ArticleMolecular cell2022
HIV integration in the human brain is linked to microglial activation and 3D genome remodeling.
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Article in Molecular cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31citing papers in PubMed
2.2field-weighted citation impact, top 10% of its field
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Who cites it
31 citing papers in PubMed, 35 citations in OpenAlex.
- Implications of HIV persistence and pathogenesis in microglia.Current opinion in HIV and AIDS · 2026Review
- The brain as an HIV reservoir: Recent findings using autopsy tissues from people with HIV.PLoS pathogens · 2026Review
- Smoldering in the sanctuary: HIV-associated brain injury in the ART era.The Journal of clinical investigation · 2026Review
- Microglial reactivity and nodule formation are associated with Synaptodendritic damage in the brains of people with HIV-1.Brain pathology (Zurich, Switzerland) · 2026Article
- Opioid-induced transcriptional reprogramming of cerebrospinal fluid immune cells is associated with neuroinflammatory signaling in antiretroviral treated SIV-infected rhesus macaques.Journal of neuroinflammation · 2026Article
- HIV gp120 induces TREM1 expression through TLR-PGE₂ signalling in human monocyte-derived microglia.Journal of neuroinflammation · 2026Article
- Cell-type specific impact of opioid use disorder and HIV on the human forebrain and cerebellum.bioRxiv : the preprint server for biology · 2026Article
- Opioid-induced transcriptional reprogramming of cerebrospinal fluid immune cells drives neuroinflammation in SIV-infected rhesus macaques.Research square · 2026Article
- NF-κB-dependent and independent inflammatory responses during acute HIV-1 infection in a model of human microglia.Frontiers in immunology · 2026Article
- Development and validation of HIV SMRTcap for the characterization of HIV-1 reservoirs across tissues and subtypes.PLoS pathogens · 2026Article
- Chronic Neuroplasticity Changes Following Neurotropic Viral Infection: Mechanisms and Implications.Cellular and molecular neurobiology · 2025Review
- Transcriptional impacts of substance use disorder and HIV on human ventral midbrain neurons and microglia.Nature communications · 2025Article
- Review
- Neurotropic Viruses as Acute and Insidious Drivers of Aging.Biomolecules · 2025Review
- Impact of chromatin on HIV-1 latency: a multi-dimensional perspective.Epigenetics & chromatin · 2025Review
- Multi-omic Characterization of HIV Effects at Single Cell Level across Human Brain Regions.bioRxiv : the preprint server for biology · 2025Article
- Transformation of brain myeloid cell populations by SIV in rhesus macaques revealed by multiomics.Communications biology · 2025Article
- The single-cell opioid responses in the context of HIV (SCORCH) consortium.Molecular psychiatry · 2024Article
- Gene expression and chromatin conformation of microglia in virally suppressed people with HIV.Life science alliance · 2024Article
- Transformation of brain myeloid cell populations by SIV in rhesus macaques revealed by multiomics.Research square · 2024Article
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Authors and funding
15 authors at 3 institutions in 1 country.
Amara L Plaza-JenningsDepartment of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Aditi ValadaDepartment of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Callan O'SheaDepartment of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Marina IskhakovaDepartment of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Benxia HuUNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
Behnam JavidfarDepartment of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Gabriella Ben HuttaDepartment of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Tova Y LambertDepartment of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Jacinta MurrayDepartment of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Bibi KassimDepartment of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Sandhya ChandrasekaranDepartment of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Benjamin K ChenDivision of Infectious Diseases, Department of Medicine, Immunology Institute, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
Susan MorgelloDepartment of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neurology, 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. Electronic address: susan.morgello@mssm.edu.
Hyejung WonUNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA. Electronic address: hyejung_won@med.unc.edu.
Schahram AkbarianDepartment of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA. Electronic address: schahram.akbarian@mssm.edu.
Allen Institute for Brain Science · USIcahn School of Medicine at Mount Sinai · USUniversity of North Carolina at Chapel Hill · US
Funding
The Manhattan HIV Brain BankU24MH100931 · NIMH · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI MORGELLO, SUSAN · 2013 to 2023
$14.0MMount Sinai Medical Scientist Training ProgramT32GM146636 · NIGMS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Talia H Swartz · 2022 to 2026
$6.8MSingle Chromatin Fiber Sequencing and Longitudinal Epigenomic Profiling in HIV+ Brain Cells Exposed to Narcotic and StimulantDP1DA056018 · NIDA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Schahram Akbarian · 2022 to 2026
$5.9MSingle nuclei transcriptome profiling in addiction circuitry of the HIV+ brainU01DA053600 · NIDA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI AKBARIAN, SCHAHRAM, MORGELLO, SUSAN · 2021 to 2025
$4.3MModeling HIV Microglia-Associated Infection and Inflammation in a Chimeric Mouse BrainR01DA054526 · NIDA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI AKBARIAN, SCHAHRAM, CHEN, BENJAMIN K · 2021 to 2025
$3.7MIdentifying Alzheimer’s Disease Causal Variants and Target Genes Using iPSC-derived MicrogliaR01AG066871 · NIA · UNIV OF NORTH CAROLINA CHAPEL HILL · PI COHEN, TODD JONATHAN, PHANSTIEL, DOUGLAS H. · 2020 to 2024
$3.7MMotor Dysfunction in cART-era HIV: Neural Circuitry and PathogenesisR01NS108801 · NINDS · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI MORGELLO, SUSAN · 2018 to 2022
$3.5MResearch Training in the Neuroscience of AgingT32AG049688 · NIA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI Joseph Michael Castellano, PATRICK R HOF · 2015 to 2026
$3.0MDeciphering Cell-type Specific Regulatory Landscape in Human BrainDP2MH122403 · NIMH · UNIV OF NORTH CAROLINA CHAPEL HILL · PI WON, HYEJUNG · 2019 to 2019
$2.3MCell migration and virological synapse formation in parenteral HIV transmissionR01DA041765 · NIDA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI CHEN, BENJAMIN K · 2016 to 2020
$2.1MCELL - AND CIRCUIT - SPECIFIC EXPLORATION OF HIV NEUROGENOMICS IN CONTEXT OF OPIATE AND COCAINE ABUSER61DA048207 · NIDA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI AKBARIAN, SCHAHRAM, MORGELLO, SUSAN · 2019 to 2021
$1.8MCELL - AND CIRCUIT - SPECIFIC EXPLORATION OF HIV NEUROGENOMICS IN CONTEXT OF OPIATE AND COCAINE ABUSER33DA048207 · NIDA · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI AKBARIAN, SCHAHRAM, MORGELLO, SUSAN · 2023 to 2024
$1.3MNIA NIH HHS R01 AG066871NIA NIH HHS T32 AG049688NIDA NIH HHS DP1 DA056018NIDA NIH HHS R01 DA041765NIDA NIH HHS R01 DA054526NIDA NIH HHS R21 DA051921NIDA NIH HHS R33 DA048207NIDA NIH HHS R61 DA048207NIDA NIH HHS U01 DA053600NIGMS NIH HHS T32 GM146636NIMH NIH HHS DP2 MH122403NIMH NIH HHS U24 MH100931NINDS NIH HHS R01 NS108801
Abstract
To explore genome organization and function in the HIV-infected brain, we applied single-nuclei transcriptomics, cell-type-specific chromosomal conformation mapping, and viral integration site sequencing (IS-seq) to frontal cortex from individuals with encephalitis (HIVE) and without (HIV+). Derepressive changes in 3D genomic compartment structures in HIVE microglia were linked to the transcriptional activation of interferon (IFN) signaling and cell migratory pathways, while transcriptional downregulation and repressive compartmentalization of neuronal health and signaling genes occurred in both HIVE and HIV+ microglia. IS-seq recovered 1,221 brain integration sites showing distinct genomic patterns compared with peripheral lymphocytes, with enrichment for sequences newly mobilized into a permissive chromatin environment after infection. Viral transcription occurred in a subset of highly activated microglia comprising 0.33% of all nuclei in HIVE brain. Our findings point to disrupted microglia-neuronal interactions in HIV and link retroviral integration to remodeling of the microglial 3D genome during infection.
Indexed as
HIV InfectionsMicrogliaBrainHumansMacrophage ActivationMacrophageschromosomal conformationsHi-CHIV encephalitishuman immunodeficiency virusinterferonmicrogliamicroglia-neuron interactionsretrovirussingle nuclei RNA-seqviral integration
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.