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Atif J, Udhesister STP, Abdelnabi MN, D’Souza S, Hung JH, Edgar RD, Gobran ST, Gomez-Escobar E, Greenwald ZR, Gallardo-Flores CE, Fontaine G, Jeong D, Lanièce-Delaunay C, Lawton D, Makuza JD, Masterman C, Marathe G, Mortazhejri S, Li J, Palmer M, Passos-Castilho AM, Sag M, Shengir M, Wallace HL, Mendlowitz AB. Impacts of the COVID-19 pandemic on hepatitis C elimination in Canada: Where do we go from here? Can Liver J 2022; 5:441-444. [PMID: 38144406 PMCID: PMC10735200 DOI: 10.3138/canlivj-2022-0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 12/26/2023]
Affiliation(s)
- Jawairia Atif
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- Co-first authors
| | - Sasha Tejna Persaud Udhesister
- Faculté de Médecine, Université de Montréal, Centre de Recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada
- Co-first authors
| | - Mohamed N Abdelnabi
- Centre de Recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Département de Microbiologie, Infectiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Simmone D’Souza
- University of Calgary Cumming School of Medicine, Calgary, Alberta, Canada
| | - Jui-Hsia Hung
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Rachel D Edgar
- University of Toronto and European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Samaa T Gobran
- Faculté de Médecine, Université de Montréal, Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Elsa Gomez-Escobar
- Centre de Recherche du Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada
| | - Zoë R Greenwald
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Carla E Gallardo-Flores
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, Ontario, Canada
| | - Guillaume Fontaine
- Clinical Epidemiology Program, Ottawa Research Institute Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Dahn Jeong
- School of Population and Public Health, University of British Columbia, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Charlotte Lanièce-Delaunay
- Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - David Lawton
- Ottawa Hospital Research Institute Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Jean Damascene Makuza
- School of Population and Public Health, University of British Columbia, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Chelsea Masterman
- Faculty of Health Sciences, University of Western Ontario, London, Ontario, Canada
| | - Gayatri Marathe
- Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Sameh Mortazhejri
- School of Epidemiology and Public Health, University of Ottawa, Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Jiafeng Li
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Chronic Disease Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Michael Palmer
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ana Maria Passos-Castilho
- Centre for Clinical Epidemiology, Lady Davis Institute, Jewish General Hospital; Department of Medicine, McGill University, Montréal, Québec, Canada
| | - Manolya Sag
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Mohamed Shengir
- Division of Experimental Medicine, Department of Medicine, McGill University, Montréal, Québec, Canada
| | - Hannah Louise Wallace
- Immunology and Infectious Diseases, Division of Biomedical Sciences, Faculty of Medicine, Memorial University, St John’s and Labrador, Newfoundland, Canada
| | - Andrew B Mendlowitz
- Toronto Centre for Liver Disease/Viral Hepatitis Care Network (VIRCAN), University Health Network, Toronto, Ontario, Canada
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Ryan CP, Jones MJ, Edgar RD, Lee NR, Kobor MS, McDade TW, Kuzawa CW. Immune cell type and DNA methylation vary with reproductive status in women: possible pathways for costs of reproduction. Evol Med Public Health 2022; 10:47-58. [PMID: 35169479 PMCID: PMC8841013 DOI: 10.1093/emph/eoac003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Abstract
Background Consistent with evolutionarily theorized costs of reproduction (CoR), reproductive history in women is associated with life expectancy and susceptibility to certain cancers, autoimmune disorders and metabolic disease. Immunological changes originating during reproduction may help explain some of these relationships. Methodology To explore the potential role of the immune system in female CoR, we characterized leukocyte composition and regulatory processes using DNA methylation (DNAm) in a cross-sectional cohort of young (20–22 years old) women differing in reproductive status. Results Compared to nulliparity, pregnancy was characterized by differential methylation at 828 sites, 96% of which were hypomethylated and enriched for genes associated with T-cell activation, innate immunity, pre-eclampsia and neoplasia. Breastfeeding was associated with differential methylation at 1107 sites (71% hypermethylated), enriched for genes involved in metabolism, immune self-recognition and neurogenesis. There were no significant differences in DNAm between nulliparous and parous women. However, compared to nullipara, pregnant women had lower proportions of B, CD4T, CD8T and natural killer (NK) cells, and higher proportions of granulocytes and monocytes. Monocyte counts were lower and NK counts higher among breastfeeding women, and remained so among parous women. Implications Our findings point to widespread differences in DNAm during pregnancy and lactation. These effects appear largely transient, but may accumulate with gravidity become detectable as women age. Nulliparous and parous women differed in leukocyte composition, consistent with more persistent effects of reproduction on cell type. These findings support transient (leukocyte DNAm) and persistent (cell composition) changes associated with reproduction in women, illuminating potential pathways contributing to CoR. Lay Summary: Evolutionary theory and epidemiology support costs of reproduction (CoR) to women’s health that may involve changes in immune function. We report differences in immune cell composition and gene regulation during pregnancy and breastfeeding. While many of these differences appear transient, immune cell composition may remain, suggesting mechanisms for female CoR.
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Affiliation(s)
- Calen P Ryan
- Department of Anthropology, Northwestern University, Evanston, IL 60208, USA
| | - Meaghan J Jones
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.,Children's Hospital Research Institute, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | | | - Nanette R Lee
- University of San Carlos Office of Population Studies Foundation Inc., Cebu City 6000, Philippines
| | - Michael S Kobor
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada.,Child and Brain Development Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8, Canada
| | - Thomas W McDade
- Department of Anthropology, Northwestern University, Evanston, IL 60208, USA.,Child and Brain Development Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1Z8, Canada.,Institute for Policy Research, Northwestern University, Evanston, IL 60208, USA
| | - Christopher W Kuzawa
- Department of Anthropology, Northwestern University, Evanston, IL 60208, USA.,Institute for Policy Research, Northwestern University, Evanston, IL 60208, USA
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Edgar RD, Perrone F, Foster AR, Payne F, Lewis S, Nayak KM, Kraiczy J, Cenier A, Torrente F, Salvestrini C, Heuschkel R, Hensel KO, Harris R, Jones DL, Zerbino DR, Zilbauer M. Culture-Associated DNA Methylation Changes Impact on Cellular Function of Human Intestinal Organoids. Cell Mol Gastroenterol Hepatol 2022; 14:1295-1310. [PMID: 36038072 PMCID: PMC9703134 DOI: 10.1016/j.jcmgh.2022.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND & AIMS Human intestinal epithelial organoids (IEOs) are a powerful tool to model major aspects of intestinal development, health, and diseases because patient-derived cultures retain many features found in vivo. A necessary aspect of the organoid model is the requirement to expand cultures in vitro through several rounds of passaging. This is of concern because the passaging of cells has been shown to affect cell morphology, ploidy, and function. METHODS Here, we analyzed 173 human IEO lines derived from the small and large bowel and examined the effect of culture duration on DNA methylation (DNAm). Furthermore, we tested the potential impact of DNAm changes on gene expression and cellular function. RESULTS Our analyses show a reproducible effect of culture duration on DNAm in a large discovery cohort as well as 2 publicly available validation cohorts generated in different laboratories. Although methylation changes were seen in only approximately 8% of tested cytosine-phosphate-guanine dinucleotides (CpGs) and global cellular function remained stable, a subset of methylation changes correlated with altered gene expression at baseline as well as in response to inflammatory cytokine exposure and withdrawal of Wnt agonists. Importantly, epigenetic changes were found to be enriched in genomic regions associated with colonic cancer and distant to the site of replication, indicating similarities to malignant transformation. CONCLUSIONS Our study shows distinct culture-associated epigenetic changes in mucosa-derived human IEOs, some of which appear to impact gene transcriptomic and cellular function. These findings highlight the need for future studies in this area and the importance of considering passage number as a potentially confounding factor.
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Affiliation(s)
- Rachel D Edgar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Francesca Perrone
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - April R Foster
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Centre for Pathway Analysis, Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
| | - Felicity Payne
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Sophia Lewis
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California; Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, California
| | - Komal M Nayak
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Judith Kraiczy
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Aurélie Cenier
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Franco Torrente
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Camilla Salvestrini
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Robert Heuschkel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Kai O Hensel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom; Witten/Herdecke University, Department of Paediatrics, Helios Medical Centre Wuppertal, Children's Hospital, Wuppertal, Germany
| | - Rebecca Harris
- Centre for Pathway Analysis, Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
| | - D Leanne Jones
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California; Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, California; Department of Anatomy and Medicine, Division of Geriatrics, University of California, San Francisco, San Francisco, California; Eli and Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, California
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.
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4
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Gasparetto M, Payne F, Nayak K, Kraiczy J, Glemas C, Philip-McKenzie Y, Ross A, Edgar RD, Zerbino DR, Salvestrini C, Torrente F, Ventham NT, Kalla R, Satsangi J, Sarkies P, Heuschkel R, Zilbauer M. Transcription and DNA Methylation Patterns of Blood-Derived CD8 + T Cells Are Associated With Age and Inflammatory Bowel Disease But Do Not Predict Prognosis. Gastroenterology 2021; 160:232-244.e7. [PMID: 32814113 PMCID: PMC7428744 DOI: 10.1053/j.gastro.2020.08.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Gene expression patterns of CD8+ T cells have been reported to correlate with clinical outcomes of adults with inflammatory bowel diseases (IBD). We aimed to validate these findings in independent patient cohorts. METHODS We obtained peripheral blood samples from 112 children with a new diagnosis of IBD (71 with Crohn's disease and 41 with ulcerative colitis) and 19 children without IBD (controls) and recorded medical information on disease activity and outcomes. CD8+ T cells were isolated from blood samples by magnetic bead sorting at the point of diagnosis and during the course of disease. Genome-wide transcription (n = 192) and DNA methylation (n = 66) profiles were generated using Affymetrix and Illumina arrays, respectively. Publicly available transcriptomes and DNA methylomes of CD8+ T cells from 3 adult patient cohorts with and without IBD were included in data analyses. RESULTS Previously reported CD8+ T-cell prognostic expression and exhaustion signatures were only found in the original adult IBD patient cohort. These signatures could not be detected in either a pediatric or a second adult IBD cohort. In contrast, an association between CD8+ T-cell gene expression with age and sex was detected across all 3 cohorts. CD8+ gene transcription was clearly associated with IBD in the 2 cohorts that included non-IBD controls. Lastly, DNA methylation profiles of CD8+ T cells from children with Crohn's disease correlated with age but not with disease outcome. CONCLUSIONS We were unable to validate previously reported findings of an association between CD8+ T-cell gene transcription and disease outcome in IBD. Our findings reveal the challenges of developing prognostic biomarkers for patients with IBD and the importance of their validation in large, independent cohorts before clinical application.
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Affiliation(s)
- Marco Gasparetto
- Department of Paediatrics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom,Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke’s, Cambridge, United Kingdom
| | - Felicity Payne
- Department of Paediatrics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom,Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke’s, Cambridge, United Kingdom
| | - Komal Nayak
- Department of Paediatrics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Judith Kraiczy
- Department of Paediatrics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Claire Glemas
- Department of Paediatrics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom,Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke’s, Cambridge, United Kingdom
| | - Yosef Philip-McKenzie
- Department of Paediatrics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Alexander Ross
- Department of Paediatrics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom,Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Rachel D. Edgar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Daniel R. Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Camilla Salvestrini
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke’s, Cambridge, United Kingdom
| | - Franco Torrente
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke’s, Cambridge, United Kingdom
| | - Nicholas T. Ventham
- Academic Coloproctology, Western General Hospital, Edinburgh, Edinburgh, United Kingdom
| | - Rahul Kalla
- Medical Research Council Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Jack Satsangi
- Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
| | - Peter Sarkies
- Medical Research Council London Institute of Medical Sciences, United Kingdom,Institute of Clinical Sciences, Imperial College London, United Kingdom
| | - Robert Heuschkel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's, Cambridge, United Kingdom.
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's, Cambridge, United Kingdom; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.
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5
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Shannon CP, Blimkie TM, Ben-Othman R, Gladish N, Amenyogbe N, Drissler S, Edgar RD, Chan Q, Krajden M, Foster LJ, Kobor MS, Mohn WW, Brinkman RR, Le Cao KA, Scheuermann RH, Tebbutt SJ, Hancock RE, Koff WC, Kollmann TR, Sadarangani M, Lee AHY. Multi-Omic Data Integration Allows Baseline Immune Signatures to Predict Hepatitis B Vaccine Response in a Small Cohort. Front Immunol 2020; 11:578801. [PMID: 33329547 PMCID: PMC7734088 DOI: 10.3389/fimmu.2020.578801] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
Background Vaccination remains one of the most effective means of reducing the burden of infectious diseases globally. Improving our understanding of the molecular basis for effective vaccine response is of paramount importance if we are to ensure the success of future vaccine development efforts. Methods We applied cutting edge multi-omics approaches to extensively characterize temporal molecular responses following vaccination with hepatitis B virus (HBV) vaccine. Data were integrated across cellular, epigenomic, transcriptomic, proteomic, and fecal microbiome profiles, and correlated to final HBV antibody titres. Results Using both an unsupervised molecular-interaction network integration method (NetworkAnalyst) and a data-driven integration approach (DIABLO), we uncovered baseline molecular patterns and pathways associated with more effective vaccine responses to HBV. Biological associations were unravelled, with signalling pathways such as JAK-STAT and interleukin signalling, Toll-like receptor cascades, interferon signalling, and Th17 cell differentiation emerging as important pre-vaccination modulators of response. Conclusion This study provides further evidence that baseline cellular and molecular characteristics of an individual's immune system influence vaccine responses, and highlights the utility of integrating information across many parallel molecular datasets.
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Affiliation(s)
- Casey P. Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence and Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- UBC Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
| | - Travis M. Blimkie
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Rym Ben-Othman
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
- Telethon Kids Institute, Perth Children’s Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Nicole Gladish
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Nelly Amenyogbe
- Telethon Kids Institute, Perth Children’s Hospital, University of Western Australia, Nedlands, WA, Australia
- Department of Experimental Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Sibyl Drissler
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Rachel D. Edgar
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Queenie Chan
- Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Mel Krajden
- British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Leonard J. Foster
- Department of Biochemistry & Molecular Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Michael S. Kobor
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - William W. Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Ryan R. Brinkman
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Kim-Anh Le Cao
- Melbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Australia
| | - Richard H. Scheuermann
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, United States
- Department of Pathology, University of California, San Diego, CA, United States
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Scott J. Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence and Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- UBC Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Robert E.W. Hancock
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | | | - Tobias R. Kollmann
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
- Telethon Kids Institute, Perth Children’s Hospital, University of Western Australia, Nedlands, WA, Australia
| | - Manish Sadarangani
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
- Vaccine Evaluation Center, BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Amy Huei-Yi Lee
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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6
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Ben-Othman R, Cai B, Liu AC, Varankovich N, He D, Blimkie TM, Lee AH, Gill EE, Novotny M, Aevermann B, Drissler S, Shannon CP, McCann S, Marty K, Bjornson G, Edgar RD, Lin DTS, Gladish N, Maclsaac J, Amenyogbe N, Chan Q, Llibre A, Collin J, Landais E, Le K, Reiss SM, Koff WC, Havenar-Daughton C, Heran M, Sangha B, Walt D, Krajden M, Crotty S, Sok D, Briney B, Burton DR, Duffy D, Foster LJ, Mohn WW, Kobor MS, Tebbutt SJ, Brinkman RR, Scheuermann RH, Hancock REW, Kollmann TR, Sadarangani M. Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults. Front Immunol 2020; 11:580373. [PMID: 33250895 PMCID: PMC7672042 DOI: 10.3389/fimmu.2020.580373] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 09/24/2020] [Indexed: 12/26/2022] Open
Abstract
Conventional vaccine design has been based on trial-and-error approaches, which have been generally successful. However, there have been some major failures in vaccine development and we still do not have highly effective licensed vaccines for tuberculosis, HIV, respiratory syncytial virus, and other major infections of global significance. Approaches at rational vaccine design have been limited by our understanding of the immune response to vaccination at the molecular level. Tools now exist to undertake in-depth analysis using systems biology approaches, but to be fully realized, studies are required in humans with intensive blood and tissue sampling. Methods that support this intensive sampling need to be developed and validated as feasible. To this end, we describe here a detailed approach that was applied in a study of 15 healthy adults, who were immunized with hepatitis B vaccine. Sampling included ~350 mL of blood, 12 microbiome samples, and lymph node fine needle aspirates obtained over a ~7-month period, enabling comprehensive analysis of the immune response at the molecular level, including single cell and tissue sample analysis. Samples were collected for analysis of immune phenotyping, whole blood and single cell gene expression, proteomics, lipidomics, epigenetics, whole blood response to key immune stimuli, cytokine responses, in vitro T cell responses, antibody repertoire analysis and the microbiome. Data integration was undertaken using different approaches-NetworkAnalyst and DIABLO. Our results demonstrate that such intensive sampling studies are feasible in healthy adults, and data integration tools exist to analyze the vast amount of data generated from a multi-omics systems biology approach. This will provide the basis for a better understanding of vaccine-induced immunity and accelerate future rational vaccine design.
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Affiliation(s)
- Rym Ben-Othman
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada.,Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Bing Cai
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Aaron C Liu
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Natallia Varankovich
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Daniel He
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Travis M Blimkie
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Amy H Lee
- Simon Fraser University, Burnaby, BC, Canada
| | - Erin E Gill
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Mark Novotny
- Department of Informatics, J. Craig Venter Institute (La Jolla), La Jolla, CA, United States
| | - Brian Aevermann
- Department of Informatics, J. Craig Venter Institute (La Jolla), La Jolla, CA, United States
| | | | - Casey P Shannon
- Prevention of Organ Failure (PROOF) Centre of Excellence and Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada
| | - Sarah McCann
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Kim Marty
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Gordean Bjornson
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Rachel D Edgar
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - David Tse Shen Lin
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Nicole Gladish
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Julia Maclsaac
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Nelly Amenyogbe
- Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Queenie Chan
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Alba Llibre
- Translational Immunology Lab, Institut Pasteur, Paris, France
| | - Joyce Collin
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Elise Landais
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Khoa Le
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Samantha M Reiss
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Wayne C Koff
- Human Vaccines Project, New York, NY, United States
| | - Colin Havenar-Daughton
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Manraj Heran
- Department of Radiology, BC Children's Hospital, Vancouver, BC, Canada
| | - Bippan Sangha
- Department of Radiology, BC Children's Hospital, Vancouver, BC, Canada
| | - David Walt
- Wyss Institute at Harvard University, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Mel Krajden
- British Columbia Centre for Disease Control, Vancouver, BC, Canada
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States.,IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Darragh Duffy
- Translational Immunology Lab, Institut Pasteur, Paris, France
| | - Leonard J Foster
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - William W Mohn
- Department of Microbiology and Immunology, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Scott J Tebbutt
- Prevention of Organ Failure (PROOF) Centre of Excellence and Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, BC, Canada.,Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Ryan R Brinkman
- Terry Fox Laboratory, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Richard H Scheuermann
- Department of Informatics, J. Craig Venter Institute (La Jolla), La Jolla, CA, United States.,Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA, United States
| | - Robert E W Hancock
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, Vancouver, BC, Canada
| | - Tobias R Kollmann
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada.,Telethon Kids Institute, University of Western Australia, Nedlands, WA, Australia
| | - Manish Sadarangani
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada
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7
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McEwen LM, O'Donnell KJ, McGill MG, Edgar RD, Jones MJ, MacIsaac JL, Lin DTS, Ramadori K, Morin A, Gladish N, Garg E, Unternaehrer E, Pokhvisneva I, Karnani N, Kee MZL, Klengel T, Adler NE, Barr RG, Letourneau N, Giesbrecht GF, Reynolds JN, Czamara D, Armstrong JM, Essex MJ, de Weerth C, Beijers R, Tollenaar MS, Bradley B, Jovanovic T, Ressler KJ, Steiner M, Entringer S, Wadhwa PD, Buss C, Bush NR, Binder EB, Boyce WT, Meaney MJ, Horvath S, Kobor MS. The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells. Proc Natl Acad Sci U S A 2020; 117:23329-23335. [PMID: 31611402 PMCID: PMC7519312 DOI: 10.1073/pnas.1820843116] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The development of biological markers of aging has primarily focused on adult samples. Epigenetic clocks are a promising tool for measuring biological age that show impressive accuracy across most tissues and age ranges. In adults, deviations from the DNA methylation (DNAm) age prediction are correlated with several age-related phenotypes, such as mortality and frailty. In children, however, fewer such associations have been made, possibly because DNAm changes are more dynamic in pediatric populations as compared to adults. To address this gap, we aimed to develop a highly accurate, noninvasive, biological measure of age specific to pediatric samples using buccal epithelial cell DNAm. We gathered 1,721 genome-wide DNAm profiles from 11 different cohorts of typically developing individuals aged 0 to 20 y old. Elastic net penalized regression was used to select 94 CpG sites from a training dataset (n = 1,032), with performance assessed in a separate test dataset (n = 689). DNAm at these 94 CpG sites was highly predictive of age in the test cohort (median absolute error = 0.35 y). The Pediatric-Buccal-Epigenetic (PedBE) clock was characterized in additional cohorts, showcasing the accuracy in longitudinal data, the performance in nonbuccal tissues and adult age ranges, and the association with obstetric outcomes. The PedBE tool for measuring biological age in children might help in understanding the environmental and contextual factors that shape the DNA methylome during child development, and how it, in turn, might relate to child health and disease.
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Affiliation(s)
- Lisa M McEwen
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Kieran J O'Donnell
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
| | - Megan G McGill
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
| | - Rachel D Edgar
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Meaghan J Jones
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Julia L MacIsaac
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - David Tse Shen Lin
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Katia Ramadori
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Alexander Morin
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Nicole Gladish
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4
| | - Elika Garg
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
| | - Eva Unternaehrer
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
| | - Irina Pokhvisneva
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR); Singapore 117609
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596
| | - Michelle Z L Kee
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR); Singapore 117609
| | - Torsten Klengel
- Department of Psychiatry, Harvard Medical School-McLean Hospital, Belmont, MA 02478
| | - Nancy E Adler
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
- Department of Psychiatry, University of California, San Francisco, CA 94143
- Department of Pediatrics, University of California, San Francisco, CA 94143
| | - Ronald G Barr
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
| | - Nicole Letourneau
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada T2N 4N1
- Faculty of Nursing, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Gerald F Giesbrecht
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada T2N 4N1
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - James N Reynolds
- Department of Biomedical and Molecular Sciences, School of Medicine, Queen's University, Kingston, ON, Canada K7L 3N6
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
| | - Jeffrey M Armstrong
- Department of Psychiatry, University of Wisconsin-Madison, Madison, WI 53706
| | - Marilyn J Essex
- Department of Psychiatry, University of Wisconsin-Madison, Madison, WI 53706
| | - Carolina de Weerth
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 HR, Nijmegen, The Netherlands
| | - Roseriet Beijers
- Behavioural Science Institute, Radboud University, 6525 HR, Nijmegen, The Netherlands
| | - Marieke S Tollenaar
- Leiden Institute for Brain and Cognition, Institute of Psychology, Leiden University, 2300 RB, Leiden, The Netherlands
| | - Bekh Bradley
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322
| | - Tanja Jovanovic
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322
| | - Kerry J Ressler
- Department of Psychiatry, Harvard Medical School-McLean Hospital, Belmont, MA 02478
| | - Meir Steiner
- Department of Psychiatry and Behavioural Neurosciences, St. Joseph's Healthcare Hamilton, McMaster University, Hamilton, ON, Canada L8S 4L8
| | - Sonja Entringer
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Institute of Medical Psychology, 10117 Berlin, Germany
- Development, Health, and Disease Research Program, University of California, Irvine, CA 92617
| | - Pathik D Wadhwa
- Development, Health, and Disease Research Program, University of California, Irvine, CA 92617
- Department of Psychiatry and Human Behavior, School of Medicine, University of California, Irvine, CA, 92617
- Department of Obstetrics and Gynecology, School of Medicine, University of California, Irvine, CA, 92617
- Department of Epidemiology, School of Medicine, University of California, Irvine, CA, 92617
| | - Claudia Buss
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Institute of Medical Psychology, 10117 Berlin, Germany
| | - Nicole R Bush
- Department of Psychiatry, University of California, San Francisco, CA 94143
| | - Elisabeth B Binder
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322
| | - W Thomas Boyce
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
- Department of Psychiatry, University of California, San Francisco, CA 94143
- Department of Pediatrics, University of California, San Francisco, CA 94143
| | - Michael J Meaney
- Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada H4H 1R3
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
- Singapore Institute for Clinical Sciences (SICS), Agency for Science, Technology and Research (A*STAR); Singapore 117609
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095;
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA 90095
| | - Michael S Kobor
- Department of Medical Genetics, University of British Columbia-BC Children's Hospital Research Institute, Vancouver, BC, Canada V5Z 4H4;
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR) Institute, Toronto, ON, Canada M5G 1M1
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8
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Bush NR, Edgar RD, Park M, MacIsaac JL, McEwen LM, Adler NE, Essex MJ, Kobor MS, Boyce WT. The biological embedding of early-life socioeconomic status and family adversity in children's genome-wide DNA methylation. Epigenomics 2018; 10:1445-1461. [PMID: 30351206 PMCID: PMC6462839 DOI: 10.2217/epi-2018-0042] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Aim: To examine variation in child DNA methylation to assess its potential as a pathway for effects of childhood social adversity on health across the life course. Materials & methods: In a diverse, prospective community sample of 178 kindergarten children, associations between three types of social experience and DNA methylation within buccal epithelial cells later in childhood were examined. Results: Family income, parental education and family psychosocial adversity each associated with increased or decreased DNA methylation (488, 354 and 102 sites, respectively) within a unique set of genomic CpG sites. Gene ontology analyses pointed to genes serving immune and developmental regulation functions. Conclusion: Findings provided support for DNA methylation as a biomarker linking early-life social experiences with later life health in humans.
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Affiliation(s)
- Nicole R Bush
- Department of Psychiatry, Center for Health & Community, Weill Neuroscience Institute, University of California, San Francisco, 3333 California Street, Suite 465, San Francisco, CA 94118, USA.,Department of Pediatrics, Division of Developmental Medicine, University of California, San Francisco, 550 16th Street, San Francisco, CA 94158, USA
| | - Rachel D Edgar
- Department of Medical Genetics, BC Children's Hospital, Centre for Molecular Medicine & Therapeutics, University of British Columbia, 950 West 28th Ave., Vancouver, BC V5Z 4H4, Canada
| | - Mina Park
- School of Population & Public Health, BC Children's Hospital, University of British Columbia, 4480 Oak St, Vancouver, BC V6H 3N1, Canada
| | - Julia L MacIsaac
- Department of Medical Genetics, BC Children's Hospital, Centre for Molecular Medicine & Therapeutics, University of British Columbia, 950 West 28th Ave., Vancouver, BC V5Z 4H4, Canada
| | - Lisa M McEwen
- Department of Medical Genetics, BC Children's Hospital, Centre for Molecular Medicine & Therapeutics, University of British Columbia, 950 West 28th Ave., Vancouver, BC V5Z 4H4, Canada
| | - Nancy E Adler
- Department of Psychiatry, Center for Health & Community, Weill Neuroscience Institute, University of California, San Francisco, 3333 California Street, Suite 465, San Francisco, CA 94118, USA
| | - Marilyn J Essex
- Department of Psychiatry, University of Wisconsin, Madison,16330 Ellendale Road, Dallas, OR 97338, USA
| | - Michael S Kobor
- Department of Medical Genetics, BC Children's Hospital, Centre for Molecular Medicine & Therapeutics, University of British Columbia, 950 West 28th Ave., Vancouver, BC V5Z 4H4, Canada
| | - W Thomas Boyce
- Department of Psychiatry, Center for Health & Community, Weill Neuroscience Institute, University of California, San Francisco, 3333 California Street, Suite 465, San Francisco, CA 94118, USA.,Department of Pediatrics, Division of Developmental Medicine, University of California, San Francisco, 550 16th Street, San Francisco, CA 94158, USA
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9
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McEwen LM, Jones MJ, Lin DTS, Edgar RD, Husquin LT, MacIsaac JL, Ramadori KE, Morin AM, Rider CF, Carlsten C, Quintana-Murci L, Horvath S, Kobor MS. Systematic evaluation of DNA methylation age estimation with common preprocessing methods and the Infinium MethylationEPIC BeadChip array. Clin Epigenetics 2018; 10:123. [PMID: 30326963 PMCID: PMC6192219 DOI: 10.1186/s13148-018-0556-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/01/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The capacity of technologies measuring DNA methylation (DNAm) is rapidly evolving, as are the options for applicable bioinformatics methods. The most commonly used DNAm microarray, the Illumina Infinium HumanMethylation450 (450K array), has recently been replaced by the Illumina Infinium HumanMethylationEPIC (EPIC array), nearly doubling the number of targeted CpG sites. Given that a subset of 450K CpG sites is absent on the EPIC array and that several tools for both data normalization and analyses were developed on the 450K array, it is important to assess their utility when applied to EPIC array data. One of the most commonly used 450K tools is the pan-tissue epigenetic clock, a multivariate predictor of biological age based on DNAm at 353 CpG sites. Of these CpGs, 19 are missing from the EPIC array, thus raising the question of whether EPIC data can be used to accurately estimate DNAm age. We also investigated a 71-CpG epigenetic age predictor, referred to as the Hannum method, which lacks 6 probes on the EPIC array. To evaluate these epigenetic clocks in EPIC data properly, a prior assessment of the effects of data preprocessing methods on DNAm age is also required. METHODS DNAm was quantified, on both the 450K and EPIC platforms, from human primary monocytes derived from 172 individuals. We calculated DNAm age from raw, and three different preprocessed data forms to assess the effects of different processing methods on the DNAm age estimate. Using an additional cohort, we also investigated DNAm age of peripheral blood mononuclear cells, bronchoalveolar lavage, and bronchial brushing samples using the EPIC array. RESULTS Using monocyte-derived data from subjects on both the 450K and EPIC, we found that DNAm age was highly correlated across both raw and preprocessing methods (r > 0.91). Thus, the correlation between chronological age and the DNAm age estimate is largely unaffected by platform differences and normalization methods. However, we found that the choice of normalization method and measurement platform can lead to a systematic offset in the age estimate which in turn leads to an increase in the median error. Comparing the 450K and EPIC DNAm age estimates, we observed that the median absolute difference was 1.44-3.10 years across preprocessing methods. CONCLUSIONS Here, we have provided evidence that the epigenetic clock is resistant to the lack of 19 CpG sites missing from the EPIC array as well as highlighted the importance of considering the technical variance of the epigenetic when interpreting group differences below the reported error. Furthermore, our study highlights the utility of epigenetic age acceleration measure, the residuals from a linear regression of DNAm age on chronological age, as the resulting values are robust with respect to normalization methods and measurement platforms.
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Affiliation(s)
- Lisa M McEwen
- BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, TRB A5-151, Vancouver, BC V5Z 4H4 Canada
| | - Meaghan J Jones
- BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, TRB A5-151, Vancouver, BC V5Z 4H4 Canada
| | - David Tse Shen Lin
- BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, TRB A5-151, Vancouver, BC V5Z 4H4 Canada
| | - Rachel D Edgar
- BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, TRB A5-151, Vancouver, BC V5Z 4H4 Canada
| | - Lucas T Husquin
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2000, 75015 Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Julia L MacIsaac
- BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, TRB A5-151, Vancouver, BC V5Z 4H4 Canada
| | - Katia E Ramadori
- BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, TRB A5-151, Vancouver, BC V5Z 4H4 Canada
| | - Alexander M Morin
- BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, TRB A5-151, Vancouver, BC V5Z 4H4 Canada
| | - Christopher F Rider
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC Canada
| | - Chris Carlsten
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC Canada
| | - Lluís Quintana-Murci
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
- Centre National de la Recherche Scientifique (CNRS) UMR2000, 75015 Paris, France
- Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Michael S Kobor
- BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia, 950 West 28th Avenue, TRB A5-151, Vancouver, BC V5Z 4H4 Canada
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O’Donnell KJ, Glover V, Lahti J, Lahti M, Edgar RD, Räikkönen K, O’Connor TG. Maternal prenatal anxiety and child COMT genotype predict working memory and symptoms of ADHD. PLoS One 2017; 12:e0177506. [PMID: 28614354 PMCID: PMC5470664 DOI: 10.1371/journal.pone.0177506] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 04/30/2017] [Indexed: 12/31/2022] Open
Abstract
Maternal prenatal anxiety is an important risk factor for altered child neurodevelopment but there is uncertainty concerning the biological mechanisms involved and sources of individual differences in children's responses. We sought to determine the role of functional genetic variation in COMT, which encodes catechol-O-methyltransferase, in the association between maternal prenatal anxiety and child symptoms of ADHD and working memory. We used the prospectively-designed ALSPAC cohort (n = 6,969) for our primary data analyses followed by replication analyses in the PREDO cohort (n = 425). Maternal prenatal anxiety was based on self-report measures; child symptoms of ADHD were collected from 4-15 years of age; working memory was assessed from in-person testing at age 8 years; and genetic variation in COMT at rs4680 was determined in both mothers and children. The association between maternal prenatal anxiety and child attention/hyperactivity symptoms and working memory was moderated by the child's rs4680 genotype, with stronger effects obtained for the val/val (G:G) genotype relative to val/met (A:G) (all p<0.01) and met/met (A:A) groups (all p<0.05). Similar findings were observed in the PREDO cohort where maternal prenatal anxiety interacted with child rs4680 to predict symptoms of ADHD at 3.5 years of age. The findings, from two cohorts, show a robust gene-environment interaction, which may contribute to inter-individual differences in the effects of maternal prenatal anxiety on developmental outcomes from childhood to mid-adolescence.
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Affiliation(s)
- Kieran J. O’Donnell
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Hospital Research Centre, Department of Psychiatry, McGill University, Montreal, Canada
- Child and Brain Development Program, Canadian Institute for Advanced Research, Toronto, Canada
| | - Vivette Glover
- Institute of Reproductive and Developmental Biology, Imperial College London, United Kingdom
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland
- Helsinki Collegium for Advanced Studies, University of Helsinki, Finland
| | - Marius Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland
- Queen's Medical Research Institute, University of Edinburgh, United Kingdom
| | - Rachel D. Edgar
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Finland
- Queen's Medical Research Institute, University of Edinburgh, United Kingdom
| | - Thomas G. O’Connor
- Wynne Center for Family Research, Department of Psychiatry, University of Rochester Medical Center, Rochester, New York, United States of America
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11
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McEwen LM, Morin AM, Edgar RD, MacIsaac JL, Jones MJ, Dow WH, Rosero-Bixby L, Kobor MS, Rehkopf DH. Differential DNA methylation and lymphocyte proportions in a Costa Rican high longevity region. Epigenetics Chromatin 2017; 10:21. [PMID: 28465725 PMCID: PMC5408416 DOI: 10.1186/s13072-017-0128-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/13/2017] [Indexed: 01/01/2023] Open
Abstract
Background The Nicoya Peninsula in Costa Rica has one of the highest old-age life expectancies in the world, but the underlying biological mechanisms of this longevity are not well understood. As DNA methylation is hypothesized to be a component of biological aging, we focused on this malleable epigenetic mark to determine its association with current residence in Nicoya versus elsewhere in Costa Rica. Examining a population’s unique DNA methylation pattern allows us to differentiate hallmarks of longevity from individual stochastic variation. These differences may be characteristic of a combination of social, biological, and environmental contexts. Methods In a cross-sectional subsample of the Costa Rican Longevity and Healthy Aging Study, we compared whole blood DNA methylation profiles of residents from Nicoya (n = 48) and non-Nicoya (other Costa Rican regions, n = 47) using the Infinium HumanMethylation450 microarray. Results We observed a number of differences that may be markers of delayed aging, such as bioinformatically derived differential CD8+ T cell proportions. Additionally, both site- and region-specific analyses revealed DNA methylation patterns unique to Nicoyans. We also observed lower overall variability in DNA methylation in the Nicoyan population, another hallmark of younger biological age. Conclusions Nicoyans represent an interesting group of individuals who may possess unique immune cell proportions as well as distinct differences in their epigenome, at the level of DNA methylation. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0128-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lisa M McEwen
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - Alexander M Morin
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - Rachel D Edgar
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - Julia L MacIsaac
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - Meaghan J Jones
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - William H Dow
- School of Public Health, University of California, Berkeley, Berkeley, CA USA
| | - Luis Rosero-Bixby
- Centro Centroamericano de Población, Universidad de Costa Rica, San José, Costa Rica
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - David H Rehkopf
- Division of General Medical Disciplines, Department of Medicine, School of Medicine, Stanford University, 1070 Arastradero Road, Suite 300, Palo Alto, CA 94304 USA
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12
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Edgar RD, Jones MJ, Robinson WP, Kobor MS. An empirically driven data reduction method on the human 450K methylation array to remove tissue specific non-variable CpGs. Clin Epigenetics 2017; 9:11. [PMID: 28184257 PMCID: PMC5290610 DOI: 10.1186/s13148-017-0320-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/31/2017] [Indexed: 11/10/2022] Open
Abstract
Background Population based epigenetic association studies of disease and exposures are becoming more common with the availability of economical genome-wide technologies for interrogation of the methylome, such as the Illumina 450K Human Methylation Array (450K). Often, the expected small number of differentially methylated cytosine-guanine pairs (CpGs) in studies of the human methylome presents a statistical challenge, as the large number of CpGs measured on the 450K necessitates careful multiple test correction. While the 450K is a highly useful tool for population epigenetic studies, many of the CpGs tested are not variable and thus of limited information content in the context of the study and tissue. CpGs with observed lack of variability in the tissue under study could be removed to reduce the data dimensionality, limit the severity of multiple test correction and allow for improved detection of differential DNA methylation. Methods Here, we performed a meta-analysis of 450K data from three commonly studied human tissues, namely blood (605 samples), buccal epithelial cells (121 samples) and placenta (157 samples). We developed lists of CpGs that are non-variable in each tissue. Results These lists are surprisingly large (blood 114,204 CpGs, buccal epithelial cells 120,009 CpGs and placenta 101,367 CpGs) and thus will be valuable filters for epigenetic association studies, considerably reducing the dimensionality of the 450K and subsequently the multiple testing correction severity. Conclusions We propose this empirically derived method for data reduction to allow for more power in detecting differential DNA methylation associated with exposures in studies on the human methylome. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0320-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rachel D Edgar
- Department of Medical Genetics, BC Children's Hospital, University of British Columbia, Vancouver, Canada
| | - Meaghan J Jones
- Department of Medical Genetics, BC Children's Hospital, University of British Columbia, Vancouver, Canada
| | - Wendy P Robinson
- Department of Medical Genetics, BC Children's Hospital, University of British Columbia, Vancouver, Canada
| | - Michael S Kobor
- Department of Medical Genetics, BC Children's Hospital, University of British Columbia, Vancouver, Canada
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Portales-Casamar E, Lussier AA, Jones MJ, MacIsaac JL, Edgar RD, Mah SM, Barhdadi A, Provost S, Lemieux-Perreault LP, Cynader MS, Chudley AE, Dubé MP, Reynolds JN, Pavlidis P, Kobor MS. DNA methylation signature of human fetal alcohol spectrum disorder. Epigenetics Chromatin 2016; 9:25. [PMID: 27358653 PMCID: PMC4926300 DOI: 10.1186/s13072-016-0074-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/17/2016] [Indexed: 02/06/2023] Open
Abstract
Background Prenatal alcohol exposure is the leading preventable cause of behavioral and cognitive deficits, which may affect between 2 and 5 % of children in North America. While the underlying mechanisms of alcohol’s effects on development remain relatively unknown, emerging evidence implicates epigenetic mechanisms in mediating the range of symptoms observed in children with fetal alcohol spectrum disorder (FASD). Thus, we investigated the effects of prenatal alcohol exposure on genome-wide DNA methylation in the NeuroDevNet FASD cohort, the largest cohort of human FASD samples to date. Methods Genome-wide DNA methylation patterns of buccal epithelial cells (BECs) were analyzed using the Illumina HumanMethylation450 array in a Canadian cohort of 206 children (110 FASD and 96 controls). Genotyping was performed in parallel using the Infinium HumanOmni2.5-Quad v1.0 BeadChip. Results After correcting for the effects of genetic background, we found 658 significantly differentially methylated sites between FASD cases and controls, with 41 displaying differences in percent methylation change >5 %. Furthermore, 101 differentially methylated regions containing two or more CpGs were also identified, overlapping with 95 different genes. The majority of differentially methylated genes were highly expressed at the level of mRNA in brain samples from the Allen Brain Atlas, and independent DNA methylation data from cortical brain samples showed high correlations with BEC DNA methylation patterns. Finally, overrepresentation analysis of genes with up-methylated CpGs revealed a significant enrichment for neurodevelopmental processes and diseases, such as anxiety, epilepsy, and autism spectrum disorders. Conclusions These findings suggested that prenatal alcohol exposure is associated with distinct DNA methylation patterns in children and adolescents, raising the possibility of an epigenetic biomarker of FASD. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0074-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Alexandre A Lussier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Meaghan J Jones
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Julia L MacIsaac
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Rachel D Edgar
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Sarah M Mah
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Amina Barhdadi
- Beaulieu-Saucier Pharmacogenomics Centre, Montreal Heart Institute, Université de Montréal, Montreal, QC Canada
| | - Sylvie Provost
- Beaulieu-Saucier Pharmacogenomics Centre, Montreal Heart Institute, Université de Montréal, Montreal, QC Canada
| | | | - Max S Cynader
- Brain Research Centre, University of British Columbia, Vancouver, BC Canada
| | - Albert E Chudley
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Manitoba, Winnipeg, MB Canada.,Department of Biochemistry and Medical Genetics, Faculty of Medicine, University of Manitoba, Winnipeg, MB Canada
| | - Marie-Pierre Dubé
- Beaulieu-Saucier Pharmacogenomics Centre, Montreal Heart Institute, Université de Montréal, Montreal, QC Canada.,Faculty of Medicine, Université de Montréal, Montreal, QC Canada
| | - James N Reynolds
- Centre for Neuroscience Studies, Queen's University, Kingston, ON Canada
| | - Paul Pavlidis
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC Canada
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada.,Human Early Learning Partnership, School of Population and Public Health, University of British Columbia, Vancouver, British Columbia Canada
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14
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Abstract
Analysis of DNA methylation in a population context has the potential to uncover novel gene and environment interactions as well as markers of health and disease. In order to find such associations it is important to control for factors which may mask or alter DNA methylation signatures. Since tissue of origin and coinciding cell type composition are major contributors to DNA methylation patterns, and can easily confound important findings, it is vital to adjust DNA methylation data for such differences across individuals. Here we describe the use of a regression method to adjust for cell type composition in DNA methylation data. We specifically discuss what information is required to adjust for cell type composition and then provide detailed instructions on how to perform cell type adjustment on high dimensional DNA methylation data. This method has been applied mainly to Illumina 450K data, but can also be adapted to pyrosequencing or genome-wide bisulfite sequencing data.
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Affiliation(s)
- Meaghan J Jones
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada, V5Z 4H4
| | - Sumaiya A Islam
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada, V5Z 4H4
| | - Rachel D Edgar
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada, V5Z 4H4
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada, V5Z 4H4.
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Abstract
The purpose of this study was to determine the effect of lengthening the anesthesia residency by the American Board of Anesthesiology on the education of anesthesia subspecialists. A survey of anesthesia residency programs was conducted from 1987 to 1991. The most frequent subspecialty practice in the clinical anesthesia (CA) 3 year is cardiovascular anesthesia. However, the percentage of CA3 residents spending extended time (greater than or equal to 6 months) in subspecialty education has significantly decreased. For example, the percentage of CA3 residents spending 12 months in subspecialty education has decreased 83%. There appears to be a slight increase in the number of CA4 or PGY5 residents (fellows) electing subspecialty practice. It is concluded that the 3-year curriculum has produced a negative impact on the education of anesthesia subspecialists.
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Affiliation(s)
- J G Reves
- Department of Anesthesiology Duke Heart Center, Duke University Medical Center, Durham, NC
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