloid leukemia (AML) promotes cancerous growth by inhibiting a tumor suppressor protein. AML cells that exhibit an abnormal coupling of segments from chromosomes 8 and 21 produce a fusion protein known as RUNX1-RUNX1T1. Erna Yang of Shenzhen University General Hospital, China, and colleagues have identified a mechanism by which this protein promotes AML progression. Experiments with AML cell lines showed that RUNX1-RUNX1T1 recruits DNA-binding proteins that introduce numerous chemical modifications to the UBXN8 gene, which inhibit production of the tumor suppressor protein it codes for. Drugs that block these modifications and stimulate UBXN8 activity also arrest tumor cell division. Experiments in mice confirmed that enhanced UBXN8 expression offers a defense against AML progression, suggesting a promising therapeutic approach.
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14
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Perrin HJ, Currin KW, Vadlamudi S, Pandey GK, Ng KK, Wabitsch M, Laakso M, Love MI, Mohlke KL. Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci. PLoS Genet 2021; 17:e1009865. [PMID: 34699533 PMCID: PMC8570510 DOI: 10.1371/journal.pgen.1009865] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/05/2021] [Accepted: 10/07/2021] [Indexed: 12/15/2022] Open
Abstract
Chromatin accessibility and gene expression in relevant cell contexts can guide identification of regulatory elements and mechanisms at genome-wide association study (GWAS) loci. To identify regulatory elements that display differential activity across adipocyte differentiation, we performed ATAC-seq and RNA-seq in a human cell model of preadipocytes and adipocytes at days 4 and 14 of differentiation. For comparison, we created a consensus map of ATAC-seq peaks in 11 human subcutaneous adipose tissue samples. We identified 58,387 context-dependent chromatin accessibility peaks and 3,090 context-dependent genes between all timepoint comparisons (log2 fold change>1, FDR<5%) with 15,919 adipocyte- and 18,244 preadipocyte-dependent peaks. Adipocyte-dependent peaks showed increased overlap (60.1%) with Roadmap Epigenomics adipocyte nuclei enhancers compared to preadipocyte-dependent peaks (11.5%). We linked context-dependent peaks to genes based on adipocyte promoter capture Hi-C data, overlap with adipose eQTL variants, and context-dependent gene expression. Of 16,167 context-dependent peaks linked to a gene, 5,145 were linked by two or more strategies to 1,670 genes. Among GWAS loci for cardiometabolic traits, adipocyte-dependent peaks, but not preadipocyte-dependent peaks, showed significant enrichment (LD score regression P<0.005) for waist-to-hip ratio and modest enrichment (P < 0.05) for HDL-cholesterol. We identified 659 peaks linked to 503 genes by two or more approaches and overlapping a GWAS signal, suggesting a regulatory mechanism at these loci. To identify variants that may alter chromatin accessibility between timepoints, we identified 582 variants in 454 context-dependent peaks that demonstrated allelic imbalance in accessibility (FDR<5%), of which 55 peaks also overlapped GWAS variants. At one GWAS locus for palmitoleic acid, rs603424 was located in an adipocyte-dependent peak linked to SCD and exhibited allelic differences in transcriptional activity in adipocytes (P = 0.003) but not preadipocytes (P = 0.09). These results demonstrate that context-dependent peaks and genes can guide discovery of regulatory variants at GWAS loci and aid identification of regulatory mechanisms. Cardiovascular and metabolic diseases are widespread, and an increased understanding of genetic mechanisms behind these diseases could improve treatment. Chromatin accessibility and gene expression in relevant cell contexts can guide identification of regulatory elements and genetic mechanisms for disease traits. A relevant context for cardiovascular and metabolic disease traits is adipocyte differentiation. To identify regulatory elements and genes that display differences in activity during adipocyte differentiation, we profiled chromatin accessibility and gene expression in a human cell model of preadipocytes and adipocytes. We identified chromatin regions that change accessibility during differentiation and predicted genes they may affect. We also linked these chromatin regions to genetic variants associated with risk of disease. At one genomic region linked to fatty acids, a chromatin region more accessible in adipocytes linked to a fatty acid synthesis gene and exhibited allelic differences in transcriptional activity in adipocytes but not preadipocytes. These results demonstrate that chromatin regions and genes that change during cell context can guide discovery of regulatory variants and aid identification of disease mechanisms.
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Affiliation(s)
- Hannah J. Perrin
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Kevin W. Currin
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Swarooparani Vadlamudi
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Gautam K. Pandey
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Kenneth K. Ng
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Martin Wabitsch
- Department of Pediatrics and Adolescent Medicine, Ulm University Hospital, Ulm, Germany
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Michael I. Love
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail:
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15
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Abstract
Genome-wide DNA methylation analysis is one of the most common epigenetic processes analysed for genome characterization and differential DNA methylation assessment. Previous genome-wide analysis has suggested an important variable in DNA methylation methods involves CpG density. The current study was designed to investigate the CpG density in a variety of different species genomes and correlate this to various DNA methylation analysis data sets. The majority of all genomes had >90% of the genome in the low density 1-3 CpG/100 bp category, while <10% of the genome was in the higher density >5 CpG/100 bp category. Similar observations with human, rat, bird, and fish genomes were observed. The methylated DNA immunoprecipitation (MeDIP) procedure uses the anti-5-methylcytosine antibody immunoprecipitation followed by next-generation sequencing (MeDIP-Seq). The MeDIP procedure is biased to lower CpG density of <5 CpG/100 bp, which corresponds to >95% of the genome. The reduced representation bisulphite (RRBS) protocol generally identifies DMRs in higher CpG density regions of ≥3 CpG/100 bp which corresponds to approximately 20% of the genome. The whole-genome bisulphite (WGBS) analyses resulted in higher CpG densities, often greater than 10 CpG/100bp. WGBS generally identifies ≥2 CpG/100bp, which corresponds to approximately 50% of the genome. Limitations and potential optimization approaches for each method are discussed. None of the procedures can provide complete genome-wide assessment of the genome, but MeDIP-Seq provides coverage of the highest percentage. Observations demonstrate that CpG density is a critical variable in DNA methylation analysis, and different molecular techniques focus on distinct genomic regions.
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Affiliation(s)
- Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, USA
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16
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Yang E, Gong D, Guan W, Li J, Gao X, Li Y, Yu L. Evaluation of acute myeloid leukemia blast percentage on MethylC-Capture Sequencing results. Exp Hematol Oncol 2021; 10:26. [PMID: 33789763 PMCID: PMC8011402 DOI: 10.1186/s40164-021-00219-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/26/2021] [Indexed: 11/10/2022] Open
Abstract
Aberrant DNA methylation is often related to the diagnosis, prognosis, and therapeutic response of acute myeloid leukemia (AML); however, relevant studies on the relationship between bone marrow myeloblast percentage and the DNA methylation level in AML have not been reported. We evaluated the effects of AML blast percentage on DNA methylation level using the MethylC-capture sequencing (MCC-Seq) approach based on next-generation sequencing (NGS) and found that the methylation level of both genome-wide and promoter regions significantly increased when the percentage of AML blasts reached ≥ 40%, indicating that an accurate DNA methylation level in cancer cells can be obtained when the bone marrow samples of AML patients have more than 40% myeloblasts.
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Affiliation(s)
- Erna Yang
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Nanshan District, Shenzhen, Guangdong, 518000, People's Republic of China
| | - Desheng Gong
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Nanshan District, Shenzhen, Guangdong, 518000, People's Republic of China
| | - Wei Guan
- Department of Hematology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jieying Li
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Nanshan District, Shenzhen, Guangdong, 518000, People's Republic of China
| | - Xuefeng Gao
- Centrol Laboratory, Shenzhen University General Hospital, Shenzhen University Health Science Center, Xueyuan AVE 1098, Nanshan District, Shenzhen, Guangdong, 518000, People's Republic of China.
| | - Yonghui Li
- Centrol Laboratory, Shenzhen University General Hospital, Shenzhen University Health Science Center, Xueyuan AVE 1098, Nanshan District, Shenzhen, Guangdong, 518000, People's Republic of China.
| | - Li Yu
- Department of Hematology and Oncology, International Cancer Center, Shenzhen Key Laboratory of Precision Medicine for Hematological Malignancies, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University Health Science Center, Shenzhen University, Xueyuan AVE 1098, Nanshan District, Shenzhen, Guangdong, 518000, People's Republic of China.
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17
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Bender A, Al Adhami H, Dahlet T, Weber M. Studying DNA Methylation Genome-Wide by Bisulfite Sequencing from Low Amounts of DNA in Mammals. Methods Mol Biol 2021; 2214:207-20. [PMID: 32944912 DOI: 10.1007/978-1-0716-0958-3_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
DNA methylation is extensively reprogrammed during mammalian embryogenesis and germ cell development. Protocols for genome-wide bisulfite sequencing enable the quantification of DNA methylation with high precision and single base-pair resolution; however they can be limited by the necessity for high amounts of DNA. Here we describe optimized reduced representation bisulfite sequencing (RRBS) and whole genome bisulfite sequencing (WGBS) protocols for low amounts of DNA, which include steps to estimate the minimal number of PCR cycles needed for the final library preparation to minimize PCR biases. These protocols require no more than 5 ng DNA and can easily be applied to mammalian cells available in small quantities such as early embryos or primordial germ cells.
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Yang E, Guan W, Gong D, Gao X, Han C, Zhang J, Wang H, Wang M, Li Y, Yu L. Epigenetic silencing of miR564 contributes to the leukemogenesis of t(8;21) acute myeloid leukemia. Clin Sci (Lond) 2020; 134:3079-91. [PMID: 33201243 DOI: 10.1042/CS20200786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 11/03/2020] [Accepted: 11/17/2020] [Indexed: 01/20/2023]
Abstract
The AML1-ETO oncoprotein, which results from t(8;21) translocation, is considered an initial event of t(8;21) acute myeloid leukemia (AML). However, the precise mechanisms of the oncogenic activity of AML1-ETO is yet to be fully determined. The present study demonstrates that AML1-ETO triggers the heterochromatic silencing of microRNA-564 (miR564) by binding at the AML1 binding site along the miR564 promoter region and recruiting chromatin-remodeling enzymes. Suppression of miR564 enhances the oncogenic activity of the AML1-ETO oncoprotein by directly inhibiting the expression of CCND1 and the DNMT3A genes. Ectopic expression of miR564 can induce retardation of G1/S transition, reperform differentiation, promote apoptosis, as well as inhibit the proliferation and colony formation of AML1-ETO+ leukemia cells in vitro. Enhanced miR564 levels can significantly inhibit the tumor proliferation of t(8;21)AML in vivo. We first identify an unexpected and important epigenetic circuitry of AML1-ETO/miR564/CCND1/DNMT3A that contributes to the leukemogenesis in vitro/vivo of AML1-ETO+ leukemia, indicating that miR564 enhancement could provide a potential therapeutic method for AML1-ETO+ leukemia.
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Abstract
The pathophysiology of obesity is complex and includes changes in eating behavior, genetic, epigenetic, environmental factors, and much more. To date, ~40 genetic polymorphisms are associated with obesity and fat distribution. However, since these options do not fully explain the inheritance of obesity, other options, such as epigenetic changes, need to be considered. Epigenetic modifications affect gene expression without changing the deoxyribonucleic acid sequence. In addition, environmental exposure during critical periods of development can affect the epigenetic tags and lead to obesity. A deeper understanding of the epigenetic mechanisms underlying obesity can aid in prevention based on lifestyle changes. This review focuses on the role of epigenetic modifications in the development of obesity and related conditions.
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Affiliation(s)
- O. M. Drapkina
- National Research Center for Therapy and Preventive Medicine
| | - O. T. Kim
- National Research Center for Therapy and Preventive Medicine
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20
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Cao M, Shao X, Chan P, Cheung W, Kwan T, Pastinen T, Robaire B. High-resolution analyses of human sperm dynamic methylome reveal thousands of novel age-related epigenetic alterations. Clin Epigenetics 2020; 12:192. [PMID: 33317634 PMCID: PMC7735420 DOI: 10.1186/s13148-020-00988-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/25/2020] [Indexed: 12/23/2022] Open
Abstract
Background Children of aged fathers are at a higher risk of developing mental disorders. Alterations in sperm DNA methylation have been implicated as a potential cause. However, age-dependent modifications of the germ cells’ epigenome remain poorly understood. Our objective was to assess the DNA methylation profile of human spermatozoa during aging.
Results We used a high throughput, customized methylC-capture sequencing (MCC-seq) approach to characterize the dynamic DNA methylation in spermatozoa from 94 fertile and infertile men, who were categorized as young, 48 men between 18–38 years or old 46 men between 46–71 years. We identified more than 150,000 age-related CpG sites that are significantly differentially methylated among 2.65 million CpG sites covered. We conducted machine learning using our dataset to predict the methylation age of subjects; the age prediction accuracy based on our assay provided a more accurate prediction than that using the 450 K chip approach. In addition, we found that there are more hypermethylated (62%) than hypomethylated (38%) CpG sites in sperm of aged men, corresponding to 798 of total differential methylated regions (DMRs), of which 483 are hypermethylated regions (HyperDMR), and 315 hypomethylated regions (HypoDMR). Moreover, the distribution of age-related hyper- and hypomethylated CpGs in sperm is not random; the CpG sites that were hypermethylated with advanced age were frequently located in the distal region to genes, whereas hypomethylated sites were near to gene transcription start sites (TSS). We identified a high density of age-associated CpG changes in chromosomes 4 and 16, particularly HyperDMRs with localized clusters, the chr4 DMR cluster overlaps PGC1α locus, a protein involved in metabolic aging and the chr16 DMR cluster overlaps RBFOX1 locus, a gene implicated in neurodevelopmental disease. Gene ontology analysis revealed that the most affected genes by age were associated with development, neuron projection, differentiation and recognition, and behaviour, suggesting a potential link to the higher risk of neurodevelopmental disorders in children of aged fathers. Conclusion We identified thousands of age-related and sperm-specific epigenetic alterations. These findings provide novel insight in understanding human sperm DNA methylation dynamics during paternal aging, and the subsequently affected genes potentially related to diseases in offspring.
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Affiliation(s)
- Mingju Cao
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir William Osler, Montreal, QC, H3G 1Y6, Canada
| | - Xiaojian Shao
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, QC, H3A 0G1, Canada.,McGill University Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, QC, H3A 0G1, Canada.,Digital Technologies Research Centre, National Research Council Canada, 1200 Montreal Road, Ottawa, ON, K1A 0R6, Canada
| | - Peter Chan
- Department of Urology, McGill University Health Centre, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada
| | - Warren Cheung
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Tony Kwan
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, QC, H3A 0G1, Canada.,McGill University Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, QC, H3A 0G1, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, QC, H3A 0G1, Canada.,McGill University Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, QC, H3A 0G1, Canada.,Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, 2401 Gilham Road, Kansas City, MO, 64108, USA
| | - Bernard Robaire
- Department of Pharmacology and Therapeutics, McGill University, 3655 Promenade Sir William Osler, Montreal, QC, H3G 1Y6, Canada. .,Department of Obstetric and Gynecology, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada.
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21
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Qi C, Vonk JM, van der Plaat DA, Nieuwenhuis MAE, Dijk FN, Aïssi D, Siroux V, Boezen HM, Xu CJ, Koppelman GH. Epigenome-wide association study identifies DNA methylation markers for asthma remission in whole blood and nasal epithelium. Clin Transl Allergy 2020; 10:60. [PMID: 33303027 PMCID: PMC7731549 DOI: 10.1186/s13601-020-00365-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/26/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Asthma is a chronic respiratory disease which is not curable, yet some patients experience spontaneous remission. We hypothesized that epigenetic mechanisms may be involved in asthma remission. METHODS Clinical remission (ClinR) was defined as the absence of asthma symptoms and medication for at least 12 months, and complete remission (ComR) was defined as ClinR with normal lung function and absence of airway hyperresponsiveness. We analyzed differential DNA methylation of ClinR and ComR comparing to persistent asthma (PersA) in whole blood samples (n = 72) and nasal brushing samples (n = 97) in a longitudinal cohort of well characterized asthma patients. Significant findings of whole blood DNA methylation were tested for replication in two independent cohorts, Lifelines and Epidemiological study on the Genetics and Environment of Asthma (EGEA). RESULTS We identified differentially methylated CpG sites associated with ClinR (7 CpG sites) and ComR (129 CpG sites) in whole blood. One CpG (cg13378519, Chr1) associated with ClinR was replicated and annotated to PEX11 (Peroxisomal Biogenesis Factor 11 Beta). The whole blood DNA methylation levels of this CpG were also different between ClinR and healthy subjects. One ComR-associated CpG (cg24788483, Chr10) that annotated to TCF7L2 (Transcription Factor 7 Like 2) was replicated and associated with expression of TCF7L2 gene. One out of seven ClinR-associated CpG sites and 8 out of 129 ComR-associated CpG sites identified from whole blood samples showed nominal significance (P < 0.05) and the same direction of effect in nasal brushes. CONCLUSION We identified DNA methylation markers possibly associated with clinical and complete asthma remission in nasal brushes and whole blood, and two CpG sites identified from whole blood can be replicated in independent cohorts and may play a role in peroxisome proliferation and Wnt signaling pathway.
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Affiliation(s)
- Cancan Qi
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, PO Box 30.001, 9700 RB, Groningen, the Netherlands.,GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Judith M Vonk
- GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Diana A van der Plaat
- GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Maartje A E Nieuwenhuis
- GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - F Nicole Dijk
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, PO Box 30.001, 9700 RB, Groningen, the Netherlands.,GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Dylan Aïssi
- University Grenoble Alpes, Inserm, CNRS, Team of environmental epidemiology applied to Reproduction and Respiratory health, IAB (Institute for Advanced Biosciences), 38000, Grenoble, France
| | - Valérie Siroux
- University Grenoble Alpes, Inserm, CNRS, Team of environmental epidemiology applied to Reproduction and Respiratory health, IAB (Institute for Advanced Biosciences), 38000, Grenoble, France
| | - H Marike Boezen
- GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Cheng-Jian Xu
- Research Group of Bioinformatics and Computational Genomics, CiiM, Centre for individualized infection medicine, A Joint Venture Between Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,Department of Gastroenterology, Hepatology and Endocrinology, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergy, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, PO Box 30.001, 9700 RB, Groningen, the Netherlands. .,GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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22
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Lin N, Liu J, Castle J, Wan J, Shendre A, Liu Y, Wang C, He C. Genome-wide DNA methylation profiling in human breast tissue by Illumina TruSeq methyl capture EPIC sequencing and infinium methylationEPIC beadchip microarray. Epigenetics 2020; 16:754-769. [PMID: 33048617 PMCID: PMC8216193 DOI: 10.1080/15592294.2020.1827703] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A newly-developed platform, the Illumina TruSeq Methyl Capture EPIC library prep (TruSeq EPIC), builds on the content of the Infinium MethylationEPIC Beadchip Microarray (EPIC-array) and leverages the power of next-generation sequencing for targeted bisulphite sequencing. We empirically examined the performance of TruSeq EPIC and EPIC-array in assessing genome-wide DNA methylation in breast tissue samples. TruSeq EPIC provided data with a much higher density in the regions when compared to EPIC-array (~2.74 million CpGs with at least 10X coverage vs ~752 K CpGs, respectively). Approximately 398 K CpGs were common and measured across the two platforms in every sample. Overall, there was high concordance in methylation levels between the two platforms (Pearson correlation r = 0.98, P < 0.0001). However, we observed that TruSeq EPIC measurements provided a wider dynamic range and likely a higher quantitative sensitivity for CpGs that were either hypo- or hyper-methylated (β close to 0 or 1, respectively). In addition, when comparing different breast tissue types TruSeq EPIC identified more differentially methylated CpGs than EPIC-array, not only out of additional sites interrogated by TruSeq EPIC alone, but also out of common sites interrogated by both platforms. Our results suggest that both platforms show high reproducibility and reliability in genome-wide DNA methylation profiling, while TruSeq EPIC had a significant improvement over EPIC-array regarding genomic resolution and coverage. The wider dynamic range and likely higher precision of the estimates by the TruSeq EPIC may lead to the identification of novel differentially methylated markers that are associated with disease risk.
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Affiliation(s)
- Nan Lin
- The Cancer Prevention and Control Research Program, University of Kentucky Markey Cancer Center, Lexington, KY, USA
| | - Jinpeng Liu
- The Cancer Prevention and Control Research Program, University of Kentucky Markey Cancer Center, Lexington, KY, USA
| | - James Castle
- The Cancer Prevention and Control Research Program, University of Kentucky Markey Cancer Center, Lexington, KY, USA
| | - Jun Wan
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Aditi Shendre
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Yunlong Liu
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Chi Wang
- The Cancer Prevention and Control Research Program, University of Kentucky Markey Cancer Center, Lexington, KY, USA
| | - Chunyan He
- The Cancer Prevention and Control Research Program, University of Kentucky Markey Cancer Center, Lexington, KY, USA.,Department of Internal Medicine, Division of Medical Oncology, College of Medicine, University of Kentucky, Lexington, KY, USA
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23
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Spracklen CN, Iyengar AK, Vadlamudi S, Raulerson CK, Jackson AU, Brotman SM, Wu Y, Cannon ME, Davis JP, Crain AT, Currin KW, Perrin HJ, Narisu N, Stringham HM, Fuchsberger C, Locke AE, Welch RP, Kuusisto JK, Pajukanta P, Scott LJ, Li Y, Collins FS, Boehnke M, Laakso M, Mohlke KL. Adiponectin GWAS loci harboring extensive allelic heterogeneity exhibit distinct molecular consequences. PLoS Genet 2020; 16:e1009019. [PMID: 32915782 DOI: 10.1371/journal.pgen.1009019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/23/2020] [Accepted: 07/29/2020] [Indexed: 02/06/2023] Open
Abstract
Loci identified in genome-wide association studies (GWAS) can include multiple distinct association signals. We sought to identify the molecular basis of multiple association signals for adiponectin, a hormone involved in glucose regulation secreted almost exclusively from adipose tissue, identified in the Metabolic Syndrome in Men (METSIM) study. With GWAS data for 9,262 men, four loci were significantly associated with adiponectin: ADIPOQ, CDH13, IRS1, and PBRM1. We performed stepwise conditional analyses to identify distinct association signals, a subset of which are also nearly independent (lead variant pairwise r2<0.01). Two loci exhibited allelic heterogeneity, ADIPOQ and CDH13. Of seven association signals at the ADIPOQ locus, two signals colocalized with adipose tissue expression quantitative trait loci (eQTLs) for three transcripts: trait-increasing alleles at one signal were associated with increased ADIPOQ and LINC02043, while trait-increasing alleles at the other signal were associated with decreased ADIPOQ-AS1. In reporter assays, adiponectin-increasing alleles at two signals showed corresponding directions of effect on transcriptional activity. Putative mechanisms for the seven ADIPOQ signals include a missense variant (ADIPOQ G90S), a splice variant, a promoter variant, and four enhancer variants. Of two association signals at the CDH13 locus, the first signal consisted of promoter variants, including the lead adipose tissue eQTL variant for CDH13, while a second signal included a distal intron 1 enhancer variant that showed ~2-fold allelic differences in transcriptional reporter activity. Fine-mapping and experimental validation demonstrated that multiple, distinct association signals at these loci can influence multiple transcripts through multiple molecular mechanisms. Many DNA variants affect common human traits, and distinct variants can have different effects on the function or expression level of the same gene. We identified variants associated with levels of adiponectin, a hormone involved in glucose regulation. Among these variants, we specifically studied the sets of variants located near two genes, ADIPOQ and CDH13, to determine how the variants affect gene expression or function. We focused on sets of variants that can be inherited together but are not always inherited together. Of the variants associated with adiponectin and located near ADIPOQ, one set were also associated with higher expression levels of the protein-coding ADIPOQ gene and a nearby non-coding gene, a second set of variants were associated with lower levels of the ADIPOQ-AS1 antisense gene, and additional variants changed the amino acid sequence or size of the adiponectin protein. Our examples show the benefits of identifying multiple sets of trait-associated variants in the same DNA region. These variants explain more trait variation, help identify genes that affect the trait, and guide studies of gene regulation and biological processes.
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Abstract
PURPOSE OF REVIEW Atherosclerosis is a chronic disease characterized by lipid retention and inflammation in the artery wall. The retention and oxidation of low-density lipoprotein (LDL) in sub-endothelial space play a critical role in atherosclerotic plaque formation and destabilization. Oxidized LDL (ox-LDL) and other modified LDL particles are avidly taken up by endothelial cells, smooth muscle cells, and macrophages mainly through several scavenger receptors, including CD36 which is a class B scavenger receptor and membrane glycoprotein. RECENT FINDINGS Animal studies performed on CD36-deficient mice suggest that deficiency of CD36 prevents the development of atherosclerosis, though with some debate. CD36 serves as a signaling hub protein at the crossroad of inflammation, lipid metabolism, and fatty acid metabolism. In addition, the level of soluble CD36 (unattached to cells) in the circulating blood was elevated in patients with atherosclerosis and other metabolic disorders. We performed a state-of-the-art review on the structure, ligands, functions, and regulation of CD36 in the context of atherosclerosis by focusing on the pathological role of CD36 in the dysfunction of endothelial cells, smooth muscle cells, monocytes/macrophages, and platelets. Finally, we highlight therapeutic possibilities to target CD36 expression/activity in atherosclerosis.
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25
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Morselli M, Farrell C, Rubbi L, Fehling HL, Henkhaus R, Pellegrini M. Targeted bisulfite sequencing for biomarker discovery. Methods 2020; 187:13-27. [PMID: 32755621 DOI: 10.1016/j.ymeth.2020.07.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/16/2020] [Accepted: 07/19/2020] [Indexed: 12/14/2022] Open
Abstract
Cytosine methylation is one of the best studied epigenetic modifications. In mammals, DNA methylation patterns vary among cells and is mainly found in the CpG context. DNA methylation is involved in important processes during development and differentiation and its dysregulation can lead to or is associated with diseases, such as cancer, loss-of-imprinting syndromes and neurological disorders. It has been also shown that DNA methylation at the cellular, tissue and organism level varies with age. To overcome the costs of Whole-Genome Bisulfite Sequencing, the gold standard method to detect 5-methylcytosines at a single base resolution, DNA methylation arrays have been developed and extensively used. This method allows one to assess the status of a fraction of the CpG sites present in the genome of an organism. In order to combine the relatively low cost of Methylation Arrays and digital signals of bisulfite sequencing, we developed a Targeted Bisulfite Sequencing method that can be applied to biomarker discovery for virtually any phenotype. Here we describe a comprehensive step-by-step protocol to build a DNA methylation-based epigenetic clock.
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Affiliation(s)
- Marco Morselli
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, United States; UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, United States; Institute for Quantitative and Computational Biosciences - The Collaboratory, University of California Los Angeles, Los Angeles, CA 90095, United States.
| | - Colin Farrell
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, United States.
| | - Liudmilla Rubbi
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, United States.
| | - Heather L Fehling
- Clinical Reference Laboratory, Inc., Lenexa, KS 66215, United States.
| | - Rebecca Henkhaus
- Clinical Reference Laboratory, Inc., Lenexa, KS 66215, United States.
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, United States; UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, United States; Institute for Quantitative and Computational Biosciences - The Collaboratory, University of California Los Angeles, Los Angeles, CA 90095, United States.
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26
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Lam D, Luu PL, Song JZ, Qu W, Risbridger GP, Lawrence MG, Lu J, Trau M, Korbie D, Clark SJ, Pidsley R, Stirzaker C. Comprehensive evaluation of targeted multiplex bisulphite PCR sequencing for validation of DNA methylation biomarker panels. Clin Epigenetics 2020; 12:90. [PMID: 32571390 PMCID: PMC7310104 DOI: 10.1186/s13148-020-00880-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/04/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND DNA methylation is a well-studied epigenetic mark that is frequently altered in diseases such as cancer, where specific changes are known to reflect the type and severity of the disease. Therefore, there is a growing interest in assessing the clinical utility of DNA methylation as a biomarker for diagnosing disease and guiding treatment. The development of an accurate loci-specific methylation assay, suitable for use on low-input clinical material, is crucial for advancing DNA methylation biomarkers into a clinical setting. A targeted multiplex bisulphite PCR sequencing approach meets these needs by allowing multiple DNA methylated regions to be interrogated simultaneously in one experiment on limited clinical material. RESULTS Here, we provide an updated protocol and recommendations for multiplex bisulphite PCR sequencing (MBPS) assays for target DNA methylation analysis. We describe additional steps to improve performance and reliability: (1) pre-sequencing PCR optimisation which includes assessing the optimal PCR cycling temperature and primer concentration and (2) post-sequencing PCR optimisation to achieve uniform coverage of each amplicon. We use a gradient of methylated controls to demonstrate how PCR bias can be assessed and corrected. Methylated controls also allow assessment of the sensitivity of methylation detection for each amplicon. Here, we show that the MBPS assay can amplify as little as 0.625 ng starting DNA and can detect methylation differences of 1% with a sequencing coverage of 1000 reads. Furthermore, the multiplex bisulphite PCR assay can comprehensively interrogate multiple regions on 1-5 ng of formalin-fixed paraffin-embedded DNA or circulating cell-free DNA. CONCLUSIONS The MBPS assay is a valuable approach for assessing methylated DNA regions in clinical samples with limited material. The optimisation and additional quality control steps described here improve the performance and reliability of this method, advancing it towards potential clinical applications in biomarker studies.
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Affiliation(s)
- Dilys Lam
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, 2010, Australia
| | - Phuc-Loi Luu
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, 2010, Australia
| | - Jenny Z Song
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, 2010, Australia
| | - Wenjia Qu
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, 2010, Australia
| | - Gail P Risbridger
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, 3800, Australia
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mitchell G Lawrence
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, 3800, Australia
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jennifer Lu
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Matt Trau
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Darren Korbie
- Centre for Personalised Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, 2010, Australia
- St Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, 2010, Australia
| | - Ruth Pidsley
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, 2010, Australia.
- St Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, 2010, Australia.
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, 2010, Australia.
- St Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, 2010, Australia.
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27
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Zhao K, Oualkacha K, Lakhal-Chaieb L, Labbe A, Klein K, Ciampi A, Hudson M, Colmegna I, Pastinen T, Zhang T, Daley D, Greenwood CMT. A novel statistical method for modeling covariate effects in bisulfite sequencing derived measures of DNA methylation. Biometrics 2020; 77:424-438. [PMID: 32438470 PMCID: PMC8359306 DOI: 10.1111/biom.13307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 02/28/2020] [Accepted: 05/08/2020] [Indexed: 01/24/2023]
Abstract
Identifying disease-associated changes in DNA methylation can help us gain a better understanding of disease etiology. Bisulfite sequencing allows the generation of high-throughput methylation profiles at single-base resolution of DNA. However, optimally modeling and analyzing these sparse and discrete sequencing data is still very challenging due to variable read depth, missing data patterns, long-range correlations, data errors, and confounding from cell type mixtures. We propose a regression-based hierarchical model that allows covariate effects to vary smoothly along genomic positions and we have built a specialized EM algorithm, which explicitly allows for experimental errors and cell type mixtures, to make inference about smooth covariate effects in the model. Simulations show that the proposed method provides accurate estimates of covariate effects and captures the major underlying methylation patterns with excellent power. We also apply our method to analyze data from rheumatoid arthritis patients and controls. The method has been implemented in R package SOMNiBUS.
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Affiliation(s)
- Kaiqiong Zhao
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada.,Lady Davis Institute for Medical Research, Montreal, QC, Canada
| | - Karim Oualkacha
- Département de Mathématiques, Université du Québec à Montrèal, Montreal, QC, Canada
| | - Lajmi Lakhal-Chaieb
- Département de Mathématiques et de Statistique, Université Laval, Quebec City, QC, Canada
| | - Aurélie Labbe
- Département des Sciences de la Décision, HEC Montrèal, Montreal, QC, Canada
| | - Kathleen Klein
- Lady Davis Institute for Medical Research, Montreal, QC, Canada
| | - Antonio Ciampi
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada.,Lady Davis Institute for Medical Research, Montreal, QC, Canada
| | - Marie Hudson
- Lady Davis Institute for Medical Research, Montreal, QC, Canada.,Department of Medicine, McGill University, Montreal, QC, Canada
| | - Inés Colmegna
- Department of Medicine, McGill University, Montreal, QC, Canada.,The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Tomi Pastinen
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, USA
| | - Tieyuan Zhang
- Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada
| | - Denise Daley
- The Centre for Heart Lung Innovation, and Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Celia M T Greenwood
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada.,Lady Davis Institute for Medical Research, Montreal, QC, Canada.,Department of Human Genetics and Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
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28
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Wang Z, Xiao Y, Guan W, Wang M, Chen J, Zhang L, Li Y, Xiong Q, Wang H, Wang M, Li Y, Lv N, Li Y, Wang L, Yu L. Acute myeloid leukemia immune escape by epigenetic CD48 silencing. Clin Sci (Lond) 2020; 134:261-71. [PMID: 31922199 DOI: 10.1042/CS20191170] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/22/2019] [Accepted: 01/10/2020] [Indexed: 02/07/2023]
Abstract
Acute myeloid leukemia (AML) is a malignant disorder of hemopoietic stem cells. AML can escape immunosurveillance of natural killer (NK) by gene mutation, fusions and epigenetic modification. The mechanism of AML immune evasion is not clearly understood. Here we show that CD48 high expression is a favorable prognosis factor that is down-regulated in AML patients, which can help AML evade from NK cell recognition and killing. Furthermore, we demonstrate that CD48 expression is regulated by methylation and that a hypomethylating agent can increase the CD48 expression, which increases the NK cells killing in vitro. Finally, we show that CD48 high expression can reverse the AML immune evasion and activate NK cells function in vivo. The present study suggests that a combination the hypomethylating agent and NK cell infusion could be a new strategy to cure AML.
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29
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Robakis TK, Zhang S, Rasgon NL, Li T, Wang T, Roth MC, Humphreys KL, Gotlib IH, Ho M, Khechaduri A, Watson K, Roat-Shumway S, Budhan VV, Davis KN, Crowe SD, Ellie Williams K, Urban AE. Epigenetic signatures of attachment insecurity and childhood adversity provide evidence for role transition in the pathogenesis of perinatal depression. Transl Psychiatry 2020; 10:48. [PMID: 32066670 PMCID: PMC7026105 DOI: 10.1038/s41398-020-0703-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/05/2019] [Accepted: 12/08/2019] [Indexed: 11/16/2022] Open
Abstract
Early life adversity and insecure attachment style are known risk factors for perinatal depression. The biological pathways linking these experiences, however, have not yet been elucidated. We hypothesized that overlap in patterns of DNA methylation in association with each of these phenomena could identify genes and pathways of importance. Specifically, we wished to distinguish between allostatic-load and role-transition hypotheses of perinatal depression. We conducted a large-scale analysis of methylation patterns across 5 × 106 individual CG dinucleotides in 54 women participating in a longitudinal prospective study of perinatal depression, using clustering-based criteria for significance to control for multiple comparisons. We identified 1580 regions in which methylation density was associated with childhood adversity, 3 in which methylation density was associated with insecure attachment style, and 6 in which methylation density was associated with perinatal depression. Shorter telomeres were observed in association with childhood trauma but not with perinatal depression or attachment insecurity. A detailed analysis of methylation density in the oxytocin receptor gene revealed similar patterns of DNA methylation in association with perinatal depression and with insecure attachment style, while childhood trauma was associated with a distinct methylation pattern in this gene. Clinically, attachment style was strongly associated with depression only in pregnancy and the early postpartum, whereas the association of childhood adversity with depression was time-invariant. We concluded that the broad DNA methylation signature and reduced telomere length associated with childhood adversity could indicate increased allostatic load across multiple body systems, whereas perinatal depression and attachment insecurity may be narrower phenotypes with more limited DNA methylation signatures outside the CNS, and no apparent association with telomere length or, by extension, allostatic load. In contrast, the finding of matching DNA methylation patterns within the oxytocin receptor gene for perinatal depression and attachment insecurity is consistent with the theory that the perinatal period is a time of activation of existing attachment schemas for the purpose of structuring the mother-child relationship, and that such activation may occur in part through specific patterns of methylation of the oxytocin receptor gene.
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Affiliation(s)
- Thalia K Robakis
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, CA, USA.
| | - Siming Zhang
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, CA, USA
- Stanford University Department of Genetics, Stanford, CA, USA
| | - Natalie L Rasgon
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, CA, USA
| | | | - Tao Wang
- AccuraScience, LLC, Johnston, IN, USA
| | - Marissa C Roth
- Vanderbilt University Department of Psychology, Nashville, TN, USA
| | | | - Ian H Gotlib
- Stanford University Department of Psychology, Stanford, CA, USA
| | - Marcus Ho
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, CA, USA
| | | | - Katherine Watson
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, CA, USA
| | - Siena Roat-Shumway
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, CA, USA
| | - Vena V Budhan
- Palo Alto University Graduate School of Psychology, Palo Alto, CA, USA
| | - Kasey N Davis
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, CA, USA
| | - Susan D Crowe
- Stanford University Department of Obstetrics & Gynecology, Stanford, CA, USA
| | | | - Alexander E Urban
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, CA, USA.
- Stanford University Department of Genetics, Stanford, CA, USA.
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30
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Tirnaz S, Batley J. DNA Methylation: Toward Crop Disease Resistance Improvement. Trends Plant Sci 2019; 24:1137-1150. [PMID: 31604599 DOI: 10.1016/j.tplants.2019.08.007] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/13/2019] [Accepted: 08/22/2019] [Indexed: 05/23/2023]
Abstract
Crop diseases, in conjunction with climate change, are a major threat to global crop production. DNA methylation is an epigenetic mark and is involved in plants' biological processes, including development, stress adaptation, and genome evolution. By providing a new source of variation, DNA methylation introduces novel direction to both scientists and breeders with its potential in disease resistance enhancement. Here, we discuss the impact of pathogen-induced DNA methylation modifications on a host's transcriptome reprogramming and genome stability, as part of the plant's defense mechanisms. We also highlight the knowledge gaps that need to be investigated for understanding the entire role of DNA methylation in plant pathogen interactions. This will ultimately assist breeders toward improving resistance and decreasing yield losses.
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Affiliation(s)
- Soodeh Tirnaz
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia.
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Abstract
Asthma is a complex trait, often associated with atopy. The genetic contribution has been evidenced by familial occurrence. Genome-wide association studies allowed for associating numerous genes with asthma, as well as identifying new loci that have a minor contribution to its phenotype. Considering the role of environmental exposure on asthma development, an increasing amount of literature has been published on epigenetic modifications associated with this pathology and especially on DNA methylation, in an attempt to better understand its missing heritability. These studies have been conducted in different tissues, but mainly in blood or its peripheral mononuclear cells. However, there is growing evidence that epigenetic changes that occur in one cell type cannot be directly translated into another one. In this review, we compare alterations in DNA methylation from different cells of the immune system and of the respiratory tract. The cell types in which data are obtained influences the global status of alteration of DNA methylation in asthmatic individuals compared to control (an increased or a decreased DNA methylation). Given that several genes were cell-type-specific, there is a great need for comparative studies on DNA methylation from different cells, but from the same individuals in order to better understand the role of epigenetics in asthma pathophysiology.
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Affiliation(s)
- Andrée-Anne Hudon Thibeault
- Département des sciences fondamentales, Université du Québec à Chicoutimi (UQAC), Saguenay, G7H 2B1 QC, Canada;
- Centre intersectoriel en santé durable (CISD), Université du Québec à Chicoutimi (UQAC), Saguenay, G7H 2B1 QC, Canada
- Quebec Respiratory Health Network, Quebec, G1V 4G5 QC, Canada
| | - Catherine Laprise
- Département des sciences fondamentales, Université du Québec à Chicoutimi (UQAC), Saguenay, G7H 2B1 QC, Canada;
- Centre intersectoriel en santé durable (CISD), Université du Québec à Chicoutimi (UQAC), Saguenay, G7H 2B1 QC, Canada
- Quebec Respiratory Health Network, Quebec, G1V 4G5 QC, Canada
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Cannon ME, Currin KW, Young KL, Perrin HJ, Vadlamudi S, Safi A, Song L, Wu Y, Wabitsch M, Laakso M, Crawford GE, Mohlke KL. Open Chromatin Profiling in Adipose Tissue Marks Genomic Regions with Functional Roles in Cardiometabolic Traits. G3 (Bethesda) 2019; 9:2521-33. [PMID: 31186305 DOI: 10.1534/g3.119.400294] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Identifying the regulatory mechanisms of genome-wide association study (GWAS) loci affecting adipose tissue has been restricted due to limited characterization of adipose transcriptional regulatory elements. We profiled chromatin accessibility in three frozen human subcutaneous adipose tissue needle biopsies and preadipocytes and adipocytes from the Simpson Golabi-Behmel Syndrome (SGBS) cell strain using an assay for transposase-accessible chromatin (ATAC-seq). We identified 68,571 representative accessible chromatin regions (peaks) across adipose tissue samples (FDR < 5%). GWAS loci for eight cardiometabolic traits were enriched in these peaks (P < 0.005), with the strongest enrichment for waist-hip ratio. Of 110 recently described cardiometabolic GWAS loci colocalized with adipose tissue eQTLs, 59 loci had one or more variants overlapping an adipose tissue peak. Annotated variants at the SNX10 waist-hip ratio locus and the ATP2A1-SH2B1 body mass index locus showed allelic differences in regulatory assays. These adipose tissue accessible chromatin regions elucidate genetic variants that may alter adipose tissue function to impact cardiometabolic traits.
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Chan D, Shao X, Dumargne MC, Aarabi M, Simon MM, Kwan T, Bailey JL, Robaire B, Kimmins S, San Gabriel MC, Zini A, Librach C, Moskovtsev S, Grundberg E, Bourque G, Pastinen T, Trasler JM. Customized MethylC-Capture Sequencing to Evaluate Variation in the Human Sperm DNA Methylome Representative of Altered Folate Metabolism. Environ Health Perspect 2019; 127:87002. [PMID: 31393794 PMCID: PMC6792365 DOI: 10.1289/ehp4812] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
BACKGROUND The sperm DNA methylation landscape is unique and critical for offspring health. If gamete-derived DNA methylation escapes reprograming in early embryos, epigenetic defects in sperm may be transmitted to the next generation. Current techniques to assess sperm DNA methylation show bias toward CpG-dense regions and do not target areas of dynamic methylation, those predicted to be environmentally sensitive and tunable regulatory elements. OBJECTIVES Our goal was to assess variation in human sperm DNA methylation and design a targeted capture panel to interrogate the human sperm methylome. METHODS To characterize variation in sperm DNA methylation, we performed whole genome bisulfite sequencing (WGBS) on an equimolar pool of sperm DNA from a wide cross section of 30 men varying in age, fertility status, methylenetetrahydrofolate reductase (MTHFR) genotype, and exposures. With our targeted capture panel, in individual samples, we examined the effect of MTHFR genotype ([Formula: see text] 677CC, [Formula: see text] 677TT), as well as high-dose folic acid supplementation ([Formula: see text], per genotype, before and after supplementation). RESULTS Through WGBS we discovered nearly 1 million CpGs possessing intermediate methylation levels (20-80%), termed dynamic sperm CpGs. These dynamic CpGs, along with 2 million commonly assessed CpGs, were used to customize a capture panel for targeted interrogation of the human sperm methylome and test its ability to detect effects of altered folate metabolism. As compared with MTHFR 677CC men, those with the 677TT genotype (50% decreased MTHFR activity) had both hyper- and hypomethylation in their sperm. High-dose folic acid supplement treatment exacerbated hypomethylation in MTHFR 677TT men compared with 677CC. In both cases, [Formula: see text] of altered methylation was found in dynamic sperm CpGs, uniquely measured by our assay. DISCUSSION Our sperm panel allowed the discovery of differential methylation following conditions affecting folate metabolism in novel dynamic sperm CpGs. Improved ability to examine variation in sperm DNA methylation can facilitate comprehensive studies of environment-epigenome interactions. https://doi.org/10.1289/EHP4812.
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Affiliation(s)
- Donovan Chan
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Xiaojian Shao
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Marie-Charlotte Dumargne
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Animal Sciences, McGill University, Montreal, Quebec, Canada
| | - Mahmoud Aarabi
- Medical Genetics & Genomics Laboratories, University of Pittsburgh Medical Center (UPMC) Magee-Womens Hospital, Pittsburgh, Pennsylvania, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | | | - Tony Kwan
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Janice L. Bailey
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Université Laval, Faculté des sciences de l’agriculture et de l’alimentation, Quebec, Quebec, Canada
| | - Bernard Robaire
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Sarah Kimmins
- Department of Animal Sciences, McGill University, Montreal, Quebec, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Maria C. San Gabriel
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Division of Urology, Department of Surgery, McGill University, Montreal, Quebec, Canada
| | - Armand Zini
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Division of Urology, Department of Surgery, McGill University, Montreal, Quebec, Canada
| | - Clifford Librach
- Canadian Reproductive Assisted Technology (CReATe) Fertility Centre, Toronto, Ontario, Canada
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada
| | - Sergey Moskovtsev
- Canadian Reproductive Assisted Technology (CReATe) Fertility Centre, Toronto, Ontario, Canada
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Ontario, Canada
| | - Elin Grundberg
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Center for Pediatric Genomic Medicine, Children’s Mercy Kansas City, Kansas City, Missouri, USA
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Center for Pediatric Genomic Medicine, Children’s Mercy Kansas City, Kansas City, Missouri, USA
| | - Jacquetta M. Trasler
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada
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Shao X, Hudson M, Colmegna I, Greenwood CMT, Fritzler MJ, Awadalla P, Pastinen T, Bernatsky S. Rheumatoid arthritis-relevant DNA methylation changes identified in ACPA-positive asymptomatic individuals using methylome capture sequencing. Clin Epigenetics 2019; 11:110. [PMID: 31366403 DOI: 10.1186/s13148-019-0699-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/24/2019] [Indexed: 12/20/2022] Open
Abstract
Objective To compare DNA methylation in subjects positive vs negative for anti-citrullinated protein antibodies (ACPA), a key serological marker of rheumatoid arthritis (RA) risk. Methods With banked serum from a random subset (N = 3600) of a large general population cohort, we identified ACPA-positive samples and compared them to age- and sex-matched ACPA-negative controls. We used a custom-designed methylome panel to conduct targeted bisulfite sequencing of 5 million CpGs located in regulatory or hypomethylated regions of DNA from whole blood (red blood cell lysed). Using binomial regression models, we investigated the differentially methylated regions (DMRs) between ACPA-positive vs ACPA-negative subjects. An independent set of T cells from RA patients was used to “validate” the differentially methylated sites. Results We measured DNA methylation in 137 subjects, of whom 63 were ACPA-positive, 66 were ACPA-negative, and 8 had self-reported RA. We identified 1303 DMRs of relevance, of which one third (402) had underlying genetic effects. These DMRs were enriched in intergenic CpG islands (CGI) and CGI shore regions. Furthermore, the genes associated with these DMRs were enriched in pathways related to Epstein-Barr virus infection and immune response. In addition, 80 (38%) of 208 RA-specific DMRs were replicated in T cells from RA samples. Conclusions Sequencing-based high-resolution methylome mapping revealed biologically relevant DNA methylation changes in asymptomatic individuals positive for ACPA that overlap with those seen in RA. Pathway analyses suggested roles for viral infections, which may represent the effect of environmental triggers upstream of disease onset. Electronic supplementary material The online version of this article (10.1186/s13148-019-0699-9) contains supplementary material, which is available to authorized users.
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Abstract
CD36 is a transmembrane protein involved in fatty acid translocation, scavenging for oxidized fatty acids acting as a receptor for adhesion molecules. It is expressed on macrophages, as well as other types of cells, such as endothelial and adipose cells. CD36 participates in muscle lipid uptake, adipose energy storage, and gut fat absorption. Recently, several preclinical and clinical studies demonstrated that upregulation of CD36 is a prerequisite for tumor metastasis. Cancer metastasis-related research emerged much later and has been less investigated, though it is equally or even more important. CD36 protein expression can be modified by epigenetic changes and post-transcriptional interference from non-coding RNAs. Some data indicate modulation of CD36 expression in specific cell types by epigenetic changes via DNA methylation patterns or histone tails, or through miRNA interference, but this is largely unexplored. The few papers addressing this topic refer mostly to lipid metabolism-related pathologies, whereas in cancer research, data are even more scarce. The aim of this review was to summarize major epigenetic and post-transcriptional mechanisms that impact CD36 expression in relation to various pathologies while highlighting the areas in need of further exploration.
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Affiliation(s)
- Cristina-Mariana Niculite
- Cell Biology Department, "Victor Babes" National Institute of Pathology, Bucharest, Romania.,Department of Cellular and Molecular Biology and Histology, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Ana-Maria Enciu
- Cell Biology Department, "Victor Babes" National Institute of Pathology, Bucharest, Romania.,Department of Cellular and Molecular Biology and Histology, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
| | - Mihail Eugen Hinescu
- Cell Biology Department, "Victor Babes" National Institute of Pathology, Bucharest, Romania.,Department of Cellular and Molecular Biology and Histology, "Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
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36
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Bradford ST, Nair SS, Statham AL, van Dijk SJ, Peters TJ, Anwar F, French HJ, von Martels JZH, Sutcliffe B, Maddugoda MP, Peranec M, Varinli H, Arnoldy R, Buckley M, Ross JP, Zotenko E, Song JZ, Stirzaker C, Bauer DC, Qu W, Swarbrick MM, Lutgers HL, Lord RV, Samaras K, Molloy PL, Clark SJ. Methylome and transcriptome maps of human visceral and subcutaneous adipocytes reveal key epigenetic differences at developmental genes. Sci Rep 2019; 9:9511. [PMID: 31266983 DOI: 10.1038/s41598-019-45777-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/11/2019] [Indexed: 12/19/2022] Open
Abstract
Adipocytes support key metabolic and endocrine functions of adipose tissue. Lipid is stored in two major classes of depots, namely visceral adipose (VA) and subcutaneous adipose (SA) depots. Increased visceral adiposity is associated with adverse health outcomes, whereas the impact of SA tissue is relatively metabolically benign. The precise molecular features associated with the functional differences between the adipose depots are still not well understood. Here, we characterised transcriptomes and methylomes of isolated adipocytes from matched SA and VA tissues of individuals with normal BMI to identify epigenetic differences and their contribution to cell type and depot-specific function. We found that DNA methylomes were notably distinct between different adipocyte depots and were associated with differential gene expression within pathways fundamental to adipocyte function. Most striking differential methylation was found at transcription factor and developmental genes. Our findings highlight the importance of developmental origins in the function of different fat depots.
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Allum F, Hedman ÅK, Shao X, Cheung WA, Vijay J, Guénard F, Kwan T, Simon MM, Ge B, Moura C, Boulier E, Rönnblom L, Bernatsky S, Lathrop M, McCarthy MI, Deloukas P, Tchernof A, Pastinen T, Vohl MC, Grundberg E. Dissecting features of epigenetic variants underlying cardiometabolic risk using full-resolution epigenome profiling in regulatory elements. Nat Commun 2019; 10:1209. [PMID: 30872577 DOI: 10.1038/s41467-019-09184-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 02/25/2019] [Indexed: 12/16/2022] Open
Abstract
Sparse profiling of CpG methylation in blood by microarrays has identified epigenetic links to common diseases. Here we apply methylC-capture sequencing (MCC-Seq) in a clinical population of ~200 adipose tissue and matched blood samples (Ntotal~400), providing high-resolution methylation profiling (>1.3 M CpGs) at regulatory elements. We link methylation to cardiometabolic risk through associations to circulating plasma lipid levels and identify lipid-associated CpGs with unique localization patterns in regulatory elements. We show distinct features of tissue-specific versus tissue-independent lipid-linked regulatory regions by contrasting with parallel assessments in ~800 independent adipose tissue and blood samples from the general population. We follow-up on adipose-specific regulatory regions under (1) genetic and (2) epigenetic (environmental) regulation via integrational studies. Overall, the comprehensive sequencing of regulatory element methylomes reveals a rich landscape of functional variants linked genetically as well as epigenetically to plasma lipid traits. Obesity and related metabolic complications represent an important health burden. Here the authors carry out a methylC-capture sequencing-based epigenome-wide association study to link circulating plasma lipid levels, CpG methylation and cardiometabolic risk across adipose and blood tissues.
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Rauch A, Haakonsson AK, Madsen JGS, Larsen M, Forss I, Madsen MR, Van Hauwaert EL, Wiwie C, Jespersen NZ, Tencerova M, Nielsen R, Larsen BD, Röttger R, Baumbach J, Scheele C, Kassem M, Mandrup S. Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis. Nat Genet 2019; 51:716-727. [PMID: 30833796 DOI: 10.1038/s41588-019-0359-1] [Citation(s) in RCA: 116] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 01/22/2019] [Indexed: 12/19/2022]
Abstract
Mesenchymal (stromal) stem cells (MSCs) constitute populations of mesodermal multipotent cells involved in tissue regeneration and homeostasis in many different organs. Here we performed comprehensive characterization of the transcriptional and epigenomic changes associated with osteoblast and adipocyte differentiation of human MSCs. We demonstrate that adipogenesis is driven by considerable remodeling of the chromatin landscape and de novo activation of enhancers, whereas osteogenesis involves activation of preestablished enhancers. Using machine learning algorithms for in silico modeling of transcriptional regulation, we identify a large and diverse transcriptional network of pro-osteogenic and antiadipogenic transcription factors. Intriguingly, binding motifs for these factors overlap with SNPs related to bone and fat formation in humans, and knockdown of single members of this network is sufficient to modulate differentiation in both directions, thus indicating that lineage determination is a delicate balance between the activities of many different transcription factors.
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Affiliation(s)
- Alexander Rauch
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Anders K Haakonsson
- Molecular Endocrinology and Stem Cell Research Unit (KMEB), Department of Endocrinology and Metabolism, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jesper G S Madsen
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Mette Larsen
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Isabel Forss
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Martin R Madsen
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Elvira L Van Hauwaert
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christian Wiwie
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Naja Z Jespersen
- Centre of Inflammation and Metabolism and Centre for Physical Activity Research, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Danish Diabetes Academy, Odense University Hospital, Odense, Denmark
| | - Michaela Tencerova
- Molecular Endocrinology and Stem Cell Research Unit (KMEB), Department of Endocrinology and Metabolism, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Ronni Nielsen
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Bjørk D Larsen
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Richard Röttger
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Jan Baumbach
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark.,Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany
| | - Camilla Scheele
- Centre of Inflammation and Metabolism and Centre for Physical Activity Research, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Moustapha Kassem
- Molecular Endocrinology and Stem Cell Research Unit (KMEB), Department of Endocrinology and Metabolism, Odense University Hospital and Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Susanne Mandrup
- Functional Genomics and Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
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Islam SA, Goodman SJ, MacIsaac JL, Obradović J, Barr RG, Boyce WT, Kobor MS. Integration of DNA methylation patterns and genetic variation in human pediatric tissues help inform EWAS design and interpretation. Epigenetics Chromatin 2019; 12:1. [PMID: 30602389 DOI: 10.1186/s13072-018-0245-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/18/2018] [Indexed: 02/06/2023] Open
Abstract
Background The widespread use of accessible peripheral tissues for epigenetic analyses has prompted increasing interest in the study of tissue-specific DNA methylation (DNAm) variation in human populations. To date, characterizations of inter-individual DNAm variability and DNAm concordance across tissues have been largely performed in adult tissues and therefore are limited in their relevance to DNAm profiles from pediatric samples. Given that DNAm patterns in early life undergo rapid changes and have been linked to a wide range of health outcomes and environmental exposures, direct investigations of tissue-specific DNAm variation in pediatric samples may help inform the design and interpretation of DNAm analyses from early life cohorts. In this study, we present a systematic comparison of genome-wide DNAm patterns between matched pediatric buccal epithelial cells (BECs) and peripheral blood mononuclear cells (PBMCs), two of the most widely used peripheral tissues in human epigenetic studies. Specifically, we assessed DNAm variability, cross-tissue DNAm concordance and genetic determinants of DNAm across two independent early life cohorts encompassing different ages. Results BECs had greater inter-individual DNAm variability compared to PBMCs and highly the variable CpGs are more likely to be positively correlated between the matched tissues compared to less variable CpGs. These sites were enriched for CpGs under genetic influence, suggesting that a substantial proportion of DNAm covariation between tissues can be attributed to genetic variation. Finally, we demonstrated the relevance of our findings to human epigenetic studies by categorizing CpGs from published DNAm association studies of pediatric BECs and peripheral blood. Conclusions Taken together, our results highlight a number of important considerations and practical implications in the design and interpretation of EWAS analyses performed in pediatric peripheral tissues. Electronic supplementary material The online version of this article (10.1186/s13072-018-0245-6) contains supplementary material, which is available to authorized users.
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40
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Wendt J, Rosenbaum H, Richmond TA, Jeddeloh JA, Burgess DL. Targeted Bisulfite Sequencing Using the SeqCap Epi Enrichment System. Methods Mol Biol 2018; 1708:383-405. [PMID: 29224155 DOI: 10.1007/978-1-4939-7481-8_20] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Cytosine methylation has been shown to have a role in a host of biological processes. In mammalian biology these include stem cell differentiation, embryonic development, genomic imprinting, inflammation, and silencing of transposable elements. Given the central importance of these processes, it is not surprising to find aberrant cytosine methylation patterns associated with many disorders in humans, including cancer, cardiovascular disease, and neurological disease. While whole genome shotgun bisulfite sequencing (WGBS) has recently become feasible, generating high sequence coverage data for the entire genome is expensive, both in terms of money and analysis time, when generally only a small subset of the genome is of interest to most researchers. This report details a procedure for the targeted enrichment of bisulfite treated DNA via SeqCap Epi, allowing high resolution focus of next generation sequencing onto a subset of the genome for high resolution cytosine methylation analysis. Regions ranging in size from only a few kb up to over 200 Mb may be targeted, including the use of the SeqCap Epi CpGiant design which is designed to target 5.5 million CpGs in the human genome. Finally, multiple samples may be multiplexed and sequenced together to provide an inexpensive method of generating methylation data for a large number of samples in a high throughput fashion.
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Affiliation(s)
- Jennifer Wendt
- Roche Sequencing Solutions, 500 S. Rosa Road, Madison, WI, 53719, USA
| | - Heidi Rosenbaum
- Roche Sequencing Solutions, 500 S. Rosa Road, Madison, WI, 53719, USA
| | - Todd A Richmond
- Roche Sequencing Solutions, 500 S. Rosa Road, Madison, WI, 53719, USA
| | | | - Daniel L Burgess
- Roche Sequencing Solutions, 500 S. Rosa Road, Madison, WI, 53719, USA.
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Zou LS, Erdos MR, Taylor DL, Chines PS, Varshney A, Parker SCJ, Collins FS, Didion JP. BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues. BMC Genomics 2018; 19:390. [PMID: 29792182 PMCID: PMC5966887 DOI: 10.1186/s12864-018-4766-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/08/2018] [Indexed: 01/14/2023] Open
Abstract
Background Bisulfite sequencing is widely employed to study the role of DNA methylation in disease; however, the data suffer from biases due to coverage depth variability. Imputation of methylation values at low-coverage sites may mitigate these biases while also identifying important genomic features associated with predictive power. Results Here we describe BoostMe, a method for imputing low-quality DNA methylation estimates within whole-genome bisulfite sequencing (WGBS) data. BoostMe uses a gradient boosting algorithm, XGBoost, and leverages information from multiple samples for prediction. We find that BoostMe outperforms existing algorithms in speed and accuracy when applied to WGBS of human tissues. Furthermore, we show that imputation improves concordance between WGBS and the MethylationEPIC array at low WGBS depth, suggesting improved WGBS accuracy after imputation. Conclusions Our findings support the use of BoostMe as a preprocessing step for WGBS analysis. Electronic supplementary material The online version of this article (10.1186/s12864-018-4766-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Luli S Zou
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael R Erdos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - D Leland Taylor
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Peter S Chines
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Arushi Varshney
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Stephen C J Parker
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Francis S Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - John P Didion
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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Taylor DL, Knowles DA, Scott LJ, Ramirez AH, Casale FP, Wolford BN, Guan L, Varshney A, Albanus RD, Parker SCJ, Narisu N, Chines PS, Erdos MR, Welch RP, Kinnunen L, Saramies J, Sundvall J, Lakka TA, Laakso M, Tuomilehto J, Koistinen HA, Stegle O, Boehnke M, Birney E, Collins FS. Interactions between genetic variation and cellular environment in skeletal muscle gene expression. PLoS One 2018; 13:e0195788. [PMID: 29659628 PMCID: PMC5901994 DOI: 10.1371/journal.pone.0195788] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 03/29/2018] [Indexed: 12/18/2022] Open
Abstract
From whole organisms to individual cells, responses to environmental conditions are influenced by genetic makeup, where the effect of genetic variation on a trait depends on the environmental context. RNA-sequencing quantifies gene expression as a molecular trait, and is capable of capturing both genetic and environmental effects. In this study, we explore opportunities of using allele-specific expression (ASE) to discover cis-acting genotype-environment interactions (GxE)—genetic effects on gene expression that depend on an environmental condition. Treating 17 common, clinical traits as approximations of the cellular environment of 267 skeletal muscle biopsies, we identify 10 candidate environmental response expression quantitative trait loci (reQTLs) across 6 traits (12 unique gene-environment trait pairs; 10% FDR per trait) including sex, systolic blood pressure, and low-density lipoprotein cholesterol. Although using ASE is in principle a promising approach to detect GxE effects, replication of such signals can be challenging as validation requires harmonization of environmental traits across cohorts and a sufficient sampling of heterozygotes for a transcribed SNP. Comprehensive discovery and replication will require large human transcriptome datasets, or the integration of multiple transcribed SNPs, coupled with standardized clinical phenotyping.
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Affiliation(s)
- D. Leland Taylor
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - David A. Knowles
- Department of Computer Science, Stanford University, Stanford, California, United States of America
| | - Laura J. Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrea H. Ramirez
- Department of Medicine, Vanderbilt University Medical Center, Tennessee, United States of America
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Brooke N. Wolford
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Li Guan
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Arushi Varshney
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ricardo D’Oliveira Albanus
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Stephen C. J. Parker
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Narisu Narisu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Peter S. Chines
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Michael R. Erdos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
| | - Ryan P. Welch
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Leena Kinnunen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Jouko Saramies
- South Karelia Social and Health Care District, Lappeenranta, Finland
| | - Jouko Sundvall
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Timo A. Lakka
- Institute of Biomedicine/Physiology, University of Eastern Finland, Kuopio, Finland
- Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, University of Eastern Finland, Kuopio, Finland
| | - Markku Laakso
- Department of Medicine, University of Eastern Finland, Kuopio, Finland
- Kuopio University Hospital, Kuopio, Finland
| | - Jaakko Tuomilehto
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Department of Neurosciences and Preventive Medicine, Danube University Krems, Krems, Austria
- Diabetes Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
- Dasman Diabetes Institute, Dasman, Kuwait
| | - Heikki A. Koistinen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Department of Medicine and Abdominal Center: Endocrinology, University of Helsinki and Helsinki University Central Hospital, Haartmaninkatu 4, Helsinki, Finland
- Minerva Foundation Institute for Medical Research, Biomedicum 2U, Tukholmankatu 8, Helsinki, Finland
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- * E-mail: (EB); (FSC)
| | - Francis S. Collins
- National Human Genome Research Institute, National Institutes of Health, Bethesda, United States of America
- * E-mail: (EB); (FSC)
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Hanghøj K, Orlando L. Ancient Epigenomics. In: Lindqvist C, Rajora OP, editors. Paleogenomics. Cham: Springer International Publishing; 2019. pp. 75-111. [DOI: 10.1007/13836_2018_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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44
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Davegårdh C, García-Calzón S, Bacos K, Ling C. DNA methylation in the pathogenesis of type 2 diabetes in humans. Mol Metab 2018; 14:12-25. [PMID: 29496428 PMCID: PMC6034041 DOI: 10.1016/j.molmet.2018.01.022] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 01/29/2018] [Accepted: 01/29/2018] [Indexed: 02/08/2023] Open
Abstract
Background Type 2 diabetes (T2D) is a multifactorial, polygenic disease caused by impaired insulin secretion and insulin resistance. Genome-wide association studies (GWAS) were expected to resolve a large part of the genetic component of diabetes; yet, the single nucleotide polymorphisms identified by GWAS explain less than 20% of the estimated heritability for T2D. There was subsequently a need to look elsewhere to find disease-causing factors. Mechanisms mediating the interaction between environmental factors and the genome, such as epigenetics, may be of particular importance in the pathogenesis of T2D. Scope of Review This review summarizes knowledge of the impact of epigenetics on the pathogenesis of T2D in humans. In particular, the review will focus on alterations in DNA methylation in four human tissues of importance for the disease; pancreatic islets, skeletal muscle, adipose tissue, and the liver. Case–control studies and studies examining the impact of non-genetic and genetic risk factors on DNA methylation in humans will be considered. These studies identified epigenetic changes in tissues from subjects with T2D versus non-diabetic controls. They also demonstrate that non-genetic factors associated with T2D such as age, obesity, energy rich diets, physical activity and the intrauterine environment impact the epigenome in humans. Additionally, interactions between genetics and epigenetics seem to influence the pathogenesis of T2D. Conclusions Overall, previous studies by our group and others support a key role for epigenetics in the growing incidence of T2D.
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Affiliation(s)
- Cajsa Davegårdh
- Epigenetics and Diabetes, Lund University Diabetes Centre (LUDC), Box 50332, 20213 Malmö, Sweden.
| | - Sonia García-Calzón
- Epigenetics and Diabetes, Lund University Diabetes Centre (LUDC), Box 50332, 20213 Malmö, Sweden
| | - Karl Bacos
- Epigenetics and Diabetes, Lund University Diabetes Centre (LUDC), Box 50332, 20213 Malmö, Sweden
| | - Charlotte Ling
- Epigenetics and Diabetes, Lund University Diabetes Centre (LUDC), Box 50332, 20213 Malmö, Sweden
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45
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Masser DR, Hadad N, Porter H, Stout MB, Unnikrishnan A, Stanford DR, Freeman WM. Analysis of DNA modifications in aging research. GeroScience 2018; 40:11-29. [PMID: 29327208 PMCID: PMC5832665 DOI: 10.1007/s11357-018-0005-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/05/2018] [Indexed: 12/22/2022] Open
Abstract
As geroscience research extends into the role of epigenetics in aging and age-related disease, researchers are being confronted with unfamiliar molecular techniques and data analysis methods that can be difficult to integrate into their work. In this review, we focus on the analysis of DNA modifications, namely cytosine methylation and hydroxymethylation, through next-generation sequencing methods. While older techniques for modification analysis performed relative quantitation across regions of the genome or examined average genome levels, these analyses lack the desired specificity, rigor, and genomic coverage to firmly establish the nature of genomic methylation patterns and their response to aging. With recent methodological advances, such as whole genome bisulfite sequencing (WGBS), bisulfite oligonucleotide capture sequencing (BOCS), and bisulfite amplicon sequencing (BSAS), cytosine modifications can now be readily analyzed with base-specific, absolute quantitation at both cytosine-guanine dinucleotide (CG) and non-CG sites throughout the genome or within specific regions of interest by next-generation sequencing. Additional advances, such as oxidative bisulfite conversion to differentiate methylation from hydroxymethylation and analysis of limited input/single-cells, have great promise for continuing to expand epigenomic capabilities. This review provides a background on DNA modifications, the current state-of-the-art for sequencing methods, bioinformatics tools for converting these large data sets into biological insights, and perspectives on future directions for the field.
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Affiliation(s)
- Dustin R Masser
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Nathan Shock Center for Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Niran Hadad
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Nathan Shock Center for Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Hunter Porter
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Nathan Shock Center for Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Michael B Stout
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Archana Unnikrishnan
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - David R Stanford
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Willard M Freeman
- Reynolds Oklahoma Center on Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma Nathan Shock Center for Aging, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Oklahoma Center for Neuroscience, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Department of Nutritional Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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46
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Li Y, Zhao H, Xu Q, Lv N, Jing Y, Wang L, Wang X, Guo J, Zhou L, Liu J, Chen G, Chen C, Li Y, Yu L. Detection of prognostic methylation markers by methylC-capture sequencing in acute myeloid leukemia. Oncotarget 2017; 8:110444-110459. [PMID: 29299160 PMCID: PMC5746395 DOI: 10.18632/oncotarget.22789] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/15/2017] [Indexed: 12/11/2022] Open
Abstract
Clinical and genetic features incompletely predict outcome in acute myeloid leukemia (AML). The value of clinical methylation assays for prognostic markers has not been extensively explored. We assess the prognostic implications of methylC-capture sequencing (MCC-Seq) in patients with de novo AML by integrating DNA methylation and genetic risk stratification. MCC-Seq assessed DNA methylation level in 44 samples. The differentially methylated regions associated with prognostic genetic information were identified. The selected prognostic DNA methylation markers were independently validated in two sets. MCC-Seq exhibited good performance in AML patients. A panel of 12 differentially methylated genes was identified with promoter hyper-differentially methylated regions associated with the outcome. Compared with a low M-value, a high M-value was associated with failure to achieve complete remission (p = 0.024), increased hazard for disease-free survival in the study set (p = 0.039) and poor overall survival in The Cancer Genome Atlas set (p = 0.038). Hematopoietic stem cell transplantation and survival outcomes were not adversely affected by a high M-value (p = 0.271). Our study establishes that MCC-Seq is a stable, reproducible, and cost-effective methylation assay in AML. A 12-gene M-value encompassing epigenetic and genetic prognostic information represented a valid prognostic marker for patients with AML.
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Affiliation(s)
- Yan Li
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, Hainan Branch of Chinese PLA General Hospital, Sanya 572013, China
| | - Hongmei Zhao
- Annoroad Gene Technology Co. Ltd., Beijing 100176, China
| | - Qingyu Xu
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Medical School of Nankai University, Tianjin 300071, China
| | - Na Lv
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, General Hospital of Shenzhen University, Shenzhen 518060, China
| | - Yu Jing
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Lili Wang
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Xiaowen Wang
- Annoroad Gene Technology Co. Ltd., Beijing 100176, China
| | - Jing Guo
- Annoroad Gene Technology Co. Ltd., Beijing 100176, China
| | - Lei Zhou
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Jing Liu
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Guofeng Chen
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Medical School of Nankai University, Tianjin 300071, China
| | - Chongjian Chen
- Annoroad Gene Technology Co. Ltd., Beijing 100176, China
| | - Yonghui Li
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Li Yu
- Department of Hematology and BMT Center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, General Hospital of Shenzhen University, Shenzhen 518060, China
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47
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Raine A, Manlig E, Wahlberg P, Syvänen AC, Nordlund J. SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing. Nucleic Acids Res 2017; 45:e36. [PMID: 27899585 PMCID: PMC5389478 DOI: 10.1093/nar/gkw1110] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 10/31/2016] [Indexed: 01/22/2023] Open
Abstract
Sodium bisulphite treatment of DNA combined with next generation sequencing (NGS) is a powerful combination for the interrogation of genome-wide DNA methylation profiles. Library preparation for whole genome bisulphite sequencing (WGBS) is challenging due to side effects of the bisulphite treatment, which leads to extensive DNA damage. Recently, a new generation of methods for bisulphite sequencing library preparation have been devised. They are based on initial bisulphite treatment of the DNA, followed by adaptor tagging of single stranded DNA fragments, and enable WGBS using low quantities of input DNA. In this study, we present a novel approach for quick and cost effective WGBS library preparation that is based on splinted adaptor tagging (SPLAT) of bisulphite-converted single-stranded DNA. Moreover, we validate SPLAT against three commercially available WGBS library preparation techniques, two of which are based on bisulphite treatment prior to adaptor tagging and one is a conventional WGBS method.
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Affiliation(s)
- Amanda Raine
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Sweden
| | - Erika Manlig
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Sweden
| | - Per Wahlberg
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Sweden
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48
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Côté JA, Lessard J, Pelletier M, Marceau S, Lescelleur O, Fradette J, Tchernof A. Role of the TGF-β pathway in dedifferentiation of human mature adipocytes. FEBS Open Bio 2017; 7:1092-1101. [PMID: 28781950 PMCID: PMC5537071 DOI: 10.1002/2211-5463.12250] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/25/2017] [Accepted: 05/11/2017] [Indexed: 11/24/2022] Open
Abstract
Dedifferentiation of adipocytes contributes to the generation of a proliferative cell population that could be useful in cellular therapy or tissue engineering. Adipocytes can dedifferentiate into precursor cells to acquire a fibroblast‐like phenotype using ceiling culture, in which the buoyancy of fat cells is exploited to allow them to adhere to the inner surface of a container. Ceiling culture is usually performed in flasks, which limits the ability to test various culture conditions. Using a new six‐well plate ceiling culture approach, we examined the relevance of TGF‐β signaling during dedifferentiation. Adipose tissue samples from patients undergoing bariatric surgery were digested with collagenase, and cell suspensions were used for ceiling cultures. Using the six‐well plate approach, cells were treated with SB431542 (an inhibitor of TGF‐β receptor ALK5) or human TGF‐β1 during dedifferentiation. Gene expression was measured in these cultures and in whole adipose tissue, the stromal–vascular fraction (SVF), mature adipocytes, and dedifferentiated fat (DFAT) cells. TGF‐β1 and collagen type I alpha 1 (COL1A1) gene expression was significantly higher in DFAT cells compared to whole adipose tissue samples and SVF cells. TGF‐β1, COL1A1, and COL6A3 gene expression was significantly higher at day 12 of dedifferentiation compared to day 0. In the six‐well plate model, treatment with TGF‐β1 or SB431542, respectively, stimulated and inhibited the TGF‐β pathway as shown by increased TGF‐β1, TGF‐β2, COL1A1, and COL6A3 gene expression and decreased expression of TGF‐β1, COL1A1, COL1A2, and COL6A3, respectively. Treatment of DFAT cells with TGF‐β1 increased the phosphorylation level of SMAD 2 and SMAD 3. Thus, a new six‐well plate model for ceiling culture allowed us to demonstrate a role for TGF‐β in modulating collagen gene expression during dedifferentiation of mature adipocytes.
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Affiliation(s)
- Julie Anne Côté
- Institut Universitaire de Cardiologie et de Pneumologie de Québec Canada.,Endocrinologie et Néphrologie CHU de Québec Canada.,École de Nutrition Université Laval Québec Canada
| | - Julie Lessard
- Institut Universitaire de Cardiologie et de Pneumologie de Québec Canada
| | - Mélissa Pelletier
- Institut Universitaire de Cardiologie et de Pneumologie de Québec Canada.,Endocrinologie et Néphrologie CHU de Québec Canada
| | - Simon Marceau
- Institut Universitaire de Cardiologie et de Pneumologie de Québec Canada
| | - Odette Lescelleur
- Institut Universitaire de Cardiologie et de Pneumologie de Québec Canada
| | - Julie Fradette
- Faculté de Médecine, Département de Chirurgie, Centre de recherche en organogénèse expérimentale de l'Université Laval/LOEX Université Laval Québec Canada.,Division de Médecine Régénérative CHU de Québec Canada
| | - André Tchernof
- Institut Universitaire de Cardiologie et de Pneumologie de Québec Canada.,Endocrinologie et Néphrologie CHU de Québec Canada.,École de Nutrition Université Laval Québec Canada
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49
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Hachiya T, Furukawa R, Shiwa Y, Ohmomo H, Ono K, Katsuoka F, Nagasaki M, Yasuda J, Fuse N, Kinoshita K, Yamamoto M, Tanno K, Satoh M, Endo R, Sasaki M, Sakata K, Kobayashi S, Ogasawara K, Hitomi J, Sobue K, Shimizu A. Genome-wide identification of inter-individually variable DNA methylation sites improves the efficacy of epigenetic association studies. NPJ Genom Med 2017; 2:11. [PMID: 29263827 DOI: 10.1038/s41525-017-0016-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 03/07/2017] [Accepted: 03/17/2017] [Indexed: 12/19/2022] Open
Abstract
Epigenome-wide association studies, which searches for blood-based DNA methylation signatures associated with environmental exposures and/or disease susceptibilities, is a promising approach to a better understanding of the molecular aetiology of common diseases. To carry out large-scale epigenome-wide association studies while avoiding false negative detection, an efficient strategy to determine target CpG sites for microarray-based or sequencing-based DNA methylation profiling is essentially needed. Here, we propose and validate a hypothesis that a strategy focusing on CpG sites with high DNA methylation level variability may attain an improved efficacy. Through whole-genome bisulfite sequencing of purified blood cells collected from > 100 apparently healthy subjects, we identified ~2.0 million inter-individually variable CpG sites as potential targets. The efficacy of our strategy was estimated to be 3.7-fold higher than that of the most frequently used strategy. Our catalogue of inter-individually variable CpG sites will accelerate the discovery of clinically relevant DNA methylation biomarkers in future epigenome-wide association studies.
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50
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Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S, Datta A, Richardson D, Burden F, Mead D, Mann AL, Fernandez JM, Rowlston S, Wilder SP, Farrow S, Shao X, Lambourne JJ, Redensek A, Albers CA, Amstislavskiy V, Ashford S, Berentsen K, Bomba L, Bourque G, Bujold D, Busche S, Caron M, Chen SH, Cheung W, Delaneau O, Dermitzakis ET, Elding H, Colgiu I, Bagger FO, Flicek P, Habibi E, Iotchkova V, Janssen-Megens E, Kim B, Lehrach H, Lowy E, Mandoli A, Matarese F, Maurano MT, Morris JA, Pancaldi V, Pourfarzad F, Rehnstrom K, Rendon A, Risch T, Sharifi N, Simon MM, Sultan M, Valencia A, Walter K, Wang SY, Frontini M, Antonarakis SE, Clarke L, Yaspo ML, Beck S, Guigo R, Rico D, Martens JHA, Ouwehand WH, Kuijpers TW, Paul DS, Stunnenberg HG, Stegle O, Downes K, Pastinen T, Soranzo N. Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells. Cell 2017; 167:1398-1414.e24. [PMID: 27863251 PMCID: PMC5119954 DOI: 10.1016/j.cell.2016.10.026] [Citation(s) in RCA: 389] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 08/19/2016] [Accepted: 10/14/2016] [Indexed: 12/20/2022]
Abstract
Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in three major human immune cell types (CD14+ monocytes, CD16+ neutrophils, and naive CD4+ T cells) from up to 197 individuals. We assess, quantitatively, the relative contribution of cis-genetic and epigenetic factors to transcription and evaluate their impact as potential sources of confounding in epigenome-wide association studies. Further, we characterize highly coordinated genetic effects on gene expression, methylation, and histone variation through quantitative trait locus (QTL) mapping and allele-specific (AS) analyses. Finally, we demonstrate colocalization of molecular trait QTLs at 345 unique immune disease loci. This expansive, high-resolution atlas of multi-omics changes yields insights into cell-type-specific correlation between diverse genomic inputs, more generalizable correlations between these inputs, and defines molecular events that may underpin complex disease risk. Genome, transcriptome, and epigenome reference panel in three human immune cell types Identified 4,418 genes associated with epigenetic changes independent of genetics Described genome-epigenome coordination defining cell-type-specific regulatory events Functionally mapped disease mechanisms at 345 unique autoimmune disease loci
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Affiliation(s)
- Lu Chen
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Bing Ge
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Louella Vasquez
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Tony Kwan
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Diego Garrido-Martín
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader, 88, Barcelona 8003, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Plaça de la Mercè, 10- 12, Barcelona 8002, Spain
| | - Stephen Watt
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Ying Yan
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Kousik Kundu
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Simone Ecker
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 3, Madrid 28029, Spain; UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Avik Datta
- Vertebrate Genomics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David Richardson
- Vertebrate Genomics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Frances Burden
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Daniel Mead
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Alice L Mann
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Jose Maria Fernandez
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 3, Madrid 28029, Spain
| | - Sophia Rowlston
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Steven P Wilder
- Genome Analysis, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Samantha Farrow
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Xiaojian Shao
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - John J Lambourne
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Adriana Redensek
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Cornelis A Albers
- Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, P.O. Box 9101, Nijmegen 6500 HB, the Netherlands; Molecular Developmental Biology, Radboud Institute for Life Sciences, Radboud University, P.O. Box 9101, Nijmegen 6500 HB, the Netherlands
| | - Vyacheslav Amstislavskiy
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63/73, Berlin 14195, Germany
| | - Sofie Ashford
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Kim Berentsen
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Lorenzo Bomba
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Guillaume Bourque
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - David Bujold
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Stephan Busche
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Maxime Caron
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Shu-Huang Chen
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Warren Cheung
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Oliver Delaneau
- Genetic Medicine and Development, University of Geneva Medical School-CMU, 1 Rue Michel-Servet, Geneva 1211, Switzerland
| | - Emmanouil T Dermitzakis
- Genetic Medicine and Development, University of Geneva Medical School-CMU, 1 Rue Michel-Servet, Geneva 1211, Switzerland
| | - Heather Elding
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Irina Colgiu
- Human Genetics Informatics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Frederik O Bagger
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Paul Flicek
- Vertebrate Genomics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ehsan Habibi
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Valentina Iotchkova
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eva Janssen-Megens
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Bowon Kim
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Hans Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63/73, Berlin 14195, Germany
| | - Ernesto Lowy
- Vertebrate Genomics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Amit Mandoli
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Filomena Matarese
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Matthew T Maurano
- Institute for Systems Genetics, New York University Langone Medical Center, ACLS West, Room 511, 430 East 29(th) Street, New York, NY 10016, USA
| | - John A Morris
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Vera Pancaldi
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 3, Madrid 28029, Spain
| | - Farzin Pourfarzad
- Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Plesmanlaan 125, Amsterdam 1066CX, the Netherlands
| | - Karola Rehnstrom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Augusto Rendon
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; Bioinformatics, Genomics England, Charterhouse Square, London EC1M 6BQ, UK
| | - Thomas Risch
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63/73, Berlin 14195, Germany
| | - Nilofar Sharifi
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Marie-Michelle Simon
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Marc Sultan
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63/73, Berlin 14195, Germany
| | - Alfonso Valencia
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 3, Madrid 28029, Spain
| | - Klaudia Walter
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Shuang-Yin Wang
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Stylianos E Antonarakis
- Genetic Medicine and Development, University of Geneva Medical School-CMU, 1 Rue Michel-Servet, Geneva 1211, Switzerland
| | - Laura Clarke
- Vertebrate Genomics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marie-Laure Yaspo
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63/73, Berlin 14195, Germany
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Roderic Guigo
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader, 88, Barcelona 8003, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Plaça de la Mercè, 10- 12, Barcelona 8002, Spain; Computational Genomics, Institut Hospital del Mar d'Investigacions Mediques (IMIM), Carrer del Dr. Aiguader, 88, Barcelona 8003, Spain
| | - Daniel Rico
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 3, Madrid 28029, Spain; Institute of Cellular Medicine, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Willem H Ouwehand
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge CB1 8RN, UK
| | - Taco W Kuijpers
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Plesmanlaan 125, Amsterdam 1066CX, the Netherlands; Emma Children's Hospital, Academic Medical Center (AMC), University of Amsterdam, Location H7-230, Meibergdreef 9, Amsterdam 1105AZ, the Netherlands
| | - Dirk S Paul
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK; Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge CB1 8RN, UK
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Tomi Pastinen
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada.
| | - Nicole Soranzo
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge CB1 8RN, UK.
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