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Seale K, Teschendorff A, Reiner AP, Voisin S, Eynon N. A comprehensive map of the aging blood methylome in humans. Genome Biol 2024; 25:240. [PMID: 39242518 PMCID: PMC11378482 DOI: 10.1186/s13059-024-03381-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 08/28/2024] [Indexed: 09/09/2024] Open
Abstract
BACKGROUND During aging, the human methylome undergoes both differential and variable shifts, accompanied by increased entropy. The distinction between variably methylated positions (VMPs) and differentially methylated positions (DMPs), their contribution to epigenetic age, and the role of cell type heterogeneity remain unclear. RESULTS We conduct a comprehensive analysis of > 32,000 human blood methylomes from 56 datasets (age range = 6-101 years). We find a significant proportion of the blood methylome that is differentially methylated with age (48% DMPs; FDR < 0.005) and variably methylated with age (37% VMPs; FDR < 0.005), with considerable overlap between the two groups (59% of DMPs are VMPs). Bivalent and Polycomb regions become increasingly methylated and divergent between individuals, while quiescent regions lose methylation more uniformly. Both chronological and biological clocks, but not pace-of-aging clocks, show a strong enrichment for CpGs undergoing both mean and variance changes during aging. The accumulation of DMPs shifting towards a methylation fraction of 50% drives the increase in entropy, smoothening the epigenetic landscape. However, approximately a quarter of DMPs exhibit anti-entropic effects, opposing this direction of change. While changes in cell type composition minimally affect DMPs, VMPs and entropy measurements are moderately sensitive to such alterations. CONCLUSION This study represents the largest investigation to date of genome-wide DNA methylation changes and aging in a single tissue, providing valuable insights into primary molecular changes relevant to chronological and biological aging.
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Affiliation(s)
- Kirsten Seale
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC, 3011, Australia
| | - Andrew Teschendorff
- CAS Key Lab of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
- UCL Cancer Institute, University College London, London, UK
| | | | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC, 3011, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Nir Eynon
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia.
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Liang X, Aouizerat BE, So‐Armah K, Cohen MH, Marconi VC, Xu K, Justice AC. DNA methylation-based telomere length is associated with HIV infection, physical frailty, cancer, and all-cause mortality. Aging Cell 2024; 23:e14174. [PMID: 38629454 PMCID: PMC11258465 DOI: 10.1111/acel.14174] [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: 12/20/2023] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 07/21/2024] Open
Abstract
Telomere length (TL) is an important indicator of cellular aging. Shorter TL is associated with several age-related diseases including coronary heart disease, heart failure, diabetes, osteoporosis, and cancer. Recently, a DNA methylation-based TL (DNAmTL) estimator has been developed as an alternative method for directly measuring TL. In this study, we examined the association of DNAmTL with cancer prevalence and mortality risk among people with and without HIV in the Veterans Aging Cohort Study Biomarker Cohort (VACS, N = 1917) and Women's Interagency HIV Study Cohort (WIHS, N = 481). We profiled DNAm in whole blood (VACS) or in peripheral blood mononuclear cells (WIHS) using an array-based method. Cancer prevalence was estimated from electronic medical records and cancer registry data. The VACS Index was used as a measure of physiologic frailty. Models were adjusted for self-reported race and ethnicity, batch, smoking status, alcohol consumption, and five cell types (CD4, CD8, NK, B cell, and monocyte). We found that people with HIV had shorter average DNAmTL than those without HIV infection [beta = -0.25, 95% confidence interval (-0.32, -0.18), p = 1.48E-12]. Greater value of VACS Index [beta = -0.002 (-0.003, -0.001), p = 2.82E-05] and higher cancer prevalence [beta = -0.07 (-0.10, -0.03), p = 1.37E-04 without adjusting age] were associated with shortened DNAmTL. In addition, one kilobase decrease in DNAmTL was associated with a 40% increase in mortality risk [hazard ratio: 0.60 (0.44, 0.82), p = 1.42E-03]. In summary, HIV infection, physiologic frailty, and cancer are associated with shortening DNAmTL, contributing to an increased risk of all-cause mortality.
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Affiliation(s)
- Xiaoyu Liang
- Department of Epidemiology and BiostatisticsMichigan State UniversityEast LansingMichiganUSA
| | - Bradley E. Aouizerat
- Translational Research Center, College of DentistryNew York UniversityNew YorkNew YorkUSA
- Department of Oral and Maxillofacial Surgery, College of DentistryNew York UniversityNew YorkNew YorkUSA
| | - Kaku So‐Armah
- Boston University School of MedicineBostonMassachusettsUSA
| | - Mardge H. Cohen
- Department of MedicineStroger Hospital of Cook CountyChicagoIllinoisUSA
| | - Vincent C. Marconi
- Emory University School of Medicine and Rollins School of Public HealthThe Atlanta Veterans Affairs Medical CenterAtlantaGeorgiaUSA
| | - Ke Xu
- Department of PsychiatryYale School of MedicineNew HavenConnecticutUSA
- VA Connecticut Healthcare SystemWest HavenConnecticutUSA
| | - Amy C. Justice
- VA Connecticut Healthcare SystemWest HavenConnecticutUSA
- Department of Internal MedicineYale School of MedicineNew HavenConnecticutUSA
- Yale School of Public HealthNew HavenConnecticutUSA
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Zhang X, Hu Y, Vandenhoudt RE, Yan C, Marconi VC, Cohen MH, Wang Z, Justice AC, Aouizerat BE, Xu K. Computationally inferred cell-type specific epigenome-wide DNA methylation analysis unveils distinct methylation patterns among immune cells for HIV infection in three cohorts. PLoS Pathog 2024; 20:e1012063. [PMID: 38466776 PMCID: PMC10957090 DOI: 10.1371/journal.ppat.1012063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 03/21/2024] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Epigenome-wide association studies (EWAS) have identified CpG sites associated with HIV infection in blood cells in bulk, which offer limited knowledge of cell-type specific methylation patterns associated with HIV infection. In this study, we aim to identify differentially methylated CpG sites for HIV infection in immune cell types: CD4+ T-cells, CD8+ T-cells, B cells, Natural Killer (NK) cells, and monocytes. METHODS Applying a computational deconvolution method, we performed a cell-type based EWAS for HIV infection in three independent cohorts (Ntotal = 1,382). DNA methylation in blood or in peripheral blood mononuclear cells (PBMCs) was profiled by an array-based method and then deconvoluted by Tensor Composition Analysis (TCA). The TCA-computed CpG methylation in each cell type was first benchmarked by bisulfite DNA methylation capture sequencing in a subset of the samples. Cell-type EWAS of HIV infection was performed in each cohort separately and a meta-EWAS was conducted followed by gene set enrichment analysis. RESULTS The meta-analysis unveiled a total of 2,021 cell-type unique significant CpG sites for five inferred cell types. Among these inferred cell-type unique CpG sites, the concordance rate in the three cohorts ranged from 96% to 100% in each cell type. Cell-type level meta-EWAS unveiled distinct patterns of HIV-associated differential CpG methylation, where 74% of CpG sites were unique to individual cell types (false discovery rate, FDR <0.05). CD4+ T-cells had the largest number of unique HIV-associated CpG sites (N = 1,624) compared to any other cell type. Genes harboring significant CpG sites are involved in immunity and HIV pathogenesis (e.g. CD4+ T-cells: NLRC5, CX3CR1, B cells: IFI44L, NK cells: IL12R, monocytes: IRF7), and in oncogenesis (e.g. CD4+ T-cells: BCL family, PRDM16, monocytes: PRDM16, PDCD1LG2). HIV-associated CpG sites were enriched among genes involved in HIV pathogenesis and oncogenesis that were enriched among interferon-α and -γ, TNF-α, inflammatory response, and apoptotic pathways. CONCLUSION Our findings uncovered computationally inferred cell-type specific modifications in the host epigenome for people with HIV that contribute to the growing body of evidence regarding HIV pathogenesis.
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Affiliation(s)
- Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut, United States of America
- VA Connecticut Healthcare System, West Haven, Connecticut, United States of America
| | - Ying Hu
- Center for Biomedical Information and Information Technology, National Cancer Institute, Rockville, Maryland, United States of America
| | - Ral E. Vandenhoudt
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut, United States of America
- VA Connecticut Healthcare System, West Haven, Connecticut, United States of America
| | - Chunhua Yan
- Center for Biomedical Information and Information Technology, National Cancer Institute, Rockville, Maryland, United States of America
| | - Vincent C. Marconi
- Division of Infectious Diseases, Emory University School of Medicine and Department of Global Health, Rollins School of Public Health, Emory University, Georgia, United States of America
- Atlanta Veterans Affairs Healthcare System, Decatur, Georgia, United States of America
| | - Mardge H. Cohen
- Department of Medicine, Stroger Hospital of Cook County, Chicago, Illinois, United States of America
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Amy C. Justice
- VA Connecticut Healthcare System, West Haven, Connecticut, United States of America
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Bradley E. Aouizerat
- Translational Research Center, College of Dentistry, New York University, New York, New York, United States of America
- Department of Oral and Maxillofacial Surgery, College of Dentistry, New York University, New York, New York, United States of America
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut, United States of America
- VA Connecticut Healthcare System, West Haven, Connecticut, United States of America
- Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, Connecticut, United States of America
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Liang X, Justice AC, Marconi VC, Aouizerat BE, Xu K. Co-occurrence of injection drug use and hepatitis C increases epigenetic age acceleration that contributes to all-cause mortality among people living with HIV. Epigenetics 2023; 18:2212235. [PMID: 37191953 PMCID: PMC10190198 DOI: 10.1080/15592294.2023.2212235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/19/2023] [Indexed: 05/17/2023] Open
Abstract
Co-occurrence of injection drug use (IDU) and hepatitis C virus infection (HCV) is common in people living with HIV (PLWH) and leads to significantly increased mortality. Epigenetic clocks derived from DNA methylation (DNAm) are associated with disease progression and all-cause mortality. In this study, we hypothesized that epigenetic age mediates the relationships between the co-occurrence of IDU and HCV with mortality risk among PLWH. We tested this hypothesis in the Veterans Aging Cohort Study (n = 927) by using four established epigenetic clocks of DNAm age (i.e., Horvath, Hannum, Pheno, Grim). Compared to individuals without IDU and HCV (IDU-HCV-), participants with IDU and HCV (IDU+HCV+) showed a 2.23-fold greater risk of mortality estimated using a Cox proportional hazards model (hazard ratio: 2.23; 95% confidence interval: 1.62-3.09; p = 1.09E-06). IDU+HCV+ was associated with a significantly increased epigenetic age acceleration (EAA) measured by 3 out of 4 epigenetic clocks, adjusting for demographic and clinical variables (Hannum: p = 8.90E-04, Pheno: p = 2.34E-03, Grim: p = 3.33E-11). Furthermore, we found that epigenetic age partially mediated the relationship between IDU+HCV+ and all-cause mortality, up to a 13.67% mediation proportion. Our results suggest that comorbid IDU with HCV increases EAA in PLWH that partially mediates the increased mortality risk.
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Affiliation(s)
- Xiaoyu Liang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA
| | - Amy C. Justice
- VA Connecticut Healthcare System, West Haven, CT, USA
- New Haven Veterans Affairs Connecticut Healthcare System, Yale University School of Medicine, New Haven, CT, USA
| | - Vincent C. Marconi
- Emory University School of Medicine and Rollins School of Public Health; the Atlanta Veterans Affairs Medical Center, Atlanta, Georgia
| | - Bradley E. Aouizerat
- Bluestone Center for Clinical Research, College of Dentistry, New York University, New York, NY, USA
- Department of Oral and Maxillofacial Surgery, College of Dentistry, New York University, New York, NY, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
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Zhang X, Hu Y, Vandenhoudt RE, Yan C, Marconi VC, Cohen MH, Justice AC, Aouizerat BE, Xu K. Cell-type specific EWAS identifies genes involved in HIV pathogenesis and oncogenesis among people with HIV infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.533691. [PMID: 36993343 PMCID: PMC10055405 DOI: 10.1101/2023.03.21.533691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Epigenome-wide association studies (EWAS) of heterogenous blood cells have identified CpG sites associated with chronic HIV infection, which offer limited knowledge of cell-type specific methylation patterns associated with HIV infection. Applying a computational deconvolution method validated by capture bisulfite DNA methylation sequencing, we conducted a cell type-based EWAS and identified differentially methylated CpG sites specific for chronic HIV infection among five immune cell types in blood: CD4+ T-cells, CD8+ T-cells, B cells, Natural Killer (NK) cells, and monocytes in two independent cohorts (N total =1,134). Differentially methylated CpG sites for HIV-infection were highly concordant between the two cohorts. Cell-type level meta-EWAS revealed distinct patterns of HIV-associated differential CpG methylation, where 67% of CpG sites were unique to individual cell types (false discovery rate, FDR <0.05). CD4+ T-cells had the largest number of HIV-associated CpG sites (N=1,472) compared to any other cell type. Genes harboring statistically significant CpG sites are involved in immunity and HIV pathogenesis (e.g. CX3CR1 in CD4+ T-cells, CCR7 in B cells, IL12R in NK cells, LCK in monocytes). More importantly, HIV-associated CpG sites were overrepresented for hallmark genes involved in cancer pathology ( FDR <0.05) (e.g. BCL family, PRDM16, PDCD1LGD, ESR1, DNMT3A, NOTCH2 ). HIV-associated CpG sites were enriched among genes involved in HIV pathogenesis and oncogenesis such as Kras-signaling, interferon-α and -γ, TNF-α, inflammatory, and apoptotic pathways. Our findings are novel, uncovering cell-type specific modifications in the host epigenome for people with HIV that contribute to the growing body of evidence regarding pathogen-induced epigenetic oncogenicity, specifically on HIV and its comorbidity with cancers.
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Oursler KK, Marconi VC, Wang Z, Xu K, Montano M, So-Armah K, Justice AC, Sun YV. Epigenetic Age Acceleration Markers Are Associated With Physiologic Frailty and All-Cause Mortality in People With Human Immunodeficiency Virus. Clin Infect Dis 2023; 76:e638-e644. [PMID: 35970820 PMCID: PMC10169393 DOI: 10.1093/cid/ciac656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/02/2022] [Accepted: 08/10/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Biomarkers that provide insight into drivers of aging are needed for people with human immunodeficiency virus (PWH). The study objective was to determine if epigenetic age acceleration (EAA) markers are associated with physiologic frailty measured by the Veterans Aging Cohort Study (VACS) Index and predict all-cause mortality for PWH. METHODS Epigenome-wide DNA methylation was profiled in VACS total white blood cell samples collected during 2005-2007 from 531 PWH to generate 6 established markers of EAA. The association of each EAA marker was tested with VACS Index 2.0. All-cause mortality was assessed over 10 years. For each EAA marker, the hazard ratio per increased year was determined using Cox regression. To evaluate mortality discrimination, C-statistics were derived. RESULTS Participants were mostly men (98.5%) and non-Hispanic Black (84.4%), with a mean age of 52.4 years (standard deviation [SD], 7.8 years). Mean VACS Index score was 59.3 (SD, 16.4) and 136 deaths occurred over a median follow-up of 8.7 years. Grim age acceleration (AA), PhenoAA, HannumAA, and extrinsic epigenetic AA were associated with the VACS Index and mortality. HorvathAA and intrinsic epigenetic AA were not associated with either outcome. GrimAA had the greatest mortality discrimination among EAA markers and predicted mortality independently of the VACS Index. One-year increase in GrimAA was associated with a 1-point increase in VACS Index and a 10% increased hazard for mortality. CONCLUSIONS The observed associations between EAA markers with physiologic frailty and mortality support future research to provide mechanistic insight into the accelerated aging process and inform interventions tailored to PWH for promoting increased healthspan.
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Affiliation(s)
- Krisann K Oursler
- Department of Internal Medicine, Virginia Tech Carilion School of Medicine and Veterans Affairs Salem Healthcare System, Roanoke, Virginia, USA
| | - Vincent C Marconi
- Department of Medicine, Emory University School of Medicine and Rollins School of Public Health, Atlanta, Georgia, USA
- Veterans Affairs Atlanta Healthcare System, Decatur, Georgia, USA
| | - Zeyuan Wang
- Department of Epidemiology, Rollins School of Public Health, Emory University,Atlanta, Georgia, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, West Haven, Connecticut, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
| | - Monty Montano
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Kaku So-Armah
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Amy C Justice
- Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
- Department of Medicine, Yale School of Medicine, West Haven, Connecticut, USA
- Division of Health Policy, Yale School of Public Health,West Haven, Connecticut, USA
| | - Yan V Sun
- Veterans Affairs Atlanta Healthcare System, Decatur, Georgia, USA
- Department of Epidemiology, Rollins School of Public Health, Emory University,Atlanta, Georgia, USA
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Krankowska DC, Załęski A, Wiercińska-Drapało A. Frailty and prefrailty in people living with HIV, with focus on women living with HIV. Int J STD AIDS 2022; 33:1106-1110. [PMID: 36217985 DOI: 10.1177/09564624221127744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
With the increasing lifespan of people living with HIV (PLWH), frailty and prefrailty are becoming topics which require more attention. The reciprocal interactions between chronic inflammation, comorbidities and frailty demonstrate the complex pathophysiology of frailty and its consequences. Female sex, HIV infection without antiretroviral treatment, reduced CD4 cell count, depression and cardiovascular disease are some of the risk factors for frailty among PLWH. Frailty predisposes to falls and can therefore lead to more frequent fractures, hospitalization and death, especially in women with osteoporosis. Continuous antiretroviral treatment, prevention of comorbidities such as depression and diagnosis of prefrailty are crucial interventions to slow the development of frailty. This review summarizes the literature on frailty in people living with HIV and discusses frailty management strategies in order to improve the health outcomes in women living with HIV.
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Affiliation(s)
- Dagny C Krankowska
- Department of Infectious and Tropical Diseases and Hepatology, 37803Medical University of Warsaw, Poland.,Hospital for Infectious Diseases, Warsaw, Poland
| | - Andrzej Załęski
- Department of Infectious and Tropical Diseases and Hepatology, 37803Medical University of Warsaw, Poland.,Hospital for Infectious Diseases, Warsaw, Poland
| | - Alicja Wiercińska-Drapało
- Department of Infectious and Tropical Diseases and Hepatology, 37803Medical University of Warsaw, Poland.,Hospital for Infectious Diseases, Warsaw, Poland
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Titanji BK, Lee M, Wang Z, Chen J, Hui Q, Lo Re III V, So-Armah K, Justice AC, Xu K, Freiberg M, Gwinn M, Marconi VC, Sun YV. Epigenome-wide association study of biomarkers of liver function identifies albumin-associated DNA methylation sites among male veterans with HIV. Front Genet 2022; 13:1020871. [PMID: 36303554 PMCID: PMC9592923 DOI: 10.3389/fgene.2022.1020871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Liver disease (LD) is an important cause of morbidity and mortality for people with HIV (PWH). The molecular factors linked with LD in PWH are varied and incompletely characterized. We performed an epigenome-wide association study (EWAS) to identify associations between DNA methylation (DNAm) and biomarkers of liver function-aspartate transaminase, alanine transaminase, albumin, total bilirubin, platelet count, FIB-4 score, and APRI score-in male United States veterans with HIV. Methods: Blood samples and clinical data were obtained from 960 HIV-infected male PWH from the Veterans Aging Cohort Study. DNAm was assessed using the Illumina 450K or the EPIC 850K array in two mutually exclusive subsets. We performed a meta-analysis for each DNAm site measured by either platform. We also examined the associations between four measures of DNAm age acceleration (AA) and liver biomarkers. Results: Nine DNAm sites were positively associated with serum albumin in the meta-analysis of the EPIC and 450K EWAS after correcting for multiple testing. Four DNAm sites (cg16936953, cg18942579, cg01409343, and cg12054453), annotated within the TMEM49 and four of the remaining five sites (cg18181703, cg03546163, cg20995564, and cg23966214) annotated to SOCS3, FKBP5, ZEB2, and SAMD14 genes, respectively. The DNAm site, cg12992827, was not annotated to any known coding sequence. No significant associations were detected for the other six liver biomarkers. Higher PhenoAA was significantly associated with lower level of serum albumin (β = -0.007, p-value = 8.6 × 10-4, CI: -0.011116, -0.002884). Conclusion: We identified epigenetic associations of both individual DNAm sites and DNAm AA with liver function through serum albumin in men with HIV. Further replication analyses in independent cohorts are warranted to confirm the epigenetic mechanisms underlying liver function and LD in PWH.
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Affiliation(s)
- Boghuma K. Titanji
- Division of Infectious Disease, Emory School of Medicine, Atlanta, GA, United States
| | - Mitch Lee
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Zeyuan Wang
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Junyu Chen
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Qin Hui
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Vincent Lo Re III
- Division of Infectious Diseases Department of Medicine and Center for Clinical Epidemiology and Biostatistics Perelman School of Medicine University of Pennsylvania, Philadelphia, PA, United States
| | - Kaku So-Armah
- Boston University Medical School, Boston, MA, United States
| | - Amy C. Justice
- Connecticut Veteran Health System, West Haven, CT, United States,Yale University School of Medicine, New Haven, CT, United States
| | - Ke Xu
- Connecticut Veteran Health System, West Haven, CT, United States,Yale University School of Medicine, New Haven, CT, United States
| | - Matthew Freiberg
- Cardiovascular Medicine Division and Tennessee Valley Healthcare System, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Marta Gwinn
- Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Vincent C. Marconi
- Division of Infectious Disease, Emory School of Medicine, Atlanta, GA, United States,Atlanta Veterans Affairs Health Care System, Decatur, GA, United States,Hubert Department of Global Health, Rollins School of Public Health, Atlanta, GA, United States,Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, United States
| | - Yan V. Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, United States,Atlanta Veterans Affairs Health Care System, Decatur, GA, United States,*Correspondence: Yan V. Sun,
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Ghanooni D, Carrico AW, Williams R, Glynn TR, Moskowitz JT, Pahwa S, Pallikkuth S, Roach ME, Dilworth S, Aouizerat BE, Flentje A. Sexual Minority Stress and Cellular Aging in Methamphetamine-Using Sexual Minority Men With Treated HIV. Psychosom Med 2022; 84:949-956. [PMID: 35980781 PMCID: PMC9553259 DOI: 10.1097/psy.0000000000001123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 06/22/2022] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Sexual minority men (e.g., gay, bisexual, and other men who have sex with men) experience stigma and sexual minority stress, which are theorized to drive negative health outcomes. Sexual minority men with treated HIV display persistent immune dysregulation, which could be amplified by sexual minority stress responses to potentiate cellular aging. METHODS This cross-sectional study included 52 sexual minority men living with HIV who had undetectable viral load (<40 copies/mL) and biologically confirmed recent methamphetamine use. Participants completed measures assessing sexual minority stress and openness about sexual minority status (i.e., outness). DNA methylation-derived outcomes included the following: the extrinsic epigenetic age acceleration clock, telomere length, naive CD4+ T-helper cells, and naive CD8+ T-cytotoxic/suppressor cells. RESULTS After adjusting for negative affect and recent stimulant use, higher sexual minority stress was associated with a faster extrinsic epigenetic age acceleration clock ( β = 0.29, p = .030), shorter telomere length ( β = -0.43, p = .002), and fewer naive CD4+ (β = -0.57, p < .001) and naive CD8+ T cells ( β = -0.57, p < .001). Greater outness was associated with higher naive CD4+ ( β = 0.32, p = .030) and naive CD8+ T cells ( β = 0.38, p = .008) as well as lower plasma interleukin 6 ( β = -0.33, p = .027). CONCLUSIONS Sexual minority stress processes are associated with markers of cellular aging and inflammation in methamphetamine-using sexual minority men living with HIV. Longitudinal research should elucidate biobehavioral mechanisms linking sexual minority stress processes with accelerated cellular aging in those with and without HIV.
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Titanji BK, Wang Z, Chen J, Hui Q, So-Armah K, Freiberg M, Justice AC, Ke X, Marconi VC, Sun YV. Soluble CD14-associated DNA methylation sites predict mortality among men with HIV infection. AIDS 2022; 36:1563-1571. [PMID: 35979830 PMCID: PMC9394925 DOI: 10.1097/qad.0000000000003279] [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] [Indexed: 02/04/2023]
Abstract
OBJECTIVES Elevated plasma levels of sCD14 predict all-cause mortality in people with HIV (PWH). Epigenetic regulation plays a key role in infection and inflammation. To reveal the epigenetic relationships between sCD14, immune function and disease progression among PWH, we conducted an epigenome-wide association study (EWAS) of sCD14 and investigated the relationship with mortality. DESIGN AND METHODS DNA methylation (DNAm) levels of peripheral blood samples from PWH in the Veterans Aging Cohort Study (VACS) were measured using the Illumina Infinium Methylation 450K (n = 549) and EPIC (850K) BeadChip (n = 526). Adjusted for covariates and multiple testing, we conducted an epigenome-wide discovery, replication, and meta-analysis to identify significant associations with sCD14. We then examined and replicated the relationship between the principal epigenetic sites and survival using Cox regression models. FINDINGS We identified 118 DNAm sites significantly associated with sCD14 in the meta-analysis of 1075 PWH. The principal associated DNAm sites mapped to genes (e.g. STAT1, PARP9, IFITM1, MX1, and IFIT1) related to inflammation and antiviral response. Adjusting for multiple testing, 10 of 118 sCD14-associated DNAm sites significantly predicted survival time conditional on sCD14 levels. CONCLUSION The identification of DNAm sites independently predicting survival may improve our understanding of prognosis and potential therapeutic targets among PWH.
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Affiliation(s)
- Boghuma K Titanji
- Division of Infectious Diseases, Emory University School of Medicine
| | - Zeyuan Wang
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA
| | - Junyu Chen
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA
| | - Qin Hui
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA
| | | | - Matthew Freiberg
- Cardiovascular Medicine Division and Tennessee Valley Healthcare System, Vanderbilt University Medical Center, Nashville, TN
| | - Amy C Justice
- Yale University School of Medicine, New Haven
- Connecticut Veteran Health System, West Haven, CT
| | - Xu Ke
- Yale University School of Medicine, New Haven
- Connecticut Veteran Health System, West Haven, CT
| | - Vincent C Marconi
- Division of Infectious Diseases, Emory University School of Medicine
- Atlanta Veterans Affairs Healthcare System, Decatur
- Hubert Department of Global Health, Rollins School of Public Health
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Yan V Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA
- Atlanta Veterans Affairs Healthcare System, Decatur
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11
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Epigenome-wide association analyses of active injection drug use. Drug Alcohol Depend 2022; 235:109431. [PMID: 35395503 DOI: 10.1016/j.drugalcdep.2022.109431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 02/28/2022] [Accepted: 03/21/2022] [Indexed: 11/20/2022]
Abstract
BACKGROUND Injection drug use (IDU) is prevalent in the US and is associated with substantial risk of blood-borne infections, morbidity, and mortality. However, the spectrum of its biologic effects on DNA methylation in blood is not well characterized. METHODS 401 participants (Mage = 47.9; 68% male; 90% African American) over several timepoints (1054 visits) were drawn from a longitudinal cohort of people who inject drugs. DNA methylation was measured among buffy coat samples from the 1054 visits. Compared to samples collected after ≥ 6 months of abstinence, separate EWAS were conducted for active injecting of any drug, quantitative injection frequency, injecting of heroin and injecting of cocaine. Linear mixed effect models were used and analyses were adjusted for repeated measurements and key technical, biological, and sociodemographic characteristics. RESULTS We found epigenome-wide significant CpG sites associated with active injection (cg10636246, AIM2, p = 2.33 × 10-8) and injection intensity (cg13117953, p = 4.30 × 10-8). We found converging evidence that cg10636246 (AIM2), cg23110600 (PRKCH), cg03546163 (FKBP5), cg04590956 (GMCL1), and cg16317961 (MAPRE2) were among the top 0.1% significantly differentially methylated CpG sites shared across the five EWAS. Top ranked CpGs among the five EWAS were enriched (p < 0.0001) in AIM2 inflammasome complex, T cell migration, insulin regulation and epinephrine synthesis pathways. During periods of active injection, samples had 0.46 years of epigenetic age acceleration relative to the abstinence period, within the same subject (p = 0.03). CONCLUSIONS Findings from this study demonstrate modest, common, and specific effects on DNA methylation during a relatively short time between periods of active drug injection and abstinence.
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12
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Liang X, Sinha R, Justice AC, Cohen MH, Aouizerat BE, Xu K. A new monocyte epigenetic clock reveals nonlinear effects of alcohol consumption on biological aging in three independent cohorts (N = 2242). Alcohol Clin Exp Res 2022; 46:736-748. [PMID: 35257385 PMCID: PMC9117474 DOI: 10.1111/acer.14803] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 02/02/2023]
Abstract
BACKGROUND Assessing the effect of alcohol consumption on biological age is essential for understanding alcohol use-related comorbidities and mortality. Previously developed epigenetic clocks are mainly based on DNA methylation in heterogeneous cell types, which provide limited knowledge on the impacts of alcohol consumption at the individual cellular level. Evidence shows that monocytes play an important role in both alcohol-induced pathophysiology and the aging process. In this study, we developed a novel monocyte-based DNA methylation clock (MonoDNAmAge) to assess the impact of alcohol consumption on monocyte age. METHODS A machine learning method was applied to select a set of chronological age-associated DNA methylation CpG sites from 1202 monocyte methylomes. Pearson correlation was tested between MonoDNAmAge and chronological age in three independent cohorts (Ntotal = 2242). Using the MonoDNAmAge clock and four established clocks (i.e., HorvathDNAmAge, HannumDNAmAge, PhenoDNAmAge, GrimDNAmAge), we then evaluated the effect of alcohol consumption on epigenetic aging in the three cohorts [i.e., Yale Stress Center Community Study (YSCCS), Veteran Aging Cohort Study (VACS), Women's Interagency HIV Study (WIHS)] using linear and quadratic models. RESULTS The MonoDNAmAge, comprised of 186 CpG sites, was moderately to strongly correlated with chronological age in the three cohorts (r = 0.90, p = 3.12E-181 in YSCCS; r = 0.54, p = 1.75E-96 in VACS; r = 0.66, p = 1.50E-60 in WIHS). More importantly, we found a nonlinear association between MonoDNAmAge and alcohol consumption (pmodel = 4.55E-08, px2 = 7.80E-08 in YSCCS; pmodel = 1.85E-02, px2 = 3.46E-02 in VACS). Heavy alcohol consumption increased EAAMonoDNAmAge up to 1.60 years while light alcohol consumption decreased EAAMonoDNAmAge up to 2.66 years. These results were corroborated by the four established epigenetic clocks (i.e., HorvathDNAmAge, HannumDNAmAge, PhenoDNAmAge, GrimDNAmAge). CONCLUSIONS The results suggest a nonlinear relationship between alcohol consumption and its effects on epigenetic age. Considering adverse effects of alcohol consumption on health, nonlinear effects of alcohol use should be interpreted with caution. The findings, for the first time, highlight the complex effects of alcohol consumption on biological aging.
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Affiliation(s)
- Xiaoyu Liang
- Department of PsychiatryYale School of MedicineNew HavenConnecticutUSA,VA Connecticut Healthcare SystemWest HavenConnecticutUSA,Department of Preventive MedicineUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Rajita Sinha
- Department of PsychiatryYale School of MedicineNew HavenConnecticutUSA,Child Study CenterYale School of MedicineNew HavenConnecticutUSA,Department of NeuroscienceYale School of MedicineNew HavenConnecticutUSA
| | - Amy C. Justice
- VA Connecticut Healthcare SystemWest HavenConnecticutUSA,Yale University School of MedicineNew Haven Veterans Affairs Connecticut Healthcare SystemNew HavenConnecticutUSA
| | - Mardge H. Cohen
- Department of MedicineStroger Hospital of Cook CountyChicagoIllinoisUSA
| | - Bradley E. Aouizerat
- Bluestone Center for Clinical ResearchCollege of DentistryNew York UniversityNew YorkNew YorkUSA,Department of Oral and Maxillofacial SurgeryCollege of DentistryNew York UniversityNew YorkNew YorkUSA
| | - Ke Xu
- Department of PsychiatryYale School of MedicineNew HavenConnecticutUSA,VA Connecticut Healthcare SystemWest HavenConnecticutUSA
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13
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Li B, Aouizerat BE, Cheng Y, Anastos K, Justice AC, Zhao H, Xu K. Incorporating local ancestry improves identification of ancestry-associated methylation signatures and meQTLs in African Americans. Commun Biol 2022; 5:401. [PMID: 35488087 PMCID: PMC9054854 DOI: 10.1038/s42003-022-03353-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 04/11/2022] [Indexed: 12/03/2022] Open
Abstract
Here we report three epigenome-wide association studies (EWAS) of DNA methylation on self-reported race, global genetic ancestry, and local genetic ancestry in admixed Americans from three sets of samples, including internal and external replications (Ntotal = 1224). Our EWAS on local ancestry (LA) identified the largest number of ancestry-associated DNA methylation sites and also featured the highest replication rate. Furthermore, by incorporating ancestry origins of genetic variations, we identified 36 methylation quantitative trait loci (meQTL) clumps for LA-associated CpGs that cannot be captured by a model that assumes identical genetic effects across ancestry origins. Lead SNPs at 152 meQTL clumps had significantly different genetic effects in the context of an African or European ancestry background. Local ancestry information enables superior capture of ancestry-associated methylation signatures and identification of ancestry-specific genetic effects on DNA methylation. These findings highlight the importance of incorporating local ancestry for EWAS in admixed samples from multi-ancestry cohorts.
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Affiliation(s)
- Boyang Li
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, United States
- VA Connecticut Healthcare System, US Department of Veterans Affairs, West Haven, CT, United States
| | - Bradley E Aouizerat
- Bluestone Center for Clinical Research, New York University, New York, NY, United States
- Department of Oral and Maxillofacial Surgery, New York University, New York, NY, United States
| | - Youshu Cheng
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, United States
| | - Kathryn Anastos
- Division of General Internal Medicine, Albert Einstein College of Medicine, Montefiore Health System, Bronx, NY, United States
| | - Amy C Justice
- VA Connecticut Healthcare System, US Department of Veterans Affairs, West Haven, CT, United States
- Department of Health Policy and Management, Yale University, New Haven, CT, United States
| | - Hongyu Zhao
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, United States.
- VA Connecticut Healthcare System, US Department of Veterans Affairs, West Haven, CT, United States.
| | - Ke Xu
- VA Connecticut Healthcare System, US Department of Veterans Affairs, West Haven, CT, United States.
- Department of Psychiatry, School of Medicine, Yale University, New Haven, CT, United States.
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14
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Tran T, Pencina KM, Schultz MB, Li Z, Ghattas C, Lau J, Sinclair DA, Montano M. Reduced Levels of NAD in Skeletal Muscle and Increased Physiologic Frailty Are Associated With Viral Coinfection in Asymptomatic Middle-Aged Adults. J Acquir Immune Defic Syndr 2022; 89:S15-S22. [PMID: 35015741 PMCID: PMC8751286 DOI: 10.1097/qai.0000000000002852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND People living with HIV (PLWH) are disproportionately burdened with multimorbidity and decline in physiologic function compared with their uninfected counterparts, but biological mechanisms that differentially contribute to the decline in muscle function in PLWH compared with uninfected people remain understudied. SETTING The study site was Brigham and Women's Hospital, Harvard Medical School, Boston, MA. METHODS We evaluated skeletal muscle tissue for levels of total nicotinamide adenine dinucleotide (NAD), NAD+, and nicotinamide adenine dinucleotide (NADH) in middle-aged asymptomatic PLWH, coinfected with hepatitis C virus and/or cytomegalovirus and compared them with uninfected control participants. RESULTS Of the 54 persons with muscle biopsy data, the mean age was 57 years with 33% women. Total NAD levels declined in skeletal muscle in association with HIV infection and was exacerbated by hepatitis C virus and cytomegalovirus coinfection, with lowest levels of total NAD, NAD+, and NADH among persons who were coinfected with all 3 viruses (P = 0.015, P = 0.014, and P = 0.076, respectively). Levels of total NAD, NAD+, and NADH in skeletal muscle were inversely associated with inflammation (P = 0.014, P = 0.013, and P = 0.055, respectively). Coinfections were also associated with measures of inflammation (CD4/CD8 ratio: P < 0.001 and sCD163: P < 0.001) and immune activation (CD38 and human leukocyte antigen-DR expression on CD8 T cells: P < 0.001). In addition, coinfection was associated with increased physiologic frailty based on the Veteran Aging Cohort Study 1.0 index assessment (P = 0.001). CONCLUSIONS Further research is warranted to determine the clinical relevance of preclinical deficits in NAD metabolites in skeletal muscle in association with viral coinfection and inflammation, as well as the observed association between viral coinfection and physiologic frailty.
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Affiliation(s)
- Thanh Tran
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Men's Health: Aging and Metabolism, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Karol M. Pencina
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Men's Health: Aging and Metabolism, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Boston Claude D. Pepper Older Americans Independence Center, Boston, MA; and
| | - Michael B. Schultz
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Labs for the Biology of Aging, Harvard Medical School, Boston, MA
| | - Zhuoying Li
- Men's Health: Aging and Metabolism, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Catherine Ghattas
- Men's Health: Aging and Metabolism, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Jackson Lau
- Men's Health: Aging and Metabolism, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - David A. Sinclair
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Labs for the Biology of Aging, Harvard Medical School, Boston, MA
| | - Monty Montano
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Men's Health: Aging and Metabolism, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Boston Claude D. Pepper Older Americans Independence Center, Boston, MA; and
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15
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Titanji BK, Gwinn M, Marconi VC, Sun YV. Epigenome-wide epidemiologic studies of human immunodeficiency virus infection, treatment, and disease progression. Clin Epigenetics 2022; 14:8. [PMID: 35016709 PMCID: PMC8750639 DOI: 10.1186/s13148-022-01230-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 01/06/2022] [Indexed: 12/12/2022] Open
Abstract
Despite significant advances in the treatment and care of people with HIV (PWH), several challenges remain in our understanding of disease pathogenesis to improve patient care. HIV infection can modify the host epigenome and as such can impact disease progression, as well as the molecular processes driving non-AIDS comorbidities in PWH. Epigenetic epidemiologic studies including epigenome-wide association studies (EWAS) offer a unique set of tools to expand our understanding of HIV disease and to identify novel strategies applicable to treatment and diagnosis in this patient population. In this review, we summarize the current state of knowledge from epigenetic epidemiologic studies of PWH, identify the main challenges of this approach, and highlight future directions for the field. Emerging epigenetic epidemiologic studies of PWH can expand our understanding of HIV infection and health outcomes, improve scientific validity through collaboration and replication, and increase the coverage of diverse populations affected by the global HIV pandemic. Through this review, we hope to highlight the potential of EWAS as a tool for HIV research and to engage more investigators to explore its application to important research questions.
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Affiliation(s)
- Boghuma K Titanji
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Marta Gwinn
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road NE #3049, Atlanta, GA, 30322, USA
| | - Vincent C Marconi
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA.,Atlanta Veterans Affairs Health Care System, Decatur, GA, USA.,Hubert Department of Global Health, Rollins School of Public Health, Atlanta, GA, USA.,Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Yan V Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road NE #3049, Atlanta, GA, 30322, USA. .,Atlanta Veterans Affairs Health Care System, Decatur, GA, USA.
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16
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Corley MJ, Sacdalan C, Pang APS, Chomchey N, Ratnaratorn N, Valcour V, Kroon E, Cho KS, Belden AC, Colby D, Robb M, Hsu D, Spudich S, Paul R, Vasan S, Ndhlovu LC, the SEARCH010/RV254 and SEARCH013/RV304 study groups. Abrupt and altered cell-type specific DNA methylation profiles in blood during acute HIV infection persists despite prompt initiation of ART. PLoS Pathog 2021; 17:e1009785. [PMID: 34388205 PMCID: PMC8386872 DOI: 10.1371/journal.ppat.1009785] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/25/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
HIV-1 disrupts the host epigenetic landscape with consequences for disease pathogenesis, viral persistence, and HIV-associated comorbidities. Here, we examined how soon after infection HIV-associated epigenetic changes may occur in blood and whether early initiation of antiretroviral therapy (ART) impacts epigenetic modifications. We profiled longitudinal genome-wide DNA methylation in monocytes and CD4+ T lymphocytes from 22 participants in the RV254/SEARCH010 acute HIV infection (AHI) cohort that diagnoses infection within weeks after estimated exposure and immediately initiates ART. We identified monocytes harbored 22,697 differentially methylated CpGs associated with AHI compared to 294 in CD4+ T lymphocytes. ART minimally restored less than 1% of these changes in monocytes and had no effect upon T cells. Monocyte DNA methylation patterns associated with viral load, CD4 count, CD4/CD8 ratio, and longitudinal clinical phenotypes. Our findings suggest HIV-1 rapidly embeds an epigenetic memory not mitigated by ART and support determining epigenetic signatures in precision HIV medicine. Trial Registration:NCT00782808 and NCT00796146. The epigenetic marker, DNA methylation, plays a key role regulating the immune system during host-pathogen interactions. Using cell-type specific DNA methylation profiling, we explored whether epigenetic changes occurred soon after HIV infection and following early treatment with anti-HIV drugs. Acute infection was associated with early DNA methylation changes in purified monocytes and CD4+ T cells isolated from blood. In monocytes, rapid anti-HIV treatment minimally restored DNA methylation changes associated with infection and unexpectedly had no impact in CD4+ T cells. DNA methylation patterns before treatment informed long term clinical outcomes including CD4+ T cell counts and favorable clinical phenotypes. These findings identify candidates for consideration in epigenome editing approaches in HIV prevention, treatment, and cure strategies.
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Affiliation(s)
- Michael J. Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine; New York, New York, United States of America
| | - Carlo Sacdalan
- Institute of HIV Research and Innovation; Bangkok, Thailand
- SEARCH, South East Asia Research Collaboration in HIV; Bangkok, Thailand
| | - Alina P. S. Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine; New York, New York, United States of America
| | - Nitiya Chomchey
- Institute of HIV Research and Innovation; Bangkok, Thailand
- SEARCH, South East Asia Research Collaboration in HIV; Bangkok, Thailand
| | | | - Victor Valcour
- Memory and Aging Center, University of California San Francisco; San Francisco, California, United States of America
| | - Eugene Kroon
- Institute of HIV Research and Innovation; Bangkok, Thailand
- SEARCH, South East Asia Research Collaboration in HIV; Bangkok, Thailand
| | - Kyu S. Cho
- Missouri Institute of Mental Health University of Missouri; St. Louis, Missouri, United States of America
| | - Andrew C. Belden
- Missouri Institute of Mental Health University of Missouri; St. Louis, Missouri, United States of America
| | - Donn Colby
- Institute of HIV Research and Innovation; Bangkok, Thailand
- SEARCH, South East Asia Research Collaboration in HIV; Bangkok, Thailand
| | - Merlin Robb
- Armed Forces Research Institute of Medical Sciences; Bangkok, Thailand
- Henry M. Jackson Foundation for the Advancement of Military Medicine; Bethesda, Maryland, United States of America
| | - Denise Hsu
- Armed Forces Research Institute of Medical Sciences; Bangkok, Thailand
- Henry M. Jackson Foundation for the Advancement of Military Medicine; Bethesda, Maryland, United States of America
| | - Serena Spudich
- Department of Neurology, Yale University; New Haven, Connecticut, United States of America
| | - Robert Paul
- Missouri Institute of Mental Health University of Missouri; St. Louis, Missouri, United States of America
| | - Sandhya Vasan
- Henry M. Jackson Foundation for the Advancement of Military Medicine; Bethesda, Maryland, United States of America
- US Military HIV Research Program; Silver Spring, Maryland, United States of America
| | - Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine; New York, New York, United States of America
- * E-mail:
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17
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Liang X, Justice AC, So-Armah K, Krystal JH, Sinha R, Xu K. DNA methylation signature on phosphatidylethanol, not on self-reported alcohol consumption, predicts hazardous alcohol consumption in two distinct populations. Mol Psychiatry 2021; 26:2238-2253. [PMID: 32034291 PMCID: PMC8440221 DOI: 10.1038/s41380-020-0668-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 12/20/2019] [Accepted: 01/28/2020] [Indexed: 12/28/2022]
Abstract
The process of diagnosing hazardous alcohol drinking (HAD) is based on self-reported data and is thereby vulnerable to bias. There has been an interest in developing epigenetic biomarkers for HAD that might complement clinical assessment. Because alcohol consumption has been previously linked to DNA methylation (DNAm), we aimed to select DNAm signatures in blood to predict HAD from two demographically and clinically distinct populations (Ntotal = 1,549). We first separately conducted an epigenome-wide association study (EWAS) for phosphatidylethanol (PEth), an objective measure of alcohol consumption, and for self-reported alcohol consumption in Cohort 1. We identified 83 PEth-associated CpGs, including 23 CpGs previously associated with alcohol consumption or alcohol use disorder. In contrast, no CpG reached epigenome-wide significance on self-reported alcohol consumption. Using a machine learning approach, two CpG subsets from EWAS on PEth and on self-reported alcohol consumption from Cohort 1 were separately tested for the prediction of HAD in Cohort 2. We found that a subset of 143 CpGs selected from the EWAS on PEth showed an excellent prediction of HAD with the area under the receiver operating characteristic curve (AUC) of 89.4% in training set and 73.9% in validation set of Cohort 2. However, CpGs preselected from the EWAS on self-reported alcohol consumption showed a poor prediction of HAD with AUC 75.2% in training set and 57.6% in validation set. Our results demonstrate that an objective measure for alcohol consumption is a more informative phenotype than self-reported data for revealing epigenetic mechanisms. The PEth-associated DNAm signature in blood could serve as a robust biomarker for alcohol consumption.
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Affiliation(s)
- Xiaoyu Liang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Amy C Justice
- VA Connecticut Healthcare System, West Haven, CT, USA
- Yale School of Medicine, New Haven, CT, USA
| | - Kaku So-Armah
- Boston University School of Medicine, Boston, MA, USA
| | - John H Krystal
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Rajita Sinha
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA
- Child Study Center, Yale School of Medicine, New Haven, CT, USA
- Stress Center, Yale School of Medicine, New Haven, CT, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.
- VA Connecticut Healthcare System, West Haven, CT, USA.
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18
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Moron-Lopez S, Urrea V, Dalmau J, Lopez M, Puertas MC, Ouchi D, Gómez A, Passaes C, Mothe B, Brander C, Saez-Cirion A, Clotet B, Esteller M, Berdasco M, Martinez-Picado J. The Genome-wide Methylation Profile of CD4+ T Cells From Individuals With Human Immunodeficiency Virus (HIV) Identifies Distinct Patterns Associated With Disease Progression. Clin Infect Dis 2021; 72:e256-e264. [PMID: 32712664 PMCID: PMC8096268 DOI: 10.1093/cid/ciaa1047] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/21/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Human genetic variation-mostly in the human leukocyte antigen (HLA) and C-C chemokine receptor type 5 (CCR5) regions-explains 25% of the variability in progression of human immunodeficiency virus (HIV) infection. However, it is also known that viral infections can modify cellular DNA methylation patterns. Therefore, changes in the methylation of cytosine-guanine (CpG) islands might modulate progression of HIV infection. METHODS In total, 85 samples were analyzed: 21 elite controllers (EC), 21 subjects with HIV before combination antiretroviral therapy (cART) (viremic, 93 325 human immunodeficiency virus type 1 [HIV-1] RNA copies/mL) and under suppressive cART (cART, median of 17 months, <50 HIV-1 RNA copies/mL), and 22 HIV-negative donors (HIVneg). We analyzed the methylation pattern of 485 577 CpG in DNA from peripheral CD4+ T lymphocytes. We selected the most differentially methylated gene (TNF) and analyzed its specific methylation, messenger RNA (mRNA) expression, and plasma protein levels in 5 individuals before and after initiation of cART. RESULTS We observed 129 methylated CpG sites (associated with 43 gene promoters) for which statistically significant differences were recorded in viremic versus HIVneg, 162 CpG sites (55 gene promoters) in viremic versus cART, 441 CpG sites (163 gene promoters) in viremic versus EC, but none in EC versus HIVneg. The TNF promoter region was hypermethylated in viremic versus HIVneg, cART, and EC. Moreover, we observed greater plasma levels of TNF in viremic individuals than in EC, cART, and HIVneg. CONCLUSIONS Our study shows that genome methylation patterns vary depending on HIV infection status and progression profile and that these variations might have an impact on controlling HIV infection in the absence of cART.
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Affiliation(s)
| | - Victor Urrea
- AIDS Research Institute IrsiCaixa, Badalona, Spain
| | | | - Miguel Lopez
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, Barcelona, Spain.,Epigenetic Therapies Group, Experimental and Clinical Hematology Program, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | | | - Dan Ouchi
- AIDS Research Institute IrsiCaixa, Badalona, Spain
| | - Antonio Gómez
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, Barcelona, Spain
| | - Caroline Passaes
- Institut Pasteur, Unité HIV, Inflammation et Persistence, Paris, France
| | - Beatriz Mothe
- AIDS Research Institute IrsiCaixa, Badalona, Spain.,Fundació Lluita Contra la Sida, University Hospital "Germans Trias i Pujol," Badalona, Spain.,University of Vic-Central University of Catalonia (UVic-UCC), Barcelona, Spain
| | - Christian Brander
- AIDS Research Institute IrsiCaixa, Badalona, Spain.,University of Vic-Central University of Catalonia (UVic-UCC), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Asier Saez-Cirion
- Institut Pasteur, Unité HIV, Inflammation et Persistence, Paris, France
| | - Bonaventura Clotet
- AIDS Research Institute IrsiCaixa, Badalona, Spain.,Fundació Lluita Contra la Sida, University Hospital "Germans Trias i Pujol," Badalona, Spain.,University of Vic-Central University of Catalonia (UVic-UCC), Barcelona, Spain
| | - Manel Esteller
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.,Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain.,Centro de Investigación Biomédica en Red Cancer (CIBERONC), Madrid, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Badalona, Spain
| | - Maria Berdasco
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, Barcelona, Spain.,Epigenetic Therapies Group, Experimental and Clinical Hematology Program, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Javier Martinez-Picado
- AIDS Research Institute IrsiCaixa, Badalona, Spain.,University of Vic-Central University of Catalonia (UVic-UCC), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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19
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Castro de Moura M, Davalos V, Planas-Serra L, Alvarez-Errico D, Arribas C, Ruiz M, Aguilera-Albesa S, Troya J, Valencia-Ramos J, Vélez-Santamaria V, Rodríguez-Palmero A, Villar-Garcia J, Horcajada JP, Albu S, Casasnovas C, Rull A, Reverte L, Dietl B, Dalmau D, Arranz MJ, Llucià-Carol L, Planas AM, Pérez-Tur J, Fernandez-Cadenas I, Villares P, Tenorio J, Colobran R, Martin-Nalda A, Soler-Palacin P, Vidal F, Pujol A, Esteller M. Epigenome-wide association study of COVID-19 severity with respiratory failure. EBioMedicine 2021; 66:103339. [PMID: 33867313 PMCID: PMC8047083 DOI: 10.1016/j.ebiom.2021.103339] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/16/2021] [Accepted: 03/26/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the coronavirus disease 2019 (COVID-19), exhibit a wide spectrum of disease behaviour. Since DNA methylation has been implicated in the regulation of viral infections and the immune system, we performed an epigenome-wide association study (EWAS) to identify candidate loci regulated by this epigenetic mark that could be involved in the onset of COVID-19 in patients without comorbidities. METHODS Peripheral blood samples were obtained from 407 confirmed COVID-19 patients ≤ 61 years of age and without comorbidities, 194 (47.7%) of whom had mild symptomatology that did not involve hospitalization and 213 (52.3%) had a severe clinical course that required respiratory support. The set of cases was divided into discovery (n = 207) and validation (n = 200) cohorts, balanced for age and sex of individuals. We analysed the DNA methylation status of 850,000 CpG sites in these patients. FINDINGS The DNA methylation status of 44 CpG sites was associated with the clinical severity of COVID-19. Of these loci, 23 (52.3%) were located in 20 annotated coding genes. These genes, such as the inflammasome component Absent in Melanoma 2 (AIM2) and the Major Histocompatibility Complex, class I C (HLA-C) candidates, were mainly involved in the response of interferon to viral infection. We used the EWAS-identified sites to establish a DNA methylation signature (EPICOVID) that is associated with the severity of the disease. INTERPRETATION We identified DNA methylation sites as epigenetic susceptibility loci for respiratory failure in COVID-19 patients. These candidate biomarkers, combined with other clinical, cellular and genetic factors, could be useful in the clinical stratification and management of patients infected with the SARS-CoV-2. FUNDING The Unstoppable campaign of the Josep Carreras Leukaemia Foundation, the Cellex Foundation and the CERCA Programme/Generalitat de Catalunya.
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Affiliation(s)
- Manuel Castro de Moura
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Catalonia, Spain
| | - Veronica Davalos
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Catalonia, Spain
| | - Laura Planas-Serra
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Damiana Alvarez-Errico
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Catalonia, Spain
| | - Carles Arribas
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Catalonia, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | | | - Jesús Troya
- Infanta Leonor University Hospital, Madrid, Spain
| | | | - Valentina Vélez-Santamaria
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain; Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Agustí Rodríguez-Palmero
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain; University Hospital Germans Trias i Pujol, Badalona, Barcelona, Catalonia, Spain
| | - Judit Villar-Garcia
- Hospital del Mar - IMIM Biomedical Research Institute, Barcelona, Catalonia, Spain
| | - Juan P Horcajada
- Hospital del Mar - IMIM Biomedical Research Institute, Barcelona, Catalonia, Spain
| | - Sergiu Albu
- Institut Guttmann Foundation, Badalona, Barcelona, Catalonia, Spain
| | - Carlos Casasnovas
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain; Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Anna Rull
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - Laia Reverte
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - Beatriz Dietl
- Servei de malalties infeccioses Hospital Universitari MutuaTerrassa, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - David Dalmau
- MutuaTerrassa Research and Innovation Foundation, HIV/AIDS Unit Hospital Universitari MutuaTerrassa, University of Barcelona, Barcelona, Catalonia, Spain
| | - Maria J Arranz
- Fundaciò Docència i Recerca Mutua Terrassa i Hospital Universitari Mutua Terrassa, Barcelona, Catalonia, Spain
| | - Laia Llucià-Carol
- Stroke Pharmacogenomics and Genetics Group, Sant Pau Institute of Research, Sant Pau Hospital, Barcelona, Catalonia, Spain
| | - Anna M Planas
- Department of Brain Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona (IIBB), Consejo Superior de Investigaciones Científicas (CSIC), Area of Neurosciences, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
| | - Jordi Pérez-Tur
- Institut de Biomedicina de València-CSIC, CIBERNED, Unitat Mixta de Neurologia i Genètica, IIS La Fe, Vallencia, Spain
| | - Israel Fernandez-Cadenas
- Stroke Pharmacogenomics and Genetics Group, Sant Pau Institute of Research, Sant Pau Hospital, Barcelona, Catalonia, Spain
| | - Paula Villares
- Internal Medicine Department, Hospital HM Sanchinarro, HM Hospitales, Madrid, Spain
| | - Jair Tenorio
- INGEMM-Instituto de Genética Médica y Molecular, Hospital Universitario La Paz, Madrid, Spain; Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Roger Colobran
- Immunology Division, Genetics Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Vall d'Hebron Barcelona Hospital Campus, UAB, Barcelona, Catalonia, Spain
| | - Andrea Martin-Nalda
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Pere Soler-Palacin
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Francesc Vidal
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain; Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Catalonia, Spain.
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20
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Shu C, Jaffe AE, Sabunciyan S, Ji H, Astemborski J, Sun J, Bakulski KM, Mehta SH, Kirk GD, Maher BS. Epigenome-wide association scan identifies methylation sites associated with HIV infection. Epigenomics 2020; 12:1917-1927. [PMID: 33232214 DOI: 10.2217/epi-2020-0123] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim: To investigate the role of epigenetics in HIV pathophysiology. Materials & methods: We conducted an epigenome-wide association scan on HIV infection status among people who inject drugs in the AIDS Linked to the IntraVenous Experience study with primary (n = 397) and validation samples (n = 390). DNA methylation from blood was measured by the Illumina EPIC BeadChip. We controlled for cell type heterogeneity by HIV status. Results: HIV infection status was associated (p < 10-8) with DNA methylation at 49 CpG sites. Sites were enriched in response to virus, interferon signaling pathway, etc. Among these sites, discovery and validation t-statistics were highly correlated (r = 0.96). Conclusion: In a cohort of people who inject drugs, HIV status was associated with differential DNA methylation at biologically meaningful sites.
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Affiliation(s)
- Chang Shu
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.,Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Andrew E Jaffe
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.,Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Sarven Sabunciyan
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Jacquie Astemborski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Jing Sun
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shruti H Mehta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Gregory D Kirk
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Brion S Maher
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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21
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Shu C, Zhang X, Aouizerat BE, Xu K. Comparison of methylation capture sequencing and Infinium MethylationEPIC array in peripheral blood mononuclear cells. Epigenetics Chromatin 2020; 13:51. [PMID: 33228774 PMCID: PMC7684759 DOI: 10.1186/s13072-020-00372-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/02/2020] [Indexed: 11/11/2022] Open
Abstract
Background Epigenome-wide association studies (EWAS) have been widely applied to identify methylation CpG sites associated with human disease. To date, the Infinium MethylationEPIC array (EPIC) is commonly used for high-throughput DNA methylation profiling. However, the EPIC array covers only 30% of the human methylome. Methylation Capture bisulfite sequencing (MC-seq) captures target regions of methylome and has advantages of extensive coverage in the methylome at an affordable price. Methods Epigenome-wide DNA methylation in four peripheral blood mononuclear cell samples was profiled by using SureSelectXT Methyl-Seq for MC-seq and EPIC platforms separately. CpG site-based reproducibility of MC-seq was assessed with DNA sample inputs ranging in quantity of high (> 1000 ng), medium (300–1000 ng), and low (150 ng–300 ng). To compare the performance of MC-seq and the EPIC arrays, we conducted a Pearson correlation and methylation value difference at each CpG site that was detected by both MC-seq and EPIC. We compared the percentage and counts in each CpG island and gene annotation between MC-seq and the EPIC array. Results After quality control, an average of 3,708,550 CpG sites per sample were detected by MC-seq with DNA quantity > 1000 ng. Reproducibility of DNA methylation in MC-seq-detected CpG sites was high among samples with high, medium, and low DNA inputs (r > 0.96). The EPIC array captured an average of 846,464 CpG sites per sample. Compared with the EPIC array, MC-seq detected more CpGs in coding regions and CpG islands. Among the 472,540 CpG sites captured by both platforms, methylation of a majority of CpG sites was highly correlated in the same sample (r: 0.98–0.99). However, methylation for a small proportion of CpGs (N = 235) differed significantly between the two platforms, with differences in beta values of greater than 0.5. Conclusions Our results show that MC-seq is an efficient and reliable platform for methylome profiling with a broader coverage of the methylome than the array-based platform. Although methylation measurements in majority of CpGs are highly correlated, a number of CpG sites show large discrepancy between the two platforms, which warrants further investigation and needs cautious interpretation.
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Affiliation(s)
- Chang Shu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, 06516, USA.,Connecticut Veteran Healthcare System, West Haven, CT, 06515, USA
| | - Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, 06516, USA.,Connecticut Veteran Healthcare System, West Haven, CT, 06515, USA
| | - Bradley E Aouizerat
- Bluestone Center for Clinical Research, College of Dentistry, New York University, New York, 10010, USA.,Department of Oral and Maxillofacial Surgery, College of Dentistry, Yale School of Medicine, New York University, New York, 10010, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, 06516, USA. .,Connecticut Veteran Healthcare System, West Haven, CT, 06515, USA.
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22
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Yang CX, Schon E, Obeidat M, Kobor MS, McEwen L, MacIsaac J, Lin D, Novak RM, Hudson F, Klinker H, Dharan N, Horvath S, Bourbeau J, Tan W, Sin DD, Man SFP, Kunisaki K, Leung JM. Occurrence of Accelerated Epigenetic Aging and Methylation Disruptions in Human Immunodeficiency Virus Infection Before Antiretroviral Therapy. J Infect Dis 2020; 223:1681-1689. [PMID: 32959881 DOI: 10.1093/infdis/jiaa599] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Whether accelerated aging develops over the course of chronic human immunodeficiency virus (HIV) infection or can be observed before significant immunosuppression on is unknown. We studied DNA methylation in blood to estimate cellular aging in persons living with HIV (PLWH) before the initiation of antiretroviral therapy (ART). METHODS A total of 378 ART-naive PLWH who had CD4 T-cell counts >500/µL and were enrolled in the Strategic Timing of Antiretroviral Therapy trial (Pulmonary Substudy) were compared with 34 HIV-negative controls. DNA methylation was performed using the Illumina MethylationEPIC BeadChip. Differentially methylated positions (DMPs) and differentially methylated regions (DMRs) in PLWH compared with controls were identified using a robust linear model. Methylation age was calculated using a previously described epigenetic clock. RESULTS There were a total of 56 639 DMPs and 6103 DMRs at a false discovery rate of <0.1. The top 5 DMPs corresponded to genes NLRC5, VRK2, B2M, and GPR6 and were highly enriched for cancer-related pathways. PLWH had significantly higher methylation age than HIV-negative controls (P = .001), with black race, low CD4 and high CD8 T-cell counts, and duration of HIV being risk factors for age acceleration. CONCLUSIONS PLWH before the initiation of ART and with preserved immune status show evidence of advanced methylation aging.
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Affiliation(s)
- Chen Xi Yang
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | - Emma Schon
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ma'en Obeidat
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada.,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lisa McEwen
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julie MacIsaac
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Lin
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Richard M Novak
- Section of Infectious Diseases, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Fleur Hudson
- MRC Clinical Trials Unit, University College London, London, United Kingdom
| | - Hartwig Klinker
- University of Würzburg Medical Center, Department of Internal Medicine II, Division of Infectious Diseases, Würzburg, Germany
| | | | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Jean Bourbeau
- Respiratory Epidemiology and Clinical Research Unit, McGill University, Montreal, Quebec, Canada
| | - Wan Tan
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada.,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Don D Sin
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada.,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - S F Paul Man
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada.,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ken Kunisaki
- Minneapolis Veterans Affairs Health Care System, Section of Pulmonary, Critical Care and Sleep Medicine, Minneapolis, Minnesota, USA.,Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Janice M Leung
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada.,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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23
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Shu C, Justice AC, Zhang X, Wang Z, Hancock DB, Johnson EO, Xu K. DNA methylation mediates the effect of cocaine use on HIV severity. Clin Epigenetics 2020; 12:140. [PMID: 32928285 PMCID: PMC7491141 DOI: 10.1186/s13148-020-00934-1] [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: 04/03/2020] [Accepted: 09/03/2020] [Indexed: 12/13/2022] Open
Abstract
Background Cocaine use accelerates human immunodeficiency virus (HIV) progression and worsens HIV outcomes. We assessed whether DNA methylation in blood mediates the association between cocaine use and HIV severity in a veteran population. Methods We analyzed 1435 HIV-positive participants from the Veterans Aging Cohort Study Biomarker Cohort (VACS-BC). HIV severity was measured by the Veteran Aging Cohort Study (VACS) index. We assessed the effect of cocaine use on VACS index and mortality among the HIV-positive participants. We selected candidate mediators that were associated with both persistent cocaine use and VACS index by epigenome-wide association (EWA) scans at a liberal p value cutoff of 0.001. Mediation analysis of the candidate CpG sites between cocaine’s effect and the VACS index was conducted, and the joint mediation effect of multiple CpGs was estimated. A two-step epigenetic Mendelian randomization (MR) analysis was conducted as validation. Results More frequent cocaine use was significantly associated with a higher VACS index (β = 1.00, p = 2.7E−04), and cocaine use increased the risk of 10-year mortality (hazard ratio = 1.10, p = 0.011) with adjustment for confounding factors. Fifteen candidate mediator CpGs were selected from the EWA scan. Twelve of these CpGs showed significant mediation effects, with each explaining 11.3–29.5% of the variation. The mediation effects for 3 of the 12 CpGs were validated by the two-step epigenetic MR analysis. The joint mediation effect of the 12 CpGs accounted for 47.2% of cocaine’s effect on HIV severity. Genes harboring these 12 CpGs are involved in the antiviral response (IFIT3, IFITM1, NLRC5, PLSCR1, PARP9) and HIV progression (CX3CR1, MX1). Conclusions We identified 12 DNA methylation CpG sites that appear to play a mediation role in the association between cocaine use and HIV severity.
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Affiliation(s)
- Chang Shu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Amy C Justice
- Connecticut Veteran Healthcare System, West Haven, CT, USA.,Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA.,Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA. .,Connecticut Veteran Healthcare System, West Haven, CT, USA.
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24
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Zhang H, Dong P, Guo S, Tao C, Chen W, Zhao W, Wang J, Cheung R, Villanueva A, Fan J, Ding H, Schrodi SJ, Zhang D, Zeng C. Hypomethylation in HBV integration regions aids non-invasive surveillance to hepatocellular carcinoma by low-pass genome-wide bisulfite sequencing. BMC Med 2020; 18:200. [PMID: 32741373 PMCID: PMC7397586 DOI: 10.1186/s12916-020-01667-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/12/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Circulating cell-free DNA (cfDNA) methylation has been demonstrated to be a promising approach for non-invasive cancer diagnosis. However, the high cost of whole genome bisulfite sequencing (WGBS) hinders the clinical implementation of a methylation-based cfDNA early detection biomarker. We proposed a novel strategy in low-pass WGBS (~ 5 million reads) to detect methylation changes in circulating cell-free DNA (cfDNA) from patients with liver diseases and hepatocellular carcinoma (HCC). METHODS The effective small sequencing depth were determined by 5 pilot cfDNA samples with relative high-depth WGBS. CfDNA of 51 patients with hepatitis, cirrhosis, and HCC were conducted using low-pass WGBS. The strategy was validated in an independent WGBS cohort of 32 healthy individuals and 26 early-stage HCC patients. Fifteen paired tumor tissue and buffy coat samples were used to characterize the methylation of hepatitis B virus (HBV) integration regions and genome distribution of cfDNA. RESULTS A significant enrichment of cfDNA in intergenic and repeat regions, especially in previously reported HBV integration sites were observed, as a feature of cfDNA and the bias of cfDNA release. Methylation profiles nearby HBV integration sites were a better indicator for hypomethylation of tumor genome comparing to Alu and LINE (long interspersed nuclear element) repeats, and were able to facilitate the cfDNA-based HCC prediction. Hypomethylation nearby HBV integration sites (5 kb flanking) was detected in HCC patients, but not in patients with hepatitis and cirrhosis (MethylHBV5k, median:0.61 vs 0.72, P = 0.0003). Methylation levels of integration sites certain candidate regions exhibited an area under the receiver operation curve (AUC) value > 0.85 to discriminate HCC from non-HCC samples. The validation cohort achieved the prediction performance with an AUC of 0.954. CONCLUSIONS Hypomethylation around viral integration sites aids low-pass cfDNA WGBS to serve as a non-invasive approach for early HCC detection, and inspire future efforts on tumor surveillance for oncovirus with integration activity.
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Affiliation(s)
- Haikun Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peiling Dong
- Department of Hepatology, Beijing You'an Hospital Affiliated with Capital Medical University, Beijing, 100069, China
| | - Shicheng Guo
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Chengcheng Tao
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Chen
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Wenmin Zhao
- Department of Hepatology, Beijing You'an Hospital Affiliated with Capital Medical University, Beijing, 100069, China
| | - Jiakang Wang
- Biology Department, Stonybrook University, Stonybrook, NY, USA
| | - Ramsey Cheung
- Department of Gastroenterology and Hepatology, VA Palo Alto Health Care System and Stanford University, Palo Alto, CA, USA
| | - Augusto Villanueva
- Liver Cancer Research Program, Division of Liver Diseases, Tisch Cancer Institute, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jian Fan
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huiguo Ding
- Department of Hepatology, Beijing You'an Hospital Affiliated with Capital Medical University, Beijing, 100069, China
| | - Steven J Schrodi
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA.
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, USA.
| | - Dake Zhang
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.
| | - Changqing Zeng
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
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25
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Ursodeoxycholic acid improves feto-placental and offspring metabolic outcomes in hypercholanemic pregnancy. Sci Rep 2020; 10:10361. [PMID: 32587408 PMCID: PMC7316783 DOI: 10.1038/s41598-020-67301-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 04/14/2020] [Indexed: 11/08/2022] Open
Abstract
Perturbations in the intrauterine environment can result in lifelong consequences for metabolic health during postnatal life. Intrahepatic cholestasis of pregnancy (ICP) can predispose offspring to metabolic disease in adulthood, likely due to a combination of the effects of increased bile acids, maternal dyslipidemia and deranged maternal and fetal lipid homeostasis. Whereas ursodeoxycholic acid (UDCA) is a commonly used treatment for ICP, no studies have yet addressed whether it can also prevent the metabolic effects of ICP in the offspring and fetoplacental unit. We therefore analyzed the lipid profile of fetal serum from untreated ICP, UDCA-treated ICP and uncomplicated pregnancies and found that UDCA ameliorates ICP-associated fetal dyslipidemia. We then investigated the effects of UDCA in a mouse model of hypercholanemic pregnancy and showed that it induces hepatoprotective mechanisms in the fetal liver, reduces hepatic fatty acid synthase (Fas) expression and improves glucose tolerance in the adult offspring. Finally, we showed that ICP leads to epigenetic changes in pathways of relevance to the offspring phenotype. We therefore conclude that UDCA can be used as an intervention in pregnancy to reduce features of metabolic disease in the offspring of hypercholanemic mothers.
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26
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Mathur R, Hui Q, Huang Y, Gwinn M, So-Armah K, Freiberg MS, Justice AC, Xu K, Marconi VC, Sun YV. DNA Methylation Markers of Type 2 Diabetes Mellitus Among Male Veterans With or Without Human Immunodeficiency Virus Infection. J Infect Dis 2020; 219:1959-1962. [PMID: 30649532 DOI: 10.1093/infdis/jiz023] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/10/2019] [Indexed: 12/20/2022] Open
Abstract
Epigenetic modifications such as DNA methylation are associated with both human immunodeficiency virus (HIV) infection and type 2 diabetes mellitus (T2DM). We investigated epigenetic associations with T2DM according to HIV infection status and assessed interaction effects among 681 male participants of the Veterans Aging Cohort Study. Methylation at previously reported sites, cg1963031 (TXNIP), cg18181703 (SOCS3), and cg09152259 (PROC), was significantly associated with T2DM in HIV-infected individuals. We identified 3 novel associations with suggestive statistical significance: cg1231141 (ADAMTS2), cg19534769 (HGFAC), and cg13163919 (TLE3). Suggestive interaction with HIV infection status was found at cg17862404 (TSC22D1). The implicated genes are involved in inflammation, pancreatic β-cell function, and T2DM pathogenesis.
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Affiliation(s)
- Raina Mathur
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta
| | - Qin Hui
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta
| | - Yunfeng Huang
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta
| | - Marta Gwinn
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta
| | - Kaku So-Armah
- Department Global Health, Emory University Rollins School of Public Health, Atlanta
| | - Matthew S Freiberg
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta
| | - Amy C Justice
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta.,Atlanta Veterans Affairs Medical Center, Georgia
| | - Ke Xu
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta.,Boston University School of Medicine, Massachusetts
| | - Vincent C Marconi
- Cardiovascular Medicine Division, Vanderbilt University School of Medicine and Tennessee Valley Healthcare System, Nashville.,Connecticut Veteran Health System, West Haven.,Department of Psychiatry, New Haven, Connecticut
| | - Yan V Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta.,Cardiovascular Medicine Division, Vanderbilt University School of Medicine and Tennessee Valley Healthcare System, Nashville.,Yale School of Medicine, New Haven, Connecticut
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Le Clerc S, Limou S, Zagury JF. Large-Scale "OMICS" Studies to Explore the Physiopatholgy of HIV-1 Infection. Front Genet 2019; 10:799. [PMID: 31572435 PMCID: PMC6754074 DOI: 10.3389/fgene.2019.00799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/30/2019] [Indexed: 12/23/2022] Open
Abstract
In this review, we present the main large-scale experimental studies that have been performed in the HIV/AIDS field. These “omics” studies are based on several technologies including genotyping, RNA interference, and transcriptome or epigenome analysis. Due to the direct connection with disease evolution, there has been a large focus on genotyping cohorts of well-characterized patients through genome-wide association studies (GWASs), but there have also been several invitro studies such as small interfering RNA (siRNA) interference or transcriptome analyses of HIV-1–infected cells. After describing the major results obtained with these omics technologies—including some with a high relevance for HIV-1 treatment—we discuss the next steps that the community needs to embrace in order to derive new actionable therapeutic or diagnostic targets. Only integrative approaches that combine all big data results and consider their complex interactions will allow us to capture the global picture of HIV molecular pathogenesis. This novel challenge will require large collaborative efforts and represents a huge open field for innovative bioinformatics approaches.
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Affiliation(s)
- Sigrid Le Clerc
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
| | - Sophie Limou
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation en Urologie et Néphrologie (ITUN), CHU de Nantes, Nantes, France.,Computer Sciences and Mathematics Department, Ecole Centrale de Nantes, Nantes, France
| | - Jean-François Zagury
- Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, HESAM Université, Paris, France
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Lei W, Xu Y, Su J, Chong CM, Su HX, Luo J, Fang EF, Bao Z, Chen G. Applications of high-throughput ‘omics’ data in the study of frailty. TRANSLATIONAL MEDICINE OF AGING 2019. [DOI: 10.1016/j.tma.2019.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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29
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Zhang X, Hu Y, Aouizerat BE, Peng G, Marconi VC, Corley MJ, Hulgan T, Bryant KJ, Zhao H, Krystal JH, Justice AC, Xu K. Machine learning selected smoking-associated DNA methylation signatures that predict HIV prognosis and mortality. Clin Epigenetics 2018; 10:155. [PMID: 30545403 PMCID: PMC6293604 DOI: 10.1186/s13148-018-0591-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/26/2018] [Indexed: 12/20/2022] Open
Abstract
Background The effects of tobacco smoking on epigenome-wide methylation signatures in white blood cells (WBCs) collected from persons living with HIV may have important implications for their immune-related outcomes, including frailty and mortality. The application of a machine learning approach to the analysis of CpG methylation in the epigenome enables the selection of phenotypically relevant features from high-dimensional data. Using this approach, we now report that a set of smoking-associated DNA-methylated CpGs predicts HIV prognosis and mortality in an HIV-positive veteran population. Results We first identified 137 epigenome-wide significant CpGs for smoking in WBCs from 1137 HIV-positive individuals (p < 1.70E−07). To examine whether smoking-associated CpGs were predictive of HIV frailty and mortality, we applied ensemble-based machine learning to build a model in a training sample employing 408,583 CpGs. A set of 698 CpGs was selected and predictive of high HIV frailty in a testing sample [(area under curve (AUC) = 0.73, 95%CI 0.63~0.83)] and was replicated in an independent sample [(AUC = 0.78, 95%CI 0.73~0.83)]. We further found an association of a DNA methylation index constructed from the 698 CpGs that were associated with a 5-year survival rate [HR = 1.46; 95%CI 1.06~2.02, p = 0.02]. Interestingly, the 698 CpGs located on 445 genes were enriched on the integrin signaling pathway (p = 9.55E−05, false discovery rate = 0.036), which is responsible for the regulation of the cell cycle, differentiation, and adhesion. Conclusion We demonstrated that smoking-associated DNA methylation features in white blood cells predict HIV infection-related clinical outcomes in a population living with HIV. Electronic supplementary material The online version of this article (10.1186/s13148-018-0591-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, 300 George Street, 950 Campbell Ave, West Haven, New Haven, CT, 06511, USA.,VA Connecticut Healthcare System, 950 Campbell Ave, West Haven, CT, 06516, USA
| | - Ying Hu
- Center for Biomedical Bioinformatics, National Cancer Institute, Rockville, MD, 20852, USA
| | - Bradley E Aouizerat
- Bluestone Center for Clinical Research, New York University, New York, NY, 10010, USA
| | - Gang Peng
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 065116, USA
| | - Vincent C Marconi
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, 30303, USA
| | - Michael J Corley
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Suite 1016B, Honolulu, 96813, USA
| | - Todd Hulgan
- School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA
| | - Kendall J Bryant
- National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD, 20852, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 065116, USA
| | - John H Krystal
- Department of Psychiatry, Yale School of Medicine, 300 George Street, 950 Campbell Ave, West Haven, New Haven, CT, 06511, USA.,VA Connecticut Healthcare System, 950 Campbell Ave, West Haven, CT, 06516, USA
| | - Amy C Justice
- VA Connecticut Healthcare System, 950 Campbell Ave, West Haven, CT, 06516, USA.,Yale University School of Medicine, New Haven, CT, 06516, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, 300 George Street, 950 Campbell Ave, West Haven, New Haven, CT, 06511, USA. .,VA Connecticut Healthcare System, 950 Campbell Ave, West Haven, CT, 06516, USA.
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Li X, Fu Y, Wang X, Qiu W. Robust joint score tests in the application of DNA methylation data analysis. BMC Bioinformatics 2018; 19:174. [PMID: 29776330 PMCID: PMC5960098 DOI: 10.1186/s12859-018-2185-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 05/02/2018] [Indexed: 12/27/2022] Open
Abstract
Background Recently differential variability has been showed to be valuable in evaluating the association of DNA methylation to the risks of complex human diseases. The statistical tests based on both differential methylation level and differential variability can be more powerful than those based only on differential methylation level. Anh and Wang (2013) proposed a joint score test (AW) to simultaneously detect for differential methylation and differential variability. However, AW’s method seems to be quite conservative and has not been fully compared with existing joint tests. Results We proposed three improved joint score tests, namely iAW.Lev, iAW.BF, and iAW.TM, and have made extensive comparisons with the joint likelihood ratio test (jointLRT), the Kolmogorov-Smirnov (KS) test, and the AW test. Systematic simulation studies showed that: 1) the three improved tests performed better (i.e., having larger power, while keeping nominal Type I error rates) than the other three tests for data with outliers and having different variances between cases and controls; 2) for data from normal distributions, the three improved tests had slightly lower power than jointLRT and AW. The analyses of two Illumina HumanMethylation27 data sets GSE37020 and GSE20080 and one Illumina Infinium MethylationEPIC data set GSE107080 demonstrated that three improved tests had higher true validation rates than those from jointLRT, KS, and AW. Conclusions The three proposed joint score tests are robust against the violation of normality assumption and presence of outlying observations in comparison with other three existing tests. Among the three proposed tests, iAW.BF seems to be the most robust and effective one for all simulated scenarios and also in real data analyses. Electronic supplementary material The online version of this article (10.1186/s12859-018-2185-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xuan Li
- Department of Mathematics and Statistics, York University, 4700 Keele Street, Toronto, M3J1P3, Canada
| | - Yuejiao Fu
- Department of Mathematics and Statistics, York University, 4700 Keele Street, Toronto, M3J1P3, Canada.
| | - Xiaogang Wang
- Department of Mathematics and Statistics, York University, 4700 Keele Street, Toronto, M3J1P3, Canada
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, 181 Longwood Avenue, Boston, 02115, USA
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