Integration features of intact latent HIV-1 in CD4+ T cell clones contribute to viral persistence
Open Access
- 12 October 2021
- journal article
- research article
- Published by Rockefeller University Press in The Journal of Experimental Medicine
- Vol. 218 (12)
- https://doi.org/10.1084/jem.20211427
Abstract
Latent intact HIV-1 proviruses persist in a small subset of long-lived CD4+ T cells that can undergo clonal expansion in vivo. Expanded clones of CD4+ T cells dominate latent reservoirs in individuals on long-term antiretroviral therapy (ART) and represent a major barrier to HIV-1 cure. To determine how integration landscape might contribute to latency, we analyzed integration sites of near full length HIV-1 genomes from individuals on long-term ART, focusing on individuals whose reservoirs are highly clonal. We find that intact proviruses in expanded CD4+ T cell clones are preferentially integrated within Krüppel-associated box (KRAB) domain–containing zinc finger (ZNF) genes. ZNF genes are associated with heterochromatin in memory CD4+ T cells; nevertheless, they are expressed in these cells under steady-state conditions. In contrast to genes carrying unique integrations, ZNF genes carrying clonal intact integrations are down-regulated upon cellular activation. Together, the data suggest selected genomic sites, including ZNF genes, can be especially permissive for maintaining HIV-1 latency during memory CD4+ T cell expansion.Keywords
Funding Information
- National Institute of Allergy and Infectious Diseases
- National Institutes of Health (UM1AI126611, 1UM1 AI100663, R01AI129795)
- Bill and Melinda Gates Foundation (OPP1092074, OPP1124068)
- Einstein–Rockefeller–City University of New York Center for AIDS Research (1P30AI124414-01A1)
- BEAT-HIV Delaney (UM1 AI126620)
- Robertson Foundation
- Robert S. Wennett Post-Doctoral Fellowship
- National Center for Advancing Translational Sciences
- National Institutes of Health (UL1 TR001866)
- Shapiro-Silverberg Fund for the Advancement of Translational Research
- National Institutes of Health (UM1AI164565)
- Howard Hughes Medical Institute
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