1
|
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.
Collapse
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
| |
Collapse
|
2
|
Gupta MK, Peng H, Li Y, Xu CJ. The role of DNA methylation in personalized medicine for immune-related diseases. Pharmacol Ther 2023; 250:108508. [PMID: 37567513 DOI: 10.1016/j.pharmthera.2023.108508] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
Epigenetics functions as a bridge between host genetic & environmental factors, aiding in human health and diseases. Many immune-related diseases, including infectious and allergic diseases, have been linked to epigenetic mechanisms, particularly DNA methylation. In this review, we summarized an updated overview of DNA methylation and its importance in personalized medicine, and demonstrated that DNA methylation has excellent potential for disease prevention, diagnosis, and treatment in a personalized manner. The future implications and limitations of the DNA methylation study have also been well-discussed.
Collapse
Affiliation(s)
- Manoj Kumar Gupta
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - He Peng
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Yang Li
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Internal Medicine and Radboud Institute for Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cheng-Jian Xu
- Centre for Individualised Infection Medicine (CiiM), a joint venture between the Helmholtz Centre for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany; TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Internal Medicine and Radboud Institute for Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands.
| |
Collapse
|
3
|
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.
Collapse
|
4
|
Esteban-Cantos A, Rodríguez-Centeno J, Silla JC, Barruz P, Sánchez-Cabo F, Saiz-Medrano G, Nevado J, Mena-Garay B, Jiménez-González M, de Miguel R, Bernardino JI, Montejano R, Cadiñanos J, Marcelo C, Gutiérrez-García L, Martínez-Martín P, Wallet C, Raffi F, Rodés B, Arribas JR. Effect of HIV infection and antiretroviral therapy initiation on genome-wide DNA methylation patterns. EBioMedicine 2023; 88:104434. [PMID: 36640455 PMCID: PMC9842861 DOI: 10.1016/j.ebiom.2022.104434] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/09/2022] [Accepted: 12/22/2022] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Previous epigenome-wide association studies have shown that HIV infection can disrupt the host DNA methylation landscape. However, it remains unclear how antiretroviral therapy (ART) affects the HIV-induced epigenetic modifications. METHODS 184 individuals with HIV from the NEAT001/ANRS143 clinical trial (with pre-ART and post-ART samples [96 weeks of follow-up]) and 44 age-and-sex matched individuals without HIV were included. We compared genome-wide DNA methylation profiles in whole blood between groups adjusting for age, sex, batch effects, and DNA methylation-based estimates of leucocyte composition. FINDINGS We identified 430 differentially methylated positions (DMPs) between HIV+ pre-ART individuals and HIV-uninfected controls. In participants with HIV, ART initiation modified the DNA methylation levels at 845 CpG positions and restored 49.3% of the changes found between HIV+ pre-ART and HIV-uninfected individuals. We only found 15 DMPs when comparing DNA methylation profiles between HIV+ post-ART individuals and participants without HIV. The Gene Ontology enrichment analysis of DMPs associated with untreated HIV infection revealed an enrichment in biological processes regulating the immune system and antiviral responses. In participants with untreated HIV infection, DNA methylation levels at top HIV-related DMPs were associated with CD4/CD8 ratios and viral loads. Changes in DNA methylation levels after ART initiation were weakly correlated with changes in CD4+ cell counts and the CD4/CD8 ratio. INTERPRETATION Control of HIV viraemia after 96 weeks of ART initiation partly restores the host DNA methylation changes that occurred before antiretroviral treatment of HIV infection. FUNDING NEAT-ID Foundation and Instituto de Salud Carlos III, co-funded by European Union.
Collapse
Affiliation(s)
- Andrés Esteban-Cantos
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Javier Rodríguez-Centeno
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Juan C Silla
- Bioinformatics Unit, Spanish National Centre for Cardiovascular Research (CNIC), Madrid, Spain
| | - Pilar Barruz
- Genomics Laboratory, Institute of Medical and Molecular Genetics, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Spanish National Centre for Cardiovascular Research (CNIC), Madrid, Spain
| | - Gabriel Saiz-Medrano
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Julián Nevado
- Genomics Laboratory, Institute of Medical and Molecular Genetics, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Beatriz Mena-Garay
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - María Jiménez-González
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Rosa de Miguel
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Jose I Bernardino
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Rocío Montejano
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Julen Cadiñanos
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Cristina Marcelo
- Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Lucía Gutiérrez-García
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Patricia Martínez-Martín
- Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Cédrick Wallet
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, CHU de Bordeaux, Bordeaux, France
| | - François Raffi
- Centre Hospitalier Universitaire de Nantes and CIC 1413 INSERM, Nantes, France
| | - Berta Rodés
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain.
| | - José R Arribas
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain.
| |
Collapse
|
5
|
Pontel LB, Bueno-Costa A, Morellato AE, Carvalho Santos J, Roué G, Esteller M. Acute lymphoblastic leukemia necessitates GSH-dependent ferroptosis defenses to overcome FSP1-epigenetic silencing. Redox Biol 2022; 55:102408. [PMID: 35944469 PMCID: PMC9364119 DOI: 10.1016/j.redox.2022.102408] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/12/2022] [Indexed: 12/03/2022] Open
Abstract
Ferroptosis is a form of cell death triggered by phospholipid hydroperoxides (PLOOH) generated from the iron-dependent oxidation of polyunsaturated fatty acids (PUFAs). To prevent ferroptosis, cells rely on the antioxidant glutathione (GSH), which serves as cofactor of the glutathione peroxidase 4 (GPX4) for the neutralization of PLOOHs. Some cancer cells can also limit ferroptosis through a GSH-independent axis, centered mainly on the ferroptosis suppressor protein 1 (FSP1). The significance of these two anti-ferroptosis pathways is still poorly understood in cancers from hematopoietic origin. Here, we report that blood-derived cancer cells are selectively sensitive to compounds that block the GSH-dependent anti-ferroptosis axis. In T- and B- acute lymphoblastic leukemia (ALL) cell lines and patient biopsies, the promoter of the gene coding for FSP1 is hypermethylated, silencing the expression of FSP1 and creating a selective dependency on GSH-centered anti-ferroptosis defenses. In-trans expression of FSP1 increases the resistance of leukemic cells to compounds targeting the GSH-dependent anti-ferroptosis pathway. FSP1 over-expression also favors ALL-tumor growth in an in vivo chick chorioallantoic membrane (CAM) model. Hence, our results reveal a metabolic vulnerability of ALL that might be of therapeutic interest.
Collapse
Affiliation(s)
- Lucas B Pontel
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain; Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina.
| | - Alberto Bueno-Costa
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Agustín E Morellato
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Juliana Carvalho Santos
- Lymphoma Translational Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Gaël Roué
- Lymphoma Translational Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain; Centro de Investigacion Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain.
| |
Collapse
|
6
|
Butyrate administration is not sufficient to improve immune reconstitution in antiretroviral-treated SIV-infected macaques. Sci Rep 2022; 12:7491. [PMID: 35523797 PMCID: PMC9076870 DOI: 10.1038/s41598-022-11122-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/13/2022] [Indexed: 12/15/2022] Open
Abstract
Defective gastrointestinal barrier function and, in turn, microbial translocation have been identified as significant contributors to persistent inflammation in antiretroviral (ARV)-treated people living with HIV. Metabolic supplementation of short-chain fatty acids (SCFAs), generally produced by the commensal microbiome, may improve these outcomes. Butyrate is a SCFA that is essential for the development and maintenance of intestinal immunity and has a known role in supporting epithelial integrity. Herein we assessed whether supplementation with the dietary supplement sodium butyrate would improve immune reconstitution and reduce inflammation in ARV-treated, simian immunodeficiency virus (SIV)-infected rhesus macaques. We demonstrate that butyrate supplementation does not significantly improve immune reconstitution, with no differences observed in systemic CD4+ T-cell frequencies, T-cell functionality or immune activation, microbial translocation, or transcriptional regulation. Our findings demonstrate that oral administration of sodium butyrate is insufficient to reduce persistent inflammation and microbial translocation in ARV-treated, SIV-infected macaques, suggesting that this therapeutic may not reduce co-morbidities and co-mortalities in treated people living with HIV.
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Arumugam T, Ramphal U, Adimulam T, Chinniah R, Ramsuran V. Deciphering DNA Methylation in HIV Infection. Front Immunol 2021; 12:795121. [PMID: 34925380 PMCID: PMC8674454 DOI: 10.3389/fimmu.2021.795121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/17/2021] [Indexed: 12/13/2022] Open
Abstract
With approximately 38 million people living with HIV/AIDS globally, and a further 1.5 million new global infections per year, it is imperative that we advance our understanding of all factors contributing to HIV infection. While most studies have focused on the influence of host genetic factors on HIV pathogenesis, epigenetic factors are gaining attention. Epigenetics involves alterations in gene expression without altering the DNA sequence. DNA methylation is a critical epigenetic mechanism that influences both viral and host factors. This review has five focal points, which examines (i) fluctuations in the expression of methylation modifying factors upon HIV infection (ii) the effect of DNA methylation on HIV viral genes and (iii) host genome (iv) inferences from other infectious and non-communicable diseases, we provide a list of HIV-associated host genes that are regulated by methylation in other disease models (v) the potential of DNA methylation as an epi-therapeutic strategy and biomarker. DNA methylation has also been shown to serve as a robust therapeutic strategy and precision medicine biomarker against diseases such as cancer and autoimmune conditions. Despite new drugs being discovered for HIV, drug resistance is a problem in high disease burden settings such as Sub-Saharan Africa. Furthermore, genetic therapies that are under investigation are irreversible and may have off target effects. Alternative therapies that are nongenetic are essential. In this review, we discuss the potential role of DNA methylation as a novel therapeutic intervention against HIV.
Collapse
Affiliation(s)
- Thilona Arumugam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Upasana Ramphal
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Theolan Adimulam
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Romona Chinniah
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| |
Collapse
|
9
|
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.
Collapse
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:
| | | |
Collapse
|
10
|
Launching a multidisciplinary European collaboration towards a cure for HIV: The EU2Cure Consortium. J Virus Erad 2021; 7:100045. [PMID: 34141442 PMCID: PMC8184646 DOI: 10.1016/j.jve.2021.100045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 11/23/2022] Open
Abstract
We felt the urgency to launch the EU2Cure Consortium to support research and find a cure for the human immunodeficiency virus (HIV) infection through intensified collaboration within Europe. This consortium is open to stakeholders on cure in Europe from academia and the community to connect. The aim of this consortium is to intensify the research collaboration amongst European HIV cure groups and the community and facilitate interactions with other academic and community cure consortia, private parties, and policy makers. Our main aim is to create a European research agenda, data sharing, and development of best practice for clinical and translational science to achieve breakthroughs with clinically feasible HIV cure strategies. This consortium should also enable setting up collaborative studies accessible to a broader group of people living with HIV. Besides reservoir studies, we have identified three overlapping scientific interests in the consortium that provide a starting point for further research within a European network: developing “shock and kill” cure strategies, defining HIV cure biomarkers, and connecting cure cohorts. This strategy should aid stakeholders to sustain progress in HIV cure research regardless of coincidental global health or political crises.
Collapse
|
11
|
Singh R, Ramsuran V, Naranbhai V, Yende-Zuma N, Garrett N, Mlisana K, Dong KL, Walker BD, Abdool Karim SS, Carrington M, Ndung'u T. Epigenetic Regulation of BST-2 Expression Levels and the Effect on HIV-1 Pathogenesis. Front Immunol 2021; 12:669241. [PMID: 34025670 PMCID: PMC8131512 DOI: 10.3389/fimmu.2021.669241] [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: 02/18/2021] [Accepted: 04/20/2021] [Indexed: 11/23/2022] Open
Abstract
HIV-1 must overcome host antiviral restriction factors for efficient replication. We hypothesized that elevated levels of bone marrow stromal cell antigen 2 (BST-2), a potent host restriction factor that interferes with HIV-1 particle release in some human cells and is antagonized by the viral protein Vpu, may associate with viral control. Using cryopreserved samples, from HIV-1 seronegative and seropositive Black women, we measured in vitro expression levels of BST-2 mRNA using a real-time PCR assay and protein levels were validated by Western blotting. The expression level of BST-2 showed an association with viral control within two independent cohorts of Black HIV infected females (r=-0.53, p=0.015, [n =21]; and r=-0.62, p=0.0006, [n=28]). DNA methylation was identified as a mechanism regulating BST-2 levels, where increased BST-2 methylation results in lower expression levels and associates with worse HIV disease outcome. We further demonstrate the ability to regulate BST-2 levels using a DNA hypomethylation drug. Our results suggest BST-2 as a factor for potential therapeutic intervention against HIV and other diseases known to involve BST-2.
Collapse
Affiliation(s)
- Ravesh Singh
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute (AHRI), Durban, South Africa.,Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, Bethesda, MD, United States.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Vivek Naranbhai
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, Bethesda, MD, United States.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nonhlanhla Yende-Zuma
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Koleka Mlisana
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Krista L Dong
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Bruce D Walker
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute (AHRI), Durban, South Africa.,The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Mary Carrington
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, Bethesda, MD, United States
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute (AHRI), Durban, South Africa.,The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Max Planck Institute for Infection Biology, Chariteplatz, Berlin, Germany.,Division of Infection and Immunity, University College London, London, United Kingdom
| |
Collapse
|