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Wang M, Yoon J, Reisert H, Das B, Orlinick B, Chiarella J, Halvas EK, Mellors J, Pang AP, Barakat LA, Fikrig M, Cyktor J, Kluger Y, Spudich S, Corley MJ, Farhadian SF. HIV-1-infected T cell clones are shared across cerebrospinal fluid and blood during ART. JCI Insight 2024; 9:e176208. [PMID: 38587074 DOI: 10.1172/jci.insight.176208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 02/27/2024] [Indexed: 04/09/2024] Open
Abstract
The central nervous system HIV reservoir is incompletely understood and is a major barrier to HIV cure. We profiled people with HIV (PWH) and uninfected controls through single-cell transcriptomic and T cell receptor (TCR) sequencing to understand the dynamics of HIV persistence in the CNS. In PWH on ART, we found that most participants had single cells containing HIV-1 RNA, which was found predominantly in CD4 central memory T cells, in both cerebrospinal fluid (CSF) and blood. HIV-1 RNA-containing cells were found more frequently in CSF than blood, indicating a higher burden of reservoir cells in the CNS than blood for some PWH. Most CD4 T cell clones containing infected cells were compartment specific, while some (22%) - including rare clones with members of the clone containing detectable HIV RNA in both blood and CSF - were found in both CSF and blood. These results suggest that infected T cells trafficked between tissue compartments and that maintenance and expansion of infected T cell clones contributed to the CNS reservoir in PWH on ART.
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Affiliation(s)
- Meng Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
| | | | | | | | | | - Jennifer Chiarella
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Elias K Halvas
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John Mellors
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alina Ps Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | | | | | - Joshua Cyktor
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yuval Kluger
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Serena Spudich
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Michael J Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Shelli F Farhadian
- Section of Infectious Diseases, and
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
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Hu W, Foord C, Hsu J, Fan L, Corley MJ, Bhatia TN, Xu S, Belchikov N, He Y, Pang AP, Lanjewar SN, Jarroux J, Joglekar A, Milner TA, Ndhlovu LC, Zhang J, Butelman E, Sloan SA, Lee VM, Gan L, Tilgner HU. ScISOr-ATAC reveals convergent and divergent splicing and chromatin specificities between matched cell types across cortical regions, evolution, and in Alzheimer's Disease. bioRxiv 2024:2024.02.24.581897. [PMID: 38464236 PMCID: PMC10925193 DOI: 10.1101/2024.02.24.581897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Multimodal measurements have become widespread in genomics, however measuring open chromatin accessibility and splicing simultaneously in frozen brain tissues remains unconquered. Hence, we devised Single-Cell-ISOform-RNA sequencing coupled with the Assay-for-Transposase-Accessible-Chromatin (ScISOr-ATAC). We utilized ScISOr-ATAC to assess whether chromatin and splicing alterations in the brain convergently affect the same cell types or divergently different ones. We applied ScISOr-ATAC to three major conditions: comparing (i) the Rhesus macaque (Macaca mulatta) prefrontal cortex (PFC) and visual cortex (VIS), (ii) cross species divergence of Rhesus macaque versus human PFC, as well as (iii) dysregulation in Alzheimer's disease in human PFC. We found that among cortical-layer biased excitatory neuron subtypes, splicing is highly brain-region specific for L3-5/L6 IT_RORB neurons, moderately specific in L2-3 IT_CUX2.RORB neurons and unspecific in L2-3 IT_CUX2 neurons. In contrast, at the chromatin level, L2-3 IT_CUX2.RORB neurons show the highest brain-region specificity compared to other subtypes. Likewise, when comparing human and macaque PFC, strong evolutionary divergence on one molecular modality does not necessarily imply strong such divergence on another molecular level in the same cell type. Finally, in Alzheimer's disease, oligodendrocytes show convergently high dysregulation in both chromatin and splicing. However, chromatin and splicing dysregulation most strongly affect distinct oligodendrocyte subtypes. Overall, these results indicate that chromatin and splicing can show convergent or divergent results depending on the performed comparison, justifying the need for their concurrent measurement to investigate complex systems. Taken together, ScISOr-ATAC allows for the characterization of single-cell splicing and chromatin patterns and the comparison of sample groups in frozen brain samples.
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Affiliation(s)
- Wen Hu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Careen Foord
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Justine Hsu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Li Fan
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Helen and Robert Appel Alzheimer's Disease Research Institute
| | - Michael J Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Tarun N Bhatia
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Siwei Xu
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Natan Belchikov
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
- Physiology, Biophysics & Systems Biology Program, Weill Cornell Medicine, New York, NY, USA
| | - Yi He
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Alina Ps Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Samantha N Lanjewar
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Julien Jarroux
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Anoushka Joglekar
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
| | - Teresa A Milner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Lishomwa C Ndhlovu
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, CA, USA
| | - Eduardo Butelman
- Neuropsychoimaging of Addiction and Related Conditions Research Program, Dept. of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven A Sloan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Virginia My Lee
- Center for Neurodegenerative Disease Research, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Li Gan
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Helen and Robert Appel Alzheimer's Disease Research Institute
| | - Hagen U Tilgner
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA
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Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea I, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A, Abdel-Mohsen M. Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging. Microbiome 2024; 12:31. [PMID: 38383483 PMCID: PMC10882811 DOI: 10.1186/s40168-024-01758-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND People living with HIV (PLWH), even when viral replication is controlled through antiretroviral therapy (ART), experience persistent inflammation. This inflammation is partly attributed to intestinal microbial dysbiosis and translocation, which may lead to non-AIDS-related aging-associated comorbidities. The extent to which living with HIV - influenced by the infection itself, ART usage, sexual orientation, or other associated factors - affects the biological age of the intestines is unclear. Furthermore, the role of microbial dysbiosis and translocation in the biological aging of PLWH remains to be elucidated. To investigate these uncertainties, we used a systems biology approach, analyzing colon and ileal biopsies, blood samples, and stool specimens from PLWH on ART and people living without HIV (PLWoH) as controls. RESULTS PLWH exhibit accelerated biological aging in the colon, ileum, and blood, as measured by various epigenetic aging clocks, compared to PLWoH. Investigating the relationship between microbial translocation and biological aging, PLWH had decreased levels of tight junction proteins in the intestines, along with increased microbial translocation. This intestinal permeability correlated with faster biological aging and increased inflammation. When investigating the relationship between microbial dysbiosis and biological aging, the intestines of PLWH had higher abundance of specific pro-inflammatory bacteria, such as Catenibacterium and Prevotella. These bacteria correlated with accelerated biological aging. Conversely, the intestines of PLWH had lower abundance of bacteria known for producing the anti-inflammatory short-chain fatty acids, such as Subdoligranulum and Erysipelotrichaceae, and these bacteria were associated with slower biological aging. Correlation networks revealed significant links between specific microbial genera in the colon and ileum (but not in feces), increased aging, a rise in pro-inflammatory microbe-related metabolites (e.g., those in the tryptophan metabolism pathway), and a decrease in anti-inflammatory metabolites like hippuric acid. CONCLUSIONS We identified specific microbial compositions and microbiota-related metabolic pathways that are intertwined with intestinal and systemic biological aging. This microbial signature of biological aging is likely reflecting various factors including the HIV infection itself, ART usage, sexual orientation, and other aspects associated with living with HIV. A deeper understanding of the mechanisms underlying these connections could offer potential strategies to mitigate accelerated aging and its associated health complications. Video Abstract.
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Affiliation(s)
- Shalini Singh
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Leila B Giron
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Maliha W Shaikh
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Shivanjali Shankaran
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
- Department of Medicine, Rush University, Chicago, IL, USA
| | - Phillip A Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Zlata R Bogin
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Simona A Bambi
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
| | - Aaron R Goldman
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Joao L L C Azevedo
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | | | | | | | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Aswin Verhoeven
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Elena Sánchez-López
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Toshitha Kannan
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA
| | - Ceylan E Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alan L Landay
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
- Department of Medicine, Rush University, Chicago, IL, USA
| | | | - Ali Keshavarzian
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, USA
- Department of Medicine, Rush University, Chicago, IL, USA
| | - Mohamed Abdel-Mohsen
- Vaccine and Immunotherapy Center, The Wistar Institute, 3601 Spruce Street, Philadelphia, PA, 19104, USA.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Promsote W, Chumpolkulwong K, Musich T, Corley MJ, Ndhlovu LC, Sopanaporn J, Inthawong D, Nadee P, Silsorn D, Sirisrisopa S, Wongsawanonkul S, Parsons MS, Cowden J, Imerbsin R, Lugo-Roman L, Vasan S, Hsu DC. Impact of sleep deprivation on neurocognition and inflammation in rhesus macaques. Brain Behav Immun Health 2023; 33:100683. [PMID: 37701789 PMCID: PMC10493883 DOI: 10.1016/j.bbih.2023.100683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/25/2023] [Accepted: 08/26/2023] [Indexed: 09/14/2023] Open
Abstract
Sleep deprivation in humans is associated with both cognitive impairment and immune dysregulation. An animal model of neuropathogenesis may provide insight to understand the effects of sleep deprivation on the brain. Human neurocognition is more closely mirrored by nonhuman primates (NHP) than other animals. As such, we developed an NHP model to assess the impact of sleep deprivation on neurocognition and markers of systemic immune activation. Six male rhesus macaques underwent three rounds of sleep deprivation (48 h without sleep) at days 0, 14, and 28. We performed domain specific cognitive assessments using the Cambridge Neuropsychological Test Automated Battery (CANTAB) via a touch screen before and after 24 and 48 h of sleep deprivation. Immune activation markers were measured in the blood by multiplex assay and flow cytometry. Although we observed variability in cognitive performance between the three rounds of sleep deprivation, cognitive impairments were identified in all six animals. We noted more cognitive impairments after 48 h than after 24 h of sleep deprivation. Following 48 h of sleep deprivation, elevations in markers of immune activation in the blood were observed in most animals. The observed impairments largely normalized after sleep. The co-occurrence of systemic immune alterations and cognitive impairment establishes this model as useful for studying the impact of sleep deprivation on neurobehavior and immune perturbations in rhesus macaques.
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Affiliation(s)
- Wanwisa Promsote
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, 20817, USA
| | | | - Thomas Musich
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Michael J. Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, 10021, USA
| | - Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, 10021, USA
| | - Jumpol Sopanaporn
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Dutsadee Inthawong
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Panupat Nadee
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Decha Silsorn
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | | | | | - Matthew S. Parsons
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, 20817, USA
| | - Jessica Cowden
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Rawiwan Imerbsin
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Luis Lugo-Roman
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Sandhya Vasan
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, 20817, USA
| | - Denise C. Hsu
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, MD, 20817, USA
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7
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Ortiz-Whittingham LR, Baumer Y, Pang APS, Sampson M, Baez AS, Rose RR, Noonan SH, Mendez-Silva J, Collins BS, Mitchell VM, Cintron MA, Farmer N, Remaley AT, Corley MJ, Powell-Wiley TM. Associations between neighborhood socioeconomic deprivation, IFNγ, and high-density lipoprotein particle size: Data from the Washington, D.C. cardiovascular health and needs assessment. Psychoneuroendocrinology 2023; 157:106346. [PMID: 37651859 PMCID: PMC10543547 DOI: 10.1016/j.psyneuen.2023.106346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/15/2023] [Accepted: 07/28/2023] [Indexed: 09/02/2023]
Abstract
INTRODUCTION Neighborhood socioeconomic deprivation is associated with increased cardiovascular risk factors, including inflammation. Inflammation plays an important role in modifying the cardioprotective function of high-density lipoprotein (HDL). Moreover, recent studies suggest that very high HDL is associated with adverse cardiovascular disease (CVD) outcomes. Thus, we sought to explore the relationships between neighborhood socioeconomic deprivation as a marker of chronic stress, inflammation, proprotein convertase subtilisin/kexin type 9 (PCSK9) (a core component of the HDL proteome), HDL characterisitcs, and biological aging as a predictor of CVD and all-cause mortality. METHODS Sixty African American subjects were recruited to the NIH Clinical Center as part of a community-based participatory research-designed observational study. Neighborhood deprivation index (NDI), a marker of neighborhood socioeconomic deprivation, was measured using US Census data. HDL characteristics (cholesterol, particle number, size, subspecies) were determined from NMR lipoprotein profiling, and plasma cytokines (IL-1β, IL-6, IL-8, TNFα, IFNγ) were measured using an ELISA-based multiplex technique. Epigenetic clock biomarkers of aging were measured using DNA methylation data obtained from participants' buffy coat samples. We used linear regression modeling adjusted for atherosclerotic cardiovascular disease (ASCVD) risk score, body mass index (BMI), and lipid-lowering medication use to investigate relationships of interest. RESULTS NDI directly associated with large HDL particle count (H7P) and IFNγ and trended toward significance with HDL-C and PCSK9. IFNγ and PCSK9 then directly associated with H7P. H7P also directly associated with higher DNA methylation phenotypic age (PhenoAge). CONCLUSION We highlight associations between neighborhood socioeconomic deprivation, IFNγ, PCSK9, HDL subspecies, and epigenetic biomarkers of aging. Taken together, our findings suggest indirect pathways linking neighborhood deprivation-related stress and inflammation to HDL and immune epigenetic changes. Moreover, these results add to recent work showing the pathogenicity of high HDL levels and underscore the need to understand how chronic stress-related inflammation and lipoprotein subspecies relate to CVD risk across diverse populations.
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Affiliation(s)
- Lola R Ortiz-Whittingham
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, United States
| | - Yvonne Baumer
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, United States
| | - Alina P S Pang
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Maureen Sampson
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Andrew S Baez
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, United States
| | - Rebecca R Rose
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, United States
| | - Sarah H Noonan
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, United States
| | - Joanna Mendez-Silva
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, United States
| | - Billy S Collins
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, United States
| | - Valerie M Mitchell
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, United States
| | - Manuel A Cintron
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, United States
| | - Nicole Farmer
- Translational Biobehavioral and Health Disparities Branch, National Institutes of Health Clinical Center, Bethesda, MD, United States
| | - Alan T Remaley
- Lipoprotein Metabolism Laboratory, Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, United States
| | - Michael J Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Tiffany M Powell-Wiley
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health, Bethesda, MD, United States; Intramural Research Program, National Institutes on Minority Health and Health Disparities (NIMHD), National Institutes of Health, Bethesda, MD, United States.
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8
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Singh S, Giron LB, Shaikh MW, Shankaran S, Engen PA, Bogin ZR, Bambi SA, Goldman AR, Azevedo JLLC, Orgaz L, de Pedro N, González P, Giera M, Verhoeven A, Sánchez-López E, Pandrea IV, Kannan T, Tanes CE, Bittinger K, Landay AL, Corley MJ, Keshavarzian A, Abdel-Mohsen M. Distinct Intestinal Microbial Signatures Linked to Accelerated Biological Aging in People with HIV. Res Sq 2023:rs.3.rs-3492242. [PMID: 37961645 PMCID: PMC10635386 DOI: 10.21203/rs.3.rs-3492242/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background People with HIV (PWH), even with controlled viral replication through antiretroviral therapy (ART), experience persistent inflammation. This is partly due to intestinal microbial dysbiosis and translocation. Such ongoing inflammation may lead to the development of non-AIDS-related aging-associated comorbidities. However, there remains uncertainty regarding whether HIV affects the biological age of the intestines and whether microbial dysbiosis and translocation influence the biological aging process in PWH on ART. To fill this knowledge gap, we utilized a systems biology approach, analyzing colon and ileal biopsies, blood samples, and stool specimens from PWH on ART and their matched HIV-negative counterparts. Results Despite having similar chronological ages, PWH on ART exhibit accelerated biological aging in the colon, ileum, and blood, as measured by various epigenetic aging clocks, compared to HIV-negative controls. Investigating the relationship between microbial translocation and biological aging, PWH on ART had decreased levels of tight junction proteins in the colon and ileum, along with increased microbial translocation. This increased intestinal permeability correlated with faster intestinal and systemic biological aging, as well as increased systemic inflammation. When investigating the relationship between microbial dysbiosis and biological aging, the intestines of PWH on ART had higher abundance of specific pro-inflammatory bacterial genera, such as Catenibacterium and Prevotella. These bacteria significantly correlated with accelerated local and systemic biological aging. Conversely, the intestines of PWH on ART had lower abundance of bacterial genera known for producing short-chain fatty acids and exhibiting anti-inflammatory properties, such as Subdoligranulum and Erysipelotrichaceae, and these bacteria taxa were associated with slower biological aging. Correlation networks revealed significant links between specific microbial genera in the colon and ileum (but not in feces), increased aging, a rise in pro-inflammatory microbial-related metabolites (e.g., those in the tryptophan metabolism pathway), and a decrease in anti-inflammatory metabolites like hippuric acid and oleic acid. Conclusions We identified a specific microbial composition and microbiome-related metabolic pathways that are intertwined with both intestinal and systemic biological aging in PWH on ART. A deeper understanding of the mechanisms underlying these connections could potentially offer strategies to counteract premature aging and its associated health complications in PWH.
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9
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Copertino DC, Holmberg CS, Weiler J, Ward AR, Howard JN, Levinger C, Pang AP, Corley MJ, Dündar F, Zumbo P, Betel D, Gandhi RT, McMahon DK, Bosch RJ, Linden N, Macatangay BJ, Cyktor JC, Eron JJ, Mellors JW, Kovacs C, Benko E, Bosque A, Jones RB. The latency-reversing agent HODHBt synergizes with IL-15 to enhance cytotoxic function of HIV-specific T cells. JCI Insight 2023; 8:e169028. [PMID: 37581929 PMCID: PMC10561764 DOI: 10.1172/jci.insight.169028] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 08/10/2023] [Indexed: 08/17/2023] Open
Abstract
IL-15 is under clinical investigation toward the goal of curing HIV infection because of its abilities to reverse HIV latency and enhance immune effector function. However, increased potency through combination with other agents may be needed. 3-Hydroxy-1,2,3-benzotriazin-4(3H)-one (HODHBt) enhances IL-15-mediated latency reversal and NK cell function by increasing STAT5 activation. We hypothesized that HODHBt would also synergize with IL-15, via STAT5, to directly enhance HIV-specific cytotoxic T cell responses. We showed that ex vivo IL-15 + HODHBt treatment markedly enhanced HIV-specific granzyme B-releasing T cell responses in PBMCs from antiretroviral therapy-suppressed (ART-suppressed) donors. We also observed upregulation of antigen processing and presentation in CD4+ T cells and increased surface MHC-I. In ex vivo PBMCs, IL-15 + HODHBt was sufficient to reduce intact proviruses in 1 of 3 ART-suppressed donors. Our findings reveal the potential for second-generation IL-15 studies incorporating HODHBt-like therapeutics. Iterative studies layering on additional latency reversal or other agents are needed to achieve consistent ex vivo reservoir reductions.
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Affiliation(s)
- Dennis C. Copertino
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Carissa S. Holmberg
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University, Washington, DC, USA
| | - Jared Weiler
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Adam R. Ward
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University, Washington, DC, USA
| | - J. Natalie Howard
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University, Washington, DC, USA
| | - Callie Levinger
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University, Washington, DC, USA
| | - Alina P.S. Pang
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Michael J. Corley
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Friederike Dündar
- Applied Bioinformatics Core and
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
- Catenion GmbH, Berlin, Germany
| | | | - Doron Betel
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
- Applied Bioinformatics Core and
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Rajesh T. Gandhi
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Deborah K. McMahon
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Ronald J. Bosch
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Noemi Linden
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Bernard J. Macatangay
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Joshua C. Cyktor
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Joseph J. Eron
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - John W. Mellors
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Colin Kovacs
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
| | - Erika Benko
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
| | - Alberto Bosque
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University, Washington, DC, USA
| | - R. Brad Jones
- Infectious Diseases Division, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
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10
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Schuetz A, Corley MJ, Sacdalan C, Phuang-Ngern Y, Nakpor T, Wansom T, Ehrenberg PK, Sriplienchan S, Thomas R, Ratnaratorn N, Sukhumvittaya S, Tragonlugsana N, Slike BM, Akapirat S, Pinyakorn S, Rerknimitr R, Pang AP, Kroon E, Teeratakulpisan N, Krebs SJ, Phanuphak N, Ndhlovu LC, Vasan S. Distinct mucosal and systemic immunological characteristics in transgender women potentially relating to HIV acquisition. JCI Insight 2023; 8:e169272. [PMID: 37432754 PMCID: PMC10543719 DOI: 10.1172/jci.insight.169272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023] Open
Abstract
Transgender women (TGW) are disproportionally affected by HIV infection, with a global estimated prevalence of 19.9%, often attributed to behavioral risk factors, with less known about biological factors. We evaluated potential biological risk factors for HIV acquisition in TGW at the sites of viral entry by assessing immune parameters of the neovaginal surface and gut mucosa. The neovagina in TGW, compared with the vagina in cisgender women (CW), shows distinct cell composition and may pose a more inflammatory environment, evidenced by increased CD4+ T cell activation and higher levels of soluble markers of inflammation (C-reactive protein, soluble CD30). Increased inflammation may be driven by microbiome composition, as shown by a greater abundance of Prevotella and a higher Shannon Diversity Index. In addition, we have observed higher frequency of CD4+CCR5+ target cells and decreased DNA methylation of the CCR5 gene in the gut mucosa of TGW compared with CW and men who have sex with men, which was inversely correlated with testosterone levels. The rectal microbiome composition in TGW appears to favor a proinflammatory milieu as well as mucosal barrier disruption. Thus, it is possible that increased inflammation and higher frequencies of CCR5-expressing target cells at sites of mucosal viral entry may contribute to increased risk of HIV acquisition in TGW, with further validation in larger studies warranted.
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Affiliation(s)
- Alexandra Schuetz
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Michael J. Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | | | | | | | - Tanyaporn Wansom
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Philip K. Ehrenberg
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | | | | | - Bonnie M. Slike
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Siriwat Akapirat
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Suteeraporn Pinyakorn
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | - Rungsun Rerknimitr
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Alina P.S. Pang
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Eugène Kroon
- Institute of HIV Research and Innovation, Bangkok, Thailand
| | | | - Shelly J. Krebs
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
| | | | - Lishomwa C. Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Sandhya Vasan
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine Inc., Bethesda, Maryland, USA
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11
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Santamaria-Garcia H, Moguilner S, Rodriguez-Villagra OA, Botero-Rodriguez F, Pina-Escudero SD, O'Donovan G, Albala C, Matallana D, Schulte M, Slachevsky A, Yokoyama JS, Possin K, Ndhlovu LC, Al-Rousan T, Corley MJ, Kosik KS, Muniz-Terrera G, Miranda JJ, Ibanez A. The impacts of social determinants of health and cardiometabolic factors on cognitive and functional aging in Colombian underserved populations. GeroScience 2023; 45:2405-2423. [PMID: 36849677 PMCID: PMC10651610 DOI: 10.1007/s11357-023-00755-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/14/2023] [Indexed: 03/01/2023] Open
Abstract
Global initiatives call for further understanding of the impact of inequity on aging across underserved populations. Previous research in low- and middle-income countries (LMICs) presents limitations in assessing combined sources of inequity and outcomes (i.e., cognition and functionality). In this study, we assessed how social determinants of health (SDH), cardiometabolic factors (CMFs), and other medical/social factors predict cognition and functionality in an aging Colombian population. We ran a cross-sectional study that combined theory- (structural equation models) and data-driven (machine learning) approaches in a population-based study (N = 23,694; M = 69.8 years) to assess the best predictors of cognition and functionality. We found that a combination of SDH and CMF accurately predicted cognition and functionality, although SDH was the stronger predictor. Cognition was predicted with the highest accuracy by SDH, followed by demographics, CMF, and other factors. A combination of SDH, age, CMF, and additional physical/psychological factors were the best predictors of functional status. Results highlight the role of inequity in predicting brain health and advancing solutions to reduce the cognitive and functional decline in LMICs.
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Affiliation(s)
- Hernando Santamaria-Garcia
- Global Brain Health Institute (GBHI), University of California San Francisco (UCSF), San Francisco, CA, USA.
- Pontificia Universidad Javeriana (Ph.D. Program in Neuroscience, Department of Psychiatry), Bogotá, Colombia.
- Center of Memory and Cognition Intellectus, Hospital Universitario San Ignacio, Bogotá, Colombia.
| | - Sebastian Moguilner
- Latin American Brain Health Institute (BrainLat), Universidad Adolfo Ibañez, Santiago de Chile, Chile
- Cognitive Neuroscience Center (CNC), Universidad de San Andrés, and CONICET, Buenos Aires, Argentina
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Felipe Botero-Rodriguez
- Pontificia Universidad Javeriana (Ph.D. Program in Neuroscience, Department of Psychiatry), Bogotá, Colombia
| | - Stefanie Danielle Pina-Escudero
- Global Brain Health Institute (GBHI), University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Neurology, Memory and Aging Center, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Gary O'Donovan
- Latin American Brain Health Institute (BrainLat), Universidad Adolfo Ibañez, Santiago de Chile, Chile
- Facultad de Medicina, Universidad de los Andes, Bogotá, Colombia
| | - Cecilia Albala
- Instituto de Nutrición Y Tecnología de los Alimentos, Universidad de Chile, Avenida El Líbano 5524, Macul, Santiago, Chile
| | - Diana Matallana
- Pontificia Universidad Javeriana (Ph.D. Program in Neuroscience, Department of Psychiatry), Bogotá, Colombia
- Center of Memory and Cognition Intellectus, Hospital Universitario San Ignacio, Bogotá, Colombia
- Mental Health Department, Hospital Universitario Fundación Santa Fe de Bogotá, Memory Clinic, Bogotá, Colombia
| | - Michael Schulte
- Latin American Brain Health Institute (BrainLat), Universidad Adolfo Ibañez, Santiago de Chile, Chile
| | - Andrea Slachevsky
- Neuropsychology and Clinical Neuroscience Laboratory (LANNEC), Physiopathology Department - Institute of Biomedical Sciences (ICBM), Neurocience and East Neuroscience Departments, Faculty of Medicine, University of Chile, Santiago de Chile, Chile
- Geroscience Center for Brain Health and Metabolism, (GERO), Santiago de Chile, Chile
- Memory and Neuropsychiatric Center (CMYN), Memory Unit - Neurology Department, Hospital del Salvador and Faculty of Medicine, University of Chile, Santiago de Chile, Chile
- Servicio de Neurología, Departamento de Medicina, Clínica Alemana-Universidad del Desarrollo, Santiago de Chile, Chile
| | - Jennifer S Yokoyama
- Global Brain Health Institute (GBHI), University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Neurology, Memory and Aging Center, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Katherine Possin
- Global Brain Health Institute (GBHI), University of California San Francisco (UCSF), San Francisco, CA, USA
- Department of Neurology, Memory and Aging Center, Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Lishomwa C Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Tala Al-Rousan
- Herbert Wertheim School of Public Health, University of California San Diego, La Jolla, CA, USA
| | - Michael J Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, NY, USA
| | - Kenneth S Kosik
- Neuroscience Research Institute. Department of Molecular Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Graciela Muniz-Terrera
- Edinburgh Dementia Prevention, University of Edinburgh, Edinburgh, UK
- Department of Primary Care, Ohio University, Athens, USA
| | - J Jaime Miranda
- CRONICAS Center of Excellence in Chronic Diseases, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of Medicine, School of Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- The George Institute for Global Health, UNSW, Sydney, Australia
| | - Agustin Ibanez
- Global Brain Health Institute (GBHI), University of California San Francisco (UCSF), San Francisco, CA, USA.
- Latin American Brain Health Institute (BrainLat), Universidad Adolfo Ibañez, Santiago de Chile, Chile.
- Cognitive Neuroscience Center (CNC), Universidad de San Andrés, and CONICET, Buenos Aires, Argentina.
- Trinity College Dublin (TCD), Dublin, Ireland.
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12
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Kroll KW, Woolley G, Terry K, Premeaux TA, Shikuma CM, Corley MJ, Bowler S, Ndhlovu LC, Reeves RK. Multiplex Analysis of Cytokines and Chemokines in Persons Aging With or Without HIV. AIDS Res Hum Retroviruses 2023; 39:367-380. [PMID: 37097212 DOI: 10.1089/aid.2022.0183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
People with HIV (PWH) on combination antiretroviral therapy (cART) are living longer lives due to modern cART advances and increased routine medical care. The full landscape of aging with HIV is unclear; given that HIV emerged relatively recently in human history and initially had a high mortality rate, there has not been a substantially aged population to evaluate. In this study, we set out to perform high-throughput plasma analyte profiling by multiplex analysis, focusing on various T helper (Th)-related cytokines, chemokines, and proinflammatory and anti-inflammatory cytokines. The primary goals being to provide reference ranges of these analytes for aging PWH cohorts, as well as testing the utility of high-throughput multiplex plasma assays. The cohort used in this study comprised age-matched healthy donors (32.6-73.5 years of age), PWH on cART (26.7-60.2 years of age), and viremic PWH (27.5-59.4 years of age). The patients in each group were then stratified across the age span to examine age-related impacts of these plasma biomarkers. Our results largely indicate feasibility of plasma analyte monitoring by multiplex and demonstrate a high degree of person-to-person variability regardless of age and HIV status. Nonetheless, we find multiple associations with age, duration of known infection, and viral load, all of which appear to be driven by either prolonged HIV disease progression or long-term use of cART.
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Affiliation(s)
- Kyle W Kroll
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University, School of Medicine, Durham, North Carolina, USA
- Department of Surgery, Duke University, School of Medicine, Durham, North Carolina, USA
| | - Griffin Woolley
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University, School of Medicine, Durham, North Carolina, USA
- Department of Surgery, Duke University, School of Medicine, Durham, North Carolina, USA
| | - Karen Terry
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University, School of Medicine, Durham, North Carolina, USA
- Department of Surgery, Duke University, School of Medicine, Durham, North Carolina, USA
| | - Thomas A Premeaux
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | | | - Michael J Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Scott Bowler
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Lishomwa C Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - R Keith Reeves
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University, School of Medicine, Durham, North Carolina, USA
- Department of Surgery, Duke University, School of Medicine, Durham, North Carolina, USA
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13
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Ortiz-Whittingham LR, Baumer Y, Collins BS, Mitchell VM, Corley MJ, Powell-Wiley TM. Abstract MP37: DNA Methylation of Leptin Mediates the Relationship Between Stress-Associated Inflammation and Insulin Resistance: Data From the Washington DC Cardiovascular Health and Needs Assessment. Circulation 2023. [DOI: 10.1161/circ.147.suppl_1.mp37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Introduction:
Chronic psychosocial stressors are associated with inflammation and cardiovascular (CV) risk, including insulin resistance (IR); however, potential DNA methylation (DNAm) mediators between stress-related inflammation and IR are not known.
Hypothesis:
DNAm biomarkers mediate the relationship between stress-related inflammation and IR.
Methods:
Participants from the DC Cardiovascular Health and Needs Assessment (DC-CHNA) underwent phenotyping at the NIH Clinical Center. Homeostatic Model Assessment for Insulin Resistance was calculated using insulin and glucose values. Social isolation, loneliness, and depression were determined using validated surveys. IL-8 was measured using an ELISA-based method. Principal component DNAm-based surrogate markers of leptin, cystatin C, and plasminogen activator inhibitor-1 were calculated from DNAm data obtained from participants' buffy coat samples. We examined relationships of interest with regression models adjusted for atherosclerotic cardiovascular disease (ASCVD) risk score and body mass index (BMI). Mediation analysis was used to evaluate DNAm measures as possible mediators.
Results:
The DC-CHNA consisted of 60 African American participants (mean age 61±11 years, 93% female) with ASCVD risk. Social isolation (β=0.34, p=0.009) and depression (β=0.30, p=0.04) associated with IL-8. IL-8 then inversely associated with DNAm-based surrogate leptin levels and directly associated with IR; leptin DNAm mediated the IL-8-IR relationship (
Figure
).
Conclusions:
We show a relationship between stress-associated IL-8 and IR mediated by DNAm-based surrogate leptin levels. While relationships between inflammation, serum leptin, and IR are documented, the impact of chronic stress on leptin DNAm in the context of CV risk requires further investigation in larger, diverse cohorts. DNAm-based surrogate markers of plasma proteins, such as leptin, could serve as a marker for increased CV risk in populations disproportionately exposed to chronic stress.
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14
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Kroll KW, Woolley G, Terry K, Premeaux TA, Shikuma CM, Corley MJ, Bowler S, Ndhlovu LC, Reeves RK. Multiplex analysis of cytokines and chemokines in persons aging with or without HIV. bioRxiv 2023:2023.01.30.526135. [PMID: 36778301 PMCID: PMC9915515 DOI: 10.1101/2023.01.30.526135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
People with HIV (PWH) on combined antiretroviral therapy (cART) are living longer lives due to modern cART advances and increased routine medical care. The full landscape of aging with HIV is unclear; given that HIV emerged relatively recently in human history and initially had a high mortality rate, there has not been a substantially aged population to evaluate. In the present study, we set out to perform high throughput plasma analyte profiling by multiplex analysis, focusing on various T helper (Th)-related cytokines, chemokines, and pro- and anti-inflammatory cytokines. The primary goals being to provide reference ranges of these analytes for aging PWH cohorts, as well as testing the utility of high throughput multiplex plasma assays. The cohort used in this study was comprised of age-matched healthy donors (aged 32.6-73.5), PWH on cART (aged 26.7-60.2), and viremic PWH (aged 27.5-59.4). The patients in each group were then stratified across the age span to examine age-related impacts of these plasma biomarkers. Our results largely indicate feasibility of plasma analyte monitoring by multiplex and demonstrate a high degree of person-to-person variability regardless of age and HIV status. Nonetheless, we find multiple associations with age, duration of known infection, and viral load, all of which appear to be driven by either prolonged HIV disease progression or long-term use of cART.
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15
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Bowler S, Papoutsoglou G, Karanikas A, Tsamardinos I, Corley MJ, Ndhlovu LC. A machine learning approach utilizing DNA methylation as an accurate classifier of COVID-19 disease severity. Sci Rep 2022; 12:17480. [PMID: 36261477 PMCID: PMC9580434 DOI: 10.1038/s41598-022-22201-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 10/11/2022] [Indexed: 01/12/2023] Open
Abstract
Since the onset of the COVID-19 pandemic, increasing cases with variable outcomes continue globally because of variants and despite vaccines and therapies. There is a need to identify at-risk individuals early that would benefit from timely medical interventions. DNA methylation provides an opportunity to identify an epigenetic signature of individuals at increased risk. We utilized machine learning to identify DNA methylation signatures of COVID-19 disease from data available through NCBI Gene Expression Omnibus. A training cohort of 460 individuals (164 COVID-19-infected and 296 non-infected) and an external validation dataset of 128 individuals (102 COVID-19-infected and 26 non-COVID-associated pneumonia) were reanalyzed. Data was processed using ChAMP and beta values were logit transformed. The JADBio AutoML platform was leveraged to identify a methylation signature associated with severe COVID-19 disease. We identified a random forest classification model from 4 unique methylation sites with the power to discern individuals with severe COVID-19 disease. The average area under the curve of receiver operator characteristic (AUC-ROC) of the model was 0.933 and the average area under the precision-recall curve (AUC-PRC) was 0.965. When applied to our external validation, this model produced an AUC-ROC of 0.898 and an AUC-PRC of 0.864. These results further our understanding of the utility of DNA methylation in COVID-19 disease pathology and serve as a platform to inform future COVID-19 related studies.
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Affiliation(s)
- Scott Bowler
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, 413 E 69th St, New York, NY, 10021, USA
| | - Georgios Papoutsoglou
- JADBio - Gnosis DA S.A, Science and Technology Park of Crete, 70013, Heraklion, Greece
| | - Aristides Karanikas
- JADBio - Gnosis DA S.A, Science and Technology Park of Crete, 70013, Heraklion, Greece
| | - Ioannis Tsamardinos
- JADBio - Gnosis DA S.A, Science and Technology Park of Crete, 70013, Heraklion, Greece
- Department of Computer Science, University of Crete, 70013, Heraklion, Greece
| | - Michael J Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, 413 E 69th St, New York, NY, 10021, USA
| | - Lishomwa C Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, 413 E 69th St, New York, NY, 10021, USA.
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16
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Kroll KW, Shah SV, Lucar OA, Premeaux TA, Shikuma CM, Corley MJ, Mosher M, Woolley G, Bowler S, Ndhlovu LC, Reeves RK. Mucosal-homing natural killer cells are associated with aging in persons living with HIV. Cell Rep Med 2022; 3:100773. [PMID: 36208628 PMCID: PMC9589002 DOI: 10.1016/j.xcrm.2022.100773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/29/2022] [Accepted: 09/16/2022] [Indexed: 11/07/2022]
Abstract
Natural killer (NK) cells are critical modulators of HIV transmission and disease. Recent evidence suggests a loss of NK cell cytotoxicity during aging, yet analysis of NK cell biology and aging in people with HIV (PWH) is lacking. Herein, we perform comprehensive analyses of people aging with and without HIV to determine age-related NK phenotypic changes. Utilizing high-dimensional flow cytometry, we analyze 30 immune-related proteins on peripheral NK cells from healthy donors, PWH with viral suppression, and viremic PWH. NK cell phenotypes are dynamic across aging but change significantly in HIV and on antiretroviral drug therapy (ART). NK cells in healthy aging show increasing ⍺4β7 and decreasing CCR7 expression and a reverse phenomenon in PWH. These HIV-associated trafficking patterns could be due to NK cell recruitment to HIV reservoir formation in lymphoid tissue or failed mucosal signaling in the HIV-infected gut but appear to be tight delineators of age-related NK cell changes.
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Affiliation(s)
- Kyle W Kroll
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University, Durham, NC, USA; Department of Surgery, Duke University, Durham, NC, USA
| | - Spandan V Shah
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Olivier A Lucar
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Thomas A Premeaux
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, NY, USA
| | | | - Michael J Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, NY, USA
| | - Matthew Mosher
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University, Durham, NC, USA; Department of Surgery, Duke University, Durham, NC, USA
| | - Griffin Woolley
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University, Durham, NC, USA; Department of Surgery, Duke University, Durham, NC, USA
| | - Scott Bowler
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, NY, USA
| | - Lishomwa C Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, NY, USA
| | - R Keith Reeves
- Division of Innate and Comparative Immunology, Center for Human Systems Immunology, Duke University, Durham, NC, USA; Department of Surgery, Duke University, Durham, NC, USA; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA.
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17
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Dye CK, Corley MJ, Ing C, Lum-Jones A, Li D, Mau MKLM, Maunakea AK. Shifts in the immunoepigenomic landscape of monocytes in response to a diabetes-specific social support intervention: a pilot study among Native Hawaiian adults with diabetes. Clin Epigenetics 2022; 14:91. [PMID: 35851422 PMCID: PMC9295496 DOI: 10.1186/s13148-022-01307-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 07/04/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Native Hawaiians are disproportionately affected by type 2 diabetes mellitus (DM), a chronic metabolic, non-communicable disease characterized by hyperglycemia and systemic inflammation. Unrelenting systemic inflammation frequently leads to a cascade of multiple comorbidities associated with DM, including cardiovascular disease, microvascular complications, and renal dysfunction. Yet few studies have examined the link between chronic inflammation at a cellular level and its relationship to standard DM therapies such as diabetes-specific lifestyle and social support education, well recognized as the cornerstone of clinical standards of diabetes care. This pilot study was initiated to explore the association of monocyte inflammation using epigenetic, immunologic, and clinical measures following a 3-month diabetes-specific social support program among high-risk Native Hawaiian adults with DM. RESULTS From a sample of 16 Native Hawaiian adults with DM, monocytes enriched from peripheral blood mononuclear cells (PBMCs) of 8 individuals were randomly selected for epigenomic analysis. Using the Illumina HumanMethylation450 BeadChip microarray, 1,061 differentially methylated loci (DML) were identified in monocytes of participants at baseline and 3 months following a DM-specific social support program (DM-SSP). Gene ontology analysis showed that these DML were enriched within genes involved in immune, metabolic, and cardiometabolic pathways, a subset of which were also significantly differentially expressed. Ex vivo analysis of immune function showed improvement post-DM-SSP compared with baseline, characterized by attenuated interleukin 1β and IL-6 secretion from monocytes. Altered cytokine secretion in response to the DM-SSP was significantly associated with changes in the methylation and gene expression states of immune-related genes in monocytes between intervention time points. CONCLUSIONS Our pilot study provides preliminary evidence of changes to inflammatory monocyte activity, potentially driven by epigenetic modifications, 3 months following a DM-specific SSP intervention. These novel alterations in the trajectory of monocyte inflammatory states were identified at loci that regulate transcription of immune and metabolic genes in high-risk Native Hawaiians with DM, suggesting a relationship between improvements in psychosocial behaviors and shifts in the immunoepigenetic patterns following a diabetes-specific SSP. Further research is warranted to investigate how social support influences systemic inflammation via immunoepigenetic modifications in chronic inflammatory diseases such as DM.
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Affiliation(s)
- Christian K Dye
- Department of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, 96822, USA
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, 96813, USA
- Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB222-K, Honolulu, HI, 96813, USA
| | - Michael J Corley
- Cornell Center for Immunology, Weill Cornell Medical Center, Cornell University, New York, NY, 10065, USA
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, 96813, USA
| | - Claire Ing
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, 96813, USA
| | - Annette Lum-Jones
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, 96813, USA
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, 96813, USA
| | - Dongmei Li
- Department of Clinical and Translational Research, School of Medicine and Dentistry, University of Rochester, Rochester, NY, 14642, USA
| | - Marjorie K L M Mau
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, 96813, USA
| | - Alika K Maunakea
- Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo St. BSB222-K, Honolulu, HI, 96813, USA.
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18
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Farhadian SF, Lindenbaum O, Zhao J, Corley MJ, Im Y, Walsh H, Vecchio A, Garcia-Milian R, Chiarella J, Chintanaphol M, Calvi R, Wang G, Ndhlovu LC, Yoon J, Trotta D, Ma S, Kluger Y, Spudich S. HIV viral transcription and immune perturbations in the CNS of people with HIV despite ART. JCI Insight 2022; 7:e160267. [PMID: 35801589 PMCID: PMC9310520 DOI: 10.1172/jci.insight.160267] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/13/2022] [Indexed: 01/12/2023] Open
Abstract
People with HIV (PWH) on antiretroviral therapy (ART) experience elevated rates of neurological impairment, despite controlling for demographic factors and comorbidities, suggesting viral or neuroimmune etiologies for these deficits. Here, we apply multimodal and cross-compartmental single-cell analyses of paired cerebrospinal fluid (CSF) and peripheral blood in PWH and uninfected controls. We demonstrate that a subset of central memory CD4+ T cells in the CSF produced HIV-1 RNA, despite apparent systemic viral suppression, and that HIV-1-infected cells were more frequently found in the CSF than in the blood. Using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), we show that the cell surface marker CD204 is a reliable marker for rare microglia-like cells in the CSF, which have been implicated in HIV neuropathogenesis, but which we did not find to contain HIV transcripts. Through a feature selection method for supervised deep learning of single-cell transcriptomes, we find that abnormal CD8+ T cell activation, rather than CD4+ T cell abnormalities, predominated in the CSF of PWH compared with controls. Overall, these findings suggest ongoing CNS viral persistence and compartmentalized CNS neuroimmune effects of HIV infection during ART and demonstrate the power of single-cell studies of CSF to better understand the CNS reservoir during HIV infection.
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Affiliation(s)
- Shelli F. Farhadian
- Department of Medicine, Section of Infectious Diseases, and
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Ofir Lindenbaum
- Program in Applied Mathematics, and
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
| | - Jun Zhao
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Michael J. Corley
- Department of Medicine, Division of Infectious Diseases, and
- Feil Family Brain & Mind Institute, Weill Cornell Medicine, New York, New York, USA
| | - Yunju Im
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Hannah Walsh
- Department of Medicine, Section of Infectious Diseases, and
| | - Alyssa Vecchio
- University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Rolando Garcia-Milian
- Bioinformatics Support Program, Cushing/Whitney Medical Library, Yale School of Medicine, New Haven, Connecticut, USA
| | - Jennifer Chiarella
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
| | | | - Rachela Calvi
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Guilin Wang
- Yale Center for Genome Analysis, Yale University, New Haven, Connecticut, USA
| | - Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, and
- Feil Family Brain & Mind Institute, Weill Cornell Medicine, New York, New York, USA
| | - Jennifer Yoon
- Department of Medicine, Section of Infectious Diseases, and
| | - Diane Trotta
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Shuangge Ma
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Yuval Kluger
- Program in Applied Mathematics, and
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Serena Spudich
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
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19
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Rathnasinghe R, Jangra S, Ye C, Cupic A, Singh G, Martínez-Romero C, Mulder LCF, Kehrer T, Yildiz S, Choi A, Yeung ST, Mena I, Gillespie V, De Vrieze J, Aslam S, Stadlbauer D, Meekins DA, McDowell CD, Balaraman V, Corley MJ, Richt JA, De Geest BG, Miorin L, Krammer F, Martinez-Sobrido L, Simon V, García-Sastre A, Schotsaert M. Characterization of SARS-CoV-2 Spike mutations important for infection of mice and escape from human immune sera. Nat Commun 2022; 13:3921. [PMID: 35798721 PMCID: PMC9261898 DOI: 10.1038/s41467-022-30763-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/13/2022] [Indexed: 12/25/2022] Open
Abstract
Due to differences in human and murine angiotensin converting enzyme 2 (ACE-2) receptor, initially available SARS-CoV-2 isolates could not infect mice. Here we show that serial passaging of USA-WA1/2020 strain in mouse lungs results in "mouse-adapted" SARS-CoV-2 (MA-SARS-CoV-2) with mutations in S, M, and N genes, and a twelve-nucleotide insertion in the S gene. MA-SARS-CoV-2 infection causes mild disease, with more pronounced morbidity depending on genetic background and in aged and obese mice. Two mutations in the S gene associated with mouse adaptation (N501Y, H655Y) are present in SARS-CoV-2 variants of concern (VoCs). N501Y in the receptor binding domain of viruses of the B.1.1.7, B.1.351, P.1 and B.1.1.529 lineages (Alpha, Beta, Gamma and Omicron variants) is associated with high transmissibility and allows VoCs to infect wild type mice. We further show that S protein mutations of MA-SARS-CoV-2 do not affect neutralization efficiency by human convalescent and post vaccination sera.
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Affiliation(s)
- Raveen Rathnasinghe
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.476726.6Present Address: Seqirus, Cambridge, MT USA
| | - Sonia Jangra
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Chengjin Ye
- grid.250889.e0000 0001 2215 0219Texas Biomedical Research Institute, San Antonio, TX USA
| | - Anastasija Cupic
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Gagandeep Singh
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Carles Martínez-Romero
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Lubbertus C. F. Mulder
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Thomas Kehrer
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Soner Yildiz
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Angela Choi
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.479574.c0000 0004 1791 3172Present Address: Moderna Therapeutics, Cambridge, MT USA
| | - Stephen T. Yeung
- grid.5386.8000000041936877XDivision of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, NY USA
| | - Ignacio Mena
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Virginia Gillespie
- grid.59734.3c0000 0001 0670 2351Center for Comparative Medicine and Surgery, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Jana De Vrieze
- grid.5342.00000 0001 2069 7798Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Sadaf Aslam
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Daniel Stadlbauer
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.479574.c0000 0004 1791 3172Present Address: Moderna Therapeutics, Cambridge, MT USA
| | - David A. Meekins
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS USA
| | - Chester D. McDowell
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS USA
| | - Velmurugan Balaraman
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS USA
| | - Michael J. Corley
- grid.5386.8000000041936877XDivision of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, NY USA
| | - Juergen A. Richt
- grid.36567.310000 0001 0737 1259Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS USA
| | - Bruno G. De Geest
- grid.5342.00000 0001 2069 7798Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Lisa Miorin
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | | | - Florian Krammer
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Luis Martinez-Sobrido
- grid.250889.e0000 0001 2215 0219Texas Biomedical Research Institute, San Antonio, TX USA
| | - Viviana Simon
- grid.59734.3c0000 0001 0670 2351Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai New York, New York, NY USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA. .,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA. .,Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA. .,The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA.
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA. .,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai New York, New York, NY, USA.
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20
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Pang APS, Higgins-Chen AT, Comite F, Raica I, Arboleda C, Went H, Mendez T, Schotsaert M, Dwaraka V, Smith R, Levine ME, Ndhlovu LC, Corley MJ. Longitudinal Study of DNA Methylation and Epigenetic Clocks Prior to and Following Test-Confirmed COVID-19 and mRNA Vaccination. Front Genet 2022; 13:819749. [PMID: 35719387 PMCID: PMC9203887 DOI: 10.3389/fgene.2022.819749] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/25/2022] [Indexed: 01/01/2023] Open
Abstract
The host epigenetic landscape rapidly changes during SARS-CoV-2 infection, and evidence suggest that severe COVID-19 is associated with durable scars to the epigenome. Specifically, aberrant DNA methylation changes in immune cells and alterations to epigenetic clocks in blood relate to severe COVID-19. However, a longitudinal assessment of DNA methylation states and epigenetic clocks in blood from healthy individuals prior to and following test-confirmed non-hospitalized COVID-19 has not been performed. Moreover, the impact of mRNA COVID-19 vaccines upon the host epigenome remains understudied. Here, we first examined DNA methylation states in the blood of 21 participants prior to and following test-confirmed COVID-19 diagnosis at a median time frame of 8.35 weeks; 756 CpGs were identified as differentially methylated following COVID-19 diagnosis in blood at an FDR adjusted p-value < 0.05. These CpGs were enriched in the gene body, and the northern and southern shelf regions of genes involved in metabolic pathways. Integrative analysis revealed overlap among genes identified in transcriptional SARS-CoV-2 infection datasets. Principal component-based epigenetic clock estimates of PhenoAge and GrimAge significantly increased in people over 50 following infection by an average of 2.1 and 0.84 years. In contrast, PCPhenoAge significantly decreased in people fewer than 50 following infection by an average of 2.06 years. This observed divergence in epigenetic clocks following COVID-19 was related to age and immune cell-type compositional changes in CD4+ T cells, B cells, granulocytes, plasmablasts, exhausted T cells, and naïve T cells. Complementary longitudinal epigenetic clock analyses of 36 participants prior to and following Pfizer and Moderna mRNA-based COVID-19 vaccination revealed that vaccination significantly reduced principal component-based Horvath epigenetic clock estimates in people over 50 by an average of 3.91 years for those who received Moderna. This reduction in epigenetic clock estimates was significantly related to chronological age and immune cell-type compositional changes in B cells and plasmablasts pre- and post-vaccination. These findings suggest the potential utility of epigenetic clocks as a biomarker of COVID-19 vaccine responses. Future research will need to unravel the significance and durability of short-term changes in epigenetic age related to COVID-19 exposure and mRNA vaccination.
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Affiliation(s)
- Alina P. S. Pang
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Albert T. Higgins-Chen
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States
- VA Connecticut Healthcare System, West Haven, CT, United States
| | - Florence Comite
- Comite Center for Precision Medicine & Health, New York, NY, United States
- Lenox Hill Hospital/Northwell, New York, NY, United States
| | - Ioana Raica
- Comite Center for Precision Medicine & Health, New York, NY, United States
| | | | | | | | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | | | - Ryan Smith
- TruDiagnostic, Lexington, KY, United States
| | - Morgan E. Levine
- Department of Pathology, Yale University School of Medicine, New Haven, CT, United States
| | - Lishomwa C. Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Michael J. Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
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21
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Chang XL, Reed JS, Webb GM, Wu HL, Le J, Bateman KB, Greene JM, Pessoa C, Waytashek C, Weber WC, Hwang J, Fischer M, Moats C, Shiel O, Bochart RM, Crank H, Siess D, Giobbi T, Torgerson J, Agnor R, Gao L, Dhody K, Lalezari JP, Bandar IS, Carnate AM, Pang AS, Corley MJ, Kelly S, Pourhassan N, Smedley J, Bimber BN, Hansen SG, Ndhlovu LC, Sacha JB. Suppression of human and simian immunodeficiency virus replication with the CCR5-specific antibody Leronlimab in two species. PLoS Pathog 2022; 18:e1010396. [PMID: 35358290 PMCID: PMC8970399 DOI: 10.1371/journal.ppat.1010396] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/25/2022] [Indexed: 12/28/2022] Open
Abstract
The CCR5-specific antibody Leronlimab is being investigated as a novel immunotherapy that can suppress HIV replication with minimal side effects. Here we studied the virological and immunological consequences of Leronlimab in chronically CCR5-tropic HIV-1 infected humans (n = 5) on suppressive antiretroviral therapy (ART) and in ART-naïve acutely CCR5-tropic SHIV infected rhesus macaques (n = 4). All five human participants transitioned from daily combination ART to self-administered weekly subcutaneous (SC) injections of 350 mg or 700 mg Leronlimab and to date all participants have sustained virologic suppression for over seven years. In all participants, Leronlimab fully occupied CCR5 receptors on peripheral blood CD4+ T cells and monocytes. In ART-naïve rhesus macaques acutely infected with CCR5-tropic SHIV, weekly SC injections of 50 mg/kg Leronlimab fully suppressed plasma viremia in half of the macaques. CCR5 receptor occupancy by Leronlimab occurred concomitant with rebound of CD4+ CCR5+ T-cells in peripheral blood, and full CCR5 receptor occupancy was found in multiple anatomical compartments. Our results demonstrate that weekly, self-administered Leronlimab was safe, well-tolerated, and efficacious for long-term virologic suppression and should be included in the arsenal of safe, easily administered, longer-acting antiretroviral treatments for people living with HIV-1. Trial Registration: ClinicalTrials.gov Identifiers: NCT02175680 and NCT02355184. With approximately 37 million people living with HIV, stopping the HIV epidemic remains a top global health priority. While daily oral antiretroviral therapy limits HIV replication, its use is a lifelong requirement and increases the likelihood for the development of drug-resistant variants. Indeed, the global prevalence of HIV drug resistance has exponentially increased in recent years, leading to a need for new drug targets. CCR5 is an ideal drug target as HIV uses this molecule to gain entry into target cells. As an example of the importance of CCR5, individuals that lack CCR5 expression due to a natural genetic mutation are naturally resistant to HIV infection. Here, we report that weekly injections of Leronlimab, an anti-CCR5 antibody that blocks the binding of HIV to CCR5, suppressed HIV replication in five HIV+ participants for over seven years. When used to treat acutely infected rhesus macaques, we found that the average amount of virus in the blood of Leronlimab-treated macaques was 10,000 times lower than in untreated macaques. These data suggest that Leronlimab is a safe and effective anti-HIV therapeutic drug.
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Affiliation(s)
- Xiao L. Chang
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
- Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Jason S. Reed
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Gabriela M. Webb
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Helen L. Wu
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Jimmy Le
- Quest Clinical Research, San Francisco, California, United States of America
| | - Katherine B. Bateman
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Justin M. Greene
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Cleiton Pessoa
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Courtney Waytashek
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Whitney C. Weber
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Joseph Hwang
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Miranda Fischer
- Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Cassandra Moats
- Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Oriene Shiel
- Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Rachele M. Bochart
- Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Hugh Crank
- Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Don Siess
- Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Travis Giobbi
- Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Jeffrey Torgerson
- Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Rebecca Agnor
- Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Lina Gao
- Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Kush Dhody
- Amarex Clinical Research LLC, Germantown, Maryland, United States of America
| | - Jacob P. Lalezari
- Quest Clinical Research, San Francisco, California, United States of America
| | - Ivo Sah Bandar
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, United States of America
| | - Alnor M. Carnate
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, United States of America
| | - Alina S. Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, United States of America
| | - Michael J. Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, United States of America
| | - Scott Kelly
- CytoDyn Inc., Vancouver, Washington, United States of America
| | | | - Jeremy Smedley
- Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Benjamin N. Bimber
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
- Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Scott G. Hansen
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, United States of America
| | - Jonah B. Sacha
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Portland, Oregon, United States of America
- Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, United States of America
- * E-mail:
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22
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Hsu DC, Chumpolkulwong K, Corley MJ, Hunsawong T, Inthawong D, Schuetz A, Imerbsin R, Silsorn D, Nadee P, Sopanaporn J, Phuang-Ngern Y, Klungthong C, Reed M, Fernandez S, Ndhlovu LC, Paul R, Lugo-Roman L, Michael NL, Modjarrad K, Vasan S. Neurocognitive impact of Zika virus infection in adult rhesus macaques. J Neuroinflammation 2022; 19:40. [PMID: 35130924 PMCID: PMC8822695 DOI: 10.1186/s12974-022-02402-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 01/24/2022] [Indexed: 12/03/2022] Open
Abstract
Background Zika virus (ZIKV) is a mosquito-transmitted flavivirus that affects many regions of the world. Infection, in utero, causes microcephaly and later developmental and neurologic impairments. The impact of ZIKV infection on neurocognition in adults has not been well described. The objective of the study was to assess the neurocognitive impact of ZIKV infection in adult rhesus macaques. Methods Neurocognitive assessments were performed using the Cambridge Neuropsychological Test Automated Battery (CANTAB) via a touch screen and modified Brinkman Board before and after subcutaneous ZIKV inoculation. Immune activation markers were measured in the blood and cerebral spinal fluid (CSF) by multiplex assay and flow cytometry. Results All animals (N = 8) had detectable ZIKV RNA in plasma at day 1 post-inoculation (PI) that peaked at day 2 PI (median 5.9, IQR 5.6–6.2 log10 genome equivalents/mL). In all eight animals, ZIKV RNA became undetectable in plasma by day 14 PI, but persisted in lymphoid tissues. ZIKV RNA was not detected in the CSF supernatant at days 4, 8, 14 and 28 PI but was detected in the brain of 2 animals at days 8 and 28 PI. Elevations in markers of immune activation in the blood and CSF were accompanied by a reduction in accuracy and reaction speed on the CANTAB in the majority of animals. Conclusions The co-occurrence of systemic and CSF immune perturbations and neurocognitive impairment establishes this model as useful for studying the impact of neuroinflammation on neurobehavior in rhesus macaques, as it pertains to ZIKV infection and potentially other pathogens. Supplementary Information The online version contains supplementary material available at 10.1186/s12974-022-02402-4.
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Affiliation(s)
- Denise C Hsu
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA. .,Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand. .,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, 20817, USA.
| | | | - Michael J Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, USA
| | - Taweewun Hunsawong
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Dutsadee Inthawong
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Alexandra Schuetz
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.,Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, 20817, USA
| | - Rawiwan Imerbsin
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Decha Silsorn
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Panupat Nadee
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Jumpol Sopanaporn
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | | | | | - Matthew Reed
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Stefan Fernandez
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Lishomwa C Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, USA.,Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Robert Paul
- Missouri Institute of Mental Health, University of Missouri, St. Louis, MO, 63143, USA
| | - Luis Lugo-Roman
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Nelson L Michael
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Kayvon Modjarrad
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
| | - Sandhya Vasan
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, 20817, USA.,Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, MD, 20910, USA
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23
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Premeaux TA, Moser CB, McKhann A, Hoenigl M, Yeung ST, Pang APS, Corley MJ, Lederman MM, Landay AL, Gianella S, Ndhlovu LC. Monitoring Circulating Immune Checkpoint Proteins as Predictors of Non-AIDS Morbid Events in People with HIV Initiating Antiretroviral Therapy. Open Forum Infect Dis 2022; 9:ofab570. [PMID: 35146038 PMCID: PMC8826032 DOI: 10.1093/ofid/ofab570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/10/2022] [Indexed: 11/28/2022] Open
Abstract
Background Although cell surface immune checkpoint proteins (ICPs) such as PD-1 expressed on T cells are associated with T-cell exhaustion, HIV disease progression, and AIDS events, they have shown limited utility in predicting non-AIDS morbidity. Given that ICPs also exist in soluble forms and are elevated in ART-treated HIV infection, we tested the hypothesis that soluble ICPs may be predictive of non-AIDS events in adults initiating ART. Methods Utilizing a nested case–control study from the AIDS Clinical Trials Group ALLRT cohort, we measured plasma levels of 15 soluble inhibitory and activating ICPs by Luminex. Participants (134 cases, 292 matched controls) were evaluated pre-ART, a year post-ART, and immediately preceding a non-AIDS event, which included myocardial infarction (MI)/stroke, malignancy, serious bacterial infection, and nonaccidental death. Results Conditional logistic regression analysis determined that higher levels of soluble CD27 were associated with increased risk of non-AIDS events at all time points. Higher levels of CD40 at baseline and pre-event and CD80 at pre-event were associated with increased risk of non-AIDS events. Examining specific non-AIDS events, multiple ICPs were associated with malignancy at baseline and pre-event, whereas only higher CD27 levels were associated with increased risk of MI/stroke at year 1 and pre-event. Conclusions While select soluble ICPs were associated with non-AIDS events, CD27 emerged as a consistent marker irrespective of ART. Our data may offer guidance on new targets for early clinical monitoring in people with HIV who remain at greater risk of specific non-AIDS events.
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Affiliation(s)
- Thomas A Premeaux
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Carlee B Moser
- Center for Biostatistics in AIDS Research in the Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ashley McKhann
- Center for Biostatistics in AIDS Research in the Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Martin Hoenigl
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Stephen T Yeung
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alina P S Pang
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Michael J Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Michael M Lederman
- Department of Medicine, Division of Infectious Diseases and HIV Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Alan L Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, USA
| | - Sara Gianella
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Lishomwa C Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
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24
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Plassmeyer M, Alpan O, Corley MJ, Premeaux TA, Lillard K, Coatney P, Vaziri T, Michalsky S, Pang APS, Bukhari Z, Yeung ST, Evering TH, Naughton G, Latterich M, Mudd P, Spada A, Rindone N, Loizou D, Ulrik Sønder S, Ndhlovu LC, Gupta R. Caspases and therapeutic potential of caspase inhibitors in moderate-severe SARS-CoV-2 infection and long COVID. Allergy 2022; 77:118-129. [PMID: 33993490 PMCID: PMC8222863 DOI: 10.1111/all.14907] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND COVID-19 can present with lymphopenia and extraordinary complex multiorgan pathologies that can trigger long-term sequela. AIMS Given that inflammasome products, like caspase-1, play a role in the pathophysiology of a number of co-morbid conditions, we investigated caspases across the spectrum of COVID-19 disease. MATERIALS & METHODS We assessed transcriptional states of multiple caspases and using flow cytometry, the expression of active caspase-1 in blood cells from COVID-19 patients in acute and convalescent stages of disease. Non-COVID-19 subject presenting with various comorbid conditions served as controls. RESULTS Single-cell RNA-seq data of immune cells from COVID-19 patients showed a distinct caspase expression pattern in T cells, neutrophils, dendritic cells, and eosinophils compared with controls. Caspase-1 was upregulated in CD4+ T-cells from hospitalized COVID-19 patients compared with unexposed controls. Post-COVID-19 patients with lingering symptoms (long-haulers) also showed upregulated caspase-1activity in CD4+ T-cells that ex vivo was attenuated with a select pan-caspase inhibitor. We observed elevated caspase-3/7levels in red blood cells from COVID-19 patients compared with controls that was reduced following caspase inhibition. DISCUSSION Our preliminary results suggest an exuberant caspase response in COVID-19 that may facilitate immune-related pathological processes leading to severe outcomes. Further clinical correlations of caspase expression in different stages of COVID-19 will be needed. CONCLUSION Pan-caspase inhibition could emerge as a therapeutic strategy to ameliorate or prevent severe COVID-19.
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Affiliation(s)
| | | | - Michael J. Corley
- Department of Medicine Division of Infectious Diseases Weill Cornell Medicine New York City NY USA
| | - Thomas A. Premeaux
- Department of Medicine Division of Infectious Diseases Weill Cornell Medicine New York City NY USA
| | | | | | | | | | - Alina P. S. Pang
- Department of Medicine Division of Infectious Diseases Weill Cornell Medicine New York City NY USA
| | - Zaheer Bukhari
- S.U.N.Y. Downstate Health Sciences University Brooklyn NY USA
| | - Stephen T. Yeung
- Department of Medicine Division of Infectious Diseases Weill Cornell Medicine New York City NY USA
| | - Teresa H. Evering
- Department of Medicine Division of Infectious Diseases Weill Cornell Medicine New York City NY USA
| | | | | | - Philip Mudd
- Department of Emergency Medicine Washington University School of Medicine Saint Louis MO USA
| | | | | | | | | | - Lishomwa C. Ndhlovu
- Department of Medicine Division of Infectious Diseases Weill Cornell Medicine New York City NY USA
| | - Raavi Gupta
- S.U.N.Y. Downstate Health Sciences University Brooklyn NY USA
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25
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Corley MJ, Pang APS, Rasmussen TA, Tolstrup M, Søgaard OS, Ndhlovu LC. Candidate host epigenetic marks predictive for HIV reservoir size, responsiveness to latency reversal, and viral rebound. AIDS 2021; 35:2269-2279. [PMID: 34482353 PMCID: PMC8563431 DOI: 10.1097/qad.0000000000003065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
OBJECTIVE This study aimed to identify candidate host epigenetic biomarkers predicting latency reversal agents (LRA) efficacy and HIV-1 rebound kinetics during analytical treatment interruption (ATI). DESIGN Retrospective longitudinal epigenetic profiling study from 13 people with HIV (PWH) on virologically suppressive antiretroviral therapy (ART) that participated in a LRA (HDAC inhibitor) clinical trial (NCT01680094) and a subsequent optional ATI to monitor for viral recrudescence after ART cessation. METHODS Genome-wide DNA methylation (DNAm) in purified CD4+ T cells was measured at single-nucleotide resolution using the Infinium MethylationEPIC array. HIV-1 DNA and RNA measures were previously assessed by PCR-based methods and the association of DNAm levels at regulatory sites of the human genome were examined with reservoir size, responsiveness to LRA, and time to viral rebound following ATI. RESULTS A distinct set of 15 candidate DNAm sites in purified CD4+ T cells at baseline pre-LRA and pre-ATI significantly correlated with time to viral rebound. Eight of these DNAm sites occurred in genes linked to HIV-1 replication dynamics including (SEPSECS, cg19113954), (MALT1, cg15968021), (CPT1C, cg14318858), (CRTAM, cg10977115), (B4GALNT4, cg04663285), (IL10, cg16284789), (TFPI2, cg19645693), and (LIFR, cg26437306); with the remaining sites at intergenic regions containing regulatory elements. Moreover, baseline DNAm states related to total HIV-1 DNA levels and the fold change in unspliced cell-associated HIV RNA following LRA treatment. CONCLUSION Preexisting host epigenetic states may determine HIV-1 rebound kinetics and reservoir maintenance. These findings suggest integrating a suite of DNA methylation markers to improve optimal participant selection and drug regimen in future HIV cure clinical trials.
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Affiliation(s)
- Michael J. Corley
- 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
| | - Thomas A. Rasmussen
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, VIC 3000, Australia
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Martin Tolstrup
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Ole S. Søgaard
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
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26
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Corley MJ, Sacdalan C, Pang APS, Chomchey N, Ratnaratorn N, Valcour V, Kroon E, Cho KS, Belden AC, Colby D, Robb M, Hsu D, Spudich S, Paul R, Vasan S, Ndhlovu LC. Abrupt and altered cell-type specific DNA methylation profiles in blood during acute HIV infection persists despite prompt initiation of ART. PLoS Pathog 2021; 17:e1009785. [PMID: 34388205 PMCID: PMC8386872 DOI: 10.1371/journal.ppat.1009785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/25/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
HIV-1 disrupts the host epigenetic landscape with consequences for disease pathogenesis, viral persistence, and HIV-associated comorbidities. Here, we examined how soon after infection HIV-associated epigenetic changes may occur in blood and whether early initiation of antiretroviral therapy (ART) impacts epigenetic modifications. We profiled longitudinal genome-wide DNA methylation in monocytes and CD4+ T lymphocytes from 22 participants in the RV254/SEARCH010 acute HIV infection (AHI) cohort that diagnoses infection within weeks after estimated exposure and immediately initiates ART. We identified monocytes harbored 22,697 differentially methylated CpGs associated with AHI compared to 294 in CD4+ T lymphocytes. ART minimally restored less than 1% of these changes in monocytes and had no effect upon T cells. Monocyte DNA methylation patterns associated with viral load, CD4 count, CD4/CD8 ratio, and longitudinal clinical phenotypes. Our findings suggest HIV-1 rapidly embeds an epigenetic memory not mitigated by ART and support determining epigenetic signatures in precision HIV medicine. Trial Registration:NCT00782808 and NCT00796146. The epigenetic marker, DNA methylation, plays a key role regulating the immune system during host-pathogen interactions. Using cell-type specific DNA methylation profiling, we explored whether epigenetic changes occurred soon after HIV infection and following early treatment with anti-HIV drugs. Acute infection was associated with early DNA methylation changes in purified monocytes and CD4+ T cells isolated from blood. In monocytes, rapid anti-HIV treatment minimally restored DNA methylation changes associated with infection and unexpectedly had no impact in CD4+ T cells. DNA methylation patterns before treatment informed long term clinical outcomes including CD4+ T cell counts and favorable clinical phenotypes. These findings identify candidates for consideration in epigenome editing approaches in HIV prevention, treatment, and cure strategies.
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Affiliation(s)
- Michael J. Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine; New York, New York, United States of America
| | - Carlo Sacdalan
- Institute of HIV Research and Innovation; Bangkok, Thailand
- SEARCH, South East Asia Research Collaboration in HIV; Bangkok, Thailand
| | - Alina P. S. Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine; New York, New York, United States of America
| | - Nitiya Chomchey
- Institute of HIV Research and Innovation; Bangkok, Thailand
- SEARCH, South East Asia Research Collaboration in HIV; Bangkok, Thailand
| | | | - Victor Valcour
- Memory and Aging Center, University of California San Francisco; San Francisco, California, United States of America
| | - Eugene Kroon
- Institute of HIV Research and Innovation; Bangkok, Thailand
- SEARCH, South East Asia Research Collaboration in HIV; Bangkok, Thailand
| | - Kyu S. Cho
- Missouri Institute of Mental Health University of Missouri; St. Louis, Missouri, United States of America
| | - Andrew C. Belden
- Missouri Institute of Mental Health University of Missouri; St. Louis, Missouri, United States of America
| | - Donn Colby
- Institute of HIV Research and Innovation; Bangkok, Thailand
- SEARCH, South East Asia Research Collaboration in HIV; Bangkok, Thailand
| | - Merlin Robb
- Armed Forces Research Institute of Medical Sciences; Bangkok, Thailand
- Henry M. Jackson Foundation for the Advancement of Military Medicine; Bethesda, Maryland, United States of America
| | - Denise Hsu
- Armed Forces Research Institute of Medical Sciences; Bangkok, Thailand
- Henry M. Jackson Foundation for the Advancement of Military Medicine; Bethesda, Maryland, United States of America
| | - Serena Spudich
- Department of Neurology, Yale University; New Haven, Connecticut, United States of America
| | - Robert Paul
- Missouri Institute of Mental Health University of Missouri; St. Louis, Missouri, United States of America
| | - Sandhya Vasan
- Henry M. Jackson Foundation for the Advancement of Military Medicine; Bethesda, Maryland, United States of America
- US Military HIV Research Program; Silver Spring, Maryland, United States of America
| | - Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine; New York, New York, United States of America
- * E-mail:
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27
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Corley MJ, Pang APS, Dody K, Mudd PA, Patterson BK, Seethamraju H, Bram Y, Peluso MJ, Torres L, Iyer NS, Premeaux TA, Yeung ST, Chandar V, Borczuk A, Schwartz RE, Henrich TJ, Deeks SG, Sacha JB, Ndhlovu LC. Genome-wide DNA methylation profiling of peripheral blood reveals an epigenetic signature associated with severe COVID-19. J Leukoc Biol 2021; 110:21-26. [PMID: 33464637 PMCID: PMC8013321 DOI: 10.1002/jlb.5hi0720-466r] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/17/2020] [Accepted: 12/29/2020] [Indexed: 01/26/2023] Open
Abstract
The global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is a highly pathogenic RNA virus causing coronavirus disease 2019 (COVID‐19) in humans. Although most patients with COVID‐19 have mild illness and may be asymptomatic, some will develop severe pneumonia, acute respiratory distress syndrome, multi‐organ failure, and death. RNA viruses such as SARS‐CoV‐2 are capable of hijacking the epigenetic landscape of host immune cells to evade antiviral defense. Yet, there remain considerable gaps in our understanding of immune cell epigenetic changes associated with severe SARS‐CoV‐2 infection pathology. Here, we examined genome‐wide DNA methylation (DNAm) profiles of peripheral blood mononuclear cells from 9 terminally‐ill, critical COVID‐19 patients with confirmed SARS‐CoV‐2 plasma viremia compared with uninfected, hospitalized influenza, untreated primary HIV infection, and mild/moderate COVID‐19 HIV coinfected individuals. Cell‐type deconvolution analyses confirmed lymphopenia in severe COVID‐19 and revealed a high percentage of estimated neutrophils suggesting perturbations to DNAm associated with granulopoiesis. We observed a distinct DNAm signature of severe COVID‐19 characterized by hypermethylation of IFN‐related genes and hypomethylation of inflammatory genes, reinforcing observations in infection models and single‐cell transcriptional studies of severe COVID‐19. Epigenetic clock analyses revealed severe COVID‐19 was associated with an increased DNAm age and elevated mortality risk according to GrimAge, further validating the epigenetic clock as a predictor of disease and mortality risk. Our epigenetic results reveal a discovery DNAm signature of severe COVID‐19 in blood potentially useful for corroborating clinical assessments, informing pathogenic mechanisms, and revealing new therapeutic targets against SARS‐CoV‐2.
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Affiliation(s)
- Michael J Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Alina P S Pang
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA.,University of Hawaii, Honolulu, Hawaii, USA
| | - Kush Dody
- Amarex Clinical Research, LLC, Germantown, Maryland, USA
| | - Philip A Mudd
- Department of Emergency Medicine, Washington University School of Medicine in St Louis, St Louis, Missouri, USA
| | | | | | - Yaron Bram
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Leonel Torres
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Nikita S Iyer
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Thomas A Premeaux
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA.,University of Hawaii, Honolulu, Hawaii, USA
| | - Stephen T Yeung
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Vasuretha Chandar
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Alain Borczuk
- Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital, Weill Cornell Medicine, New York, New York, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Jonah B Sacha
- Vaccine & Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Portland, Oregon, USA
| | - Lishomwa C Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York, USA
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Chew GM, Padua AJP, Chow DC, Souza SA, Clements DM, Corley MJ, Pang AP, Alejandria MM, Gerschenson M, Shikuma CM, Ndhlovu LC. Effects of Brief Adjunctive Metformin Therapy in Virologically Suppressed HIV-Infected Adults on Polyfunctional HIV-Specific CD8 T Cell Responses to PD-L1 Blockade. AIDS Res Hum Retroviruses 2021; 37:24-33. [PMID: 33019813 DOI: 10.1089/aid.2020.0172] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Targeting inhibitory immune checkpoint receptor pathways has shown remarkable success in improving anticancer T cell responses for the elimination of tumors. Such immunotherapeutic strategies are being pursued for HIV remission. Metformin has shown favorable clinical outcomes in enhancing the efficacy of programmed cell death-1 (PD-1) blockade and restoring antitumor T cell immunity. Furthermore, monocytes are known to be a strong predictor of progression-free survival in response to anti-PD-1 immunotherapy. In a single-arm clinical trial, we evaluated the immunological effects over an 8-week course of metformin therapy in seven euglycemic, virally suppressed HIV-infected participants on combination antiretroviral therapy (cART). We assessed changes in peripheral HIV-Gag-specific T cell responses to immune checkpoint blockade (ICB) with anti-PD-L1 and anti-T cell immunoreceptor with immunoglobulin and ITIM domain (TIGIT) monoclonal antibodies (mAbs) and changes in CD8 T cell and monocyte subsets using flow cytometry. Study participants were all male, 71% (5/7) Caucasian, with a median age of 61 years, CD4 count of 739 cells/μL, and plasma HIV RNA of <50 copies/mL on stable cART for >1 year. Ex vivo polyfunctional HIV-Gag-specific CD8 T cell responses to anti-PD-L1 mAb significantly improved (p < .05) over the 8-week course of metformin therapy. Moreover, frequencies of both intermediate (CD14+CD16+; r = 0.89, p = .01) and nonclassical (CD14lowCD16+; r = 0.92, p = .01) monocytes at entry were predictive of the magnitude of the anti-HIV CD8 T cell responses to PD-L1 blockade. Collectively, these findings highlight that 8-week course of metformin increases the polyfunctionality of CD8 T cells and that baseline monocyte subset frequencies may be a potential determinant of PD-L1 blockade efficacy. These data provide valuable information for HIV remission trials that utilize ICB strategies to enhance anti-HIV CD8 T cell immunity.
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Affiliation(s)
- Glen M. Chew
- John A. Burns School of Medicine, University of Hawai'i, Honolulu, Hawaii, USA
| | - Ana Joy P. Padua
- College of Medicine, University of the Philippines, Manila, Philippines
| | - Dominic C. Chow
- John A. Burns School of Medicine, University of Hawai'i, Honolulu, Hawaii, USA
| | - Scott A. Souza
- John A. Burns School of Medicine, University of Hawai'i, Honolulu, Hawaii, USA
| | | | - Michael J. Corley
- John A. Burns School of Medicine, University of Hawai'i, Honolulu, Hawaii, USA
| | - Alina P.S. Pang
- John A. Burns School of Medicine, University of Hawai'i, Honolulu, Hawaii, USA
| | | | - Mariana Gerschenson
- John A. Burns School of Medicine, University of Hawai'i, Honolulu, Hawaii, USA
| | - Cecilia M. Shikuma
- John A. Burns School of Medicine, University of Hawai'i, Honolulu, Hawaii, USA
| | - Lishomwa C. Ndhlovu
- John A. Burns School of Medicine, University of Hawai'i, Honolulu, Hawaii, USA
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Suárez-Fariñas M, Tokuyama M, Wei G, Huang R, Livanos A, Jha D, Levescot A, Irizar H, Kosoy R, Cording S, Wang W, Losic B, Ungaro RC, Di’Narzo A, Martinez-Delgado G, Suprun M, Corley MJ, Stojmirovic A, Houten SM, Peters L, Curran M, Brodmerkel C, Perrigoue J, Friedman JR, Hao K, Schadt EE, Zhu J, Ko HM, Cho J, Dubinsky MC, Sands BE, Ndhlovu L, Cerf-Bensusan N, Kasarskis A, Colombel JF, Harpaz N, Argmann C, Mehandru S. Intestinal Inflammation Modulates the Expression of ACE2 and TMPRSS2 and Potentially Overlaps With the Pathogenesis of SARS-CoV-2-related Disease. Gastroenterology 2021; 160:287-301.e20. [PMID: 32980345 PMCID: PMC7516468 DOI: 10.1053/j.gastro.2020.09.029] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/14/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS The presence of gastrointestinal symptoms and high levels of viral RNA in the stool suggest active severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication within enterocytes. METHODS Here, in multiple, large cohorts of patients with inflammatory bowel disease (IBD), we have studied the intersections between Coronavirus Disease 2019 (COVID-19), intestinal inflammation, and IBD treatment. RESULTS A striking expression of ACE2 on the small bowel enterocyte brush border supports intestinal infectivity by SARS-CoV-2. Commonly used IBD medications, both biologic and nonbiologic, do not significantly impact ACE2 and TMPRSS2 receptor expression in the uninflamed intestines. In addition, we have defined molecular responses to COVID-19 infection that are also enriched in IBD, pointing to shared molecular networks between COVID-19 and IBD. CONCLUSIONS These data generate a novel appreciation of the confluence of COVID-19- and IBD-associated inflammation and provide mechanistic insights supporting further investigation of specific IBD drugs in the treatment of COVID-19. Preprint doi: https://doi.org/10.1101/2020.05.21.109124.
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Affiliation(s)
- Mayte Suárez-Fariñas
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York,Icahn Institute for Data Science and Genomic Technology, New York City, New York
| | - Minami Tokuyama
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Gabrielle Wei
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ruiqi Huang
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York,Icahn Institute for Data Science and Genomic Technology, New York City, New York
| | - Alexandra Livanos
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Divya Jha
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Anais Levescot
- Inserm, UMR1163, Laboratory of Intestinal Immunity and Institute Imagine, Paris, France,Université de Paris, Paris, France
| | - Haritz Irizar
- University College London, Department Mental Health Sciences Unit, London, UK
| | - Roman Kosoy
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Sascha Cording
- Inserm, UMR1163, Laboratory of Intestinal Immunity and Institute Imagine, Paris, France,Université de Paris, Paris, France
| | - Wenhui Wang
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bojan Losic
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ryan C. Ungaro
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Antonio Di’Narzo
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Gustavo Martinez-Delgado
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Maria Suprun
- Center for Biostatistics, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michael J. Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
| | | | - Sander M. Houten
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lauren Peters
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | | | | | - Ke Hao
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Eric E. Schadt
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jun Zhu
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Huaibin M. Ko
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Judy Cho
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York,The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marla C. Dubinsky
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bruce E. Sands
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lishomwa Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, New York
| | | | - Andrew Kasarskis
- Icahn Institute for Data Science and Genomic Technology, New York City, New York,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jean-Frederic Colombel
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Noam Harpaz
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Carmen Argmann
- Icahn Institute for Data Science and Genomic Technology, New York City, New York; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Saurabh Mehandru
- The Dr. Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, New York.
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30
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Patterson BK, Seethamraju H, Dhody K, Corley MJ, Kazempour K, Lalezari J, Pang APS, Sugai C, Mahyari E, Francisco EB, Pise A, Rodrigues H, Wu HL, Webb GM, Park BS, Kelly S, Pourhassan N, Lelic A, Kdouh L, Herrera M, Hall E, Bimber BN, Plassmeyer M, Gupta R, Alpan O, O'Halloran JA, Mudd PA, Akalin E, Ndhlovu LC, Sacha JB. CCR5 inhibition in critical COVID-19 patients decreases inflammatory cytokines, increases CD8 T-cells, and decreases SARS-CoV2 RNA in plasma by day 14. Int J Infect Dis 2020; 103:25-32. [PMID: 33186704 PMCID: PMC7654230 DOI: 10.1016/j.ijid.2020.10.101] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVE Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is now a global pandemic. Emerging results indicate a dysregulated immune response. Given the role of CCR5 in immune cell migration and inflammation, we investigated the impact of CCR5 blockade via the CCR5-specific antibody leronlimab on clinical, immunological, and virological parameters in severe COVID-19 patients. METHODS In March 2020, 10 terminally ill, critical COVID-19 patients received two doses of leronlimab via individual emergency use indication. We analyzed changes in clinical presentation, immune cell populations, inflammation, as well as SARS-CoV-2 plasma viremia before and 14 days after treatment. RESULTS Over the 14-day study period, six patients survived, two were extubated, and one discharged. We observed complete CCR5 receptor occupancy in all donors by day 7. Compared with the baseline, we observed a concomitant statistically significant reduction in plasma IL-6, restoration of the CD4/CD8 ratio, and resolution of SARS-CoV2 plasma viremia (pVL). Furthermore, the increase in the CD8 percentage was inversely correlated with the reduction in pVL (r = -0.77, p = 0.0013). CONCLUSIONS Our study design precludes clinical efficacy inferences but the results implicate CCR5 as a therapeutic target for COVID-19 and they form the basis for ongoing randomized clinical trials.
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Affiliation(s)
| | | | - Kush Dhody
- Amarex Clinical Research LLC, Germantown, MD, USA
| | - Michael J Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | - Alina P S Pang
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Eisa Mahyari
- Vaccine & Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR, USA
| | | | | | | | - Helen L Wu
- Vaccine & Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR, USA
| | - Gabriela M Webb
- Vaccine & Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR, USA
| | - Byung S Park
- Vaccine & Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR, USA
| | | | | | | | | | | | | | - Benjamin N Bimber
- Vaccine & Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR, USA
| | | | - Raavi Gupta
- State University of New York-University Hospital of Brooklyn, NY, USA
| | | | - Jane A O'Halloran
- Division of Infectious Diseases, Department of Internal Medicine, USA
| | - Philip A Mudd
- Department of Emergency Medicine, Washington University in Saint Louis School of Medicine, Saint Louis, MO, USA
| | | | - Lishomwa C Ndhlovu
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jonah B Sacha
- Vaccine & Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Portland, OR, USA
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31
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SahBandar IN, Chew GM, Corley MJ, Pang APS, Tsai N, Hanks N, Khadka VS, Klatt NR, Hensley-McBain T, Somsouk M, Vujkovic-Cvijin I, Chow DC, Shikuma CM, Ndhlovu LC. Changes in gastrointestinal microbial communities influence HIV-specific CD8+ T-cell responsiveness to immune checkpoint blockade. AIDS 2020; 34:1451-1460. [PMID: 32675558 PMCID: PMC7371239 DOI: 10.1097/qad.0000000000002557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVES The aim of this study was to examine the relationship between gut microbial communities in HIV-infected individuals on suppressive antiretroviral therapy (cART), and the peripheral HIV-Gag-specific CD8 T-cell responses before and after ex-vivo immune checkpoint blockade (ICB). DESIGN Thirty-four HIV-seropositive, 10 HIV-seronegative and 12 HIV-seropositive receiving faecal microbiota transplant (FMT) participants were included. Gut microbial communities, peripheral and gut associated negative checkpoint receptors (NCRs) and peripheral effector functions were assessed. METHODS Bacterial 16s rRNA sequencing for gut microbiome study and flow-based assays for peripheral and gut NCR and their cognate ligand expression, including peripheral HIV-Gag-specific CD8 T-cell responses before and after ex-vivo anti-PD-L1 and anti-TIGIT ICB were performed. RESULTS Fusobacteria abundance was significantly higher in HIV-infected donors compared to uninfected controls. In HIV-infected participants receiving Fusobacteria-free FMT, Fusobacteria persisted up to 24 weeks in stool post FMT. PD-1 TIGIT and their ligands were expanded in mucosal vs. peripheral T cells and dendritic cells, respectively. PD-L1 and TIGIT blockade significantly increased the magnitude of peripheral anti-HIV-Gag-specific CD8 T-cell responses. Higher gut Fusobacteria abundance was associated with lower magnitude of peripheral IFN-γ+ HIV-Gag-specific CD8 T-cell responses following ICB. CONCLUSION The gut colonization of Fusobacteria in HIV infection is persistent and may influence anti-HIV T-cell immunity to PD-1 or TIGIT blockade. Strategies modulating Fusobacteria colonization may elicit a favourable mucosal immune landscape to enhance the efficacy of ICB for HIV cure.
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Affiliation(s)
| | - Glen M Chew
- Department of Tropical Medicine
- Hawaii Center for AIDS
| | | | | | | | | | - Vedbar S Khadka
- Department of Biostatistics and Quantitative Health Science, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Nichole R Klatt
- Department of Pharmaceutics, University of Washington, Seattle, Washington
| | | | - Ma Somsouk
- Division of Gastroenterology, Department of Medicine, Zuckerberg San Francisco General Hospital, University of California, San Francisco, California
| | - Ivan Vujkovic-Cvijin
- Metaorganism Immunity Section, National Institute of Allergy & Infectious Disease, National Institutes of Health, Bethesda, Maryland, USA
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32
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Go RCP, Corley MJ, Ross GW, Petrovitch H, Masaki KH, Maunakea AK, He Q, Tiirikainen MI. Genome-wide epigenetic analyses in Japanese immigrant plantation workers with Parkinson's disease and exposure to organochlorines reveal possible involvement of glial genes and pathways involved in neurotoxicity. BMC Neurosci 2020; 21:31. [PMID: 32650713 PMCID: PMC7350633 DOI: 10.1186/s12868-020-00582-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 07/07/2020] [Indexed: 12/29/2022] Open
Abstract
Background Parkinson’s disease (PD) is a disease of the central nervous system that progressively affects the motor system. Epidemiological studies have provided evidence that exposure to agriculture-related occupations or agrichemicals elevate a person’s risk for PD. Here, we sought to examine the possible epigenetic changes associated with working on a plantation on Oahu, HI and/or exposure to organochlorines (OGC) in PD cases. Results We measured genome-wide DNA methylation using the Illumina Infinium HumanMethylation450K BeadChip array in matched peripheral blood and postmortem brain biospecimens in PD cases (n = 20) assessed for years of plantation work and presence of organochlorines in brain tissue. The comparison of 10+ to 0 years of plantation work exposure detected 7 and 123 differentially methylated loci (DML) in brain and blood DNA, respectively (p < 0.0001). The comparison of cases with 4+ to 0–2 detectable levels of OGCs, identified 8 and 18 DML in brain and blood DNA, respectively (p < 0.0001). Pathway analyses revealed links to key neurotoxic and neuropathologic pathways related to impaired immune and proinflammatory responses as well as impaired clearance of damaged proteins, as found in the predominantly glial cell population in these environmental exposure-related PD cases. Conclusions These results suggest that distinct DNA methylation biomarker profiles related to environmental exposures in PD cases with previous exposure can be found in both brain and blood.
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Affiliation(s)
- Rodney C P Go
- Pacific Health Research and Education Institute, 3375 Koapaka Street, Suite I-540, Honolulu, HI, 96819, USA.,Kuakini Health Systems, 347 N Kuakini St, Honolulu, HI, 96817, USA.,Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, AL, 35294, USA
| | - Michael J Corley
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawai'i at Manoa, 650 Ilalo St, Honolulu, HI, 96813, USA
| | - G Webster Ross
- Pacific Health Research and Education Institute, 3375 Koapaka Street, Suite I-540, Honolulu, HI, 96819, USA.,Veterans Affairs Pacific Islands Health Care System, 459 Patterson Rd, Honolulu, HI, 96819, USA.,Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii at Manoa, 650 Ilalo St, Honolulu, HI, 96817, USA
| | - Helen Petrovitch
- Pacific Health Research and Education Institute, 3375 Koapaka Street, Suite I-540, Honolulu, HI, 96819, USA.,Veterans Affairs Pacific Islands Health Care System, 459 Patterson Rd, Honolulu, HI, 96819, USA.,Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii at Manoa, 650 Ilalo St, Honolulu, HI, 96817, USA
| | - Kamal H Masaki
- Kuakini Health Systems, 347 N Kuakini St, Honolulu, HI, 96817, USA.,Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii at Manoa, 650 Ilalo St, Honolulu, HI, 96817, USA
| | - Alika K Maunakea
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawai'i at Manoa, 650 Ilalo St, Honolulu, HI, 96813, USA
| | - Qimei He
- Pacific Health Research and Education Institute, 3375 Koapaka Street, Suite I-540, Honolulu, HI, 96819, USA.,Kuakini Health Systems, 347 N Kuakini St, Honolulu, HI, 96817, USA.,Veterans Affairs Pacific Islands Health Care System, 459 Patterson Rd, Honolulu, HI, 96819, USA
| | - Maarit I Tiirikainen
- University of Hawaii Cancer Center, University of Hawaii at Manoa, 701 Ilalo St, Honolulu, HI, 96813, USA.
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Premeaux TA, Javandel S, Hosaka KRJ, Greene M, Therrien N, Allen IE, Corley MJ, Valcour VG, Ndhlovu LC. Associations Between Plasma Immunomodulatory and Inflammatory Mediators With VACS Index Scores Among Older HIV-Infected Adults on Antiretroviral Therapy. Front Immunol 2020; 11:1321. [PMID: 32695109 PMCID: PMC7338430 DOI: 10.3389/fimmu.2020.01321] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/26/2020] [Indexed: 12/13/2022] Open
Abstract
The prevalence of age-related comorbidities is increased in people living with HIV, even in those well-controlled on combination antiretroviral therapy (ART). Persistent immune activation and inflammation may play pivotal roles in the pathogenesis; however, the burden of morbidities in the older HIV infected population may be exacerbated and driven by distinct mechanisms. In a cross sectional study of 45 HIV-infected participants 60 years or older, we examined the relationships between 14 immunomodulatory and inflammatory factors and the Veterans Aging Cohort Study (VACS) Index, a metric of multimorbidity and mortality comprised of age, CD4 count, hemoglobin, Fibrosis-4 [FIB-4], and estimated glomerular filtration rate [eGFR], by linear regression analysis. All participants were virally suppressed (<50 HIV RNA copies/mL), on ART, and primarily Caucasian (86.7%), and male (91.1%). Plasma levels of monocyte/macrophage-associated (neopterin, IP-10, sCD163, sCD14, and MCP-1) and glycan-binding immunomodulatory factors (galectin (Gal)-1, Gal-3, and Gal-9) were assessed, as well as inflammatory biomarkers previously linked to the VACS Index (i.e., CRP, cystatin C, TNF-α, TNFRI, IL-6, and D-dimer) for comparison. In regression analysis, higher VACS index scores were associated with higher levels of neopterin, cystatin C, TNFRI, and Gal-9 (all p < 0.05), potentially driven by correlations found with individual VACS components, including age, CD4 count, FIB-4, and eGFR. Gal-9, cystatin C, and TNFRI directly correlated with the extent of multimorbidity. Multiple correlations among markers were observed, suggesting an interplay of overlapping, but distinct, pathways. Collectively, in addition to cystatin C and TNFRI, both galectin-9 and neopterin, independently emerged as novel fluid markers of the VACS Index and burden of comorbidity and may further guide in understanding pathogenic mechanisms of age-related disorders in older HIV-infected individuals on suppressive ART.
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Affiliation(s)
- Thomas A Premeaux
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Shireen Javandel
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, San Francisco, CA, United States
| | - Kalei R J Hosaka
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Meredith Greene
- Division of Geriatric Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Nicholas Therrien
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Isabel E Allen
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
| | - Michael J Corley
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Victor G Valcour
- Department of Neurology, Memory and Aging Center, University of California, San Francisco, San Francisco, CA, United States.,Division of Geriatric Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Lishomwa C Ndhlovu
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States.,Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
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34
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Patterson BK, Seethamraju H, Dhody K, Corley MJ, Kazempour K, Lalezari JP, Pang AP, Sugai C, Francisco EB, Pise A, Rodrigues H, Ryou M, Wu HL, Webb GM, Park BS, Kelly S, Pourhassan N, Lelic A, Kdouh L, Herrera M, Hall E, Aklin E, Ndhlovu L, Sacha JB. Disruption of the CCL5/RANTES-CCR5 Pathway Restores Immune Homeostasis and Reduces Plasma Viral Load in Critical COVID-19. medRxiv 2020:2020.05.02.20084673. [PMID: 32511656 PMCID: PMC7277012 DOI: 10.1101/2020.05.02.20084673] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), is now pandemic with nearly three million cases reported to date. Although the majority of COVID-19 patients experience only mild or moderate symptoms, a subset will progress to severe disease with pneumonia and acute respiratory distress syndrome (ARDS) requiring mechanical ventilation. Emerging results indicate a dysregulated immune response characterized by runaway inflammation, including cytokine release syndrome (CRS), as the major driver of pathology in severe COVID-19. With no treatments currently approved for COVID-19, therapeutics to prevent or treat the excessive inflammation in severe disease caused by SARS-CoV-2 infection are urgently needed. Here, in 10 terminally-ill, critical COVID-19 patients we report profound elevation of plasma IL-6 and CCL5 (RANTES), decreased CD8+ T cell levels, and SARS-CoV-2 plasma viremia. Following compassionate care treatment with the CCR5 blocking antibody leronlimab, we observed complete CCR5 receptor occupancy on macrophage and T cells, rapid reduction of plasma IL-6, restoration of the CD4/CD8 ratio, and a significant decrease in SARS-CoV-2 plasma viremia. Consistent with reduction of plasma IL-6, single-cell RNA-sequencing revealed declines in transcriptomic myeloid cell clusters expressing IL-6 and interferon-related genes. These results demonstrate a novel approach to resolving unchecked inflammation, restoring immunologic deficiencies, and reducing SARS-CoV-2 plasma viral load via disruption of the CCL5-CCR5 axis, and support randomized clinical trials to assess clinical efficacy of leronlimab-mediated inhibition of CCR5 for COVID-19.
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Corley MJ, Chew G, Pang APS, Ndhlovu L. DNA Methylation Tightly Regulates TIGIT Expression in CD8+ T cells During Chronic HIV Infection. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.95.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The T cell Ig and ITIM domain (TIGIT) receptor is a next generation negative immune checkpoint that is unregulated on exhausted CD8+ T cells in cancer and in chronic HIV-1 infection. TIGIT is currently being pursued in Phase 1 human clinical studies for immune restoration using targeted monoclonal antibodies. However, the regulation of TIGIT expression on T cells still remain unclear. We characterized and compared genome-wide epigenetic and transcriptional profiles in sorted TIGIT+ and TIGIT− CD4 and CD8 T cells in peripheral blood obtained from three virally-suppressed chronic HIV participants on antiretroviral therapy. Unsupervised hierarchical clustering analysis of differentially methylated loci indicated TIGIT+ T cells stratified from TIGIT− T cells based on cellular DNA methylation profiles. Compared to cell sorted purified TIGIT− T cells, 86.5% of CpG loci exhibiting hypomethylated states in TIGIT+ T cells. Specifically, the levels of DNA methylation at the nine CpG loci on the methylation array related to the TIGIT gene showed significant demethylation in TIGIT+ compared to TIGIT− T cells. We found 6/7 sites located at the TIGIT promotor were significantly decreased in methylation in TIGIT + compared to TIGIT− cells (cg19959917: TIGIT+ = 0.605, TIGIT− = 0.715, P = 0.002). Moreover, the CpG located intergenic (cg19959917: TIGIT+ = 0.605, TIGIT− = 0.715, P = 0.002 and at the 3′ UTR (cg19959917: TIGIT+ = 0.605, TIGIT− = 0.715, P = 0.002) were significantly demethylated in TIGIT+ compared to TIGIT− T cells. DNA methylation changes correlated significantly with mRNA expression and surface protein expression. These reference methylomes expose a distinct DNA methylation state of TIGIT+ T cells and reference for epigenetic targeting.
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Fujimoto BA, Young M, Carter L, Pang APS, Corley MJ, Fogelgren B, Polgar N. The exocyst complex regulates insulin-stimulated glucose uptake of skeletal muscle cells. Am J Physiol Endocrinol Metab 2019; 317:E957-E972. [PMID: 31593505 PMCID: PMC6962504 DOI: 10.1152/ajpendo.00109.2019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 10/02/2019] [Accepted: 10/02/2019] [Indexed: 01/16/2023]
Abstract
Skeletal muscle handles ~80-90% of the insulin-induced glucose uptake. In skeletal muscle, insulin binding to its cell surface receptor triggers redistribution of intracellular glucose transporter GLUT4 protein to the cell surface, enabling facilitated glucose uptake. In adipocytes, the eight-protein exocyst complex is an indispensable constituent in insulin-induced glucose uptake, as it is responsible for the targeted trafficking and plasma membrane-delivery of GLUT4. However, the role of the exocyst in skeletal muscle glucose uptake has never been investigated. Here we demonstrate that the exocyst is a necessary factor in insulin-induced glucose uptake in skeletal muscle cells as well. The exocyst complex colocalizes with GLUT4 storage vesicles in L6-GLUT4myc myoblasts at a basal state and associates with these vesicles during their translocation to the plasma membrane after insulin signaling. Moreover, we show that the exocyst inhibitor endosidin-2 and a heterozygous knockout of Exoc5 in skeletal myoblast cells both lead to impaired GLUT4 trafficking to the plasma membrane and hinder glucose uptake in response to an insulin stimulus. Our research is the first to establish that the exocyst complex regulates insulin-induced GLUT4 exocytosis and glucose metabolism in muscle cells. A deeper knowledge of the role of the exocyst complex in skeletal muscle tissue may help our understanding of insulin resistance in type 2 diabetes.
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Affiliation(s)
- Brent A Fujimoto
- Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Madison Young
- Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Lamar Carter
- Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Alina P S Pang
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Michael J Corley
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Ben Fogelgren
- Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Noemi Polgar
- Department of Anatomy, Biochemistry and Physiology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
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D'Antoni ML, Kallianpur KJ, Premeaux TA, Corley MJ, Fujita T, Laws EI, Ogata-Arakaki D, Chow DC, Khadka VS, Shikuma CM, Ndhlovu LC. Lower Interferon Regulatory Factor-8 Expression in Peripheral Myeloid Cells Tracks With Adverse Central Nervous System Outcomes in Treated HIV Infection. Front Immunol 2019; 10:2789. [PMID: 31849969 PMCID: PMC6895026 DOI: 10.3389/fimmu.2019.02789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/14/2019] [Indexed: 11/23/2022] Open
Abstract
Cognitive dysfunction persists in 30–50% of chronically HIV-infected individuals despite combination antiretroviral therapy (ART). Although monocytes are implicated in poor cognitive performance, distinct biological mechanisms associated with cognitive dysfunction in HIV infection are unclear. We previously showed that a regulatory region of the interferon regulatory factor-8 (IRF8) gene is hyper-methylated in HIV-infected individuals with cognitive impairment compared to those with normal cognition. Here, we investigated IRF-8 protein expression and assessed relationships with multiple parameters associated with brain health. Intracellular IRF-8 expression was measured in cryopreserved peripheral blood mononuclear cells from chronically HIV-infected individuals on ART using flow cytometry. Neuropsychological performance was assessed by generating domain-specific standardized (NPZ) scores, with a global score defined by aggregating individual domain scores. Regional brain volumes were obtained by magnetic resonance imaging and soluble inflammatory factors were assessed by immunosorbent assays. Non-parametric analyses were conducted and statistical significance was defined as p < 0.05. Twenty aviremic (HIV RNA<50 copies/ml) participants, 84% male, median age 51 [interquartile range (IQR) 46, 55], median CD4 count 548 [439, 700] were evaluated. IRF-8 expression was highest in plasmacytoid dendritic cells (pDCs). Assessing cognitive function, lower IRF-8 density in classical monocytes significantly correlated with worse NPZ_learning memory (LM; rho = 0.556) and NPZ_working memory (WM; rho = 0.612) scores, in intermediate monocytes with worse NPZ_LM (rho = 0.532) scores, and in non-classical monocytes, lower IRF-8 correlated with worse global NPZ (rho = 0.646), NPZ_LM (rho = 0.536), NPZ_WM (rho = 0.647), and NPZ_executive function (rho = 0.605) scores. In myeloid DCs (mDCs) lower IRF-8 correlated with worse NPZ_WM (rho = 0.48) scores and in pDCs with worse NPZ_WM (rho = 0.561) scores. Declines in IRF-8 in classical monocytes significantly correlated with smaller hippocampal volume (rho = 0.573) and in intermediate and non-classical monocytes with smaller cerebral white matter volume (rho = 0.509 and rho = 0.473, respectively). IRF-8 density in DCs did not significantly correlate with brain volumes. Among biomarkers tested, higher soluble ICAM-1 levels significantly correlated with higher IRF-8 in all monocyte and DC subsets. These data may implicate IRF-8 as a novel transcription factor in the neuropathophysiology of brain abnormalities in treated HIV and serve as a potential therapeutic target to decrease the burden of cognitive dysfunction in this population.
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Affiliation(s)
- Michelle L D'Antoni
- Department of Tropical Medicine, University of Hawai'i, Honolulu, HI, United States.,Hawaii Center for AIDS, University of Hawai'i, Honolulu, HI, United States
| | - Kalpana J Kallianpur
- Department of Tropical Medicine, University of Hawai'i, Honolulu, HI, United States.,Hawaii Center for AIDS, University of Hawai'i, Honolulu, HI, United States
| | - Thomas A Premeaux
- Department of Tropical Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Michael J Corley
- Department of Native Hawaiian Health, University of Hawai'i, Honolulu, HI, United States
| | - Tsuyoshi Fujita
- Department of Tropical Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Elizabeth I Laws
- Department of Tropical Medicine, University of Hawai'i, Honolulu, HI, United States
| | | | - Dominic C Chow
- Hawaii Center for AIDS, University of Hawai'i, Honolulu, HI, United States
| | - Vedbar S Khadka
- Office of Biostatistics and Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI, United States
| | - Cecilia M Shikuma
- Hawaii Center for AIDS, University of Hawai'i, Honolulu, HI, United States
| | - Lishomwa C Ndhlovu
- Department of Tropical Medicine, University of Hawai'i, Honolulu, HI, United States.,Hawaii Center for AIDS, University of Hawai'i, Honolulu, HI, United States
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38
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Mu C, Corley MJ, Lee RWY, Wong M, Pang A, Arakaki G, Miyamoto R, Rho JM, Mickiewicz B, Dowlatabadi R, Vogel HJ, Korchemagin Y, Shearer J. Metabolic Framework for the Improvement of Autism Spectrum Disorders by a Modified Ketogenic Diet: A Pilot Study. J Proteome Res 2019; 19:382-390. [PMID: 31696714 DOI: 10.1021/acs.jproteome.9b00581] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The ketogenic diet (KD) can improve the core features of autism spectrum disorders (ASD) in some children, but the effects on the overall metabolism remain unclear. This pilot study investigated the behavioral parameters in relation to blood metabolites and trace elements in a cohort of 10 typically developed controls (TC) and 17 children with ASD at baseline and following 3 months of treatment with a modified KD regimen. A nontargeted, multiplatform metabolomic approach was employed, including gas chromatography-mass spectrometry, 1H nuclear magnetic resonance spectroscopy, and inductively coupled plasma-mass spectrometry. The associations among plasma metabolites, trace elements, and behavior scores were investigated. Employing a combination of metabolomic platforms, 118 named metabolites and 73 trace elements were assessed. Relative to TC, a combination of glutamate, galactonate, and glycerol discriminated ASD with 88% accuracy. ASD had higher concentrations of galactose intermediates, gut microbe-derived trimethylamine N-oxide and N-acetylserotonin, and lower concentrations of 3-hydroxybutyrate and selenium at baseline. Following 3 months of KD intervention, the levels of circulating ketones and acetylcarnitine were increased. KD restored lower selenium levels in ASD to that of controls, and correlation analysis identified a novel negative correlation between the changes in selenium and behavior scores. Based on the different behavior responses to KD, we found that high responders had greater concentrations of 3-hydroxybutyrate and ornithine, with lower galactose. These findings enhance our current understanding of the metabolic derangements present in ASD and may be of utility in predicting favorable responses to KD intervention.
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Affiliation(s)
| | - Michael J Corley
- John A. Burns School of Medicine, Department of Native Hawaiian Health , University of Hawaii , Honolulu , Hawaii 96822 , United States
| | - Ryan W Y Lee
- Shriners Hospitals for Children , Honolulu , Hawaii 96826 , United States
| | - Miki Wong
- Shriners Hospitals for Children , Honolulu , Hawaii 96826 , United States
| | - Alina Pang
- John A. Burns School of Medicine, Department of Native Hawaiian Health , University of Hawaii , Honolulu , Hawaii 96822 , United States
| | - Gaye Arakaki
- Shriners Hospitals for Children , Honolulu , Hawaii 96826 , United States
| | - Rob Miyamoto
- Shriners Hospitals for Children , Honolulu , Hawaii 96826 , United States
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Uzzan M, Tokuyama M, Rosenstein AK, Tomescu C, SahBandar IN, Ko HM, Leyre L, Chokola A, Kaplan-Lewis E, Rodriguez G, Seki A, Corley MJ, Aberg J, La Porte A, Park EY, Ueno H, Oikonomou I, Doron I, Iliev ID, Chen BK, Lui J, Schacker TW, Furtado GC, Lira SA, Colombel JF, Horowitz A, Lim JK, Chomont N, Rahman AH, Montaner LJ, Ndhlovu LC, Mehandru S. Anti-α4β7 therapy targets lymphoid aggregates in the gastrointestinal tract of HIV-1-infected individuals. Sci Transl Med 2019; 10:10/461/eaau4711. [PMID: 30282696 DOI: 10.1126/scitranslmed.aau4711] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/11/2018] [Indexed: 12/12/2022]
Abstract
Gut homing CD4+ T cells expressing the integrin α4β7 are early viral targets and contribute to HIV-1 pathogenesis, likely by seeding the gastrointestinal (GI) tract with HIV. Although simianized anti-α4β7 monoclonal antibodies have shown promise in preventing or attenuating the disease course of simian immunodeficiency virus in nonhuman primate studies, the mechanisms of drug action remain elusive. We present a cohort of individuals with mild inflammatory bowel disease and concomitant HIV-1 infection receiving anti-α4β7 treatment. By sampling the immune inductive and effector sites of the GI tract, we have discovered that anti-α4β7 therapy led to a significant and unexpected attenuation of lymphoid aggregates, most notably in the terminal ileum. Given that lymphoid aggregates serve as important sanctuary sites for maintaining viral reservoirs, their attrition by anti-α4β7 therapy has important implications for HIV-1 therapeutics and eradication efforts and defines a rational basis for the use of anti-α4β7 therapy in HIV-1 infection.
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Affiliation(s)
- Mathieu Uzzan
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Minami Tokuyama
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adam K Rosenstein
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Ivo N SahBandar
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
| | - Huaibin M Ko
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Louise Leyre
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, Québec H2X 0A9, Canada
| | - Anupa Chokola
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Emma Kaplan-Lewis
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gabriela Rodriguez
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Akihiro Seki
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael J Corley
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
| | - Judith Aberg
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Annalena La Porte
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eun-Young Park
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
| | - Hideki Ueno
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ioannis Oikonomou
- Division of Gastroenterology, Rush University, Chicago, IL 60612, USA
| | - Itai Doron
- Gastroenterology and Hepatology Divison, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Divison, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Benjamin K Chen
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jennifer Lui
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Timothy W Schacker
- Department of Medicine, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
| | - Glaucia C Furtado
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sergio A Lira
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Amir Horowitz
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jean K Lim
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicolas Chomont
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, Québec H2X 0A9, Canada
| | - Adeeb H Rahman
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Lishomwa C Ndhlovu
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
| | - Saurabh Mehandru
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. .,Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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40
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Corley MJ, Vargas-Maya N, Pang APS, Lum-Jones A, Li D, Khadka V, Sultana R, Blanchard DC, Maunakea AK. Epigenetic Delay in the Neurodevelopmental Trajectory of DNA Methylation States in Autism Spectrum Disorders. Front Genet 2019; 10:907. [PMID: 31681403 PMCID: PMC6797928 DOI: 10.3389/fgene.2019.00907] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 08/28/2019] [Indexed: 12/16/2022] Open
Abstract
Autism spectrum disorders (ASD) are hypothesized to originate in utero from perturbations in neural stem cell niche regions of the developing brain. Dynamic epigenetic processes including DNA methylation are integral to coordinating typical brain development. However, the extent and consequences of alterations to DNA methylation states in neural stem cell compartments in ASD are unknown. Here, we report significant DNA methylation defects in the subventricular zone of the lateral ventricles from postmortem brain of 17 autism diagnosed compared to 17 age- and gender-matched typically developing individuals. Both array- and sequencing-based genome-wide methylome analyses independently revealed that these alterations were preferentially targeted to intragenic and bivalently modified chromatin domains of genes predominately involved in neurodevelopment, which associated with aberrant precursor messenger RNA splicing events of ASD-relevant genes. Integrative analysis of our ASD and typically developing postmortem brain methylome datasets with that from fetal brain at different neurodevelopmental stages revealed that the methylation states of differentially methylated loci associated with ASD remarkably resemble the methylation states at earlier time points in fetal brain development. This observation was confirmed using additional methylome datasets from three other brain regions. Altogether, these findings implicate an epigenetic delay in the trajectory of normal DNA methylation states during the course of brain development that may consequently lead to deleterious transcriptomic events in ASD and support the hypothesis of an early developmental origin of ASD.
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Affiliation(s)
- Michael J Corley
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Nauru Vargas-Maya
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Alina P S Pang
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Annette Lum-Jones
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Dongmei Li
- Department of Clinical and Translational Research, University of Rochester Medical Center, Rochester, NY, United States
| | - Vedbar Khadka
- Office of Biostatistics & Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - Razvan Sultana
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
| | - D Caroline Blanchard
- Bekesy Neurobiology Laboratory, Pacific Biosciences Research Center, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Alika K Maunakea
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States
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Zhang X, Hu Y, Aouizerat BE, Peng G, Marconi VC, Corley MJ, Hulgan T, Bryant KJ, Zhao H, Krystal JH, Justice AC, Xu K. Machine learning selected smoking-associated DNA methylation signatures that predict HIV prognosis and mortality. Clin Epigenetics 2018; 10:155. [PMID: 30545403 PMCID: PMC6293604 DOI: 10.1186/s13148-018-0591-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/26/2018] [Indexed: 12/20/2022] Open
Abstract
Background The effects of tobacco smoking on epigenome-wide methylation signatures in white blood cells (WBCs) collected from persons living with HIV may have important implications for their immune-related outcomes, including frailty and mortality. The application of a machine learning approach to the analysis of CpG methylation in the epigenome enables the selection of phenotypically relevant features from high-dimensional data. Using this approach, we now report that a set of smoking-associated DNA-methylated CpGs predicts HIV prognosis and mortality in an HIV-positive veteran population. Results We first identified 137 epigenome-wide significant CpGs for smoking in WBCs from 1137 HIV-positive individuals (p < 1.70E−07). To examine whether smoking-associated CpGs were predictive of HIV frailty and mortality, we applied ensemble-based machine learning to build a model in a training sample employing 408,583 CpGs. A set of 698 CpGs was selected and predictive of high HIV frailty in a testing sample [(area under curve (AUC) = 0.73, 95%CI 0.63~0.83)] and was replicated in an independent sample [(AUC = 0.78, 95%CI 0.73~0.83)]. We further found an association of a DNA methylation index constructed from the 698 CpGs that were associated with a 5-year survival rate [HR = 1.46; 95%CI 1.06~2.02, p = 0.02]. Interestingly, the 698 CpGs located on 445 genes were enriched on the integrin signaling pathway (p = 9.55E−05, false discovery rate = 0.036), which is responsible for the regulation of the cell cycle, differentiation, and adhesion. Conclusion We demonstrated that smoking-associated DNA methylation features in white blood cells predict HIV infection-related clinical outcomes in a population living with HIV. Electronic supplementary material The online version of this article (10.1186/s13148-018-0591-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, 300 George Street, 950 Campbell Ave, West Haven, New Haven, CT, 06511, USA.,VA Connecticut Healthcare System, 950 Campbell Ave, West Haven, CT, 06516, USA
| | - Ying Hu
- Center for Biomedical Bioinformatics, National Cancer Institute, Rockville, MD, 20852, USA
| | - Bradley E Aouizerat
- Bluestone Center for Clinical Research, New York University, New York, NY, 10010, USA
| | - Gang Peng
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 065116, USA
| | - Vincent C Marconi
- Division of Infectious Diseases, Emory University School of Medicine, Atlanta, GA, 30303, USA
| | - Michael J Corley
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Suite 1016B, Honolulu, 96813, USA
| | - Todd Hulgan
- School of Medicine, Vanderbilt University, Nashville, TN, 37232, USA
| | - Kendall J Bryant
- National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD, 20852, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 065116, USA
| | - John H Krystal
- Department of Psychiatry, Yale School of Medicine, 300 George Street, 950 Campbell Ave, West Haven, New Haven, CT, 06511, USA.,VA Connecticut Healthcare System, 950 Campbell Ave, West Haven, CT, 06516, USA
| | - Amy C Justice
- VA Connecticut Healthcare System, 950 Campbell Ave, West Haven, CT, 06516, USA.,Yale University School of Medicine, New Haven, CT, 06516, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, 300 George Street, 950 Campbell Ave, West Haven, New Haven, CT, 06511, USA. .,VA Connecticut Healthcare System, 950 Campbell Ave, West Haven, CT, 06516, USA.
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Balaan C, Corley MJ, Eulalio T, Leite-Ahyo K, Pang APS, Fang R, Khadka VS, Maunakea AK, Ward MA. Juvenile Shank3b deficient mice present with behavioral phenotype relevant to autism spectrum disorder. Behav Brain Res 2018; 356:137-147. [PMID: 30134148 DOI: 10.1016/j.bbr.2018.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 08/07/2018] [Accepted: 08/08/2018] [Indexed: 12/19/2022]
Abstract
Autism spectrum disorder (ASD) is a pervasive, multifactorial neurodevelopmental disorder diagnosed according to deficits in three behavioral domains: communication, social interaction, and stereotyped/repetitive behaviors. Mutations in Shank genes account for ∼1% of clinical ASD cases with Shank3 being the most common gene variant. In addition to maintaining synapses and facilitating dendritic maturation, Shank genes encode master scaffolding proteins that build core complexes in the postsynaptic densities of glutamatergic synapses. Male mice with a deletion of the PDZ domain of Shank3 (Shank3B KO) were previously shown to display ASD-like behavioral phenotypes with reported self-injurious repetitive grooming and aberrant social interactions. Our goal was to extend these previous findings and use a comprehensive battery of highly detailed ASD-relevant behavioral assays including an assessment of mouse ultrasonic communication carried out on key developmental days and male and female Shank3B KO mice. We demonstrate that ASD-related behaviors, atypical reciprocal social interaction and indiscriminate repetitive grooming, are apparent in juvenile stages of development of Shank3B KO mice. Our findings underscore the importance of utilizing Shank mutant models to understand the impact of this gene in ASD etiology, whichmay enable future studies focusing on etiological gene-environment interactions in ASD.
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Affiliation(s)
- Chantell Balaan
- Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawai'i, 1960 East-West Rd, Honolulu, HI, 96822, United States
| | - Michael J Corley
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawai'i, 651 Ilalo St, Honolulu, HI, 96813, United States
| | - Tiffany Eulalio
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawai'i, 651 Ilalo St, Honolulu, HI, 96813, United States
| | - Ka'ahukane Leite-Ahyo
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawai'i, 651 Ilalo St, Honolulu, HI, 96813, United States
| | - Alina P S Pang
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawai'i, 651 Ilalo St, Honolulu, HI, 96813, United States
| | - Rui Fang
- Department of Complementary & Integrative Medicine, John A. Burns School of Medicine, University of Hawai'i, 651 Ilalo St, Honolulu, HI, 96813, United States
| | - Vedbar S Khadka
- Department of Complementary & Integrative Medicine, John A. Burns School of Medicine, University of Hawai'i, 651 Ilalo St, Honolulu, HI, 96813, United States
| | - Alika K Maunakea
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawai'i, 651 Ilalo St, Honolulu, HI, 96813, United States
| | - Monika A Ward
- Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawai'i, 1960 East-West Rd, Honolulu, HI, 96822, United States.
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Lee RWY, Corley MJ, Pang A, Arakaki G, Abbott L, Nishimoto M, Miyamoto R, Lee E, Yamamoto S, Maunakea AK, Lum-Jones A, Wong M. A modified ketogenic gluten-free diet with MCT improves behavior in children with autism spectrum disorder. Physiol Behav 2018; 188:205-211. [PMID: 29421589 PMCID: PMC5863039 DOI: 10.1016/j.physbeh.2018.02.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/27/2018] [Accepted: 02/03/2018] [Indexed: 02/08/2023]
Abstract
Purpose The ketogenic diet is a low-carbohydrate, moderate protein, high-fat diet that has emerged as a potential treatment for autism spectrum disorder. Autism spectrum disorder is a neurodevelopmental disorder of social communication, and restricted, repetitive behaviors and interests in need of novel therapies. An open-label clinical trial was done in Honolulu, Hawaii to test a modified ketogenic diet for improvement of core clinical impairments in children with ASD. Intervention A modified ketogenic gluten-free diet regimen with supplemental MCT was completed in 15 children ages 2 to 17 years for 3 months. Clinical (ADOS-2, CARS-2) and biochemical measures were performed at baseline and 3-months on the ketogenic diet. Main outcome Children administered a modified ketogenic gluten-free diet with supplemental MCT significantly improved core autism features assessed from the ADOS-2 after 3 months on diet (P = 0.006). No significant difference was observed in restricted and repetitive behavior score (P = 0.125) after 3 months on the diet protocol. Substantial improvement (> 30% decrease ADOS-2 total score) was observed in six participants, moderate improvement (> 3 units) in two participants, and minor/no improvement in seven participants. Ten participants assessed at a six-month time point sustained improvement in total ADOS-2 and social affect subdomain scores comparing baseline and 6 months (P = 0.019; P = 0.023), but no significant improvement in restricted and repetitive behavior scores were noted (P = 0.197). Significant improvements in CARS-2 items after 3 months of the modified ketogenic protocol were observed in imitation, body use, and fear or nervousness (P = 0.031, P = 0.008, P = 0.039). The percent change on ADOS-2 score from baseline to 3 months was associated with baseline high-density lipoprotein levels (ρ = −0.67, P = 0.007) and albumin levels (ρ = −0.60, P = 0.019). Moreover, the percent change from baseline to 3 months in ADOS-2 scores was significantly associated with percent change in high-density lipoprotein levels (ρ = 0.54, P = 0.049) and albumin levels (ρ = 0.67, P = 0.010). Conclusions A modified gluten-free ketogenic diet with supplemental MCT is a potentially beneficial treatment option to improve the core features of autism spectrum disorder and warrants further investigation. Trial registration Trial Registry: Clinicaltrials.gov Registration Number: NCT02477904 URL: https://www.clinicaltrials.gov/ct2/show/NCT02477904?term=ketogenic+diet&cond=Autism&rank=1
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Affiliation(s)
- Ryan W Y Lee
- Shriners Hospitals for Children, Medical Staff Department, Honolulu, Hawaii, United States; University of Hawaii, John A. Burns School of Medicine, Department of Pediatrics, Honolulu, Hawaii, United States; Shriners Hospitals for Children, Research Department, Honolulu, Hawaii, United States.
| | - Michael J Corley
- University of Hawaii, John A. Burns School of Medicine, Department of Native Hawaiian Health, Honolulu, Hawaii, United States.
| | - Alina Pang
- University of Hawaii, John A. Burns School of Medicine, Department of Native Hawaiian Health, Honolulu, Hawaii, United States.
| | - Gaye Arakaki
- Shriners Hospitals for Children, Rehabilitation Department, Honolulu, Hawaii, United States.
| | - Lisa Abbott
- Shriners Hospitals for Children, Research Department, Honolulu, Hawaii, United States
| | - Michael Nishimoto
- Shriners Hospitals for Children, Medical Staff Department, Honolulu, Hawaii, United States.
| | - Rob Miyamoto
- Shriners Hospitals for Children, Research Department, Honolulu, Hawaii, United States.
| | - Erica Lee
- University of Hawaii, John A. Burns School of Medicine, Department of Native Hawaiian Health, Honolulu, Hawaii, United States.
| | - Susan Yamamoto
- Shriners Hospitals for Children, Research Department, Honolulu, Hawaii, United States.
| | - Alika K Maunakea
- University of Hawaii, John A. Burns School of Medicine, Department of Native Hawaiian Health, Honolulu, Hawaii, United States.
| | - Annette Lum-Jones
- University of Hawaii, John A. Burns School of Medicine, Department of Native Hawaiian Health, Honolulu, Hawaii, United States.
| | - Miki Wong
- Shriners Hospitals for Children, Research Department, Honolulu, Hawaii, United States; Shriners Hospitals for Children, Nutrition Services Department, Honolulu, Hawaii, United States.
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Madagula KK, Ginwala R, Caruso B, Khan ZK, Chew GM, Pattekar A, Corley MJ, Loonawat R, Jacobson S, Sreedhar S, Ndhlovu LC, Jain P. HTLV-1 infection and neuropathogenesis in the context of Rag1−/−γc−/− (RAG1-hu) and BLT mice. The Journal of Immunology 2017. [DOI: 10.4049/jimmunol.198.supp.78.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
To date, the lack of a suitable small animal model has hindered our quest to understand the immuno- and neuropathogenesis of HTLV-1, the causative agent of chronic disabling neuroinflammatory disease HAM/TSP. Host immune response that plays a critical role in the outcome of HTLV-1 infection could be better tested in the context of humanized (hu) mice. Thus, we infected neonatal and adult Balb/c-Rag1−/−γc−/− (Rag1) as well as Bone marrow-Liver-Thymic (BLT) mice with HTLV-1. Proviral load (PVL) was determined in the peripheral blood, spleen, and other organs by droplet digital PCR. Within blood, PVL and viral protein Tax was detected as early as 2 wks post-infection (wpi). Tax showed peak expression at 14 wpi in Rag1 mice with continued expression until 16 weeks. Both PVL and Tax expression was considerably higher in the adult Rag1 mice as compared to the neonates with the latter showing less than 20% PVL in the peripheral blood, brain, and liver. Moreover, signs of lymphocytic infiltration with concomitant Tax expression and resulting myelin disruption were observed in the spinal cord and brain of infected mice. Thus far, several members of the CD28:B7 family of co-signaling molecules have been associated with T-cell dysfunctions in HTLV-infected patients. We found increased expression of PD-1, TIGIT and TIM-3 on CD8+ T cells in the CNS of infected hu-mice. This represents the first attempt to establish HTLV-1 neuropathogenesis in the context of Rag-1 and BLT hu-mice suggesting the possibility of developing a small animal model of HAM/TSP for testing groundbreaking therapies.
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Corley MJ, Dye C, D'Antoni ML, Byron MM, Yo KLA, Lum-Jones A, Nakamoto B, Valcour V, SahBandar I, Shikuma CM, Ndhlovu LC, Maunakea AK. Comparative DNA Methylation Profiling Reveals an Immunoepigenetic Signature of HIV-related Cognitive Impairment. Sci Rep 2016; 6:33310. [PMID: 27629381 PMCID: PMC5024304 DOI: 10.1038/srep33310] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 08/24/2016] [Indexed: 11/20/2022] Open
Abstract
Monocytes/macrophages contribute to the neuropathogenesis of HIV-related cognitive impairment (CI); however, considerable gaps in our understanding of the precise mechanisms driving this relationship remain. Furthermore, whether a distinct biological profile associated with HIV-related CI resides in immune cell populations remains unknown. Here, we profiled DNA methylomes and transcriptomes of monocytes derived from HIV-infected individuals with and without CI using genome-wide DNA methylation and gene expression profiling. We identified 1,032 CI-associated differentially methylated loci in monocytes. These loci related to gene networks linked to the central nervous system (CNS) and interactions with HIV. Most (70.6%) of these loci exhibited higher DNA methylation states in the CI group and were preferentially distributed over gene bodies and intergenic regions of the genome. CI-associated DNA methylation states at 12 CpG sites associated with neuropsychological testing performance scores. CI-associated DNA methylation also associated with gene expression differences including CNS genes CSRNP1 (P = 0.017), DISC1 (P = 0.012), and NR4A2 (P = 0.005); and a gene known to relate to HIV viremia, THBS1 (P = 0.003). This discovery cohort data unveils cell type-specific DNA methylation patterns related to HIV-associated CI and provide an immunoepigenetic DNA methylation “signature” potentially useful for corroborating clinical assessments, informing pathogenic mechanisms, and revealing new therapeutic targets against CI.
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Affiliation(s)
- Michael J Corley
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
| | - Christian Dye
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
| | - Michelle L D'Antoni
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB325C, Honolulu, HI 96813, USA
| | - Mary Margaret Byron
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB325C, Honolulu, HI 96813, USA
| | - Kaahukane Leite-Ah Yo
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
| | - Annette Lum-Jones
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
| | - Beau Nakamoto
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB, Honolulu, HI 96815, USA
| | - Victor Valcour
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA, USA
| | - Ivo SahBandar
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB325C, Honolulu, HI 96813, USA
| | - Cecilia M Shikuma
- Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB, Honolulu, HI 96815, USA
| | - Lishomwa C Ndhlovu
- Department of Tropical Medicine, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB325C, Honolulu, HI 96813, USA.,Hawaii Center for AIDS, John A. Burns School of Medicine, University of Hawaii, 651 Ilalo Street, BSB, Honolulu, HI 96815, USA
| | - Alika K Maunakea
- Department of Native Hawaiian Health, John A. Burns School of Medicine, Suite 1016B, University of Hawaii, Honolulu, HI 96813, USA
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Fong KSK, Hufnagel RB, Khadka VS, Corley MJ, Maunakea AK, Fogelgren B, Ahmed ZM, Lozanoff S. A mutation in the tuft mouse disrupts TET1 activity and alters the expression of genes that are crucial for neural tube closure. Dis Model Mech 2016; 9:585-96. [PMID: 26989192 PMCID: PMC4892663 DOI: 10.1242/dmm.024109] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/09/2016] [Indexed: 01/19/2023] Open
Abstract
Genetic variations affecting neural tube closure along the head result in malformations of the face and brain. Neural tube defects (NTDs) are among the most common birth defects in humans. We previously reported a mouse mutant called tuft that arose spontaneously in our wild-type 3H1 colony. Adult tuft mice present midline craniofacial malformations with or without an anterior cephalocele. In addition, affected embryos presented neural tube closure defects resulting in insufficient closure of the anterior neuropore or exencephaly. Here, through whole-genome sequencing, we identified a nonsense mutation in the Tet1 gene, which encodes a methylcytosine dioxygenase (TET1), co-segregating with the tuft phenotype. This mutation resulted in premature termination that disrupts the catalytic domain that is involved in the demethylation of cytosine. We detected a significant loss of TET enzyme activity in the heads of tuft embryos that were homozygous for the mutation and had NTDs. RNA-Seq transcriptome analysis indicated that multiple gene pathways associated with neural tube closure were dysregulated in tuft embryo heads. Among them, the expressions of Cecr2, Epha7 and Grhl2 were significantly reduced in some embryos presenting neural tube closure defects, whereas one or more components of the non-canonical WNT signaling pathway mediating planar cell polarity and convergent extension were affected in others. We further show that the recombinant mutant TET1 protein was capable of entering the nucleus and affected the expression of endogenous Grhl2 in IMCD-3 (inner medullary collecting duct) cells. These results indicate that TET1 is an epigenetic determinant for regulating genes that are crucial to closure of the anterior neural tube and its mutation has implications to craniofacial development, as presented by the tuft mouse. Summary: We propose an epigenetic mechanism establishing the regulation of genes that are crucial for neural tube closure. This mechanism could be a novel target for resolving such birth defects and associated disorders.
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Affiliation(s)
- Keith S K Fong
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI 96813, USA
| | - Robert B Hufnagel
- Department of Pediatrics, Division of Human Genetics, Cincinnati Children's Hospital, College of Medicine, University of Cincinnati, 3333 Burnet Ave, ML 7003, Cincinnati, OH 45229, USA Unit on Pediatric, Development & Genetic Ophthalmology, Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vedbar S Khadka
- Office of Biostatistics and Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI 96813, USA
| | - Michael J Corley
- Epigenomics Research Program, Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI 96813, USA
| | - Alika K Maunakea
- Epigenomics Research Program, Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI 96813, USA
| | - Ben Fogelgren
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI 96813, USA
| | - Zubair M Ahmed
- Department of Pediatrics, Division of Human Genetics, Cincinnati Children's Hospital, College of Medicine, University of Cincinnati, 3333 Burnet Ave, ML 7003, Cincinnati, OH 45229, USA Department of Otorhinolaryngology Head and Neck Surgery, School of Medicine, University of Maryland, BioPark Bldg1, 800 West Baltimore Street, Room 404, Baltimore, MD 21201, USA
| | - Scott Lozanoff
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, University of Hawai'i, Honolulu, HI 96813, USA
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Corley MJ, Zhang W, Zheng X, Lum-Jones A, Maunakea AK. Semiconductor-based sequencing of genome-wide DNA methylation states. Epigenetics 2015; 10:153-66. [PMID: 25602802 PMCID: PMC4622511 DOI: 10.1080/15592294.2014.1003747] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 12/15/2014] [Accepted: 12/22/2014] [Indexed: 12/17/2022] Open
Abstract
Methylated DNA immunoprecipitation sequencing (MeDIP-Seq) is a widely used approach to study DNA methylation genome-wide. Here, we developed a MeDIP-Seq protocol compatible with the Ion Torrent semiconductor-based sequencing platform that is low cost, rapid, and scalable. We applied this protocol to demonstrate MeDIP-Seq on the Ion Torrent platform provides adequate coverage of CpG cytosines, the methylation states of which we validated at single-base resolution on the Infinium HumanMethylation450 BeadChip array, and accurately identifies sites of differential DNA methylation. Furthermore, we applied an integrative approach to further investigate and confirm the role of DNA methylation in alternative splicing and to profile 5mC and 5hmC variants of DNA methylation in normal human brain tissue that is localized over distinct genomic regions. These applications of MeDIP-Seq on the Ion Torrent platform have broad utility and add to the current methodologies for profiling genome-wide DNA methylation states in normal and disease conditions.
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Affiliation(s)
- Michael J Corley
- Department of Native Hawaiian Health; John A. Burns School of Medicine; University of Hawaii; Honolulu, HI USA
| | - Wei Zhang
- Department of Native Hawaiian Health; John A. Burns School of Medicine; University of Hawaii; Honolulu, HI USA
| | - Xin Zheng
- Department of Native Hawaiian Health; John A. Burns School of Medicine; University of Hawaii; Honolulu, HI USA
| | - Annette Lum-Jones
- Department of Native Hawaiian Health; John A. Burns School of Medicine; University of Hawaii; Honolulu, HI USA
| | - Alika K Maunakea
- Department of Native Hawaiian Health; John A. Burns School of Medicine; University of Hawaii; Honolulu, HI USA
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Pearson BL, Corley MJ, Vasconcellos A, Blanchard DC, Blanchard RJ. Heparan sulfate deficiency in autistic postmortem brain tissue from the subventricular zone of the lateral ventricles. Behav Brain Res 2013; 243:138-45. [PMID: 23318464 DOI: 10.1016/j.bbr.2012.12.062] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 12/12/2012] [Accepted: 12/14/2012] [Indexed: 01/20/2023]
Abstract
Abnormal cellular growth and organization have been characterized in postmortem tissue from brains of autistic individuals, suggestive of pathology in a critical neurogenic niche, the subventricular zone (SVZ) of the brain lateral ventricles (LV). We examined cellular organization, cell proliferation, and constituents of the extracellular matrix such as N-sulfated heparan sulfate (HS) and laminin (LAM) in postmortem brain tissue from the LV-SVZ of young to elderly individuals with autism (n=4) and age-matched typically developing (TD) individuals (n=4) using immunofluorescence techniques. Strong and systematic reductions in HS immunofluorescence were observed in the LV-SVZ of the TD individuals with increasing age. For young through mature, but not elderly, autistic pair members, HS was reduced compared to their matched TDs. Cellular proliferation (Ki67+) was higher in the autistic individual of the youngest age-matched pair. These preliminary data suggesting that HS may be reduced in young to mature autistic individuals are in agreement with previous findings from the BTBR T+tf/J mouse, an animal model of autism; from mice with genetic modifications reducing HS; and with genetic variants in HS-related genes in autism. They suggest that aberrant extracellular matrix glycosaminoglycan function localized to the subventricular zone of the lateral ventricles may be a biomarker for autism, and potentially involved in the etiology of the disorder.
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Affiliation(s)
- Brandon L Pearson
- Department of Psychology, University of Hawaii, 2530 Dole Street, Honolulu, HI 96822, USA
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Meyza KZ, Defensor EB, Jensen AL, Corley MJ, Pearson BL, Pobbe RLH, Bolivar VJ, Blanchard DC, Blanchard RJ. The BTBR T+ tf/J mouse model for autism spectrum disorders-in search of biomarkers. Behav Brain Res 2012; 251:25-34. [PMID: 22958973 DOI: 10.1016/j.bbr.2012.07.021] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 07/11/2012] [Accepted: 07/12/2012] [Indexed: 12/28/2022]
Abstract
Autism spectrum disorders (ASD) form a common group of neurodevelopmental disorders appearing to be under polygenic control, but also strongly influenced by multiple environmental factors. The brain mechanisms responsible for ASD are not understood and animal models paralleling related emotional and cognitive impairments may prove helpful in unraveling them. BTBR T+ tf/J (BTBR) mice display behaviors consistent with the three diagnostic categories for ASD. They show impaired social interaction and communication as well as increased repetitive behaviors. This review covers much of the data available to date on BTBR behavior, neuroanatomy and physiology in search for candidate biomarkers, which could both serve as diagnostic tools and help to design effective treatments for the behavioral symptoms of ASD.
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Affiliation(s)
- Ksenia Z Meyza
- Pacific Biosciences Research Center, University of Hawaii, 1993 East-west Road, Honolulu, HI 96822, USA
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Corley MJ, Meyza KZ, Blanchard DC, Blanchard RJ. Reduced sulfate plasma concentrations in the BTBR T+tf/J mouse model of autism. Physiol Behav 2012; 107:663-5. [PMID: 22538115 DOI: 10.1016/j.physbeh.2012.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 04/10/2012] [Accepted: 04/10/2012] [Indexed: 12/13/2022]
Abstract
Clinical studies have shown that children diagnosed with autism show abnormal sulfate chemistry, which is critical for cellular and metabolic processes. To determine if the inbred BTBR T+tf/J mouse shows autism-relevant aberrations in sulfate chemistry, the present study examined plasma sulfate concentrations in BTBR T+tf/J, inbred C57BL/6J, and outbred CD-1 mice. Results showed that the BTBR T+tf/J mouse exhibits significantly lower plasma sulfate concentrations in comparison to both C57BL/6J and CD-1 mice. These results suggest that the BTBR mouse shows autism-relevant abnormalities in sulfate chemistry and may serve additional utility in examining the role of sulfate and sulfate-dependent systems in relation to autism-relevant behavioral aberrations.
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Affiliation(s)
- Michael J Corley
- Department of Psychology, University of Hawaii, Honolulu, HI, USA.
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