351
|
Accelerated epigenetic aging and inflammatory/immunological profile (ipAGE) in patients with chronic kidney disease. GeroScience 2022; 44:817-834. [PMID: 35237926 DOI: 10.1007/s11357-022-00540-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/23/2022] [Indexed: 12/13/2022] Open
Abstract
Chronic kidney disease (CKD) is defined by a reduced estimated glomerular filtration rate (eGFR). This failure can be related to a phenotype of accelerated aging. In this work, we considered 76 patients with end-stage renal disease (ESRD) and 83 healthy controls. We concomitantly evaluated for the first time two measures that can be informative of the rate of aging, i.e., whole blood DNA methylation using the Illumina Infinium EPIC array and plasma levels of a selection of inflammatory/immunological proteins using multiplex immunoassays. First of all, we demonstrated accelerated aging in terms of the most common epigenetic age estimators in CKD patients. Moreover, we developed a new clock/predictor of age based on the inflammatory/immunological profile (ipAGE) and identified the inflammatory/immunological biomarkers differentially expressed between cases and controls. IpAGE appeared to be more sensitive than epigenetic clocks in quantifying the accelerated aging phenotype of ESRD patients. Interestingly, we did not find any correlation between the age acceleration evaluated according to the epigenetic clocks and ipAGE in either the ESRD group or the control group. On the whole, our data show a consistent accelerated aging phenotype in ESRD patients, which is better appreciated by quantifying the underlying inflammatory processes (inflammaging) by ipAGE than by using epigenetic clocks.
Collapse
|
352
|
Ehrlich M. Risks and rewards of big-data in epigenomics research: an interview with Melanie Ehrlich. Epigenomics 2022; 14:351-358. [PMID: 35255735 DOI: 10.2217/epi-2022-0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Melanie Ehrlich, PhD, is a professor in the Tulane Cancer Center, the Tulane Center for Medical Bioinformatics and Genomics and the Hayward Human Genetics Program at Tulane Medical School, New Orleans, LA. She obtained her PhD in molecular biology in 1971 from the State University of New York at Stony Brook and completed postdoctoral research at Albert Einstein College of Medicine in 1972. She has been working on various aspects of epigenetics, starting with DNA methylation, since 1973. Her group made many first findings about DNA methylation (see below). For example, in 1982 and 1983, in collaboration with Charles Gehrke at the University of Missouri, she was the first to report tissue-specific and cancer-specific differences in overall DNA methylation in humans. In 1985, Xian-Yang Zhang and Richard Wang in her lab discovered a class of human DNA sequences specifically hypomethylated in sperm. In 1998, her group was the first to describe extensive losses of DNA methylation in pericentromeric and centromeric DNA repeats in human cancer. Her lab's many publications on the prevalence of both DNA hypermethylation and hypomethylation in the same cancers brought needed balance to our understanding of the epigenetics of cancer and to its clinical implications [1]. Besides working on cancer epigenetics, her research group has helped elucidate cytogenetic and gene expression abnormalities in the immunodeficiency, centromeric and facial anomalies (ICF) syndrome, a rare recessive disease often caused by mutations in DNMT3B. Her group also studied the epigenetics and transcriptomics of facioscapulohumeral muscular dystrophy (FSHD), whose disease locus is a tandem 3.3-kb repeat at subtelomeric 4q (that happens to be hypomethylated in ICF DNA [2]). Her study of FSHD has taken her in the direction of muscle (skeletal muscle, heart and aorta) epigenetics [3-6]. Recently, she has led research that applies epigenetics much more rigorously than usual to the evaluation of genetic variants from genome-wide association studies (GWAS) of osteoporosis and obesity. In continued collaboration with Sriharsa Pradhan at New England Biolabs and Michelle Lacey at Tulane University, she has compared 5-hydroxymethylcytosine and 5-methylcytosine clustering in various human tissues [7] and is studying myoblast methylomes that they generated by a new high-resolution enzymatic technique (enzymatic methyl-seq).
Collapse
Affiliation(s)
- Melanie Ehrlich
- Tulane Cancer Center, Center for Medical Bioinformatics & Genomics, & Hayward Genetics Center, Tulane University, New Orleans, LA 70112, USA
| |
Collapse
|
353
|
Liu Y, Eliot MN, Papandonatos GD, Kelsey KT, Fore R, Langevin S, Buckley J, Chen A, Lanphear BP, Cecil KM, Yolton K, Hivert MF, Sagiv SK, Baccarelli AA, Oken E, Braun JM. Gestational Perfluoroalkyl Substance Exposure and DNA Methylation at Birth and 12 Years of Age: A Longitudinal Epigenome-Wide Association Study. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:37005. [PMID: 35266797 PMCID: PMC8911098 DOI: 10.1289/ehp10118] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 05/31/2023]
Abstract
BACKGROUND DNA methylation alterations may underlie associations between gestational perfluoroalkyl substances (PFAS) exposure and later-life health outcomes. To the best of our knowledge, no longitudinal studies have examined the associations between gestational PFAS and DNA methylation. OBJECTIVES We examined associations of gestational PFAS exposure with longitudinal DNA methylation measures at birth and in adolescence using the Health Outcomes and Measures of the Environment (HOME) Study (2003-2006; Cincinnati, Ohio). METHODS We quantified serum concentrations of perfluorooctanoate (PFOA), perfluorooctane sulfonate (PFOS), perfluorononanoate (PFNA), and perfluorohexane sulfonate (PFHxS) in mothers during pregnancy. We measured DNA methylation in cord blood (n=266) and peripheral leukocytes at 12 years of age (n=160) using the Illumina HumanMethylation EPIC BeadChip. We analyzed associations between log2-transformed PFAS concentrations and repeated DNA methylation measures using linear regression with generalized estimating equations. We included interaction terms between children's age and gestational PFAS. We performed Gene Ontology enrichment analysis to identify molecular pathways. We used Project Viva (1999-2002; Boston, Massachusetts) to replicate significant associations. RESULTS After adjusting for covariates, 435 cytosine-guanine dinucleotide (CpG) sites were associated with PFAS (false discovery rate, q<0.05). Specifically, we identified 2 CpGs for PFOS, 12 for PFOA, 8 for PFHxS, and 413 for PFNA; none overlapped. Among these, 2 CpGs for PFOA and 4 for PFNA were replicated in Project Viva. Some of the PFAS-associated CpG sites annotated to gene regions related to cancers, cognitive health, cardiovascular disease, and kidney function. We found little evidence that the associations between PFAS and DNA methylation differed by children's age. DISCUSSION In these longitudinal data, PFAS biomarkers were associated with differences in several CpGs at birth and at 12 years of age in or near genes linked to some PFAS-associated health outcomes. Future studies should examine whether DNA methylation mediates associations between gestational PFAS exposure and health. https://doi.org/10.1289/EHP10118.
Collapse
Affiliation(s)
- Yun Liu
- Department of Epidemiology, Brown University School of Public Health, Providence, Rhode Island, USA
| | - Melissa N. Eliot
- Department of Epidemiology, Brown University School of Public Health, Providence, Rhode Island, USA
| | - George D. Papandonatos
- Department of Biostatistics, Brown University School of Public Health, Providence, Rhode Island, USA
| | - Karl T. Kelsey
- Department of Epidemiology, Brown University School of Public Health, Providence, Rhode Island, USA
- Department of Laboratory Medicine and Pathology, Brown University, Providence, Rhode Island, USA
| | - Ruby Fore
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Scott Langevin
- Department of Environmental & Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jessie Buckley
- Department of Environmental Health and Engineering, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Aimin Chen
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Bruce P. Lanphear
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Kim M. Cecil
- Department of Environmental & Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Department of Radiology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Kimberly Yolton
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, Massachusetts, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sharon K. Sagiv
- Department of Epidemiology, Berkeley School of Public Health, University of California, Berkeley, California, USA
| | - Andrea A. Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, USA
| | - Emily Oken
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph M. Braun
- Department of Epidemiology, Brown University School of Public Health, Providence, Rhode Island, USA
| |
Collapse
|
354
|
Tobi EW, Juvinao-Quintero DL, Ronkainen J, Ott R, Alfano R, Canouil M, Geurtsen ML, Khamis A, Küpers LK, Lim IY, Perron P, Pesce G, Tuhkanen J, Starling AP, Andrew T, Binder E, Caiazzo R, Chan JK, Gaillard R, Gluckman PD, Keikkala E, Karnani N, Mustaniemi S, Nawrot TS, Pattou F, Plusquin M, Raverdy V, Tan KH, Tzala E, Raikkonen K, Winkler C, Ziegler AG, Annesi-Maesano I, Bouchard L, Chong YS, Dabelea D, Felix JF, Heude B, Jaddoe VW, Lahti J, Reimann B, Vääräsmäki M, Bonnefond A, Froguel P, Hummel S, Kajantie E, Jarvelin MR, Steegers-Theunissen RP, Howe CG, Hivert MF, Sebert S. Maternal Glycemic Dysregulation During Pregnancy and Neonatal Blood DNA Methylation: Meta-analyses of Epigenome-Wide Association Studies. Diabetes Care 2022; 45:614-623. [PMID: 35104326 PMCID: PMC8918264 DOI: 10.2337/dc21-1701] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/10/2021] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Maternal glycemic dysregulation during pregnancy increases the risk of adverse health outcomes in her offspring, a risk thought to be linearly related to maternal hyperglycemia. It is hypothesized that changes in offspring DNA methylation (DNAm) underline these associations. RESEARCH DESIGN AND METHODS To address this hypothesis, we conducted fixed-effects meta-analyses of epigenome-wide association study (EWAS) results from eight birth cohorts investigating relationships between cord blood DNAm and fetal exposure to maternal glucose (Nmaximum = 3,503), insulin (Nmaximum = 2,062), and area under the curve of glucose (AUCgluc) following oral glucose tolerance tests (Nmaximum = 1,505). We performed lookup analyses for identified cytosine-guanine dinucleotides (CpGs) in independent observational cohorts to examine associations between DNAm and cardiometabolic traits as well as tissue-specific gene expression. RESULTS Greater maternal AUCgluc was associated with lower cord blood DNAm at neighboring CpGs cg26974062 (β [SE] -0.013 [2.1 × 10-3], P value corrected for false discovery rate [PFDR] = 5.1 × 10-3) and cg02988288 (β [SE]-0.013 [2.3 × 10-3], PFDR = 0.031) in TXNIP. These associations were attenuated in women with GDM. Lower blood DNAm at these two CpGs near TXNIP was associated with multiple metabolic traits later in life, including type 2 diabetes. TXNIP DNAm in liver biopsies was associated with hepatic expression of TXNIP. We observed little evidence of associations between either maternal glucose or insulin and cord blood DNAm. CONCLUSIONS Maternal hyperglycemia, as reflected by AUCgluc, was associated with lower cord blood DNAm at TXNIP. Associations between DNAm at these CpGs and metabolic traits in subsequent lookup analyses suggest that these may be candidate loci to investigate in future causal and mediation analyses.
Collapse
Affiliation(s)
- Elmar W. Tobi
- Division of Obstetrics and Prenatal Medicine, Department of Obstetrics and Gynaecology, Erasmus MC, Rotterdam, the Netherlands
| | - Diana L. Juvinao-Quintero
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, MA
| | - Justiina Ronkainen
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Raffael Ott
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- Forschergruppe Diabetes, Technical University Munich, Klinikum rechts der Isar, Munich, Germany
- Forschergruppe Diabetes e.V., Helmholtz Zentrum München, Munich-Neuherberg, Germany
| | - Rossella Alfano
- Center for Environmental Sciences, University of Hasselt, Hasselt, Belgium
| | - Mickaël Canouil
- INSERM U1283, CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- University of Lille, Lille University Hospital, Lille, France
| | - Madelon L. Geurtsen
- The Generation R Study Group, Erasmus MC, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, Rotterdam, the Netherlands
| | - Amna Khamis
- INSERM U1283, CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- University of Lille, Lille University Hospital, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Leanne K. Küpers
- The Generation R Study Group, Erasmus MC, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, Rotterdam, the Netherlands
| | - Ives Y. Lim
- Bioinformatics Institute, A*STAR, Singapore
- Singapore Institute for Clinical Sciences, A*STAR, Singapore
| | - Patrice Perron
- Department of Medicine, Universite de Sherbrooke, Sherbrooke, Canada
- Research Center, Centre hospitalier Universitaire de Sherbrooke, Sherbrooke, Canada
| | - Giancarlo Pesce
- Paris-Saclay University, Paris-South University, UVSQ, Center for Research in Epidemiology and Population Health (CESP), INSERM, Villejuif, France
- Sorbonne Université and INSERM, Team EPAR, Institut Pierre Louis D’Épidémiologie et de Santé Publique, Paris, France
| | - Johanna Tuhkanen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Anne P. Starling
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO
- Lifecourse Epidemiology of Adiposity and Diabetes Center, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Toby Andrew
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Elisabeth Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA
| | - Robert Caiazzo
- University of Lille, CHU Lille, Inserm, Institut Pasteur Lille, U1190 Translational Research for Diabetes, Lille, France
| | - Jerry K.Y. Chan
- Department of Reproductive Medicine, KK Women’s and Children’s Hospital, Singapore
- Academic Clinical Program in Obstetrics and Gynaecology, Duke-NUS Medical School, Singapore
| | - Romy Gaillard
- The Generation R Study Group, Erasmus MC, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, Rotterdam, the Netherlands
| | - Peter D. Gluckman
- Singapore Institute for Clinical Sciences, A*STAR, Singapore
- Liggins Institute, University of Auckland, Aukland, New Zealand
| | - Elina Keikkala
- Population Health Unit, Finnish Institute for Health and Welfare, Oulu, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Neerja Karnani
- Bioinformatics Institute, A*STAR, Singapore
- Singapore Institute for Clinical Sciences, A*STAR, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Sanna Mustaniemi
- Population Health Unit, Finnish Institute for Health and Welfare, Oulu, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Tim S. Nawrot
- Center for Environmental Sciences, University of Hasselt, Hasselt, Belgium
| | - François Pattou
- University of Lille, CHU Lille, Inserm, Institut Pasteur Lille, U1190 Translational Research for Diabetes, Lille, France
| | - Michelle Plusquin
- Center for Environmental Sciences, University of Hasselt, Hasselt, Belgium
| | - Violeta Raverdy
- University of Lille, CHU Lille, Inserm, Institut Pasteur Lille, U1190 Translational Research for Diabetes, Lille, France
| | - Kok Hian Tan
- Academic Clinical Program in Obstetrics and Gynaecology, Duke-NUS Medical School, Singapore
- Department of Maternal Fetal Medicine, KK Women’s and Children’s Hospital, Singapore
| | - Evangelia Tzala
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, U.K
| | - Katri Raikkonen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Christiane Winkler
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- Forschergruppe Diabetes, Technical University Munich, Klinikum rechts der Isar, Munich, Germany
- Forschergruppe Diabetes e.V., Helmholtz Zentrum München, Munich-Neuherberg, Germany
| | - Anette-G. Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- Forschergruppe Diabetes, Technical University Munich, Klinikum rechts der Isar, Munich, Germany
- Forschergruppe Diabetes e.V., Helmholtz Zentrum München, Munich-Neuherberg, Germany
| | - Isabella Annesi-Maesano
- Montpellier University, INSERM, Institut Desbrest d’Épidémiologie et de Santé Publique (IDESP), Montpellier, France
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Universite de Sherbrooke, Sherbrooke, Canada
- Department of Laboratory Medicine, CIUSSS du Saguenay–Lac-St-Jean, Hôpital Universitaire de Chicoutimi, Canada
| | - Yap Seng Chong
- Singapore Institute for Clinical Sciences, A*STAR, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore
| | - Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO
- Lifecourse Epidemiology of Adiposity and Diabetes Center, University of Colorado Anschutz Medical Campus, Aurora, CO
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO
| | - Janine F. Felix
- The Generation R Study Group, Erasmus MC, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, Rotterdam, the Netherlands
| | - Barbara Heude
- Université de Paris, Inserm, INRAE, Centre for Research in Epidemiology and Statistics (CRESS), Paris, France
| | - Vincent W.V. Jaddoe
- The Generation R Study Group, Erasmus MC, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, Rotterdam, the Netherlands
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Brigitte Reimann
- Center for Environmental Sciences, University of Hasselt, Hasselt, Belgium
| | - Marja Vääräsmäki
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Amélie Bonnefond
- INSERM U1283, CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- University of Lille, Lille University Hospital, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Philippe Froguel
- INSERM U1283, CNRS UMR 8199, European Genomic Institute for Diabetes, Institut Pasteur de Lille, Lille, France
- University of Lille, Lille University Hospital, Lille, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Sandra Hummel
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- Forschergruppe Diabetes, Technical University Munich, Klinikum rechts der Isar, Munich, Germany
- Forschergruppe Diabetes e.V., Helmholtz Zentrum München, Munich-Neuherberg, Germany
| | - Eero Kajantie
- Population Health Unit, Finnish Institute for Health and Welfare, Oulu, Finland
- PEDEGO Research Unit, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Children’s Hospital, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Marjo-Riita Jarvelin
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, U.K
- Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, U.K
| | - Regine P.M. Steegers-Theunissen
- Division of Obstetrics and Prenatal Medicine, Department of Obstetrics and Gynaecology, Erasmus MC, Rotterdam, the Netherlands
| | - Caitlin G. Howe
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, MA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA
| | - Sylvain Sebert
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| |
Collapse
|
355
|
Beltrán-García J, Osca-Verdegal R, Jávega B, Herrera G, O’Connor JE, García-López E, Casabó-Vallés G, Rodriguez-Gimillo M, Ferreres J, Carbonell N, Pallardó FV, García-Giménez JL. Characterization of Early Peripheral Immune Responses in Patients with Sepsis and Septic Shock. Biomedicines 2022; 10:525. [PMID: 35327327 PMCID: PMC8945007 DOI: 10.3390/biomedicines10030525] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/22/2022] Open
Abstract
(1) Background: Sepsis is a life-threatening condition caused by an abnormal host response to infection that produces altered physiological responses causing tissue damage and can result in organ dysfunction and, in some cases, death. Although sepsis is characterized by a malfunction of the immune system leading to an altered immune response and immunosuppression, the high complexity of the pathophysiology of sepsis requires further investigation to characterize the immune response in sepsis and septic shock. (2) Methods: This study analyzes the immune-related responses occurring during the early stages of sepsis by comparing the amounts of cytokines, immune modulators and other endothelial mediators of a control group and three types of severe patients: critically ill non-septic patients, septic and septic shock patients. (3) Results: We showed that in the early stages of sepsis the innate immune system attempts to counteract infection, probably via neutrophils. Conversely, the adaptive immune system is not yet fully activated, either in septic or in septic shock patients. In addition, immunosuppressive responses and pro-coagulation signals are active in patients with septic shock. (4) Conclusions: The highest levels of IL-6 and pyroptosis-related cytokines (IL-18 and IL-1α) were found in septic shock patients, which correlated with D-dimer. Moreover, endothelial function may be affected as shown by the overexpression of adhesion molecules such as s-ICAM1 and E-Selectin during septic shock.
Collapse
Affiliation(s)
- Jesús Beltrán-García
- Center for Biomedical Research Network on Rare Diseases (CIBERER), Carlos III Health Institute, 46010 Valencia, Spain; (J.B.-G.); (R.O.-V.); (E.G.-L.); (F.V.P.)
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (M.R.-G.); (J.F.); (N.C.)
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
| | - Rebeca Osca-Verdegal
- Center for Biomedical Research Network on Rare Diseases (CIBERER), Carlos III Health Institute, 46010 Valencia, Spain; (J.B.-G.); (R.O.-V.); (E.G.-L.); (F.V.P.)
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (M.R.-G.); (J.F.); (N.C.)
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
| | - Beatriz Jávega
- Laboratory of Cytomics, Joint Research Unit CIPF-UVEG, University of Valencia, 46010 Valencia, Spain; (B.J.); (J.-E.O.)
| | - Guadalupe Herrera
- Flow Cytometry Unit, IIS INCLIVA, Fundación Investigación Hospital Clínico Valencia, 46010 Valencia, Spain;
| | - José-Enrique O’Connor
- Laboratory of Cytomics, Joint Research Unit CIPF-UVEG, University of Valencia, 46010 Valencia, Spain; (B.J.); (J.-E.O.)
| | - Eva García-López
- Center for Biomedical Research Network on Rare Diseases (CIBERER), Carlos III Health Institute, 46010 Valencia, Spain; (J.B.-G.); (R.O.-V.); (E.G.-L.); (F.V.P.)
- EpiDisease S.L. (Spin-Off CIBER-ISCIII), Parc Científic de la Universitat de València, 46980 Paterna, Spain;
| | - Germán Casabó-Vallés
- EpiDisease S.L. (Spin-Off CIBER-ISCIII), Parc Científic de la Universitat de València, 46980 Paterna, Spain;
| | - María Rodriguez-Gimillo
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (M.R.-G.); (J.F.); (N.C.)
- Intensive Care Unit, Clinical University Hospital of Valencia (HCUV), 46010 Valencia, Spain
| | - José Ferreres
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (M.R.-G.); (J.F.); (N.C.)
- Intensive Care Unit, Clinical University Hospital of Valencia (HCUV), 46010 Valencia, Spain
| | - Nieves Carbonell
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (M.R.-G.); (J.F.); (N.C.)
- Intensive Care Unit, Clinical University Hospital of Valencia (HCUV), 46010 Valencia, Spain
| | - Federico V. Pallardó
- Center for Biomedical Research Network on Rare Diseases (CIBERER), Carlos III Health Institute, 46010 Valencia, Spain; (J.B.-G.); (R.O.-V.); (E.G.-L.); (F.V.P.)
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (M.R.-G.); (J.F.); (N.C.)
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
| | - José Luis García-Giménez
- Center for Biomedical Research Network on Rare Diseases (CIBERER), Carlos III Health Institute, 46010 Valencia, Spain; (J.B.-G.); (R.O.-V.); (E.G.-L.); (F.V.P.)
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (M.R.-G.); (J.F.); (N.C.)
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain
| |
Collapse
|
356
|
Wagner W. How to Translate DNA Methylation Biomarkers Into Clinical Practice. Front Cell Dev Biol 2022; 10:854797. [PMID: 35281115 PMCID: PMC8905294 DOI: 10.3389/fcell.2022.854797] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/04/2022] [Indexed: 12/14/2022] Open
Abstract
Recent advances in sequencing technologies provide unprecedented opportunities for epigenetic biomarker development. Particularly the DNA methylation pattern-which is modified at specific sites in the genome during cellular differentiation, aging, and disease-holds high hopes for a wide variety of diagnostic applications. While many epigenetic biomarkers have been described, only very few of them have so far been successfully translated into clinical practice and almost exclusively in the field of oncology. This discrepancy might be attributed to the different demands of either publishing a new finding or establishing a standardized and approved diagnostic procedure. This is exemplified for epigenetic leukocyte counts and epigenetic age-predictions. To ease later clinical translation, the following hallmarks should already be taken into consideration when designing epigenetic biomarkers: 1) Identification of best genomic regions, 2) pre-analytical processing, 3) accuracy of DNA methylation measurements, 4) identification of confounding parameters, 5) accreditation as diagnostic procedure, 6) standardized data analysis, 7) turnaround time, and 8) costs and customer requirements. While the initial selection of relevant genomic regions is usually performed on genome wide DNA methylation profiles, it might be advantageous to subsequently establish targeted assays that focus on specific genomic regions. Development of an epigenetic biomarker for clinical application is a long and cumbersome process that is only initiated with the identification of an epigenetic signature.
Collapse
Affiliation(s)
- Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen University Medical School, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| |
Collapse
|
357
|
Raffington L, Belsky DW. Integrating DNA Methylation Measures of Biological Aging into Social Determinants of Health Research. Curr Environ Health Rep 2022; 9:196-210. [PMID: 35181865 DOI: 10.1007/s40572-022-00338-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2022] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW Acceleration of biological processes of aging is hypothesized to drive excess morbidity and mortality in socially disadvantaged populations. DNA methylation measures of biological aging provide tools for testing this hypothesis. RECENT FINDINGS Next-generation DNA methylation measures of biological aging developed to predict mortality risk and physiological decline are more predictive of morbidity and mortality than the original epigenetic clocks developed to predict chronological age. These new measures show consistent evidence of more advanced and faster biological aging in people exposed to socioeconomic disadvantage and may be able to record the emergence of socially determined health inequalities as early as childhood. Next-generation DNA methylation measures of biological aging also indicate race/ethnic disparities in biological aging. More research is needed on these measures in samples of non-Western and non-White populations. New DNA methylation measures of biological aging open opportunities for refining inference about the causes of social disparities in health and devising policies to eliminate them. Further refining measures of biological aging by including more diversity in samples used for measurement development is a critical priority for the field.
Collapse
Affiliation(s)
- Laurel Raffington
- Department of Psychology, University of Texas at Austin, Austin, TX, USA
- Population Research Center, The University of Texas at Austin, Austin, TX, USA
| | - Daniel W Belsky
- Department of Epidemiology, Columbia University Mailman School of Public Health, 722 W 168th St. Rm 413, New York, NY, 10032, USA.
- Robert N Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, NY, USA.
| |
Collapse
|
358
|
Shepherd R, Bretherton I, Pang K, Mansell T, Czajko A, Kim B, Vlahos A, Zajac JD, Saffery R, Cheung A, Novakovic B. Gender-affirming hormone therapy induces specific DNA methylation changes in blood. Clin Epigenetics 2022; 14:24. [PMID: 35177097 PMCID: PMC8851870 DOI: 10.1186/s13148-022-01236-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 01/13/2022] [Indexed: 11/10/2022] Open
Abstract
Background DNA methylation is an epigenetic mark that is influenced by underlying genetic profile, environment, and ageing. In addition to X-linked DNA methylation, sex-specific methylation patterns are widespread across autosomal chromosomes and can be present from birth or arise over time. In individuals where gender identity and sex assigned at birth are markedly incongruent, as in the case of transgender people, feminization or masculinization may be sought through gender-affirming hormone therapy (GAHT). GAHT is a cornerstone of transgender care, yet no studies to date have investigated its effect on genome-wide methylation. We profiled genome-wide DNA methylation in blood of transgender women (n = 13) and transgender men (n = 13) before and during GAHT (6 months and 12 months into feminizing or masculinizing hormone therapy). Results We identified several thousand differentially methylated CpG sites (DMPs) (Δβ ≥ 0.02, unadjusted p value < 0.05) and several differentially methylated regions (DMRs) in both people undergoing feminizing and masculinizing GAHT, the vast majority of which were progressive changes over time. X chromosome and sex-specific autosomal DNA methylation patterns established in early development are largely refractory to change in association with GAHT, with only 3% affected (Δβ ≥ 0.02, unadjusted p value < 0.05). The small number of sex-specific DMPs that were affected by GAHT were those that become sex-specific during the lifetime, known as sex-and-age DMPs, including DMRs in PRR4 and VMP1 genes. The GAHT-induced changes at these sex-associated probes consistently demonstrated a shift towards the methylation signature of the GAHT-naïve opposite sex, and we observed enrichment of previously reported adolescence-associated methylation changes. Conclusion We provide evidence for GAHT inducing a unique blood methylation signature in transgender people. This study advances our understanding of the complex interplay between sex hormones, sex chromosomes, and DNA methylation in the context of immunity. We highlight the need to broaden the field of ‘sex-specific’ immunity beyond cisgender males and cisgender females, as transgender people on GAHT exhibit a unique molecular profile. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01236-4.
Collapse
Affiliation(s)
- Rebecca Shepherd
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Ingrid Bretherton
- Department of Medicine (Austin Health), The University of Melbourne, Parkville, VIC, Australia.,Department of Endocrinology, Austin Health, Heidelberg, VIC, Australia
| | - Ken Pang
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Adolescent Medicine, Royal Children's Hospital, Parkville, VIC, Australia
| | - Toby Mansell
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Anna Czajko
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Bowon Kim
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Amanda Vlahos
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Jeffrey D Zajac
- Department of Medicine (Austin Health), The University of Melbourne, Parkville, VIC, Australia.,Department of Endocrinology, Austin Health, Heidelberg, VIC, Australia
| | - Richard Saffery
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Ada Cheung
- Department of Medicine (Austin Health), The University of Melbourne, Parkville, VIC, Australia.,Department of Endocrinology, Austin Health, Heidelberg, VIC, Australia
| | - Boris Novakovic
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia. .,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.
| |
Collapse
|
359
|
Arneson A, Haghani A, Thompson MJ, Pellegrini M, Kwon SB, Vu H, Maciejewski E, Yao M, Li CZ, Lu AT, Morselli M, Rubbi L, Barnes B, Hansen KD, Zhou W, Breeze CE, Ernst J, Horvath S. A mammalian methylation array for profiling methylation levels at conserved sequences. Nat Commun 2022; 13:783. [PMID: 35145108 PMCID: PMC8831611 DOI: 10.1038/s41467-022-28355-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/20/2022] [Indexed: 12/12/2022] Open
Abstract
Infinium methylation arrays are not available for the vast majority of non-human mammals. Moreover, even if species-specific arrays were available, probe differences between them would confound cross-species comparisons. To address these challenges, we developed the mammalian methylation array, a single custom array that measures up to 36k CpGs per species that are well conserved across many mammalian species. We designed a set of probes that can tolerate specific cross-species mutations. We annotate the array in over 200 species and report CpG island status and chromatin states in select species. Calibration experiments demonstrate the high fidelity in humans, rats, and mice. The mammalian methylation array has several strengths: it applies to all mammalian species even those that have not yet been sequenced, it provides deep coverage of conserved cytosines facilitating the development of epigenetic biomarkers, and it increases the probability that biological insights gained in one species will translate to others.
Collapse
Affiliation(s)
- Adriana Arneson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Amin Haghani
- Dept. of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Michael J Thompson
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Soo Bin Kwon
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ha Vu
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Emily Maciejewski
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Computer Science Department, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mingjia Yao
- Dept. of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Caesar Z Li
- Dept. of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Ake T Lu
- Dept. of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Marco Morselli
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Liudmilla Rubbi
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Bret Barnes
- Illumina, Inc, 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Kasper D Hansen
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, USA
| | | | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA.
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.
- Computer Science Department, University of California, Los Angeles, Los Angeles, CA, USA.
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Steve Horvath
- Dept. of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Dept. of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Altos Labs, San Diego, CA, USA.
| |
Collapse
|
360
|
Cristoferi I, Giacon TA, Boer K, van Baardwijk M, Neri F, Campisi M, Kimenai HJAN, Clahsen-van Groningen MC, Pavanello S, Furian L, Minnee RC. The applications of DNA methylation as a biomarker in kidney transplantation: a systematic review. Clin Epigenetics 2022; 14:20. [PMID: 35130936 PMCID: PMC8822833 DOI: 10.1186/s13148-022-01241-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/27/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Although kidney transplantation improves patient survival and quality of life, long-term results are hampered by both immune- and non-immune-mediated complications. Current biomarkers of post-transplant complications, such as allograft rejection, chronic renal allograft dysfunction, and cutaneous squamous cell carcinoma, have a suboptimal predictive value. DNA methylation is an epigenetic modification that directly affects gene expression and plays an important role in processes such as ischemia/reperfusion injury, fibrosis, and alloreactive immune response. Novel techniques can quickly assess the DNA methylation status of multiple loci in different cell types, allowing a deep and interesting study of cells' activity and function. Therefore, DNA methylation has the potential to become an important biomarker for prediction and monitoring in kidney transplantation. PURPOSE OF THE STUDY The aim of this study was to evaluate the role of DNA methylation as a potential biomarker of graft survival and complications development in kidney transplantation. MATERIAL AND METHODS: A systematic review of several databases has been conducted. The Newcastle-Ottawa scale and the Jadad scale have been used to assess the risk of bias for observational and randomized studies, respectively. RESULTS Twenty articles reporting on DNA methylation as a biomarker for kidney transplantation were included, all using DNA methylation for prediction and monitoring. DNA methylation pattern alterations in cells isolated from different tissues, such as kidney biopsies, urine, and blood, have been associated with ischemia-reperfusion injury and chronic renal allograft dysfunction. These alterations occurred in different and specific loci. DNA methylation status has also proved to be important for immune response modulation, having a crucial role in regulatory T cell definition and activity. Research also focused on a better understanding of the role of this epigenetic modification assessment for regulatory T cells isolation and expansion for future tolerance induction-oriented therapies. CONCLUSIONS Studies included in this review are heterogeneous in study design, biological samples, and outcome. More coordinated investigations are needed to affirm DNA methylation as a clinically relevant biomarker important for prevention, monitoring, and intervention.
Collapse
Affiliation(s)
- Iacopo Cristoferi
- Division of HPB and Transplant Surgery, Department of Surgery, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015GD, Rotterdam, the Netherlands.
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015GD, Rotterdam, the Netherlands.
- Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015GD, Rotterdam, the Netherlands.
| | - Tommaso Antonio Giacon
- Kidney and Pancreas Transplantation Unit, Department of Surgical, Oncological and Gastroenterological Sciences, Padua University Hospital, Via Giustiniani 2, 35128, Padua, Italy
- Occupational Medicine, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, Padua University, Via Giustiniani 2, 35128, Padua, Italy
- Environmental and Respiratory Physiology Laboratory, Department of Biomedical Sciences, Padua University, Via Marzolo 3, 35131, Padua, Italy
- Institute of Anaesthesia and Intensive Care, Department of Medicine - DIMED, Padua University Hospital, Via Cesare Battisti 267, 35128, Padua, Italy
| | - Karin Boer
- Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015GD, Rotterdam, the Netherlands
- Division of Nephrology and Transplantation, Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015GD, Rotterdam, The Netherlands
| | - Myrthe van Baardwijk
- Division of HPB and Transplant Surgery, Department of Surgery, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015GD, Rotterdam, the Netherlands
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015GD, Rotterdam, the Netherlands
- Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015GD, Rotterdam, the Netherlands
| | - Flavia Neri
- Kidney and Pancreas Transplantation Unit, Department of Surgical, Oncological and Gastroenterological Sciences, Padua University Hospital, Via Giustiniani 2, 35128, Padua, Italy
| | - Manuela Campisi
- Occupational Medicine, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, Padua University, Via Giustiniani 2, 35128, Padua, Italy
| | - Hendrikus J A N Kimenai
- Division of HPB and Transplant Surgery, Department of Surgery, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015GD, Rotterdam, the Netherlands
- Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015GD, Rotterdam, the Netherlands
| | - Marian C Clahsen-van Groningen
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015GD, Rotterdam, the Netherlands
- Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015GD, Rotterdam, the Netherlands
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Sofia Pavanello
- Occupational Medicine, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, Padua University, Via Giustiniani 2, 35128, Padua, Italy
| | - Lucrezia Furian
- Kidney and Pancreas Transplantation Unit, Department of Surgical, Oncological and Gastroenterological Sciences, Padua University Hospital, Via Giustiniani 2, 35128, Padua, Italy
| | - Robert C Minnee
- Division of HPB and Transplant Surgery, Department of Surgery, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015GD, Rotterdam, the Netherlands
- Erasmus MC Transplant Institute, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, 3015GD, Rotterdam, the Netherlands
| |
Collapse
|
361
|
Bhattacharya A, Freedman AN, Avula V, Harris R, Liu W, Pan C, Lusis AJ, Joseph RM, Smeester L, Hartwell HJ, Kuban KCK, Marsit CJ, Li Y, O'Shea TM, Fry RC, Santos HP. Placental genomics mediates genetic associations with complex health traits and disease. Nat Commun 2022; 13:706. [PMID: 35121757 PMCID: PMC8817049 DOI: 10.1038/s41467-022-28365-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/15/2021] [Indexed: 01/09/2023] Open
Abstract
As the master regulator in utero, the placenta is core to the Developmental Origins of Health and Disease (DOHaD) hypothesis but is historically understudied. To identify placental gene-trait associations (GTAs) across the life course, we perform distal mediator-enriched transcriptome-wide association studies (TWAS) for 40 traits, integrating placental multi-omics from the Extremely Low Gestational Age Newborn Study. At [Formula: see text], we detect 248 GTAs, mostly for neonatal and metabolic traits, across 176 genes, enriched for cell growth and immunological pathways. In aggregate, genetic effects mediated by placental expression significantly explain 4 early-life traits but no later-in-life traits. 89 GTAs show significant mediation through distal genetic variants, identifying hypotheses for distal regulation of GTAs. Investigation of one hypothesis in human placenta-derived choriocarcinoma cells reveal that knockdown of mediator gene EPS15 upregulates predicted targets SPATA13 and FAM214A, both associated with waist-hip ratio in TWAS, and multiple genes involved in metabolic pathways. These results suggest profound health impacts of placental genomic regulation in developmental programming across the life course.
Collapse
Affiliation(s)
- Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
- Institute for Quantitative and Computational Biosciences, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
| | - Anastasia N Freedman
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Vennela Avula
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Rebeca Harris
- Biobehavioral Laboratory, School of Nursing, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Weifang Liu
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Calvin Pan
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Aldons J Lusis
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Robert M Joseph
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Lisa Smeester
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Hadley J Hartwell
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Karl C K Kuban
- Department of Pediatrics, Division of Pediatric Neurology, Boston University Medical Center, Boston, MA, 02118, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health Emory University, Atlanta, GA, 30322, USA
| | - Yun Li
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27514, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - T Michael O'Shea
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA.
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA.
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina, Chapel Hill, NC, 27514, USA.
| | - Hudson P Santos
- Biobehavioral Laboratory, School of Nursing, University of North Carolina, Chapel Hill, NC, 27514, USA.
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27514, USA.
| |
Collapse
|
362
|
Li L, Zhang H, Holloway JW, Ewart S, Relton CL, Arshad SH, Karmaus W. Does DNA methylation mediate the association of age at puberty with FVC or FEV1? ERJ Open Res 2022; 8:00476-2021. [PMID: 35237685 PMCID: PMC8883177 DOI: 10.1183/23120541.00476-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 12/30/2021] [Indexed: 11/05/2022] Open
Abstract
Background Age of pubertal onset is associated with lung function in adulthood. However, the underlying role of epigenetics as a mediator of this association remains unknown. Methods DNA methylation (DNAm) in peripheral blood was measured at age 18 years in the Isle of Wight birth cohort (IOWBC) along with data on age of pubertal events, forced vital capacity (FVC) and forced expiratory volume in 1 s (FEV1) at 26 years. Structural equation models were applied to examine mediation effects of DNAm on the association of age at pubertal events with FVC and FEV1. Findings were further tested in the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. Results In the IOWBC, for females, 21 cytosine-phosphate-guanine sites (CpGs) were shown to mediate the association of age at puberty with FVC or FEV1 at 26 years (p<0.05). In males, DNAm at 20 CpGs was found to mediate the association of age at puberty with FVC (p<0.05). At almost all these CpGs, indirect effects (effects of age at pubertal events on FVC or FEV1via DNAm) contributed a smaller portion to the total effects compared to direct effects (e.g. at cg08680129, ∼22% of the estimated total effect of age at menarche on FVC at age 26 was contributed by an indirect effect). Among the IOWBC-discovered CpGs available in ALSPAC, none of them was replicated in ALSPAC (p>0.05). Conclusions Our findings suggest that post-adolescence DNAm in peripheral blood is likely not to mediate the association of age at pubertal onset with young adulthood FVC or FEV1. The association between age at pubertal onset and lung function parameters FVC or FEV1 in young adulthood is not likely to be mediated by DNA methylation in peripheral bloodhttps://bit.ly/31G8hDi
Collapse
|
363
|
The WID-BC-index identifies women with primary poor prognostic breast cancer based on DNA methylation in cervical samples. Nat Commun 2022; 13:449. [PMID: 35105882 PMCID: PMC8807602 DOI: 10.1038/s41467-021-27918-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023] Open
Abstract
Genetic and non-genetic factors contribute to breast cancer development. An epigenome-based signature capturing these components in easily accessible samples could identify women at risk. Here, we analyse the DNA methylome in 2,818 cervical, 357 and 227 matched buccal and blood samples respectively, and 42 breast tissue samples from women with and without breast cancer. Utilising cervical liquid-based cytology samples, we develop the DNA methylation-based Women’s risk IDentification for Breast Cancer index (WID-BC-index) that identifies women with breast cancer with an AUROC (Area Under the Receiver Operator Characteristic) of 0.84 (95% CI: 0.80–0.88) and 0.81 (95% CI: 0.76–0.86) in internal and external validation sets, respectively. CpGs at progesterone receptor binding sites hypomethylated in normal breast tissue of women with breast cancer or in BRCA mutation carriers are also hypomethylated in cervical samples of women with poor prognostic breast cancer. Our data indicate that a systemic epigenetic programming defect is highly prevalent in women who develop breast cancer. Further studies validating the WID-BC-index may enable clinical implementation for monitoring breast cancer risk. Breast cancer is most commonly diagnosed via a needle biopsy. In this study, the authors show that cervical samples from women with breast cancer have a methylation signature different to that of healthy controls.
Collapse
|
364
|
Barrett JE, Jones A, Evans I, Reisel D, Herzog C, Chindera K, Kristiansen M, Leavy OC, Manchanda R, Bjørge L, Zikan M, Cibula D, Widschwendter M. The DNA methylome of cervical cells can predict the presence of ovarian cancer. Nat Commun 2022; 13:448. [PMID: 35105887 PMCID: PMC8807742 DOI: 10.1038/s41467-021-26615-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 10/04/2021] [Indexed: 02/03/2023] Open
Abstract
The vast majority of epithelial ovarian cancer arises from tissues that are embryologically derived from the Müllerian Duct. Here, we demonstrate that a DNA methylation signature in easy-to-access Müllerian Duct-derived cervical cells from women with and without ovarian cancer (i.e. referred to as the Women's risk IDentification for Ovarian Cancer index or WID-OC-index) is capable of identifying women with an ovarian cancer in the absence of tumour DNA with an AUC of 0.76 and women with an endometrial cancer with an AUC of 0.81. This and the observation that the cervical cell WID-OC-index mimics the epigenetic program of those cells at risk of becoming cancerous in BRCA1/2 germline mutation carriers (i.e. mammary epithelium, fallopian tube fimbriae, prostate) further suggest that the epigenetic misprogramming of cervical cells is an indicator for cancer predisposition. This concept has the potential to advance the field of risk-stratified cancer screening and prevention.
Collapse
Affiliation(s)
- James E Barrett
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, 6060, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Allison Jones
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Iona Evans
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Daniel Reisel
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Chiara Herzog
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, 6060, Hall in Tirol, Austria
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria
| | - Kantaraja Chindera
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK
| | - Mark Kristiansen
- UCL Genomics, Zayed Centre for Research into Rare Disease in Children, University College London, London, WC1N 1DZ, UK
| | - Olivia C Leavy
- Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
- Department of Non-communicable Disease Epidemiology, The London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Ranjit Manchanda
- Department of Gynaecological Oncology, Barts Health NHS Trust, Royal London Hospital, London, E1 1BB, UK
- Centre for Prevention, Detection & Diagnosis, Wolfson Institute of Population Health, Queen Mary University of London, London, EC1M 6BQ, UK
- Department of Health Services Research, The London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Line Bjørge
- Department of Obstetrics and Gynaecology, Haukeland University Hospital, Bergen, Norway
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Michal Zikan
- Hospital Na Bulovce, Prague, Czech Republic
- Department of Obstetrics and Gynecology, General University Hospital in Prague, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - David Cibula
- Department of Obstetrics and Gynecology, General University Hospital in Prague, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Martin Widschwendter
- European Translational Oncology Prevention and Screening (EUTOPS) Institute, 6060, Hall in Tirol, Austria.
- Research Institute for Biomedical Aging Research, Universität Innsbruck, 6020, Innsbruck, Austria.
- Department of Women's Cancer, UCL EGA Institute for Women's Health, University College London, 74 Huntley Street, London, WC1E 6AU, UK.
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
365
|
Kular L, Ewing E, Needhamsen M, Pahlevan Kakhki M, Covacu R, Gomez-Cabrero D, Brundin L, Jagodic M. DNA methylation changes in glial cells of the normal-appearing white matter in Multiple Sclerosis patients. Epigenetics 2022; 17:1311-1330. [PMID: 35094644 PMCID: PMC9586622 DOI: 10.1080/15592294.2021.2020436] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Multiple Sclerosis (MS), the leading cause of non-traumatic neurological disability in young adults, is a chronic inflammatory and neurodegenerative disease of the central nervous system (CNS). Due to the poor accessibility to the target organ, CNS-confined processes underpinning the later progressive form of MS remain elusive thereby limiting treatment options. We aimed to examine DNA methylation, a stable epigenetic mark of genome activity, in glial cells to capture relevant molecular changes underlying MS neuropathology. We profiled DNA methylation in nuclei of non-neuronal cells, isolated from 38 post-mortem normal-appearing white matter (NAWM) specimens of MS patients (n = 8) in comparison to white matter of control individuals (n = 14), using Infinium MethylationEPIC BeadChip. We identified 1,226 significant (genome-wide adjusted P-value < 0.05) differentially methylated positions (DMPs) between MS patients and controls. Functional annotation of the altered DMP-genes uncovered alterations of processes related to cellular motility, cytoskeleton dynamics, metabolic processes, synaptic support, neuroinflammation and signaling, such as Wnt and TGF-β pathways. A fraction of the affected genes displayed transcriptional differences in the brain of MS patients, as reported by publically available transcriptomic data. Cell type-restricted annotation of DMP-genes attributed alterations of cytoskeleton rearrangement and extracellular matrix remodelling to all glial cell types, while some processes, including ion transport, Wnt/TGF-β signaling and immune processes were more specifically linked to oligodendrocytes, astrocytes and microglial cells, respectively. Our findings strongly suggest that NAWM glial cells are highly altered, even in the absence of lesional insult, collectively exhibiting a multicellular reaction in response to diffuse inflammation.
Collapse
Affiliation(s)
- Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ewoud Ewing
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Majid Pahlevan Kakhki
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ruxandra Covacu
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - David Gomez-Cabrero
- Department of Medicine, Unit of Computational Medicine, Center for Molecular Medicine, Karolinska Institutet, Solna, Sweden
- Mucosal and Salivary Biology Division, King’s College London Dental Institute, London, UK
- Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (Chn), Universidad Pública de Navarra (Upna), IdiSNA, Pamplona, Spain
- Biological & Environmental Sciences & Engineering Division, King Abdullah University of Science & Technology, Thuwal, Kingdom of Saudi Arabia
| | - Lou Brundin
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
366
|
Rees WD, Telkar N, Lin DTS, Wong MQ, Poloni C, Fathi A, Kobor M, Zachos NC, Steiner TS. An in vitro chronic damage model impairs inflammatory and regenerative responses in human colonoid monolayers. Cell Rep 2022; 38:110283. [PMID: 35045294 DOI: 10.1016/j.celrep.2021.110283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/20/2021] [Accepted: 12/28/2021] [Indexed: 12/18/2022] Open
Abstract
Acute damage to the intestinal epithelium can be repaired via de-differentiation of mature intestinal epithelial cells (IECs) to a stem-like state, but there is a lack of knowledge on how intestinal stem cells function after chronic injury, such as in inflammatory bowel disease (IBD). We developed a chronic-injury model in human colonoid monolayers by repeated rounds of air-liquid interface and submerged culture. We use this model to understand how chronic intestinal damage affects the ability of IECs to (1) respond to microbial stimulation, using the Toll-like receptor 5 (TLR5) agonist FliC and (2) regenerate and protect the epithelium from further damage. Repeated rounds of damage impair the ability of IECs to regrow and respond to TLR stimulation. We also identify mRNA expression and DNA methylation changes in genes associated with IBD and colon cancer. This methodology results in a human model of recurrent IEC injury like that which occurs in IBD.
Collapse
Affiliation(s)
- William D Rees
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada; Division of Hematology, Department of Medicine, Stanford University, Palo Alto, CA, USA
| | - Nikita Telkar
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada; BC Cancer Agency, University of British Columbia, Vancouver, BC, Canada
| | - David T S Lin
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada
| | - May Q Wong
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada
| | - Chad Poloni
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada
| | - Ayda Fathi
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada
| | - Michael Kobor
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada
| | - Nicholas C Zachos
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Theodore S Steiner
- BC Children's Hospital Research Institute, University of British Columbia, Rm. C328 HP East, VGH, Vancouver, BC V5Z 3J5, Canada.
| |
Collapse
|
367
|
Levy MA, McConkey H, Kerkhof J, Barat-Houari M, Bargiacchi S, Biamino E, Bralo MP, Cappuccio G, Ciolfi A, Clarke A, DuPont BR, Elting MW, Faivre L, Fee T, Fletcher RS, Cherik F, Foroutan A, Friez MJ, Gervasini C, Haghshenas S, Hilton BA, Jenkins Z, Kaur S, Lewis S, Louie RJ, Maitz S, Milani D, Morgan AT, Oegema R, Østergaard E, Pallares NR, Piccione M, Pizzi S, Plomp AS, Poulton C, Reilly J, Relator R, Rius R, Robertson S, Rooney K, Rousseau J, Santen GWE, Santos-Simarro F, Schijns J, Squeo GM, St John M, Thauvin-Robinet C, Traficante G, van der Sluijs PJ, Vergano SA, Vos N, Walden KK, Azmanov D, Balci T, Banka S, Gecz J, Henneman P, Lee JA, Mannens MMAM, Roscioli T, Siu V, Amor DJ, Baynam G, Bend EG, Boycott K, Brunetti-Pierri N, Campeau PM, Christodoulou J, Dyment D, Esber N, Fahrner JA, Fleming MD, Genevieve D, Kerrnohan KD, McNeill A, Menke LA, Merla G, Prontera P, Rockman-Greenberg C, Schwartz C, Skinner SA, Stevenson RE, Vitobello A, Tartaglia M, Alders M, Tedder ML, Sadikovic B. Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders. HGG ADVANCES 2022; 3:100075. [PMID: 35047860 PMCID: PMC8756545 DOI: 10.1016/j.xhgg.2021.100075] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023] Open
Abstract
Overlapping clinical phenotypes and an expanding breadth and complexity of genomic associations are a growing challenge in the diagnosis and clinical management of Mendelian disorders. The functional consequences and clinical impacts of genomic variation may involve unique, disorder-specific, genomic DNA methylation episignatures. In this study, we describe 19 novel episignature disorders and compare the findings alongside 38 previously established episignatures for a total of 57 episignatures associated with 65 genetic syndromes. We demonstrate increasing resolution and specificity ranging from protein complex, gene, sub-gene, protein domain, and even single nucleotide-level Mendelian episignatures. We show the power of multiclass modeling to develop highly accurate and disease-specific diagnostic classifiers. This study significantly expands the number and spectrum of disorders with detectable DNA methylation episignatures, improves the clinical diagnostic capabilities through the resolution of unsolved cases and the reclassification of variants of unknown clinical significance, and provides further insight into the molecular etiology of Mendelian conditions.
Collapse
Affiliation(s)
- Michael A Levy
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Mouna Barat-Houari
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Sara Bargiacchi
- Medical Genetics Unit, "A. Meyer" Children's Hospital of Florence, Florence, Italy
| | - Elisa Biamino
- Department of Pediatrics, University of Turin, Turin, Italy
| | - María Palomares Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Gerarda Cappuccio
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Angus Clarke
- Cardiff University School of Medicine, Cardiff, UK
| | | | - Mariet W Elting
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Laurence Faivre
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Timothy Fee
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | | | - Florian Cherik
- Genetic medical center, CHU Clermont Ferrand, France.,Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | | | - Cristina Gervasini
- Division of Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | | | - Zandra Jenkins
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Suzanne Lewis
- BC Children's and Women's Hospital and Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | | | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Donatella Milani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela T Morgan
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Nathalie Ruiz Pallares
- Autoinflammatory and Rare Diseases Unit, Medical Genetic Department for Rare Diseases and Personalized Medicine, CHU Montpellier, Montpellier, France
| | - Maria Piccione
- Medical Genetics Unit Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Simone Pizzi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Astrid S Plomp
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia
| | - Jack Reilly
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Rocio Rius
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Stephen Robertson
- Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Justine Rousseau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Gijs W E Santen
- Department of Clinical Genetics, LUMC, Leiden, the Netherlands
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Josephine Schijns
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Gabriella Maria Squeo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Miya St John
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Christel Thauvin-Robinet
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France.,Centre de Référence Déficiences Intellectuelles de Causes Rares, Hôpital D'Enfants, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Giovanna Traficante
- Medical Genetics Unit, "A. Meyer" Children's Hospital of Florence, Florence, Italy
| | | | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, VA, USA.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Niels Vos
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, Amsterdam, the Netherlands
| | | | - Dimitar Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Perth, Australia
| | - Tugce Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5W9, Canada
| | - Siddharth Banka
- Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.,Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Jozef Gecz
- School of Medicine, Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA 5005, Australia
| | - Peter Henneman
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | | | - Marcel M A M Mannens
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, Australia.,Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia.,New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, Australia
| | - Victoria Siu
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A 3K7, Canada.,Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5W9, Canada
| | - David J Amor
- Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Undiagnosed Diseases Program, Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Australia.,Division of Paediatrics and Telethon Kids Institute, Faculty of Health and Medical Sciences, Perth, Australia
| | | | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - David Dyment
- Children's Hospital of Eastern Ontario, Ottawa, Canada
| | | | - Jill A Fahrner
- Departments of Genetic Medicine and Pediatrics, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mark D Fleming
- Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - David Genevieve
- Montpellier University, Reference Center for Rare Disease, Medical Genetic Department for Rare Disease and Personalize Medicine, Inserm Unit 1183, CHU Montpellier, Montpellier, France
| | - Kristin D Kerrnohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Alisdair McNeill
- Department of Neuroscience, University of Sheffield, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy.,Laboratory of Regulatory and Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Paolo Prontera
- Medical Genetics Unit, University of Perugia Hospital SM della Misericordia, Perugia, Italy
| | - Cheryl Rockman-Greenberg
- Department of Pediatrics and Child Health, Rady Faculty of Health Sciences, University of Manitoba and Program in Genetics and Metabolism, Shared Health MB, Winnipeg, MB, Canada
| | | | | | | | - Antonio Vitobello
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France.,Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marielle Alders
- Amsterdam UMC, University of Amsterdam, Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre; London Health Sciences Centre, London, ON N6A 5W9, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| |
Collapse
|
368
|
Paweł K, Maria Małgorzata S. CpG Island Methylator Phenotype-A Hope for the Future or a Road to Nowhere? Int J Mol Sci 2022; 23:ijms23020830. [PMID: 35055016 PMCID: PMC8777692 DOI: 10.3390/ijms23020830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 02/06/2023] Open
Abstract
The CpG island methylator phenotype (CIMP) can be regarded as the most notable emanation of epigenetic instability in cancer. Since its discovery in the late 1990s, CIMP has been extensively studied, mainly in colorectal cancers (CRC) and gliomas. Consequently, knowledge on molecular and pathological characteristics of CIMP in CRC and other tumour types has rapidly expanded. Concordant and widespread hypermethylation of multiple CpG islands observed in CIMP in multiple cancers raised hopes for future epigenetically based diagnostics and treatments of solid tumours. However, studies on CIMP in solid tumours were hampered by a lack of generalisability and reproducibility of epigenetic markers. Moreover, CIMP was not a satisfactory marker in predicting clinical outcomes. The idea of targeting epigenetic abnormalities such as CIMP for cancer therapy has not been implemented for solid tumours, either. Twenty-one years after its discovery, we aim to cover both the fundamental and new aspects of CIMP and its future application as a diagnostic marker and target in anticancer therapies.
Collapse
|
369
|
Assessment of the Molecular Heterogeneity of E-Cadherin Expression in Invasive Lobular Breast Cancer. Cancers (Basel) 2022; 14:cancers14020295. [PMID: 35053458 PMCID: PMC8773871 DOI: 10.3390/cancers14020295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/16/2021] [Accepted: 12/23/2021] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Invasive lobular breast cancers (ILCs) are histologically classified by their discohesive growth pattern, due to loss of the cell adhesion glycoprotein E-cadherin (CDH1), which arises via mutation in CDH1 in around half of these tumours. A subset of these tumours, however, show mixed levels of E-cadherin expression. Here, we sought to address whether the distinct parts of individual tumours showing heterogeneous E-cadherin expression harbour distinct driver alterations. Using whole genome sequencing and methylation profiling of nine such cases, we identified that these tumours are clonally related, suggesting that they are part of the spectrum of ILC tumours. CDH1 mutant tumours showed a higher mutational burden indicative of APOBEC-mediated mutagenesis. In some cases, known clinically actionable driver mutations, such as PIK3CA, were exclusive to one component. Together, these results highlight the heterogeneity underpinning this special histological breast cancer. Abstract Mutations and loss of E-cadherin protein expression define the vast majority of invasive lobular carcinomas. In a subset of these cases, the heterogeneous expression of E-cadherin is observed either as wild-type (strong membranous) expression or aberrant expression (cytoplasmic expression). However, it is unclear as to whether the two components would be driven by distinct genetic or epigenetic alterations. Here, we used whole genome DNA sequencing and methylation array profiling of two separately dissected components of nine invasive lobular carcinomas with heterogeneous E-cadherin expression. E-cadherin negative and aberrant/positive components of E-cadherin heterogeneous tumours showed a similar mutational, copy number and promoter methylation repertoire, suggesting they arise from a common ancestor, as opposed to the collision of two independent tumours. We found that the majority of E-cadherin heterogeneous tumours harboured CDH1 mutations in both the E-cadherin negative and aberrant/positive components together with somatic mutations in additional driver genes known to be enriched in both pure invasive carcinomas of no special type and invasive lobular breast cancers, whereas these were less commonly observed in CDH1 wild-type tumours. CDH1 mutant tumours also exhibited a higher mutation burden as well as increased presence of APOBEC-dependent mutational signatures 2 and 13 compared to CDH1 wild-type tumours. Together, our results suggest that regardless of E-cadherin protein expression, tumours showing heterogeneous expression of E-cadherin should be considered as part of the spectrum of invasive lobular breast cancers.
Collapse
|
370
|
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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
371
|
Wang WJ, Huang R, Zheng T, Du Q, Yang MN, Xu YJ, Liu X, Tao MY, He H, Fang F, Li F, Fan JG, Zhang J, Briollais L, Ouyang F, Luo ZC. Genome-Wide Placental Gene Methylations in Gestational Diabetes Mellitus, Fetal Growth and Metabolic Health Biomarkers in Cord Blood. Front Endocrinol (Lausanne) 2022; 13:875180. [PMID: 35721735 PMCID: PMC9204344 DOI: 10.3389/fendo.2022.875180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/21/2022] [Indexed: 12/03/2022] Open
Abstract
Gestational diabetes mellitus (GDM) "program" an elevated risk of metabolic syndrome in the offspring. Epigenetic alterations are a suspected mechanism. GDM has been associated with placental DNA methylation changes in some epigenome-wide association studies. It remains unclear which genes or pathways are affected, and whether any placental differential gene methylations are correlated to fetal growth or circulating metabolic health biomarkers. In an epigenome-wide association study using the Infinium MethylationEPIC Beadchip, we sought to identify genome-wide placental differentially methylated genes and enriched pathways in GDM, and to assess the correlations with fetal growth and metabolic health biomarkers in cord blood. The study samples were 30 pairs of term placentas in GDM vs. euglycemic pregnancies (controls) matched by infant sex and gestational age at delivery in the Shanghai Birth Cohort. Cord blood metabolic health biomarkers included insulin, C-peptide, proinsulin, IGF-I, IGF-II, leptin and adiponectin. Adjusting for maternal age, pre-pregnancy BMI, parity, mode of delivery and placental cell type heterogeneity, 256 differentially methylated positions (DMPs,130 hypermethylated and 126 hypomethylated) were detected between GDM and control groups accounting for multiple tests with false discovery rate <0.05 and beta-value difference >0.05. WSCD2 was identified as a differentially methylated gene in both site- and region-level analyses. We validated 7 hypermethylated (CYP1A2, GFRA1, HDAC4, LIMS2, NAV3, PAX6, UPK1B) and 10 hypomethylated (DPP10, CPLX1, CSMD2, GPR133, NRXN1, PCSK9, PENK, PRDM16, PTPRN2, TNXB) genes reported in previous epigenome-wide association studies. We did not find any enriched pathway accounting for multiple tests. DMPs in 11 genes (CYP2D7P1, PCDHB15, ERG, SIRPB1, DKK2, RAPGEF5, CACNA2D4, PCSK9, TSNARE1, CADM2, KCNAB2) were correlated with birth weight (z score) accounting for multiple tests. There were no significant correlations between placental gene methylations and cord blood biomarkers. In conclusions, GDM was associated with DNA methylation changes in a number of placental genes, but these placental gene methylations were uncorrelated to the observed metabolic health biomarkers (fetal growth factors, leptin and adiponectin) in cord blood. We validated 17 differentially methylated placental genes in GDM, and identified 11 differentially methylated genes relevant to fetal growth.
Collapse
Affiliation(s)
- Wen-Juan Wang
- Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, and Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
- Lunenfeld-Tanenbaum Research Institute, Prosserman Centre for Population Health Research, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Clinical Skills Center, School of Clinical Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Rong Huang
- Lunenfeld-Tanenbaum Research Institute, Prosserman Centre for Population Health Research, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Tao Zheng
- Department of Obstetrics and Gynecology, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Qinwen Du
- Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, and Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meng-Nan Yang
- Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, and Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Ya-Jie Xu
- Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, and Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Xin Liu
- Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, and Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Min-Yi Tao
- Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, and Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Hua He
- Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, and Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Fang Fang
- Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, and Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Fei Li
- Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, and Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Jian-Gao Fan
- Center for Fatty Liver, Shanghai Key Lab of Pediatric Gastroenterology and Nutrition, Department of Gastroenterology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Zhang
- Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, and Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
| | - Laurent Briollais
- Lunenfeld-Tanenbaum Research Institute, Prosserman Centre for Population Health Research, Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Fengxiu Ouyang
- Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, and Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
- *Correspondence: Zhong-Cheng Luo, ; Fengxiu Ouyang,
| | - Zhong-Cheng Luo
- Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Early Life Health Institute, and Department of Pediatrics, Xinhua Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai, China
- Lunenfeld-Tanenbaum Research Institute, Prosserman Centre for Population Health Research, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- *Correspondence: Zhong-Cheng Luo, ; Fengxiu Ouyang,
| |
Collapse
|
372
|
Williams LA, LaSalle JM. Future Prospects for Epigenetics in Autism Spectrum Disorder. Mol Diagn Ther 2022; 26:569-579. [PMID: 35962910 PMCID: PMC9626414 DOI: 10.1007/s40291-022-00608-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2022] [Indexed: 12/30/2022]
Abstract
Despite decades of investigation into the genetics of autism spectrum disorder (ASD), a current consensus in the field persists that ASD risk is too heterogeneous to be diagnosed by a single set of genetic variants. As such, ASD research has broadened to include assessment of other molecular biomarkers implicated in the condition that may be reflective of environmental exposures or gene by environment interactions. Epigenetic variance, and specifically differential DNA methylation, have emerged as areas of particularly high interest to ASD, as the epigenetic markers from specific chromatin loci collectively can reflect influences of multiple genetic and environmental factors and can also result in differential gene expression patterns. This review examines recent studies of the ASD epigenome, detailing common gene pathways found to be differentially methylated in people with ASD, and considers how these discoveries may inform our understanding of ASD etiology. We also consider future applications of epigenetics in ASD research and clinical practice, focusing on substratification, biomarker development, and experimental preclinical models of ASD that test causality. In combination with other -omics approaches, epigenomics allows an improved conceptualization of the multifactorial nature of ASD, and opens future lines of inquiry for both basic research and clinical practice.
Collapse
Affiliation(s)
- Logan A. Williams
- grid.27860.3b0000 0004 1936 9684Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Perinatal Origins of Disparities Center, University of California Davis, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684MIND Institute, University of California Davis, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Genome Center, University of California Davis, Davis, CA USA
| | - Janine M. LaSalle
- grid.27860.3b0000 0004 1936 9684Department of Medical Microbiology and Immunology, University of California Davis School of Medicine, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Perinatal Origins of Disparities Center, University of California Davis, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684MIND Institute, University of California Davis, Davis, CA USA ,grid.27860.3b0000 0004 1936 9684Genome Center, University of California Davis, Davis, CA USA
| |
Collapse
|
373
|
Zhang Z, Zeng C, Zhang W. Characterization of the Illumina EPIC Array for Optimal Applications in Epigenetic Research Targeting Diverse Human Populations. EPIGENETICS COMMUNICATIONS 2022; 2:7. [PMCID: PMC9718568 DOI: 10.1186/s43682-022-00015-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The Illumina EPIC array is widely used for high-throughput profiling of DNA cytosine modifications in human samples, covering more than 850,000 modification sites across various genomic features. The application of this platform is expected to provide novel insights into the epigenetic contribution to human complex traits and diseases. Considering the diverse inter-population genetic and epigenetic variation, it will benefit the research community with a comprehensive characterization of this platform for its applicability to major global populations. Specifically, we mapped 866,836 CpG probes from the EPIC array to the human genome reference. We detected 91,034 CpG probes that did not align reliably to the human genome reference. In addition, 21,256 CpG probes were found to ambiguously map to multiple loci in the human genome, and 448 probes showing inaccurate genomic information from the original Illumina annotations. We further characterized those uniquely mapped CpG probes in terms of whether they contained common genetic variants, i.e., single nucleotide polymorphisms (SNPs), in major global populations, by utilizing the 1000 Genomes Project data. A list of optimal CpG probes on the EPIC array was generated for major global populations, with the aim of providing a resource to facilitate future studies of diverse human populations. In conclusion, our analysis indicated that studies of diverse human populations using the EPIC array would be benefited by taking into account of the technical features of this platform.
Collapse
Affiliation(s)
- Zhou Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Chang Zeng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| | - Wei Zhang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA.,The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| |
Collapse
|
374
|
Cunningham JM, Winham SJ, Wang C, Weiglt B, Fu Z, Armasu SM, McCauley BM, Brand AH, Chiew YE, Elishaev E, Gourley C, Kennedy CJ, Laslavic A, Lester J, Piskorz A, Sekowska M, Brenton JD, Churchman M, DeFazio A, Drapkin R, Elias KM, Huntsman DG, Karlan BY, Köbel M, Konner J, Lawrenson K, Papaemmanuil E, Bolton KL, Modugno F, Goode EL. DNA Methylation Profiles of Ovarian Clear Cell Carcinoma. Cancer Epidemiol Biomarkers Prev 2022; 31:132-141. [PMID: 34697060 PMCID: PMC8755592 DOI: 10.1158/1055-9965.epi-21-0677] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/18/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Ovarian clear cell carcinoma (OCCC) is a rare ovarian cancer histotype that tends to be resistant to standard platinum-based chemotherapeutics. We sought to better understand the role of DNA methylation in clinical and biological subclassification of OCCC. METHODS We interrogated genome-wide methylation using DNA from fresh frozen tumors from 271 cases, applied nonsmooth nonnegative matrix factorization (nsNMF) clustering, and evaluated clinical associations and biological pathways. RESULTS Two approximately equally sized clusters that associated with several clinical features were identified. Compared with Cluster 2 (N = 137), Cluster 1 cases (N = 134) presented at a more advanced stage, were less likely to be of Asian ancestry, and tended to have poorer outcomes including macroscopic residual disease following primary debulking surgery (P < 0.10). Subset analyses of targeted tumor sequencing and IHC data revealed that Cluster 1 tumors showed TP53 mutation and abnormal p53 expression, and Cluster 2 tumors showed aneuploidy and ARID1A/PIK3CA mutation (P < 0.05). Cluster-defining CpGs included 1,388 CpGs residing within 200 bp of the transcription start sites of 977 genes; 38% of these genes (N = 369 genes) were differentially expressed across cluster in transcriptomic subset analysis (P < 10-4). Differentially expressed genes were enriched for six immune-related pathways, including IFNα and IFNγ responses (P < 10-6). CONCLUSIONS DNA methylation clusters in OCCC correlate with disease features and gene expression patterns among immune pathways. IMPACT This work serves as a foundation for integrative analyses that better understand the complex biology of OCCC in an effort to improve potential for development of targeted therapeutics.
Collapse
Affiliation(s)
- Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
| | - Stacey J Winham
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Chen Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Britta Weiglt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zhuxuan Fu
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | - Sebastian M Armasu
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Bryan M McCauley
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Alison H Brand
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- University of Sydney, Sydney, New South Wales, Australia
| | - Yoke-Eng Chiew
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Esther Elishaev
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Catherine J Kennedy
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Angela Laslavic
- Womens Cancer Research Center, Magee-Womens Research Institute and Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Jenny Lester
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, California
| | - Anna Piskorz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Magdalena Sekowska
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Michael Churchman
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Anna DeFazio
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- University of Sydney, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | - David G Huntsman
- British Columbia's Ovarian Cancer Research (OVCARE) Program, BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Beth Y Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, California
| | - Martin Köbel
- Department of Laboratory and Pathology Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jason Konner
- Weill Cornell Medical College of Cornell University, New York, New York
- Department of Medicine, Washington University, St. Louis, Missouri
| | - Kate Lawrenson
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Women's Cancer Program at the Samuel Oschin Cancer Institute Cedars-Sinai Medical Center, Los Angeles, California
| | - Elli Papaemmanuil
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kelly L Bolton
- Department of Medicine, Washington University, St. Louis, Missouri
| | - Francesmary Modugno
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
- Womens Cancer Research Center, Magee-Womens Research Institute and Hillman Cancer Center, Pittsburgh, Pennsylvania
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Ellen L Goode
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| |
Collapse
|
375
|
Edgar RD, Perrone F, Foster AR, Payne F, Lewis S, Nayak KM, Kraiczy J, Cenier A, Torrente F, Salvestrini C, Heuschkel R, Hensel KO, Harris R, Jones DL, Zerbino DR, Zilbauer M. Culture-Associated DNA Methylation Changes Impact on Cellular Function of Human Intestinal Organoids. Cell Mol Gastroenterol Hepatol 2022; 14:1295-1310. [PMID: 36038072 PMCID: PMC9703134 DOI: 10.1016/j.jcmgh.2022.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND & AIMS Human intestinal epithelial organoids (IEOs) are a powerful tool to model major aspects of intestinal development, health, and diseases because patient-derived cultures retain many features found in vivo. A necessary aspect of the organoid model is the requirement to expand cultures in vitro through several rounds of passaging. This is of concern because the passaging of cells has been shown to affect cell morphology, ploidy, and function. METHODS Here, we analyzed 173 human IEO lines derived from the small and large bowel and examined the effect of culture duration on DNA methylation (DNAm). Furthermore, we tested the potential impact of DNAm changes on gene expression and cellular function. RESULTS Our analyses show a reproducible effect of culture duration on DNAm in a large discovery cohort as well as 2 publicly available validation cohorts generated in different laboratories. Although methylation changes were seen in only approximately 8% of tested cytosine-phosphate-guanine dinucleotides (CpGs) and global cellular function remained stable, a subset of methylation changes correlated with altered gene expression at baseline as well as in response to inflammatory cytokine exposure and withdrawal of Wnt agonists. Importantly, epigenetic changes were found to be enriched in genomic regions associated with colonic cancer and distant to the site of replication, indicating similarities to malignant transformation. CONCLUSIONS Our study shows distinct culture-associated epigenetic changes in mucosa-derived human IEOs, some of which appear to impact gene transcriptomic and cellular function. These findings highlight the need for future studies in this area and the importance of considering passage number as a potentially confounding factor.
Collapse
Affiliation(s)
- Rachel D Edgar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Francesca Perrone
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - April R Foster
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Centre for Pathway Analysis, Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
| | - Felicity Payne
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Sophia Lewis
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California; Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, California
| | - Komal M Nayak
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Judith Kraiczy
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Aurélie Cenier
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Franco Torrente
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Camilla Salvestrini
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Robert Heuschkel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Kai O Hensel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom; Witten/Herdecke University, Department of Paediatrics, Helios Medical Centre Wuppertal, Children's Hospital, Wuppertal, Germany
| | - Rebecca Harris
- Centre for Pathway Analysis, Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
| | - D Leanne Jones
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California; Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, California; Department of Anatomy and Medicine, Division of Geriatrics, University of California, San Francisco, San Francisco, California; Eli and Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, California
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.
| |
Collapse
|
376
|
Bhat B, Jones GT. Data Analysis of DNA Methylation Epigenome-Wide Association Studies (EWAS): A Guide to the Principles of Best Practice. Methods Mol Biol 2022; 2458:23-45. [PMID: 35103960 DOI: 10.1007/978-1-0716-2140-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Array-based EWAS have become an increasingly popular technique to identify population epigenetic effects, particularly in humans. With the arrival of nonhuman species arrays, such as the mouse, this is likely to become an even more widely used technology. This chapter provides the less experienced researcher a guide to the analysis of data from the most widely used platform, the Illumina Infinium Methylation assay. This includes an overview of quality filtering, data normalization, analysis options, and techniques to improve the interpretation of results.
Collapse
Affiliation(s)
- Basharat Bhat
- Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Gregory T Jones
- Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
| |
Collapse
|
377
|
Park J, Lee Y, Won CW. CEND1 and MIR885 methylation changes associated with successful cognitive aging in community-dwelling older adults. Exp Gerontol 2022; 160:111704. [DOI: 10.1016/j.exger.2022.111704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/14/2021] [Accepted: 01/11/2022] [Indexed: 11/26/2022]
|
378
|
Borinskaya SA, Rubanovich AV, Larin AK, Kazantseva AV, Davydova YD, Generozov EV, Khusnutdinova EK, Yankovsky NK. Epigenome-Wide Association Study of CpG Methylation in Aggressive Behavior. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421120048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
379
|
Shanthikumar S, Neeland MR, Saffery R, Ranganathan SC, Oshlack A, Maksimovic J. DNA Methylation Profiles of Purified Cell Types in Bronchoalveolar Lavage: Applications for Mixed Cell Paediatric Pulmonary Studies. Front Immunol 2021; 12:788705. [PMID: 35003108 PMCID: PMC8727592 DOI: 10.3389/fimmu.2021.788705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 12/03/2021] [Indexed: 01/15/2023] Open
Abstract
In epigenome-wide association studies analysing DNA methylation from samples containing multiple cell types, it is essential to adjust the analysis for cell type composition. One well established strategy for achieving this is reference-based cell type deconvolution, which relies on knowledge of the DNA methylation profiles of purified constituent cell types. These are then used to estimate the cell type proportions of each sample, which can then be incorporated to adjust the association analysis. Bronchoalveolar lavage is commonly used to sample the lung in clinical practice and contains a mixture of different cell types that can vary in proportion across samples, affecting the overall methylation profile. A current barrier to the use of bronchoalveolar lavage in DNA methylation-based research is the lack of reference DNA methylation profiles for each of the constituent cell types, thus making reference-based cell composition estimation difficult. Herein, we use bronchoalveolar lavage samples collected from children with cystic fibrosis to define DNA methylation profiles for the four most common and clinically relevant cell types: alveolar macrophages, granulocytes, lymphocytes and alveolar epithelial cells. We then demonstrate the use of these methylation profiles in conjunction with an established reference-based methylation deconvolution method to estimate the cell type composition of two different tissue types; a publicly available dataset derived from artificial blood-based cell mixtures and further bronchoalveolar lavage samples. The reference DNA methylation profiles developed in this work can be used for future reference-based cell type composition estimation of bronchoalveolar lavage. This will facilitate the use of this tissue in studies examining the role of DNA methylation in lung health and disease.
Collapse
Affiliation(s)
- Shivanthan Shanthikumar
- Respiratory and Sleep Medicine, Royal Children’s Hospital, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Respiratory Diseases, Murdoch Children’s Research Institute, Parkville, VIC, Australia
- *Correspondence: Shivanthan Shanthikumar,
| | - Melanie R. Neeland
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Molecular Immunity, Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Richard Saffery
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Molecular Immunity, Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Sarath C. Ranganathan
- Respiratory and Sleep Medicine, Royal Children’s Hospital, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Respiratory Diseases, Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Alicia Oshlack
- Computational Biology Program, Peter MacCallum Cancer Centre, Parkville, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- School of BioScience, University of Melbourne, Parkville, VIC, Australia
| | - Jovana Maksimovic
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Respiratory Diseases, Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Computational Biology Program, Peter MacCallum Cancer Centre, Parkville, VIC, Australia
| |
Collapse
|
380
|
Murgas KA, Ma Y, Shahidi LK, Mukherjee S, Allen AS, Shibata D, Ryser MD. A Bayesian hierarchical model to estimate DNA methylation conservation in colorectal tumors. Bioinformatics 2021; 38:22-29. [PMID: 34487148 DOI: 10.1093/bioinformatics/btab637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 07/30/2021] [Accepted: 09/01/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Conservation is broadly used to identify biologically important (epi)genomic regions. In the case of tumor growth, preferential conservation of DNA methylation can be used to identify areas of particular functional importance to the tumor. However, reliable assessment of methylation conservation based on multiple tissue samples per patient requires the decomposition of methylation variation at multiple levels. RESULTS We developed a Bayesian hierarchical model that allows for variance decomposition of methylation on three levels: between-patient normal tissue variation, between-patient tumor-effect variation and within-patient tumor variation. We then defined a model-based conservation score to identify loci of reduced within-tumor methylation variation relative to between-patient variation. We fit the model to multi-sample methylation array data from 21 colorectal cancer (CRC) patients using a Monte Carlo Markov Chain algorithm (Stan). Sets of genes implicated in CRC tumorigenesis exhibited preferential conservation, demonstrating the model's ability to identify functionally relevant genes based on methylation conservation. A pathway analysis of preferentially conserved genes implicated several CRC relevant pathways and pathways related to neoantigen presentation and immune evasion. Our findings suggest that preferential methylation conservation may be used to identify novel gene targets that are not consistently mutated in CRC. The flexible structure makes the model amenable to the analysis of more complex multi-sample data structures. AVAILABILITY AND IMPLEMENTATION The data underlying this article are available in the NCBI GEO Database, under accession code GSE166212. The R analysis code is available at https://github.com/kevin-murgas/DNAmethylation-hierarchicalmodel. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Kevin A Murgas
- Department of Biomedical Informatics, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA
| | - Yanlin Ma
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Lidea K Shahidi
- Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - Sayan Mukherjee
- Department of Statistical Science, Duke University, Durham, NC 27708, USA
- Department of Computer Science, Duke University, Durham, NC 27708, USA
- Department of Mathematics, Duke University, Durham, NC 27708, USA
- Department of Bioinformatics and Biostatistics, Duke University, Durham, NC 27710, USA
| | - Andrew S Allen
- Department of Bioinformatics and Biostatistics, Duke University, Durham, NC 27710, USA
- Duke Center for Statistical Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Darryl Shibata
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Marc D Ryser
- Department of Mathematics, Duke University, Durham, NC 27708, USA
- Department of Population Health Sciences, Duke University Medical Center, Durham, NC 27701, USA
| |
Collapse
|
381
|
Harville EW, Mishra PP, Kähönen M, Raitoharju E, Marttila S, Raitakari O, Lehtimäki T. Reproductive history and blood cell DNA methylation later in life: the Young Finns Study. Clin Epigenetics 2021; 13:227. [PMID: 34930449 PMCID: PMC8690999 DOI: 10.1186/s13148-021-01215-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/09/2021] [Indexed: 01/16/2023] Open
Abstract
Background Women with a history of complications of pregnancy, including hypertensive disorders, gestational diabetes or an infant fetal growth restriction or preterm birth, are at higher risk for cardiovascular disease later in life. We aimed to examine differences in maternal DNA methylation following pregnancy complications. Methods Data on women participating in the Young Finns study (n = 836) were linked to the national birth registry. DNA methylation in whole blood was assessed using the Infinium Methylation EPIC BeadChip. Epigenome-wide analysis was conducted on differential CpG methylation at 850 K sites. Reproductive history was also modeled as a predictor of four epigenetic age indices. Results Fourteen significant differentially methylated sites were found associated with both history of pre-eclampsia and overall hypertensive disorders of pregnancy. No associations were found between reproductive history and any epigenetic age acceleration measure. Conclusions Differences in epigenetic methylation profiles could represent pre-existing risk factors, or changes that occurred as a result of experiencing these complications. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01215-1.
Collapse
Affiliation(s)
- Emily W Harville
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA. .,Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland.
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland.,Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, 33521, Tampere, Finland.,Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, 33521, Tampere, Finland
| | - Emma Raitoharju
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland.,Department of Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Saara Marttila
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland.,Department of Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Gerontology Research Center, Tampere University, Tampere, Finland
| | - Olli Raitakari
- Research Center of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland.,Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, 33521, Tampere, Finland.,Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| |
Collapse
|
382
|
Meyer B, Clifton S, Locke W, Luu PL, Du Q, Lam D, Armstrong NJ, Kumar B, Deng N, Harvey K, Swarbrick A, Ganju V, Clark SJ, Pidsley R, Stirzaker C. Identification of DNA methylation biomarkers with potential to predict response to neoadjuvant chemotherapy in triple-negative breast cancer. Clin Epigenetics 2021; 13:226. [PMID: 34922619 PMCID: PMC8684655 DOI: 10.1186/s13148-021-01210-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/07/2021] [Indexed: 12/31/2022] Open
Abstract
Neoadjuvant chemotherapy (NAC) is used to treat triple-negative breast cancer (TNBC) prior to resection. Biomarkers that accurately predict a patient's response to NAC are needed to individualise therapy and avoid chemotoxicity from unnecessary chemotherapy. We performed whole-genome DNA methylation profiling on diagnostic TNBC biopsy samples from the Sequential Evaluation of Tumours Undergoing Preoperative (SETUP) NAC study. We found 9 significantly differentially methylated regions (DMRs) at diagnosis which were associated with response to NAC. We show that 4 of these DMRs are associated with TNBC overall survival (P < 0.05). Our results highlight the potential of DNA methylation biomarkers for predicting NAC response in TNBC.
Collapse
Affiliation(s)
- Braydon Meyer
- Epigenetics Research Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia
| | - Samuel Clifton
- Epigenetics Research Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia
| | - Warwick Locke
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, New South Wales, North Ryde, 2113 Australia
| | - Phuc-Loi Luu
- Epigenetics Research Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia
- St. Vincent’s Clinical School, UNSW Australia, Sydney, NSW 2010 Australia
| | - Qian Du
- Epigenetics Research Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia
- St. Vincent’s Clinical School, UNSW Australia, Sydney, NSW 2010 Australia
| | - Dilys Lam
- Epigenetics Research Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia
| | - Nicola J. Armstrong
- Department of Mathematics and Statistics, Curtin University, Perth, WA 6103 Australia
| | - Beena Kumar
- Hudson Institute of Medical Research, Clayton, VIC 3168 Australia
- Monash Health Pathology, Monash Health, Victoria, 3168 Australia
- Monash University, Melbourne, VIC 3168 Australia
| | - Niantao Deng
- St. Vincent’s Clinical School, UNSW Australia, Sydney, NSW 2010 Australia
- Cancer Research Theme, Garvan Institute of Medical Research, Sydney, NSW 2010 Australia
| | - Kate Harvey
- Cancer Research Theme, Garvan Institute of Medical Research, Sydney, NSW 2010 Australia
| | - Alex Swarbrick
- St. Vincent’s Clinical School, UNSW Australia, Sydney, NSW 2010 Australia
- Cancer Research Theme, Garvan Institute of Medical Research, Sydney, NSW 2010 Australia
| | - Vinod Ganju
- Hudson Institute of Medical Research, Clayton, VIC 3168 Australia
| | - Susan J. Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia
- St. Vincent’s Clinical School, UNSW Australia, Sydney, NSW 2010 Australia
| | - Ruth Pidsley
- Epigenetics Research Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia
- St. Vincent’s Clinical School, UNSW Australia, Sydney, NSW 2010 Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics and Epigenetics Theme, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010 Australia
- St. Vincent’s Clinical School, UNSW Australia, Sydney, NSW 2010 Australia
| |
Collapse
|
383
|
Nwanaji-Enwerem JC, Chung FFL, Van der Laan L, Novoloaca A, Cuenin C, Johansson H, Bonanni B, Hubbard AE, Smith MT, Hartman SJ, Cardenas A, Sears DD, Herceg Z. An epigenetic aging analysis of randomized metformin and weight loss interventions in overweight postmenopausal breast cancer survivors. Clin Epigenetics 2021; 13:224. [PMID: 34920739 PMCID: PMC8684118 DOI: 10.1186/s13148-021-01218-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 12/13/2021] [Indexed: 11/10/2022] Open
Abstract
Metformin and weight loss relationships with epigenetic age measures-biological aging biomarkers-remain understudied. We performed a post-hoc analysis of a randomized controlled trial among overweight/obese breast cancer survivors (N = 192) assigned to metformin, placebo, weight loss with metformin, or weight loss with placebo interventions for 6 months. Epigenetic age was correlated with chronological age (r = 0.20-0.86; P < 0.005). However, no significant epigenetic aging associations were observed by intervention arms. Consistent with published reports in non-cancer patients, 6 months of metformin therapy may be inadequate to observe expected epigenetic age deceleration. Longer duration studies are needed to better characterize these relationships.Trial Registration: Registry Name: ClincialTrials.Gov.Registration Number: NCT01302379.Date of Registration: February 2011.URL: https://clinicaltrials.gov/ct2/show/NCT01302379.
Collapse
Affiliation(s)
- Jamaji C Nwanaji-Enwerem
- Department of Emergency Medicine, Gangarosa Department of Environmental Health, Emory University School of Medicine, Emory Rollins School of Public Health, 1518 Clifton Rd. NE, Atlanta, GA, 30322, USA.
- Division of Environmental Health Sciences, School of Public Health and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
| | - Felicia Fei-Lei Chung
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Lars Van der Laan
- Division of Environmental Health Sciences, School of Public Health and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Alexei Novoloaca
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Cyrille Cuenin
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Harriet Johansson
- Division of Cancer Prevention and Genetics, IEO European Institute of Oncology IRCCS, Via Ripamonti, 435 - 20141, Milan, Italy
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, IEO European Institute of Oncology IRCCS, Via Ripamonti, 435 - 20141, Milan, Italy
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - Alan E Hubbard
- Division of Environmental Health Sciences, School of Public Health and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Martyn T Smith
- Division of Environmental Health Sciences, School of Public Health and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Sheri J Hartman
- Herbert Wertheim School of Public Health, University of California, San Diego, CA, USA
- Moores Cancer Center, University of California, San Diego, CA, USA
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health and Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Dorothy D Sears
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Moores Cancer Center, University of California, San Diego, CA, USA
- Department Medicine, University of California, San Diego, CA, USA
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| |
Collapse
|
384
|
Epigenetic Age Acceleration Is Not Associated with Age-Related Macular Degeneration. Int J Mol Sci 2021; 22:ijms222413457. [PMID: 34948253 PMCID: PMC8705580 DOI: 10.3390/ijms222413457] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 01/01/2023] Open
Abstract
DNA methylation age (DNAm age) estimation is a powerful biomarker of human ageing. To date, epigenetic clocks have not been evaluated in age-related macular degeneration (AMD). Here, we perform genome-wide DNA methylation analyses in blood of AMD patients with a documented smoking history (14 AMD, 16 Normal), identifying loci of differential methylation (DML) with a relaxed p-value criterion (p ≤ 10−4). We conduct DNAm age analyses using the Horvath-multi tissue, Hannum and Skin & Blood epigenetic clocks in both blood and retinal pigment epithelium (RPE). We perform Ingenuity Pathway Analysis Causal Network Analysis (IPA CNA) on the topmost significantly differentially methylated CpG probes in blood and RPE. Results show poor performance of epigenetic clocks in RPE. Epigenetic age acceleration (EAA) was not observed in AMD. However, we observe positive EAA in blood of smokers, and in smokers with AMD. DML analysis revealed hypomethylation at cg04953735 within RPTOR (p = 6.51 × 10−5; Δβ = −11.95%). IPA CNA in the RPE also identified RPTOR as the putative master regulator, predicted to be inhibited in AMD. In conclusion, this is the first study evaluating an association of epigenetic ageing in AMD. We posit a role for RPTOR as a common master regulator of methylation changes in the RPE in AMD.
Collapse
|
385
|
Reduced NCOR2 expression accelerates androgen deprivation therapy failure in prostate cancer. Cell Rep 2021; 37:110109. [PMID: 34910907 PMCID: PMC8889623 DOI: 10.1016/j.celrep.2021.110109] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 09/21/2021] [Accepted: 11/17/2021] [Indexed: 01/27/2023] Open
Abstract
This study addresses the roles of nuclear receptor corepressor 2 (NCOR2) in prostate cancer (PC) progression in response to androgen deprivation therapy (ADT). Reduced NCOR2 expression significantly associates with shorter disease-free survival in patients with PC receiving adjuvant ADT. Utilizing the CWR22 xenograft model, we demonstrate that stably reduced NCOR2 expression accelerates disease recurrence following ADT, associates with gene expression patterns that include neuroendocrine features, and induces DNA hypermethylation. Stably reduced NCOR2 expression in isogenic LNCaP (androgen-sensitive) and LNCaP-C4–2 (androgen-independent) cells revealed that NCOR2 reduction phenocopies the impact of androgen treatment and induces global DNA hypermethylation patterns. NCOR2 genomic binding is greatest in LNCaP-C4–2 cells and most clearly associates with forkhead box (FOX) transcription factor FOXA1 binding. NCOR2 binding significantly associates with transcriptional regulation most when in active enhancer regions. These studies reveal robust roles for NCOR2 in regulating the PC transcriptome and epigenome and underscore recent mutational studies linking NCOR2 loss of function to PC disease progression. Long et al. show that reduced levels of NCOR2 lead to accelerated prostate cancer recurrence during androgen withdrawal in a patient-derived xenograft model. NCOR2 reduction is characterized by incomplete response to androgen withdrawal, and recurrent tumors show increased neuroendocrine traits. These phenotypic changes are associated with hypermethylated enhancers.
Collapse
|
386
|
Locus-Specific Methylation of GSTP1, RNF219, and KIAA1539 Genes with Single Molecule Resolution in Cell-Free DNA from Healthy Donors and Prostate Tumor Patients: Application in Diagnostics. Cancers (Basel) 2021; 13:cancers13246234. [PMID: 34944854 PMCID: PMC8699300 DOI: 10.3390/cancers13246234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Prostate cancer (PCa) is the second most commonly diagnosed cancer in men, which is constantly accompanied by benign prostate hyperplasia (BPH). To reach a 100% 5-year survival rate in PCa, which is characteristic for PCa if it is diagnosed in early stages, efficient PCa diagnostics against the background of BPH are demanded. The article describes a liquid biopsy approach to differential PCa diagnostics based on the data on locus-specific methylation of the three genes (GSTP1, RNF219, and KIAA1539) obtained with NGS of cell-free DNA from blood plasma of PCa, BPH, and healthy individuals. We offered a diagnostic approach including the analysis of simultaneous methylation status of two CpGs in one cell-free DNA molecule, allowing the discrimination of all patients with absolute sensitivity and specificity. Abstract The locus-specific methylation of three genes (GSTP1, RNF219, and KIAA1539 (also known as FAM214B)) in the blood plasma cell-free DNA (cfDNA) of 20 patients with prostate cancer (PCa), 18 healthy donors (HDs), and 17 patients with benign prostatic hyperplasia (BPH) was studied via the MiSeq platform. The methylation status of two CpGs within the same loci were used as the diagnostic feature for discriminating the patient groups. Many variables had good diagnostic characteristics, e.g., each of the variables GSTP1.C3.C9, GSTP1.C9, and GSTP1.C9.T17 demonstrated an 80% sensitivity at a 100% specificity for PCa patients vs. the others comparison. The analysis of RNF219 gene loci methylation allowed discriminating BPH patients with absolute sensitivity and specificity. The data on the methylation of the genes GSTP1 and RNF219 allowed discriminating PCa patients, as well as HDs, with absolute sensitivity and specificity. Thus, the data on the locus-specific methylation of cfDNA (with single-molecule resolution) combined with a diagnostic approach considering the simultaneous methylation of several CpGs in one locus enabled the discrimination of HD, BPH, and PCa patients.
Collapse
|
387
|
Weiss E, Vlahos A, Kim B, Wijegunasekara S, Shanmuganathan D, Aitken T, Joo JHE, Imran S, Shepherd R, Craig JM, Green M, Hiden U, Novakovic B, Saffery R. Transcriptomic Remodelling of Fetal Endothelial Cells During Establishment of Inflammatory Memory. Front Immunol 2021; 12:757393. [PMID: 34867995 PMCID: PMC8640490 DOI: 10.3389/fimmu.2021.757393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/03/2021] [Indexed: 12/11/2022] Open
Abstract
Inflammatory memory involves the molecular and cellular ‘reprogramming’ of innate immune cells following exogenous stimuli, leading to non-specific protection against subsequent pathogen exposure. This phenomenon has now also been described in non-hematopoietic cells, such as human fetal and adult endothelial cells. In this study we mapped the cell-specific DNA methylation profile and the transcriptomic remodelling during the establishment of inflammatory memory in two distinct fetal endothelial cell types – a progenitor cell (ECFC) and a differentiated cell (HUVEC) population. We show that both cell types have a core transcriptional response to an initial exposure to a viral-like ligand, Poly(I:C), characterised by interferon responsive genes. There was also an ECFC specific response, marked by the transcription factor ELF1, suggesting a non-canonical viral response pathway in progenitor endothelial cells. Next, we show that both ECFCs and HUVECs establish memory in response to an initial viral exposure, resulting in an altered subsequent response to lipopolysaccharide. While the capacity to train or tolerize the induction of specific sets of genes was similar between the two cell types, the progenitor ECFCs show a higher capacity to establish memory. Among tolerized cellular pathways are those involved in endothelial barrier establishment and leukocyte migration, both important for regulating systemic immune-endothelial cell interactions. These findings suggest that the capacity for inflammatory memory may be a common trait across different endothelial cell types but also indicate that the specific downstream targets may vary by developmental stage.
Collapse
Affiliation(s)
- Elisa Weiss
- Perinatal Research Laboratory, Department of Obstetrics & Gynaecology, Medical University of Graz, Graz, Austria
| | - Amanda Vlahos
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Bowon Kim
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Sachintha Wijegunasekara
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Dhanya Shanmuganathan
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Thomas Aitken
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Biosciences, University of Melbourne, Parkville, VIC, Australia
| | - Ji-Hoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia.,University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Samira Imran
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC, Australia
| | - Rebecca Shepherd
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Jeffrey M Craig
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC, Australia.,Molecular Epidemiology, Murdoch Children's Research Institute, Parkville, VIC, Australia.,The Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, VIC, Australia
| | - Mark Green
- Department of Biosciences, University of Melbourne, Parkville, VIC, Australia
| | - Ursula Hiden
- Perinatal Research Laboratory, Department of Obstetrics & Gynaecology, Medical University of Graz, Graz, Austria
| | - Boris Novakovic
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC, Australia
| | - Richard Saffery
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC, Australia
| |
Collapse
|
388
|
Ou K, Hamo D, Schulze A, Roemhild A, Kaiser D, Gasparoni G, Salhab A, Zarrinrad G, Amini L, Schlickeiser S, Streitz M, Walter J, Volk HD, Schmueck-Henneresse M, Reinke P, Polansky JK. Strong Expansion of Human Regulatory T Cells for Adoptive Cell Therapy Results in Epigenetic Changes Which May Impact Their Survival and Function. Front Cell Dev Biol 2021; 9:751590. [PMID: 34869339 PMCID: PMC8639223 DOI: 10.3389/fcell.2021.751590] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/12/2021] [Indexed: 12/27/2022] Open
Abstract
Adoptive transfer of regulatory T cells (Treg) is a promising new therapeutic option to treat detrimental inflammatory conditions after transplantation and during autoimmune disease. To reach sufficient cell yield for treatment, ex vivo isolated autologous or allogenic Tregs need to be expanded extensively in vitro during manufacturing of the Treg product. However, repetitive cycles of restimulation and prolonged culture have been shown to impact T cell phenotypes, functionality and fitness. It is therefore critical to scrutinize the molecular changes which occur during T cell product generation, and reexamine current manufacturing practices. We performed genome-wide DNA methylation profiling of cells throughout the manufacturing process of a polyclonal Treg product that has proven safety and hints of therapeutic efficacy in kidney transplant patients. We found progressive DNA methylation changes over the duration of culture, which were donor-independent and reproducible between manufacturing runs. Differentially methylated regions (DMRs) in the final products were significantly enriched at promoters and enhancers of genes implicated in T cell activation. Additionally, significant hypomethylation did also occur in promoters of genes implicated in functional exhaustion in conventional T cells, some of which, however, have been reported to strengthen immunosuppressive effector function in Tregs. At the same time, a set of reported Treg-specific demethylated regions increased methylation levels with culture, indicating a possible destabilization of Treg identity during manufacturing, which was independent of the purity of the starting material. Together, our results indicate that the repetitive TCR-mediated stimulation lead to epigenetic changes that might impact functionality of Treg products in multiple ways, by possibly shifting to an effector Treg phenotype with enhanced functional activity or by risking destabilization of Treg identity and impaired TCR activation. Our analyses also illustrate the value of epigenetic profiling for the evaluation of T cell product manufacturing pipelines, which might open new avenues for the improvement of current adoptive Treg therapies with relevance for conventional effector T cell products.
Collapse
Affiliation(s)
- Kristy Ou
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Dania Hamo
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Anne Schulze
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Andy Roemhild
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Daniel Kaiser
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Gilles Gasparoni
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken, Germany
| | - Abdulrahman Salhab
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken, Germany
| | - Ghazaleh Zarrinrad
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Leila Amini
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Stephan Schlickeiser
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Mathias Streitz
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jörn Walter
- Department of Genetics and Epigenetics, Saarland University, Saarbrücken, Germany
| | - Hans-Dieter Volk
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.,Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Schmueck-Henneresse
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Petra Reinke
- Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Julia K Polansky
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.,German Rheumatism Research Centre (DRFZ) Berlin, Berlin, Germany
| |
Collapse
|
389
|
Foox J, Nordlund J, Lalancette C, Gong T, Lacey M, Lent S, Langhorst BW, Ponnaluri VKC, Williams L, Padmanabhan KR, Cavalcante R, Lundmark A, Butler D, Mozsary C, Gurvitch J, Greally JM, Suzuki M, Menor M, Nasu M, Alonso A, Sheridan C, Scherer A, Bruinsma S, Golda G, Muszynska A, Łabaj PP, Campbell MA, Wos F, Raine A, Liljedahl U, Axelsson T, Wang C, Chen Z, Yang Z, Li J, Yang X, Wang H, Melnick A, Guo S, Blume A, Franke V, Ibanez de Caceres I, Rodriguez-Antolin C, Rosas R, Davis JW, Ishii J, Megherbi DB, Xiao W, Liao W, Xu J, Hong H, Ning B, Tong W, Akalin A, Wang Y, Deng Y, Mason CE. The SEQC2 epigenomics quality control (EpiQC) study. Genome Biol 2021; 22:332. [PMID: 34872606 PMCID: PMC8650396 DOI: 10.1186/s13059-021-02529-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA's Epigenomics Quality Control Group. RESULTS Each sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms. CONCLUSIONS The data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.
Collapse
Affiliation(s)
- Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Jessica Nordlund
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Claudia Lalancette
- BRCF Epigenomics Core, University of Michigan Medicine, Ann Arbor, MI, 48109, USA
| | - Ting Gong
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | | | - Samantha Lent
- AbbVie Genomics Research Center, 1 N. Waukegan Rd, North Chicago, IL, 60036, USA
| | | | | | | | | | - Raymond Cavalcante
- BRCF Epigenomics Core, University of Michigan Medicine, Ann Arbor, MI, 48109, USA
| | - Anders Lundmark
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Justin Gurvitch
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - John M Greally
- Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Masako Suzuki
- Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Mark Menor
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | - Masaki Nasu
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | - Alicia Alonso
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Caroline Sheridan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
- Division of Hematology/Oncology, Department of Medicine, Epigenomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Andreas Scherer
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - Gosia Golda
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Agata Muszynska
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Paweł P Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Frank Wos
- New York Genome Center, New York, NY, 10013, USA
| | - Amanda Raine
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Ulrika Liljedahl
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Tomas Axelsson
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Charles Wang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Zhong Chen
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Zhaowei Yang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jing Li
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaopeng Yang
- Department of Neurology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China
| | - Hongwei Wang
- Development of Medicine, the University of Chicago, Chicago, IL, 60637, USA
| | - Ari Melnick
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Shang Guo
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China
| | - Alexander Blume
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Vedran Franke
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Inmaculada Ibanez de Caceres
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Carlos Rodriguez-Antolin
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Rocio Rosas
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Justin Wade Davis
- AbbVie Genomics Research Center, 1 N. Waukegan Rd, North Chicago, IL, 60036, USA
| | | | - Dalila B Megherbi
- CMINDS Research Center, Francis College of Engineering, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Wenming Xiao
- Center for Devices and Radiological Health, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - Will Liao
- New York Genome Center, New York, NY, 10013, USA
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Baitang Ning
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Yunliang Wang
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China.
| | - Youping Deng
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA.
- The Feil Family Brain and Mind Research Institute, New York, New York, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
390
|
Campagna MP, Xavier A, Lechner-Scott J, Maltby V, Scott RJ, Butzkueven H, Jokubaitis VG, Lea RA. Epigenome-wide association studies: current knowledge, strategies and recommendations. Clin Epigenetics 2021; 13:214. [PMID: 34863305 PMCID: PMC8645110 DOI: 10.1186/s13148-021-01200-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 11/19/2021] [Indexed: 02/06/2023] Open
Abstract
The aetiology and pathophysiology of complex diseases are driven by the interaction between genetic and environmental factors. The variability in risk and outcomes in these diseases are incompletely explained by genetics or environmental risk factors individually. Therefore, researchers are now exploring the epigenome, a biological interface at which genetics and the environment can interact. There is a growing body of evidence supporting the role of epigenetic mechanisms in complex disease pathophysiology. Epigenome-wide association studies (EWASes) investigate the association between a phenotype and epigenetic variants, most commonly DNA methylation. The decreasing cost of measuring epigenome-wide methylation and the increasing accessibility of bioinformatic pipelines have contributed to the rise in EWASes published in recent years. Here, we review the current literature on these EWASes and provide further recommendations and strategies for successfully conducting them. We have constrained our review to studies using methylation data as this is the most studied epigenetic mechanism; microarray-based data as whole-genome bisulphite sequencing remains prohibitively expensive for most laboratories; and blood-based studies due to the non-invasiveness of peripheral blood collection and availability of archived DNA, as well as the accessibility of publicly available blood-cell-based methylation data. Further, we address multiple novel areas of EWAS analysis that have not been covered in previous reviews: (1) longitudinal study designs, (2) the chip analysis methylation pipeline (ChAMP), (3) differentially methylated region (DMR) identification paradigms, (4) methylation quantitative trait loci (methQTL) analysis, (5) methylation age analysis and (6) identifying cell-specific differential methylation from mixed cell data using statistical deconvolution.
Collapse
Affiliation(s)
- Maria Pia Campagna
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Alexandre Xavier
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - Jeannette Lechner-Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
- Department of Neurology, Division of Medicine, John Hunter Hospital, Newcastle, Australia
| | - Vicky Maltby
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - Rodney J Scott
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
- Division of Molecular Medicine, New South Wales Health Pathology North, Newcastle, Australia
| | - Helmut Butzkueven
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Melbourne, Australia
| | - Vilija G Jokubaitis
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Melbourne, Australia
| | - Rodney A Lea
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia.
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.
| |
Collapse
|
391
|
Xu Y, Tsai CW, Chang WS, Han Y, Huang M, Pettaway CA, Bau DT, Gu J. Epigenome-Wide Association Study of Prostate Cancer in African Americans Identifies DNA Methylation Biomarkers for Aggressive Disease. Biomolecules 2021; 11:1826. [PMID: 34944472 PMCID: PMC8698937 DOI: 10.3390/biom11121826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/22/2021] [Accepted: 12/01/2021] [Indexed: 12/14/2022] Open
Abstract
DNA methylation plays important roles in prostate cancer (PCa) development and progression. African American men have higher incidence and mortality rates of PCa than other racial groups in U.S. The goal of this study was to identify differentially methylated CpG sites and genes between clinically defined aggressive and nonaggressive PCa in African Americans. We performed genome-wide DNA methylation profiling in leukocyte DNA from 280 African American PCa patients using Illumina MethylationEPIC array that contains about 860K CpG sties. There was a slight increase of overall methylation level (mean β value) with the increasing Gleason scores (GS = 6, GS = 7, GS ≥ 8, P for trend = 0.002). There were 78 differentially methylated CpG sites with P < 10-4 and 9 sites with P < 10-5 in the trend test. We also found 77 differentially methylated regions/genes (DMRs), including 10 homeobox genes and six zinc finger protein genes. A gene ontology (GO) molecular pathway enrichment analysis of these 77 DMRs found that the main enriched pathway was DNA-binding transcriptional factor activity. A few representative DMRs include HOXD8, SOX11, ZNF-471, and ZNF-577. Our study suggests that leukocyte DNA methylation may be valuable biomarkers for aggressive PCa and the identified differentially methylated genes provide biological insights into the modulation of immune response by aggressive PCa.
Collapse
Affiliation(s)
- Yifan Xu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.X.); (C.-W.T.); (W.-S.C.); (M.H.)
| | - Chia-Wen Tsai
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.X.); (C.-W.T.); (W.-S.C.); (M.H.)
- Terry Fox Cancer Research Laboratory, China Medical University Hospital, Taichung 404332, Taiwan;
| | - Wen-Shin Chang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.X.); (C.-W.T.); (W.-S.C.); (M.H.)
- Terry Fox Cancer Research Laboratory, China Medical University Hospital, Taichung 404332, Taiwan;
| | - Yuyan Han
- School of Biological Sciences, University of Northern Colorado, Greeley, CO 80639, USA;
| | - Maosheng Huang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.X.); (C.-W.T.); (W.-S.C.); (M.H.)
| | - Curtis A. Pettaway
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Da-Tian Bau
- Terry Fox Cancer Research Laboratory, China Medical University Hospital, Taichung 404332, Taiwan;
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung 41354, Taiwan
| | - Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; (Y.X.); (C.-W.T.); (W.-S.C.); (M.H.)
| |
Collapse
|
392
|
van Rheenen W, van der Spek RAA, Bakker MK, van Vugt JJFA, Hop PJ, Zwamborn RAJ, de Klein N, Westra HJ, Bakker OB, Deelen P, Shireby G, Hannon E, Moisse M, Baird D, Restuadi R, Dolzhenko E, Dekker AM, Gawor K, Westeneng HJ, Tazelaar GHP, van Eijk KR, Kooyman M, Byrne RP, Doherty M, Heverin M, Al Khleifat A, Iacoangeli A, Shatunov A, Ticozzi N, Cooper-Knock J, Smith BN, Gromicho M, Chandran S, Pal S, Morrison KE, Shaw PJ, Hardy J, Orrell RW, Sendtner M, Meyer T, Başak N, van der Kooi AJ, Ratti A, Fogh I, Gellera C, Lauria G, Corti S, Cereda C, Sproviero D, D'Alfonso S, Sorarù G, Siciliano G, Filosto M, Padovani A, Chiò A, Calvo A, Moglia C, Brunetti M, Canosa A, Grassano M, Beghi E, Pupillo E, Logroscino G, Nefussy B, Osmanovic A, Nordin A, Lerner Y, Zabari M, Gotkine M, Baloh RH, Bell S, Vourc'h P, Corcia P, Couratier P, Millecamps S, Meininger V, Salachas F, Mora Pardina JS, Assialioui A, Rojas-García R, Dion PA, Ross JP, Ludolph AC, Weishaupt JH, Brenner D, Freischmidt A, Bensimon G, Brice A, Durr A, Payan CAM, Saker-Delye S, Wood NW, Topp S, Rademakers R, Tittmann L, Lieb W, Franke A, Ripke S, Braun A, Kraft J, Whiteman DC, Olsen CM, Uitterlinden AG, Hofman A, Rietschel M, Cichon S, Nöthen MM, Amouyel P, Traynor BJ, Singleton AB, Mitne Neto M, Cauchi RJ, Ophoff RA, Wiedau-Pazos M, Lomen-Hoerth C, van Deerlin VM, Grosskreutz J, Roediger A, Gaur N, Jörk A, Barthel T, Theele E, Ilse B, Stubendorff B, Witte OW, Steinbach R, Hübner CA, Graff C, Brylev L, Fominykh V, Demeshonok V, Ataulina A, Rogelj B, Koritnik B, Zidar J, Ravnik-Glavač M, Glavač D, Stević Z, Drory V, Povedano M, Blair IP, Kiernan MC, Benyamin B, Henderson RD, Furlong S, Mathers S, McCombe PA, Needham M, Ngo ST, Nicholson GA, Pamphlett R, Rowe DB, Steyn FJ, Williams KL, Mather KA, Sachdev PS, Henders AK, Wallace L, de Carvalho M, Pinto S, Petri S, Weber M, Rouleau GA, Silani V, Curtis CJ, Breen G, Glass JD, Brown RH, Landers JE, Shaw CE, Andersen PM, Groen EJN, van Es MA, Pasterkamp RJ, Fan D, Garton FC, McRae AF, Davey Smith G, Gaunt TR, Eberle MA, Mill J, McLaughlin RL, Hardiman O, Kenna KP, Wray NR, Tsai E, Runz H, Franke L, Al-Chalabi A, Van Damme P, van den Berg LH, Veldink JH. Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology. Nat Genet 2021; 53:1636-1648. [PMID: 34873335 PMCID: PMC8648564 DOI: 10.1038/s41588-021-00973-1] [Citation(s) in RCA: 219] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 10/18/2021] [Indexed: 02/01/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with a lifetime risk of one in 350 people and an unmet need for disease-modifying therapies. We conducted a cross-ancestry genome-wide association study (GWAS) including 29,612 patients with ALS and 122,656 controls, which identified 15 risk loci. When combined with 8,953 individuals with whole-genome sequencing (6,538 patients, 2,415 controls) and a large cortex-derived expression quantitative trait locus (eQTL) dataset (MetaBrain), analyses revealed locus-specific genetic architectures in which we prioritized genes either through rare variants, short tandem repeats or regulatory effects. ALS-associated risk loci were shared with multiple traits within the neurodegenerative spectrum but with distinct enrichment patterns across brain regions and cell types. Of the environmental and lifestyle risk factors obtained from the literature, Mendelian randomization analyses indicated a causal role for high cholesterol levels. The combination of all ALS-associated signals reveals a role for perturbations in vesicle-mediated transport and autophagy and provides evidence for cell-autonomous disease initiation in glutamatergic neurons.
Collapse
Affiliation(s)
- Wouter van Rheenen
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
| | - Rick A A van der Spek
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Mark K Bakker
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Joke J F A van Vugt
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Paul J Hop
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Ramona A J Zwamborn
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Niek de Klein
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Harm-Jan Westra
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Olivier B Bakker
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Patrick Deelen
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Gemma Shireby
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Matthieu Moisse
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Denis Baird
- Translational Biology, Biogen, Boston, MA, USA
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol, UK
| | - Restuadi Restuadi
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | | | - Annelot M Dekker
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Klara Gawor
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Henk-Jan Westeneng
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Gijs H P Tazelaar
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Kristel R van Eijk
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Maarten Kooyman
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Ross P Byrne
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Mark Doherty
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Mark Heverin
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- National Institute for Health Research Biomedical Research Centre and Dementia Unit, South London and Maudsley NHS Foundation Trust and King's College London, London, UK
| | - Aleksey Shatunov
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Nicola Ticozzi
- Department of Neurology, Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Bradley N Smith
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Marta Gromicho
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Siddharthan Chandran
- Euan MacDonald Centre for Motor Neurone Disease Research, Edinburgh, UK
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
| | - Suvankar Pal
- Euan MacDonald Centre for Motor Neurone Disease Research, Edinburgh, UK
- UK Dementia Research Institute, University of Edinburgh, Edinburgh, UK
| | - Karen E Morrison
- School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - John Hardy
- Department of Molecular Neuroscience, Institute of Neurology, University College London, London, UK
| | - Richard W Orrell
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Michael Sendtner
- Institute of Clinical Neurobiology, University Hospital Würzburg, Würzburg, Germany
| | - Thomas Meyer
- Charité University Hospital, Humboldt University, Berlin, Germany
| | - Nazli Başak
- Koç University, School of Medicine, KUTTAM-NDAL, Istanbul, Turkey
| | | | - Antonia Ratti
- Department of Neurology, Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Isabella Fogh
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Cinzia Gellera
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', Milan, Italy
| | - Giuseppe Lauria
- 3rd Neurology Unit, Motor Neuron Diseases Center, Fondazione IRCCS Istituto Neurologico 'Carlo Besta', MIlan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Stefania Corti
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
- Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Daisy Sproviero
- Genomic and Post-Genomic Center, IRCCS Mondino Foundation, Pavia, Italy
| | - Sandra D'Alfonso
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Gianni Sorarù
- Department of Neurosciences, University of Padova, Padova, Italy
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Massimiliano Filosto
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Alessandro Padovani
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Adriano Chiò
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Neurologia 1, Azienda Ospedaliero Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Andrea Calvo
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Neurologia 1, Azienda Ospedaliero Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Cristina Moglia
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Neurologia 1, Azienda Ospedaliero Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Maura Brunetti
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
| | - Antonio Canosa
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
- Neurologia 1, Azienda Ospedaliero Universitaria Città della Salute e della Scienza, Turin, Italy
| | - Maurizio Grassano
- 'Rita Levi Montalcini' Department of Neuroscience, ALS Centre, University of Torino, Turin, Italy
| | - Ettore Beghi
- Laboratory of Neurological Diseases, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Elisabetta Pupillo
- Laboratory of Neurological Diseases, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
| | - Giancarlo Logroscino
- Department of Clinical Research in Neurology, University of Bari at 'Pia Fondazione Card G. Panico' Hospital, Bari, Italy
| | - Beatrice Nefussy
- Neuromuscular Diseases Unit, Department of Neurology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Alma Osmanovic
- Department of Neurology, Hannover Medical School, Hannover, Germany
- Essener Zentrum für Seltene Erkrankungen (EZSE), University Hospital Essen, Essen, Germany
| | - Angelica Nordin
- Department of Clinical Sciences, Neurosciences, Umeå University, Umeå, Sweden
| | - Yossef Lerner
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Neurology, the Agnes Ginges Center for Human Neurogenetics, Hadassah Medical Center, Jerusalem, Israel
| | - Michal Zabari
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Neurology, the Agnes Ginges Center for Human Neurogenetics, Hadassah Medical Center, Jerusalem, Israel
| | - Marc Gotkine
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Neurology, the Agnes Ginges Center for Human Neurogenetics, Hadassah Medical Center, Jerusalem, Israel
| | - Robert H Baloh
- Center for Neural Science and Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Neurology, Neuromuscular Division, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Shaughn Bell
- Center for Neural Science and Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Neurology, Neuromuscular Division, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Patrick Vourc'h
- Service de Biochimie et Biologie Moléculaire, CHU de Tours, Tours, France
- UMR 1253, Université de Tours, Inserm, Tours, France
| | - Philippe Corcia
- UMR 1253, Université de Tours, Inserm, Tours, France
- Centre de référence sur la SLA, CHU de Tours, Tours, France
| | - Philippe Couratier
- Centre de référence sur la SLA, CHRU de Limoges, Limoges, France
- UMR 1094, Université de Limoges, Inserm, Limoges, France
| | - Stéphanie Millecamps
- ICM, Institut du Cerveau, Inserm, CNRS, Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
| | | | - François Salachas
- ICM, Institut du Cerveau, Inserm, CNRS, Sorbonne Université, Hôpital Pitié-Salpêtrière, Paris, France
- Département de Neurologie, Centre de référence SLA Ile de France, Hôpital de la Pitié-Salpêtrière, AP-HP, Paris, France
| | | | - Abdelilah Assialioui
- Functional Unit of Amyotrophic Lateral Sclerosis (UFELA), Service of Neurology, Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ricardo Rojas-García
- MND Clinic, Neurology Department, Hospital de la Santa Creu i Sant Pau de Barcelona, Universitat Autonoma de Barcelona, Barcelona, Spain
| | - Patrick A Dion
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Jay P Ross
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Jochen H Weishaupt
- Division of Neurodegeneration, Department of Neurology, University Medicine Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - David Brenner
- Division of Neurodegeneration, Department of Neurology, University Medicine Mannheim, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Axel Freischmidt
- Department of Neurology, Ulm University, Ulm, Germany
- German Center for Neurodegenerative Diseases (DZNE) Ulm, Ulm, Germany
| | - Gilbert Bensimon
- Département de Pharmacologie Clinique, Hôpital de la Pitié-Salpêtrière, UPMC Pharmacologie, AP-HP, Paris, France
- Pharmacologie Sorbonne Université, Paris, France
- Institut du Cerveau, Paris Brain Institute ICM, Paris, France
- Laboratoire de Biostatistique, Epidémiologie Clinique, Santé Publique Innovation et Méthodologie (BESPIM), CHU-Nîmes, Nîmes, France
| | - Alexis Brice
- Sorbonne Université, Paris Brain Institute, APHP, INSERM, CNRS, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Alexandra Durr
- Sorbonne Université, Paris Brain Institute, APHP, INSERM, CNRS, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Christine A M Payan
- Département de Pharmacologie Clinique, Hôpital de la Pitié-Salpêtrière, UPMC Pharmacologie, AP-HP, Paris, France
| | | | - Nicholas W Wood
- Department of Clinical and Movement Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Simon Topp
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Rosa Rademakers
- Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, FL, USA
| | - Lukas Tittmann
- Popgen Biobank and Institute of Epidemiology, Christian Albrechts-University Kiel, Kiel, Germany
| | - Wolfgang Lieb
- Popgen Biobank and Institute of Epidemiology, Christian Albrechts-University Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
| | - Alice Braun
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
| | - Julia Kraft
- Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin, Berlin, Germany
| | - David C Whiteman
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Catherine M Olsen
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Andre G Uitterlinden
- Department of Internal Medicine, Genetics Laboratory, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Marcella Rietschel
- Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany
- Central Institute of Mental Health, Mannheim, Germany
| | - Sven Cichon
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life and Brain Center, Bonn, Germany
- Division of Medical Genetics, University Hospital Basel and Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Neuroscience and Medicine INM-1, Research Center Juelich, Juelich, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life and Brain Center, Bonn, Germany
| | - Philippe Amouyel
- INSERM UMR1167-RID-AGE LabEx DISTALZ-Risk Factors and Molecular Determinants of Aging-Related Diseases, University of Lille, Centre Hospitalier of the University of Lille, Institut Pasteur de Lille, Lille, France
| | - Bryan J Traynor
- Neuromuscular Diseases Research Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, NIH, Porter Neuroscience Research Center, Bethesda, MD, USA
| | | | - Ruben J Cauchi
- Centre for Molecular Medicine and Biobanking and Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Roel A Ophoff
- University Medical Center Utrecht, Department of Psychiatry, Rudolf Magnus Institute of Neuroscience, Utrecht, the Netherlands
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Martina Wiedau-Pazos
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | | | - Vivianna M van Deerlin
- Center for Neurodegenerative Disease Research, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Julian Grosskreutz
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
- Precision Neurology Unit, Department of Neurology, University Hospital Schleswig-Holstein, University of Luebeck, Luebeck, Germany
| | | | - Nayana Gaur
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Alexander Jörk
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Tabea Barthel
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Erik Theele
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Benjamin Ilse
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | | | - Otto W Witte
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - Robert Steinbach
- Hans Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | | | - Caroline Graff
- Department of Geriatric Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Lev Brylev
- Department of Neurology, Bujanov Moscow Clinical Hospital, Moscow, Russia
- Moscow Research and Clinical Center for Neuropsychiatry of the Healthcare Department, Moscow, Russia
- Department of Functional Biochemistry of the Nervous System, Institute of Higher Nervous Activity and Neurophysiology Russian Academy of Sciences, Moscow, Russia
| | - Vera Fominykh
- Department of Neurology, Bujanov Moscow Clinical Hospital, Moscow, Russia
- Department of Functional Biochemistry of the Nervous System, Institute of Higher Nervous Activity and Neurophysiology Russian Academy of Sciences, Moscow, Russia
| | - Vera Demeshonok
- ALS-Care Center, 'GAOORDI', Medical Clinic of the St. Petersburg, St. Petersburg, Russia
| | - Anastasia Ataulina
- Department of Neurology, Bujanov Moscow Clinical Hospital, Moscow, Russia
| | - Boris Rogelj
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
- Biomedical Research Institute BRIS, Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Blaž Koritnik
- Ljubljana ALS Centre, Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Janez Zidar
- Ljubljana ALS Centre, Institute of Clinical Neurophysiology, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Metka Ravnik-Glavač
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Damjan Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Zorica Stević
- Clinic of Neurology, Clinical Center of Serbia, School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Vivian Drory
- Neuromuscular Diseases Unit, Department of Neurology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Monica Povedano
- Functional Unit of Amyotrophic Lateral Sclerosis (UFELA), Service of Neurology, Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Matthew C Kiernan
- Brain and Mind Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Beben Benyamin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- Australian Centre for Precision Health and Allied Health and Human Performance, University of South Australia, Adelaide, South Australia, Australia
| | - Robert D Henderson
- Centre for Clinical Research, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Sarah Furlong
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Susan Mathers
- Calvary Health Care Bethlehem, Parkdale, Victoria, Australia
| | - Pamela A McCombe
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Merrilee Needham
- Fiona Stanley Hospital, Perth, Western Australia, Australia
- Notre Dame University, Fremantle, Western Australia, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, Western Australia, Australia
| | - Shyuan T Ngo
- Centre for Clinical Research, Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Garth A Nicholson
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, New South Wales, Australia
- Molecular Medicine Laboratory, Concord Repatriation General Hospital, Concord, New South Wales, Australia
| | - Roger Pamphlett
- Discipline of Pathology and Department of Neuropathology, Brain and Mind Centre, University of Sydney, Sydney, New South Wales, Australia
| | - Dominic B Rowe
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Frederik J Steyn
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- The School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
- Neuroscience Research Australia Institute, Randwick, New South Wales, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
- Neuropsychiatric Institute, the Prince of Wales Hospital, UNSW, Randwick, New South Wales, Australia
| | - Anjali K Henders
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Mamede de Carvalho
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Susana Pinto
- Instituto de Fisiologia, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Susanne Petri
- Department of Neurology, Hannover Medical School, Hannover, Germany
| | - Markus Weber
- Neuromuscular Diseases Unit/ALS Clinic, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Guy A Rouleau
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Vincenzo Silani
- Department of Neurology, Stroke Unit and Laboratory of Neuroscience, Istituto Auxologico Italiano IRCCS, Milan, Italy
- Department of Pathophysiology and Transplantation, 'Dino Ferrari' Center, Università degli Studi di Milano, Milan, Italy
| | - Charles J Curtis
- Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
- NIHR BioResource Centre Maudsley, NIHR Maudsley Biomedical Research Centre (BRC) at South London and Maudsley NHS Foundation Trust (SLaM) & Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
| | - Gerome Breen
- Social Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
- NIHR BioResource Centre Maudsley, NIHR Maudsley Biomedical Research Centre (BRC) at South London and Maudsley NHS Foundation Trust (SLaM) & Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
| | - Jonathan D Glass
- Department Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Robert H Brown
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Christopher E Shaw
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Peter M Andersen
- Department of Clinical Sciences, Neurosciences, Umeå University, Umeå, Sweden
| | - Ewout J N Groen
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Michael A van Es
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - R Jeroen Pasterkamp
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Dongsheng Fan
- Department of Neurology, Third Hospital, Peking University, Beijing, China
| | - Fleur C Garton
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, Bristol, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit (IEU), Population Health Sciences, University of Bristol, Bristol, UK
- Population Health Science, Bristol Medical School, Bristol, UK
| | | | - Jonathan Mill
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Russell L McLaughlin
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Kevin P Kenna
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Department of Translational Neuroscience, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Naomi R Wray
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Ellen Tsai
- Translational Biology, Biogen, Boston, MA, USA
| | - Heiko Runz
- Translational Biology, Biogen, Boston, MA, USA
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- King's College Hospital, London, UK
| | - Philip Van Damme
- Department of Neurosciences, Experimental Neurology and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven, Belgium
- Laboratory of Neurobiology, VIB, Center for Brain & Disease Research, Leuven, Belgium
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium
| | - Leonard H van den Berg
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jan H Veldink
- Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
| |
Collapse
|
393
|
Ritonja JA, Aronson KJ, Flaten L, Topouza DG, Duan QL, Durocher F, Tranmer JE, Bhatti P. Exploring the impact of night shift work on methylation of circadian genes. Epigenetics 2021; 17:1259-1268. [PMID: 34825628 DOI: 10.1080/15592294.2021.2009997] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Night shift work is associated with increased breast cancer risk, but the molecular mechanisms are not well-understood. The objective of this study was to explore the relationship between night shift work parameters (current status, duration/years, and intensity) and methylation in circadian genes as a potential mechanism underlying the carcinogenic effects of night shift work. A cross-sectional study was conducted among 74 female healthcare employees (n = 38 day workers, n = 36 night shift workers). The Illumina Infinium MethylationEPIC beadchip was applied to DNA extracted from blood samples to measure methylation using a candidate gene approach at 1150 CpG loci across 22 circadian genes. Linear regression models were used to examine the association between night shift work parameters and continuous methylation measurements (β-values) for each CpG site. The false-discovery rate (q = 0.2) was used to account for multiple comparisons. Compared to day workers, current night shift workers demonstrated hypermethylation in the 5'UTR region of CSNK1E (q = 0.15). Individuals that worked night shifts for ≥10 years exhibited hypomethylation in the gene body of NR1D1 (q = 0.08) compared to those that worked <10 years. Hypermethylation in the gene body of ARNTL was also apparent in those who worked ≥3 consecutive night shifts a week (q = 0.18). These findings suggest that night shift work is associated with differential methylation in core circadian genes, including CSNK1E, NR1D1 and ARNTL. Future, larger-scale studies with long-term follow-up and detailed night shift work assessment are needed to confirm and expand on these findings.
Collapse
Affiliation(s)
- Jennifer A Ritonja
- Department of Public Health Sciences, Queen's University, Kingston, Canada
| | - Kristan J Aronson
- Department of Public Health Sciences, Queen's University, Kingston, Canada.,Division of Cancer Care and Epidemiology, Cancer Research Institute, Queen's University, Kingston, Canada
| | - Lisa Flaten
- Department of Public Health Sciences, Queen's University, Kingston, Canada
| | - Danai G Topouza
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada
| | - Qing Ling Duan
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Canada.,School of Computing, Queen's University, Kingston, Canada
| | - Francine Durocher
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Kingston, Canada.,Centre de Recherche Sur Le Cancer, Centre de Recherche Du Chu de Québec-Université Laval, Quebec, Canada
| | - Joan E Tranmer
- Department of Public Health Sciences, Queen's University, Kingston, Canada.,The School of Nursing is the department, School of Nursing, Queen's University, Kingston, Canada
| | | |
Collapse
|
394
|
Nöthling J, Abrahams N, Toikumo S, Suderman M, Mhlongo S, Lombard C, Seedat S, Hemmings SMJ. Genome-wide differentially methylated genes associated with posttraumatic stress disorder and longitudinal change in methylation in rape survivors. Transl Psychiatry 2021; 11:594. [PMID: 34799556 PMCID: PMC8604994 DOI: 10.1038/s41398-021-01608-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 08/01/2021] [Accepted: 09/02/2021] [Indexed: 12/24/2022] Open
Abstract
Rape is associated with a high risk for posttraumatic stress disorder (PTSD). DNA methylation changes may confer risk or protection for PTSD following rape by regulating the expression of genes implicated in pathways affected by PTSD. We aimed to: (1) identify epigenome-wide differences in methylation profiles between rape-exposed women with and without PTSD at 3-months post-rape, in a demographically and ethnically similar group, drawn from a low-income setting; (2) validate and replicate the findings of the epigenome-wide analysis in selected genes (BRSK2 and ADCYAP1); and (3) investigate baseline and longitudinal changes in BRSK2 and ADCYAP1 methylation over six months in relation to change in PTSD symptom scores over 6 months, in the combined discovery/validation and replication samples (n = 96). Rape-exposed women (n = 852) were recruited from rape clinics in the Rape Impact Cohort Evaluation (RICE) umbrella study. Epigenome-wide differentially methylated CpG sites between rape-exposed women with (n = 24) and without (n = 24) PTSD at 3-months post-rape were investigated using the Illumina EPIC BeadChip in a discovery cohort (n = 48). Validation (n = 47) and replication (n = 49) of BRSK2 and ADCYAP1 methylation findings were investigated using EpiTYPER technology. Longitudinal change in BRSK2 and ADCYAP1 was also investigated using EpiTYPER technology in the combined sample (n = 96). In the discovery sample, after adjustment for multiple comparisons, one differentially methylated CpG site (chr10: 61385771/ cg01700569, p = 0.049) and thirty-four differentially methylated regions were associated with PTSD status at 3-months post-rape. Decreased BRSK2 and ADCYAP1 methylation at 3-months and 6-months post-rape were associated with increased PTSD scores at the same time points, but these findings did not remain significant in adjusted models. In conclusion, decreased methylation of BRSK2 may result in abnormal neuronal polarization, synaptic development, vesicle formation, and disrupted neurotransmission in individuals with PTSD. PTSD symptoms may also be mediated by differential methylation of the ADCYAP1 gene which is involved in stress regulation. Replication of these findings is required to determine whether ADCYAP1 and BRSK2 are biomarkers of PTSD and potential therapeutic targets.
Collapse
Affiliation(s)
- Jani Nöthling
- Department of Psychiatry, Faculty of Medicine and Health Sciences Stellenbosch University, Cape Town, South Africa.
- Gender and Health Research Unit, South African Medical Research Council, Cape Town, South Africa.
- South African Medical Research Council Unit on the Genomics of Brain Disorders, Stellenbosch University, Cape Town, South Africa.
| | - Naeemah Abrahams
- Gender and Health Research Unit, South African Medical Research Council, Cape Town, South Africa
- Division of Social and Behavioural Sciences, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Sylvanus Toikumo
- Department of Psychiatry, Faculty of Medicine and Health Sciences Stellenbosch University, Cape Town, South Africa
- South African Medical Research Council Unit on the Genomics of Brain Disorders, Stellenbosch University, Cape Town, South Africa
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, United Kingdom
| | - Shibe Mhlongo
- Gender and Health Research Unit, South African Medical Research Council, Cape Town, South Africa
| | - Carl Lombard
- Biostatistics Unit, South African Medical Research Council, Cape Town, South Africa
- Division of Epidemiology and Biostatistics, Department of Global Health, Stellenbosch University, Cape Town, South Africa
| | - Soraya Seedat
- Department of Psychiatry, Faculty of Medicine and Health Sciences Stellenbosch University, Cape Town, South Africa
- South African Medical Research Council Unit on the Genomics of Brain Disorders, Stellenbosch University, Cape Town, South Africa
| | - Sian Megan Joanna Hemmings
- Department of Psychiatry, Faculty of Medicine and Health Sciences Stellenbosch University, Cape Town, South Africa
- South African Medical Research Council Unit on the Genomics of Brain Disorders, Stellenbosch University, Cape Town, South Africa
| |
Collapse
|
395
|
Laaksonen J, Mishra PP, Seppälä I, Raitoharju E, Marttila S, Mononen N, Lyytikäinen LP, Kleber ME, Delgado GE, Lepistö M, Almusa H, Ellonen P, Lorkowski S, März W, Hutri-Kähönen N, Raitakari O, Kähönen M, Salonen JT, Lehtimäki T. Mitochondrial genome-wide analysis of nuclear DNA methylation quantitative trait loci. Hum Mol Genet 2021; 31:1720-1732. [PMID: 35077545 PMCID: PMC9122653 DOI: 10.1093/hmg/ddab339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 11/13/2022] Open
Abstract
Abstract
Mitochondria have a complex communication network with the surrounding cell and can alter nuclear DNA methylation (DNAm). Variation in the mitochondrial DNA (mtDNA) has also been linked to differential DNAm. Genome-wide association studies have identified numerous DNAm quantitative trait loci, but these studies have not examined the mitochondrial genome. Herein, we quantified nuclear DNAm from blood and conducted a mitochondrial genome-wide association study of DNAm, with an additional emphasis on sex- and prediabetes-specific heterogeneity. We used the Young Finns Study (n = 926) with sequenced mtDNA genotypes as a discovery sample and sought replication in the Ludwigshafen Risk and Cardiovascular Health study (n = 2317). We identified numerous significant associations in the discovery phase (P < 10−9), but they were not replicated when accounting for multiple testing. In total, 27 associations were nominally replicated with a P < 0.05. The replication analysis presented no evidence of sex- or prediabetes-specific heterogeneity. The 27 associations were included in a joint meta-analysis of the two cohorts, and 19 DNAm sites associated with mtDNA variants, while four other sites showed haplogroup associations. An expression quantitative trait methylation analysis was performed for the identified DNAm sites, pinpointing two statistically significant associations. This study provides evidence of a mitochondrial genetic control of nuclear DNAm with little evidence found for sex- and prediabetes-specific effects. The lack of a comparable mtDNA data set for replication is a limitation in our study and further studies are needed to validate our results.
Collapse
Affiliation(s)
- Jaakko Laaksonen
- To whom correspondence should be addressed at: Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, PO Box 100, Tampere FI-33014, Finland. Tel: +358 504080774; E-mail:
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Emma Raitoharju
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Saara Marttila
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
- Gerontology Research Center, Tampere University, Tampere 33520, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany
| | - Graciela E Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany
| | - Maija Lepistö
- Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki 00290, Finland
| | - Henrikki Almusa
- Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki 00290, Finland
| | - Pekka Ellonen
- Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki 00290, Finland
| | - Stefan Lorkowski
- Institute of Nutritional Sciences, Friedrich Schiller University Jena, Jena 07743, Germany
- Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena 07743, Germany
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany
- Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena 07743, Germany
- SYNLAB Academy, SYNLAB Holding Deutschland GmbH, Augsburg 86156, Germany
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz 8010, Austria
| | - Nina Hutri-Kähönen
- Tampere Centre for Skills Training and Simulation, Tampere University, Tampere 33520, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku 20520, Finland
- Research Centre for Applied and Preventive Cardiovascular Medicine, University of Turku, Turku 20520, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20520, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere 33520, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| | - Jukka T Salonen
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
- MAS-Metabolic Analytical Services Oy, Helsinki 00990, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere 33520, Finland
| |
Collapse
|
396
|
Aevermann BD, Shannon CP, Novotny M, Ben-Othman R, Cai B, Zhang Y, Ye JC, Kobor MS, Gladish N, Lee AHY, Blimkie TM, Hancock RE, Llibre A, Duffy D, Koff WC, Sadarangani M, Tebbutt SJ, Kollmann TR, Scheuermann RH. Machine Learning-Based Single Cell and Integrative Analysis Reveals That Baseline mDC Predisposition Correlates With Hepatitis B Vaccine Antibody Response. Front Immunol 2021; 12:690470. [PMID: 34777332 PMCID: PMC8588842 DOI: 10.3389/fimmu.2021.690470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 08/25/2021] [Indexed: 01/23/2023] Open
Abstract
Vaccination to prevent infectious disease is one of the most successful public health interventions ever developed. And yet, variability in individual vaccine effectiveness suggests that a better mechanistic understanding of vaccine-induced immune responses could improve vaccine design and efficacy. We have previously shown that protective antibody levels could be elicited in a subset of recipients with only a single dose of the hepatitis B virus (HBV) vaccine and that a wide range of antibody levels were elicited after three doses. The immune mechanisms responsible for this vaccine response variability is unclear. Using single cell RNA sequencing of sorted innate immune cell subsets, we identified two distinct myeloid dendritic cell subsets (NDRG1-expressing mDC2 and CDKN1C-expressing mDC4), the ratio of which at baseline (pre-vaccination) correlated with the immune response to a single dose of HBV vaccine. Our results suggest that the participants in our vaccine study were in one of two different dendritic cell dispositional states at baseline – an NDRG2-mDC2 state in which the vaccine elicited an antibody response after a single immunization or a CDKN1C-mDC4 state in which the vaccine required two or three doses for induction of antibody responses. To explore this correlation further, genes expressed in these mDC subsets were used for feature selection prior to the construction of predictive models using supervised canonical correlation machine learning. The resulting models showed an improved correlation with serum antibody titers in response to full vaccination. Taken together, these results suggest that the propensity of circulating dendritic cells toward either activation or suppression, their “dispositional endotype” at pre-vaccination baseline, could dictate response to vaccination.
Collapse
Affiliation(s)
- Brian D Aevermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Casey P Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada.,The University of British Columbia (UBC) Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada
| | - Mark Novotny
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Rym Ben-Othman
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.,Telethon Kids Institute, Perth Children's Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Bing Cai
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Yun Zhang
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
| | - Jamie C Ye
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada.,The University of British Columbia (UBC) Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada
| | - Michael S Kobor
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Nicole Gladish
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Amy Huei-Yi Lee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Travis M Blimkie
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Robert E Hancock
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Alba Llibre
- Translational Immunology Lab, Institut Pasteur, Paris, France
| | - Darragh Duffy
- Translational Immunology Lab, Institut Pasteur, Paris, France
| | - Wayne C Koff
- Human Vaccines Project, New York, NY, United States
| | - Manish Sadarangani
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.,Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence, St. Paul's Hospital, Vancouver, BC, Canada.,The University of British Columbia (UBC) Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada.,Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Tobias R Kollmann
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada.,Telethon Kids Institute, Perth Children's Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States.,Department of Pathology, University of California, San Diego, San Diego, CA, United States.,Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| |
Collapse
|
397
|
Roy R, Ramamoorthy S, Shapiro BD, Kaileh M, Hernandez D, Sarantopoulou D, Arepalli S, Boller S, Singh A, Bektas A, Kim J, Moore AZ, Tanaka T, McKelvey J, Zukley L, Nguyen C, Wallace T, Dunn C, Wersto R, Wood W, Piao Y, Becker KG, Coletta C, De S, Sen JM, Battle A, Weng NP, Grosschedl R, Ferrucci L, Sen R. DNA methylation signatures reveal that distinct combinations of transcription factors specify human immune cell epigenetic identity. Immunity 2021; 54:2465-2480.e5. [PMID: 34706222 DOI: 10.1016/j.immuni.2021.10.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 06/06/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022]
Abstract
Epigenetic reprogramming underlies specification of immune cell lineages, but patterns that uniquely define immune cell types and the mechanisms by which they are established remain unclear. Here, we identified lineage-specific DNA methylation signatures of six immune cell types from human peripheral blood and determined their relationship to other epigenetic and transcriptomic patterns. Sites of lineage-specific hypomethylation were associated with distinct combinations of transcription factors in each cell type. By contrast, sites of lineage-specific hypermethylation were restricted mostly to adaptive immune cells. PU.1 binding sites were associated with lineage-specific hypo- and hypermethylation in different cell types, suggesting that it regulates DNA methylation in a context-dependent manner. These observations indicate that innate and adaptive immune lineages are specified by distinct epigenetic mechanisms via combinatorial and context-dependent use of key transcription factors. The cell-specific epigenomics and transcriptional patterns identified serve as a foundation for future studies on immune dysregulation in diseases and aging.
Collapse
Affiliation(s)
- Roshni Roy
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | | | - Benjamin D Shapiro
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Mary Kaileh
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, Baltimore, MD, USA
| | - Dimitra Sarantopoulou
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Sampath Arepalli
- Laboratory of Neurogenetics, National Institute on Aging, Baltimore, MD, USA
| | - Sören Boller
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Amit Singh
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Arsun Bektas
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Jaekwan Kim
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Ann Zenobia Moore
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Julia McKelvey
- Clinical Research Core, National Institute on Aging, Baltimore, MD, USA
| | - Linda Zukley
- Clinical Research Core, National Institute on Aging, Baltimore, MD, USA
| | - Cuong Nguyen
- Flow Cytometry Unit, National Institute on Aging, Baltimore, MD, USA
| | - Tonya Wallace
- Flow Cytometry Unit, National Institute on Aging, Baltimore, MD, USA
| | - Christopher Dunn
- Flow Cytometry Unit, National Institute on Aging, Baltimore, MD, USA
| | - Robert Wersto
- Flow Cytometry Unit, National Institute on Aging, Baltimore, MD, USA
| | - William Wood
- Laboratory of Genetics & Genomics, National Institute on Aging, Baltimore, MD, USA
| | - Yulan Piao
- Laboratory of Genetics & Genomics, National Institute on Aging, Baltimore, MD, USA
| | - Kevin G Becker
- Laboratory of Genetics & Genomics, National Institute on Aging, Baltimore, MD, USA
| | - Christopher Coletta
- Laboratory of Genetics & Genomics, National Institute on Aging, Baltimore, MD, USA
| | - Supriyo De
- Laboratory of Genetics & Genomics, National Institute on Aging, Baltimore, MD, USA
| | - Jyoti Misra Sen
- Laboratory of Clinical Investigation, National Institute on Aging, Baltimore, MD, USA
| | - Alexis Battle
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Nan-Ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA
| | - Rudolf Grosschedl
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, USA.
| |
Collapse
|
398
|
Charras A, Garau J, Hofmann SR, Carlsson E, Cereda C, Russ S, Abraham S, Hedrich CM. DNA Methylation Patterns in CD8 + T Cells Discern Psoriasis From Psoriatic Arthritis and Correlate With Cutaneous Disease Activity. Front Cell Dev Biol 2021; 9:746145. [PMID: 34746142 PMCID: PMC8567019 DOI: 10.3389/fcell.2021.746145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/16/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Psoriasis is a T cell-mediated chronic autoimmune/inflammatory disease. While some patients experience disease limited to the skin (skin psoriasis), others develop joint involvement (psoriatic arthritis; PsA). In the absence of disease- and/or outcome-specific biomarkers, and as arthritis can precede skin manifestations, diagnostic and therapeutic delays are common and contribute to disease burden and damage accrual. Objective: Altered epigenetic marks, including DNA methylation, contribute to effector T cell phenotypes and altered cytokine expression in autoimmune/inflammatory diseases. This project aimed at the identification of disease-/outcome-specific DNA methylation signatures in CD8+ T cells from patients with psoriasis and PsA as compared to healthy controls. Method: Peripheral blood CD8+ T cells from nine healthy controls, 10 psoriasis, and seven PsA patients were collected to analyze DNA methylation marks using Illumina Human Methylation EPIC BeadChips (>850,000 CpGs per sample). Bioinformatic analysis was performed using R (minfi, limma, ChAMP, and DMRcate packages). Results: DNA methylation profiles in CD8+ T cells differentiate healthy controls from psoriasis patients [397 Differentially Methylated Positions (DMPs); 9 Differentially Methylated Regions (DMRs) when ≥CpGs per DMR were considered; 2 DMRs for ≥10 CpGs]. Furthermore, patients with skin psoriasis can be discriminated from PsA patients [1,861 DMPs, 20 DMRs (≥5 CpGs per region), 4 DMRs (≥10 CpGs per region)]. Gene ontology (GO) analyses considering genes with ≥1 DMP in their promoter delivered methylation defects in skin psoriasis and PsA primarily affecting the BMP signaling pathway and endopeptidase regulator activity, respectively. GO analysis of genes associated with DMRs between skin psoriasis and PsA demonstrated an enrichment of GABAergic neuron and cortex neuron development pathways. Treatment with cytokine blockers associated with DNA methylation changes [2,372 DMPs; 1,907 DMPs within promoters, 7 DMRs (≥5 CpG per regions)] affecting transforming growth factor beta receptor and transmembrane receptor protein serine/threonine kinase signaling pathways. Lastly, a methylation score including TNF and IL-17 pathway associated DMPs inverse correlates with skin disease activity scores (PASI). Conclusion: Patients with skin psoriasis exhibit DNA methylation patterns in CD8+ T cells that allow differentiation from PsA patients and healthy individuals, and reflect clinical activity of skin disease. Thus, DNA methylation profiling promises potential as diagnostic and prognostic tool to be used for molecular patient stratification toward individualized treatment.
Collapse
Affiliation(s)
- Amandine Charras
- Department of Women's and Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Jessica Garau
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Sigrun R Hofmann
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Emil Carlsson
- Department of Women's and Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Cristina Cereda
- Genomic and Post-Genomic Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Susanne Russ
- Klinik und Poliklinik für Kinder- und Jugendmedizin, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Susanne Abraham
- Klinik und Poliklinik für Dermatologie, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Christian M Hedrich
- Department of Women's and Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom.,Department of Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust Hospital, Liverpool, United Kingdom
| |
Collapse
|
399
|
Lecamwasam A, Novakovic B, Meyer B, Ekinci EI, Dwyer KM, Saffery R. DNA methylation profiling identifies epigenetic differences between early versus late stages of diabetic chronic kidney disease. Nephrol Dial Transplant 2021; 36:2027-2038. [PMID: 33146725 DOI: 10.1093/ndt/gfaa226] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND We investigated a cross-sectional epigenome-wide association study of patients with early and late diabetes-associated chronic kidney disease (CKD) to identify possible epigenetic differences between the two groups as well as changes in methylation across all stages of diabetic CKD. We also evaluated the potential of using a panel of identified 5'-C-phosphate-G-3' (CpG) sites from this cohort to predict the progression of diabetic CKD. METHODS This cross-sectional study recruited 119 adults. DNA was extracted from blood using the Qiagen QIAampDNA Mini Spin Kit. Genome-wide methylation analysis was performed using Illumina Infinium MethylationEPIC BeadChips (HM850K). Intensity data files were processed and analysed using the minfi and MissMethyl packages for R. We examined the degree of methylation of CpG sites in early versus late diabetic CKD patients for CpG sites with an unadjusted P-value <0.01 and an absolute change in methylation of 5% (n = 239 CpG sites). RESULTS Hierarchical clustering of the 239 CpG sites largely separated the two groups. A heat map for all 239 CpG sites demonstrated distinct methylation patterns in the early versus late groups, with CpG sites showing evidence of progressive change. Based on our differentially methylated region (DMR) analysis of the 239 CpG sites, we highlighted two DMRs, namely the cysteine-rich secretory protein 2 (CRISP2) and piwi-like RNA-mediated gene silencing 1 (PIWIL1) genes. The best predictability for the two groups involved a receiver operating characteristics curve of eight CpG sites alone and achieved an area under the curve of 0.976. CONCLUSIONS We have identified distinct DNA methylation patterns between early and late diabetic CKD patients as well as demonstrated novel findings of potential progressive methylation changes across all stages (1-5) of diabetic CKD at specific CpG sites. We have also identified associated genes CRISP2 and PIWIL1, which may have the potential to act as stage-specific diabetes-associated CKD markers, and showed that the use of a panel of eight identified CpG sites alone helps to increase the predictability for the two groups.
Collapse
Affiliation(s)
| | - Boris Novakovic
- Epigenetics Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Braydon Meyer
- Epigenetics Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Elif I Ekinci
- Department of Endocrinology, Austin Health, Melbourne, Victoria, Australia.,Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Karen M Dwyer
- School of Medicine, Faculty of Health, Deakin University, Melbourne, Victoria, Australia
| | - Richard Saffery
- Epigenetics Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| |
Collapse
|
400
|
Wu N, Yuan F, Yue S, Jiang F, Ren D, Liu L, Bi Y, Guo Z, Ji L, Han K, Yang X, Feng M, Su K, Yang F, Wu X, Lu Q, Li X, Wang R, Liu B, Le S, Shi Y, He G. Effect of exercise and diet intervention in NAFLD and NASH via GAB2 methylation. Cell Biosci 2021; 11:189. [PMID: 34736535 PMCID: PMC8569968 DOI: 10.1186/s13578-021-00701-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/25/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Nonalcoholic fatty liver disease (NAFLD) is a disorder that extends from simple hepatic steatosis to nonalcoholic steatohepatitis (NASH), which is effectively alleviated by lifestyle intervention. Nevertheless, DNA methylation mechanism underling the effect of environmental factors on NAFLD and NASH is still obscure. The aim of this study was to investigate the effect of exercise and diet intervention in NAFLD and NASH via DNA methylation of GAB2. METHODS Methylation of genomic DNA in human NAFLD was quantified using Infinium Methylation EPIC BeadChip assay after exercise (Ex), low carbohydrate diet (LCD) and exercise plus low carbohydrate diet (ELCD) intervention. The output Idat files were processed using ChAMP package. False discovery rate on genome-wide analysis of DNA methylation (q < 0.05), and cytosine-guanine dinucleotides (CpGs) which are located in promoters were used for subsequent analysis (|Δβ|≥ 0.1). K-means clustering was used to cluster differentially methylated genes according to 3D genome information from Human embryonic stem cell. To quantify DNA methylation and mRNA expression of GRB2 associated binding protein 2 (GAB2) in NASH mice after Ex, low fat diet (LFD) and exercise plus low fat diet (ELFD), MassARRAY EpiTYPER and quantitative reverse transcription polymerase chain reaction were used. RESULTS Both LCD and ELCD intervention on human NAFLD can induce same DNA methylation alterations at critical genes in blood, e.g., GAB2, which was also validated in liver and adipose of NASH mice after LFD and ELFD intervention. Moreover, methylation of CpG units (i.e., CpG_10.11.12) inversely correlated with mRNA expression GAB2 in adipose tissue of NASH mice after ELFD intervention. CONCLUSIONS We highlighted the susceptibility of DNA methylation in GAB2 to ELFD intervention, through which exercise and diet can protect against the progression of NAFLD and NASH on the genome level, and demonstrated that the DNA methylation variation in blood could mirror epigenetic signatures in target tissues of important biological function, i.e., liver and adipose tissue. Trial registration International Standard Randomized Controlled Trial Number Register (ISRCTN 42622771).
Collapse
Affiliation(s)
- Na Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Fan Yuan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Siran Yue
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Fengyan Jiang
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Decheng Ren
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Liangjie Liu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Bi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Zhenming Guo
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Ji
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Ke Han
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Mofan Feng
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Kai Su
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Fengping Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xi Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Qing Lu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Xingwang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China.,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Ruirui Wang
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Baocheng Liu
- Shanghai Innovation Center of Traditional Chinese Medicine Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shenglong Le
- Exercise Translational Medicine Center, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Yi Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China. .,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China.
| | - Guang He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030, China. .,Shanghai Key Laboratory of Psychotic Disorders, and Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|