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Pilkay S, Riffer A, Carroll A. Trauma context exerts intergenerational effects on child mental health via DNA methylation. Epigenetics 2024; 19:2333654. [PMID: 38577817 PMCID: PMC11000619 DOI: 10.1080/15592294.2024.2333654] [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: 09/15/2023] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
Many people experience traumatic or negative events, but few develop mental health issues as a result. This study investigated whether newborn DNA methylation (DNAm) previously associated with maternal childhood physical abuse by her father affected the child's mental health and physical growth, as well as whether it mediated or moderated developmental outcomes. METHODS Study sample (N = 903) and data came from Bristol University's Avon Longitudinal Study of Parents and Children. DNAm was measured in cord blood at birth. DNAm data was preprocessed, normalized, and quality controlled before subsetting to 60 CpG sites of interest from previous research. Linear regression analysis examined newborn DNAm and child development outcome associations. Sobel test examined the mediating relationship between mother's history of childhood abuse by father, newborn targeted gene DNAm of significant CpG sites, and child's mental health and physical growth. Moderation analyses examined the interaction effects between the significant CpG sites and mothers' physical abuse by their fathers on child's mental health and physical growth. RESULTS Full cohort analyses showed that newborn DNAm of several different CpG sites associates with separation anxiety, fear, and unhappy/tearful presentations in children aged 6-7 y. Sex-specific associations emerged with boys showing associations with anxiety and fear, and girls showing associations with fear and unhappiness. In boys only, cord blood DNAm mediates the effect of maternal childhood trauma on offspring mental health. No moderation effects emerged. CONCLUSION Intergenerational effects of mother's relationship to her abuser present in newborn DNAm associate with 7-year-old child's mental health, show sex-specific effects, and newborn DNAm does mediate maternal childhood trauma effects on offspring mental health in early-life.
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Affiliation(s)
- Stefanie Pilkay
- Falk College of Sport and Human Dynamics, School of Social Work, Syracuse University, Syracuse, NYUSA
| | - Andie Riffer
- Jane Addams College of Social Work, University of Illinois at Chicago, Chicago, IL, USA
| | - Andrew Carroll
- Falk College of Sport and Human Dynamics, School of Social Work, Syracuse University, Syracuse, NYUSA
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Lu DQ, Yao XY, Ren YT, Zhang KY, Zhu XC, Hong T, Yu X, Xie ZM, Chen LY, Wang XC. Genome-wide DNA methylation sequencing reveals epigenetic features and potential biomarkers of Sjögren syndrome. Int J Rheum Dis 2023; 26:2223-2232. [PMID: 37740638 DOI: 10.1111/1756-185x.14918] [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: 02/07/2023] [Revised: 08/08/2023] [Accepted: 09/03/2023] [Indexed: 09/24/2023]
Abstract
AIM Sjögren syndrome (SS) is a slowly progressive, inflammatory, autoimmune disease. The aim of this study was to construct the DNA methylation profiles of whole blood of SS patients and healthy controls (HC), and to explore the role of differentially methylated genes in the pathogenesis of the disease. METHODS Whole-genome bisulfite sequencing was performed on three SS patients and four HC. The biological function of genes associated with differentially methylated regions (DMRs) was investigated using Gene Ontology functional analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis, using network-based key driver analysis (KDA) to find KDA genes. In clinical samples of SS patients and controls, the expression levels of KDA genes were validated by quantitative real-time polymerase chain reaction and immunohistochemical analysis. Moreover, the diagnostic value of KDA genes for SS was confirmed using receiver operating characteristic curves. RESULTS We identified 322 DMRs, annotated as 162 associated genes. Six genes were selected via the number of networks of KDA genes. Differential expression of genes such as human leukocyte antigen (HLA) class I, ADAR, and OAS2 was observed in patients' peripheral blood mononuclear cells and the minor salivary glands, which can be used as potential diagnostic biomarkers for SS. CONCLUSION Clinical sample validation suggested that HLA class I, ADAR, and OAS2 might play a role in the development of SS. Our study shows epigenetic regulatory mechanisms and potential disease markers associated with SS, which in turn will enable us to identify new therapeutic targets.
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Affiliation(s)
- Ding-Qi Lu
- Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Xin-Yi Yao
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Ya-Ting Ren
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Kai-Yuan Zhang
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Xin-Chao Zhu
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Tao Hong
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Xue Yu
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Zhi-Min Xie
- The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Li-Ying Chen
- The Second Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Xin-Chang Wang
- The Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
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3
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Teruel M, Barturen G, Martínez-Bueno M, Castellini-Pérez O, Barroso-Gil M, Povedano E, Kerick M, Català-Moll F, Makowska Z, Buttgereit A, Pers JO, Marañón C, Ballestar E, Martin J, Carnero-Montoro E, Alarcón-Riquelme ME. Integrative epigenomics in Sjögren´s syndrome reveals novel pathways and a strong interaction between the HLA, autoantibodies and the interferon signature. Sci Rep 2021; 11:23292. [PMID: 34857786 PMCID: PMC8640069 DOI: 10.1038/s41598-021-01324-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 10/19/2021] [Indexed: 12/24/2022] Open
Abstract
Primary Sjögren's syndrome (SS) is a systemic autoimmune disease characterized by lymphocytic infiltration and damage of exocrine salivary and lacrimal glands. The etiology of SS is complex with environmental triggers and genetic factors involved. By conducting an integrated multi-omics study, we confirmed a vast coordinated hypomethylation and overexpression effects in IFN-related genes, what is known as the IFN signature. Stratified and conditional analyses suggest a strong interaction between SS-associated HLA genetic variation and the presence of Anti-Ro/SSA autoantibodies in driving the IFN epigenetic signature and determining SS. We report a novel epigenetic signature characterized by increased DNA methylation levels in a large number of genes enriched in pathways such as collagen metabolism and extracellular matrix organization. We identified potential new genetic variants associated with SS that might mediate their risk by altering DNA methylation or gene expression patterns, as well as disease-interacting genetic variants that exhibit regulatory function only in the SS population. Our study sheds new light on the interaction between genetics, autoantibody profiles, DNA methylation and gene expression in SS, and contributes to elucidate the genetic architecture of gene regulation in an autoimmune population.
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Affiliation(s)
- María Teruel
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Guillermo Barturen
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Manuel Martínez-Bueno
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Olivia Castellini-Pérez
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Miguel Barroso-Gil
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Elena Povedano
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Martin Kerick
- IPBLN-CSIC, Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, 18016, Granada, Spain
| | - Francesc Català-Moll
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
- IDIBELL, Bellvitge Biomedical Research Institute 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Zuzanna Makowska
- Pharmaceuticals Division, Bayer Pharma Aktiengesellschaft, Berlin, Germany
| | - Anne Buttgereit
- Pharmaceuticals Division, Bayer Pharma Aktiengesellschaft, Berlin, Germany
| | | | - Concepción Marañón
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
- IDIBELL, Bellvitge Biomedical Research Institute 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Javier Martin
- IPBLN-CSIC, Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, 18016, Granada, Spain
| | - Elena Carnero-Montoro
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain.
| | - Marta E Alarcón-Riquelme
- GENYO, Center for Genomics and Oncological Research Pfizer/University of Granada/Andalusian Regional Government, 18016, Granada, Spain.
- Institute for Environmental Medicine, Karolinska Institutet, 171 67, Solna, Sweden.
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Seiler Vellame D, Castanho I, Dahir A, Mill J, Hannon E. Characterizing the properties of bisulfite sequencing data: maximizing power and sensitivity to identify between-group differences in DNA methylation. BMC Genomics 2021; 22:446. [PMID: 34126923 PMCID: PMC8204428 DOI: 10.1186/s12864-021-07721-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/13/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The combination of sodium bisulfite treatment with highly-parallel sequencing is a common method for quantifying DNA methylation across the genome. The power to detect between-group differences in DNA methylation using bisulfite-sequencing approaches is influenced by both experimental (e.g. read depth, missing data and sample size) and biological (e.g. mean level of DNA methylation and difference between groups) parameters. There is, however, no consensus about the optimal thresholds for filtering bisulfite sequencing data with implications for the reproducibility of findings in epigenetic epidemiology. RESULTS We used a large reduced representation bisulfite sequencing (RRBS) dataset to assess the distribution of read depth across DNA methylation sites and the extent of missing data. To investigate how various study variables influence power to identify DNA methylation differences between groups, we developed a framework for simulating bisulfite sequencing data. As expected, sequencing read depth, group size, and the magnitude of DNA methylation difference between groups all impacted upon statistical power. The influence on power was not dependent on one specific parameter, but reflected the combination of study-specific variables. As a resource to the community, we have developed a tool, POWEREDBiSeq, which utilizes our simulation framework to predict study-specific power for the identification of DNAm differences between groups, taking into account user-defined read depth filtering parameters and the minimum sample size per group. CONCLUSIONS Our data-driven approach highlights the importance of filtering bisulfite-sequencing data by minimum read depth and illustrates how the choice of threshold is influenced by the specific study design and the expected differences between groups being compared. The POWEREDBiSeq tool, which can be applied to different types of bisulfite sequencing data (e.g. RRBS, whole genome bisulfite sequencing (WGBS), targeted bisulfite sequencing and amplicon-based bisulfite sequencing), can help users identify the level of data filtering needed to optimize power and aims to improve the reproducibility of bisulfite sequencing studies.
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Affiliation(s)
- Dorothea Seiler Vellame
- College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, EX2 5DW, UK.
| | - Isabel Castanho
- College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, EX2 5DW, UK
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline-Avenue, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Aisha Dahir
- College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, EX2 5DW, UK
| | - Jonathan Mill
- College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, EX2 5DW, UK.
| | - Eilis Hannon
- College of Medicine and Health, University of Exeter, Royal Devon and Exeter Hospital, Exeter, EX2 5DW, UK.
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5
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Wang M, Ibeagha-Awemu EM. Impacts of Epigenetic Processes on the Health and Productivity of Livestock. Front Genet 2021; 11:613636. [PMID: 33708235 PMCID: PMC7942785 DOI: 10.3389/fgene.2020.613636] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/21/2020] [Indexed: 12/23/2022] Open
Abstract
The dynamic changes in the epigenome resulting from the intricate interactions of genetic and environmental factors play crucial roles in individual growth and development. Numerous studies in plants, rodents, and humans have provided evidence of the regulatory roles of epigenetic processes in health and disease. There is increasing pressure to increase livestock production in light of increasing food needs of an expanding human population and environment challenges, but there is limited related epigenetic data on livestock to complement genomic information and support advances in improvement breeding and health management. This review examines the recent discoveries on epigenetic processes due to DNA methylation, histone modification, and chromatin remodeling and their impacts on health and production traits in farm animals, including bovine, swine, sheep, goat, and poultry species. Most of the reports focused on epigenome profiling at the genome-wide or specific genic regions in response to developmental processes, environmental stressors, nutrition, and disease pathogens. The bulk of available data mainly characterized the epigenetic markers in tissues/organs or in relation to traits and detection of epigenetic regulatory mechanisms underlying livestock phenotype diversity. However, available data is inadequate to support gainful exploitation of epigenetic processes for improved animal health and productivity management. Increased research effort, which is vital to elucidate how epigenetic mechanisms affect the health and productivity of livestock, is currently limited due to several factors including lack of adequate analytical tools. In this review, we (1) summarize available evidence of the impacts of epigenetic processes on livestock production and health traits, (2) discuss the application of epigenetics data in livestock production, and (3) present gaps in livestock epigenetics research. Knowledge of the epigenetic factors influencing livestock health and productivity is vital for the management and improvement of livestock productivity.
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Affiliation(s)
- Mengqi Wang
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
- Department of Animal Science, Laval University, Quebec, QC, Canada
| | - Eveline M. Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
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6
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Lanata CM, Blazer A, Criswell LA. The Contribution of Genetics and Epigenetics to Our Understanding of Health Disparities in Rheumatic Diseases. Rheum Dis Clin North Am 2020; 47:65-81. [PMID: 34042055 DOI: 10.1016/j.rdc.2020.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Socioeconomic determinants of health are associated with worse outcomes in the rheumatic diseases and contribute significantly to health disparities. However, genetic and epigenetic risk factors may affect different populations disproportionally and further exacerbate health disparities. We discuss the role of genetics and epigenetics to the health disparities observed in rheumatic diseases. We review concepts of population genetics and natural selection, current genome-wide genetic and epigenetic studies of several autoimmune diseases, and environmental exposures associated with disease risk in different populations. To understand how genomics influence health disparities in the rheumatic diseases, further studies in different populations worldwide are needed.
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Affiliation(s)
- Cristina M Lanata
- Russell/Engleman Rheumatology Research Center, University of California, San Francisco, 513 Parnassus Avenue, MSB S865, San Francisco, CA, USA
| | - Ashira Blazer
- Department of Medicine, Division of Rheumatology, NYU Langone Health, 550 1st Avenue, MSB 606, New York, NY 10029, USA
| | - Lindsey A Criswell
- Russell/Engleman Rheumatology Research Center, University of California, San Francisco, 513 Parnassus Avenue, MSB S864, San Francisco, CA, USA.
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7
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Feng X, Hao X, Shi R, Xia Z, Huang L, Yu Q, Zhou F. Detection and Comparative Analysis of Methylomic Biomarkers of Rheumatoid Arthritis. Front Genet 2020; 11:238. [PMID: 32292416 PMCID: PMC7119472 DOI: 10.3389/fgene.2020.00238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 02/28/2020] [Indexed: 01/05/2023] Open
Abstract
Rheumatoid arthritis (RA) is a common autoimmune disorder influenced by both genetic and environmental factors. To investigate possible contributions of DNA methylation to the etiology of RA with minimum confounding genetic heterogeneity, we investigated genome-wide DNA methylation in disease-discordant monozygotic twin pairs. This study hypothesized that methylomic biomarkers might facilitate accurate RA detection. A comprehensive series of biomarker detection algorithms were utilized to find the best methylomic biomarkers for detecting RA patients using the methylomic data of the peripheral blood samples. The best model achieved 100.00% in accuracy (Acc) with 81 methylomic biomarkers and a 10-fold cross-validation (10FCV) strategy. Some of the methylomic biomarkers were experimentally confirmed to be associated with the onset or development of RA. It is also interesting to observe that many of the detected biomarkers were from chromosome Y, supporting the knowledge that RA has a significant gender discrepancy.
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Affiliation(s)
- Xin Feng
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China.,Jilin Institute of Chemical Technology, Jilin, China.,BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Xubing Hao
- BioKnow Health Informatics Lab, College of Software, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Ruoyao Shi
- BioKnow Health Informatics Lab, College of Life Sciences, Jilin University, Changchun, China
| | - Zhiqiang Xia
- BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Lan Huang
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Qiong Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China
| | - Fengfeng Zhou
- BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
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8
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Miller-Archie SA, Izmirly PM, Berman JR, Brite J, Walker DJ, Dasilva RC, Petrsoric LJ, Cone JE. Systemic Autoimmune Disease Among Adults Exposed to the September 11, 2001 Terrorist Attack. Arthritis Rheumatol 2020; 72:849-859. [PMID: 31762219 PMCID: PMC7216890 DOI: 10.1002/art.41175] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 11/19/2019] [Indexed: 12/18/2022]
Abstract
Objective Autoimmune disease is an emerging condition among persons exposed to the September 11, 2001 attack on the World Trade Center (WTC). Components of the dust cloud resulting from the collapse of the WTC have been associated with development of a systemic autoimmune disease, as has posttraumatic stress disorder (PTSD). We undertook this study to determine whether dust exposure and PTSD were associated with an increased risk of systemic autoimmune disease in a 9/11‐exposed cohort. Methods Among 43,133 WTC Health Registry enrollees, 2,786 self‐reported having a post‐9/11 systemic autoimmune disease. We obtained informed consent to review medical records to validate systemic autoimmune disease diagnoses for 1,041 enrollees. Diagnoses of systemic autoimmune diseases were confirmed by classification criteria, rheumatologist diagnosis, or having been prescribed systemic autoimmune disease medication. Controls were enrollees who denied having an autoimmune disease diagnosis (n = 37,017). We used multivariable log‐binomial regression to examine the association between multiple 9/11 exposures and risk of post‐9/11 systemic autoimmune disease, stratifying by responders (rescue, recovery, and clean‐up workers) and community members (e.g., residents, area workers). Results We identified 118 persons with systemic autoimmune disease. Rheumatoid arthritis was most frequent (n = 71), followed by Sjӧgren's syndrome (n = 22), systemic lupus erythematosus (n = 20), myositis (n = 9), mixed connective tissue disease (n = 7), and scleroderma (n = 4). Among 9/11 responders, those with intense dust cloud exposure had almost twice the risk of systemic autoimmune disease (adjusted risk ratio 1.86 [95% confidence interval 1.02–3.40]). Community members with PTSD had a nearly 3‐fold increased risk of systemic autoimmune disease. Conclusion Intense dust cloud exposure among responders and PTSD among community members were associated with a statistically significant increased risk of new‐onset systemic autoimmune disease. Clinicians treating 9/11 survivors should be aware of the potential increased risk of systemic autoimmune disease in this population.
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Affiliation(s)
| | | | - Jessica R Berman
- Hospital for Special Surgery and Weill Cornell Medical College, New York, New York
| | - Jennifer Brite
- New York City Department of Health and Mental Hygiene, New York, New York
| | - Deborah J Walker
- New York City Department of Health and Mental Hygiene, New York, New York
| | - Renato C Dasilva
- New York City Department of Health and Mental Hygiene, New York, New York
| | - Lysa J Petrsoric
- New York City Department of Health and Mental Hygiene, New York, New York
| | - James E Cone
- New York City Department of Health and Mental Hygiene, New York, New York
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9
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Demirkaya E, Arici ZS, Romano M, Berard RA, Aksentijevich I. Current State of Precision Medicine in Primary Systemic Vasculitides. Front Immunol 2019; 10:2813. [PMID: 31921111 PMCID: PMC6927998 DOI: 10.3389/fimmu.2019.02813] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/15/2019] [Indexed: 12/12/2022] Open
Abstract
Precision medicine (PM) is an emerging data-driven health care approach that integrates phenotypic, genomic, epigenetic, and environmental factors unique to an individual. The goal of PM is to facilitate diagnosis, predict effective therapy, and avoid adverse reactions specific for each patient. The forefront of PM is in oncology; nonetheless, it is developing in other fields of medicine, including rheumatology. Recent studies on elucidating the genetic architecture of polygenic and monogenic rheumatological diseases have made PM possible by enabling physicians to customize medical treatment through the incorporation of clinical features and genetic data. For complex inflammatory disorders, the prevailing paradigm is that disease susceptibility is due to additive effects of common reduced-penetrance gene variants and environmental factors. Efforts have been made to calculate cumulative genetic risk score (GRS) and to relate specific susceptibility alleles for use of target therapies. The discovery of rare patients with single-gene high-penetrance mutations informed our understanding of pathways driving systemic inflammation. Here, we review the advances in practicing PM in patients with primary systemic vasculitides (PSVs). We summarize recent genetic studies and discuss current knowledge on the contribution of epigenetic factors and extracellular vesicles (EVs) in disease progression and treatment response. Implementation of PM in PSVs is a developing field that will require analysis of a large cohort of patients to validate data from genomics, transcriptomics, metabolomics, proteomics, and epigenomics studies for accurate disease profiling. This multi-omics approach to study disease pathogeneses should ultimately provide a powerful tool for stratification of patients to receive tailored optimal therapies and for monitoring their disease activity.
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Affiliation(s)
- Erkan Demirkaya
- Division of Paediatric Rheumatology, Department of Paediatrics, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - Zehra Serap Arici
- Department of Paediatric Rheumatology, Sanliurfa Training and Research Hospital, Sanliurfa, Turkey
| | - Micol Romano
- Division of Paediatric Rheumatology, Department of Paediatrics, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada.,Department of Pediatric Rheumatology, Istituto Ortopedico Gaetano Pini, Milan, Italy
| | - Roberta Audrey Berard
- Division of Paediatric Rheumatology, Department of Paediatrics, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, Canada
| | - Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
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10
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Interferons ( IFN-A/-B/-G) Genetic Variants in Patients with Mixed Connective Tissue Disease (MCTD). J Clin Med 2019; 8:jcm8122046. [PMID: 31766529 PMCID: PMC6947393 DOI: 10.3390/jcm8122046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/06/2019] [Accepted: 11/20/2019] [Indexed: 12/27/2022] Open
Abstract
Mixed connective tissue disease (MCTD) is a rare complex autoimmune disease in which autoantigens are recognized by endosomal TLRs. Their activation induces a higher secretion of the type I interferons, IFN-γ and the up-regulation of the INF-inducible genes. The present study aimed to investigate whether SNPs that are located in the IFN-A, IFN-B, and IFN-G genes are associated with MCTD. 145 MCTD patients and 281 healthy subjects were examined for IFN-A, IFN-B, and IFN-G genetic variants by TaqMan SNP genotyping assay. ELISA determined IFN-α/-β/-γ serum levels. Among the seven tested SNPs, four polymorphisms: IFN-A rs10757212, IFN-A rs3758236, IFN-G rs2069705, IFN-G rs2069718, as well as INF-G rs1861493A/rs2069705A/rs2069718G haplotype were significantly associated with a predisposition for MCTD. Raynaud's phenomenon, erosive arthritis, swollen hands and fingers, and sclerodactyly were significantly more frequently observed in MCTD patients with IFN-G rs2069718 G allele than in patients with IFN-G rs2069718 A allele. We also found that anti-U1-A autoantibodies most frequently occurred in MCTD patients with rs2069718 GA genotype, while the IFN-G rs2069705 AG and rs2069718 GA genotypes might be a marker of anti-Ro60 presence in MCTD patients. Our results indicate that IFN-G genetic variants may be potential genetic biomarkers for MCTD susceptibility and severity.
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Carnero-Montoro E, Barturen G, Povedano E, Kerick M, Martinez-Bueno M, Ballestar E, Martin J, Teruel M, Alarcón-Riquelme ME. Epigenome-Wide Comparative Study Reveals Key Differences Between Mixed Connective Tissue Disease and Related Systemic Autoimmune Diseases. Front Immunol 2019; 10:1880. [PMID: 31440254 PMCID: PMC6693476 DOI: 10.3389/fimmu.2019.01880] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/24/2019] [Indexed: 11/26/2022] Open
Abstract
Mixed Connective Tissue Disease (MCTD) is a rare complex systemic autoimmune disease (SAD) characterized by the presence of increased levels of anti-U1 ribonucleoprotein autoantibodies and signs and symptoms that resemble other SADs such as systemic sclerosis (SSc), rheumatoid arthritis (RA), and systemic lupus erythematosus (SLE). Due to its low prevalence, this disease has been very poorly studied at the molecular level. We performed for the first time an epigenome-wide association study interrogating DNA methylation data obtained with the Infinium MethylationEPIC array from whole blood samples in 31 patients diagnosed with MCTD and 255 healthy subjects. We observed a pervasive hypomethylation involving 170 genes enriched for immune-related function such as those involved in type I interferon signaling pathways or in negative regulation of viral genome replication. We mostly identified epigenetic signals at genes previously implicated in other SADs, for example MX1, PARP9, DDX60, or IFI44L, for which we also observed that MCTD patients exhibit higher DNA methylation variability compared with controls, suggesting that these sites might be involved in plastic immune responses that are relevant to the disease. Through methylation quantitative trait locus (meQTL) analysis we identified widespread local genetic effects influencing DNA methylation variability at MCTD-associated sites. Interestingly, for IRF7, IFI44 genes, and the HLA region we have evidence that they could be exerting a genetic risk on MCTD mediated through DNA methylation changes. Comparison of MCTD-associated epigenome with patients diagnosed with SLE, or Sjögren's Syndrome, reveals a common interferon-related epigenetic signature, however we find substantial epigenetic differences when compared with patients diagnosed with rheumatoid arthritis and systemic sclerosis. Furthermore, we show that MCTD-associated CpGs are potential epigenetic biomarkers with high diagnostic value. Our study serves to reveal new genes and pathways involved in MCTD, to illustrate the important role of epigenetic modifications in MCTD pathology, in mediating the interaction between different genetic and environmental MCTD risk factors, and as potential biomarkers of SADs.
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Affiliation(s)
- Elena Carnero-Montoro
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Guillermo Barturen
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Elena Povedano
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Martin Kerick
- CSIC-IBPLN, Consejo Superior de Investigaciones Científicas, Instituto de Parasitología y Biomedicina López-Neyra, Granada, Spain
| | - Manuel Martinez-Bueno
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | | | - Esteban Ballestar
- IDIBELL, Bellvitge Biomedical Research Institute L'Hospitalet de Llobregat, Barcelona, Spain
| | - Javier Martin
- CSIC-IBPLN, Consejo Superior de Investigaciones Científicas, Instituto de Parasitología y Biomedicina López-Neyra, Granada, Spain
| | - María Teruel
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Marta E Alarcón-Riquelme
- GENYO, Center for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain.,Institute for Environmental Medicine, Karolinska Institutet, Solna, Sweden
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Imgenberg-Kreuz J, Almlöf JC, Leonard D, Sjöwall C, Syvänen AC, Rönnblom L, Sandling JK, Nordmark G. Shared and Unique Patterns of DNA Methylation in Systemic Lupus Erythematosus and Primary Sjögren's Syndrome. Front Immunol 2019; 10:1686. [PMID: 31428085 PMCID: PMC6688520 DOI: 10.3389/fimmu.2019.01686] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/04/2019] [Indexed: 12/14/2022] Open
Abstract
Objectives: To perform a cross-comparative analysis of DNA methylation in patients with systemic lupus erythematosus (SLE), patients with primary Sjögren's syndrome (pSS), and healthy controls addressing the question of epigenetic sharing and aiming to detect disease-specific alterations. Methods: DNA extracted from peripheral blood from 347 cases with SLE, 100 cases with pSS, and 400 healthy controls were analyzed on the Human Methylation 450k array, targeting 485,000 CpG sites across the genome. A linear regression model including age, sex, and blood cell type distribution as covariates was fitted, and association p-values were Bonferroni corrected. A random forest machine learning classifier was designed for prediction of disease status based on DNA methylation data. Results: We established a combined set of 4,945 shared differentially methylated CpG sites (DMCs) in SLE and pSS compared to controls. In pSS, hypomethylation at type I interferon induced genes was mainly driven by patients who were positive for Ro/SSA and/or La/SSB autoantibodies. Analysis of differential methylation between SLE and pSS identified 2,244 DMCs with a majority of sites showing decreased methylation in SLE compared to pSS. The random forest classifier demonstrated good performance in discerning between disease status with an area under the curve (AUC) between 0.83 and 0.96. Conclusions: The majority of differential DNA methylation is shared between SLE and pSS, however, important quantitative differences exist. Our data highlight neutrophil dysregulation as a shared mechanism, emphasizing the role of neutrophils in the pathogenesis of systemic autoimmune diseases. The current study provides evidence for genes and molecular pathways driving common and disease-specific pathogenic mechanisms.
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Affiliation(s)
- Juliana Imgenberg-Kreuz
- Section of Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Jonas Carlsson Almlöf
- Molecular Medicine and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Dag Leonard
- Section of Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Christopher Sjöwall
- Rheumatology, Division of Neuro and Inflammation Sciences, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Ann-Christine Syvänen
- Molecular Medicine and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Lars Rönnblom
- Section of Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Johanna K Sandling
- Section of Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Gunnel Nordmark
- Section of Rheumatology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
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13
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He W, Wang B, Li Q, Yao Q, Jia X, Song R, Li S, Zhang JA. Aberrant Expressions of Co-stimulatory and Co-inhibitory Molecules in Autoimmune Diseases. Front Immunol 2019; 10:261. [PMID: 30842773 PMCID: PMC6391512 DOI: 10.3389/fimmu.2019.00261] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/29/2019] [Indexed: 12/26/2022] Open
Abstract
Co-signaling molecules include co-stimulatory and co-inhibitory molecules and play important roles in modulating immune responses. The roles of co-signaling molecules in autoimmune diseases have not been clearly defined. We assessed the expressions of co-stimulatory and co-inhibitory molecules in autoimmune diseases through a bioinformatics-based study. By using datasets of whole-genome transcriptome, the expressions of 54 co-stimulatory or co-inhibitory genes in common autoimmune diseases were analyzed using Robust rank aggregation (RRA) method. Nineteen array datasets and 6 RNA-seq datasets were included in the RRA discovery study and RRA validation study, respectively. Significant genes were further validated in several autoimmune diseases including Graves' disease (GD). RRA discovery study suggested that CD160 was the most significant gene aberrantly expressed in autoimmune diseases (Adjusted P = 5.9E-12), followed by CD58 (Adjusted P = 5.7E-06) and CD244 (Adjusted P = 9.5E-05). RRA validation study also identified CD160 as the most significant gene aberrantly expressed in autoimmune diseases (Adjusted P = 5.9E-09). We further found that the aberrant expression of CD160 was statistically significant in multiple autoimmune diseases including GD (P < 0.05), and CD160 had a moderate role in diagnosing those autoimmune diseases. Flow cytometry confirmed that CD160 was differentially expressed on the surface of CD8+ T cells between GD patients and healthy controls (P = 0.002), which proved the aberrant expression of CD160 in GD at the protein level. This study suggests that CD160 is the most significant co-signaling gene aberrantly expressed in autoimmune diseases. Treatment strategy targeting CD160-related pathway may be promising for the therapy of autoimmune diseases.
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Affiliation(s)
- Weiwei He
- Department of Endocrinology, Affiliated Hospital of Yanan Medical University, Yanan, China
| | - Bin Wang
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai, China
| | - Qian Li
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai, China
| | - Qiuming Yao
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai, China
| | - Xi Jia
- Department of Endocrinology, Jinshan Hospital of Fudan University, Shanghai, China
| | - Ronghua Song
- Department of Endocrinology and Rheumatology, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Sheli Li
- Department of Endocrinology, Affiliated Hospital of Yanan Medical University, Yanan, China
| | - Jin-An Zhang
- Department of Endocrinology and Rheumatology, Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
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14
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Affiliation(s)
- Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA..
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