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Hellbach F, Freuer D, Meisinger C, Peters A, Winkelmann J, Costeira R, Hauner H, Baumeister SE, Bell JT, Waldenberger M, Linseisen J. Usual dietary intake and change in DNA methylation over years: EWAS in KORA FF4 and KORA fit. Front Nutr 2024; 10:1295078. [PMID: 38249614 PMCID: PMC10799384 DOI: 10.3389/fnut.2023.1295078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction Changes in DNA methylation can increase or suppress the expression of health-relevant genes. We investigated for the first time the relationship between habitual food consumption and changes in DNA methylation. Methods The German KORA FF4 and KORA Fit studies were used to study the change in methylation over a median follow-up of 4 years. Only subjects participating in both surveys and with available dietary and methylation data were included in the analysis (n = 465). DNA methylation was measured using the Infinium MethylationEPIC BeadChip (Illumina), resulting in 735,527 shared CpGs across both studies. Generalized estimating equation models with an interaction term of exposure and time point were used to analyze the association of 34 food groups, folic acid, and two dietary patterns with changes in DNA methylation over time. Results The results were corrected for genomic inflation. Significant interaction terms indicate different effects between both time points. We observed only a few significant associations between food intake and change in DNA methylation, except for cream and spirit consumption. The annotated genes include CLN3, PROM1, DLEU7, TLL2, and UGT1A10. Discussion We identified weak associations between food consumption and DNA methylation change. The differential results for cream and spirits, both consumed in low quantities, require replication in independent studies.
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Affiliation(s)
- Fabian Hellbach
- Department of Epidemiology, Faculty of Medicine, University of Augsburg, University Hospital Augsburg, Augsburg, Germany
- Medical Faculty, Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilian University Munich, Munich, Germany
| | - Dennis Freuer
- Department of Epidemiology, Faculty of Medicine, University of Augsburg, University Hospital Augsburg, Augsburg, Germany
| | - Christa Meisinger
- Department of Epidemiology, Faculty of Medicine, University of Augsburg, University Hospital Augsburg, Augsburg, Germany
| | - Annette Peters
- Medical Faculty, Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilian University Munich, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Juliane Winkelmann
- Institute of Neurogenomic, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Technical University of Munich, Institute of Human Genetics, Klinikum Rechts der Isar, Munich, Germany
| | - Ricardo Costeira
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Hans Hauner
- Else Kröner-Fresenius-Center for Nutritional Medicine, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- School of Medicine, Institute of Nutritional Medicine, Technical University of Munich, Munich, Germany
| | - Sebastian-Edgar Baumeister
- Medical Faculty, Institute of Health Services Research in Dentistry, University of Münster, Münster, Germany
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Melanie Waldenberger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Jakob Linseisen
- Department of Epidemiology, Faculty of Medicine, University of Augsburg, University Hospital Augsburg, Augsburg, Germany
- Medical Faculty, Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilian University Munich, Munich, Germany
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Beltrán-García J, Casabó-Vallés G, Osca-Verdegal R, Navarrete-López P, Rodriguez-Gimillo M, Nacher-Sendra E, Ferrando-Sánchez C, García-López E, Pallardó FV, Carbonell N, Mena-Mollá S, García-Giménez JL. Alterations in leukocyte DNA methylome are associated to immunosuppression in severe clinical phenotypes of septic patients. Front Immunol 2024; 14:1333705. [PMID: 38235139 PMCID: PMC10791922 DOI: 10.3389/fimmu.2023.1333705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024] Open
Abstract
Introduction Sepsis patients experience a complex interplay of host pro- and anti-inflammatory processes which compromise the clinical outcome. Despite considering the latest clinical and scientific research, our comprehension of the immunosuppressive events in septic episodes remains incomplete. Additionally, a lack of data exists regarding the role of epigenetics in modulating immunosuppression, subsequently impacting patient survival. Methods To advance the current understanding of the mechanisms underlying immunosuppression, in this study we explored the dynamics of DNA methylation using the Infinium Methylation EPIC v1.0 BeadChip Kit in leukocytes from patients suffering from sepsis, septic shock, and critically ill patients as controls, within the first 24 h after admission in the Intensive Care Unit of a tertiary hospital. Results and discussion Employing two distinct analysis approaches (DMRcate and mCSEA) in comparing septic shock and critically ill patients, we identified 1,256 differentially methylated regions (DMRs) intricately linked to critical immune system pathways. The examination of the top 100 differentially methylated positions (DMPs) between septic shock and critically ill patients facilitated a clear demarcation among the three patient groups. Notably, the top 6,657 DMPs exhibited associations with organ dysfunction and lactate levels. Among the individual genes displaying significant differential methylation, IL10, TREM1, IL1B, and TNFAIP8 emerged with the most pronounced methylation alterations across the diverse patient groups when subjected to DNA bisulfite pyrosequencing analysis. These findings underscore the dynamic nature of DNA methylation profiles, highlighting the most pronounced alterations in patients with septic shock, and revealing their close association with the disease.
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Affiliation(s)
- Jesús Beltrán-García
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Carlos III Health Institute, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
- Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Germán Casabó-Vallés
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
- EpiDisease S. L. (Spin-Off CIBER-ISCIII), Parc Científic de la Universitat de València, Valencia, Spain
| | - Rebeca Osca-Verdegal
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Carlos III Health Institute, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
- Salk Institute for Biological Studies, San Diego, CA, United States
| | - Paula Navarrete-López
- Department of Animal Reproduction, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)-Centro Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - María Rodriguez-Gimillo
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Intensive Care Unit, Hospital Clínico Universitario de Valencia (HCUV), Valencia, Spain
| | - Elena Nacher-Sendra
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Carolina Ferrando-Sánchez
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Intensive Care Unit, Hospital Clínico Universitario de Valencia (HCUV), Valencia, Spain
| | - Eva García-López
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Carlos III Health Institute, Valencia, Spain
- EpiDisease S. L. (Spin-Off CIBER-ISCIII), Parc Científic de la Universitat de València, Valencia, Spain
| | - Federico V Pallardó
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Carlos III Health Institute, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Nieves Carbonell
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Intensive Care Unit, Hospital Clínico Universitario de Valencia (HCUV), Valencia, Spain
| | - Salvador Mena-Mollá
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - José Luis García-Giménez
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Carlos III Health Institute, Valencia, Spain
- INCLIVA Biomedical Research Institute, Valencia, Spain
- Department of Physiology, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
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103
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Farrell C, Hu C, Lapborisuth K, Pu K, Snir S, Pellegrini M. Identifying epigenetic aging moderators using the epigenetic pacemaker. FRONTIERS IN BIOINFORMATICS 2024; 3:1308680. [PMID: 38235295 PMCID: PMC10791860 DOI: 10.3389/fbinf.2023.1308680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/04/2023] [Indexed: 01/19/2024] Open
Abstract
Epigenetic clocks are DNA methylation-based chronological age prediction models that are commonly employed to study age-related biology. The difference between the predicted and observed age is often interpreted as a form of biological age acceleration, and many studies have measured the impact of environmental and disease-associated factors on epigenetic age. Most epigenetic clocks are fit using approaches that minimize the error between the predicted and observed chronological age, and as a result, they may not accurately model the impact of factors that moderate the relationship between the actual and epigenetic age. Here, we compare epigenetic clocks that are constructed using penalized regression methods to an evolutionary framework of epigenetic aging with the epigenetic pacemaker (EPM), which directly models DNA methylation as a function of a time-dependent epigenetic state. In simulations, we show that the value of the epigenetic state is impacted by factors such as age, sex, and cell-type composition. Next, in a dataset aggregated from previous studies, we show that the epigenetic state is also moderated by sex and the cell type. Finally, we demonstrate that the epigenetic state is also moderated by toxins in a study on polybrominated biphenyl exposure. Thus, we find that the pacemaker provides a robust framework for the study of factors that impact epigenetic age acceleration and that the effect of these factors may be obscured in traditional clocks based on linear regression models.
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Affiliation(s)
- Colin Farrell
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Chanyue Hu
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kalsuda Lapborisuth
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kyle Pu
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Sagi Snir
- Department of Evolutionary Biology, University of Haifa, Haifa, Israel
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
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104
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Schöpf J, Uhrig S, Heilig CE, Lee KS, Walther T, Carazzato A, Dobberkau AM, Weichenhan D, Plass C, Hartmann M, Diwan GD, Carrero ZI, Ball CR, Hohl T, Kindler T, Rudolph-Hähnel P, Helm D, Schneider M, Nilsson A, Øra I, Imle R, Banito A, Russell RB, Jones BC, Lipka DB, Glimm H, Hübschmann D, Hartmann W, Fröhling S, Scholl C. Multi-omic and functional analysis for classification and treatment of sarcomas with FUS-TFCP2 or EWSR1-TFCP2 fusions. Nat Commun 2024; 15:51. [PMID: 38168093 PMCID: PMC10761971 DOI: 10.1038/s41467-023-44360-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Linking clinical multi-omics with mechanistic studies may improve the understanding of rare cancers. We leverage two precision oncology programs to investigate rhabdomyosarcoma with FUS/EWSR1-TFCP2 fusions, an orphan malignancy without effective therapies. All tumors exhibit outlier ALK expression, partly accompanied by intragenic deletions and aberrant splicing resulting in ALK variants that are oncogenic and sensitive to ALK inhibitors. Additionally, recurrent CKDN2A/MTAP co-deletions provide a rationale for PRMT5-targeted therapies. Functional studies show that FUS-TFCP2 blocks myogenic differentiation, induces transcription of ALK and truncated TERT, and inhibits DNA repair. Unlike other fusion-driven sarcomas, TFCP2-rearranged tumors exhibit genomic instability and signs of defective homologous recombination. DNA methylation profiling demonstrates a close relationship with undifferentiated sarcomas. In two patients, sarcoma was preceded by benign lesions carrying FUS-TFCP2, indicating stepwise sarcomagenesis. This study illustrates the potential of linking precision oncology with preclinical research to gain insight into the classification, pathogenesis, and therapeutic vulnerabilities of rare cancers.
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Affiliation(s)
- Julia Schöpf
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), and National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sebastian Uhrig
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg, and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Christoph E Heilig
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Kwang-Seok Lee
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Tatjana Walther
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Alexander Carazzato
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Anna Maria Dobberkau
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | | | | | - Mark Hartmann
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Gaurav D Diwan
- Bioquant, Heidelberg University, Heidelberg, Germany
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Zunamys I Carrero
- Department for Translational Medical Oncology, NCT, NCT/UCC Dresden, a Partnership Between DKFZ, Heidelberg Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
| | - Claudia R Ball
- Department for Translational Medical Oncology, NCT, NCT/UCC Dresden, a Partnership Between DKFZ, Heidelberg Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD, Dresden, Germany
- Faculty of Biology, TUD Dresden University of Technology, Dresden, Germany
| | - Tobias Hohl
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), and National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Thomas Kindler
- University Cancer Center Mainz, Johannes Gutenberg University Mainz, Mainz, Germany
- Department of Hematology, Medical Oncology and Pneumology, University Medical Center, Mainz, Germany
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Patricia Rudolph-Hähnel
- University Cancer Center Mainz, Johannes Gutenberg University Mainz, Mainz, Germany
- Department of Hematology, Medical Oncology and Pneumology, University Medical Center, Mainz, Germany
- German Cancer Consortium (DKTK), Mainz, Germany
| | - Dominic Helm
- Proteomics Core Facility, DKFZ, Heidelberg, Germany
| | | | - Anna Nilsson
- Pediatric Oncology and Coagulation, Karolinska University Hospital, Stockholm, Sweden
| | - Ingrid Øra
- Pediatric Oncology and Hematology, Skåne University Hospital, Lund University, Lund, Sweden
| | - Roland Imle
- Soft-Tissue Sarcoma Junior Research Group, DKFZ, Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ) and NCT Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ana Banito
- Soft-Tissue Sarcoma Junior Research Group, DKFZ, Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ) and NCT Heidelberg, Heidelberg, Germany
| | - Robert B Russell
- Bioquant, Heidelberg University, Heidelberg, Germany
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Barbara C Jones
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Hopp Children's Cancer Center (KiTZ) and NCT Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Daniel B Lipka
- Section of Translational Cancer Epigenomics, Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany
| | - Hanno Glimm
- Department for Translational Medical Oncology, NCT, NCT/UCC Dresden, a Partnership Between DKFZ, Heidelberg Faculty of Medicine and University Hospital Carl Gustav Carus, TUD Dresden University of Technology, and Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- German Cancer Consortium (DKTK), Dresden, Germany
- Translational Medical Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TUD, Dresden, Germany
- Translational Functional Cancer Genomics, DKFZ, Heidelberg, Germany
| | - Daniel Hübschmann
- Computational Oncology Group, Molecular Precision Oncology Program, NCT Heidelberg, and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Pattern Recognition and Digital Medicine Group, Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | - Wolfgang Hartmann
- Gerhard Domagk Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Stefan Fröhling
- Division of Translational Medical Oncology, DKFZ, and NCT Heidelberg, Heidelberg, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.
| | - Claudia Scholl
- Division of Applied Functional Genomics, German Cancer Research Center (DKFZ), and National Center for Tumor Diseases (NCT), NCT Heidelberg, a Partnership Between DKFZ and Heidelberg University Hospital, Heidelberg, Germany.
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Stone TC, Ward V, Hogan A, Alexander Ho KM, Wilson A, McBain H, Duku M, Wolfson P, Cheung S, Rosenfeld A, Lovat LB. Using saliva epigenetic data to develop and validate a multivariable predictor of esophageal cancer status. Epigenomics 2024; 16:109-125. [PMID: 38226541 PMCID: PMC10825730 DOI: 10.2217/epi-2023-0248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 01/04/2024] [Indexed: 01/17/2024] Open
Abstract
Background: Salivary epigenetic biomarkers may detect esophageal cancer. Methods: A total of 256 saliva samples from esophageal adenocarcinoma patients and matched volunteers were analyzed with Illumina EPIC methylation arrays. Three datasets were created, using 64% for discovery, 16% for testing and 20% for validation. Modules of gene-based methylation probes were created using weighted gene coexpression network analysis. Module significance to disease and gene importance to module were determined and a random forest classifier generated using best-scoring gene-related epigenetic probes. A cost-sensitive wrapper algorithm maximized cancer diagnosis. Results: Using age, sex and seven probes, esophageal adenocarcinoma was detected with area under the curve of 0.72 in discovery, 0.73 in testing and 0.75 in validation datasets. Cancer sensitivity was 88% with specificity of 31%. Conclusion: We have demonstrated a potentially clinically viable classifier of esophageal cancer based on saliva methylation.
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Affiliation(s)
- Timothy C Stone
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Vanessa Ward
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Aine Hogan
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Kai Man Alexander Ho
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
- Wellcome/EPSRC Centre for Interventional & Surgical Sciences (WEISS), University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Ash Wilson
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Hazel McBain
- Wellcome/EPSRC Centre for Interventional & Surgical Sciences (WEISS), University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Margaret Duku
- Wellcome/EPSRC Centre for Interventional & Surgical Sciences (WEISS), University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Paul Wolfson
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Sharon Cheung
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
| | - Avi Rosenfeld
- Department of Computer Science, Jerusalem College of Technology, Havaad Haleumi 21, Givat Mordechai, 91160, Jerusalem, Israel
| | - Laurence B Lovat
- Division of Surgery & Interventional Science, University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
- Wellcome/EPSRC Centre for Interventional & Surgical Sciences (WEISS), University College London, Charles Bell House, 43-45 Foley Street, London, W1W 7TY, UK
- Department of Gastrointestinal Services, University College London Hospital, 235 Euston Road, London, NW1 2BU, UK
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106
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Hong X, Miao K, Cao W, Lv J, Yu C, Huang T, Sun D, Liao C, Pang Y, Hu R, Pang Z, Yu M, Wang H, Wu X, Liu Y, Gao W, Li L. Association of psychological distress and DNA methylation: A 5-year longitudinal population-based twin study. Psychiatry Clin Neurosci 2024; 78:51-59. [PMID: 37793011 DOI: 10.1111/pcn.13606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/06/2023]
Abstract
AIM To identify the psychological distress (PD)-associated 5'-cytosine-phosphate-guanine-3' sites (CpGs), and investigate the temporal relationship between dynamic changes in DNA methylation (DNAm) and PD. METHODS This study included 1084 twins from the Chinese National Twin Register (CNTR). The CNTR conducted epidemiological investigations and blood withdrawal twice in 2013 and 2018. These included twins were used to perform epigenome-wide association studies (EWASs) and to validate the previously reported PD-associated CpGs selected from previous EWASs in PubMed, Embase, and the EWAS catalog. Next, a cross-lagged study was performed to examine the temporality between changes in DNAm and PD in 308 twins who completed both 2013 and 2018 surveys. RESULTS The EWAS analysis of our study identified 25 CpGs. In the validation analysis, 741 CpGs from 29 previous EWASs on PD were selected for validation, and 101 CpGs were validated to be significant at a false discovery rate <0.05. The cross-lagged analysis found a unidirectional path from PD to DNAm at 14 CpGs, while no sites showed significance from DNAm to PD. CONCLUSIONS This study identified and validated PD-related CpGs in a Chinese twin population, and suggested that PD may be the cause of changes in DNAm over time. The findings provide new insights into the molecular mechanisms underlying PD pathophysiology.
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Affiliation(s)
- Xuanming Hong
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, China
| | - Ke Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, China
| | - Weihua Cao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, China
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, China
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, China
| | - Tao Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, China
| | - Dianjianyi Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, China
| | - Chunxiao Liao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, China
| | - Yuanjie Pang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, China
| | - Runhua Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, China
| | - Zengchang Pang
- Qingdao Center for Disease Control and Prevention, Qingdao, China
| | - Min Yu
- Zhejiang Center for Disease Control and Prevention, Hangzhou, China
| | - Hua Wang
- Jiangsu Center for Disease Control and Prevention, Nanjing, China
| | - Xianping Wu
- Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Yu Liu
- Heilongjiang Center for Disease Control and Prevention, Harbin, China
| | - Wenjing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, China
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Epidemiology of Major Diseases, Ministry of Education, Peking University, Beijing, China
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Patel RA, Sayar E, Coleman I, Roudier MP, Hanratty B, Low JY, Jaiswal N, Ajkunic A, Dumpit R, Ercan C, Salama N, O’Brien VP, Isaacs WB, Epstein JI, De Marzo AM, Trock BJ, Luo J, Brennen WN, Tretiakova M, Vakar-Lopez F, True LD, Goodrich DW, Corey E, Morrissey C, Nelson PS, Hurley PJ, Gulati R, Haffner MC. Characterization of HOXB13 expression patterns in localized and metastatic castration-resistant prostate cancer. J Pathol 2024; 262:105-120. [PMID: 37850574 PMCID: PMC10871027 DOI: 10.1002/path.6216] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/16/2023] [Accepted: 09/08/2023] [Indexed: 10/19/2023]
Abstract
HOXB13 is a key lineage homeobox transcription factor that plays a critical role in the differentiation of the prostate gland. Several studies have suggested that HOXB13 alterations may be involved in prostate cancer development and progression. Despite its potential biological relevance, little is known about the expression of HOXB13 across the disease spectrum of prostate cancer. To this end, we validated a HOXB13 antibody using genetic controls and investigated HOXB13 protein expression in murine and human developing prostates, localized prostate cancers, and metastatic castration-resistant prostate cancers. We observed that HOXB13 expression increases during later stages of murine prostate development. All localized prostate cancers showed HOXB13 protein expression. Interestingly, lower HOXB13 expression levels were observed in higher-grade tumors, although no significant association between HOXB13 expression and recurrence or disease-specific survival was found. In advanced metastatic prostate cancers, HOXB13 expression was retained in the majority of tumors. While we observed lower levels of HOXB13 protein and mRNA levels in tumors with evidence of lineage plasticity, 84% of androgen receptor-negative castration-resistant prostate cancers and neuroendocrine prostate cancers (NEPCs) retained detectable levels of HOXB13. Notably, the reduced expression observed in NEPCs was associated with a gain of HOXB13 gene body CpG methylation. In comparison to the commonly used prostate lineage marker NKX3.1, HOXB13 showed greater sensitivity in detecting advanced metastatic prostate cancers. Additionally, in a cohort of 837 patients, 383 with prostatic and 454 with non-prostatic tumors, we found that HOXB13 immunohistochemistry had a 97% sensitivity and 99% specificity for prostatic origin. Taken together, our studies provide valuable insight into the expression pattern of HOXB13 during prostate development and cancer progression. Furthermore, our findings support the utility of HOXB13 as a diagnostic biomarker for prostate cancer, particularly to confirm the prostatic origin of advanced metastatic castration-resistant tumors. © 2023 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Radhika A. Patel
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Erolcan Sayar
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ilsa Coleman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Brian Hanratty
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jin-Yih Low
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Neha Jaiswal
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Azra Ajkunic
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ruth Dumpit
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Caner Ercan
- Institute of Pathology and Medical Genetics, University Hospital Basel, Basel, Switzerland
| | - Nina Salama
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Valerie P. O’Brien
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - William B. Isaacs
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Jonathan I. Epstein
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Department of Pathology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Angelo M. De Marzo
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Department of Pathology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Bruce J. Trock
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Jun Luo
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - W Nathaniel Brennen
- Department of Urology, Johns Hopkins University School of Medicine, MD, Baltimore, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, MD, Baltimore, USA
| | - Maria Tretiakova
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Funda Vakar-Lopez
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Lawrence D. True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - David W. Goodrich
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Paula J. Hurley
- Departments of Medicine and Urology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Roman Gulati
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, WA, USA
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108
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Gallardo-Gómez M, Costas-Ríos L, Garcia-Prieto CA, Álvarez-Rodríguez L, Bujanda L, Barrero M, Castells A, Balaguer F, Jover R, Esteller M, Tardío Baiges A, González-Carreró Fojón J, Cubiella J, De Chiara L. Serum DNA methylome of the colorectal cancer serrated pathway enables non-invasive detection. Mol Oncol 2023. [PMID: 38129291 DOI: 10.1002/1878-0261.13573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/07/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023] Open
Abstract
The clinical relevance of the colorectal cancer serrated pathway is evident, but the screening of serrated lesions remains challenging. We aimed to characterize the serum methylome of the serrated pathway and to evaluate circulating cell-free DNA (cfDNA) methylomes as a potential source of biomarkers for the non-invasive detection of serrated lesions. We collected serum samples from individuals with serrated adenocarcinoma (SAC), traditional serrated adenomas, sessile serrated lesions, hyperplastic polyps and individuals with no colorectal findings. First, we quantified cfDNA methylation with the MethylationEPIC array. Then, we compared the methylation profiles with tissue and serum datasets. Finally, we evaluated the utility of serum cfDNA methylation biomarkers. We identified a differential methylation profile able to distinguish high-risk serrated lesions from no serrated neoplasia, showing concordance with tissue methylation from SAC and sessile serrated lesions. Serum methylation profiles are pathway-specific, clearly separating serrated lesions from conventional adenomas. The combination of ninjurin 2 (NINJ2) and glutamate-rich 1 (ERICH1) methylation discriminated high-risk serrated lesions and SAC with 91.4% sensitivity (64.4% specificity), while zinc finger protein 718 (ZNF718) methylation reported 100% sensitivity for the detection of SAC (96% specificity). This is the first study exploring the serum methylome of serrated lesions. Differential methylation of cfDNA can be used for the non-invasive detection of colorectal serrated lesions.
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Affiliation(s)
- María Gallardo-Gómez
- CINBIO, Universidade de Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
| | - Lara Costas-Ríos
- CINBIO, Universidade de Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Spain
| | - Carlos A Garcia-Prieto
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Spain
| | - Lara Álvarez-Rodríguez
- CINBIO, Universidade de Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Spain
| | - Luis Bujanda
- Department of Gastroenterology, Biodonostia Health Research Institute, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad del País Vasco (UPV/EHU), San Sebastián, Spain
| | - Maialen Barrero
- Department of Oncology, Hospital Universitario Donostia, San Sebastián, Spain
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Spain
| | - Rodrigo Jover
- Servicio de Medicina Digestiva, Hospital General Universitario Dr. Balmis ISABIAL, Universidad Miguel Hernández, Alicante, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Spain
| | - Antoni Tardío Baiges
- Department of Pathology, Hospital Álvaro Cunqueiro, Instituto de Investigación Biomédica Galicia Sur, Vigo, Spain
| | | | - Joaquín Cubiella
- Department of Gastroenterology, Complexo Hospitalario Universitario de Ourense, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Ourense, Spain
| | - Loretta De Chiara
- CINBIO, Universidade de Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Spain
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109
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Chatterjee K, Mal S, Ghosh M, Chattopadhyay NR, Roy SD, Chakraborty K, Mukherjee S, Aier M, Choudhuri T. Blood-based DNA methylation in advanced Nasopharyngeal Carcinoma exhibited distinct CpG methylation signature. Sci Rep 2023; 13:22086. [PMID: 38086861 PMCID: PMC10716134 DOI: 10.1038/s41598-023-45001-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 10/14/2023] [Indexed: 12/18/2023] Open
Abstract
The TNM staging system is currently used to detect cancer stages. Regardless, a small proportion of cancer patients recur even after therapy, suggesting more specific molecular tools are required to justify the stage-specific detection and prompt cancer diagnosis. Thus, we aimed to explore the blood-based DNA methylation signature of metastatic nasopharyngeal carcinoma (NPC) to establish a holistic methylation biomarker panel. For the identification of methylation signature, the EPIC BeadChip-based array was performed. Comparative analysis for identifying unique probes, validation, and functional studies was investigated by analyzing GEO and TCGA datasets. We observed 4093 differentially methylated probes (DMPs), 1232 hydroxymethylated probes, and 25 CpG islands. Gene expression study revealed both upregulated and downregulated genes. Correlation analysis suggested a positive (with a positive r, p ≤ 0.05) and negative (with a negative r, p ≤ 0.05) association with different cancers. TFBS analysis exhibited the binding site for many TFs. Furthermore, gene enrichment analysis indicated the involvement of those identified genes in biological pathways. However, blood-based DNA methylation data uncovered a distinct DNA methylation pattern, which might have an additive role in NPC progression by altering the TFs binding. Moreover, based on tissue-specificity, a variation of correlation between methylation and gene expression was noted in different cancers.
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Affiliation(s)
- Koustav Chatterjee
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235
| | - Sudipa Mal
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235
| | - Monalisha Ghosh
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235
| | | | - Sankar Deb Roy
- Department of Radiation Oncology, Eden Medical Center, Dimapur, Nagaland, India
| | - Koushik Chakraborty
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235
| | - Syamantak Mukherjee
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235
| | - Moatoshi Aier
- Department of Pathology, Eden Medical Center, Dimapur, Nagaland, India
| | - Tathagata Choudhuri
- Department of Biotechnology, Visva-Bharati, Santiniketan, Birbhum, West Bengal, India, 731235.
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110
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Casella C, Kiles F, Urquhart C, Michaud DS, Kirwa K, Corlin L. Methylomic, Proteomic, and Metabolomic Correlates of Traffic-Related Air Pollution in the Context of Cardiorespiratory Health: A Systematic Review, Pathway Analysis, and Network Analysis. TOXICS 2023; 11:1014. [PMID: 38133415 PMCID: PMC10748071 DOI: 10.3390/toxics11121014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/18/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
A growing body of literature has attempted to characterize how traffic-related air pollution (TRAP) affects molecular and subclinical biological processes in ways that could lead to cardiorespiratory disease. To provide a streamlined synthesis of what is known about the multiple mechanisms through which TRAP could lead to cardiorespiratory pathology, we conducted a systematic review of the epidemiological literature relating TRAP exposure to methylomic, proteomic, and metabolomic biomarkers in adult populations. Using the 139 papers that met our inclusion criteria, we identified the omic biomarkers significantly associated with short- or long-term TRAP and used these biomarkers to conduct pathway and network analyses. We considered the evidence for TRAP-related associations with biological pathways involving lipid metabolism, cellular energy production, amino acid metabolism, inflammation and immunity, coagulation, endothelial function, and oxidative stress. Our analysis suggests that an integrated multi-omics approach may provide critical new insights into the ways TRAP could lead to adverse clinical outcomes. We advocate for efforts to build a more unified approach for characterizing the dynamic and complex biological processes linking TRAP exposure and subclinical and clinical disease and highlight contemporary challenges and opportunities associated with such efforts.
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Affiliation(s)
- Cameron Casella
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA; (C.C.); (F.K.); (C.U.); (D.S.M.); (K.K.)
| | - Frances Kiles
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA; (C.C.); (F.K.); (C.U.); (D.S.M.); (K.K.)
| | - Catherine Urquhart
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA; (C.C.); (F.K.); (C.U.); (D.S.M.); (K.K.)
| | - Dominique S. Michaud
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA; (C.C.); (F.K.); (C.U.); (D.S.M.); (K.K.)
| | - Kipruto Kirwa
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA; (C.C.); (F.K.); (C.U.); (D.S.M.); (K.K.)
- Department of Environmental Health, Boston University School of Public Health, Boston, MA 02118, USA
| | - Laura Corlin
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA; (C.C.); (F.K.); (C.U.); (D.S.M.); (K.K.)
- Department of Civil and Environmental Engineering, Tufts University School of Engineering, Medford, MA 02155, USA
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111
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Tuminello S, Nguyen E, Durmus N, Alptekin R, Yilmaz M, Crisanti MC, Snuderl M, Chen Y, Shao Y, Reibman J, Taioli E, Arslan AA. World Trade Center Exposure, DNA Methylation Changes, and Cancer: A Review of Current Evidence. EPIGENOMES 2023; 7:31. [PMID: 38131903 PMCID: PMC10742700 DOI: 10.3390/epigenomes7040031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/22/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction: Known carcinogens in the dust and fumes from the destruction of the World Trade Center (WTC) towers on 9 November 2001 included metals, asbestos, and organic pollutants, which have been shown to modify epigenetic status. Epigenome-wide association analyses (EWAS) using uniform (Illumina) methodology have identified novel epigenetic profiles of WTC exposure. Methods: We reviewed all published data, comparing differentially methylated gene profiles identified in the prior EWAS studies of WTC exposure. This included DNA methylation changes in blood-derived DNA from cases of cancer-free "Survivors" and those with breast cancer, as well as tissue-derived DNA from "Responders" with prostate cancer. Emerging molecular pathways related to the observed DNA methylation changes in WTC-exposed groups were explored and summarized. Results: WTC dust exposure appears to be associated with DNA methylation changes across the genome. Notably, WTC dust exposure appears to be associated with increased global DNA methylation; direct dysregulation of cancer genes and pathways, including inflammation and immune system dysregulation; and endocrine system disruption, as well as disruption of cholesterol homeostasis and lipid metabolism. Conclusion: WTC dust exposure appears to be associated with biologically meaningful DNA methylation changes, with implications for carcinogenesis and development of other chronic diseases.
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Affiliation(s)
- Stephanie Tuminello
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; (S.T.)
| | - Emelie Nguyen
- Institute for Translational Epidemiology, Icahn School of Medicine at Mount Sinai, New York, NY 10016, USA
| | - Nedim Durmus
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Ramazan Alptekin
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Muhammed Yilmaz
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | | | - Matija Snuderl
- Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Yu Chen
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; (S.T.)
- NYU Perlmutter Comprehensive Cancer Center, New York, NY 10016, USA
| | - Yongzhao Shao
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; (S.T.)
- NYU Perlmutter Comprehensive Cancer Center, New York, NY 10016, USA
| | - Joan Reibman
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
- Division of Environmental Medicine, Department of Medicine, NYU Grossman School of Medicine, New York University, New York, NY 10016, USA
| | - Emanuela Taioli
- Institute for Translational Epidemiology, Icahn School of Medicine at Mount Sinai, New York, NY 10016, USA
| | - Alan A. Arslan
- Department of Population Health, NYU Grossman School of Medicine, New York, NY 10016, USA; (S.T.)
- NYU Perlmutter Comprehensive Cancer Center, New York, NY 10016, USA
- Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York, NY 10016, USA
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112
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Ndhlovu LC, Bendall ML, Dwaraka V, Pang APS, Dopkins N, Carreras N, Smith R, Nixon DF, Corley MJ. Retroelement-Age Clocks: Epigenetic Age Captured by Human Endogenous Retrovirus and LINE-1 DNA methylation states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570422. [PMID: 38106164 PMCID: PMC10723416 DOI: 10.1101/2023.12.06.570422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Human endogenous retroviruses (HERVs), the remnants of ancient viral infections embedded within the human genome, and long interspersed nuclear elements 1 (LINE-1), a class of autonomous retrotransposons, are silenced by host epigenetic mechanisms including DNA methylation. The resurrection of particular retroelements has been linked to biological aging. Whether the DNA methylation states of locus specific HERVs and LINEs can be used as a biomarker of chronological age in humans remains unclear. We show that highly predictive epigenetic clocks of chronological age can be constructed from retroelement DNA methylation states in the immune system, across human tissues, and pan-mammalian species. We found retroelement epigenetic clocks were reversed during transient epigenetic reprogramming, accelerated in people living with HIV-1, responsive to antiretroviral therapy, and accurate in estimating long-term culture ages of human brain organoids. Our findings support the hypothesis of epigenetic dysregulation of retroelements as a potential contributor to the biological hallmarks of aging.
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Affiliation(s)
- Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Matthew L. Bendall
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | | | - Alina PS Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Nicholas Dopkins
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | | | | | - Douglas F. Nixon
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Michael J. Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
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113
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Kalyakulina A, Yusipov I, Kondakova E, Bacalini MG, Giuliani C, Sivtseva T, Semenov S, Ksenofontov A, Nikolaeva M, Khusnutdinova E, Zakharova R, Vedunova M, Franceschi C, Ivanchenko M. Epigenetics of the far northern Yakutian population. Clin Epigenetics 2023; 15:189. [PMID: 38053163 PMCID: PMC10699032 DOI: 10.1186/s13148-023-01600-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Yakuts are one of the indigenous populations of the subarctic and arctic territories of Siberia characterized by a continental subarctic climate with severe winters, with the regular January average temperature in the regional capital city of Yakutsk dipping below - 40 °C. The epigenetic mechanisms of adaptation to such ecologies and environments and, in particular, epigenetic age acceleration in the local population have not been studied before. RESULTS This work reports the first epigenetic study of the Yakutian population using whole-blood DNA methylation data, supplemented with the comparison to the residents of Central Russia. Gene set enrichment analysis revealed, among others, geographic region-specific differentially methylated regions associated with adaptation to climatic conditions (water consumption, digestive system regulation), aging processes (actin filament activity, cell fate), and both of them (channel activity, regulation of steroid and corticosteroid hormone secretion). Further, it is demonstrated that the epigenetic age acceleration of the Yakutian representatives is significantly higher than that of Central Russia counterparts. For both geographic regions, we showed that epigenetically males age faster than females, whereas no significant sex differences were found between the regions. CONCLUSIONS We performed the first study of the epigenetic data of the Yakutia cohort, paying special attention to region-specific features, aging processes, age acceleration, and sex specificity.
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Affiliation(s)
- Alena Kalyakulina
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia.
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia.
| | - Igor Yusipov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Elena Kondakova
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | | | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126, Bologna, Italy
| | - Tatiana Sivtseva
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Sergey Semenov
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Artem Ksenofontov
- State Budgetary Institution of the Republic of Sakha (Yakutia) Republican Center for Public Health and Medical Prevention, Yakutsk, 677001, Russia
| | - Maria Nikolaeva
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia, 450054
| | - Raisa Zakharova
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Maria Vedunova
- Institute of Biology and Biomedicine, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
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114
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Merzbacher C, Ryan B, Goldsborough T, Hillary RF, Campbell A, Murphy L, McIntosh AM, Liewald D, Harris SE, McRae AF, Cox SR, Cannings TI, Vallejos CA, McCartney DL, Marioni RE. Integration of datasets for individual prediction of DNA methylation-based biomarkers. Genome Biol 2023; 24:278. [PMID: 38053194 PMCID: PMC10696831 DOI: 10.1186/s13059-023-03114-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 11/20/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Epigenetic scores (EpiScores) can provide biomarkers of lifestyle and disease risk. Projecting new datasets onto a reference panel is challenging due to separation of technical and biological variation with array data. Normalisation can standardise data distributions but may also remove population-level biological variation. RESULTS We compare two birth cohorts (Lothian Birth Cohorts of 1921 and 1936 - nLBC1921 = 387 and nLBC1936 = 498) with blood-based DNA methylation assessed at the same chronological age (79 years) and processed in the same lab but in different years and experimental batches. We examine the effect of 16 normalisation methods on a novel BMI EpiScore (trained in an external cohort, n = 18,413), and Horvath's pan-tissue DNA methylation age, when the cohorts are normalised separately and together. The BMI EpiScore explains a maximum variance of R2=24.5% in BMI in LBC1936 (SWAN normalisation). Although there are cross-cohort R2 differences, the normalisation method makes a minimal difference to within-cohort estimates. Conversely, a range of absolute differences are seen for individual-level EpiScore estimates for BMI and age when cohorts are normalised separately versus together. While within-array methods result in identical EpiScores whether a cohort is normalised on its own or together with the second dataset, a range of differences is observed for between-array methods. CONCLUSIONS Normalisation methods returning similar EpiScores, whether cohorts are analysed separately or together, will minimise technical variation when projecting new data onto a reference panel. These methods are important for cases where raw data is unavailable and joint normalisation of cohorts is computationally expensive.
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Affiliation(s)
| | - Barry Ryan
- School of Informatics, University of Edinburgh, Edinburgh, EH8 9AB, UK
| | | | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrew M McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - David Liewald
- Department of Psychology, Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Sarah E Harris
- Department of Psychology, Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Allan F McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Simon R Cox
- Department of Psychology, Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Timothy I Cannings
- Maxwell Institute for Mathematical Sciences, School of Mathematics, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Catalina A Vallejos
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
- The Alan Turing Institute, London, UK
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK.
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK.
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Awada Z, Cahais V, Cuenin C, Akika R, Silva Almeida Vicente AL, Makki M, Tamim H, Herceg Z, Khoueiry Zgheib N, Ghantous A. Waterpipe and cigarette epigenome analysis reveals markers implicated in addiction and smoking type inference. ENVIRONMENT INTERNATIONAL 2023; 182:108260. [PMID: 38006773 PMCID: PMC10716859 DOI: 10.1016/j.envint.2023.108260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/02/2023] [Accepted: 10/09/2023] [Indexed: 11/27/2023]
Abstract
Waterpipe smoking is frequent in the Middle East and Africa with emerging prevalence worldwide. The epigenome acts as a molecular sensor to exposures and a crucial driver in several diseases. With the widespread use of waterpipe smoking, it is timely to investigate its epigenomic markers and their role in addiction, as a central player in disease prevention and therapeutic strategies. DNA methylome-wide profiling was performed on an exposure-rich population from the Middle East, constituting of 216 blood samples split equally between never, cigarette-only and waterpipe-only smokers. Waterpipe smokers showed predominantly distinct epigenetic markers from cigarette smokers, even though both smoking forms are tobacco-based. Moreover, each smoking form could be accurately (∼90 %) inferred from the DNA methylome using machine learning. Top markers showed dose-response relationship with extent of smoking and were validated using independent technologies and additional samples (total N = 284). Smoking markers were enriched in regulatory regions and several biological pathways, primarily addiction. The epigenetically altered genes were not associated with genetic etiology of tobacco use, and the methylation levels of addiction genes, in particular, were more likely to reverse after smoking cessation. In contrast, other epigenetic markers continued to feature smoking exposure after cessation, which may explain long-term health effects observed in former smokers. This study reports, for the first time, blood epigenome-wide markers of waterpipe smokers and reveals new markers of cigarette smoking, with implications in mechanisms of addiction and the capacity to discriminate between different smoking types. These markers may offer actionable targets to reverse the epigenetic memory of addiction and can guide future prevention strategies for tobacco smoking as the most preventable cause of illnesses worldwide.
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Affiliation(s)
- Zainab Awada
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Vincent Cahais
- 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
| | - Reem Akika
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Anna Luiza Silva Almeida Vicente
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France; Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Maha Makki
- Clinical Research Institute, American University of Beirut Medical Center, Beirut, Lebanon
| | - Hani Tamim
- Clinical Research Institute, American University of Beirut Medical Center, Beirut, Lebanon; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France
| | - Nathalie Khoueiry Zgheib
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.
| | - Akram Ghantous
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer, Lyon, France.
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116
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Bakulski KM, Blostein F, London SJ. Linking Prenatal Environmental Exposures to Lifetime Health with Epigenome-Wide Association Studies: State-of-the-Science Review and Future Recommendations. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:126001. [PMID: 38048101 PMCID: PMC10695268 DOI: 10.1289/ehp12956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 12/05/2023]
Abstract
BACKGROUND The prenatal environment influences lifetime health; epigenetic mechanisms likely predominate. In 2016, the first international consortium paper on cigarette smoking during pregnancy and offspring DNA methylation identified extensive, reproducible exposure signals. This finding raised expectations for epigenome-wide association studies (EWAS) of other exposures. OBJECTIVE We review the current state-of-the-science for DNA methylation associations across prenatal exposures in humans and provide future recommendations. METHODS We reviewed 134 prenatal environmental EWAS of DNA methylation in newborns, focusing on 51 epidemiological studies with meta-analysis or replication testing. Exposures spanned cigarette smoking, alcohol consumption, air pollution, dietary factors, psychosocial stress, metals, other chemicals, and other exogenous factors. Of the reproducible DNA methylation signatures, we examined implementation as exposure biomarkers. RESULTS Only 19 (14%) of these prenatal EWAS were conducted in cohorts of 1,000 or more individuals, reflecting the still early stage of the field. To date, the largest perinatal EWAS sample size was 6,685 participants. For comparison, the most recent genome-wide association study for birth weight included more than 300,000 individuals. Replication, at some level, was successful with exposures to cigarette smoking, folate, dietary glycemic index, particulate matter with aerodynamic diameter < 10 μ m and < 2.5 μ m , nitrogen dioxide, mercury, cadmium, arsenic, electronic waste, PFAS, and DDT. Reproducible effects of a more limited set of prenatal exposures (smoking, folate) enabled robust methylation biomarker creation. DISCUSSION Current evidence demonstrates the scientific premise for reproducible DNA methylation exposure signatures. Better powered EWAS could identify signatures across many exposures and enable comprehensive biomarker development. Whether methylation biomarkers of exposures themselves cause health effects remains unclear. We expect that larger EWAS with enhanced coverage of epigenome and exposome, along with improved single-cell technologies and evolving methods for integrative multi-omics analyses and causal inference, will expand mechanistic understanding of causal links between environmental exposures, the epigenome, and health outcomes throughout the life course. https://doi.org/10.1289/EHP12956.
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Affiliation(s)
| | - Freida Blostein
- University of Michigan, Ann Arbor, Michigan, USA
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Stephanie J. London
- National Institute of Environmental Health Sciences, National Institutes of Health, U.S. Department of Health and Human Services, Research Triangle Park, North Carolina, USA
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117
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Apsley AT, Ye Q, Etzel L, Wolf S, Hastings WJ, Mattern BC, Siegel SR, Shalev I. Biological stability of DNA methylation measurements over varying intervals of time and in the presence of acute stress. Epigenetics 2023; 18:2230686. [PMID: 37393564 PMCID: PMC10316737 DOI: 10.1080/15592294.2023.2230686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/13/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023] Open
Abstract
Identifying factors that influence the stability of DNA methylation measurements across biological replicates is of critical importance in basic and clinical research. Using a within-person between-group experimental design (n = 31, number of observations = 192), we report the stability of biological replicates over a variety of unique temporal scenarios, both in the absence and presence of acute psychosocial stress, and between individuals who have experienced early life adversity (ELA) and non-exposed individuals. We found that varying time intervals, acute stress, and ELA exposure influenced the stability of repeated DNA methylation measurements. In the absence of acute stress, probes were less stable as time passed; however, stress exerted a stabilizing influence on probes over longer time intervals. Compared to non-exposed individuals, ELA-exposed individuals had significantly lower probe stability immediately following acute stress. Additionally, we found that across all scenarios, probes used in most epigenetic-based algorithms for estimating epigenetic age or immune cell proportions had average or below-average stability, except for the Principal Component and DunedinPACE epigenetic ageing clocks, which were enriched for more stable probes. Finally, using highly stable probes in the absence of stress, we identified multiple probes that were hypomethylated in the presence of acute stress, regardless of ELA status. Two hypomethylated probes are located near the transcription start site of the glutathione-disulfide reductase gene (GSR), which has previously been shown to be an integral part of the stress response to environmental toxins. We discuss implications for future studies concerning the reliability and reproducibility of DNA methylation measurements.Abbreviations: DNAm - DNA methylation, CpG - 5'-cytosine-phosphate-guanine-3,' ICC - Interclass correlation coefficient, ELA - Early-life adversity, PBMCs - Peripheral blood mononuclear cells, mQTL - Methylation quantitative trait loci, TSS - Transcription start site, GSR - Glutathione-disulfide reductase gene, TSST - Trier social stress test, PC - Principal component.
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Affiliation(s)
- Abner T. Apsley
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
- Department of Molecular, Cellular and Integrative Biological Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Qiaofeng Ye
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Laura Etzel
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Sarah Wolf
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Waylon J. Hastings
- Department of Psychiatry, Tulane University School of Medicine, New Orleans, LA, USA
| | - Brooke C. Mattern
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Sue Rutherford Siegel
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Idan Shalev
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
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118
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Zheng Y, Lunetta KL, Liu C, Smith AK, Sherva R, Miller MW, Logue MW. A novel principal component based method for identifying differentially methylated regions in Illumina Infinium MethylationEPIC BeadChip data. Epigenetics 2023; 18:2207959. [PMID: 37196182 PMCID: PMC10193914 DOI: 10.1080/15592294.2023.2207959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 03/22/2023] [Accepted: 04/19/2023] [Indexed: 05/19/2023] Open
Abstract
Differentially methylated regions (DMRs) are genomic regions with methylation patterns across multiple CpG sites that are associated with a phenotype. In this study, we proposed a Principal Component (PC) based DMR analysis method for use with data generated using the Illumina Infinium MethylationEPIC BeadChip (EPIC) array. We obtained methylation residuals by regressing the M-values of CpGs within a region on covariates, extracted PCs of the residuals, and then combined association information across PCs to obtain regional significance. Simulation-based genome-wide false positive (GFP) rates and true positive rates were estimated under a variety of conditions before determining the final version of our method, which we have named DMRPC. Then, DMRPC and another DMR method, coMethDMR, were used to perform epigenome-wide analyses of several phenotypes known to have multiple associated methylation loci (age, sex, and smoking) in a discovery and a replication cohort. Among regions that were analysed by both methods, DMRPC identified 50% more genome-wide significant age-associated DMRs than coMethDMR. The replication rate for the loci that were identified by only DMRPC was higher than the rate for those that were identified by only coMethDMR (90% for DMRPC vs. 76% for coMethDMR). Furthermore, DMRPC identified replicable associations in regions of moderate between-CpG correlation which are typically not analysed by coMethDMR. For the analyses of sex and smoking, the advantage of DMRPC was less clear. In conclusion, DMRPC is a new powerful DMR discovery tool that retains power in genomic regions with moderate correlation across CpGs.
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Affiliation(s)
- Yuanchao Zheng
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Chunyu Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Alicia K. Smith
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Richard Sherva
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Mark W. Miller
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Biomedical Genetics, Boston University School of Medicine, Boston, MA, USA
| | - Mark W. Logue
- National Center for PTSD, VA Boston Healthcare System, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
- Biomedical Genetics, Boston University School of Medicine, Boston, MA, USA
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119
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Noguera-Castells A, García-Prieto CA, Álvarez-Errico D, Esteller M. Validation of the new EPIC DNA methylation microarray (900K EPIC v2) for high-throughput profiling of the human DNA methylome. Epigenetics 2023; 18:2185742. [PMID: 36871255 PMCID: PMC9988339 DOI: 10.1080/15592294.2023.2185742] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
DNA methylation, one of the best characterized epigenetic marks in the human genome, plays a pivotal role in gene transcription regulation and other biological processes in humans. On top of that, the DNA methylome undergoes profound changes in cancer and other disorders. However, large-scale and population-based studies are limited by high costs and the need for considerable expertise in data analysis for whole-genome bisulphite-sequencing methodologies. Following the success of the EPIC DNA methylation microarray, the newly developed Infinium HumanMethylationEPIC version 2.0 (900K EPIC v2) is now available. This new array contains more than 900,000 CpG probes covering the human genome and excluding masked probes from the previous version. The 900K EPIC v2 microarray adds more than 200,000 probes covering extra DNA cis-regulatory regions such as enhancers, super-enhancers and CTCF binding regions. Herein, we have technically and biologically validated the new methylation array to show its high reproducibility and consistency among technical replicates and with DNA extracted from FFPE tissue. In addition, we have hybridized primary normal and tumoural tissues and cancer cell lines from different sources and tested the robustness of the 900K EPIC v2 microarray when analysing the different DNA methylation profiles. The validation highlights the improvements offered by the new array and demonstrates the versatility of this updated tool for characterizing the DNA methylome in human health and disease.
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Affiliation(s)
- Aleix Noguera-Castells
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain.,Department of Biosciences, Faculty of Science, Technology and Engineering, University of Vic - Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Carlos A García-Prieto
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain.,Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Damiana Álvarez-Errico
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
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120
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Bhat B, Jones GT. Gaps in current methods to detect polymorphic CpGs from Illumina Infinium human methylation microarrays and exploring their potential impact in multi-EWAS analyses. Epigenetics 2023; 18:2281153. [PMID: 37983305 PMCID: PMC10732615 DOI: 10.1080/15592294.2023.2281153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023] Open
Abstract
DNA methylation (DNAm) epigenome-wide association studies (EWAS) have been performed on diverse ethnicities to discover novel biomarkers associated with various diseases, such as cancers, autoimmune diseases, and neurological disorders. However, genetic polymorphisms can influence DNAm levels resulting in methylation quantitative trait loci (meQTL). These can be either direct effects, by altering the sequence of the methylation (CpG) site itself, or, in the case of array-based measures, indirectly altering the detection probe-binding site interaction. Given that genetic variant frequencies associated with meQTL can differ between population groups, these have the potential to confound EWAS observations, particularly in multi-ethnic populations. In this study, we analysed publicly available DNA methylation profiles (450K array), consisting of 1342 individuals from 6 distinct ancestral groups. We investigate two distinct tools (GapHunter and MethylToSNP) specifically designed to identify CpG sites that may be influenced by genetic variation. Results from this aggregated trans-ancestral epigenome-wide dataset suggest that both tools fail to consistently identify not only rarer (MAF < 0.05) genetic variant effects but also more than half of sites predicted to be associated with variants with much higher allele frequencies (MAF >0.2). In addition, there is a relatively low concordance in the detection of polymorphic CpGs between GapHunter and MethylToSNP. Screening of CpG site associations from EWAS using either of these tools is unlikely to be a robust or comprehensive means of identifying all genetic variant confounding effects.
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Affiliation(s)
- Basharat Bhat
- Departments of Surgical Sciences, University of Otago, Dunedin, New Zealand
| | - Gregory T Jones
- Departments of Surgical Sciences, University of Otago, Dunedin, New Zealand
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121
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Ponce D, Rodríguez F, Miranda JP, Binder AM, Santos JL, Michels KB, Cutler GB, Pereira A, Iñiguez G, Mericq V. Differential methylation pattern in pubertal girls associated with biochemical premature adrenarche. Epigenetics 2023; 18:2200366. [PMID: 37053179 PMCID: PMC10114989 DOI: 10.1080/15592294.2023.2200366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Biochemical premature adrenarche is defined by elevated serum DHEAS [≥40 μg/dL] before age 8 y in girls. This condition is receiving more attention due to its association with obesity, hyperinsulinemia, dyslipidemia, and polycystic ovary syndrome. Nevertheless, the link between early androgen excess and these risk factors remains unknown. Epigenetic modifications, and specifically DNA methylation, have been associated with the initiation and progression of numerous disorders, including obesity and insulin resistance. The aim of this study was to determine if prepubertal androgen exposure is associated with a different methylation profile in pubertal girls. Eighty-six healthy girls were studied. At age 7 y, anthropometric measurements were begun and DHEAS levels were determined. Girls were classified into Low DHEAS (LD) [<42 μg/dL] and High DHEAS (HD) [≥42 μg/dL] groups. At Tanner stages 2 and 4 a DNA methylation microarray was performed to identify differentially methylated CpG positions (DMPs) between HD and LD groups. We observed a differential methylation pattern between pubertal girls with and without biochemical PA. Moreover, a set of DNA methylation markers, selected by the LASSO method, successfully distinguished between HD and LD girls regardless of Tanner stage. Additionally, a subset of these markers were significantly associated with glucose-related measures such as insulin level, HOMA-IR, and glycaemia. This pilot study provides evidence consistent with the hypothesis that high DHEAS concentration, or its hormonally active metabolites, may induce a unique blood methylation signature in pubertal girls, and that this methylation pattern is associated with altered glucose metabolism.
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Affiliation(s)
- Diana Ponce
- Institute of Maternal and Child Research, School of Medicine, Universidad de Chile, Santiago, Chile
| | - Fernando Rodríguez
- Institute of Maternal and Child Research, School of Medicine, Universidad de Chile, Santiago, Chile
| | - José P Miranda
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Advanced Center for Chronic Diseases (ACCDiS), Pontificia Universidad Católica de Chile & Universidad de Chile, Santiago, Chile
| | - Alexandra M Binder
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, USA
- Population Sciences in the Pacific Program (Cancer Epidemiology), University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, USA
| | - José L Santos
- Department of Nutrition, Diabetes, and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Karin B Michels
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | | | - Ana Pereira
- Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Germán Iñiguez
- Institute of Maternal and Child Research, School of Medicine, Universidad de Chile, Santiago, Chile
| | - Verónica Mericq
- Institute of Maternal and Child Research, School of Medicine, Universidad de Chile, Santiago, Chile
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122
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Meyer OS, Andersen MM, Børsting C, Morling N, Wulf HC, Philipsen PA, Lerche CM, Dyrberg Andersen J. Comparison of global DNA methylation analysis by whole genome bisulfite sequencing and the Infinium Mouse Methylation BeadChip using fresh and fresh-frozen mouse epidermis. Epigenetics 2023; 18:2144574. [PMID: 36373380 PMCID: PMC9980693 DOI: 10.1080/15592294.2022.2144574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Until recently, studying the murine methylome was restricted to sequencing-based methods. In this study we compared the global DNA methylation levels of hairless mouse epidermis using the recently released Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulphite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of 123,851 CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.999) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study's aims and the available resources in the laboratory.
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Affiliation(s)
- Olivia Strunge Meyer
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100Copenhagen, Denmark,CONTACT Olivia Strunge Meyer Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Heafth and Medical Sciences, University of Copenhagen. Frederik V's vej 11, 2100 Copenhagen, Denmark
| | - Mikkel Meyer Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100Copenhagen, Denmark,Department of Mathematical Sciences, Aalborg University, 9220Aalborg, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100Copenhagen, Denmark,Department of Mathematical Sciences, Aalborg University, 9220Aalborg, Denmark
| | - Hans Christian Wulf
- Department of Dermatology, Copenhagen University Hospital - Bispebjerg and Frederiksberg, 2400Copenhagen, Denmark
| | - Peter Alshede Philipsen
- Department of Dermatology, Copenhagen University Hospital - Bispebjerg and Frederiksberg, 2400Copenhagen, Denmark
| | - Catharina Margrethe Lerche
- Department of Dermatology, Copenhagen University Hospital - Bispebjerg and Frederiksberg, 2400Copenhagen, Denmark,Department of Pharmacy, University of Copenhagen, 2100Copenhagen, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100Copenhagen, Denmark
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Harbs J, Rinaldi S, Keski-Rahkonen P, Liu X, Palmqvist R, Van Guelpen B, Harlid S. An epigenome-wide analysis of sex hormone levels and DNA methylation in male blood samples. Epigenetics 2023; 18:2196759. [PMID: 36994855 PMCID: PMC10072117 DOI: 10.1080/15592294.2023.2196759] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
Endogenous sex hormones and DNA methylation both play important roles in various diseases. However, their interplay is largely unknown. A deeper understanding of their interrelationships could provide new insights into the pathology of disease development. We, therefore, investigated associations between circulating sex hormones, sex hormone binding globulin (SHBG), and DNA methylation in blood, using samples from 77 men (65 with repeated samples), from the population-based Northern Sweden Health and Disease Study (NSHDS). DNA methylation was measured in buffy coat using the Infinium Methylation EPIC BeadChip (Illumina). Sex hormone (oestradiol, oestrone, testosterone, androstenedione, dehydroepiandrosterone, and progesterone) and SHBG concentrations were measured in plasma using a high-performance liquid chromatography tandem mass spectrometry (LC/MS-MS) method and an enzyme-linked immunoassay, respectively. Associations between sex hormones, SHBG, and DNA methylation were estimated using both linear regression and mixed-effects models. Additionally, we used the comb-p method to identify differentially methylated regions based on nearby P values. We identified one novel CpG site (cg14319657), at which DNA methylation was associated with dehydroepiandrosterone, surpassing a genome-wide significance level. In addition, more than 40 differentially methylated regions were associated with levels of sex hormones and SHBG and several of these mapped to genes involved in hormone-related diseases. Our findings support a relationship between circulating sex hormones and DNA methylation and suggest that further investigation is warranted, both for validation, further exploration and to gain a deeper understanding of the mechanisms and potential consequences for health and disease.
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Affiliation(s)
- Justin Harbs
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
| | - Sabina Rinaldi
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Pekka Keski-Rahkonen
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Xijia Liu
- Department of Statistics, Umeå University, Umeå, Sweden
| | - Richard Palmqvist
- Deparment of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Bethany Van Guelpen
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Sophia Harlid
- Department of Radiation Sciences, Oncology Unit, Umeå University, Umeå, Sweden
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124
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Rabotnick MH, Ehlinger J, Haidari A, Goodrich JM. Prenatal exposures to endocrine disrupting chemicals: The role of multi-omics in understanding toxicity. Mol Cell Endocrinol 2023; 578:112046. [PMID: 37598796 PMCID: PMC10592024 DOI: 10.1016/j.mce.2023.112046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 08/22/2023]
Abstract
Endocrine disrupting chemicals (EDCs) are a diverse group of toxicants detected in populations globally. Prenatal EDC exposures impact birth and childhood outcomes. EDCs work through persistent changes at the molecular, cellular, and organ level. Molecular and biochemical signals or 'omics' can be measured at various functional levels - including the epigenome, transcriptome, proteome, metabolome, and the microbiome. In this narrative review, we introduce each omics and give examples of associations with prenatal EDC exposures. There is substantial research on epigenomic modifications in offspring exposed to EDCs during gestation, and a growing number of studies evaluating the transcriptome, proteome, metabolome, or microbiome in response to these exposures. Multi-omics, integrating data across omics layers, may improve understanding of disrupted function pathways related to early life exposures. We highlight several data integration methods to consider in multi-omics studies. Information from multi-omics can improve understanding of the biological processes and mechanisms underlying prenatal EDC toxicity.
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Affiliation(s)
- Margaret H Rabotnick
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Jessa Ehlinger
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Ariana Haidari
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA.
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James EA, Holers VM, Iyer R, Prideaux EB, Rao NL, Rims C, Muir VS, Posso SE, Bloom MS, Zia A, Elliott SE, Adamska JZ, Ai R, Brewer RC, Seifert JA, Moss L, Barzideh S, Demoruelle MK, Striebich CC, Okamoto Y, Sainbayar E, Crook AA, Peterson RA, Vanderlinden LA, Wang W, Boyle DL, Robinson WH, Buckner JH, Firestein GS, Deane KD. Multifaceted immune dysregulation characterizes individuals at-risk for rheumatoid arthritis. Nat Commun 2023; 14:7637. [PMID: 37993439 PMCID: PMC10665556 DOI: 10.1038/s41467-023-43091-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
Molecular markers of autoimmunity, such as antibodies to citrullinated protein antigens (ACPA), are detectable prior to inflammatory arthritis (IA) in rheumatoid arthritis (RA) and may define a state that is 'at-risk' for future RA. Here we present a cross-sectional comparative analysis among three groups that include ACPA positive individuals without IA (At-Risk), ACPA negative individuals and individuals with early, ACPA positive clinical RA (Early RA). Differential methylation analysis among the groups identifies non-specific dysregulation in peripheral B, memory and naïve T cells in At-Risk participants, with more specific immunological pathway abnormalities in Early RA. Tetramer studies show increased abundance of T cells recognizing citrullinated (cit) epitopes in At-Risk participants, including expansion of T cells reactive to citrullinated cartilage intermediate layer protein I (cit-CILP); these T cells have Th1, Th17, and T stem cell memory-like phenotypes. Antibody-antigen array analyses show that antibodies targeting cit-clusterin, cit-fibrinogen and cit-histone H4 are elevated in At-Risk and Early RA participants, with the highest levels of antibodies detected in those with Early RA. These findings indicate that an ACPA positive at-risk state is associated with multifaceted immune dysregulation that may represent a potential opportunity for targeted intervention.
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Affiliation(s)
- Eddie A James
- Benaroya Research Institute, Seattle, WA, 98101, USA
| | - V Michael Holers
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Radhika Iyer
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, 94304, USA
- VA Palo Alto Health Care System, Palo Alto, CA, 94550, USA
| | - E Barton Prideaux
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Navin L Rao
- Janssen Research and Development, Spring House, PA, 19477, USA
| | - Cliff Rims
- Benaroya Research Institute, Seattle, WA, 98101, USA
| | | | | | - Michelle S Bloom
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, 94304, USA
- VA Palo Alto Health Care System, Palo Alto, CA, 94550, USA
| | - Amin Zia
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, 94304, USA
- VA Palo Alto Health Care System, Palo Alto, CA, 94550, USA
| | - Serra E Elliott
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, 94304, USA
- VA Palo Alto Health Care System, Palo Alto, CA, 94550, USA
| | - Julia Z Adamska
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, 94304, USA
- VA Palo Alto Health Care System, Palo Alto, CA, 94550, USA
| | - Rizi Ai
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - R Camille Brewer
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, 94304, USA
- VA Palo Alto Health Care System, Palo Alto, CA, 94550, USA
| | - Jennifer A Seifert
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - LauraKay Moss
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Saman Barzideh
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - M Kristen Demoruelle
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Christopher C Striebich
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Yuko Okamoto
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
- Division of Rheumatology, Department of Internal Medicine, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Enkhtsogt Sainbayar
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Alexandra A Crook
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Ryan A Peterson
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Lauren A Vanderlinden
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - David L Boyle
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - William H Robinson
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA, 94304, USA
- VA Palo Alto Health Care System, Palo Alto, CA, 94550, USA
| | | | - Gary S Firestein
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Kevin D Deane
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
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126
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Rajasekar P, Hall RJ, Binaya KC, Mahapatra PS, Puppala SP, Thakker D, MacIsaac JL, Lin D, Kobor M, Bolton CE, Sayers I, Hall IP, Clifford RL. Nepalese indoor cookstove smoke extracts alter human airway epithelial gene expression, DNA methylation and hydroxymethylation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 337:122561. [PMID: 37742862 DOI: 10.1016/j.envpol.2023.122561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/26/2023]
Abstract
Household air pollution caused by inefficient cooking practices causes 4 million deaths a year worldwide. In Nepal, 86% of the rural population use solid fuels for cooking. Over 25% of premature deaths associated with air pollution are respiratory in nature. Here we aimed to identify molecular signatures of different cookstove and fuel type exposures in human airway epithelial cells, to understand the mechanisms mediating cook stove smoke induced lung disease. Primary human airway epithelial cells in submerged culture were exposed to traditional cook stove (TCS), improved cook stove (ICS) and liquefied petroleum gas (LPG) stove smoke extracts. Changes to gene expression, DNA methylation and hydroxymethylation were measured by bulk RNA sequencing and HumanMethylationEPIC BeadChip following oxidative bisulphite conversion, respectively. TCS smoke extract alone reproducibly caused changes in the expression of 52 genes enriched for oxidative stress pathways. TCS, ICS and LPG smoke extract exposures were associated with distinct changes to DNA methylation and hydroxymethylation. A subset of TCS induced genes were associated with differentially methylated and/or hydroxymethylated CpGs sites, and enriched for the ferroptosis pathway and the upstream regulator NFE2L2. DNA methylation and hydroxymethylation changes not associated with a concurrent change in gene expression, were linked to biological processes and molecular pathways important to airway health, including neutrophil function, transforming growth factor beta signalling, GTPase activity, and cell junction organisation. Our data identified differential impacts of TCS, ICS and LPG cook stove smoke on the human airway epithelium transcriptome, DNA methylome and hydroxymethylome and provide further insight into the association between indoor air pollution exposure and chronic lung disease mechanisms.
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Affiliation(s)
- Poojitha Rajasekar
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK
| | - Robert J Hall
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK
| | - K C Binaya
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Water and Air Theme, Atmosphere Initiative, International Centre for Integrated Mountain Development, Kathmandu, Nepal
| | - Parth S Mahapatra
- Water and Air Theme, Atmosphere Initiative, International Centre for Integrated Mountain Development, Kathmandu, Nepal
| | - Siva P Puppala
- Water and Air Theme, Atmosphere Initiative, International Centre for Integrated Mountain Development, Kathmandu, Nepal
| | - Dhruma Thakker
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK
| | - Julia L MacIsaac
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Lin
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael Kobor
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Charlotte E Bolton
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK
| | - Ian Sayers
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK
| | - Ian P Hall
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK
| | - Rachel L Clifford
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, University of Nottingham, UK; Nottingham NIHR Biomedical Research Centre, Nottingham, UK; Biodiscovery Institute, University Park, University of Nottingham, UK.
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127
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Coltell O, Asensio EM, Sorlí JV, Ortega-Azorín C, Fernández-Carrión R, Pascual EC, Barragán R, González JI, Estruch R, Alzate JF, Pérez-Fidalgo A, Portolés O, Ordovas JM, Corella D. Associations between the New DNA-Methylation-Based Telomere Length Estimator, the Mediterranean Diet and Genetics in a Spanish Population at High Cardiovascular Risk. Antioxidants (Basel) 2023; 12:2004. [PMID: 38001857 PMCID: PMC10669035 DOI: 10.3390/antiox12112004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Biological aging is a relevant risk factor for chronic diseases, and several indicators for measuring this factor have been proposed, with telomere length (TL) among the most studied. Oxidative stress may regulate telomere shortening, which is implicated in the increased risk. Using a novel estimator for TL, we examined whether adherence to the Mediterranean diet (MedDiet), a highly antioxidant-rich dietary pattern, is associated with longer TL. We determined TL using DNA methylation algorithms (DNAmTL) in 414 subjects at high cardiovascular risk from Spain. Adherence to the MedDiet was assessed by a validated score, and genetic variants in candidate genes and at the genome-wide level were analyzed. We observed several significant associations (p < 0.05) between DNAmTL and candidate genes (TERT, TERF2, RTEL1, and DCAF4), contributing to the validity of DNAmTL as a biomarker in this population. Higher adherence to the MedDiet was associated with lower odds of having a shorter TL in the whole sample (OR = 0.93; 95% CI: 0.85-0.99; p = 0.049 after fully multivariate adjustment). Nevertheless, this association was stronger in women than in men. Likewise, in women, we observed a direct association between adherence to the MedDiet score and DNAmTL as a continuous variable (beta = 0.015; SE: 0.005; p = 0.003), indicating that a one-point increase in adherence was related to an average increase of 0.015 ± 0.005 kb in TL. Upon examination of specific dietary items within the global score, we found that fruits, fish, "sofrito", and whole grains exhibited the strongest associations in women. The novel score combining these items was significantly associated in the whole population. In the genome-wide association study (GWAS), we identified ten polymorphisms at the suggestive level of significance (p < 1 × 10-5) for DNAmTL (intergenics, in the IQSEC1, NCAPG2, and ABI3BP genes) and detected some gene-MedDiet modulations on DNAmTL. As this is the first study analyzing the DNAmTL estimator, genetics, and modulation by the MedDiet, more studies are needed to confirm these findings.
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Affiliation(s)
- Oscar Coltell
- Department of Computer Languages and Systems, Universitat Jaume I, 12071 Castellón, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
| | - Eva M. Asensio
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - José V. Sorlí
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Carolina Ortega-Azorín
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Rebeca Fernández-Carrión
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Eva C. Pascual
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Rocío Barragán
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - José I. González
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Ramon Estruch
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Internal Medicine, Institut d’Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain
| | - Juan F. Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia
- Facultad de Medicina, Centro Nacional de Secuenciación Genómica—CNSG, Sede de Investigación Universitaria—SIU, Universidad de Antioquia, Medellín 050010, Colombia
| | - Alejandro Pérez-Fidalgo
- Department of Medical Oncology, University Clinic Hospital of Valencia, 46010 Valencia, Spain; (A.P.-F.)
- Biomedical Research Networking Centre on Cancer (CIBERONC), Health Institute Carlos III, 28029 Madrid, Spain
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain
| | - Olga Portolés
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Jose M. Ordovas
- Department of Medical Oncology, University Clinic Hospital of Valencia, 46010 Valencia, Spain; (A.P.-F.)
- Nutrition and Genomics, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA 02111, USA
- Nutritional Control of the Epigenome Group, Precision Nutrition and Obesity Program, IMDEA Food, UAM + CSIC, 28049 Madrid, Spain
| | - Dolores Corella
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.M.A.); (C.O.-A.); (J.I.G.); (R.E.)
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
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Jung AM, Furlong MA, Goodrich JM, Cardenas A, Beitel SC, Littau SR, Caban-Martinez AJ, Gulotta JJ, Wallentine DD, Urwin D, Gabriel J, Hughes J, Graber JM, Grant C, Burgess JL. Associations Between Epigenetic Age Acceleration and microRNA Expression Among U.S. Firefighters. Epigenet Insights 2023; 16:25168657231206301. [PMID: 37953967 PMCID: PMC10634256 DOI: 10.1177/25168657231206301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 09/20/2023] [Indexed: 11/14/2023] Open
Abstract
Epigenetic changes may be biomarkers of health. Epigenetic age acceleration (EAA), the discrepancy between epigenetic age measured via epigenetic clocks and chronological age, is associated with morbidity and mortality. However, the intersection of epigenetic clocks with microRNAs (miRNAs) and corresponding miRNA-based health implications have not been evaluated. We analyzed DNA methylation and miRNA profiles from blood sampled among 332 individuals enrolled across 2 U.S.-based firefighter occupational studies (2015-2018 and 2018-2020). We considered 7 measures of EAA in leukocytes (PhenoAge, GrimAge, Horvath, skin-blood, and Hannum epigenetic clocks, and extrinsic and intrinsic epigenetic age acceleration). We identified miRNAs associated with EAA using individual linear regression models, adjusted for sex, race/ethnicity, chronological age, and cell type estimates, and investigated downstream effects of associated miRNAs with miRNA enrichment analyses and genomic annotations. On average, participants were 38 years old, 88% male, and 75% non-Hispanic white. We identified 183 of 798 miRNAs associated with EAA (FDR q < 0.05); 126 with PhenoAge, 59 with GrimAge, 1 with Horvath, and 1 with the skin-blood clock. Among miRNAs associated with Horvath and GrimAge, there were 61 significantly enriched disease annotations including age-related metabolic and cardiovascular conditions and several cancers. Enriched pathways included those related to proteins and protein modification. We identified miRNAs associated with EAA of multiple epigenetic clocks. PhenoAge had more associations with individual miRNAs, but GrimAge and Horvath had greater implications for miRNA-associated pathways. Understanding the relationship between these epigenetic markers could contribute to our understanding of the molecular underpinnings of aging and aging-related diseases.
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Affiliation(s)
- Alesia M Jung
- Department of Community, Environment & Policy, Mel & Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
- Department of Pharmacology & Toxicology, R. Ken Coit College of Pharmacy, College of Public Health, Tucson, AZ, USA
| | - Melissa A Furlong
- Department of Community, Environment & Policy, Mel & Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Andres Cardenas
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Shawn C Beitel
- Department of Community, Environment & Policy, Mel & Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | - Sally R Littau
- Department of Community, Environment & Policy, Mel & Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
| | - Alberto J Caban-Martinez
- Department of Public Health Sciences, Miller School of Medicine, University of Miami, Miami, FL, USA
| | | | | | - Derek Urwin
- Los Angeles County Fire Department, Los Angeles, CA, USA
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- Division of Health Safety and Medicine, International Association of Fire Fighters, Washington, DC, USA
| | - Jamie Gabriel
- Los Angeles County Fire Department, Los Angeles, CA, USA
| | | | - Judith M Graber
- Department of Biostatistics & Epidemiology, School of Public Health, Rutgers University, Piscataway, NJ, USA
| | - Casey Grant
- Fire Protection Research Foundation, Quincy, MA, USA
| | - Jefferey L Burgess
- Department of Community, Environment & Policy, Mel & Enid Zuckerman College of Public Health, University of Arizona, Tucson, AZ, USA
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129
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deSteiguer AJ, Raffington L, Sabhlok A, Tanksley P, Tucker-Drob EM, Harden KP. Stability of DNA-Methylation Profiles of Biological Aging in Children and Adolescents. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564766. [PMID: 37961459 PMCID: PMC10635005 DOI: 10.1101/2023.10.30.564766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background and Objectives Methylation profile scores (MPSs) index biological aging and aging-related disease in adults and are cross-sectionally associated with social determinants of health in childhood. MPSs thus provide an opportunity to trace how aging-related biology responds to environmental changes in early life. Information regarding the stability of MPSs in early life is currently lacking. Method We use longitudinal data from children and adolescents ages 8-18 (N = 428, M age = 12.15 years) from the Texas Twin Project. Participants contributed two waves of salivary DNA-methylation data (mean lag = 3.94 years), which were used to construct four MPSs reflecting multi-system physiological decline and mortality risk (PhenoAgeAccel and GrimAgeAccel), pace of biological aging (DunedinPACE), and cognitive function (Epigenetic-g). Furthermore, we exploit variation among participants in whether they were exposed to the COVID-19 pandemic during the course of study participation, in order to test how a historical period characterized by environmental disruption might affect children's aging-related MPSs. Results All MPSs showed moderate longitudinal stability (test-retest rs = 0.42, 0.44, 0.46, 0.51 for PhenoAgeAccel, GrimAgeAccel, and Epigenetic-g, and DunedinPACE, respectively). No differences in the stability of MPSs were apparent between those whose second assessment took place after the onset of the COVID-19 pandemic vs. those for whom both assessments took place prior to the pandemic. Conclusions Aging-related DNA-methylation patterns are less stable in childhood than has been previously observed in adulthood. Further developmental research on the methylome is necessary to understand which environmental perturbations in childhood impact trajectories of biological aging and when children are most sensitive to those impacts.
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Affiliation(s)
- Abby J. deSteiguer
- Department of Psychology, University of Texas at Austin, Austin, TX, USA
| | - Laurel Raffington
- Max Planck Research Group Biosocial – Biology, Social Disparities, and Development, Max Planck Institute for Human Development, Berlin, Germany
| | - Aditi Sabhlok
- Department of Psychology, University of Texas at Austin, Austin, TX, USA
| | - Peter Tanksley
- Population Research Center, The University of Texas at Austin, Austin, TX, USA
| | - Elliot M. Tucker-Drob
- Department of Psychology, University of Texas at Austin, Austin, TX, USA
- Population Research Center, The University of Texas at Austin, Austin, TX, USA
| | - K. Paige Harden
- Department of Psychology, University of Texas at Austin, Austin, TX, USA
- Population Research Center, The University of Texas at Austin, Austin, TX, USA
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130
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Beaumont RN, Flatley C, Vaudel M, Wu X, Chen J, Moen GH, Skotte L, Helgeland Ø, Solé-Navais P, Banasik K, Albiñana C, Ronkainen J, Fadista J, Stinson SE, Trajanoska K, Wang CA, Westergaard D, Srinivasan S, Sánchez-Soriano C, Bilbao JR, Allard C, Groleau M, Kuulasmaa T, Leirer DJ, White F, Jacques PÉ, Cheng H, Hao K, Andreassen OA, Åsvold BO, Atalay M, Bhatta L, Bouchard L, Brumpton BM, Brunak S, Bybjerg-Grauholm J, Ebbing C, Elliott P, Engelbrechtsen L, Erikstrup C, Estarlich M, Franks S, Gaillard R, Geller F, Grove J, Hougaard DM, Kajantie E, Morgen CS, Nohr EA, Nyegaard M, Palmer CNA, Pedersen OB, Rivadeneira F, Sebert S, Shields BM, Stoltenberg C, Surakka I, Thørner LW, Ullum H, Vaarasmaki M, Vilhjalmsson BJ, Willer CJ, Lakka TA, Gybel-Brask D, Bustamante M, Hansen T, Pearson ER, Reynolds RM, Ostrowski SR, Pennell CE, Jaddoe VWV, Felix JF, Hattersley AT, Melbye M, Lawlor DA, Hveem K, Werge T, Nielsen HS, Magnus P, Evans DM, Jacobsson B, Järvelin MR, Zhang G, Hivert MF, Johansson S, Freathy RM, Feenstra B, Njølstad PR. Genome-wide association study of placental weight identifies distinct and shared genetic influences between placental and fetal growth. Nat Genet 2023; 55:1807-1819. [PMID: 37798380 PMCID: PMC10632150 DOI: 10.1038/s41588-023-01520-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 08/31/2023] [Indexed: 10/07/2023]
Abstract
A well-functioning placenta is essential for fetal and maternal health throughout pregnancy. Using placental weight as a proxy for placental growth, we report genome-wide association analyses in the fetal (n = 65,405), maternal (n = 61,228) and paternal (n = 52,392) genomes, yielding 40 independent association signals. Twenty-six signals are classified as fetal, four maternal and three fetal and maternal. A maternal parent-of-origin effect is seen near KCNQ1. Genetic correlation and colocalization analyses reveal overlap with birth weight genetics, but 12 loci are classified as predominantly or only affecting placental weight, with connections to placental development and morphology, and transport of antibodies and amino acids. Mendelian randomization analyses indicate that fetal genetically mediated higher placental weight is causally associated with preeclampsia risk and shorter gestational duration. Moreover, these analyses support the role of fetal insulin in regulating placental weight, providing a key link between fetal and placental growth.
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Affiliation(s)
- Robin N Beaumont
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Christopher Flatley
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Xiaoping Wu
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jing Chen
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Gunn-Helen Moen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Line Skotte
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Øyvind Helgeland
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Pol Solé-Navais
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Clara Albiñana
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
| | | | - João Fadista
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Sciences, Lund University Diabetes Centre, Malmö, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Sara Elizabeth Stinson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Katerina Trajanoska
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Carol A Wang
- School of Medicine and Public Health, College of Medicine, Public Health and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, Newcastle, New South Wales, Australia
| | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Methods and Analysis, Statistics Denmark, Copenhagen, Denmark
| | - Sundararajan Srinivasan
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | | | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Barcelona, Spain
| | - Catherine Allard
- Centre de recherche du Centre Hospitalier de l'Universite de Sherbrooke, Sherbrooke, Québec, Canada
| | - Marika Groleau
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Teemu Kuulasmaa
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
| | - Daniel J Leirer
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Frédérique White
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Pierre-Étienne Jacques
- Centre de recherche du Centre Hospitalier de l'Universite de Sherbrooke, Sherbrooke, Québec, Canada
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Haoxiang Cheng
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Ke Hao
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Ole A Andreassen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Bjørn Olav Åsvold
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Department of Endocrinology, Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Mustafa Atalay
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
| | - Laxmi Bhatta
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Clinical Department of Laboratory Medicine, Centre intégré universitaire de santé et de services sociaux (CIUSSS) du Saguenay-Lac-St-Jean-Hôpital Universitaire de Chicoutimi, Saguenay, Québec, Canada
| | - Ben Michael Brumpton
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
- Clinic of Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Cathrine Ebbing
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Gynecology and Obstetrics, Haukeland University Hospital, Bergen, Norway
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Line Engelbrechtsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Obstetrics and Gynecology, Herlev Hospital, Herlev, Denmark
| | - Christian Erikstrup
- Department Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Marisa Estarlich
- Faculty of Nursing and Chiropody, Universitat de València, C/Menendez Pelayo, Valencia, Spain
- Epidemiology and Environmental Health Joint Research Unit, Foundation for the Promotion of Health and Biomedical Research in the Valencian Region, FISABIO-Public Health, FISABIO-Universitat Jaume I-Universitat de València, Valencia, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Stephen Franks
- Institute of Reproductive and Developmental Biology, Imperial College London, London, UK
| | - Romy Gaillard
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jakob Grove
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Biomedicine-Human Genetics and the iSEQ Center, Aarhus University, Aarhus, Denmark
- Center for Genomics and Personalized Medicine, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - David M Hougaard
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
| | - Eero Kajantie
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki and Oulu, Oulu, Finland
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Camilla S Morgen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- National Institute of Public Health, University of Southern Denmark, Copenhagen, Denmark
| | - Ellen A Nohr
- Institute of Clinical research, University of Southern Denmark, Odense, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Colin N A Palmer
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Ole Birger Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Sylvain Sebert
- Research Unit of Population Health, University of Oulu, Oulu, Finland
| | - Beverley M Shields
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Camilla Stoltenberg
- Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Ida Surakka
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
| | - Lise Wegner Thørner
- Department of Clinical Immunology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | | | - Marja Vaarasmaki
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Department of Obstetrics and Gynaecology, Oulu University Hospital, Oulu, Finland
| | - Bjarni J Vilhjalmsson
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiology, University of Michigan, Ann Arbor, MI, USA
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Timo A Lakka
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
- Department of Clinical Physiology and Nuclear Medicine, Kuopio University Hospital, Kuopio, Finland
- Foundation for Research in Health Exercise and Nutrition, Kuopio Research Institute of Exercise Medicine, Kuopio, Finland
| | - Dorte Gybel-Brask
- Psychotherapeutic Outpatient Clinic, Mental Health Services, Capital Region, Copenhagen, Denmark
| | - Mariona Bustamante
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Madrid, Spain
- ISGlobal, Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ewan R Pearson
- Division of Population Health and Genomics, School of Medicine, University of Dundee, Dundee, UK
| | - Rebecca M Reynolds
- Centre for Cardiovascular Science, The University of Edinburgh, Edinburgh, UK
| | - Sisse R Ostrowski
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Craig E Pennell
- School of Medicine and Public Health, College of Medicine, Public Health and Wellbeing, The University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, New Lambton Heights, Newcastle, New South Wales, Australia
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Andrew T Hattersley
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Mads Melbye
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Danish Cancer Institute, Copenhagen, Denmark
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Deborah A Lawlor
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Kristian Hveem
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- HUNT Research Centre, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Levanger, Norway
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark
- Lundbeck Center for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Henriette Svarre Nielsen
- Department of Obstetrics and Gynecology, Copenhagen University Hospital, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - David M Evans
- Frazer Institute, The University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, University of Oulu, Oulu, Finland
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Unit of Primary Health Care, Oulu University Hospital, OYS, Oulu, Finland
| | - Ge Zhang
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Stefan Johansson
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| | - Rachel M Freathy
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK.
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.
- Department of Clinical Immunology, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark.
| | - Pål R Njølstad
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Children and Youth Clinic, Haukeland University Hospital, Bergen, Norway.
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Ott R, Stein R, Hauta-Alus HH, Ronkainen J, Fernández-Barrés S, Spielau U, Kirsten H, Poulain T, Melton PE, Küpers LK, Azaryah H, Colombo M, Landgraf K, Tobi EW, O'Sullivan T, Huang RC, Campoy C, Winkler C, Vioque J, Vrijheid M, Kiess W, Körner A, Sebert S, Jarvelin MR, Ziegler AG, Hummel S. Epigenome-Wide Meta-analysis Reveals Associations Between Dietary Glycemic Index and Glycemic Load and DNA Methylation in Children and Adolescents of Different Body Sizes. Diabetes Care 2023; 46:2067-2075. [PMID: 37756535 DOI: 10.2337/dc23-0474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023]
Abstract
OBJECTIVE Dietary glycemic index (GI) and glycemic load (GL) are associated with cardiometabolic health in children and adolescents, with potential distinct effects in people with increased BMI. DNA methylation (DNAm) may mediate these effects. Thus, we conducted meta-analyses of epigenome-wide association studies (EWAS) between dietary GI and GL and blood DNAm of children and adolescents. RESEARCH DESIGN AND METHODS We calculated dietary GI and GL and performed EWAS in children and adolescents (age range: 4.5-17 years) from six cohorts (N = 1,187). We performed stratified analyses of participants with normal weight (n = 801) or overweight or obesity (n = 386). We performed look-ups for the identified cytosine-phosphate-guanine (CpG) sites (false discovery rate [FDR] <0.05) with tissue-specific gene expression of 832 blood and 223 subcutaneous adipose tissue samples from children and adolescents. RESULTS Dietary GL was positively associated with DNAm of cg20274553 (FDR <0.05), annotated to WDR27. Several CpGs were identified in the normal-weight (GI: 85; GL: 17) and overweight or obese (GI: 136; GL: 298; FDR <0.05) strata, and none overlapped between strata. In participants with overweight or obesity, identified CpGs were related to RNA expression of genes associated with impaired metabolism (e.g., FRAT1, CSF3). CONCLUSIONS We identified 537 associations between dietary GI and GL and blood DNAm, mainly in children and adolescents with overweight or obesity. High-GI and/or -GL diets may influence epigenetic gene regulation and thereby promote metabolic derangements in young people with increased BMI.
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Affiliation(s)
- Raffael Ott
- Institute of Diabetes Research, Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes e.V. at Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
| | - Robert Stein
- Medical Faculty, University of Leipzig, University Hospital for Children and Adolescents, Center for Pediatric Research, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Helena H Hauta-Alus
- PEDEGO Research Unit, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
- Population Health Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
- Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Justiina Ronkainen
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Sílvia Fernández-Barrés
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Carlos III Institute, Madrid, Spain
| | - Ulrike Spielau
- Medical Faculty, University of Leipzig, University Hospital for Children and Adolescents, Center for Pediatric Research, Leipzig, Germany
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Tanja Poulain
- LIFE Child Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Phillip E Melton
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
- University of Western Australia, School of Population and Global Health, Perth, Western Australia, Australia
| | - Leanne K Küpers
- The Generation R Study Group, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus Medical Center, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Hatim Azaryah
- Department of Paediatrics, School of Medicine, University of Granada, Granada, Spain
- EURISTIKOS Excellence Centre for Paediatric Research, Biomedical Research Centre, University of Granada, Granada, Spain
| | - Marco Colombo
- Medical Faculty, University of Leipzig, University Hospital for Children and Adolescents, Center for Pediatric Research, Leipzig, Germany
| | - Kathrin Landgraf
- Medical Faculty, University of Leipzig, University Hospital for Children and Adolescents, Center for Pediatric Research, Leipzig, Germany
| | - Elmar W Tobi
- Periconceptional Epidemiology, Department of Obstetrics and Gynaecology, Division of Obstetrics and Prenatal Medicine, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Therese O'Sullivan
- Nutrition and Health Innovation Research Institute, Edith Cowan University, Perth, Western Australia, Australia
| | - Rae-Chi Huang
- Nutrition and Health Innovation Research Institute, Edith Cowan University, Perth, Western Australia, Australia
| | - Cristina Campoy
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Carlos III Institute, Madrid, Spain
- Department of Paediatrics, School of Medicine, University of Granada, Granada, Spain
- EURISTIKOS Excellence Centre for Paediatric Research, Biomedical Research Centre, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (Ibs-Granada), Granada, Spain
| | - Christiane Winkler
- Institute of Diabetes Research, Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes e.V. at Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes, School of Medicine, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Jesus Vioque
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Carlos III Institute, Madrid, Spain
- Alicante Institute for Health and Biomedical Research, University Miguel Hernandez, Alicante, Spain
| | - Martine Vrijheid
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Spanish Consortium for Research on Epidemiology and Public Health (CIBERESP), Carlos III Institute, Madrid, Spain
| | - Wieland Kiess
- Medical Faculty, University of Leipzig, University Hospital for Children and Adolescents, Center for Pediatric Research, Leipzig, Germany
- LIFE Child Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Antje Körner
- Medical Faculty, University of Leipzig, University Hospital for Children and Adolescents, Center for Pediatric Research, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
- LIFE Child Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Sylvain Sebert
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Marjo-Riitta Jarvelin
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, U.K
- Medical Research Council-Public Health England Centre for Environment and Health, School of Public Health, Imperial College, London, U.K
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Middlesex, U.K
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes e.V. at Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes, School of Medicine, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Sandra Hummel
- Institute of Diabetes Research, Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes e.V. at Helmholtz Munich, German Research Center for Environmental Health, Munich, Germany
- Forschergruppe Diabetes, School of Medicine, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
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132
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Kocher K, Bhattacharya S, Niforatos-Andescavage N, Almalvez M, Henderson D, Vilain E, Limperopoulos C, Délot EC. Genome-wide neonatal epigenetic changes associated with maternal exposure to the COVID-19 pandemic. BMC Med Genomics 2023; 16:268. [PMID: 37899449 PMCID: PMC10614377 DOI: 10.1186/s12920-023-01707-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 10/17/2023] [Indexed: 10/31/2023] Open
Abstract
BACKGROUND During gestation, stressors to the fetus, including viral exposure or maternal psychological distress, can fundamentally alter the neonatal epigenome, and may be associated with long-term impaired developmental outcomes. The impact of in utero exposure to the COVID-19 pandemic on the newborn epigenome has yet to be described. METHODS This study aimed to determine whether there are unique epigenetic signatures in newborns who experienced otherwise healthy pregnancies that occurred during the COVID-19 pandemic (Project RESCUE). The pre-pandemic control and pandemic cohorts (Project RESCUE) included in this study are part of a prospective observational and longitudinal cohort study that evaluates the impact of elevated prenatal maternal stress during the COVID-19 pandemic on early childhood neurodevelopment. Using buccal swabs collected at birth, differential DNA methylation analysis was performed using the Infinium MethylationEPIC arrays and linear regression analysis. Pathway analysis and gene ontology enrichment were performed on resultant gene lists. RESULTS Widespread differential methylation was found between neonates exposed in utero to the pandemic and pre-pandemic neonates. In contrast, there were no apparent epigenetic differences associated with maternal COVID-19 infection during pregnancy. Differential methylation was observed among genomic sites that underpin important neurological pathways that have been previously reported in the literature to be differentially methylated because of prenatal stress, such as NR3C1. CONCLUSIONS The present study reveals potential associations between exposure to the COVID-19 pandemic during pregnancy and subsequent changes in the newborn epigenome. While this finding warrants further investigation, it is a point that should be considered in any study assessing newborn DNA methylation studies obtained during this period, even in otherwise healthy pregnancies.
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Affiliation(s)
- Kristen Kocher
- Center for Genetic Medicine Research, Children's National Research & Innovation Campus, Washington, DC, USA
- Department of Genomics & Precision Medicine, George Washington University, Washington, DC, USA
| | - Surajit Bhattacharya
- Center for Genetic Medicine Research, Children's National Research & Innovation Campus, Washington, DC, USA
| | | | - Miguel Almalvez
- Institute for Clinical and Translational Science, University of California, Irvine, CA, USA
| | - Diedtra Henderson
- Developing Brain Institute, Children's National Hospital, Washington, DC, USA
| | - Eric Vilain
- Institute for Clinical and Translational Science, University of California, Irvine, CA, USA.
| | | | - Emmanuèle C Délot
- Center for Genetic Medicine Research, Children's National Research & Innovation Campus, Washington, DC, USA.
- Department of Genomics & Precision Medicine, George Washington University, Washington, DC, USA.
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133
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Burton MA, Garratt ES, Hewitt MO, Sharkh HY, Antoun E, Westbury LD, Dennison EM, Harvey NC, Cooper C, MacIsaac JL, Kobor MS, Patel HP, Godfrey KM, Lillycrop KA. DNA methylation of insulin signaling pathways is associated with HOMA2-IR in primary myoblasts from older adults. Skelet Muscle 2023; 13:17. [PMID: 37898813 PMCID: PMC10612387 DOI: 10.1186/s13395-023-00326-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 10/09/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND While ageing is associated with increased insulin resistance (IR), the molecular mechanisms underlying increased IR in the muscle, the primary organ for glucose clearance, have yet to be elucidated in older individuals. As epigenetic processes are suggested to contribute to the development of ageing-associated diseases, we investigated whether differential DNA methylation was associated with IR in human primary muscle stem cells (myoblasts) from community-dwelling older individuals. METHODS We measured DNA methylation (Infinium HumanMethylationEPIC BeadChip) in myoblast cultures from vastus lateralis biopsies (119 males/females, mean age 78.24 years) from the Hertfordshire Sarcopenia Study extension (HSSe) and examined differentially methylated cytosine phosphate guanine (CpG) sites (dmCpG), regions (DMRs) and gene pathways associated with HOMA2-IR, an index for the assessment of insulin resistance, and levels of glycated hemoglobin HbA1c. RESULTS Thirty-eight dmCpGs (false discovery rate (FDR) < 0.05) were associated with HOMA2-IR, with dmCpGs enriched in genes linked with JNK, AMPK and insulin signaling. The methylation signal associated with HOMA2-IR was attenuated after the addition of either BMI (6 dmCpGs), appendicular lean mass index (ALMi) (7 dmCpGs), grip strength (15 dmCpGs) or gait speed (23 dmCpGs) as covariates in the model. There were 8 DMRs (Stouffer < 0.05) associated with HOMA2-IR, including DMRs within T-box transcription factor (TBX1) and nuclear receptor subfamily-2 group F member-2 (NR2F2); the DMRs within TBX1 and NR2F2 remained associated with HOMA2-IR after adjustment for BMI, ALMi, grip strength or gait speed. Forty-nine dmCpGs and 21 DMRs were associated with HbA1c, with cg13451048, located within exoribonuclease family member 3 (ERI3) associated with both HOMA2-IR and HbA1c. HOMA2-IR and HbA1c were not associated with accelerated epigenetic ageing. CONCLUSIONS These findings suggest that insulin resistance is associated with differential DNA methylation in human primary myoblasts with both muscle mass and body composition making a significant contribution to the methylation changes associated with IR.
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Affiliation(s)
- Mark A Burton
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Emma S Garratt
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University of Southampton & University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Matthew O Hewitt
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Hanan Y Sharkh
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
- Biological Sciences, University of Southampton, Southampton, UK
| | - Elie Antoun
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Leo D Westbury
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
| | - Elaine M Dennison
- NIHR Southampton Biomedical Research Centre, University of Southampton & University Hospital Southampton NHS Foundation Trust, Southampton, UK
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
| | - Nicholas C Harvey
- NIHR Southampton Biomedical Research Centre, University of Southampton & University Hospital Southampton NHS Foundation Trust, Southampton, UK
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
| | - Cyrus Cooper
- NIHR Southampton Biomedical Research Centre, University of Southampton & University Hospital Southampton NHS Foundation Trust, Southampton, UK
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Julia L MacIsaac
- Department of Medical Genetics, Faculty of Medicine, Edwin S.H. Leong Healthy Aging Program, University of British Columbia, Vancouver, Canada
| | - Michael S Kobor
- Department of Medical Genetics, Faculty of Medicine, Edwin S.H. Leong Healthy Aging Program, University of British Columbia, Vancouver, Canada
| | - Harnish P Patel
- NIHR Southampton Biomedical Research Centre, University of Southampton & University Hospital Southampton NHS Foundation Trust, Southampton, UK
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
- Faculty of Medicine, Academic Geriatric Medicine, University of Southampton, Southampton, UK
| | - Keith M Godfrey
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University of Southampton & University Hospital Southampton NHS Foundation Trust, Southampton, UK
- MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, UK
| | - Karen A Lillycrop
- Human Development and Health Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK.
- NIHR Southampton Biomedical Research Centre, University of Southampton & University Hospital Southampton NHS Foundation Trust, Southampton, UK.
- Biological Sciences, University of Southampton, Southampton, UK.
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Widayati TA, Schneider J, Panteleeva K, Chernysheva E, Hrbkova N, Beck S, Voloshin V, Chervova O. Open access-enabled evaluation of epigenetic age acceleration in colorectal cancer and development of a classifier with diagnostic potential. Front Genet 2023; 14:1258648. [PMID: 37953923 PMCID: PMC10634722 DOI: 10.3389/fgene.2023.1258648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023] Open
Abstract
Aberrant DNA methylation (DNAm) is known to be associated with the aetiology of cancer, including colorectal cancer (CRC). In the past, the availability of open access data has been the main driver of innovative method development and research training. However, this is increasingly being eroded by the move to controlled access, particularly of medical data, including cancer DNAm data. To rejuvenate this valuable tradition, we leveraged DNAm data from 1,845 samples (535 CRC tumours, 522 normal colon tissues adjacent to tumours, 72 colorectal adenomas, and 716 normal colon tissues from healthy individuals) from 14 open access studies deposited in NCBI GEO and ArrayExpress. We calculated each sample's epigenetic age (EA) using eleven epigenetic clock models and derived the corresponding epigenetic age acceleration (EAA). For EA, we observed that most first- and second-generation epigenetic clocks reflect the chronological age in normal tissues adjacent to tumours and healthy individuals [e.g., Horvath (r = 0.77 and 0.79), Zhang elastic net (EN) (r = 0.70 and 0.73)] unlike the epigenetic mitotic clocks (EpiTOC, HypoClock, MiAge) (r < 0.3). For EAA, we used PhenoAge, Wu, and the above mitotic clocks and found them to have distinct distributions in different tissue types, particularly between normal colon tissues adjacent to tumours and cancerous tumours, as well as between normal colon tissues adjacent to tumours and normal colon tissue from healthy individuals. Finally, we harnessed these associations to develop a classifier using elastic net regression (with lasso and ridge regularisations) that predicts CRC diagnosis based on a patient's sex and EAAs calculated from histologically normal controls (i.e., normal colon tissues adjacent to tumours and normal colon tissue from healthy individuals). The classifier demonstrated good diagnostic potential with ROC-AUC = 0.886, which suggests that an EAA-based classifier trained on relevant data could become a tool to support diagnostic/prognostic decisions in CRC for clinical professionals. Our study also reemphasises the importance of open access clinical data for method development and training of young scientists. Obtaining the required approvals for controlled access data would not have been possible in the timeframe of this study.
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Affiliation(s)
- Tyas Arum Widayati
- Medical Genomics Lab, Cancer Institute, University College London, London, United Kingdom
| | - Jadesada Schneider
- Medical Genomics Lab, Cancer Institute, University College London, London, United Kingdom
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Kseniia Panteleeva
- School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Elizabeth Chernysheva
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Natalie Hrbkova
- Medical Genomics Lab, Cancer Institute, University College London, London, United Kingdom
| | - Stephan Beck
- Medical Genomics Lab, Cancer Institute, University College London, London, United Kingdom
| | - Vitaly Voloshin
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, United Kingdom
| | - Olga Chervova
- Medical Genomics Lab, Cancer Institute, University College London, London, United Kingdom
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135
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Kunkle B, Martin ER, Wang L. Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC BeadChip microarrays. RESEARCH SQUARE 2023:rs.3.rs-3068938. [PMID: 37461726 PMCID: PMC10350239 DOI: 10.21203/rs.3.rs-3068938/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC arrays. We conducted a comprehensive assessment of the EPIC array probe reliability using 138 duplicated blood DNAm samples generated by the Alzheimer's Disease Neuroimaging Initiative study. We introduced a novel statistical measure, the modified intraclass correlation, to better account for the disagreement in duplicate measurements. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliable information for probes on the EPIC array, will serve as a valuable resource for future DNAm studies.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I. Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michael A. Schmidt
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Achintya Varma
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - X. Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Brian Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R. Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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136
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Kunkle B, Martin ER, Wang L. Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC BeadChip microarrays. RESEARCH SQUARE 2023:rs.3.rs-3068938. [PMID: 37461726 PMCID: PMC10350239 DOI: 10.21203/rs.3.rs-3068938/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC arrays. We conducted a comprehensive assessment of the EPIC array probe reliability using 138 duplicated blood DNAm samples generated by the Alzheimer's Disease Neuroimaging Initiative study. We introduced a novel statistical measure, the modified intraclass correlation, to better account for the disagreement in duplicate measurements. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliable information for probes on the EPIC array, will serve as a valuable resource for future DNAm studies.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I. Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michael A. Schmidt
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Achintya Varma
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - X. Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Brian Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R. Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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137
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LaFlamme CW, Rastin C, Sengupta S, Pennington HE, Russ-Hall SJ, Schneider AL, Bonkowski ES, Almanza Fuerte EP, Galey M, Goffena J, Gibson SB, Allan TJ, Nyaga DM, Lieffering N, Hebbar M, Walker EV, Darnell D, Olsen SR, Kolekar P, Djekidel N, Rosikiewicz W, McConkey H, Kerkhof J, Levy MA, Relator R, Lev D, Lerman-Sagie T, Park KL, Alders M, Cappuccio G, Chatron N, Demain L, Genevieve D, Lesca G, Roscioli T, Sanlaville D, Tedder ML, Hubshman MW, Ketkar S, Dai H, Worley KC, Rosenfeld JA, Chao HT, Neale G, Carvill GL, Wang Z, Berkovic SF, Sadleir LG, Miller DE, Scheffer IE, Sadikovic B, Mefford HC. Diagnostic Utility of Genome-wide DNA Methylation Analysis in Genetically Unsolved Developmental and Epileptic Encephalopathies and Refinement of a CHD2 Episignature. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.11.23296741. [PMID: 37873138 PMCID: PMC10592992 DOI: 10.1101/2023.10.11.23296741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Sequence-based genetic testing currently identifies causative genetic variants in ∼50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. Rare epigenetic variations ("epivariants") can drive disease by modulating gene expression at single loci, whereas genome-wide DNA methylation changes can result in distinct "episignature" biomarkers for monogenic disorders in a growing number of rare diseases. Here, we interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 516 individuals with genetically unsolved DEEs who had previously undergone extensive genetic testing. We identified rare differentially methylated regions (DMRs) and explanatory episignatures to discover causative and candidate genetic etiologies in 10 individuals. We then used long-read sequencing to identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and two copy number variants. We also identify pathogenic sequence variants associated with episignatures; some had been missed by previous exome sequencing. Although most DEE genes lack known episignatures, the increase in diagnostic yield for DNA methylation analysis in DEEs is comparable to the added yield of genome sequencing. Finally, we refine an episignature for CHD2 using an 850K methylation array which was further refined at higher CpG resolution using bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate genetic causes as ∼2% (10/516) for unsolved DEE cases.
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138
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Kuiper LM, Polinder-Bos HA, Bizzarri D, Vojinovic D, Vallerga CL, Beekman M, Dollé MET, Ghanbari M, Voortman T, Reinders MJT, Verschuren WMM, Slagboom PE, van den Akker EB, van Meurs JBJ. Epigenetic and Metabolomic Biomarkers for Biological Age: A Comparative Analysis of Mortality and Frailty Risk. J Gerontol A Biol Sci Med Sci 2023; 78:1753-1762. [PMID: 37303208 PMCID: PMC10562890 DOI: 10.1093/gerona/glad137] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Indexed: 06/13/2023] Open
Abstract
Biological age captures a person's age-related risk of unfavorable outcomes using biophysiological information. Multivariate biological age measures include frailty scores and molecular biomarkers. These measures are often studied in isolation, but here we present a large-scale study comparing them. In 2 prospective cohorts (n = 3 222), we compared epigenetic (DNAm Horvath, DNAm Hannum, DNAm Lin, DNAm epiTOC, DNAm PhenoAge, DNAm DunedinPoAm, DNAm GrimAge, and DNAm Zhang) and metabolomic-based (MetaboAge and MetaboHealth) biomarkers in reflection of biological age, as represented by 5 frailty measures and overall mortality. Biomarkers trained on outcomes with biophysiological and/or mortality information outperformed age-trained biomarkers in frailty reflection and mortality prediction. DNAm GrimAge and MetaboHealth, trained on mortality, showed the strongest association with these outcomes. The associations of DNAm GrimAge and MetaboHealth with frailty and mortality were independent of each other and of the frailty score mimicking clinical geriatric assessment. Epigenetic, metabolomic, and clinical biological age markers seem to capture different aspects of aging. These findings suggest that mortality-trained molecular markers may provide novel phenotype reflecting biological age and strengthen current clinical geriatric health and well-being assessment.
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Affiliation(s)
- Lieke M Kuiper
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Center for Nutrition, Prevention and Health Services, Bilthoven, The Netherlands
| | | | - Daniele Bizzarri
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Centre, Leiden, The Netherlands
- Pattern Recognition and Bioinformatics, Delft University of Technology, Delft, The Netherlands
| | - Dina Vojinovic
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Centre, Leiden, The Netherlands
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | | | - Marian Beekman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Centre, Leiden, The Netherlands
| | - Martijn E T Dollé
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, The Netherlands
| | - Marcel J T Reinders
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Centre, Leiden, The Netherlands
- Pattern Recognition and Bioinformatics, Delft University of Technology, Delft, The Netherlands
| | - W M Monique Verschuren
- Center for Nutrition, Prevention and Health Services, Bilthoven, The Netherlands
- Julius Center for Health Sciences and Primary Care Utrecht, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Centre, Leiden, The Netherlands
- Max Planck Institute for the Biology of Ageing, Cologne, Germany
| | - Erik B van den Akker
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Centre, Leiden, The Netherlands
- Pattern Recognition and Bioinformatics, Delft University of Technology, Delft, The Netherlands
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus MC, Rotterdam, The Netherlands
- Department of Orthopaedics and Sports Medicine, Erasmus MC, Rotterdam, The Netherlands
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139
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Mouat JS, Li S, Myint SS, Laufer BI, Lupo PJ, Schraw JM, Woodhouse JP, de Smith AJ, LaSalle JM. Epigenomic signature of major congenital heart defects in newborns with Down syndrome. Hum Genomics 2023; 17:92. [PMID: 37803336 PMCID: PMC10559462 DOI: 10.1186/s40246-023-00540-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/02/2023] [Indexed: 10/08/2023] Open
Abstract
BACKGROUND Congenital heart defects (CHDs) affect approximately half of individuals with Down syndrome (DS), but the molecular reasons for incomplete penetrance are unknown. Previous studies have largely focused on identifying genetic risk factors associated with CHDs in individuals with DS, but comprehensive studies of the contribution of epigenetic marks are lacking. We aimed to identify and characterize DNA methylation differences from newborn dried blood spots (NDBS) of DS individuals with major CHDs compared to DS individuals without CHDs. METHODS We used the Illumina EPIC array and whole-genome bisulfite sequencing (WGBS) to quantitate DNA methylation for 86 NDBS samples from the California Biobank Program: (1) 45 DS-CHD (27 female, 18 male) and (2) 41 DS non-CHD (27 female, 14 male). We analyzed global CpG methylation and identified differentially methylated regions (DMRs) in DS-CHD versus DS non-CHD comparisons (both sex-combined and sex-stratified) corrected for sex, age of blood collection, and cell-type proportions. CHD DMRs were analyzed for enrichment in CpG and genic contexts, chromatin states, and histone modifications by genomic coordinates and for gene ontology enrichment by gene mapping. DMRs were also tested in a replication dataset and compared to methylation levels in DS versus typical development (TD) WGBS NDBS samples. RESULTS We found global CpG hypomethylation in DS-CHD males compared to DS non-CHD males, which was attributable to elevated levels of nucleated red blood cells and not seen in females. At a regional level, we identified 58, 341, and 3938 CHD-associated DMRs in the Sex Combined, Females Only, and Males Only groups, respectively, and used machine learning algorithms to select 19 Males Only loci that could distinguish CHD from non-CHD. DMRs in all comparisons were enriched for gene exons, CpG islands, and bivalent chromatin and mapped to genes enriched for terms related to cardiac and immune functions. Lastly, a greater percentage of CHD-associated DMRs than background regions were differentially methylated in DS versus TD samples. CONCLUSIONS A sex-specific signature of DNA methylation was detected in NDBS of DS-CHD compared to DS non-CHD individuals. This supports the hypothesis that epigenetics can reflect the variability of phenotypes in DS, particularly CHDs.
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Affiliation(s)
- Julia S Mouat
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Swe Swe Myint
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Benjamin I Laufer
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA
- Genome Center, University of California, Davis, CA, USA
- MIND Institute, University of California, Davis, CA, USA
| | - Philip J Lupo
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jeremy M Schraw
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - John P Woodhouse
- Division of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA, USA.
- Perinatal Origins of Disparities Center, University of California, Davis, CA, USA.
- Genome Center, University of California, Davis, CA, USA.
- MIND Institute, University of California, Davis, CA, USA.
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140
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Perez-Garcia J, Pino-Yanes M, Plender EG, Everman JL, Eng C, Jackson ND, Moore CM, Beckman KB, Medina V, Sharma S, Winnica DE, Holguin F, Rodríguez-Santana J, Villar J, Ziv E, Seibold MA, Burchard EG. Epigenomic response to albuterol treatment in asthma-relevant airway epithelial cells. Clin Epigenetics 2023; 15:156. [PMID: 37784136 PMCID: PMC10546710 DOI: 10.1186/s13148-023-01571-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/25/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Albuterol is the first-line asthma medication used in diverse populations. Although DNA methylation (DNAm) is an epigenetic mechanism involved in asthma and bronchodilator drug response (BDR), no study has assessed whether albuterol could induce changes in the airway epithelial methylome. We aimed to characterize albuterol-induced DNAm changes in airway epithelial cells, and assess potential functional consequences and the influence of genetic variation and asthma-related clinical variables. RESULTS We followed a discovery and validation study design to characterize albuterol-induced DNAm changes in paired airway epithelial cultures stimulated in vitro with albuterol. In the discovery phase, an epigenome-wide association study using paired nasal epithelial cultures from Puerto Rican children (n = 97) identified 22 CpGs genome-wide associated with repeated-use albuterol treatment (p < 9 × 10-8). Albuterol predominantly induced a hypomethylation effect on CpGs captured by the EPIC array across the genome (probability of hypomethylation: 76%, p value = 3.3 × 10-5). DNAm changes on the CpGs cg23032799 (CREB3L1), cg00483640 (MYLK4-LINC01600), and cg05673431 (KSR1) were validated in nasal epithelia from 10 independent donors (false discovery rate [FDR] < 0.05). The effect on the CpG cg23032799 (CREB3L1) was cross-tissue validated in bronchial epithelial cells at nominal level (p = 0.030). DNAm changes in these three CpGs were shown to be influenced by three independent genetic variants (FDR < 0.05). In silico analyses showed these polymorphisms regulated gene expression of nearby genes in lungs and/or fibroblasts including KSR1 and LINC01600 (6.30 × 10-14 ≤ p ≤ 6.60 × 10-5). Additionally, hypomethylation at the CpGs cg10290200 (FLNC) and cg05673431 (KSR1) was associated with increased gene expression of the genes where they are located (FDR < 0.05). Furthermore, while the epigenetic effect of albuterol was independent of the asthma status, severity, and use of medication, BDR was nominally associated with the effect on the CpG cg23032799 (CREB3L1) (p = 0.004). Gene-set enrichment analyses revealed that epigenomic modifications of albuterol could participate in asthma-relevant processes (e.g., IL-2, TNF-α, and NF-κB signaling pathways). Finally, nine differentially methylated regions were associated with albuterol treatment, including CREB3L1, MYLK4, and KSR1 (adjusted p value < 0.05). CONCLUSIONS This study revealed evidence of epigenetic modifications induced by albuterol in the mucociliary airway epithelium. The epigenomic response induced by albuterol might have potential clinical implications by affecting biological pathways relevant to asthma.
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Grants
- R01 ES015794 NIEHS NIH HHS
- R01 HL120393 NHLBI NIH HHS
- R01ES015794, R21ES24844 NIEHS NIH HHS
- UM1 HG008901 NHGRI NIH HHS
- R01MD010443, R56MD013312 NIMHD NIH HHS
- R01 HL135156 NHLBI NIH HHS
- R01 HL128439 NHLBI NIH HHS
- R01 HL117004 NHLBI NIH HHS
- R21 ES024844 NIEHS NIH HHS
- R01 HL117626 NHLBI NIH HHS
- R56 MD013312 NIMHD NIH HHS
- R01 MD010443 NIMHD NIH HHS
- R01 HL155024 NHLBI NIH HHS
- R01HL155024-01, HHSN268201600032I, 3R01HL-117626-02S1, HHSN268201800002I, 3R01HL117004-02S3, 3R01HL-120393-02S1, R01HL117004, R01HL128439, R01HL135156, X01HL134589 NHLBI NIH HHS
- HHSN268201600032C NHLBI NIH HHS
- U24 HG008956 NHGRI NIH HHS
- Ministerio de Universidades
- Ministerio de Ciencia e Innovación
- Instituto de Salud Carlos III
- National Heart, Lung, and Blood Institute
- National Human Genome Research Institute
- National Institute of Environmental Health Sciences
- National Institute on Minority Health and Health Disparities
- The Centers for Common Disease Genomics of the Genome Sequencing Program
- Tobacco-Related Disease Research Program
- Sandler Family Foundation
- American Asthma Foundation
- Amos Medical Faculty Development Program from the Robert Wood Johnson Foundation
- Harry Wm. and Diana V. Hind Distinguished Professor in Pharmaceutical Sciences II
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Affiliation(s)
- Javier Perez-Garcia
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Canary Islands, Spain.
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology, and Genetics, Universidad de La Laguna (ULL), La Laguna, Tenerife, Canary Islands, Spain.
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna (ULL), La Laguna, Spain.
| | - Elizabeth G Plender
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Jamie L Everman
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Celeste Eng
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Nathan D Jackson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Camille M Moore
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Department of Biomedical Research, National Jewish Health, Denver, CO, USA
- Department of Biostatistics and Informatics, University of Colorado, Denver, CO, USA
| | - Kenneth B Beckman
- University of Minnesota Genomics Center (UMNGC), Minneapolis, MN, USA
| | | | - Sunita Sharma
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Daniel Efrain Winnica
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Fernando Holguin
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Jesús Villar
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Multidisciplinary Organ Dysfunction Evaluation Research Network (MODERN), Research Unit, Hospital Universitario Dr. Negrín, Las Palmas de Gran Canaria, Spain
- Li Ka Shing Knowledge Institute at the St. Michael's Hospital, Toronto, ON, Canada
| | - Elad Ziv
- Institute for Human Genetics, University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Max A Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Esteban G Burchard
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco (UCSF), San Francisco, CA, USA
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141
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Casella C, Kiles F, Urquhart C, Michaud DS, Kirwa K, Corlin L. Methylomic, proteomic, and metabolomic correlates of traffic-related air pollution: A systematic review, pathway analysis, and network analysis relating traffic-related air pollution to subclinical and clinical cardiorespiratory outcomes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.30.23296386. [PMID: 37873294 PMCID: PMC10592990 DOI: 10.1101/2023.09.30.23296386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
A growing body of literature has attempted to characterize how traffic-related air pollution (TRAP) affects molecular and subclinical biological processes in ways that could lead to cardiorespiratory disease. To provide a streamlined synthesis of what is known about the multiple mechanisms through which TRAP could lead cardiorespiratory pathology, we conducted a systematic review of the epidemiological literature relating TRAP exposure to methylomic, proteomic, and metabolomic biomarkers in adult populations. Using the 139 papers that met our inclusion criteria, we identified the omic biomarkers significantly associated with short- or long-term TRAP and used these biomarkers to conduct pathway and network analyses. We considered the evidence for TRAP-related associations with biological pathways involving lipid metabolism, cellular energy production, amino acid metabolism, inflammation and immunity, coagulation, endothelial function, and oxidative stress. Our analysis suggests that an integrated multi-omics approach may provide critical new insights into the ways TRAP could lead to adverse clinical outcomes. We advocate for efforts to build a more unified approach for characterizing the dynamic and complex biological processes linking TRAP exposure and subclinical and clinical disease, and highlight contemporary challenges and opportunities associated with such efforts.
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Affiliation(s)
- Cameron Casella
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Frances Kiles
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Catherine Urquhart
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Dominique S. Michaud
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Kipruto Kirwa
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
- Department of Environmental Health, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Laura Corlin
- Department of Public Health and Community Medicine, Tufts University School of Medicine, Boston, MA 02111, USA
- Department of Civil and Environmental Engineering, Tufts University School of Engineering, Medford, MA 02155, USA
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142
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Shi D, Zhou X, Cai L, Wei X, Zhang L, Sun Q, Zhou F, Sun L. Placental DNA methylation analysis of selective fetal growth restriction in monochorionic twins reveals aberrant methylated CYP11A1 gene for fetal growth restriction. FASEB J 2023; 37:e23207. [PMID: 37732623 DOI: 10.1096/fj.202300742r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 08/04/2023] [Accepted: 09/07/2023] [Indexed: 09/22/2023]
Abstract
Fetal growth restriction (FGR) is associated with increased susceptibility to perinatal morbidity and mortality. Evidence suggests that epigenetic changes play critical roles in the regulation of fetal growth. We sought to present a comprehensive analysis of the associations between placental DNA methylation and selective fetal growth restriction (sFGR), which is a severe complication of monochorionic twin pregnancies, characterized by one fetus experiencing restricted growth. Genome-wide methylation analysis was performed on 24 placental samples obtained from 12 monochorionic twins with sFGR (Cohort 1) using Illumina Infinium MethylationEPIC BeadChip. Integrative analysis of our EPIC data and two previous placental methylation studies of sFGR (a total of 30 placental samples from 15 sFGR twins) was used to identify convincing differential promoter methylation. Validation analysis was performed on the placentas from 15 sFGR twins (30 placental samples), 15 FGR singletons, and 14 control singletons (Cohort 2) using pyrosequencing, quantitative real-time polymerase chain reaction, western blot, and immunohistochemistry (IHC). A globe shift toward hypomethylation was identified in the placentas of growth-restricted fetuses compared with the placentas of normal fetuses in monochorionic twins, including 5625 hypomethylated CpGs and 452 hypermethylated CpGs, especially in the regions of CpG islands, gene-body and promoters. The analysis of pathways revealed dysregulation primarily in steroid hormone biosynthesis, metabolism, cell adhesion, signaling transduction, and immune response. Integrative analysis revealed a differentially methylated promoter region in the CYP11A1 gene, encoding a rate-limiting enzyme of steroidogenesis converting cholesterol to pregnenolone. The CYP11A1 gene was validated to have hypomethylation and higher mRNA expression in sFGR twins and FGR singletons. In conclusion, our findings suggested that the changes in placental DNA methylation pattern in sFGR may have functional implications for differentially methylated genes and regulatory regions. The study provides reliable evidence for identifying abnormally methylated CYP11A1 gene in the placenta of sFGR.
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Affiliation(s)
- Dayuan Shi
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xinyao Zhou
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Luyao Cai
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xing Wei
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Luye Zhang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qianqian Sun
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fenhe Zhou
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Luming Sun
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
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143
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Ehlinger JV, Goodrich JM, Dolinoy DC, Watkins DJ, Cantoral A, Mercado-García A, Téllez-Rojo MM, Peterson KE. Associations between blood leukocyte DNA methylation and sustained attention in mid-to-late childhood. Epigenomics 2023; 15:965-981. [PMID: 37942546 PMCID: PMC10718163 DOI: 10.2217/epi-2023-0169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 10/20/2023] [Indexed: 11/10/2023] Open
Abstract
Aims: To identify associations between DNA methylation (DNAm) across the epigenome and symptoms related to attention-deficit/hyperactivity disorder in a population of Hispanic children. Materials & methods: Among 517 participants in the ELEMENT study aged 9-18 years, we conducted an epigenome-wide association study examining associations between blood leukocyte DNAm and performance on the Conners' continuous performance test (CPT3). Results: DNAm at loci in or near ZNF814, ELF4 and OR6K6 and functional enrichment for gene pathways pertaining to ferroptosis, inflammation, immune response and neurotransmission were significantly related to CPT3 scores. Conclusion: DNAm was associated with CPT3 performance. Further analysis is warranted to understand how these genes and enriched pathways contribute to attention-deficit/hyperactivity disorder.
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Affiliation(s)
- Jessa V Ehlinger
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jaclyn M Goodrich
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Deborah J Watkins
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | | | | | | | - Karen E Peterson
- Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan, Ann Arbor, MI 48109, USA
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144
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Naue J. Getting the chronological age out of DNA: using insights of age-dependent DNA methylation for forensic DNA applications. Genes Genomics 2023; 45:1239-1261. [PMID: 37253906 PMCID: PMC10504122 DOI: 10.1007/s13258-023-01392-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/15/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND DNA analysis for forensic investigations has a long tradition with important developments and optimizations since its first application. Traditionally, short tandem repeats analysis has been the most powerful method for the identification of individuals. However, in addition, epigenetic changes, i.e., DNA methylation, came into focus of forensic DNA research. Chronological age prediction is one promising application to allow for narrowing the pool of possible individuals who caused a trace, as well as to support the identification of unknown bodies and for age verification of living individuals. OBJECTIVE This review aims to provide an overview of the current knowledge, possibilities, and (current) limitations about DNA methylation-based chronological age prediction with emphasis on forensic application. METHODS The development, implementation and application of age prediction tools requires a deep understanding about the biological background, the analysis methods, the age-dependent DNA methylation markers, as well as the mathematical models for age prediction and their evaluation. Furthermore, additional influences can have an impact. Therefore, the literature was evaluated in respect to these diverse topics. CONCLUSION The numerous research efforts in recent years have led to a rapid change in our understanding of the application of DNA methylation for chronological age prediction, which is now on the way to implementation and validation. Knowledge of the various aspects leads to a better understanding and allows a more informed interpretation of DNAm quantification results, as well as the obtained results by the age prediction tools.
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Affiliation(s)
- Jana Naue
- Institute of Forensic Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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145
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Lu YT, Plets M, Morrison G, Cunha AT, Cen SY, Rhie SK, Siegmund KD, Daneshmand S, Quinn DI, Meeks JJ, Lerner SP, Petrylak DP, McConkey D, Flaig TW, Thompson IM, Goldkorn A. Cell-free DNA Methylation as a Predictive Biomarker of Response to Neoadjuvant Chemotherapy for Patients with Muscle-invasive Bladder Cancer in SWOG S1314. Eur Urol Oncol 2023; 6:516-524. [PMID: 37087309 PMCID: PMC10587361 DOI: 10.1016/j.euo.2023.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 03/09/2023] [Accepted: 03/27/2023] [Indexed: 04/24/2023]
Abstract
BACKGROUND Neoadjuvant chemotherapy (NAC) is the standard of care in muscle-invasive bladder cancer (MIBC). However, treatment is intense, and the overall benefit is small, necessitating effective biomarkers to identify patients who will benefit most. OBJECTIVE To characterize cell-free DNA (cfDNA) methylation in patients receiving NAC in SWOG S1314, a prospective cooperative group trial, and to correlate the methylation signatures with pathologic response at radical cystectomy. DESIGN, SETTING, AND PARTICIPANTS SWOG S1314 is a prospective cooperative group trial for patients with MIBC (cT2-T4aN0M0, ≥5 mm of viable tumor), with a primary objective of evaluating the coexpression extrapolation (COXEN) gene expression signature as a predictor of NAC response, defined as achieving pT0N0 or ≤pT1N0 at radical cystectomy. For the current exploratory analysis, blood samples were collected prospectively from 72 patients in S1314 before and during NAC, and plasma cfDNA methylation was measured using the Infinium MethylationEPIC BeadChip array. INTERVENTION No additional interventions besides plasma collection. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Differential methylation between pathologic responders (≤pT1N0) and nonresponders was analyzed, and a classifier predictive of treatment response was generated using the Random Forest machine learning algorithm. RESULTS AND LIMITATIONS Using prechemotherapy plasma cfDNA, we developed a methylation-based response score (mR-score) predictive of pathologic response. Plasma samples collected after the first cycle of NAC yielded mR-scores with similar predictive ability. Furthermore, we used cfDNA methylation data to calculate the circulating bladder DNA fraction, which had a modest but independent predictive ability for treatment response. In a model combining mR-score and circulating bladder DNA fraction, we correctly predicted pathologic response in 79% of patients based on their plasma collected at baseline and after one cycle of chemotherapy. Limitations of this study included a limited sample size and relatively low circulating bladder DNA levels. CONCLUSIONS Our study provides the proof of concept that cfDNA methylation can be used to generate classifiers of NAC response in bladder cancer patients. PATIENT SUMMARY In this exploratory analysis of S1314, we demonstrated that cell-free DNA methylation can be profiled to generate biomarker signatures associated with neoadjuvant chemotherapy response. With validation in additional cohorts, this minimally invasive approach may be used to predict chemotherapy response in locally advanced bladder cancer and perhaps also in metastatic disease.
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Affiliation(s)
- Yi-Tsung Lu
- Division of Medical Oncology, Department of Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Melissa Plets
- SWOG Statistics and Data Management Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Gareth Morrison
- Division of Medical Oncology, Department of Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Alexander T Cunha
- Division of Medical Oncology, Department of Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Steven Y Cen
- Department of Radiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Suhn K Rhie
- Department of Biochemistry and Molecular Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Kimberly D Siegmund
- Department of Population and Public Health Science, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Siamak Daneshmand
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David I Quinn
- Division of Medical Oncology, Department of Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Joshua J Meeks
- Departments of Urology, Biochemistry, and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Seth P Lerner
- Scott Department of Urology, Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Thomas W Flaig
- University of Colorado, School of Medicine, Aurora, CO, USA
| | - Ian M Thompson
- CHRISTUS Medical Center Hospital, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Amir Goldkorn
- Division of Medical Oncology, Department of Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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146
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Sullivan ADW, Bozack AK, Cardenas A, Comer JS, Bagner DM, Forehand R, Parent J. Parenting Practices May Buffer the Impact of Adversity on Epigenetic Age Acceleration Among Young Children With Developmental Delays. Psychol Sci 2023; 34:1173-1185. [PMID: 37733001 PMCID: PMC10626625 DOI: 10.1177/09567976231194221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/26/2023] [Indexed: 09/22/2023] Open
Abstract
This study examined whether children exposed to adversity would exhibit lower epigenetic age acceleration in the context of improved parenting. Children with developmental delays and externalizing behavior problems (N = 62; Mage = 36.26 months; 70.97% boys, 29.03% girls; 71% Latinx, 22.6% Black) were drawn from a larger randomized controlled trial (RCT), which randomized them to receive Internet-delivered parent-child interaction therapy (iPCIT; n = 30) or community referrals as usual (RAU; n = 32). Epigenetic age acceleration was estimated with the pediatric buccal epigenetic clock, using saliva. Adversity was assessed using parent, family, and neighborhood-level cumulative-risk indicators. Adversity interacted with Time 2 (T2) observations of positive and negative-parenting practices to predict epigenetic age acceleration 1.5 years later, regardless of treatment assignment. Children exposed to more adversity displayed lower epigenetic age acceleration when parents evidenced increased positive (b = -0.15, p = .001) and decreased negative (b = -0.12, p = .01) parenting practices.
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Affiliation(s)
- Alexandra D. W. Sullivan
- Department of Psychological Science, University of Vermont
- Department of Psychiatry, Center for Health and Community, University of California, San Francisco
| | - Anne K. Bozack
- Department of Epidemiology and Population Health, School of Medicine, Stanford University
| | - Andres Cardenas
- Department of Epidemiology and Population Health, School of Medicine, Stanford University
- Department of Pediatrics, School of Medicine, Stanford University
| | - Jonathan S. Comer
- Department of Psychology and Center for Children and Families, Florida International University
| | - Daniel M. Bagner
- Department of Psychology and Center for Children and Families, Florida International University
| | - Rex Forehand
- Department of Psychological Science, University of Vermont
| | - Justin Parent
- Bradley-Hasbro Children’s Research Center, E. P. Bradley Hospital, Providence, RI
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University
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147
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Sandalova E, Goh J, Lim ZX, Lim ZM, Barardo D, Dorajoo R, Kennedy BK, Maier AB. Alpha-ketoglutarate supplementation and BiologicaL agE in middle-aged adults (ABLE)-intervention study protocol. GeroScience 2023; 45:2897-2907. [PMID: 37217632 PMCID: PMC10643463 DOI: 10.1007/s11357-023-00813-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Targeting molecular processes of aging will enable people to live healthier and longer lives by preventing age-related diseases. Geroprotectors are compounds with the potential to increase healthspan and lifespan. Even though many of them have been tested in animal models, the translation to humans is limited. Alpha-Ketoglutarate (AKG) has been studied widely in model animals, but there are few studies testing its geroprotective properties in humans. ABLE is a double blinded placebo-controlled randomized trial (RCT) of 1 g sustained release Ca-AKG versus placebo for 6 months of intervention and 3 months follow up including 120 40-60-year-old healthy individuals with a higher DNA methylation age compared to their chronological age. The primary outcome is the decrease in DNA methylation age from baseline to the end of the intervention. A total of 120 participants will be randomized to receive either sustained release Ca-AKG or placebo. Secondary outcomes include changes in the inflammatory and metabolic parameters in blood, handgrip strength and leg extension strength, arterial stiffness, skin autofluorescence, and aerobic capacity from baseline to 3 months, 6 months, and 9 months. This study will recruit middle-aged participants with an older DNA methylation age compared to their chronological age, and test whether supplementation with Ca-AKG can reduce DNA methylation age. This study is unique in its inclusion of biologically older participants.
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Affiliation(s)
- Elena Sandalova
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore.
- Centre for Healthy Longevity, National University Health System (NUHS), Singapore, Singapore.
| | - Jorming Goh
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore
- Centre for Healthy Longevity, National University Health System (NUHS), Singapore, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Zi Xiang Lim
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore
- Centre for Healthy Longevity, National University Health System (NUHS), Singapore, Singapore
| | - Zhi Meng Lim
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore
- Centre for Healthy Longevity, National University Health System (NUHS), Singapore, Singapore
| | - Diogo Barardo
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore
- Centre for Healthy Longevity, National University Health System (NUHS), Singapore, Singapore
| | - Rajkumar Dorajoo
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Health Services and Systems Research, Duke-NUS Medical School, Singapore, Singapore
| | - Brian K Kennedy
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore
- Centre for Healthy Longevity, National University Health System (NUHS), Singapore, Singapore
| | - Andrea B Maier
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117456, Singapore.
- Centre for Healthy Longevity, National University Health System (NUHS), Singapore, Singapore.
- Department of Human Movement Sciences, @AgeAmsterdam, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam, Netherlands.
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148
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Dupont ME, Jacobsen SB, Christiansen SNN, Tfelt-Hansen J, Smerup MH, Andersen JD, Morling N. Fresh and frozen cardiac tissue are comparable in DNA methylation array β-values, but formalin-fixed, paraffin-embedded tissue may overestimate DNA methylation levels. Sci Rep 2023; 13:16381. [PMID: 37773256 PMCID: PMC10541404 DOI: 10.1038/s41598-023-43788-2] [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] [Received: 08/09/2023] [Accepted: 09/28/2023] [Indexed: 10/01/2023] Open
Abstract
Untreated fresh cardiac tissue is the optimal tissue material for investigating DNA methylation patterns of cardiac biology and diseases. However, fresh tissue is difficult to obtain. Therefore, tissue stored as frozen or formalin-fixed, paraffin-embedded (FFPE) is widely used for DNA methylation studies. It is unknown whether storage conditions alter the DNA methylation in cardiac tissue. In this study, we compared the DNA methylation patterns of fresh, frozen, and FFPE cardiac tissue to investigate if the storage method affected the DNA methylation results. We used the Infinium MethylationEPIC assay to obtain genome-wide methylation levels in fresh, frozen, and FFPE tissues from nine individuals. We found that the DNA methylation levels of 21.4% of the examined CpG sites were overestimated in the FFPE samples compared to that of fresh and frozen tissue, whereas 5.7% were underestimated. Duplicate analyses of the DNA methylation patterns showed high reproducibility (precision) for frozen and FFPE tissues. In conclusion, we found that frozen and FFPE tissues gave reproducible DNA methylation results and that frozen and fresh tissues gave similar results.
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Affiliation(s)
- Mikkel Eriksen Dupont
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Stine Bøttcher Jacobsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Steffan Noe Niikanoff Christiansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Morten Holdgaard Smerup
- Department of Cardiothoracic Surgery, Rigshospitalet Copenhagen University Hospital, Copenhagen, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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149
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Kaur D, Lee SM, Goldberg D, Spix NJ, Hinoue T, Li HT, Dwaraka VB, Smith R, Shen H, Liang G, Renke N, Laird PW, Zhou W. Comprehensive Evaluation of The Infinium Human MethylationEPIC v2 BeadChip. EPIGENETICS COMMUNICATIONS 2023; 3:6. [PMID: 38455390 PMCID: PMC10919401 DOI: 10.1186/s43682-023-00021-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/18/2023] [Indexed: 03/09/2024]
Abstract
Infinium Methylation BeadChips are widely used to profile DNA cytosine modifications in large cohort studies for reasons of cost-effectiveness, accurate quantification, and user-friendly data analysis in characterizing these canonical epigenetic marks. In this work, we conducted a comprehensive evaluation of the updated Infinium MethylationEPIC v2 BeadChip (EPICv2). Our evaluation revealed that EPICv2 offers significant improvements over its predecessors, including expanded enhancer coverage, applicability to diverse ancestry groups, support for low-input DNA down to one nanogram, coverage of existing epigenetic clocks, cell type deconvolution panels, and human trait associations, while maintaining accuracy and reproducibility. Using EPICv2, we were able to identify epigenome and sequence signatures in cell line models of DNMT and SETD2 loss and/or hypomorphism. Furthermore, we provided probe-wise evaluation and annotation to facilitate the use of new features on this array for studying the interplay between somatic mutations and epigenetic landscape in cancer genomics. In conclusion, EPICv2 provides researchers with a valuable tool for studying epigenetic modifications and their role in development and disease.
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Affiliation(s)
- Diljeet Kaur
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA, 19104, USA
- These authors contribute equally
| | - Sol Moe Lee
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA, 19104, USA
- These authors contribute equally
| | - David Goldberg
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA, 19104, USA
| | - Nathan J Spix
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Toshinori Hinoue
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Hong-Tao Li
- Department of Urology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | | | - Ryan Smith
- TruDiagnostic Inc, Lexington, KY 40503, USA
| | - Hui Shen
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Gangning Liang
- Department of Urology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Nicole Renke
- Illumina, Inc., Product Management Department, San Diego, CA 92122, USA
| | - Peter W Laird
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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150
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Shi H, Chen S, Meng FW, Ossip DJ, Yan C, Li D. Epigenome-wide DNA methylation profiling in comparison between pathological and physiological hypertrophy of human cardiomyocytes. Front Genet 2023; 14:1264382. [PMID: 37829282 PMCID: PMC10565041 DOI: 10.3389/fgene.2023.1264382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/11/2023] [Indexed: 10/14/2023] Open
Abstract
Background: Physiological and pathological stimuli result in distinct forms of cardiac hypertrophy, but the molecular regulation comparing the two, especially at the DNA methylation level, is not well understood. Methods: We conducted an in vitro study using human cardiomyocytes exposed to angiotensin II (AngII) and insulin-like growth factor 1 (IGF-1) to mimic pathologically and physiologically hypertrophic heart models, respectively. Whole genome DNA methylation patterns were profiled by the Infinium human MethylationEPIC platform with >850 K DNA methylation loci. Two external datasets were used for comparisons and qRT-PCR was performed for examining expression of associated genes of those identified DNA methylation loci. Results: We detected 194 loci that are significantly differentially methylated after AngII treatment, and 206 significant loci after IGF-1 treatment. Mapping the significant loci to genes, we identified 158 genes corresponding to AngII treatment and 175 genes to IGF-1 treatment. Using the gene-set enrichment analysis, the PI3K-Akt signaling pathway was identified to be significantly enriched for both AngII and IGF-1 treatment. The Hippo signaling pathway was enriched after IGF-1 treatment, but not for AngII treatment. CDK6 and RPTOR are components of the PI3K-Akt pathway but have different DNA methylation patterns in response to AngII and IGF-1. qRT-PCR confirmed the different gene expressions of CDK6 and PRTOR. Conclusion: Our study is pioneering in profiling epigenome DNA methylation changes in adult human cardiomyocytes under distinct stress conditions: pathological (AngII) and physiological (IGF-1). The identified DNA methylation loci, genes, and pathways might have the potential to distinguish between pathological and physiological cardiac hypertrophy.
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Affiliation(s)
- Hangchuan Shi
- Department of Clinical and Translational Research, University of Rochester Medical Center, Rochester, NY, United States
- Department of Public Health Sciences, University of Rochester Medical Center, Rochester, NY, United States
| | - Si Chen
- Aab Cardiovascular Research Institute, University of Rochester, School of Medicine and Dentistry, Rochester, NY, United States
| | - Fanju W. Meng
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, United States
| | - Deborah J. Ossip
- Department of Public Health Sciences, University of Rochester Medical Center, Rochester, NY, United States
| | - Chen Yan
- Aab Cardiovascular Research Institute, University of Rochester, School of Medicine and Dentistry, Rochester, NY, United States
| | - Dongmei Li
- Department of Clinical and Translational Research, University of Rochester Medical Center, Rochester, NY, United States
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