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Vabalas A, Hartonen T, Vartiainen P, Jukarainen S, Viippola E, Rodosthenous RS, Liu A, Hägg S, Perola M, Ganna A. Deep learning-based prediction of one-year mortality in Finland is an accurate but unfair aging marker. NATURE AGING 2024:10.1038/s43587-024-00657-5. [PMID: 38914859 DOI: 10.1038/s43587-024-00657-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 05/27/2024] [Indexed: 06/26/2024]
Abstract
Short-term mortality risk, which is indicative of individual frailty, serves as a marker for aging. Previous age clocks focused on predicting either chronological age or longer-term mortality. Aging clocks predicting short-term mortality are lacking and their algorithmic fairness remains unexamined. We developed a deep learning model to predict 1-year mortality using nationwide longitudinal data from the Finnish population (FinRegistry; n = 5.4 million), incorporating more than 8,000 features spanning up to 50 years. We achieved an area under the curve (AUC) of 0.944, outperforming a baseline model that included only age and sex (AUC = 0.897). The model generalized well to different causes of death (AUC > 0.800 for 45 of 50 causes), including coronavirus disease 2019, which was absent in the training data. Performance varied among demographics, with young females exhibiting the best and older males the worst results. Extensive prediction fairness analyses highlighted disparities among disadvantaged groups, posing challenges to equitable integration into public health interventions. Our model accurately identified short-term mortality risk, potentially serving as a population-wide aging marker.
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Affiliation(s)
- Andrius Vabalas
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Tuomo Hartonen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Pekka Vartiainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Pediatric Research Center, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Sakari Jukarainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Essi Viippola
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | | | - Aoxing Liu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Markus Perola
- The Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
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Xia Q, Zhou T, Xu H, Ge S, Tang X. The Relationship Between Alcohol Consumption and Frailty Among Older Adults in China: Results From the Chinese Longitudinal Healthy Longevity Survey. J Transcult Nurs 2024:10436596241259196. [PMID: 38872344 DOI: 10.1177/10436596241259196] [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: 06/15/2024] Open
Abstract
INTRODUCTION Alcohol consumption has an impact on the frailty, but current research in China lacks a detailed classification of alcohol use. This study aimed to explore the relationship between different drinking patterns and frailty in older adults. METHODOLOGY The data came from the 2018 Chinese Longitudinal Healthy Longevity Survey (CLHLS) study, which included older adults (aged ≧ 60). Their demographic data, drinking status, and frailty index were collected in CLHLS. Through logistic regression models to analyze the correlation between alcohol consumption and frailty. RESULTS A total of 14,931 participants were included in the analysis. The prevalence of frailty was 29.1%, 35.2%, and 14.9% among risk-free, past risky, and now risky drinkers, respectively. After adjusting for covariates, past risky drinking was a risk factor for frailty (p = .003). DISCUSSION High-risk alcohol consumption is positively correlated with frailty. Prevention and reduction of risky drinking in older adults may help protect them from developing frailty.
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Affiliation(s)
- Qiujie Xia
- Xuzhou Medical University, Xuzhou, China
| | - Tian Zhou
- Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Hui Xu
- Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Song Ge
- University of Houston-Downtown, USA
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Hu W, Chen S, Cai J, Yang Y, Yan H, Chen F. High-dimensional mediation analysis for continuous outcome with confounders using overlap weighting method in observational epigenetic study. BMC Med Res Methodol 2024; 24:125. [PMID: 38831262 PMCID: PMC11145821 DOI: 10.1186/s12874-024-02254-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/22/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND Mediation analysis is a powerful tool to identify factors mediating the causal pathway of exposure to health outcomes. Mediation analysis has been extended to study a large number of potential mediators in high-dimensional data settings. The presence of confounding in observational studies is inevitable. Hence, it's an essential part of high-dimensional mediation analysis (HDMA) to adjust for the potential confounders. Although the propensity score (PS) related method such as propensity score regression adjustment (PSR) and inverse probability weighting (IPW) has been proposed to tackle this problem, the characteristics with extreme propensity score distribution of the PS-based method would result in the biased estimation. METHODS In this article, we integrated the overlapping weighting (OW) technique into HDMA workflow and proposed a concise and powerful high-dimensional mediation analysis procedure consisting of OW confounding adjustment, sure independence screening (SIS), de-biased Lasso penalization, and joint-significance testing underlying the mixture null distribution. We compared the proposed method with the existing method consisting of PS-based confounding adjustment, SIS, minimax concave penalty (MCP) variable selection, and classical joint-significance testing. RESULTS Simulation studies demonstrate the proposed procedure has the best performance in mediator selection and estimation. The proposed procedure yielded the highest true positive rate, acceptable false discovery proportion level, and lower mean square error. In the empirical study based on the GSE117859 dataset in the Gene Expression Omnibus database using the proposed method, we found that smoking history may lead to the estimated natural killer (NK) cell level reduction through the mediation effect of some methylation markers, mainly including methylation sites cg13917614 in CNP gene and cg16893868 in LILRA2 gene. CONCLUSIONS The proposed method has higher power, sufficient false discovery rate control, and precise mediation effect estimation. Meanwhile, it is feasible to be implemented with the presence of confounders. Hence, our method is worth considering in HDMA studies.
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Affiliation(s)
- Weiwei Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Shiyu Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Jiaxin Cai
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Yuhui Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Hong Yan
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Fangyao Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
- Department of Radiology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China.
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Zhu T, Tong H, Du Z, Beck S, Teschendorff AE. An improved epigenetic counter to track mitotic age in normal and precancerous tissues. Nat Commun 2024; 15:4211. [PMID: 38760334 PMCID: PMC11101651 DOI: 10.1038/s41467-024-48649-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 05/09/2024] [Indexed: 05/19/2024] Open
Abstract
The cumulative number of stem cell divisions in a tissue, known as mitotic age, is thought to be a major determinant of cancer-risk. Somatic mutational and DNA methylation (DNAm) clocks are promising tools to molecularly track mitotic age, yet their relationship is underexplored and their potential for cancer risk prediction in normal tissues remains to be demonstrated. Here we build and validate an improved pan-tissue DNAm counter of total mitotic age called stemTOC. We demonstrate that stemTOC's mitotic age proxy increases with the tumor cell-of-origin fraction in each of 15 cancer-types, in precancerous lesions, and in normal tissues exposed to major cancer risk factors. Extensive benchmarking against 6 other mitotic counters shows that stemTOC compares favorably, specially in the preinvasive and normal-tissue contexts. By cross-correlating stemTOC to two clock-like somatic mutational signatures, we confirm the mitotic-like nature of only one of these. Our data points towards DNAm as a promising molecular substrate for detecting mitotic-age increases in normal tissues and precancerous lesions, and hence for developing cancer-risk prediction strategies.
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Affiliation(s)
- Tianyu Zhu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Huige Tong
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Zhaozhen Du
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Stephan Beck
- Medical Genomics Group, UCL Cancer Institute, University College London, 72 Huntley Street, WC1E 6BT, London, UK
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institute for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
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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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Ruderman SA, Odden MC, Webel AR, Fitzpatrick AL, Crane PK, Nance RM, Drumright LN, Whitney BM, Mixson LS, Ma J, Willig AL, Haidar L, Eltonsy S, Mayer KH, O'Cleirigh C, Cropsey KL, Eron JJ, Napravnik S, Greene M, McCaul M, Chander G, Cachay E, Lober WB, Kritchevsky SB, Austad S, Landay A, Pandya C, Cartujano-Barrera F, Saag MS, Kamen C, Hahn AW, Kitahata MM, Delaney JAC, Crane HM. Tobacco Smoking and Pack-Years Are Associated With Frailty Among People With HIV. J Acquir Immune Defic Syndr 2023; 94:135-142. [PMID: 37368939 PMCID: PMC10527292 DOI: 10.1097/qai.0000000000003242] [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: 08/05/2022] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND Tobacco smoking increases frailty risk among the general population and is common among people with HIV (PWH) who experience higher rates of frailty at younger ages than the general population. METHODS We identified 8608 PWH across 6 Centers for AIDS Research Network of Integrated Clinical Systems sites who completed ≥2 patient-reported outcome assessments, including a frailty phenotype measuring unintentional weight loss, poor mobility, fatigue, and inactivity, and scored 0-4. Smoking was measured as baseline pack-years and time-updated never, former, or current use with cigarettes/day. We used Cox models to associate smoking with risk of incident frailty (score ≥3) and deterioration (frailty score increase by ≥2 points), adjusted for demographics, antiretroviral medication, and time-updated CD4 count. RESULTS The mean follow-up of PWH was 5.3 years (median: 5.0), the mean age at baseline was 45 years, 15% were female, and 52% were non-White. At baseline, 60% reported current or former smoking. Current (HR: 1.79; 95% confidence interval: 1.54 to 2.08) and former (HR: 1.31; 95% confidence interval: 1.12 to 1.53) smoking were associated with higher incident frailty risk, as were higher pack-years. Current smoking (among younger PWH) and pack-years, but not former smoking, were associated with higher risk of deterioration. CONCLUSIONS Among PWH, smoking status and duration are associated with incident and worsening frailty.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jimmy Ma
- University of Washington, Seattle, WA, USA
| | | | - Lara Haidar
- University of Manitoba, Winnipeg, Manitoba, CA
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7
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Cheng Y, Justice A, Wang Z, Li B, Hancock DB, Johnson EO, Xu K. Cis-meQTL for cocaine use-associated DNA methylation in an HIV-positive cohort show pleiotropic effects on multiple traits. BMC Genomics 2023; 24:556. [PMID: 37730558 PMCID: PMC10510240 DOI: 10.1186/s12864-023-09661-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/08/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Cocaine use (CU) is associated with psychiatric and medical diseases. Little is known about the mechanisms of CU-related comorbidities. Findings from preclinical and clinical studies have suggested that CU is associated with aberrant DNA methylation (DNAm) that may be influenced by genetic variants [i.e., methylation quantitative trait loci (meQTLs)]. In this study, we mapped cis-meQTLs for CU-associated DNAm sites (CpGs) in an HIV-positive cohort (Ntotal = 811) and extended the meQTLs to multiple traits. RESULTS We conducted cis-meQTL analysis for 224 candidate CpGs selected for their association with CU in blood. We identified 7,101 significant meQTLs [false discovery rate (FDR) < 0.05], which mostly mapped to genes involved in immunological functions and were enriched in immune pathways. We followed up the meQTLs using phenome-wide association study and trait enrichment analyses, which revealed 9 significant traits. We tested for causal effects of CU on these 9 traits using Mendelian Randomization and found evidence that CU plays a causal role in increasing hypertension (p-value = 2.35E-08) and decreasing heel bone mineral density (p-value = 1.92E-19). CONCLUSIONS These findings suggest that genetic variants for CU-associated DNAm have pleiotropic effects on other relevant traits and provide new insights into the causal relationships between cocaine use and these complex traits.
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Affiliation(s)
- Youshu Cheng
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
- VA Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Amy Justice
- VA Connecticut Healthcare System, West Haven, CT, 06516, USA
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06511, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
| | - Boyang Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06511, USA
- VA Connecticut Healthcare System, West Haven, CT, 06516, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC, USA
- Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Ke Xu
- VA Connecticut Healthcare System, West Haven, CT, 06516, USA.
- Department of Psychiatry, Yale School of Medicine, 300 George Street, New Haven, CT, 06511, USA.
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Luo Q, Dwaraka VB, Chen Q, Tong H, Zhu T, Seale K, Raffaele JM, Zheng SC, Mendez TL, Chen Y, Carreras N, Begum S, Mendez K, Voisin S, Eynon N, Lasky-Su JA, Smith R, Teschendorff AE. A meta-analysis of immune-cell fractions at high resolution reveals novel associations with common phenotypes and health outcomes. Genome Med 2023; 15:59. [PMID: 37525279 PMCID: PMC10388560 DOI: 10.1186/s13073-023-01211-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/10/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND Changes in cell-type composition of tissues are associated with a wide range of diseases and environmental risk factors and may be causally implicated in disease development and progression. However, these shifts in cell-type fractions are often of a low magnitude, or involve similar cell subtypes, making their reliable identification challenging. DNA methylation profiling in a tissue like blood is a promising approach to discover shifts in cell-type abundance, yet studies have only been performed at a relatively low cellular resolution and in isolation, limiting their power to detect shifts in tissue composition. METHODS Here we derive a DNA methylation reference matrix for 12 immune-cell types in human blood and extensively validate it with flow-cytometric count data and in whole-genome bisulfite sequencing data of sorted cells. Using this reference matrix, we perform a directional Stouffer and fixed effects meta-analysis comprising 23,053 blood samples from 22 different cohorts, to comprehensively map associations between the 12 immune-cell fractions and common phenotypes. In a separate cohort of 4386 blood samples, we assess associations between immune-cell fractions and health outcomes. RESULTS Our meta-analysis reveals many associations of cell-type fractions with age, sex, smoking and obesity, many of which we validate with single-cell RNA sequencing. We discover that naïve and regulatory T-cell subsets are higher in women compared to men, while the reverse is true for monocyte, natural killer, basophil, and eosinophil fractions. Decreased natural killer counts associated with smoking, obesity, and stress levels, while an increased count correlates with exercise and sleep. Analysis of health outcomes revealed that increased naïve CD4 + T-cell and N-cell fractions associated with a reduced risk of all-cause mortality independently of all major epidemiological risk factors and baseline co-morbidity. A machine learning predictor built only with immune-cell fractions achieved a C-index value for all-cause mortality of 0.69 (95%CI 0.67-0.72), which increased to 0.83 (0.80-0.86) upon inclusion of epidemiological risk factors and baseline co-morbidity. CONCLUSIONS This work contributes an extensively validated high-resolution DNAm reference matrix for blood, which is made freely available, and uses it to generate a comprehensive map of associations between immune-cell fractions and common phenotypes, including health outcomes.
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Affiliation(s)
- Qi Luo
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Varun B Dwaraka
- TruDiagnostics, 881 Corporate Dr., Lexington, KY, 40503, USA
| | - Qingwen Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Huige Tong
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Tianyu Zhu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Kirsten Seale
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC, 3011, Australia
| | - Joseph M Raffaele
- PhysioAge LLC, 30 Central Park South / Suite 8A, New York, NY, 10019, USA
| | - Shijie C Zheng
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Tavis L Mendez
- TruDiagnostics, 881 Corporate Dr., Lexington, KY, 40503, USA
| | - Yulu Chen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | | | - Sofina Begum
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Kevin Mendez
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Footscray, VIC, 3011, Australia
| | - Nir Eynon
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Jessica A Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Ryan Smith
- TruDiagnostics, 881 Corporate Dr., Lexington, KY, 40503, USA.
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
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9
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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] [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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11
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Krittanawong C, Singh NK, Scheuring RA, Urquieta E, Bershad EM, Macaulay TR, Kaplin S, Dunn C, Kry SF, Russomano T, Shepanek M, Stowe RP, Kirkpatrick AW, Broderick TJ, Sibonga JD, Lee AG, Crucian BE. Human Health during Space Travel: State-of-the-Art Review. Cells 2022; 12:cells12010040. [PMID: 36611835 PMCID: PMC9818606 DOI: 10.3390/cells12010040] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
The field of human space travel is in the midst of a dramatic revolution. Upcoming missions are looking to push the boundaries of space travel, with plans to travel for longer distances and durations than ever before. Both the National Aeronautics and Space Administration (NASA) and several commercial space companies (e.g., Blue Origin, SpaceX, Virgin Galactic) have already started the process of preparing for long-distance, long-duration space exploration and currently plan to explore inner solar planets (e.g., Mars) by the 2030s. With the emergence of space tourism, space travel has materialized as a potential new, exciting frontier of business, hospitality, medicine, and technology in the coming years. However, current evidence regarding human health in space is very limited, particularly pertaining to short-term and long-term space travel. This review synthesizes developments across the continuum of space health including prior studies and unpublished data from NASA related to each individual organ system, and medical screening prior to space travel. We categorized the extraterrestrial environment into exogenous (e.g., space radiation and microgravity) and endogenous processes (e.g., alteration of humans' natural circadian rhythm and mental health due to confinement, isolation, immobilization, and lack of social interaction) and their various effects on human health. The aim of this review is to explore the potential health challenges associated with space travel and how they may be overcome in order to enable new paradigms for space health, as well as the use of emerging Artificial Intelligence based (AI) technology to propel future space health research.
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Affiliation(s)
- Chayakrit Krittanawong
- Department of Medicine and Center for Space Medicine, Section of Cardiology, Baylor College of Medicine, Houston, TX 77030, USA
- Translational Research Institute for Space Health, Houston, TX 77030, USA
- Department of Cardiovascular Diseases, New York University School of Medicine, New York, NY 10016, USA
- Correspondence: or (C.K.); (B.E.C.); Tel.: +1-713-798-4951 (C.K.); +1-281-483-0123 (B.E.C.)
| | - Nitin Kumar Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | | | - Emmanuel Urquieta
- Translational Research Institute for Space Health, Houston, TX 77030, USA
- Department of Emergency Medicine and Center for Space Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric M. Bershad
- Department of Neurology, Center for Space Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Scott Kaplin
- Department of Cardiovascular Diseases, New York University School of Medicine, New York, NY 10016, USA
| | - Carly Dunn
- Department of Dermatology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephen F. Kry
- Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Marc Shepanek
- Office of the Chief Health and Medical Officer, NASA, Washington, DC 20546, USA
| | | | - Andrew W. Kirkpatrick
- Department of Surgery and Critical Care Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | | | - Jean D. Sibonga
- Division of Biomedical Research and Environmental Sciences, NASA Lyndon B. Johnson Space Center, Houston, TX 77058, USA
| | - Andrew G. Lee
- Department of Ophthalmology, University of Texas Medical Branch School of Medicine, Galveston, TX 77555, USA
- Department of Ophthalmology, Blanton Eye Institute, Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Ophthalmology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Ophthalmology, Texas A and M College of Medicine, College Station, TX 77807, USA
- Department of Ophthalmology, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
- Departments of Ophthalmology, Neurology, and Neurosurgery, Weill Cornell Medicine, New York, NY 10021, USA
| | - Brian E. Crucian
- National Aeronautics and Space Administration (NASA) Johnson Space Center, Human Health and Performance Directorate, Houston, TX 77058, USA
- Correspondence: or (C.K.); (B.E.C.); Tel.: +1-713-798-4951 (C.K.); +1-281-483-0123 (B.E.C.)
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12
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Robinson KG, Marsh AG, Lee SK, Hicks J, Romero B, Batish M, Crowgey EL, Shrader MW, Akins RE. DNA Methylation Analysis Reveals Distinct Patterns in Satellite Cell-Derived Myogenic Progenitor Cells of Subjects with Spastic Cerebral Palsy. J Pers Med 2022; 12:jpm12121978. [PMID: 36556199 PMCID: PMC9780849 DOI: 10.3390/jpm12121978] [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: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
Spastic type cerebral palsy (CP) is a complex neuromuscular disorder that involves altered skeletal muscle microanatomy and growth, but little is known about the mechanisms contributing to muscle pathophysiology and dysfunction. Traditional genomic approaches have provided limited insight regarding disease onset and severity, but recent epigenomic studies indicate that DNA methylation patterns can be altered in CP. Here, we examined whether a diagnosis of spastic CP is associated with intrinsic DNA methylation differences in myoblasts and myotubes derived from muscle resident stem cell populations (satellite cells; SCs). Twelve subjects were enrolled (6 CP; 6 control) with informed consent/assent. Skeletal muscle biopsies were obtained during orthopedic surgeries, and SCs were isolated and cultured to establish patient-specific myoblast cell lines capable of proliferation and differentiation in culture. DNA methylation analyses indicated significant differences at 525 individual CpG sites in proliferating SC-derived myoblasts (MB) and 1774 CpG sites in differentiating SC-derived myotubes (MT). Of these, 79 CpG sites were common in both culture types. The distribution of differentially methylated 1 Mbp chromosomal segments indicated distinct regional hypo- and hyper-methylation patterns, and significant enrichment of differentially methylated sites on chromosomes 12, 13, 14, 15, 18, and 20. Average methylation load across 2000 bp regions flanking transcriptional start sites was significantly different in 3 genes in MBs, and 10 genes in MTs. SC derived MBs isolated from study participants with spastic CP exhibited fundamental differences in DNA methylation compared to controls at multiple levels of organization that may reveal new targets for studies of mechanisms contributing to muscle dysregulation in spastic CP.
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Affiliation(s)
- Karyn G. Robinson
- Nemours Children’s Research, Nemours Children’s Health System, Wilmington, DE 19803, USA
| | - Adam G. Marsh
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA
| | - Stephanie K. Lee
- Nemours Children’s Research, Nemours Children’s Health System, Wilmington, DE 19803, USA
| | - Jonathan Hicks
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716, USA
| | - Brigette Romero
- Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Mona Batish
- Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA
| | - Erin L. Crowgey
- Nemours Children’s Research, Nemours Children’s Health System, Wilmington, DE 19803, USA
| | - M. Wade Shrader
- Department of Orthopedics, Nemours Children’s Hospital Delaware, Wilmington, DE 19803, USA
| | - Robert E. Akins
- Nemours Children’s Research, Nemours Children’s Health System, Wilmington, DE 19803, USA
- Correspondence: ; Tel.: +1-302-651-6779
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13
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Marttila S, Tamminen H, Rajić S, Mishra PP, Lehtimäki T, Raitakari O, Kähönen M, Kananen L, Jylhävä J, Hägg S, Delerue T, Peters A, Waldenberger M, Kleber ME, März W, Luoto R, Raitanen J, Sillanpää E, Laakkonen EK, Heikkinen A, Ollikainen M, Raitoharju E. Methylation status of VTRNA2-1/ nc886 is stable across populations, monozygotic twin pairs and in majority of tissues. Epigenomics 2022; 14:1105-1124. [PMID: 36200237 DOI: 10.2217/epi-2022-0228] [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: 11/21/2022] Open
Abstract
Aims & methods: The aim of this study was to characterize the methylation level of a polymorphically imprinted gene, VTRNA2-1/nc886, in human populations and somatic tissues.48 datasets, consisting of more than 30 tissues and >30,000 individuals, were used. Results: nc886 methylation status is associated with twin status and ethnic background, but the variation between populations is limited. Monozygotic twin pairs present concordant methylation, whereas ∼30% of dizygotic twin pairs present discordant methylation in the nc886 locus. The methylation levels of nc886 are uniform across somatic tissues, except in cerebellum and skeletal muscle. Conclusion: The nc886 imprint may be established in the oocyte, and, after implantation, the methylation status is stable, excluding a few specific tissues.
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Affiliation(s)
- Saara Marttila
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Gerontology Research Center, Tampere University, Tampere, 33014, Finland
| | - Hely Tamminen
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Sonja Rajić
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Fimlab Laboratories, Arvo Ylpön katu 4, Tampere, 33520, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Fimlab Laboratories, Arvo Ylpön katu 4, Tampere, 33520, Finland
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku & Turku University Hospital, Turku, 20014, Finland.,Research Centre of Applied & Preventive Cardiovascular Medicine, University of Turku, Turku, 20014, Finland.,Department of Clinical Physiology & Nuclear Medicine, Turku University Hospital, Turku, 20014, Finland
| | - Mika Kähönen
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Department of Clinical Physiology, Tampere University Hospital, Tampere, 33521, Finland
| | - Laura Kananen
- Faculty of Medicine & Health Technology, & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520,Finland.,Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden.,Faculty of Social Sciences (Health Sciences), & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Juulia Jylhävä
- Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden.,Faculty of Social Sciences (Health Sciences), & Gerontology Research Center, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Sara Hägg
- Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Thomas Delerue
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764,, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, D-85764,, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany.,SYNLAB MVZ Humangenetik Mannheim, Mannheim, Germany
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, 68167, Germany.,Competence Cluster for Nutrition & Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Jena, 07743, Germany.,SYNLAB Academy, SYNLAB Holding Deutschland GmbH, Augsburg, 86156, Germany.,Clinical Institute of Medical & Chemical Laboratory Diagnostics, Medical University of Graz, Graz, 8010, Austria
| | - Riitta Luoto
- The Social Insurance Institute of Finland (Kela), Helsinki, 00250, Finland.,The UKK Institute for Health Promotion Research, Kaupinpuistonkatu 1, Tampere, 33500, Finland
| | - Jani Raitanen
- The UKK Institute for Health Promotion Research, Kaupinpuistonkatu 1, Tampere, 33500, Finland.,Faculty of Social Sciences (Health Sciences), Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
| | - Elina Sillanpää
- Gerontology Research Center & Faculty of Sport & Health Sciences, University of Jyväskylä, Jyväskylä, 40014, Finland.,Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Eija K Laakkonen
- Gerontology Research Center & Faculty of Sport & Health Sciences, University of Jyväskylä, Jyväskylä, 40014, Finland
| | - Aino Heikkinen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland, FIMM, HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Emma Raitoharju
- Molecular Epidemiology, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland.,Finnish Cardiovascular Research Center Tampere, Faculty of Medicine & Health Technology, Tampere University, Arvo Ylpön katu 34, Tampere, 33520, Finland
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14
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Wang T, Xia P, Su P. High-Dimensional DNA Methylation Mediates the Effect of Smoking on Crohn's Disease. Front Genet 2022; 13:831885. [PMID: 35450213 PMCID: PMC9016182 DOI: 10.3389/fgene.2022.831885] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Epigenome-wide mediation analysis aims to identify high-dimensional DNA methylation at cytosine–phosphate–guanine (CpG) sites that mediate the causal effect of linking smoking with Crohn’s disease (CD) outcome. Studies have shown that smoking has significant detrimental effects on the course of CD. So we assessed whether DNA methylation mediates the association between smoking and CD. Among 103 CD cases and 174 controls, we estimated whether the effects of smoking on CD are mediated through DNA methylation CpG sites, which we referred to as causal mediation effect. Based on the causal diagram, we first implemented sure independence screening (SIS) to reduce the pool of potential mediator CpGs from a very large to a moderate number; then, we implemented variable selection with de-sparsifying the LASSO regression. Finally, we carried out a comprehensive mediation analysis and conducted sensitivity analysis, which was adjusted for potential confounders of age, sex, and blood cell type proportions to estimate the mediation effects. Smoking was significantly associated with CD under odds ratio (OR) of 2.319 (95% CI: 1.603, 3.485, p < 0.001) after adjustment for confounders. Ninety-nine mediator CpGs were selected from SIS, and then, seven candidate CpGs were obtained by de-sparsifying the LASSO regression. Four of these CpGs showed statistical significance, and the average causal mediation effects (ACME) were attenuated from 0.066 to 0.126. Notably, three significant mediator CpGs had absolute sensitivity parameters of 0.40, indicating that these mediation effects were robust even when the assumptions were slightly violated. Genes (BCL3 and FKBP5) harboring these four CpGs were related to CD. These findings suggest that changes in methylation are involved in the mechanism by which smoking increases risk of CD.
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Affiliation(s)
- Tingting Wang
- Institute of Medical Sciences, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Pingtian Xia
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ping Su
- Institute of Medical Sciences, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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15
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Rodés B, Cadiñanos J, Esteban-Cantos A, Rodríguez-Centeno J, Arribas JR. Ageing with HIV: Challenges and biomarkers. EBioMedicine 2022; 77:103896. [PMID: 35228014 PMCID: PMC8889090 DOI: 10.1016/j.ebiom.2022.103896] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/13/2022] Open
Abstract
The antiretroviral treatment (ART) developed to control HIV infection led to a revolution in the prognosis of people living with HIV (PLWH). PLWH underwent from suffering severe disease and often fatal complications at young ages to having a chronic condition and a life expectancy close to the general population. Nevertheless, chronic age-related diseases increase as PLWH age. The harmful effect of HIV infection on the individual's immune system adds to its deterioration during ageing, exacerbating comorbidities. In addition, PLWH are more exposed to risk factors affecting ageing, such as coinfections or harmful lifestyles. The ART initiation reverses the biological ageing process but only partially, and additionally can have some toxicities that influence ageing. Observational studies suggest premature ageing in PLWH. Therefore, there is considerable interest in the early prediction of unhealthy ageing through validated biomarkers, easy to implement in HIV-clinical settings. The most promising biomarkers are second-generation epigenetic clocks and integrative algorithms.
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Affiliation(s)
- Berta Rodés
- HIV/AIDS and Infectious Diseases Research Group, Hospital Universitario La Paz Institute for Health Research-IdiPAZ, Paseo de la Castellana 261, Madrid 28046, Spain; CIBER of Infectious Diseases (CIBER-INFECT), 28029 Madrid, Spain.
| | - Julen Cadiñanos
- HIV/AIDS and Infectious Diseases Research Group, Hospital Universitario La Paz Institute for Health Research-IdiPAZ, Paseo de la Castellana 261, Madrid 28046, Spain; Infectious Diseases Unit, Department of Internal Medicine, Hospital Universitario La Paz, Paseo de la Castellana 261, Madrid 28046, Spain; CIBER of Infectious Diseases (CIBER-INFECT), 28029 Madrid, Spain
| | - Andrés Esteban-Cantos
- HIV/AIDS and Infectious Diseases Research Group, Hospital Universitario La Paz Institute for Health Research-IdiPAZ, Paseo de la Castellana 261, Madrid 28046, Spain; CIBER of Infectious Diseases (CIBER-INFECT), 28029 Madrid, Spain
| | - Javier Rodríguez-Centeno
- HIV/AIDS and Infectious Diseases Research Group, Hospital Universitario La Paz Institute for Health Research-IdiPAZ, Paseo de la Castellana 261, Madrid 28046, Spain; CIBER of Infectious Diseases (CIBER-INFECT), 28029 Madrid, Spain
| | - José Ramón Arribas
- HIV/AIDS and Infectious Diseases Research Group, Hospital Universitario La Paz Institute for Health Research-IdiPAZ, Paseo de la Castellana 261, Madrid 28046, Spain; Infectious Diseases Unit, Department of Internal Medicine, Hospital Universitario La Paz, Paseo de la Castellana 261, Madrid 28046, Spain; CIBER of Infectious Diseases (CIBER-INFECT), 28029 Madrid, Spain.
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16
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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: 1.5] [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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17
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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. 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: 4] [Impact Index Per Article: 1.3] [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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18
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Meier R, Nissen E, Koestler DC. Low variability in the underlying cellular landscape adversely affects the performance of interaction-based approaches for conducting cell-specific analyses of DNA methylation in bulk samples. Stat Appl Genet Mol Biol 2021; 20:73-84. [PMID: 34378875 PMCID: PMC9125800 DOI: 10.1515/sagmb-2021-0004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/19/2021] [Indexed: 11/15/2022]
Abstract
Statistical methods that allow for cell type specific DNA methylation (DNAm) analyses based on bulk-tissue methylation data have great potential to improve our understanding of human disease and have created unprecedented opportunities for new insights using the wealth of publicly available bulk-tissue methylation data. These methodologies involve incorporating interaction terms formed between the phenotypes/exposures of interest and proportions of the cell types underlying the bulk-tissue sample used for DNAm profiling. Despite growing interest in such "interaction-based" methods, there has been no comprehensive assessment how variability in the cellular landscape across study samples affects their performance. To answer this question, we used numerous publicly available whole-blood DNAm data sets along with extensive simulation studies and evaluated the performance of interaction-based approaches in detecting cell-specific methylation effects. Our results show that low cell proportion variability results in large estimation error and low statistical power for detecting cell-specific effects of DNAm. Further, we identified that many studies targeting methylation profiling in whole-blood may be at risk to be underpowered due to low variability in the cellular landscape across study samples. Finally, we discuss guidelines for researchers seeking to conduct studies utilizing interaction-based approaches to help ensure that their studies are adequately powered.
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Affiliation(s)
- Richard Meier
- Department of Biostatistics & Data Science, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City66160, KS, USA
| | - Emily Nissen
- Department of Biostatistics & Data Science, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City66160, KS, USA
| | - Devin C. Koestler
- Department of Biostatistics & Data Science, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City66160, KS, USA
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19
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Kucher AN, Babushkina NP, Sleptcov AA, Nazarenko MS. Genetic Control of Human Infection with SARS-CoV-2. RUSS J GENET+ 2021; 57:627-641. [PMID: 34248311 PMCID: PMC8254434 DOI: 10.1134/s1022795421050057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/26/2020] [Accepted: 08/25/2020] [Indexed: 01/21/2023]
Abstract
In 2019, the SARS-CoV-2 beta-coronavirus, which caused a pandemic of severe acute respiratory viral infection COVID-19 (from COronaVIrus Disease 2019), was first detected. The susceptibility to SARS-CoV-2 and the nature of the course of the COVID-19 clinical picture are determined by many factors, including genetic characteristics of both the pathogen and the human. The SARS-CoV-2 genome has a similarity to the genomes of other coronaviruses, which are pathogenic for humans and cause a severe course of infection: 79% to the SARS-CoV genome and 50% to the MERS-CoV genome. The most significant differences between SARS-CoV-2 and other coronaviruses are recorded in the structure of the gene of the S protein, a key protein responsible for the virus binding to the receptor of the host organism cells. In particular, substitutions in the S protein of SARS-CoV-2, leading to the formation of the furin cleavage site that is absent in other SARS-like coronaviruses, were identified, which may explain the high pathogenicity of SARS-CoV-2. In humans, the genes that are significant for the initial stages of infection include ACE2, ANPEP, DPP4 (encode receptors for coronavirus binding); TMPRSS2, FURIN, TMPRSS11D, CTSL, CTSB (encode proteases involved in the entry of the coronavirus into the cell); DDX1 (the gene of ATP-dependent RNA helicase DDX1, which promotes replication of coronaviruses); and IFITM1, IFITM2, and IFITM3 (encode interferon-induced transmembrane proteins with an antiviral effect). These genes are expressed in many tissues (including those susceptible to the effects of SARS-CoV-2); rare and frequent variants that affect the structure of the encoded protein and its properties and expression level are described in them. A number of common genetic variants with proven functional significance are characterized by the variability in the allele frequency in the world's populations, which can determine interpopulation differences in the prevalence of COVID-19 and in the clinical features of the course of this pathology. The expression level of genes that are important for the formation of the susceptibility to SARS-CoV-2 is affected by epigenetic modifications, comorbidities at the time of infection, taking medications, and bad habits.
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Affiliation(s)
- A. N. Kucher
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, 634050 Tomsk, Russia
| | - N. P. Babushkina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, 634050 Tomsk, Russia
| | - A. A. Sleptcov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, 634050 Tomsk, Russia
| | - M. S. Nazarenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, 634050 Tomsk, Russia
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20
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Xu S, Yuan H, Li L, Bai F, Yang K, Zhao L. Identification potential epigenetic biomarkers of a human immunodeficiency virus/tuberculosis co-infection based on weighted gene co-expression network analysis. Microbiol Immunol 2021; 65:422-431. [PMID: 34125446 DOI: 10.1111/1348-0421.12926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/17/2021] [Accepted: 06/12/2021] [Indexed: 01/14/2023]
Abstract
Tuberculosis (TB) is one of the most common opportunistic infections and a leading cause of death in patients infected with human immunodeficiency virus (HIV). However, conventional diagnostic tools have several limitations. The aim of this study was to screen key DNA methylated cytosine-phosphate-guanine dinucleotide (CpG) islands (CGIs) to identify potential diagnosis biomarkers in HIV mono-infected patients and HIV/TB co-infected patients based on a network analysis. The GSE50835 DNA methylation microarray data were downloaded from the Gene Expression Omnibus (GEO) database. Differentially methylated CpG islands analysis, weighted gene co-expression network analysis (WGCNA), and least absolute shrinkage and selection operator (LASSO) logistic regression were performed in 19 HIV mono-infected patients and 20 HIV/TB co-infected patients. In total, 1950 differentially methylated CpG islands were identified, and weighted co-methylation network construction and module preservation revealed one network module that can distinguish the HIV/TB co-infected patients from the HIV mono-infected patients. Based on the LASSO logistic regression, an eight-methylated CpG island diagnosis model was established that can accurately distinguish HIV/TB co-infected patients from HIV mono-infected patients with a sensitivity of 87.2%, a specificity of 88.7%, and an area under the receiver operating characteristic (ROC) curve (AUC) of 0.948. Alteration in the eight-DNA methylated CpG sites might be involved in the pathology of an HIV/TB co-infection and could be used as potential diagnosis biomarkers in HIV/TB co-infected patients.
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Affiliation(s)
- Shaohua Xu
- Drug Clinical Trial Center, Gansu Wuwei Tumor Hospital, Wuwei, Gansu, China
| | - Huicheng Yuan
- Drug Clinical Trial Center, Gansu Wuwei Tumor Hospital, Wuwei, Gansu, China
| | - Ling Li
- Drug Clinical Trial Center, Gansu Wuwei Tumor Hospital, Wuwei, Gansu, China
| | - Feng Bai
- Drug Clinical Trial Center, Gansu Wuwei Tumor Hospital, Wuwei, Gansu, China
| | - Kai Yang
- Drug Clinical Trial Center, Gansu Wuwei Tumor Hospital, Wuwei, Gansu, China
| | - Liangcun Zhao
- Drug Clinical Trial Center, Gansu Wuwei Tumor Hospital, Wuwei, Gansu, China
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21
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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: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 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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22
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Quan Y, Liang F, Deng SM, Zhu Y, Chen Y, Xiong J. Mining the Selective Remodeling of DNA Methylation in Promoter Regions to Identify Robust Gene-Level Associations With Phenotype. Front Mol Biosci 2021; 8:597513. [PMID: 33842534 PMCID: PMC8034267 DOI: 10.3389/fmolb.2021.597513] [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: 08/21/2020] [Accepted: 02/01/2021] [Indexed: 11/13/2022] Open
Abstract
Epigenetics is an essential biological frontier linking genetics to the environment, where DNA methylation is one of the most studied epigenetic events. In recent years, through the epigenome-wide association study (EWAS), researchers have identified thousands of phenotype-related methylation sites. However, the overlaps of identified phenotype-related DNA methylation sites between various studies are often quite small, and it might be due to the fact that methylation remodeling has a certain degree of randomness within the genome. Thus, the identification of robust gene-phenotype associations is crucial to interpreting pathogenesis. How to integrate the methylation values of different sites on the same gene and to mine the DNA methylation at the gene level remains a challenge. A recent study found that the DNA methylation difference of the gene body and promoter region has a strong correlation with gene expression. In this study, we proposed a Statistical difference of DNA Methylation between Promoter and Other Body Region (SIMPO) algorithm to extract DNA methylation values at the gene level. First, by choosing to smoke as an environmental exposure factor, our method led to significant improvements in gene overlaps (from 5 to 17%) between different datasets. In addition, the biological significance of phenotype-related genes identified by SIMPO algorithm is comparable to that of the traditional probe-based methods. Then, we selected two disease contents (e.g., insulin resistance and Parkinson's disease) to show that the biological efficiency of disease-related gene identification increased from 15.43 to 44.44% (p-value = 1.20e-28). In summary, our results declare that mining the selective remodeling of DNA methylation in promoter regions can identify robust gene-level associations with phenotype, and the characteristic remodeling of a given gene's promoter region can reflect the essence of disease.
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Affiliation(s)
- Yuan Quan
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
- Lab of Epigenetics and Advanced Health Technology, Space Science and Technology Institute, Shenzhen, China
| | - Fengji Liang
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
| | - Si-Min Deng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Yuexing Zhu
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
- Aromability Inc., Beijing, China
| | - Ying Chen
- Lab of Epigenetics and Advanced Health Technology, Space Science and Technology Institute, Shenzhen, China
| | - Jianghui Xiong
- Lab of Epigenetics and Advanced Health Technology, Space Science and Technology Institute, Shenzhen, China
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
- Aromability Inc., Beijing, China
- Jiangsu Industrial Technology Research Institute (JITRI), Applied Adaptome Immunology Institute, Nanjing, Jiangsu, China
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23
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Zhang W, Yang R, Liang F, Liu G, Chen A, Wu H, Lai S, Ding W, Wei X, Zhen X, Jiang X. Prediction of Microvascular Invasion in Hepatocellular Carcinoma With a Multi-Disciplinary Team-Like Radiomics Fusion Model on Dynamic Contrast-Enhanced Computed Tomography. Front Oncol 2021; 11:660629. [PMID: 33796471 PMCID: PMC8008108 DOI: 10.3389/fonc.2021.660629] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 02/25/2021] [Indexed: 12/24/2022] Open
Abstract
Objective To investigate microvascular invasion (MVI) of HCC through a noninvasive multi-disciplinary team (MDT)-like radiomics fusion model on dynamic contrast enhanced (DCE) computed tomography (CT). Methods This retrospective study included 111 patients with pathologically proven hepatocellular carcinoma, which comprised 57 MVI-positive and 54 MVI-negative patients. Target volume of interest (VOI) was delineated on four DCE CT phases. The volume of tumor core (Vtc) and seven peripheral tumor regions (Vpt, with varying distances of 2, 4, 6, 8, 10, 12, and 14 mm to tumor margin) were obtained. Radiomics features extracted from different combinations of phase(s) and VOI(s) were cross-validated by 150 classification models. The best phase and VOI (or combinations) were determined. The top predictive models were ranked and screened by cross-validation on the training/validation set. The model fusion, a procedure analogous to multidisciplinary consultation, was performed on the top-3 models to generate a final model, which was validated on an independent testing set. Results Image features extracted from Vtc+Vpt(12mm) in the portal venous phase (PVP) showed dominant predictive performances. The top ranked features from Vtc+Vpt(12mm) in PVP included one gray level size zone matrix (GLSZM)-based feature and four first-order based features. Model fusion outperformed a single model in MVI prediction. The weighted fusion method achieved the best predictive performance with an AUC of 0.81, accuracy of 78.3%, sensitivity of 81.8%, and specificity of 75% on the independent testing set. Conclusion Image features extracted from the PVP with Vtc+Vpt(12mm) are the most reliable features indicative of MVI. The MDT-like radiomics fusion model is a promising tool to generate accurate and reproducible results in MVI status prediction in HCC.
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Affiliation(s)
- Wanli Zhang
- Department of Radiology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Radiology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Ruimeng Yang
- Department of Radiology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Radiology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Fangrong Liang
- School of Biomedical Engineering, Southern Medical University, Guangzhou, China
| | - Guoshun Liu
- Department of Radiology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Radiology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Amei Chen
- Department of Radiology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Radiology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Hongzhen Wu
- Department of Radiology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Radiology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Shengsheng Lai
- School of Medical Equipment, Guangdong Food and Drug Vocational College, Guangzhou, China
| | - Wenshuang Ding
- Department of Pathology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Xinhua Wei
- Department of Radiology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Radiology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Xin Zhen
- School of Biomedical Engineering, Southern Medical University, Guangzhou, China
| | - Xinqing Jiang
- Department of Radiology, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Radiology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
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24
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Shu C, Justice AC, Zhang X, Marconi VC, Hancock DB, Johnson EO, Xu K. DNA methylation biomarker selected by an ensemble machine learning approach predicts mortality risk in an HIV-positive veteran population. Epigenetics 2020; 16:741-753. [PMID: 33092459 PMCID: PMC8216205 DOI: 10.1080/15592294.2020.1824097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Background: With the improved life expectancy of people living with HIV (PLWH), identifying vulnerable subpopulations at high mortality risk is important. Evidences showed that DNA methylation (DNAm) is associated with mortality in non-HIV populations. Here, we established a panel of DNAm biomarkers that can predict mortality risk among PLWH. Methods: 1,081 HIV-positive participants from the Veterans Ageing Cohort Study (VACS) were divided into training (N = 460), validation (N = 114), and testing (N = 507) sets. VACS index was used as a measure of mortality risk among PLWH. Model training and fine-tuning were conducted using the ensemble method in the training and validation sets and prediction performance was assessed in the testing set. The survival analysis comparing the predicted high and low mortality risk groups and the Gene Ontology enrichment analysis of the predictive CpG sites were performed. Results: We selected a panel of 393 CpGs for the ensemble prediction model that showed excellent performance in predicting high mortality risk with an auROC of 0.809 (95%CI: 0.767,0.851) and a balanced accuracy of 0.653 (95%CI: 0.611, 0.693) in the testing set. The high mortality risk group was significantly associated with 10-year mortality (hazard ratio = 1.79, p = 4E-05) compared with low risk group. These 393 CpGs were located in 280 genes enriched in immune and inflammation response pathways. Conclusions: We identified a panel of DNAm features associated with mortality risk in PLWH. These DNAm features may serve as predictive biomarkers for mortality risk among PLWH. Abbreviations: AUC: Area Under Curve; CI: Confidence interval; DMR: differentially methylated region; DNA: Deoxyribonucleic acid; DNAm: DNA methylation; DAVID: Database for Annotation, Visualization, and Integrated Discovery; EWA: epigenome-wide association; FDR: False discovery rate; FWER: Family-wise error rate; GLMNET: elastic-net-regularized generalized linear models; GO: Gene ontology; HIV: Human immunodeficiency virus; HM450K: Human Methylation 450 K BeadChip; k-NN: k-nearest neighbours; NK: Natural killer; PC: Principal component; PLWH: people living with HIV; QC: Quality control; SVM: Support Vector Machines; VACS: Veterans Ageing Cohort Study; XGBoost: Extreme Gradient Boosting Tree
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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
| | - Vincent C Marconi
- Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, 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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25
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Cai J, Xu Y, Zhang W, Ding S, Sun Y, Lyu J, Duan M, Liu S, Huang L, Zhou F. A comprehensive comparison of residue-level methylation levels with the regression-based gene-level methylation estimations by ReGear. Brief Bioinform 2020; 22:5921981. [PMID: 33048108 DOI: 10.1093/bib/bbaa253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/10/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
MOTIVATION DNA methylation is a biological process impacting the gene functions without changing the underlying DNA sequence. The DNA methylation machinery usually attaches methyl groups to some specific cytosine residues, which modify the chromatin architectures. Such modifications in the promoter regions will inactivate some tumor-suppressor genes. DNA methylation within the coding region may significantly reduce the transcription elongation efficiency. The gene function may be tuned through some cytosines are methylated. METHODS This study hypothesizes that the overall methylation level across a gene may have a better association with the sample labels like diseases than the methylations of individual cytosines. The gene methylation level is formulated as a regression model using the methylation levels of all the cytosines within this gene. A comprehensive evaluation of various feature selection algorithms and classification algorithms is carried out between the gene-level and residue-level methylation levels. RESULTS A comprehensive evaluation was conducted to compare the gene and cytosine methylation levels for their associations with the sample labels and classification performances. The unsupervised clustering was also improved using the gene methylation levels. Some genes demonstrated statistically significant associations with the class label, even when no residue-level methylation features have statistically significant associations with the class label. So in summary, the trained gene methylation levels improved various methylome-based machine learning models. Both methodology development of regression algorithms and experimental validation of the gene-level methylation biomarkers are worth of further investigations in the future studies. The source code, example data files and manual are available at http://www.healthinformaticslab.org/supp/.
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26
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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: 2.5] [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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Oriol-Tordera B, Berdasco M, Llano A, Mothe B, Gálvez C, Martinez-Picado J, Carrillo J, Blanco J, Duran-Castells C, Ganoza C, Sanchez J, Clotet B, Calle ML, Sánchez-Pla A, Esteller M, Brander C, Ruiz-Riol M. Methylation regulation of Antiviral host factors, Interferon Stimulated Genes (ISGs) and T-cell responses associated with natural HIV control. PLoS Pathog 2020; 16:e1008678. [PMID: 32760119 PMCID: PMC7410168 DOI: 10.1371/journal.ppat.1008678] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/03/2020] [Indexed: 01/21/2023] Open
Abstract
GWAS, immune analyses and biomarker screenings have identified host factors associated with in vivo HIV-1 control. However, there is a gap in the knowledge about the mechanisms that regulate the expression of such host factors. Here, we aimed to assess DNA methylation impact on host genome in natural HIV-1 control. To this end, whole DNA methylome in 70 untreated HIV-1 infected individuals with either high (>50,000 HIV-1-RNA copies/ml, n = 29) or low (<10,000 HIV-1-RNA copies/ml, n = 41) plasma viral load (pVL) levels were compared and identified 2,649 differentially methylated positions (DMPs). Of these, a classification random forest model selected 55 DMPs that correlated with virologic (pVL and proviral levels) and HIV-1 specific adaptive immunity parameters (IFNg-T cell responses and neutralizing antibodies capacity). Then, cluster and functional analyses identified two DMP clusters: cluster 1 contained hypo-methylated genes involved in antiviral and interferon response (e.g. PARP9, MX1, and USP18) in individuals with high viral loads while in cluster 2, genes related to T follicular helper cell (Tfh) commitment (e.g. CXCR5 and TCF7) were hyper-methylated in the same group of individuals with uncontrolled infection. For selected genes, mRNA levels negatively correlated with DNA methylation, confirming an epigenetic regulation of gene expression. Further, these gene expression signatures were also confirmed in early and chronic stages of infection, including untreated, cART treated and elite controllers HIV-1 infected individuals (n = 37). These data provide the first evidence that host genes critically involved in immune control of the virus are under methylation regulation in HIV-1 infection. These insights may offer new opportunities to identify novel mechanisms of in vivo virus control and may prove crucial for the development of future therapeutic interventions aimed at HIV-1 cure.
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Affiliation(s)
- Bruna Oriol-Tordera
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Maria Berdasco
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute, L'Hospitalet de Llobregat, Barcelona, Spain
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Anuska Llano
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Beatriz Mothe
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
- University of Vic—Central University of Catalonia, Catalonia, Vic, Spain
- Fundació Lluita contra la Sida, Infectious Disease Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Cristina Gálvez
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
- University of Vic—Central University of Catalonia, Catalonia, Vic, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Julià Blanco
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
- University of Vic—Central University of Catalonia, Catalonia, Vic, Spain
| | - Clara Duran-Castells
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Carmela Ganoza
- Asociación Civil IMPACTA Salud y Educacion, Lima, Peru
- Alberto Hurtado School of Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jorge Sanchez
- Asociación Civil IMPACTA Salud y Educacion, Lima, Peru
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales, CITBM, Lima, Peru
| | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
- University of Vic—Central University of Catalonia, Catalonia, Vic, Spain
- Fundació Lluita contra la Sida, Infectious Disease Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Maria Luz Calle
- University of Vic—Central University of Catalonia, Catalonia, Vic, Spain
| | - Alex Sánchez-Pla
- Statistics Department, Biology Faculty, University of Barcelona, Spain
- Statistics and Bioinformatics Unit Vall d'Hebron Institut de Recerca (VHIR), Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Christian Brander
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
- University of Vic—Central University of Catalonia, Catalonia, Vic, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
- AELIX Therapeutics, Barcelona, Spain
| | - Marta Ruiz-Riol
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
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Ivanov S, Lagunin A, Filimonov D, Tarasova O. Network-Based Analysis of OMICs Data to Understand the HIV-Host Interaction. Front Microbiol 2020; 11:1314. [PMID: 32625189 PMCID: PMC7311653 DOI: 10.3389/fmicb.2020.01314] [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: 04/09/2020] [Accepted: 05/25/2020] [Indexed: 12/22/2022] Open
Abstract
The interaction of human immunodeficiency virus with human cells is responsible for all stages of the viral life cycle, from the infection of CD4+ cells to reverse transcription, integration, and the assembly of new viral particles. To date, a large amount of OMICs data as well as information from functional genomics screenings regarding the HIV–host interaction has been accumulated in the literature and in public databases. We processed databases containing HIV–host interactions and found 2910 HIV-1-human protein-protein interactions, mostly related to viral group M subtype B, 137 interactions between human and HIV-1 coding and non-coding RNAs, essential for viral lifecycle and cell defense mechanisms, 232 transcriptomics, 27 proteomics, and 34 epigenomics HIV-related experiments. Numerous studies regarding network-based analysis of corresponding OMICs data have been published in recent years. We overview various types of molecular networks, which can be created using OMICs data, including HIV–human protein–protein interaction networks, co-expression networks, gene regulatory and signaling networks, and approaches for the analysis of their topology and dynamics. The network-based analysis can be used to determine the critical pathways and key proteins involved in the HIV life cycle, cellular and immune responses to infection, viral escape from host defense mechanisms, and mechanisms mediating different susceptibility of humans to infection. The proteins and pathways identified in these studies represent a basis for developing new anti-HIV therapeutic strategies such as new drugs preventing infection of CD4+ cells and viral replication, effective vaccines, “shock and kill” and “block and lock” approaches to cure latent infection.
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Affiliation(s)
- Sergey Ivanov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia.,Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexey Lagunin
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia.,Department of Bioinformatics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry Filimonov
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
| | - Olga Tarasova
- Department of Bioinformatics, Institute of Biomedical Chemistry, Moscow, Russia
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