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Horvath S, Singh K, Raj K, Khairnar SI, Sanghavi A, Shrivastava A, Zoller JA, Li CZ, Herenu CB, Canatelli-Mallat M, Lehmann M, Habazin S, Novokmet M, Vučković F, Solberg Woods LC, Martinez AG, Wang T, Chiavellini P, Levine AJ, Chen H, Brooke RT, Gordevicius J, Lauc G, Goya RG, Katcher HL. Reversal of biological age in multiple rat organs by young porcine plasma fraction. GeroScience 2024; 46:367-394. [PMID: 37875652 PMCID: PMC10828479 DOI: 10.1007/s11357-023-00980-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023] Open
Abstract
Young blood plasma is known to confer beneficial effects on various organs in mice and rats. However, it was not known whether plasma from young adult pigs rejuvenates old rat tissues at the epigenetic level; whether it alters the epigenetic clock, which is a highly accurate molecular biomarker of aging. To address this question, we developed and validated six different epigenetic clocks for rat tissues that are based on DNA methylation values derived from n = 613 tissue samples. As indicated by their respective names, the rat pan-tissue clock can be applied to DNA methylation profiles from all rat tissues, while the rat brain, liver, and blood clocks apply to the corresponding tissue types. We also developed two epigenetic clocks that apply to both human and rat tissues by adding n = 1366 human tissue samples to the training data. We employed these six rat clocks to investigate the rejuvenation effects of a porcine plasma fraction treatment in different rat tissues. The treatment more than halved the epigenetic ages of blood, heart, and liver tissue. A less pronounced, but statistically significant, rejuvenation effect could be observed in the hypothalamus. The treatment was accompanied by progressive improvement in the function of these organs as ascertained through numerous biochemical/physiological biomarkers, behavioral responses encompassing cognitive functions. An immunoglobulin G (IgG) N-glycosylation pattern shift from pro- to anti-inflammatory also indicated reversal of glycan aging. Overall, this study demonstrates that a young porcine plasma-derived treatment markedly reverses aging in rats according to epigenetic clocks, IgG glycans, and other biomarkers of aging.
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Affiliation(s)
- Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA.
- Altos Labs, Cambridge, UK.
| | - Kavita Singh
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM's NMIMS University, Mumbai, India
| | | | - Shraddha I Khairnar
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM's NMIMS University, Mumbai, India
| | | | | | - Joseph A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Caesar Z Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA
| | - Claudia B Herenu
- Institute for Experimental Pharmacology of Cordoba (IFEC), School of Chemical Sciences, National University of Cordoba, Cordoba, Argentina
| | - Martina Canatelli-Mallat
- Biochemistry Research Institute of La Plata-Histology B, Pathology B, School of Medicine, University of La Plata, La Plata, Argentina
| | - Marianne Lehmann
- Biochemistry Research Institute of La Plata-Histology B, Pathology B, School of Medicine, University of La Plata, La Plata, Argentina
| | | | | | | | - Leah C Solberg Woods
- Wake Forest University School of Medicine, Medical Center Drive, Winston Salem, NC, USA
| | - Angel Garcia Martinez
- Department of Pharmacology, Addiction Science and Toxicology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Tengfei Wang
- Department of Pharmacology, Addiction Science and Toxicology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Priscila Chiavellini
- Biochemistry Research Institute of La Plata-Histology B, Pathology B, School of Medicine, University of La Plata, La Plata, Argentina
| | - Andrew J Levine
- Department of Neurology, David Geffen School of Medicine at the University of California, Los Angeles, CA, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | | | | | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Rodolfo G Goya
- Biochemistry Research Institute of La Plata-Histology B, Pathology B, School of Medicine, University of La Plata, La Plata, Argentina
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Zoller JA, Parasyraki E, Lu AT, Haghani A, Niehrs C, Horvath S. DNA methylation clocks for clawed frogs reveal evolutionary conservation of epigenetic aging. GeroScience 2024; 46:945-960. [PMID: 37270437 PMCID: PMC10828168 DOI: 10.1007/s11357-023-00840-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/25/2023] [Indexed: 06/05/2023] Open
Abstract
To address how conserved DNA methylation-based epigenetic aging is in diverse branches of the tree of life, we generated DNA methylation data from African clawed frogs (Xenopus laevis) and Western clawed frogs (Xenopus tropicalis) and built multiple epigenetic clocks. Dual species clocks were developed that apply to both humans and frogs (human-clawed frog clocks), supporting that epigenetic aging processes are evolutionary conserved outside mammals. Highly conserved positively age-related CpGs are located in neural-developmental genes such as uncx, tfap2d as well as nr4a2 implicated in age-associated disease. We conclude that signatures of epigenetic aging are evolutionary conserved between frogs and mammals and that the associated genes relate to neural processes, altogether opening opportunities to employ Xenopus as a model organism to study aging.
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Affiliation(s)
- Joseph A Zoller
- Department of Biostatistics, School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany.
- German Cancer Research Center (DKFZ), Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Steve Horvath
- Department of Biostatistics, School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego, CA, USA.
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3
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Comley-White N, Ntsiea V, Potterton J. Physical functioning in adolescents with perinatal HIV. AIDS Care 2024; 36:60-69. [PMID: 37229771 DOI: 10.1080/09540121.2023.2214862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/11/2023] [Indexed: 05/27/2023]
Abstract
Perinatal HIV impacts on growth and development in childhood, with physical impairments such as growth limitations, decreased physical activity, reduced exercise tolerance and cardiopulmonary dysfunction continuing into adolescence. There is limited data on other physical functioning domains in perinatally HIV-infected adolescents (PHIVA) thus the aim of this study was to establish the physical sequelae of perinatal HIV in adolescents. This South African cross-sectional study compared PHIVA with HIV-negative adolescents, assessing anthropometry, muscle strength, endurance and motor performance. All ethical considerations were adhered to. The study included 147 PHIVA and 102 HIV-negative adolescents, aged 10-16 years. The majority (87.1%) of PHIVA were virally suppressed however, they still showed significant deficits in height (p < 0.001), weight (p < 0.001) and BMI (p = 0.004). Both groups performed poorly in muscle strength and endurance but did not differ significantly. In motor performance, the PHIVA scored significantly lower for manual dexterity and balance, with significantly more PHIVA with motor difficulty. A regression analysis showed that viral suppression predicted muscle strength (p = 0.032) and age positively predicted endurance (p = 0.044) and negatively predicated aiming and catching (p = 0.009). In conclusion, PHIVA face growth deficits and challenges with motor performance, especially with manual dexterity and balance.
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Affiliation(s)
- Nicolette Comley-White
- Department of Physiotherapy, University of the Witwatersrand, Johannesburg, South Africa
| | - Veronica Ntsiea
- Department of Physiotherapy, University of the Witwatersrand, Johannesburg, South Africa
| | - Joanne Potterton
- Department of Physiotherapy, University of the Witwatersrand, Johannesburg, South Africa
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4
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Corley MJ, Pang APS, Shikuma CM, Ndhlovu LC. Cell-type specific impact of metformin on monocyte epigenetic age reversal in virally suppressed older people living with HIV. Aging Cell 2024; 23:e13926. [PMID: 37675817 PMCID: PMC10776116 DOI: 10.1111/acel.13926] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 09/08/2023] Open
Abstract
The anti-diabetic drug metformin may promote healthy aging. However, few clinical trials of metformin assessing biomarkers of aging have been completed. In this communication, we retrospectively examined the effect of metformin on epigenetic age using principal component (PC)-based epigenetic clocks, mitotic clocks, and pace of aging in peripheral monocytes and CD8+ T cells from participants in two clinical trials of virologically-suppressed people living with HIV (PLWH) with normal glucose receiving metformin. In a small 24-week clinical trial that randomized participants to receive either adjunctive metformin or observation, we observed significantly decreased PCPhenoAge and PCGrimAge estimates of monocytes from only participants in the metformin arm by a mean decrease of 3.53 and 1.84 years from baseline to Week 24. In contrast, we observed no significant differences in all PC clocks for participants in the observation arm over 24 weeks. Notably, our analysis of epigenetic mitotic clocks revealed significant increases for monocytes in the metformin arm when comparing baseline to Week 24, suggesting an impact of metformin on myeloid cell kinetics. Analysis of a single-arm clinical trial of adjunctive metformin in eight PLWH revealed no significant differences across all epigenetic clocks assessed in CD8+ T cells at 4- and 8-week time points. Our results suggest cell-type-specific myeloid effects of metformin captured by PC-based epigenetic clock biomarkers. Larger clinical studies of metformin are needed to validate these observations and this report highlights the need for further inclusion of PLWH in geroscience trials evaluating the effect of metformin on increasing healthspan and lifespan.
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Affiliation(s)
- Michael J. Corley
- Department of Medicine, Division of Infectious DiseasesWeill Cornell MedicineNew York CityNew YorkUSA
| | - Alina P. S. Pang
- Department of Medicine, Division of Infectious DiseasesWeill Cornell MedicineNew York CityNew YorkUSA
| | - Cecilia M. Shikuma
- Hawaii Center for AIDS, John A. Burns School of MedicineUniversity of HawaiiHonoluluHawaiiUSA
| | - Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious DiseasesWeill Cornell MedicineNew York CityNew YorkUSA
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Ndhlovu LC, Bendall ML, Dwaraka V, Pang APS, Dopkins N, Carreras N, Smith R, Nixon DF, Corley MJ. Retroelement-Age Clocks: Epigenetic Age Captured by Human Endogenous Retrovirus and LINE-1 DNA methylation states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570422. [PMID: 38106164 PMCID: PMC10723416 DOI: 10.1101/2023.12.06.570422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Human endogenous retroviruses (HERVs), the remnants of ancient viral infections embedded within the human genome, and long interspersed nuclear elements 1 (LINE-1), a class of autonomous retrotransposons, are silenced by host epigenetic mechanisms including DNA methylation. The resurrection of particular retroelements has been linked to biological aging. Whether the DNA methylation states of locus specific HERVs and LINEs can be used as a biomarker of chronological age in humans remains unclear. We show that highly predictive epigenetic clocks of chronological age can be constructed from retroelement DNA methylation states in the immune system, across human tissues, and pan-mammalian species. We found retroelement epigenetic clocks were reversed during transient epigenetic reprogramming, accelerated in people living with HIV-1, responsive to antiretroviral therapy, and accurate in estimating long-term culture ages of human brain organoids. Our findings support the hypothesis of epigenetic dysregulation of retroelements as a potential contributor to the biological hallmarks of aging.
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Affiliation(s)
- Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Matthew L. Bendall
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | | | - Alina PS Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Nicholas Dopkins
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | | | | | - Douglas F. Nixon
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Michael J. Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
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Mohammadzadeh N, Chomont N, Estaquier J, Cohen EA, Power C. Is the Central Nervous System Reservoir a Hurdle for an HIV Cure? Viruses 2023; 15:2385. [PMID: 38140626 PMCID: PMC10747469 DOI: 10.3390/v15122385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 11/28/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023] Open
Abstract
There is currently no cure for HIV infection although adherence to effective antiretroviral therapy (ART) suppresses replication of the virus in blood, increases CD4+ T-cell counts, reverses immunodeficiency, and increases life expectancy. Despite these substantial advances, ART is a lifelong treatment for people with HIV (PWH) and upon cessation or interruption, the virus quickly rebounds in plasma and anatomic sites, including the central nervous system (CNS), resulting in disease progression. With recent advances in quantifying viral burden, detection of genetically intact viral genomes, and isolation of replication-competent virus from brain tissues of PWH receiving ART, it has become apparent that the CNS viral reservoir (largely comprised of macrophage type cells) poses a substantial challenge for HIV cure strategies. Other obstacles impacting the curing of HIV include ageing populations, substance use, comorbidities, limited antiretroviral drug efficacy in CNS cells, and ART-associated neurotoxicity. Herein, we review recent findings, including studies of the proviral integration sites, reservoir decay rates, and new treatment/prevention strategies in the context of the CNS, together with highlighting the next steps for investigations of the CNS as a viral reservoir.
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Affiliation(s)
- Nazanin Mohammadzadeh
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada;
| | - Nicolas Chomont
- Department of Immunopathology, Research Centre of the Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC H2X 0A9, Canada;
- Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada;
| | - Jerome Estaquier
- Department of Microbiology and Immunology, CHU de Québec-Université Laval Research Center, Québec, QC G1V 4G2, Canada;
| | - Eric A. Cohen
- Department of Microbiology, Infectiology and Immunology, Faculty of Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada;
- Institut de Recherches Cliniques de Montreal, Montreal, QC H2W 1R7, Canada
| | - Christopher Power
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2R3, Canada;
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Horvath S, Haghani A, Zoller JA, Lu AT, Ernst J, Pellegrini M, Jasinska AJ, Mattison JA, Salmon AB, Raj K, Horvath M, Paul KC, Ritz BR, Robeck TR, Spriggs M, Ehmke EE, Jenkins S, Li C, Nathanielsz PW. Pan-primate studies of age and sex. GeroScience 2023; 45:3187-3209. [PMID: 37493860 PMCID: PMC10643767 DOI: 10.1007/s11357-023-00878-3] [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: 06/08/2023] [Accepted: 07/16/2023] [Indexed: 07/27/2023] Open
Abstract
Age and sex have a profound effect on cytosine methylation levels in humans and many other species. Here we analyzed DNA methylation profiles of 2400 tissues derived from 37 primate species including 11 haplorhine species (baboons, marmosets, vervets, rhesus macaque, chimpanzees, gorillas, orangutan, humans) and 26 strepsirrhine species (suborders Lemuriformes and Lorisiformes). From these we present here, pan-primate epigenetic clocks which are highly accurate for all primates including humans (age correlation R = 0.98). We also carried out in-depth analysis of baboon DNA methylation profiles and generated five epigenetic clocks for baboons (Olive-yellow baboon hybrid), one of which, the pan-tissue epigenetic clock, was trained on seven tissue types (fetal cerebral cortex, adult cerebral cortex, cerebellum, adipose, heart, liver, and skeletal muscle) with ages ranging from late fetal life to 22.8 years of age. Using the primate data, we characterize the effect of age and sex on individual cytosines in highly conserved regions. We identify 11 sex-related CpGs on autosomes near genes (POU3F2, CDYL, MYCL, FBXL4, ZC3H10, ZXDC, RRAS, FAM217A, RBM39, GRIA2, UHRF2). Low overlap can be observed between age- and sex-related CpGs. Overall, this study advances our understanding of conserved age- and sex-related epigenetic changes in primates, and provides biomarkers of aging for all primates.
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Affiliation(s)
- Steve Horvath
- Altos Labs, San Diego, CA, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
| | | | - Joseph A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Jason Ernst
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and BiobehavioralSciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Julie A Mattison
- Translational Gerontology Branch, National Institute On Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Adam B Salmon
- The Sam and Ann Barshop Institute for Longevity and Aging Studies, and Department of Molecular Medicine, UT Health San Antonio, and the Geriatric Research Education and Clinical Center, South Texas Veterans Healthcare System, San Antonio, TX, USA
| | | | | | - Kimberly C Paul
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Beate R Ritz
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Epidemiology, UCLA Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Todd R Robeck
- Corporate Zoological Operations, SeaWorld Parks, Orlando, FL, USA
| | - Maria Spriggs
- Busch Gardens Tampa, SeaWorld Parks, Tampa, FL, 33612, USA
| | | | - Susan Jenkins
- Texas Pregnancy & Life-Course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources Department, Laramie, WY, USA
| | - Cun Li
- Texas Pregnancy & Life-Course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources Department, Laramie, WY, USA
| | - Peter W Nathanielsz
- Texas Pregnancy & Life-Course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources Department, Laramie, WY, USA
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Musci RJ, Raghunathan RS, Johnson SB, Klein L, Ladd-Acosta C, Ansah R, Hassoun R, Voegtline KM. Using Epigenetic Clocks to Characterize Biological Aging in Studies of Children and Childhood Exposures: a Systematic Review. PREVENTION SCIENCE : THE OFFICIAL JOURNAL OF THE SOCIETY FOR PREVENTION RESEARCH 2023; 24:1398-1423. [PMID: 37477807 PMCID: PMC10964791 DOI: 10.1007/s11121-023-01576-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2023] [Indexed: 07/22/2023]
Abstract
Biological age, measured via epigenetic clocks, offers a unique and useful tool for prevention scientists to explore the short- and long-term implications of age deviations for health, development, and behavior. The use of epigenetic clocks in pediatric research is rapidly increasing, and there is a need to review the landscape of this work to understand the utility of these clocks for prevention scientists. We summarize the current state of the literature on the use of specific epigenetic clocks in childhood. Using systematic review methods, we identified studies published through February 2023 that used one of three epigenetic clocks as a measure of biological aging. These epigenetic clocks could either be used as a predictor of health outcomes or as a health outcome of interest. The database search identified 982 records, 908 of which were included in a title and abstract review. After full-text screening, 68 studies were eligible for inclusion. While findings were somewhat mixed, a majority of included studies found significant associations between the epigenetic clock used and the health outcome of interest or between an exposure and the epigenetic clock used. From these results, we propose the use of epigenetic clocks as a tool to understand how exposures impact biologic aging pathways and development in early life, as well as to monitor the effectiveness of preventive interventions that aim to reduce exposure and associated adverse health outcomes.
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Affiliation(s)
- Rashelle J Musci
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, Baltimore, MD, 21205, USA.
| | | | - Sara B Johnson
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, Baltimore, MD, 21205, USA
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, USA
- Department of Population, Family and Reproductive Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Lauren Klein
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, USA
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
| | - Rosemary Ansah
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, USA
| | - Ronda Hassoun
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, 624 N. Broadway, Baltimore, MD, 21205, USA
| | - Kristin M Voegtline
- Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, USA
- Department of Population, Family and Reproductive Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
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Mastrotheodoros S, Boks MP, Rousseau C, Meeus W, Branje S. Negative parenting, epigenetic age, and psychological problems: prospective associations from adolescence to young adulthood. J Child Psychol Psychiatry 2023; 64:1446-1461. [PMID: 37203368 DOI: 10.1111/jcpp.13821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND Epigenetic clocks are based on DNA methylation levels of several genomic loci and have been developed as indices of biological aging. Studies examining the effects of stressful environmental exposures have shown that stress is associated with differences between epigenetic age and chronological age (i.e., Epigenetic Age acceleration, EA). This pre-registered longitudinal study examined the long-term effects of negative parenting and psychological problems throughout adolescence (ages 13-17 years) on EA in late adolescence (age 17 years) and EA changes from late adolescence to young adulthood (age 25 years). Further, it examined how (change in) EA is related to changes in psychological problems from adolescence to young adulthood. METHODS We used data from a sample of 434 participants followed from age 13 to age 25, with saliva collected at ages 17 and 25. We estimated EA using four commonly used epigenetic clocks and analyzed the data using Structural Equation Modeling. RESULTS While negative parenting was not related to EA nor change in EA, (change in) EA was related to developmental indices such as externalizing problems and self-concept clarity. CONCLUSIONS Declining psychological well-being during young adulthood was preceded by EA.
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Affiliation(s)
- Stefanos Mastrotheodoros
- Department of Youth and Family, Utrecht University, Utrecht, The Netherlands
- Department of Psychology, University of Crete, Rethymno, Greece
| | - Marco P Boks
- Department of Psychiatry, Brain Center University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Céline Rousseau
- Department of Psychiatry, Brain Center University Medical Center Utrecht, University Utrecht, Utrecht, The Netherlands
| | - Wim Meeus
- Department of Youth and Family, Utrecht University, Utrecht, The Netherlands
| | - Susan Branje
- Department of Youth and Family, Utrecht University, Utrecht, The Netherlands
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10
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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.
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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.
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Haghani A, Li CZ, Robeck TR, Zhang J, Lu AT, Ablaeva J, Acosta-Rodríguez VA, Adams DM, Alagaili AN, Almunia J, Aloysius A, Amor NM, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter G, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chavez AS, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke S, Cook JA, Cooper LN, Cossette ML, Day J, DeYoung J, Dirocco S, Dold C, Dunnum JL, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Fei Z, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Goya RG, Grant MJ, Green CB, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Belmonte JCI, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaître JF, Levine AJ, Li X, Li C, Lim AR, Lin DTS, Lindemann DM, Liphardt SW, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Murphy WJ, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, Nyamsuren B, O’Brien JK, Ginn PO, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pedersen AB, Pellegrini M, Peters KJ, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Shafer AB, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmohammadi E, Spangler ML, Spriggs M, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Vu H, Wallingford MC, Wang N, Wilkinson GS, Williams RW, Yan Q, Yao M, Young BG, Zhang B, Zhang Z, Zhao Y, Zhao P, Zhou W, Zoller JA, Ernst J, Seluanov A, Gorbunova V, Yang XW, Raj K, Horvath S. DNA methylation networks underlying mammalian traits. Science 2023; 381:eabq5693. [PMID: 37561875 PMCID: PMC11180965 DOI: 10.1126/science.abq5693] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/21/2023] [Indexed: 08/12/2023]
Abstract
Using DNA methylation profiles (n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all samples, we identified 55 distinct cytosine modules, of which 30 are related to traits such as maximum life span, adult weight, age, sex, and human mortality risk. Maximum life span is associated with methylation levels in HOXL subclass homeobox genes and developmental processes and is potentially regulated by pluripotency transcription factors. The methylation state of some modules responds to perturbations such as caloric restriction, ablation of growth hormone receptors, consumption of high-fat diets, and expression of Yamanaka factors. This study reveals an intertwined evolution of the genome and epigenome that mediates the biological characteristics and traits of different mammalian species.
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Affiliation(s)
- Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Caesar Z. Li
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Janssen Research & Development, Spring House, PA, USA
| | - Todd R. Robeck
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - Joshua Zhang
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ake T. Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Julia Ablaeva
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Victoria A. Acosta-Rodríguez
- Department of Neuroscience, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Danielle M. Adams
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Abdulaziz N. Alagaili
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Javier Almunia
- Loro Parque Fundacion, Avenida Loro Parque, Puerto de la Cruz, Tenerife, Spain
| | - Ajoy Aloysius
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Nabil M.S. Amor
- Laboratory of Biodiversity, Parasitology, and Ecology, University of Tunis El Manar, Tunis, Tunisia
| | - Reza Ardehali
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Adriana Arneson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - C. Scott Baker
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - Gareth Banks
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Science and Innovation Campus, Oxfordshire, UK
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Nigel C. Bennett
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | | | - Daniel T. Blumstein
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
- The Rocky Mountain Biological Laboratory, Crested Butte, CO, USA
| | - Eleanor K. Bors
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | | | | | - Janine L. Brown
- Center for Species Survival, Smithsonian National Zoo and Conservation Biology, Front Royal, VA, USA
| | - Gerald Carter
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Alex Caulton
- AgResearch, Invermay Agricultural Centre, Mosgiel, Otago, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand
| | - Julie M. Cavin
- Gulf World Marine Park - Dolphin Company, Panama City Beach, FL, USA
| | - Lisa Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - Ioulia Chatzistamou
- Department of Pathology, Microbiology & Immunology, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - Andreas S. Chavez
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, The University of Tennessee Health Science Center, Memphis, TN, USA
| | - Kaiyang Cheng
- Medical Informatics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Priscila Chiavellini
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - Oi-Wa Choi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Shannon Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel, Otago, New Zealand
| | - Joseph A. Cook
- University of New Mexico, Department of Biology and Museum of Southwestern Biology, Albuquerque, NM, USA
| | - Lisa N. Cooper
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, USA
| | - Marie-Laurence Cossette
- Department of Environmental & Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - Joanna Day
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - Joseph DeYoung
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Christopher Dold
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - Jonathan L. Dunnum
- University of New Mexico, Department of Biology and Museum of Southwestern Biology, Albuquerque, NM, USA
| | | | - Candice K. Emmons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Stephan Emmrich
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Ebru Erbay
- Altos Labs, Bay Area Institute of Science, Redwood City, CA, USA
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | | | - Chris G. Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Zhe Fei
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
- Department of Statistics, University of California, Riverside, CA, USA
| | - Steven H. Ferguson
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada
| | - Carrie J. Finno
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | | | - Jean-Michel Gaillard
- University of Lyon, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - Eva Garde
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Livia Gerber
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
- Australian National Wildlife Collection, CSIRO, Canberra, Australia
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Rodolfo G. Goya
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - Matthew J Grant
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Carla B. Green
- Department of Neuroscience, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - M. Bradley Hanson
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Daniel W. Hart
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | | | | | - Andrew N. Hogan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Carolyn J. Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Timothy A. Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Taosheng Huang
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | | | - Anna J. Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Gareth Jones
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Olga Kashpur
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
| | | | | | - Vimala Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
| | - Hippokratis Kiaris
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Michael S. Kobor
- Edwin S. H. Leong Healthy Aging Program, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pawel Kordowitzki
- Institute of Veterinary Medicine, Nicolaus Copernicus University, Torun, Poland
| | | | - Michael Krützen
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Zurich, Switzerland
| | - Soo Bin Kwon
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Brenda Larison
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Marianne Lehmann
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - Jean-François Lemaître
- University of Lyon, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - Andrew J. Levine
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xinmin Li
- Technology Center for Genomics and Bioinformatics, Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Cun Li
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - Andrea R. Lim
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - David T. S. Lin
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Thomas J. Little
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | | | | | - Julie A. Mattison
- Translational Gerontology Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | | | - June Mergl
- Marineland of Canada, Niagara Falls, Ontario, Canada
| | - Jennifer J. Meudt
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin Madison, Madison, WI, USA
| | - Gisele A. Montano
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - Khyobeni Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - Jason Munshi-South
- Louis Calder Center - Biological Field Station, Department of Biological Sciences, Fordham University, Armonk, NY, USA
| | - William J. Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | - Asieh Naderi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - Martina Nagy
- Museum fur Naturkunde, Leibniz-Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Pritika Narayan
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Peter W. Nathanielsz
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - Ngoc B. Nguyen
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | | | - Justine K. O’Brien
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | | | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Deutsches Krebsforschungszentrum, Division of Regulatory Genomics and Cancer Evolution, Heidelberg, Germany
| | | | | | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kim M. Parsons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Kimberly C. Paul
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Amy B. Pedersen
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Matteo Pellegrini
- Department Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Katharina J. Peters
- Evolutionary Genetics Group, Department of Anthropology, University of Zurich, Zurich, Switzerland
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | | | - Darren W. Pietersen
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - Gabriela M. Pinho
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Jocelyn Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jesse R. Poganik
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Natalia A. Prado
- Department of Biology, College of Arts and Science, Adelphi University, Garden City, NY, USA
- Center for Species Survival, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - Pradeep Reddy
- Altos Labs, San Diego, CA, USA
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Benjamin Rey
- University of Lyon, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - Beate R. Ritz
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Environmental Health Sciences, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | | | | | | | - Elena Rydkina
- Department of Biology, University of Rochester, Rochester, NY, USA
| | | | - Adam B. Salmon
- The Sam and Ann Barshop Institute for Longevity and Aging Studies and Department of Molecular Medicine, UT Health San Antonio, and the Geriatric Research Education and Clinical Center, South Texas Veterans Healthcare System, San Antonio, TX, USA
| | | | - Kyle M. Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Dennis Schmitt
- College of Agriculture, Missouri State University, Springfield, MO, USA
| | | | | | - Lawrence B. Schook
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Karen E. Sears
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Aaron B.A. Shafer
- Department of Forensic Science, Environmental & Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - Anastasia V. Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Kavita Singh
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, SVKM’S NMIMS University, Mumbai, India
| | - Ishani Sinha
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Jesse Slone
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - Russel G. Snell
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of Auckland, Auckland, New Zealand
| | - Elham Soltanmohammadi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | | | | | | | | | - Karen J. Steinman
- Species Preservation Laboratory, SeaWorld San Diego, San Diego, CA, USA
| | - Donald T Stewart
- Biology Department, Acadia University, Wolfville, Nova Scotia, Canada
| | | | - Balazs Szladovits
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - Joseph S. Takahashi
- Department of Neuroscience, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Masaki Takasugi
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin, Ireland
| | - Michael J. Thompson
- Department Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Bill Van Bonn
- Animal Care and Science Division, John G. Shedd Aquarium, Chicago, IL, USA
| | - Sonja C. Vernes
- School of Biology, The University of St. Andrews, Fife, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
| | - Diego Villar
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Harry V. Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ha Vu
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Nan Wang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Robert W. Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - Qi Yan
- Altos Labs, San Diego, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Mingjia Yao
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Bohan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhihui Zhang
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Yang Zhao
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Peng Zhao
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, CA, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Andrei Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - X. William Yang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
- Altos Labs, Cambridge, UK
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Horvath S, Singh K, Raj K, Khairnar S, Sanghavi A, Shrivastava A, Zoller JA, Li CZ, Herenu CB, Canatelli-Mallat M, Lehmann M, Habazin S, Novokmet M, Vučković F, Woods LCS, Martinez AG, Wang T, Chiavellini P, Levine AJ, Chen H, Brooke RT, Gordevicius J, Lauc G, Goya RG, Katcher HL. Reversal of Biological Age in Multiple Rat Organs by Young Porcine Plasma Fraction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.06.552148. [PMID: 37609328 PMCID: PMC10441355 DOI: 10.1101/2023.08.06.552148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Young blood plasma is known to confer beneficial effects on various organs in mice and rats. However, it was not known whether plasma from young pigs rejuvenates old rat tissues at the epigenetic level; whether it alters the epigenetic clock, which is a highly accurate molecular biomarker of aging. To address this question, we developed and validated six different epigenetic clocks for rat tissues that are based on DNA methylation values derived from n=613 tissue samples. As indicated by their respective names, the rat pan-tissue clock can be applied to DNA methylation profiles from all rat tissues, while the rat brain-, liver-, and blood clocks apply to the corresponding tissue types. We also developed two epigenetic clocks that apply to both human and rat tissues by adding n=1366 human tissue samples to the training data. We employed these six rat clocks to investigate the rejuvenation effects of a porcine plasma fraction treatment in different rat tissues. The treatment more than halved the epigenetic ages of blood, heart, and liver tissue. A less pronounced, but statistically significant, rejuvenation effect could be observed in the hypothalamus. The treatment was accompanied by progressive improvement in the function of these organs as ascertained through numerous biochemical/physiological biomarkers and behavioral responses to assess cognitive functions. An immunoglobulin G (IgG) N-glycosylation pattern shift from pro- to anti-inflammatory also indicated reversal of glycan aging. Overall, this study demonstrates that a young porcine plasma-derived treatment markedly reverses aging in rats according to epigenetic clocks, IgG glycans, and other biomarkers of aging.
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Affiliation(s)
- Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California, USA
- Altos Labs, Cambridge, UK
| | - Kavita Singh
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM’S NMIMS University, Mumbai, India
| | | | - Shraddha Khairnar
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM’S NMIMS University, Mumbai, India
| | | | | | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California, USA
| | - Caesar Z. Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California, USA
| | - Claudia B. Herenu
- Institute for Experimental Pharmacology of Cordoba (IFEC), School of Chemical Sciences, National University of Cordoba, Cordoba, Argentina
| | - Martina Canatelli-Mallat
- Biochemistry Research Institute of La Plata – Histology B, Pathology B, School of Medicine, University of La Plata, La Plata CC 455 (zip 1900), Argentina
| | - Marianne Lehmann
- Biochemistry Research Institute of La Plata – Histology B, Pathology B, School of Medicine, University of La Plata, La Plata CC 455 (zip 1900), Argentina
| | | | | | | | - Leah C. Solberg Woods
- Wake Forest University School of Medicine, 1 Medical Center Drive, Winston Salem, NC 27157, USA
| | - Angel Garcia Martinez
- Department of Pharmacology, Addiction Science and Toxicology, The University of Tennessee Health Science Center, Memphis, TN 3993, USA
| | - Tengfei Wang
- Department of Pharmacology, Addiction Science and Toxicology, The University of Tennessee Health Science Center, Memphis, TN 3993, USA
| | - Priscila Chiavellini
- Biochemistry Research Institute of La Plata – Histology B, Pathology B, School of Medicine, University of La Plata, La Plata CC 455 (zip 1900), Argentina
| | - Andrew J. Levine
- Department of Neurology, David Geffen School of Medicine at the University of California, Los Angeles, CA, 90095, USA
| | - Hao Chen
- Department of Pharmacology, Addiction Science and Toxicology, The University of Tennessee Health Science Center, Memphis, TN 3993, USA
| | - Robert T Brooke
- Epigenetic Clock Development Foundation, Torrance, California, USA
| | | | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
- Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
| | - Rodolfo G. Goya
- Biochemistry Research Institute of La Plata – Histology B, Pathology B, School of Medicine, University of La Plata, La Plata CC 455 (zip 1900), Argentina
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13
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Woods SP, Teixeira AL, Martins LB, Fries GR, Colpo GD, Rocha NP. Accelerated epigenetic aging in older adults with HIV disease: associations with serostatus, HIV clinical factors, and health literacy. GeroScience 2023; 45:2257-2265. [PMID: 36820957 PMCID: PMC10651616 DOI: 10.1007/s11357-023-00759-9] [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: 02/02/2023] [Accepted: 02/18/2023] [Indexed: 02/24/2023] Open
Abstract
The prevalence of older persons with HIV (PWH) disease has increased considerably in the last 20 years, but our understanding of biological factors of aging and their clinical correlates among PWH remains limited. Study participants were 149 persons aged 50 and older, including 107 PWH and 42 seronegatives. All participants completed a blood draw, research medical evaluation, structured psychiatric interview, neurocognitive assessment, questionnaires, and measures of health literacy. Four epigenetic clocks were generated from stored blood samples using standardized laboratory methods. In regression models adjusting for sex and smoking status, PWH had significantly higher epigenetic aging acceleration values than seronegatives on all four indicators. Within the PWH sample, higher levels of epigenetic aging acceleration were moderately associated with lower current CD4 count, AIDS diagnoses, higher scores on the Veterans Aging Cohort Study Index, and lower telomere values. Higher epigenetic aging acceleration indices were also associated with lower health literacy among PWH. PWH experience accelerated aging as measured by a series of epigenetic clocks, which may be linked to immune compromise and risk of all-cause mortality. Health literacy may be a modifiable target for mitigating the risk of accelerated aging among older PWH.
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Affiliation(s)
- Steven Paul Woods
- Department of Psychology, University of Houston, 3695 Cullen Blvd., 126 Heyne Bldg. (Ste. 239d), Houston, Texas, 77004, USA.
| | - Antonio L Teixeira
- Department of Psychiatry & Behavioral Science, University of Texas Health Sciences Center at Houston, 1941 East Rd., Houston, Texas, 77054, USA
| | - Lais B Martins
- Department of Psychiatry & Behavioral Science, University of Texas Health Sciences Center at Houston, 1941 East Rd., Houston, Texas, 77054, USA
| | - Gabriel R Fries
- Department of Psychiatry & Behavioral Science, University of Texas Health Sciences Center at Houston, 1941 East Rd., Houston, Texas, 77054, USA
| | - Gabriela D Colpo
- Department of Neurology, University of Texas Health Sciences Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
| | - Natalia P Rocha
- Department of Neurology, University of Texas Health Sciences Center at Houston, 6431 Fannin St., Houston, Texas, 77030, USA
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14
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Guo S, Zhang J, Yang X, Weissman S, Olatosi B, Patel RC, Li X. Impact of HIV on COVID-19 Outcomes: A Propensity Score Matching Analysis with Varying Age Differences. AIDS Behav 2023:10.1007/s10461-023-04088-y. [PMID: 37289345 PMCID: PMC10249542 DOI: 10.1007/s10461-023-04088-y] [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] [Accepted: 05/15/2023] [Indexed: 06/09/2023]
Abstract
To exploratorily test (1) the impact of HIV and aging process among PLWH on COVID-19 outcomes; and (2) whether the effects of HIV on COVID-19 outcomes differed by immunity level. The data used in this study was retrieved from the COVID-19 positive cohort in National COVID Cohort Collaborative (N3C). Multivariable logistic regression models were conducted on populations that were matched using either exact matching or propensity score matching (PSM) with varying age difference between PLWH and non-PLWH to examine the impact of HIV and aging process on all-cause mortality and hospitalization among COVID-19 patients. Subgroup analyses by CD4 counts and viral load (VL) levels were conducted using similar approaches. Among the 2,422,864 adults with a COVID-19 diagnosis, 15,188 were PLWH. PLWH had a significantly higher odds of death compared to non-PLWH until age difference reached 6 years or more, while PLWH were still at an elevated risk of hospitalization across all matched cohorts. The odds of both severe outcomes were persistently higher among PLWH with CD4 < 200 cells/mm3. VL ≥ 200 copies/ml was only associated with higher hospitalization, regardless of the predefined age differences. Age advancement in HIV might significantly contribute to the higher risk of COVID-19 mortality and HIV infection may still impact COVID-19 hospitalization independent of the age advancement in HIV.
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Affiliation(s)
- Siyuan Guo
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Jiajia Zhang
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Xueying Yang
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA.
- Department of Health Promotion, Education and Behavior, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA.
| | - Sharon Weissman
- Department of Internal Medicine, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - Bankole Olatosi
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
- Department of Health Services Policy and Management, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Rena C Patel
- Departments of Medicine and Global Health, University of Washington, Seattle, WA, USA
| | - Xiaoming Li
- South Carolina SmartState Center for Healthcare Quality, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
- Department of Health Promotion, Education and Behavior, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
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15
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Horvath S, Lu AT, Haghani A, Zoller JA, Li CZ, Lim AR, Brooke RT, Raj K, Serres-Armero A, Dreger DL, Hogan AN, Plassais J, Ostrander EA. DNA methylation clocks for dogs and humans. Proc Natl Acad Sci U S A 2022; 119:e2120887119. [PMID: 35580182 PMCID: PMC9173771 DOI: 10.1073/pnas.2120887119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/05/2022] [Indexed: 12/24/2022] Open
Abstract
DNA methylation profiles have been used to develop biomarkers of aging known as epigenetic clocks, which predict chronological age with remarkable accuracy and show promise for inferring health status as an indicator of biological age. Epigenetic clocks were first built to monitor human aging, but their underlying principles appear to be evolutionarily conserved, as they have now been successfully developed for many mammalian species. Here, we describe reliable and highly accurate epigenetic clocks shown to apply to 93 domestic dog breeds. The methylation profiles were generated using the mammalian methylation array, which utilizes DNA sequences that are conserved across all mammalian species. Canine epigenetic clocks were constructed to estimate age and also average time to death. We also present two highly accurate human–dog dual species epigenetic clocks (R = 0.97), which may facilitate the ready translation from canine to human use (or vice versa) of antiaging treatments being developed for longevity and preventive medicine. Finally, epigenome-wide association studies here reveal individual methylation sites that may underlie the inverse relationship between breed weight and lifespan. Overall, we describe robust biomarkers to measure aging and, potentially, health status in canines.
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Affiliation(s)
- Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA 90095
| | - Ake T. Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA 90095
| | - Caesar Z. Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA 90095
| | - Andrea R. Lim
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | | | - Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot OX11 0RQ, United Kingdom
| | | | - Dayna L. Dreger
- National Human Genome Research Institute, NIH, Bethesda, MD 20892
| | - Andrew N. Hogan
- National Human Genome Research Institute, NIH, Bethesda, MD 20892
| | - Jocelyn Plassais
- National Human Genome Research Institute, NIH, Bethesda, MD 20892
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16
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Musa J, Kim K, Zheng Y, Qu Y, Joyce BT, Wang J, Nannini DR, Gursel DB, Silas O, Abdulkareem FB, Imade G, Akanmu AS, Wei JJ, Kocherginsky M, Kim KYA, Wehbe F, Achenbach CJ, Anorlu R, Simon MA, Sagay A, Ogunsola FT, Murphy RL, Hou L. Accelerated Epigenetic Age Among Women with Invasive Cervical Cancer and HIV-Infection in Nigeria. Front Public Health 2022; 10:834800. [PMID: 35570901 PMCID: PMC9099239 DOI: 10.3389/fpubh.2022.834800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Background Invasive cervical cancer (ICC) is a serious public health burden in Nigeria, where human immunodeficiency virus (HIV) remains highly prevalent. Previous research suggested that epigenetic age acceleration (EAA) could play a role in detection of HIV-associated ICC. However, little research has been conducted on this topic in Africa where the population is most severely affected by HIV-associated ICC. Here, we investigated the association between ICC and EAA using cervical tissues of ICC-diagnosed Nigerian women living with HIV. Methods We included 116 cervical tissue samples from three groups of Nigerian women in this study: (1) HIV+/ICC+ (n = 39); (2) HIV+/ICC- (n = 53); and (3) HIV-/ICC + (n = 24). We utilized four DNA methylation-based EAA estimators; IEAA, EEAA, GrimAA, and PhenoAA. We compared EAA measurements across the 3 HIV/ICC groups using multiple linear regression models. We also compared EAA between 26 tumor tissues and their surrounding normal tissues using paired t-tests. We additionally performed a receiver operating characteristics (ROC) curve analysis to illustrate the area under the curve (AUC) of EAA in ICC. Results We found the most striking associations between HIV/ICC status and PhenoAge acceleration (PhenoAA). Among HIV-positive women, PhenoAA was on average 13.4 years higher in women with ICC compared to cancer-free women (P = 0.005). PhenoAA was 20.7 and 7.1 years higher in tumor tissues compared to surrounding normal tissues among HIV-positive women (P = 0.009) and HIV-negative women (P = 0.284), respectively. We did not find substantial differences in PhenoAA between HIV-positive and HIV-negative women with ICC. Conclusion PhenoAA is associated with ICC in HIV-infected women in our study. Our findings suggest that PhenoAA may serve as a potential biomarker for further risk stratification of HIV-associated ICC in Nigeria and similar resource-constrained settings.
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Affiliation(s)
- Jonah Musa
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Obstetrics and Gynecology, College of Health Sciences, University of Jos, Jos, Nigeria
| | - Kyeezu Kim
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Yinan Zheng
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Yishu Qu
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Brian T. Joyce
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Jun Wang
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Drew R. Nannini
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Demirkan B. Gursel
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | | | | | - Godwin Imade
- Department of Obstetrics and Gynecology, College of Health Sciences, University of Jos, Jos, Nigeria
| | - Alani S. Akanmu
- Department of Hematology and Blood Transfusion, Lagos University Teaching Hospital and College of Medicine, University of Lagos, Lagos, Nigeria
| | - Jian-Jun Wei
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Masha Kocherginsky
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Kwang-Youn A. Kim
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Firas Wehbe
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Department of Preventive Medicine, Division of Health and Biomedical Informatics, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Chad J. Achenbach
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Rose Anorlu
- Department of Obstetrics and Gynecology, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Melissa A. Simon
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Atiene Sagay
- Department of Obstetrics and Gynecology, College of Health Sciences, University of Jos, Jos, Nigeria
| | - Folasade T. Ogunsola
- Department of Medical Microbiology, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Robert L. Murphy
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Lifang Hou
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
- Center for Global Oncology, Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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17
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Epigenetic clock and methylation studies in marsupials: opossums, Tasmanian devils, kangaroos, and wallabies. GeroScience 2022; 44:1825-1845. [PMID: 35449380 PMCID: PMC9213610 DOI: 10.1007/s11357-022-00569-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 04/10/2022] [Indexed: 11/13/2022] Open
Abstract
The opossum (Monodelphis domestica), with its sequenced genome, ease of laboratory care and experimental manipulation, and unique biology, is the most used laboratory marsupial. Using the mammalian methylation array, we generated DNA methylation data from n = 100 opossum samples from the ear, liver, and tail. We contrasted postnatal development and later aging effects in the opossum methylome with those in mouse (Mus musculus, C57BL/6 J strain) and other marsupial species such as Tasmanian devil, kangaroos, and wallabies. While the opossum methylome is similar to that of mouse during postnatal development, it is distinct from that shared by other mammals when it comes to the age-related gain of methylation at target sites of polycomb repressive complex 2. Our immunohistochemical staining results provide additional support for the hypothesis that PRC2 activity increases with later aging in mouse tissues but remains constant in opossum tissues. We present several epigenetic clocks for opossums that are distinguished by their compatibility with tissue type (pan-tissue and blood clock) and species (opossum and human). Two dual-species human-opossum pan-tissue clocks accurately measure chronological age and relative age, respectively. The human-opossum epigenetic clocks are expected to provide a significant boost to the attractiveness of opossum as a biological model. Additional epigenetic clocks for Tasmanian devil, red kangaroos and other species of the genus Macropus may aid species conservation efforts.
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18
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Cao X, Li W, Wang T, Ran D, Davalos V, Planas-Serra L, Pujol A, Esteller M, Wang X, Yu H. Accelerated biological aging in COVID-19 patients. Nat Commun 2022; 13:2135. [PMID: 35440567 PMCID: PMC9018863 DOI: 10.1038/s41467-022-29801-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/30/2022] [Indexed: 01/01/2023] Open
Abstract
Chronological age is a risk factor for SARS-CoV-2 infection and severe COVID-19. Previous findings indicate that epigenetic age could be altered in viral infection. However, the epigenetic aging in COVID-19 has not been well studied. In this study, DNA methylation of the blood samples from 232 healthy individuals and 413 COVID-19 patients is profiled using EPIC methylation array. Epigenetic ages of each individual are determined by applying epigenetic clocks and telomere length estimator to the methylation profile of the individual. Epigenetic age acceleration is calculated and compared between groups. We observe strong correlations between the epigenetic clocks and individual's chronological age (r > 0.8, p < 0.0001). We also find the increasing acceleration of epigenetic aging and telomere attrition in the sequential blood samples from healthy individuals and infected patients developing non-severe and severe COVID-19. In addition, the longitudinal DNA methylation profiling analysis find that the accumulation of epigenetic aging from COVID-19 syndrome could be partly reversed at late clinic phases in some patients. In conclusion, accelerated epigenetic aging is associated with the risk of SARS-CoV-2 infection and developing severe COVID-19. In addition, the accumulation of epigenetic aging from COVID-19 may contribute to the post-COVID-19 syndrome among survivors.
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Affiliation(s)
- Xue Cao
- Department of Oncology, Guizhou Provincial People's Hospital, Guiyang, Guizhou, China.,Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenjuan Li
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ting Wang
- Research & Development, Thermo Fisher Scientific Inc., Los Angeles, CA, USA
| | - Dongzhi Ran
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, USA.,Key Laboratory of Biochemistry and Molecular Pharmacology, Department of Pharmacology, Chongqing Medical University, Chongqing, China
| | - Veronica Davalos
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
| | - Laura Planas-Serra
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.,Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.,Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.,Institucio Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Catalonia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain.,Institucio Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Madrid, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Xiaolin Wang
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Huichuan Yu
- Guangdong Institute of Gastroenterology, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Disease, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China. .,Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
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19
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Horvath S, Lin DTS, Kobor MS, Zoller JA, Said JW, Morgello S, Singer E, Yong WH, Jamieson BD, Levine AJ. HIV, pathology and epigenetic age acceleration in different human tissues. GeroScience 2022; 44:1609-1620. [PMID: 35411474 PMCID: PMC9213580 DOI: 10.1007/s11357-022-00560-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/30/2022] [Indexed: 11/29/2022] Open
Abstract
Epigenetic clocks based on patterns of DNA methylation have great importance in understanding aging and disease; however, there are basic questions to be resolved in their application. It remains unknown whether epigenetic age acceleration (EAA) within an individual shows strong correlation between different primary tissue sites, the extent to which tissue pathology and clinical illness correlate with EAA in the target organ, and if EAA variability across tissues differs according to sex. Considering the outsized role of age-related illness in Human Immunodeficiency Virus-1 (HIV), these questions were pursued in a sample enriched for tissue from HIV-infected individuals. We used a custom methylation array to generate DNA methylation data from 661 samples representing 11 human tissues (adipose, blood, bone marrow, heart, kidney, liver, lung, lymph node, muscle, spleen and pituitary gland) from 133 clinically characterized, deceased individuals, including 75 infected with HIV. We developed a multimorbidity index based on the clinical disease history. Epigenetic age was moderately correlated across tissues. Blood had the greatest number and degree of correlation, most notably with spleen and bone marrow. However, blood did not correlate with epigenetic age of liver. EAA in liver was weakly correlated with EAA in kidney, adipose, lung and bone marrow. Clinically, hypertension was associated with EAA in several tissues, consistent with the multiorgan impacts of this illness. HIV infection was associated with positive age acceleration in kidney and spleen. Male sex was associated with increased epigenetic acceleration in several tissues. Preliminary evidence indicates that amyotrophic lateral sclerosis is associated with positive EAA in muscle tissue. Finally, greater multimorbidity was associated with greater EAA across all tissues. Blood alone will often fail to detect EAA in other tissues. While hypertension is associated with increased EAA in several tissues, many pathologies are associated with organ-specific age acceleration.
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Affiliation(s)
- Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA. .,Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA.
| | - David T S Lin
- Centre for Molecular Medicine and Therapeutics, BC Childrens Hospital Research Institute, Vancouver, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, BC Childrens Hospital Research Institute, Vancouver, Canada
| | - Joseph A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Jonathan W Said
- Department of Pathology and Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, Los Angeles, USA
| | - Susan Morgello
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Departments of Neuroscience and Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elyse Singer
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - William H Yong
- Department of Pathology and Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, Los Angeles, USA
| | - Beth D Jamieson
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Andrew J Levine
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, USA
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20
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Sehl ME, Breen EC, Shih R, Chen L, Wang R, Horvath S, Bream JH, Duggal P, Martinson J, Wolinsky SM, Martinez-Maza O, Ramirez CM, Jamieson BD. Increased Rate of Epigenetic Aging in Men Living With HIV Prior to Treatment. Front Genet 2022; 12:796547. [PMID: 35295196 PMCID: PMC8919029 DOI: 10.3389/fgene.2021.796547] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 12/06/2021] [Indexed: 01/26/2023] Open
Abstract
Background: Epigenetic aging is accelerated in tissues of persons living with HIV (PLWH) and may underlie the early onset of age-related illnesses. This study examines the rate-of-change in epigenetic age in PLWH following HIV infection but before HAART, using archived longitudinal samples from the Multicenter AIDS Cohort Study. Methods: DNA was isolated from cryopreserved peripheral blood mononuclear cells from 101 men living with HIV, with baseline visit <2.5 years after HIV seroconversion (Visit 1) and follow-up visit <1.5 years before the initiation of HAART (Visit 2), and 100 HIV-uninfected men matched on age and visits with comparable time intervals. DNA methylation (DNAm) age was estimated for five clocks (Pan-tissue, Extrinsic, Phenotypic, Grim, and Skin & Blood age), and a DNAm-based estimate of telomere length (DNAmTL). Multivariate linear regression models were used to examine baseline factors associated with rate-of-aging, defined as (DNAm age visit 2-DNAm age visit 1)/(age visit 2-age visit 1). Results: Epigenetic age increased approximately twice as fast in PLWH as uninfected controls (Pan-tissue, Extrinsic, and Phenotypic clocks). Shortening of DNAmTL was nearly 3-fold faster in PLWH than controls. Faster rate-of-aging was associated with HIV status (Pan-Tissue, Extrinsic, Phenotypic, and DNAmTL), white race (Extrinsic, DNAmTL), higher cumulative HIV viral load (Grim), and lower baseline DNAm age (Phenotypic, Skin & Blood). Conclusion: Epigenetic rates-of-aging were significantly faster for untreated PLWH. Our findings expand on the important impact of HIV infection on biologic aging, both in elevating epigenetic age and increasing the rate-of-aging in the years following infection.
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Affiliation(s)
- Mary E. Sehl
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, United States
| | - Elizabeth Crabb Breen
- Cousins Center for Psychoneuroimmunology, Department of Psychiatry and Behavioral Sciences, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, United States
| | - Roger Shih
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, United States
| | - Larry Chen
- UCLA Computational and Systems Biology Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ruibin Wang
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jay H. Bream
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Immunology Training Program, Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Jeremy Martinson
- Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Steven M. Wolinsky
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Otoniel Martinez-Maza
- Departments of Obstetrics and Gynecology and Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, United States
- Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, United States
| | - Christina M. Ramirez
- Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, United States
| | - Beth D. Jamieson
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, United States
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21
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Nichols SL. Central Nervous System Impact of Perinatally Acquired HIV in Adolescents and Adults: an Update. Curr HIV/AIDS Rep 2022; 19:121-132. [PMID: 35107809 PMCID: PMC8904346 DOI: 10.1007/s11904-021-00598-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2021] [Indexed: 11/24/2022]
Abstract
Purpose of Review Perinatally acquired HIV infection (PHIV) can confer neurodevelopmental risk. As children with PHIV increasingly survive through adolescence and into adulthood, understanding its long-term central nervous system (CNS) impacts is critical for maximizing adult outcomes and quality of life. Recent Findings Recently published neurocognitive and neuroimaging findings show impacts on the CNS associated with early HIV disease progression that endure into adolescence and young adulthood. Although developmental trajectories in adolescence largely appear stable, further research on maturational processes is indicated. Summary Although early antiretroviral therapy in infancy appears to be protective, it is not universally available and current youth largely developed without its benefit. The neurocognitive effects of HIV and the multiple other risks to neurodevelopment experienced by youth with PHIV call for further longitudinal research and a multifaceted approach to prevention and intervention.
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Affiliation(s)
- Sharon L Nichols
- Department of Neurosciences, University of California, San Diego 9500 Gilman Drive, #0935, CA, 92093, La Jolla, USA.
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22
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Horvath S, Haghani A, Zoller JA, Naderi A, Soltanmohammadi E, Farmaki E, Kaza V, Chatzistamou I, Kiaris H. Methylation studies in Peromyscus: aging, altitude adaptation, and monogamy. GeroScience 2022; 44:447-461. [PMID: 34698996 PMCID: PMC8810952 DOI: 10.1007/s11357-021-00472-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/07/2021] [Indexed: 11/18/2022] Open
Abstract
DNA methylation-based biomarkers of aging have been developed for humans and many other mammals and could be used to assess how stress factors impact aging. Deer mice (Peromyscus) are long-living rodents that have emerged as an informative model to study aging, adaptation to extreme environments, and monogamous behavior. In the present study, we have undertaken an exhaustive, genome-wide analysis of DNA methylation in Peromyscus, spanning different species, stocks, sexes, tissues, and age cohorts. We describe DNA methylation-based estimators of age for different species of deer mice based on novel DNA methylation data generated on highly conserved mammalian CpGs measured with a custom array. The multi-tissue epigenetic clock for deer mice was trained on 3 tissues (tail, liver, and brain). Two human-Peromyscus clocks accurately measure age and relative age, respectively. We present CpGs and enriched pathways that relate to different conditions such as chronological age, high altitude, and monogamous behavior. Overall, this study provides a first step towards studying the epigenetic correlates of monogamous behavior and adaptation to high altitude in Peromyscus. The human-Peromyscus epigenetic clocks are expected to provide a significant boost to the attractiveness of Peromyscus as a biological model.
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Affiliation(s)
- Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA USA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA USA
| | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA USA
| | - Asieh Naderi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC USA
| | - Elham Soltanmohammadi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC USA
| | - Elena Farmaki
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC USA
| | - Vimala Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC USA
| | - Ioulia Chatzistamou
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC USA
| | - Hippokratis Kiaris
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC USA
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC USA
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23
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Rinaldi S, Pallikkuth S, De Armas L, Richardson B, Pan L, Pahwa R, Williams S, Cameron M, Pahwa S. Distinct Molecular Signatures of Aging in Healthy and HIV-Infected Individuals. J Acquir Immune Defic Syndr 2022; 89:S47-S55. [PMID: 35015745 PMCID: PMC8751284 DOI: 10.1097/qai.0000000000002864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Virally suppressed chronic HIV-infected individuals on antiretroviral therapy experience similar immune impairments as HIV-uninfected elderly. However, they manifest symptoms of premature immune aging such as suboptimal responses to vaccination at a younger age. Mechanisms underlying premature immune aging are unclear. SETTING The study site was University of Miami Miller School of Medicine. METHODS In this study, we aimed to identify molecular signatures of aging in HIV-infected (HIV) individuals compared with age-matched healthy control (HC) participants. Transcriptomic profiles of peripheral blood mononuclear cells collected cross-sectionally from study participants were evaluated using RNA sequencing, and genes and pathways associated with age and HIV status were identified and compared between study groups. Generalized linear modeling was used to identify transcriptional signatures associated with age. RESULTS Despite that fewer differentially expressed genes between young (<40 yrs) and old (>59 yrs) were observed in the HIV group, metabolic and innate immune activation pathways were associated with increasing age in both HIV and HC. Age was also associated with pathways involved with T-cell immune activation in HC and with interferon signaling pathways in HIV. We observed signs of precocious immune aging at the transcriptional level in HIV and defined a transcriptional perturbation associated with innate immunity and glucose metabolism induced by aging in both HC and HIV. CONCLUSION In this study, we identified distinct molecular signatures predictive of age in HIV versus HC, which suggest precocious immune aging in HIV. Overall, our results highlight the molecular pathways of immune aging in both HC and HIV that may be targeted for additional mechanistic insights or in a therapeutic setting.
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Affiliation(s)
- Stefano Rinaldi
- Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL
| | - Suresh Pallikkuth
- Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL
- Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL
| | - Lesley De Armas
- Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL
| | - Brian Richardson
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH.
| | - Li Pan
- Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL
| | - Rajendra Pahwa
- Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL
| | - Sion Williams
- Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL
- Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL
| | - Mark Cameron
- Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL
- Department of Population & Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH.
| | - Savita Pahwa
- Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL
- Miami Center for AIDS Research, University of Miami Miller School of Medicine, Miami, FL
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24
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Horvath S, Haghani A, Peng S, Hales EN, Zoller JA, Raj K, Larison B, Robeck TR, Petersen JL, Bellone RR, Finno CJ. DNA methylation aging and transcriptomic studies in horses. Nat Commun 2022; 13:40. [PMID: 35013267 PMCID: PMC8748428 DOI: 10.1038/s41467-021-27754-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022] Open
Abstract
Cytosine methylation patterns have not yet been thoroughly studied in horses. Here, we profile n = 333 samples from 42 horse tissue types at loci that are highly conserved between mammalian species using a custom array (HorvathMammalMethylChip40). Using the blood and liver tissues from horses, we develop five epigenetic aging clocks: a multi-tissue clock, a blood clock, a liver clock and two dual-species clocks that apply to both horses and humans. In addition, using blood methylation data from three additional equid species (plains zebra, Grevy's zebras and Somali asses), we develop another clock that applies across all equid species. Castration does not significantly impact the epigenetic aging rate of blood or liver samples from horses. Methylation and RNA data from the same tissues define the relationship between methylation and RNA expression across horse tissues. We expect that the multi-tissue atlas will become a valuable resource.
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Affiliation(s)
- Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Sichong Peng
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | - Erin N Hales
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | - Joseph A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, UK
| | - Brenda Larison
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| | - Todd R Robeck
- Zoological Operations, SeaWorld Parks and Entertainment, 7007 SeaWorld Drive, Orlando, FL, USA
| | | | - Rebecca R Bellone
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
- Veterinary Genetics Laboratory, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | - Carrie J Finno
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA.
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25
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Horvath S, Haghani A, Macoretta N, Ablaeva J, Zoller JA, Li CZ, Zhang J, Takasugi M, Zhao Y, Rydkina E, Zhang Z, Emmrich S, Raj K, Seluanov A, Faulkes CG, Gorbunova V. DNA methylation clocks tick in naked mole rats but queens age more slowly than nonbreeders. NATURE AGING 2022; 2:46-59. [PMID: 35368774 PMCID: PMC8975251 DOI: 10.1038/s43587-021-00152-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Naked mole rats (NMRs) live an exceptionally long life, appear not to exhibit age-related decline in physiological capacity and are resistant to age-related diseases. However, it has been unknown whether NMRs also evade aging according to a primary hallmark of aging: epigenetic changes. To address this question, we profiled n = 385 samples from 11 tissue types at loci that are highly conserved between mammalian species using a custom array (HorvathMammalMethylChip40). We observed strong epigenetic aging effects and developed seven highly accurate epigenetic clocks for several tissues (pan-tissue, blood, kidney, liver, skin clocks) and two dual-species (human-NMR) clocks. The skin clock correctly estimated induced pluripotent stem cells derived from NMR fibroblasts to be of prenatal age. The NMR epigenetic clocks revealed that breeding NMR queens age more slowly than nonbreeders, a feature that is also observed in some eusocial insects. Our results show that despite a phenotype of negligible senescence, the NMR ages epigenetically.
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Affiliation(s)
- Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
- These authors contributed equally: Steve Horvath, Amin Haghani
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- These authors contributed equally: Steve Horvath, Amin Haghani
| | - Nicholas Macoretta
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Julia Ablaeva
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Caesar Z. Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Joshua Zhang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Masaki Takasugi
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Yang Zhao
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Elena Rydkina
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Zhihui Zhang
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Stephan Emmrich
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, UK
| | - Andrei Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
- These authors jointly supervised this work: Andrei Seluanov, Chris G. Faulkes, Vera Gorbunova
| | - Chris G. Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- These authors jointly supervised this work: Andrei Seluanov, Chris G. Faulkes, Vera Gorbunova
| | - Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
- These authors jointly supervised this work: Andrei Seluanov, Chris G. Faulkes, Vera Gorbunova
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26
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Shiau S, Arpadi SM, Shen Y, Cantos A, Ramon CV, Shah J, Jang G, Manly JJ, Brickman AM, Baccarelli AA, Yin MT. Epigenetic Aging Biomarkers Associated With Cognitive Impairment in Older African American Adults With Human Immunodeficiency Virus (HIV). Clin Infect Dis 2021; 73:1982-1991. [PMID: 34143869 PMCID: PMC8664485 DOI: 10.1093/cid/ciab563] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Accelerated epigenetic aging using DNA methylation (DNAm)-based biomarkers has been reported in people with human immunodeficiency virus (HIV, PWH), but limited data are available among African Americans (AA), women, and older PWH. METHODS DNAm was measured using Illumina EPIC Arrays for 107 (69 PWH and 38 HIV-seronegative controls) AA adults ≥60 years in New York City. Six DNAm-based biomarkers of aging were estimated: (1) epigenetic age acceleration (EAA), (2) extrinsic epigenetic age acceleration (EEAA), (3) intrinsic epigenetic age acceleration (IEAA), (4) GrimAge, (5) PhenoAge, and (6) DNAm-estimated telomere length (DNAm-TL). The National Institutes of Health (NIH) Toolbox Cognition Battery (domains: executive function, attention, working memory, processing speed, and language) and Montreal Cognitive Assessment (MoCA) were administered. Participants were assessed for frailty by the Fried criteria. RESULTS The PWH and control groups did not differ by sex, chronological age, or ethnicity. In total, 83% of PWH had a viral load <50 copies/mL, and 94% had a recent CD4 ≥200 cells/µL. The PWH group had a higher EAA, EEAA, GrimAge, and PhenoAge, and a lower DNAm-TL compared to the controls. IEAA was not different between groups. For PWH, there were significant negative correlations between IEAA and executive function, attention, and working memory and PhenoAge and attention. No associations between biomarkers and frailty were detected. CONCLUSIONS Evidence of epigenetic age acceleration was observed in AA older PWH using DNAm-based biomarkers of aging. There was no evidence of age acceleration independent of cell type National Institutes of Health composition (IEAA) associated with HIV, but this measure was associated with decreased cognitive function among PWH.
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Affiliation(s)
- Stephanie Shiau
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey, USA
| | - Stephen M Arpadi
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA.,Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA.,ICAP at Columbia, Mailman School of Public Health, Columbia University Irving Medical Center, New York, New York, USA
| | - Yanhan Shen
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Anyelina Cantos
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Christian Vivar Ramon
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Jayesh Shah
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Grace Jang
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Jennifer J Manly
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA.,Taub Institute for Research in Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, USA.,Department of Neurology, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Adam M Brickman
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA.,Taub Institute for Research in Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, New York, USA.,Department of Neurology, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Irving Medical Center, New York, New York, USA
| | - Michael T Yin
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
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27
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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.
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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
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28
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Horvath S, Zoller JA, Haghani A, Jasinska AJ, Raj K, Breeze CE, Ernst J, Vaughan KL, Mattison JA. Epigenetic clock and methylation studies in the rhesus macaque. GeroScience 2021; 43:2441-2453. [PMID: 34487267 PMCID: PMC8599607 DOI: 10.1007/s11357-021-00429-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/01/2021] [Indexed: 11/28/2022] Open
Abstract
Methylation levels at specific CpG positions in the genome have been used to develop accurate estimators of chronological age in humans, mice, and other species. Although epigenetic clocks are generally species-specific, the principles underpinning them appear to be conserved at least across the mammalian class. This is exemplified by the successful development of epigenetic clocks for mice and several other mammalian species. Here, we describe epigenetic clocks for the rhesus macaque (Macaca mulatta), the most widely used nonhuman primate in biological research. Using a custom methylation array (HorvathMammalMethylChip40), we profiled n = 281 tissue samples (blood, skin, adipose, kidney, liver, lung, muscle, and cerebral cortex). From these data, we generated five epigenetic clocks for macaques. These clocks differ with regard to applicability to different tissue types (pan-tissue, blood, skin), species (macaque only or both humans and macaques), and measure of age (chronological age versus relative age). Additionally, the age-based human-macaque clock exhibits a high age correlation (R = 0.89) with the vervet monkey (Chlorocebus sabaeus), another Old World species. Four CpGs within the KLF14 promoter were consistently altered with age in four tissues (adipose, blood, cerebral cortex, skin). Future studies will be needed to evaluate whether these epigenetic clocks predict age-related conditions in the rhesus macaque.
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Affiliation(s)
- Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA USA
| | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA USA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA USA
| | - Anna J. Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA Los Angeles, USA
| | - Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, , Didcot, UK
| | | | - Jason Ernst
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Kelli L. Vaughan
- Translational Gerontology Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, 16701 Elmer School Rd., MD 20842 Dickerson, USA
| | - Julie A. Mattison
- Translational Gerontology Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, 16701 Elmer School Rd., MD 20842 Dickerson, USA
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Horvath S, Zoller JA, Haghani A, Lu AT, Raj K, Jasinska AJ, Mattison JA, Salmon AB. DNA methylation age analysis of rapamycin in common marmosets. GeroScience 2021; 43:2413-2425. [PMID: 34482522 PMCID: PMC8599537 DOI: 10.1007/s11357-021-00438-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/09/2021] [Indexed: 01/10/2023] Open
Abstract
Human DNA methylation data have previously been used to develop highly accurate biomarkers of aging ("epigenetic clocks"). Subsequent studies demonstrate that similar epigenetic clocks can also be developed for mice and many other mammals. Here, we describe epigenetic clocks for common marmosets (Callithrix jacchus) based on novel DNA methylation data generated from highly conserved mammalian CpGs that were profiled using a custom Infinium array (HorvathMammalMethylChip40). From these, we developed and present here two epigenetic clocks for marmosets that are applicable to whole blood samples. We find that the human-marmoset clock for relative age exhibits moderately high age correlations in two other non-human primate species: vervet monkeys and rhesus macaques. In a separate cohort of marmosets, we tested whether intervention with rapamycin, a drug shown to extend lifespan in mice, would alter the epigenetic age of marmosets, as measured by the marmoset epigenetic clocks. These clocks did not detect significant effects of rapamycin on the epigenetic age of marmoset blood. The common marmoset stands out from other mammals in that it is not possible to build accurate estimators of sex based on DNA methylation data: the accuracy of a random forest predictor of sex (66%) was substantially lower than that observed for other mammals (which is close to 100%). Overall, the epigenetic clocks developed here for the common marmoset are expected to be useful for age estimation of wild-born animals and for anti-aging studies in this species.
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Affiliation(s)
- Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Gonda Building, 695 Charles Young Drive South, Los Angeles, CA USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Gonda Building, 695 Charles Young Drive South, Los Angeles, CA USA
| | - Ake T. Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Gonda Building, 695 Charles Young Drive South, Los Angeles, CA USA
| | - Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, UK
| | - Anna J. Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA USA
| | - Julie A. Mattison
- Translational Gerontology Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, Dickerson, MD USA
| | - Adam B. Salmon
- The Sam and Ann Barshop Institute for Longevity and Aging Studies, and Department of Molecular Medicine, UT Health San Antonio, and the Geriatric Research Education and Clinical Center, South Texas Veterans Healthcare System, San Antonio, TX USA
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30
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Schachtschneider KM, Schook LB, Meudt JJ, Shanmuganayagam D, Zoller JA, Haghani A, Li CZ, Zhang J, Yang A, Raj K, Horvath S. Epigenetic clock and DNA methylation analysis of porcine models of aging and obesity. GeroScience 2021; 43:2467-2483. [PMID: 34523051 PMCID: PMC8599541 DOI: 10.1007/s11357-021-00439-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/09/2021] [Indexed: 12/29/2022] Open
Abstract
DNA-methylation profiles have been used successfully to develop highly accurate biomarkers of age, epigenetic clocks, for many species. Using a custom methylation array, we generated DNA methylation data from n = 238 porcine tissues including blood, bladder, frontal cortex, kidney, liver, and lung, from domestic pigs (Sus scrofa domesticus) and minipigs (Wisconsin Miniature Swine™). Samples used in this study originated from Large White X Landrace crossbred pigs, Large White X Minnesota minipig crossbred pigs, and Wisconsin Miniature Swine™. We present 4 epigenetic clocks for pigs that are distinguished by their compatibility with tissue type (pan-tissue and blood clock) and species (pig and human). Two dual-species human-pig pan-tissue clocks accurately measure chronological age and relative age, respectively. We also characterized CpGs that differ between minipigs and domestic pigs. Strikingly, several genes implicated by our epigenetic studies of minipig status overlap with genes (ADCY3, TFAP2B, SKOR1, and GPR61) implicated by genetic studies of body mass index in humans. In addition, CpGs with different levels of methylation between the two pig breeds were identified proximal to genes involved in blood LDL levels and cholesterol synthesis, of particular interest given the minipig's increased susceptibility to cardiovascular disease compared to domestic pigs. Thus, breed-specific differences of domestic and minipigs may potentially help to identify biological mechanisms underlying weight gain and aging-associated diseases. Our porcine clocks are expected to be useful for elucidating the role of epigenetics in aging and obesity, and the testing of anti-aging interventions.
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Affiliation(s)
- Kyle M. Schachtschneider
- Department of Radiology, University of Illinois At Chicago, Chicago, IL USA
- Department of Biochemistry and Molecular Genetics, University of Illinois At Chicago, Chicago, IL USA
- National Center for Supercomputing Applications, University of Illinois At Urbana-Champaign, Urban, IL USA
| | - Lawrence B. Schook
- Department of Radiology, University of Illinois At Chicago, Chicago, IL USA
- Department of Animal Sciences, University of Illinois At Urbana-Champaign, Urbana, IL USA
| | - Jennifer J. Meudt
- Biomedical & Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin – Madison, Madison, WI USA
| | - Dhanansayan Shanmuganayagam
- Biomedical & Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin – Madison, Madison, WI USA
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI USA
| | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA USA
| | - Amin Haghani
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA USA
| | - Caesar Z. Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA USA
| | - Joshua Zhang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Gonda Building, 695 Charles Young Drive South, Los Angeles, CA 90095 USA
| | - Andrew Yang
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA USA
| | - Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, UK
| | - Steve Horvath
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Gonda Building, 695 Charles Young Drive South, Los Angeles, CA 90095 USA
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Raj K, Szladovits B, Haghani A, Zoller JA, Li CZ, Black P, Maddox D, Robeck TR, Horvath S. Epigenetic clock and methylation studies in cats. GeroScience 2021; 43:2363-2378. [PMID: 34463900 PMCID: PMC8599556 DOI: 10.1007/s11357-021-00445-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/17/2021] [Indexed: 12/21/2022] Open
Abstract
Human DNA methylation profiles have been used successfully to develop highly accurate biomarkers of aging ("epigenetic clocks"). Although these human epigenetic clocks are not immediately applicable to all species of the animal kingdom, the principles underpinning them appear to be conserved even in animals that are evolutionarily far removed from humans. This is exemplified by recent development of epigenetic clocks for mice and other mammalian species. Here, we describe epigenetic clocks for the domestic cat (Felis catus), based on methylation profiles of CpGs with flanking DNA sequences that are highly conserved between multiple mammalian species. Methylation levels of these CpGs are measured using a custom-designed Infinium array (HorvathMammalMethylChip40). From these, we present 3 epigenetic clocks for cats; of which, one applies only to blood samples from cats, while the remaining two dual-species human-cat clocks apply both to cats and humans. We demonstrate that these domestic cat clocks also lead to high age correlations in cheetahs, tigers, and lions. It is expected that these epigenetic clocks for cats possess the potential to be further developed for monitoring feline health as well as being used for identifying and validating anti-aging interventions.
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Affiliation(s)
- Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, UK
| | - Balazs Szladovits
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, 695 Charles E. Young Drive South, Los Angeles, CA 90095 USA
| | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Gonda Building, Los Angeles, CA 90095 USA
| | - Caesar Z. Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Gonda Building, Los Angeles, CA 90095 USA
| | | | | | - Todd R. Robeck
- Corporate Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, 695 Charles E. Young Drive South, Los Angeles, CA 90095 USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Gonda Building, Los Angeles, CA 90095 USA
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Epigenetic clock and methylation studies in vervet monkeys. GeroScience 2021; 44:699-717. [PMID: 34591235 PMCID: PMC9135907 DOI: 10.1007/s11357-021-00466-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/20/2021] [Indexed: 11/26/2022] Open
Abstract
DNA methylation-based biomarkers of aging have been developed for many mammals but not yet for the vervet monkey (Chlorocebus sabaeus), which is a valuable non-human primate model for biomedical studies. We generated novel DNA methylation data from vervet cerebral cortex, blood, and liver using highly conserved mammalian CpGs represented on a custom array (HorvathMammalMethylChip40). We present six DNA methylation-based estimators of age: vervet multi-tissue epigenetic clock and tissue-specific clocks for brain cortex, blood, and liver. In addition, we developed two dual species clocks (human-vervet clocks) for measuring chronological age and relative age, respectively. Relative age was defined as ratio of chronological age to maximum lifespan to address the species differences in maximum lifespan. The high accuracy of the human-vervet clocks demonstrates that epigenetic aging processes are evolutionary conserved in primates. When applying these vervet clocks to tissue samples from another primate species, rhesus macaque, we observed high age correlations but strong offsets. We characterized CpGs that correlate significantly with age in the vervet. CpG probes that gain methylation with age across tissues were located near the targets of Polycomb proteins SUZ12 and EED and genes possessing the trimethylated H3K27 mark in their promoters. The epigenetic clocks are expected to be useful for anti-aging studies in vervets.
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Oblak L, van der Zaag J, Higgins-Chen AT, Levine ME, Boks MP. A systematic review of biological, social and environmental factors associated with epigenetic clock acceleration. Ageing Res Rev 2021; 69:101348. [PMID: 33930583 DOI: 10.1016/j.arr.2021.101348] [Citation(s) in RCA: 183] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 04/01/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023]
Abstract
Aging involves a diverse set of biological changes accumulating over time that leads to increased risk of morbidity and mortality. Epigenetic clocks are now widely used to quantify biological aging, in order to investigate determinants that modify the rate of aging and to predict age-related outcomes. Numerous biological, social and environmental factors have been investigated for their relationship to epigenetic clock acceleration and deceleration. The aim of this review was to synthesize general trends concerning the associations between human epigenetic clocks and these investigated factors. We conducted a systematic review of all available literature and included 156 publications across 4 resource databases. We compiled a list of all presently existing blood-based epigenetic clocks. Subsequently, we created an extensive dataset of over 1300 study findings in which epigenetic clocks were utilized in blood tissue of human subjects to assess the relationship between these clocks and numeral environmental exposures and human traits. Statistical analysis was possible on 57 such relationships, measured across 4 different epigenetic clocks (Hannum, Horvath, Levine and GrimAge). We found that the Horvath, Hannum, Levine and GrimAge epigenetic clocks tend to agree in direction of effects, but vary in size. Body mass index, HIV infection, and male sex were significantly associated with acceleration of one or more epigenetic clocks. Acceleration of epigenetic clocks was also significantly related to mortality, cardiovascular disease, cancer and diabetes. Our findings provide a graphical and numerical synopsis of the past decade of epigenetic age estimation research and indicate areas where further attention could be focused in the coming years.
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Shiau S, Cantos A, Ramon CV, Shen Y, Shah J, Jang G, Baccarelli AA, Arpadi SM, Yin MT. Epigenetic Age in Young African American Adults With Perinatally Acquired HIV. J Acquir Immune Defic Syndr 2021; 87:1102-1109. [PMID: 33765682 PMCID: PMC8217147 DOI: 10.1097/qai.0000000000002687] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/01/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Prior studies have measured accelerated aging in people with HIV using a DNA methylation (DNAm)-based biomarker of aging, "epigenetic age," but data are limited in African American (AA) young adults with perinatally acquired HIV infection (PHIV). METHODS We performed a cross-sectional study of AA young adults aged 20-35 years with PHIV (N = 31) and seronegative controls (N = 30) using DNAm measured in whole blood and cognitive function measured by the NIH Toolbox. Illumina EPIC array was used to measure DNAm age and accelerated aging markers including epigenetic age acceleration (EAA), as well as extrinsic (EEAA) and intrinsic (IEAA) EAA. RESULTS PHIV and controls did not differ by sex (45 vs. 43% male), chronological age (26.2 vs. 28.0 years), or ethnicity. Chronological age and DNAm age were correlated (r = 0.56, P < 0.01). PHIV had a higher mean EAA (2.86 ± 6.5 vs. -2.96 ± 3.9, P < 0.01) and EEAA (4.57 ± 13.0 vs. -4.72 ± 6.0, P < 0.01) than controls; however, IEAA was not different between groups. Among PHIV, EAA and EEAA were higher in those with HIV viral load ≥50 copies/mL than <50 copies/mL (EEA: 8.1 ± 5.2 vs. 0.11 ± 5.5, P = 0 < 0.01 and EEAA: 16.1 ± 10.6 vs. -1.83 ± 9.7, P < 0.01). We observed negative correlations (r = -0.36 to -0.31) between EEAA and executive function, attention, and language scores. CONCLUSIONS In conclusion, EAA in blood was observed in AA young adults with PHIV on ART using 2 measures, including EEAA which upweights the contribution of immunosenescent cell types. However, there was no evidence of age acceleration with a measure independent of cell type composition.
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Affiliation(s)
- Stephanie Shiau
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ
| | - Anyelina Cantos
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Christian V Ramon
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Yanhan Shen
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Jayesh Shah
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Grace Jang
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - Stephen M Arpadi
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY; and
- ICAP at Columbia, Mailman School of Public Health, Columbia University Irving Medical Center, New York, NY
| | - Michael T Yin
- Department of Medicine, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
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Noroozi R, Ghafouri-Fard S, Pisarek A, Rudnicka J, Spólnicka M, Branicki W, Taheri M, Pośpiech E. DNA methylation-based age clocks: From age prediction to age reversion. Ageing Res Rev 2021; 68:101314. [PMID: 33684551 DOI: 10.1016/j.arr.2021.101314] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 12/12/2022]
Abstract
Aging as an irretrievable occurrence throughout the entire life is characterized by a progressive decline in physiological functionality and enhanced disease vulnerability. Numerous studies have demonstrated that epigenetic modifications, particularly DNA methylation (DNAm), correlate with aging and age-related diseases. Several investigations have attempted to predict chronological age using the age-related alterations in the DNAm of certain CpG sites. Here we categorize different studies that tracked the aging process in the DNAm landscape to show how epigenetic age clocks evolved from a chronological age estimator to an indicator of lifespan and healthspan. We also describe the health and disease predictive potential of estimated epigenetic age acceleration regarding different clinical conditions and lifestyle factors. Considering the revealed age-related epigenetic changes, the recent age-reprogramming strategies are discussed which are promising methods for resetting the aging clocks.
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Affiliation(s)
- Rezvan Noroozi
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Aleksandra Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Joanna Rudnicka
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
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Prado NA, Brown JL, Zoller JA, Haghani A, Yao M, Bagryanova LR, Campana MG, E. Maldonado J, Raj K, Schmitt D, Robeck TR, Horvath S. Epigenetic clock and methylation studies in elephants. Aging Cell 2021; 20:e13414. [PMID: 34118182 PMCID: PMC8282242 DOI: 10.1111/acel.13414] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/15/2021] [Accepted: 05/08/2021] [Indexed: 11/30/2022] Open
Abstract
Age-associated DNA-methylation profiles have been used successfully to develop highly accurate biomarkers of age ("epigenetic clocks") in humans, mice, dogs, and other species. Here we present epigenetic clocks for African and Asian elephants. These clocks were developed using novel DNA methylation profiles of 140 elephant blood samples of known age, at loci that are highly conserved between mammalian species, using a custom Infinium array (HorvathMammalMethylChip40). We present epigenetic clocks for Asian elephants (Elephas maximus), African elephants (Loxodonta africana), and both elephant species combined. Two additional human-elephant clocks were constructed by combining human and elephant samples. Epigenome-wide association studies identified elephant age-related CpGs and their proximal genes. The products of these genes play important roles in cellular differentiation, organismal development, metabolism, and circadian rhythms. Intracellular events observed to change with age included the methylation of bivalent chromatin domains, and targets of polycomb repressive complexes. These readily available epigenetic clocks can be used for elephant conservation efforts where accurate estimates of age are needed to predict demographic trends.
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Affiliation(s)
- Natalia A. Prado
- Center for Species SurvivalSmithsonian Conservation Biology InstituteFront RoyalVAUSA
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonDCUSA
| | - Janine L. Brown
- Center for Species SurvivalSmithsonian Conservation Biology InstituteFront RoyalVAUSA
| | - Joseph A. Zoller
- Department of BiostatisticsFielding School of Public HealthUniversity of CaliforniaLos AngelesCAUSA
| | - Amin Haghani
- Department of Human GeneticsDavid Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
| | - Mingjia Yao
- Department of BiostatisticsFielding School of Public HealthUniversity of CaliforniaLos AngelesCAUSA
| | - Lora R. Bagryanova
- Department of EpidemiologyFielding School of Public HealthUniversity of CaliforniaLos Angeles, Los AngelesCAUSA
| | - Michael G. Campana
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonDCUSA
| | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonDCUSA
| | - Ken Raj
- Radiation Effects DepartmentCentre for Radiation, Chemical and Environmental HazardsPublic Health EnglandDidcotUK
| | - Dennis Schmitt
- College of AgricultureMissouri State UniversitySpringfieldMOUSA
| | | | - Steve Horvath
- Department of BiostatisticsFielding School of Public HealthUniversity of CaliforniaLos AngelesCAUSA
- Department of Human GeneticsDavid Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
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Esteban-Cantos A, Montejano R, Rodríguez-Centeno J, Saiz-Medrano G, De Miguel R, Barruz P, Bernardino JI, Mena-Garay B, Cadiñanos J, Jiménez-González M, Nevado J, Valencia E, Mayoral-Muñoz M, Arribas JR, Rodés B. Longitudinal changes in epigenetic age acceleration in aviremic HIV-infected recipients of long-term antiretroviral treatment. J Infect Dis 2021; 225:287-294. [PMID: 34166509 DOI: 10.1093/infdis/jiab338] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/22/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND HIV infection induces epigenetic age acceleration (EAA), but it remains unclear whether epigenetic aging continues to accelerate during successful ART and prolonged virological suppression. METHODS We longitudinally analyzed 63 long-term aviremic HIV-infected adults. Using blood DNA methylation patterns, we calculated EAA measures based on three epigenetic clocks (Horvath´s clock, PhenoAge and GrimAge). We recorded the emergence of serious AIDS-related and non-AIDS-related events throughout the study to assess its association with EAA. RESULTS All participants were on stable ART and were virologically suppressed. After 4 years of follow-up, PhenoAge-EAA and GrimAge-EAA showed no differences, whereas Horvath-EAA slightly decreased (median difference; -0.53 years, p=0.015). Longitudinal changes in EAA measures were independent of changes in CD4 counts, the antiretroviral regimen or other HIV related factors. 19% of participants experienced a serious clinical event during the study. Horvath-EAA was significantly higher at baseline in participants with clinical events (p=0.027). After adjusting for confounders, we found a trend towards an association of higher levels of all EAA measures at baseline with serious clinical events. CONCLUSIONS Epigenetic aging did not accelerate in long-term aviremic HIV-infected adults after four years of successful ART. EAA measures deserve further study as potential tools for predicting clinical events.
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Affiliation(s)
- Andrés Esteban-Cantos
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid 28046, Spain
| | - Rocio Montejano
- Infectious Diseases Unit, Department of Internal Medicine, La Paz University Hospital-IdiPAZ, Madrid 28046, Spain
| | - Javier Rodríguez-Centeno
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid 28046, Spain
| | - Gabriel Saiz-Medrano
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid 28046, Spain
| | - Rosa De Miguel
- Infectious Diseases Unit, Department of Internal Medicine, La Paz University Hospital-IdiPAZ, Madrid 28046, Spain
| | - Pilar Barruz
- Genomics Laboratory, INGEMM, La Paz University Hospital-IdiPAZ, Madrid 28046, Spain
| | - Jose I Bernardino
- HIV Unit, Department of Internal Medicine, La Paz University Hospital-IdiPAZ, Madrid 28046, Spain
| | - Beatriz Mena-Garay
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid 28046, Spain
| | - Julen Cadiñanos
- Infectious Diseases Unit, Department of Internal Medicine, La Paz University Hospital-IdiPAZ, Madrid 28046, Spain
| | - María Jiménez-González
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid 28046, Spain
| | - Julián Nevado
- Genomics Laboratory, INGEMM, La Paz University Hospital-IdiPAZ, Madrid 28046, Spain
| | - Eulalia Valencia
- HIV Unit, Department of Internal Medicine, La Paz University Hospital-IdiPAZ, Madrid 28046, Spain
| | - Mario Mayoral-Muñoz
- HIV Unit, Department of Internal Medicine, La Paz University Hospital-IdiPAZ, Madrid 28046, Spain
| | - Jose R Arribas
- Infectious Diseases Unit, Department of Internal Medicine, La Paz University Hospital-IdiPAZ, Madrid 28046, Spain
| | - Berta Rodés
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid 28046, Spain
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Nwosu EC, Holmes MJ, Cotton MF, Dobbels E, Little F, Laughton B, van der Kouwe A, Meintjes EM, Robertson F. Cortical structural changes related to early antiretroviral therapy (ART) interruption in perinatally HIV-infected children at 5 years of age. IBRO Neurosci Rep 2021; 10:161-170. [PMID: 34179869 PMCID: PMC8211921 DOI: 10.1016/j.ibneur.2021.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 02/03/2021] [Indexed: 12/21/2022] Open
Abstract
ART interruption in children can occur especially in resource-limited settings for reasons including poor adherence, stock-outs, ART intolerance of non-pediatric formulas and pill size, as well as ultimately to test for HIV remission. Although early ART initiation is now standard of care in pediatric HIV management, very little is known on the effect of early ART initiation or subsequent interruption on brain development. This study aimed to investigate the effect of ART interruption on brain cortical thickness (CT) and folding in a subset of children from the Children with HIV Early antiRetroviral therapy (CHER) trial cohort who all started ART before 18 months of age. CHER participants in the neuroimaging follow-up study had magnetic resonance (MRI) scans on a 3T Siemens Allegra brain scanner at age 5.44 ± 0.37 years. MR images were processed using the automated cross-sectional stream in FreeSurfer v6.0 and vertex wise comparisons of CT and local gyrification indices (LGIs) were performed between HIV+ children and HIV- controls, as well as between HIV+ children on interrupted or continuous ART and controls. HIV+ children (n = 46) showed thicker cortex than HIV- children (n = 29) in bilateral frontal and left temporo-insular regions but lower LGIs in left superior and bilateral medial orbitofrontal cortex extending into rostral anterior cingulate. Children on interrupted ART (n = 21) had thicker cortex than HIV- controls in left frontal and right insular regions, but children on continuous treatment (n = 25) showed no difference from controls. Children on both interrupted and continuous ART showed region-specific alterations in LGI relative to controls. Cortical folding appears more sensitive than CT to early life events including early ART and interruption. However, immune health resilience in children can translate to long term preservation of morphometric brain development, especially for those on early and continuous treatment.
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Affiliation(s)
- Emmanuel C. Nwosu
- UCT Medical Imaging Research Unit, Division of Biomedical Engineering, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, South Africa
- Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Martha J. Holmes
- UCT Medical Imaging Research Unit, Division of Biomedical Engineering, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, South Africa
- Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Mark F. Cotton
- Family Centre for Research with Ubuntu, Department of Paediatrics & Child Health, Tygerberg Children’s Hospital and Faculty of Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Els Dobbels
- Family Centre for Research with Ubuntu, Department of Paediatrics & Child Health, Tygerberg Children’s Hospital and Faculty of Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Francesca Little
- Department of Statistical Sciences, Faculty of Sciences, University of Cape Town, South Africa
| | - Barbara Laughton
- Family Centre for Research with Ubuntu, Department of Paediatrics & Child Health, Tygerberg Children’s Hospital and Faculty of Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Andre van der Kouwe
- A.A. Martinos Centre for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Radiology, Harvard Medical School, Boston, MA, USA
| | - Ernesta M. Meintjes
- UCT Medical Imaging Research Unit, Division of Biomedical Engineering, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, South Africa
- Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Frances Robertson
- UCT Medical Imaging Research Unit, Division of Biomedical Engineering, Department of Human Biology, Faculty of Health Sciences, University of Cape Town, South Africa
- Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, South Africa
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Nwanaji-Enwerem JC, Colicino E, Gao X, Wang C, Vokonas P, Boyer EW, Baccarelli AA, Schwartz J. Associations of Plasma Folate and Vitamin B6 With Blood DNA Methylation Age: An Analysis of One-Carbon Metabolites in the VA Normative Aging Study. J Gerontol A Biol Sci Med Sci 2021; 76:760-769. [PMID: 33027507 DOI: 10.1093/gerona/glaa257] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Indexed: 02/01/2023] Open
Abstract
One-carbon metabolism is an important contributor to aging-related diseases; nevertheless, relationships of one-carbon metabolites with novel DNA methylation-based measures of biological aging remain poorly characterized. We examined relationships of one-carbon metabolites with 3 DNA methylation-based measures of biological aging: DNAmAge, GrimAge, and PhenoAge. We measured plasma levels of 4 common one-carbon metabolites (vitamin B6, vitamin B12, folate, and homocysteine) in 715 VA Normative Aging Study participants with at least 1 visit between 1999 and 2008 (observations = 1153). DNA methylation age metrics were calculated using the HumanMethylation450 BeadChip. We utilized Bayesian Kernel Machine Regression models adjusted for chronological age, lifestyle factors, age-related diseases, and study visits to determine metabolites important to the aging outcomes. Bayesian Kernel Machine Regression models allowed for the estimation of the relationships of single metabolites and the cumulative metabolite mixture with methylation age. Log vitamin B6 was selected as important to PhenoAge (β = -1.62 years, 95% CI: -2.28, -0.96). Log folate was selected as important to GrimAge (β = 0.75 years, 95% CI: 0.41, 1.09) and PhenoAge (β = 1.62 years, 95% CI: 0.95, 2.29). Compared to a model where each metabolite in the mixture is set to its 50th percentile, the log cumulative mixture with each metabolite at its 30th (β = -0.13 years, 95% CI: -0.26, -0.005) and 40th percentile (β = -0.06 years, 95% CI: -0.11, -0.005) was associated with decreased GrimAge. Our results provide novel characterizations of the relationships between one-carbon metabolites and DNA methylation age in a human population study. Further research is required to confirm these findings and establish their generalizability.
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Affiliation(s)
- Jamaji C Nwanaji-Enwerem
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, and MD/PhD Program, Harvard Medical School, Boston, Massachusetts
| | - Elena Colicino
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Xu Gao
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, New York
| | - Cuicui Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Pantel Vokonas
- VA Normative Aging Study, Veterans Affairs Boston Healthcare System and the Department of Medicine, Boston University School of Medicine, Massachusetts
| | - Edward W Boyer
- Division of Medical Toxicology, Department of Emergency Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, New York
| | - Joel Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
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Epigenetic age acceleration changes 2 years after antiretroviral therapy initiation in adults with HIV: a substudy of the NEAT001/ANRS143 randomised trial. Lancet HIV 2021; 8:e197-e205. [PMID: 33794182 DOI: 10.1016/s2352-3018(21)00006-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/04/2020] [Accepted: 11/20/2020] [Indexed: 01/24/2023]
Abstract
BACKGROUND DNA methylation-based estimators of biological age are reliable biomarkers of the ageing process. We aimed to investigate a range of epigenetic ageing biomarkers in a substudy of the NEAT001/ANRS143 clinical trial, which compared ritonavir-boosted darunavir with either raltegravir or tenofovir disoproxil fumarate and emtricitabine in antiretroviral therapy (ART)-naive adults. METHODS We analysed frozen whole blood samples from 168 ART-naive participants with HIV from the NEAT001/ANRS143 trial, before ART initiation and after 2 years of ART (84 participants on ritonavir-boosted darunavir with raltegravir and 84 participants on ritonavir-boosted darunavir with tenofovir disoproxil fumarate and emtricitabine). We also included 44 participants without HIV with a similar age and sex distribution. We analysed DNA methylation. Epigenetic age estimators (Horvath's clock, Hannum's clock, GrimAge, and PhenoAge) and estimated leucocyte compositions were generated using Horvath's New Online Methylation Age Calculator and Houseman's method. We calculated epigenetic age acceleration measures for each estimator of epigenetic age. The NEAT001/ANRS143 trial is registered with ClinicalTrials.gov, NCT01066962. FINDINGS Compared with the HIV-uninfected group, ART-naive participants with HIV showed higher epigenetic age acceleration (EAA) according to all EAA estimators (mean 2·5 years, 95% CI 1·89-3·22 for Horvath-EAA; 1·4 years, 0·74-1·99 for Hannum-EAA; 2·8 years, 1·97-3·68 for GrimAge-EAA; and 7·3 years, 6·40-8·13 for PhenoAge-EAA), with all differences being statistically significant except for Hannum-EAA (Horvath-EAA p=0·0008; Hannum-EAA p=0·059; GrimAge-EAA p=0·0021; and PhenoAge-EAA p<0·0001). Epigenetic ageing was more pronounced in participants who had CD4 counts less than 200 cells per μL (significant for PhenoAge and Hannum's clock, p=0·0015 and p=0·034, respectively) or viral loads over 100 000 copies per mL at baseline (significant for PhenoAge, p=0·017). After 2 years of ART, epigenetic age acceleration was reduced, although PhenoAge and GrimAge remained significantly higher in participants with HIV compared with participants without HIV (mean difference 3·69 years, 95% CI 1·77-5·61; p=0·0002 and 2·2 years, 0·47-3·99; p=0·013, respectively). There were no significant differences in the ART effect on epigenetic ageing between treatment regimens. At baseline, participants with HIV showed dysregulation of DNA methylation-based estimated leucocyte subsets towards more differentiated T-cell phenotypes and proinflammatory leucocytes, which was also partly restored with ART. INTERPRETATION ART initiation partly reversed epigenetic ageing associated with untreated HIV infection. Further studies are needed to understand the long-term dynamics and clinical relevance of epigenetic ageing biomarkers in people with HIV. FUNDING NEAT-ID Foundation.
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Lew BJ, Schantell MD, O'Neill J, Morsey B, Wang T, Ideker T, Swindells S, Fox HS, Wilson TW. Reductions in Gray Matter Linked to Epigenetic HIV-Associated Accelerated Aging. Cereb Cortex 2021; 31:3752-3763. [PMID: 33822880 DOI: 10.1093/cercor/bhab045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 01/12/2023] Open
Abstract
A growing literature suggests a relationship between HIV-infection and a molecular profile of age acceleration. However, despite the widely known high prevalence of HIV-related brain atrophy and HIV-associated neurocognitive disorder (HAND), epigenetic age acceleration has not been linked to HIV-related changes in structural MRI. We applied morphological MRI methods to study the brain structure of 110 virally suppressed participants with HIV infection and 122 uninfected controls age 22-72. All participants were assessed for cognitive impairment, and blood samples were collected from a subset of 86 participants with HIV and 83 controls to estimate epigenetic age. We examined the group-level interactive effects of HIV and chronological age and then used individual estimations of epigenetic age to understand the relationship between age acceleration and brain structure. Finally, we studied the effects of HAND. HIV-infection was related to gray matter reductions, independent of age. However, using epigenetic age as a biomarker for age acceleration, individual HIV-related age acceleration was associated with reductions in total gray matter. HAND was associated with decreases in thalamic and hippocampal gray matter. In conclusion, despite viral suppression, accentuated gray matter loss is evident with HIV-infection, and greater biological age acceleration specifically relates to such gray matter loss.
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Affiliation(s)
- Brandon J Lew
- Institute for Human Neuroscience, Boys Town National Research Hospital, Omaha, NE 68010, USA.,Department of Neurological Sciences, University of Nebraska Medical Center (UNMC), Omaha, NE 68198-8440, USA
| | - Mikki D Schantell
- Institute for Human Neuroscience, Boys Town National Research Hospital, Omaha, NE 68010, USA
| | - Jennifer O'Neill
- Department of Internal Medicine, Division of Infectious Diseases, UNMC, Omaha, NE 68198-8440, USA
| | - Brenda Morsey
- Department of Neurological Sciences, University of Nebraska Medical Center (UNMC), Omaha, NE 68198-8440, USA
| | - Tina Wang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Susan Swindells
- Department of Internal Medicine, Division of Infectious Diseases, UNMC, Omaha, NE 68198-8440, USA
| | - Howard S Fox
- Department of Neurological Sciences, University of Nebraska Medical Center (UNMC), Omaha, NE 68198-8440, USA
| | - Tony W Wilson
- Institute for Human Neuroscience, Boys Town National Research Hospital, Omaha, NE 68010, USA.,Department of Neurological Sciences, University of Nebraska Medical Center (UNMC), Omaha, NE 68198-8440, USA
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Shiau S, Brummel SS, Kennedy EM, Hermetz K, Spector SA, Williams PL, Kacanek D, Smith R, Drury SS, Agwu A, Ellis A, Patel K, Seage GR, Van Dyke RB, Marsit CJ. Longitudinal changes in epigenetic age in youth with perinatally acquired HIV and youth who are perinatally HIV-exposed uninfected. AIDS 2021; 35:811-819. [PMID: 33587437 PMCID: PMC7969428 DOI: 10.1097/qad.0000000000002805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVES To quantify the rate of change in epigenetic age compared with chronological age over time in youth with perinatally acquired HIV (YPHIV) and youth who are perinatally HIV-exposed uninfected (YPHEU). DESIGN Longitudinal study of 32 YPHIV and 8 YPHEU with blood samples collected at two time points at least 3 years apart. METHODS DNA methylation was measured using the Illumina MethylationEPIC array and epigenetic age was calculated using the Horvath method. Linear mixed effects models were fit to estimate the average change in epigenetic age for a 1-year change in chronological age separately for YPHIV and YPHEU. RESULTS Median age was 10.9 and 16.8 years at time 1 and 2, respectively. Groups were balanced by sex (51% male) and race (67% black). Epigenetic age increased by 1.23 years (95% CI 1.03--1.43) for YPHIV and 0.95 years (95% CI 0.74--1.17) for YPHEU per year increase in chronological age. Among YPHIV, in a model with chronological age, a higher area under the curve (AUC) viral load was associated with an increase in epigenetic age over time [2.19 years per log10 copies/ml, (95% CI 0.65--3.74)], whereas a higher time-averaged AUC CD4+ T-cell count was associated with a decrease in epigenetic age over time [-0.34 years per 100 cells/μl, (95% CI -0.63 to -0.06)] in YPHIV. CONCLUSION We observed an increase in the rate of epigenetic aging over time in YPHIV, but not in YPHEU. In YPHIV, higher viral load and lower CD4+ T-cell count were associated with accelerated epigenetic aging, emphasizing the importance of early and sustained suppressive treatment for YPHIV, who will receive lifelong ART.
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Affiliation(s)
- Stephanie Shiau
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey
| | - Sean S Brummel
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Elizabeth M Kennedy
- Gangarosa Department of Environ mental Health, Emory University Rollins School of Public Health, Atlanta, Georgia
| | - Karen Hermetz
- Gangarosa Department of Environ mental Health, Emory University Rollins School of Public Health, Atlanta, Georgia
| | - Stephen A Spector
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Rady Children's Hospital, San Diego, California
| | - Paige L Williams
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Deborah Kacanek
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Renee Smith
- Department of Pediatrics, University of Illinois at Chicago, Chicago, Illinois
| | - Stacy S Drury
- Department of Child and Adolescent Psychiatry, Tulane University School of Medicine, New Orleans, Louisiana
| | - Allison Agwu
- Departments of Pediatric and Adult Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Angela Ellis
- Frontier Science & Technology, Amherst, New York
| | - Kunjal Patel
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - George R Seage
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Russell B Van Dyke
- Department of Pediatrics, Tulane School of Medicine, New Orleans, Louisiana, USA
| | - Carmen J Marsit
- Gangarosa Department of Environ mental Health, Emory University Rollins School of Public Health, Atlanta, Georgia
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Yusuf H, Agwu A. Adolescents and young adults with early acquired HIV infection in the united states: unique challenges in treatment and secondary prevention. Expert Rev Anti Infect Ther 2021; 19:457-471. [PMID: 32990092 PMCID: PMC8084860 DOI: 10.1080/14787210.2021.1829473] [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: 05/29/2020] [Accepted: 09/24/2020] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Worldwide, children who acquired human immunodeficiency virus (HIV) at an early age, either perinatally or through blood transfusion, are reaching adolescence and adulthood due to successful antiretroviral treatment (ART). While many are thriving, a significant proportion face unprecedented multilevel challenges that can affect their long-term outcomes. Specifically, longstanding and poorly controlled HIV resulting from inadequate early regimens and nonadherence, along with the toxicities of some ART agents, can predispose them to sequelae including HIV-associated complications and other comorbidities. AREAS COVERED This paper reviews and summarizes the unique issues facing adolescents and young adults with early acquired HIV (AYA-EAHIV), including ART challenges, emerging comorbidities, and complications, including mental health comorbidities, secondary prevention, and transition from pediatric/adolescent to adult care. EXPERT OPINION AYA-EAHIV are a special population that have lived their entire lives with the physical and psychological toll of HIV mandating targeted and purposeful approaches to optimize their management and outcomes. Multifaceted inclusive and context-specific approaches focusing on heightened research, risk reduction interventions, and 'outside the box' thinking will be required to optimize treatment and reduce morbidity and mortality.
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Affiliation(s)
- Hasiya Yusuf
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Allison Agwu
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Chiavellini P, Canatelli-Mallat M, Lehmann M, Gallardo MD, Herenu CB, Cordeiro JL, Clement J, Goya RG. Aging and rejuvenation - a modular epigenome model. Aging (Albany NY) 2021; 13:4734-4746. [PMID: 33627519 PMCID: PMC7950254 DOI: 10.18632/aging.202712] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/08/2021] [Indexed: 12/21/2022]
Abstract
The view of aging has evolved in parallel with the advances in biomedical sciences. Long considered as an irreversible process where interventions were only aimed at slowing down its progression, breakthrough discoveries like animal cloning and cell reprogramming have deeply changed our understanding of postnatal development, giving rise to the emerging view that the epigenome is the driver of aging. The idea was significantly strengthened by the converging discovery that DNA methylation (DNAm) at specific CpG sites could be used as a highly accurate biomarker of age defined by an algorithm known as the Horvath clock. It was at this point where epigenetic rejuvenation came into play as a strategy to reveal to what extent biological age can be set back by making the clock tick backwards. Initial evidence suggests that when the clock is forced to tick backwards in vivo, it is only able to drag the phenotype to a partially rejuvenated condition. In order to explain the results, a bimodular epigenome is proposed, where module A represents the DNAm clock component and module B the remainder of the epigenome. Epigenetic rejuvenation seems to hold the key to arresting or even reversing organismal aging.
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Affiliation(s)
- Priscila Chiavellini
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Martina Canatelli-Mallat
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Marianne Lehmann
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Maria D Gallardo
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Claudia B Herenu
- Institute for Experimental Pharmacology (IFEC), School of Chemical Sciences, National University of Cordoba, Cordoba, Argentina
| | - Jose L Cordeiro
- World Academy of Art and Science (WAAS), Napa, CA 94558, USA
| | | | - Rodolfo G Goya
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
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Accelerated epigenetic aging in adolescents living with HIV is associated with altered development of brain structures. J Neurovirol 2021; 28:208-216. [PMID: 33554325 DOI: 10.1007/s13365-021-00947-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 12/22/2020] [Accepted: 01/15/2021] [Indexed: 01/09/2023]
Abstract
We recently demonstrated that adolescents perinatally infected with HIV-1 (PHIV+) have accelerated aging as measured by a highly accurate epigenetic biomarker of aging known as the epigenetic clock. However, whether epigenetic age acceleration in PHIV+ impacts brain development at the macro- and microstructural levels of brain anatomy has not been studied. We report on a cross-sectional study of PHIV+ enrolled in the Cape Town Adolescent Antiretroviral Cohort (CTAAC). The Illumina Infinium Methylation EPIC array was used to generate DNA methylation data from the blood samples of 180 PHIV+ aged 9 to 12 years. The epigenetic clock software and method was used to estimate two measures, epigenetic age acceleration (AgeAccelerationResidual) and extrinsic epigenetic age acceleration (EEAA). Each participant underwent T1 structural magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI). In order to investigate the associations of chronological age, sex, epigenetic age acceleration and treatment variables (CNS penetration effectiveness score (CPE)) of antiretroviral regimen on brain structure in PHIV+, we developed stepwise multiple regression models in R (version 3.4.3, 2017) including grey and white matter volumes, cortical thickness, cortical surface area and DTI measures of white matter microstructural integrity. The mean DNAm age (16.01 years) of the participants was higher than their mean chronological age (10.77 years). Epigenetic age acceleration contributed more to regional alterations of brain volumes, cortical thickness, cortical surface areas and neuronal microstructure than chronological age, in a range of regions. CPE positively contributed to volume of the brain stem. Understanding the drivers of epigenetic age acceleration could lead to valuable insights into structural brain alterations, and the persistence of neurocognitive disorders in seen in PHIV+ .
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Mahtab S, Zar HJ, Ntusi NAB, Joubert S, Asafu-Agyei NAA, Luff NJ, Jele N, Zuhlke L, Myer L, Jao J. Endothelial Dysfunction in South African Youth Living With Perinatally Acquired Human Immunodeficiency Virus on Antiretroviral Therapy. Clin Infect Dis 2020; 71:e672-e679. [PMID: 32285090 PMCID: PMC7744981 DOI: 10.1093/cid/ciaa396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 04/10/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus (HIV) and antiretroviral therapy (ART) confer cardiovascular disease (CVD) risk in adults with HIV. Few studies have assessed endothelial dysfunction (ED), an early marker of subclinical CVD risk, in youth living with perinatally acquired HIV (YLPHIV). METHODS Using peripheral arterial tonometry, we compared ED in YLPHIV and age-matched youth without HIV. A reactive hyperemic index ≤1.35 was defined as ED. Eligible participants included those aged 9-14 years and on ART ≥6 months at enrollment. RESULTS Overall, 431 YLPHIV and 93 youth without HIV with a median age of 14.1 versus 13.9 years, respectively, were included. YLPHIV had a lower BMI z score (BMIZ; -0.2 vs 0.4; P < .01) but higher rates of hypercholesterolemia (10% vs 1%; P = .01) than youth without HIV. Among YLPHIV, mean log viral load (VL) was 4.83 copies/mL with 21.7% having a CD4 count <500 cell/mm3; median duration on ART was 9.8 years with 38% initiating at <2 years of age. YLPHIV had higher rates of ED than youth without HIV (50% vs 34%; P = .01); this relationship persisted after adjusting for age, sex, BMIZ, elevated BP, and hypercholesterolemia (RR, 1.43; P = .02). Among YLPHIV, CD4 count >500 cell/mm3 (RR, 1.04; P = .76), VL (RR, 1.01; P = .78), and current ART class (protease inhibitor based vs nonnucleoside inhibitor based: relative risk, 0.90; P = .186) were not associated with ED after adjustment. CONCLUSIONS Even after adjusting for physiologic differences, YLPHIV appear to be at increased risk of ED compared with age-matched youth without HIV. These findings have important implications for the life course of YLPHIV who may be at increased risk of premature CVD and complications.
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Affiliation(s)
- Sana Mahtab
- Department of Pediatrics and Child Health, Red Cross War Memorial Hospital, University of Cape Town, Cape Town, South Africa.,SA MRC unit on child and adolescent Health, Red Cross War Memorial Hospital, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Pediatrics and Child Health, Red Cross War Memorial Hospital, University of Cape Town, Cape Town, South Africa.,SA MRC unit on child and adolescent Health, Red Cross War Memorial Hospital, University of Cape Town, Cape Town, South Africa
| | - Ntobeko A B Ntusi
- Division of Cardiology, Department of Medicine, Groote Schuur Hospital and Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Susan Joubert
- Department of Pediatrics and Child Health, Red Cross War Memorial Hospital, University of Cape Town, Cape Town, South Africa.,SA MRC unit on child and adolescent Health, Red Cross War Memorial Hospital, University of Cape Town, Cape Town, South Africa
| | - Nana Akua A Asafu-Agyei
- Department of Pediatrics and Child Health, Red Cross War Memorial Hospital, University of Cape Town, Cape Town, South Africa.,SA MRC unit on child and adolescent Health, Red Cross War Memorial Hospital, University of Cape Town, Cape Town, South Africa
| | - Norme J Luff
- Department of Pediatrics and Child Health, Red Cross War Memorial Hospital, University of Cape Town, Cape Town, South Africa.,SA MRC unit on child and adolescent Health, Red Cross War Memorial Hospital, University of Cape Town, Cape Town, South Africa
| | - Nomawethu Jele
- Department of Pediatrics and Child Health, Red Cross War Memorial Hospital, University of Cape Town, Cape Town, South Africa.,SA MRC unit on child and adolescent Health, Red Cross War Memorial Hospital, University of Cape Town, Cape Town, South Africa
| | - Liesl Zuhlke
- Division of Pediatric Cardiology, Red Cross War Memorial Children's Hospital, Rondebosch, Cape Town, South Africa
| | - Landon Myer
- Division of Epidemiology and Biostatistics, School of Public Health and Family Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jennifer Jao
- Department of Pediatrics, Division of Infectious Diseases, Northwestern Feinberg School of Medicine, Chicago, Illinois, USA
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Hoare J, Stein DJ, Heany SJ, Fouche JP, Phillips N, Er S, Myer L, Zar HJ, Horvath S, Levine AJ. Accelerated epigenetic aging in adolescents from low-income households is associated with altered development of brain structures. Metab Brain Dis 2020; 35:1287-1298. [PMID: 32671535 PMCID: PMC7606536 DOI: 10.1007/s11011-020-00589-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 06/23/2020] [Indexed: 10/23/2022]
Abstract
The relationship between cognitive performance, macro and microstructural brain anatomy and accelerated aging as measured by a highly accurate epigenetic biomarker of aging known as the epigenetic clock in healthy adolescents has not been studied. Healthy adolescents enrolled in the Cape Town Adolescent Antiretroviral Cohort Study were studied cross sectionally. The Illumina Infinium Methylation EPIC array was used to generate DNA methylation data from the blood samples of 44 adolescents aged 9 to 12 years old. The epigenetic clock software and method was used to estimate two measures, epigenetic age acceleration residual (AAR) and extrinsic epigenetic age acceleration (EEAA). Each participant underwent neurocognitive testing, T1 structural magnetic resonance imaging (MRI), and diffusion tensor imaging (DTI). Correlation tests were run between the two epigenetic aging measures and 10 cognitive functioning domains, to assess for differences in cognitive performance as epigenetic aging increases. In order to investigate the associations of epigenetic age acceleration on brain structure, we developed stepwise multiple regression models in R (version 3.4.3, 2017) including grey and white matter volumes, cortical thickness, and cortical surface area, as well as DTI measures of white matter microstructural integrity. In addition to negatively affecting two cognitive domains, visual memory (p = .026) and visual spatial acuity (p = .02), epigenetic age acceleration was associated with alterations of brain volumes, cortical thickness, cortical surface areas and abnormalities in neuronal microstructure in a range of regions. Stress was a significant predictor (p = .029) of AAR. Understanding the drivers of epigenetic age acceleration in adolescents could lead to valuable insights into the development of neurocognitive impairment in adolescents.
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Affiliation(s)
- Jacqueline Hoare
- Department of Psychiatry and Mental Health, University of Cape Town, Groote Schuur Hospital, Observatory, Cape Town, 7925, South Africa.
| | - Dan J Stein
- Department of Psychiatry and Mental Health, University of Cape Town, Groote Schuur Hospital, Observatory, Cape Town, 7925, South Africa
- SA MRC Unit on Risk & Resilience in Mental Disorders, Cape Town, South Africa
| | - Sarah J Heany
- Department of Psychiatry and Mental Health, University of Cape Town, Groote Schuur Hospital, Observatory, Cape Town, 7925, South Africa
| | - Jean-Paul Fouche
- Department of Psychiatry and Mental Health, University of Cape Town, Groote Schuur Hospital, Observatory, Cape Town, 7925, South Africa
| | - Nicole Phillips
- Department of Psychiatry and Mental Health, University of Cape Town, Groote Schuur Hospital, Observatory, Cape Town, 7925, South Africa
| | - Sebnem Er
- Department of Statistics, University of Cape Town, Rondebosch, Cape Town, South Africa
| | - Landon Myer
- Centre for Infectious Disease Epidemiology and Research, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa
- Division of Epidemiology and Biostatistics, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- SA Medical Research Council Unit on Child and Adolescent Health, Cape Town, South Africa
| | - Steve Horvath
- Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Biostatistics, School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Andrew J Levine
- SA MRC Unit on Risk & Resilience in Mental Disorders, Cape Town, South Africa
- Department of Neurology, David Geffen School of Medicine at the University of California, Los Angeles, CA, USA
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48
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Yang CX, Schon E, Obeidat M, Kobor MS, McEwen L, MacIsaac J, Lin D, Novak RM, Hudson F, Klinker H, Dharan N, Horvath S, Bourbeau J, Tan W, Sin DD, Man SFP, Kunisaki K, Leung JM. Occurrence of Accelerated Epigenetic Aging and Methylation Disruptions in Human Immunodeficiency Virus Infection Before Antiretroviral Therapy. J Infect Dis 2020; 223:1681-1689. [PMID: 32959881 DOI: 10.1093/infdis/jiaa599] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Whether accelerated aging develops over the course of chronic human immunodeficiency virus (HIV) infection or can be observed before significant immunosuppression on is unknown. We studied DNA methylation in blood to estimate cellular aging in persons living with HIV (PLWH) before the initiation of antiretroviral therapy (ART). METHODS A total of 378 ART-naive PLWH who had CD4 T-cell counts >500/µL and were enrolled in the Strategic Timing of Antiretroviral Therapy trial (Pulmonary Substudy) were compared with 34 HIV-negative controls. DNA methylation was performed using the Illumina MethylationEPIC BeadChip. Differentially methylated positions (DMPs) and differentially methylated regions (DMRs) in PLWH compared with controls were identified using a robust linear model. Methylation age was calculated using a previously described epigenetic clock. RESULTS There were a total of 56 639 DMPs and 6103 DMRs at a false discovery rate of <0.1. The top 5 DMPs corresponded to genes NLRC5, VRK2, B2M, and GPR6 and were highly enriched for cancer-related pathways. PLWH had significantly higher methylation age than HIV-negative controls (P = .001), with black race, low CD4 and high CD8 T-cell counts, and duration of HIV being risk factors for age acceleration. CONCLUSIONS PLWH before the initiation of ART and with preserved immune status show evidence of advanced methylation aging.
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Affiliation(s)
- Chen Xi Yang
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | - Emma Schon
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ma'en Obeidat
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada.,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lisa McEwen
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julie MacIsaac
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Lin
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Richard M Novak
- Section of Infectious Diseases, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Fleur Hudson
- MRC Clinical Trials Unit, University College London, London, United Kingdom
| | - Hartwig Klinker
- University of Würzburg Medical Center, Department of Internal Medicine II, Division of Infectious Diseases, Würzburg, Germany
| | | | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Jean Bourbeau
- Respiratory Epidemiology and Clinical Research Unit, McGill University, Montreal, Quebec, Canada
| | - Wan Tan
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada.,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Don D Sin
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada.,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - S F Paul Man
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada.,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ken Kunisaki
- Minneapolis Veterans Affairs Health Care System, Section of Pulmonary, Critical Care and Sleep Medicine, Minneapolis, Minnesota, USA.,Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Janice M Leung
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada.,Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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49
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Sehl ME, Rickabaugh TM, Shih R, Martinez-Maza O, Horvath S, Ramirez CM, Jamieson BD. The Effects of Anti-retroviral Therapy on Epigenetic Age Acceleration Observed in HIV-1-infected Adults. Pathog Immun 2020; 5:291-311. [PMID: 33501399 PMCID: PMC7815056 DOI: 10.20411/pai.v5i1.376] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/08/2020] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND HIV-1 infection is associated with acceleration of age-related methylation patterns in peripheral blood and brain of infected individuals although the relative contributions of HIV-1 infection versus its treatment to the observed accelerations in biological aging have not yet been investigated. METHODS In this longitudinal study of the effects of antiretroviral therapy (ART) on epigenetic aging patterns, we extracted DNA from peripheral blood mononuclear cells from 15 HIV-1-infected individuals infected at three time points: 6 months-1year pre-ART, 6-12 months post-initiation of ART, and 18-24 months after initiating ART. We compared these trajectories with those of 15 age-matched uninfected control participants at three time points with similar intervals. Methylation studies were performed using the Infinium methylation 450 arrays. We examined four epigenetic clock measurements: Age acceleration residual (AAR), Extrinsic (EEAA), Phenotypic (PEAA), and Grim (GEAA) epigenetic age acceleration. Weighted correlation network (WGCNA) analysis was used to identify clusters of highly co-methylated CpGs. RESULTS We found that prior to the initiation of ART all four epigenetic measures were significantly higher in HIV-1-infected individuals compared with uninfected individuals (P<0.001 for AAR, P=0.008 for EEAA, P=0.012 for GEAA, P<0.001 for PEAA using Wilcoxon rank sum tests between serostatus groups). These effects persisted after the initiation of ART, although the magnitude of these differences diminished. At 18-24 months post-ART initiation (time point 3), PEAA and GEAA were no longer significantly different between HIV-1-infected and uninfected individuals (P=0.059 for PEAA, P=0.11 for GEAA), while AAR and EEAA remained significantly higher in HIV-1-infected individuals compared with uninfected individuals. We further examined for global patterns of methylation differences between HIV-1-infected and uninfected at each time point, and found 14 groups of co-methylated CpGs that were significantly different between groups at baseline, and remained different after the initiation of ART. Conclusion: We confirm that epigenetic age acceleration associated with HIV-1 infection is most dramatic before ART initiation, and this observation is consistent across four epigenetic clock measurements, as well as in additional groups of co-methylated CpGs identified using WGCNA. Following initiation of ART, there is a partial reduction in age acceleration in all measures, with loss of any significant difference in PEAA and GEAA between serostatus groups. Our findings support the need for future studies examining for a link between epigenetic age acceleration and clinical outcomes in HIV-1-infected individuals.
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Affiliation(s)
- Mary E. Sehl
- Department of Medicine, Division of Hematology-Oncology, David Geffen School of Medicine, UCLA
- Department of Computational Medicine, David Geffen School of Medicine, UCLA
- These authors contributed equally to this work
| | - Tammy M. Rickabaugh
- Department of Pediatrics, Division of Hematology-Oncology, David Geffen School of Medicine, UCLA
- These authors contributed equally to this work
| | - Roger Shih
- Department of Pediatrics, Division of Hematology-Oncology, David Geffen School of Medicine, UCLA
| | | | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, UCLA
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, UCLA
| | - Christina M. Ramirez
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, UCLA
| | - Beth D. Jamieson
- Department of Medicine, Division of Hematology-Oncology, David Geffen School of Medicine, UCLA
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50
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Sil S, Niu F, Chivero ET, Singh S, Periyasamy P, Buch S. Role of Inflammasomes in HIV-1 and Drug Abuse Mediated Neuroinflammaging. Cells 2020; 9:cells9081857. [PMID: 32784383 PMCID: PMC7464640 DOI: 10.3390/cells9081857] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
Despite the effectiveness of combined antiretroviral therapy (cART) in suppressing virus replication, chronic inflammation remains one of the cardinal features intersecting HIV-1, cART, drug abuse, and likely contributes to the accelerated neurocognitive decline and aging in people living with HIV-1 (PLWH) that abuse drugs. It is also estimated that ~30–60% of PLWH on cART develop cognitive deficits associated with HIV-1-associated neurocognitive disorders (HAND), with symptomatology ranging from asymptomatic to mild, neurocognitive impairments. Adding further complexity to HAND is the comorbidity of drug abuse in PLWH involving activated immune responses and the release of neurotoxins, which, in turn, mediate neuroinflammation. Premature or accelerated aging is another feature of drug abusing PLWH on cART regimes. Emerging studies implicate the role of HIV-1/HIV-1 proteins, cART, and abused drugs in altering the inflammasome signaling in the central nervous system (CNS) cells. It is thus likely that exposure of these cells to HIV-1/HIV-1 proteins, cART, and/or abused drugs could have synergistic/additive effects on the activation of inflammasomes, in turn, leading to exacerbated neuroinflammation, ultimately resulting in premature aging referred to as “inflammaging” In this review, we summarize the current knowledge of inflammasome activation, neuroinflammation, and aging in central nervous system (CNS) cells such as microglia, astrocytes, and neurons in the context of HIV-1 and drug abuse.
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Affiliation(s)
| | | | | | | | | | - Shilpa Buch
- Correspondence: (P.P.); (S.B.); Tel.: +1-402-559-3165 (S.B.)
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