Antigen specificities and proviral integration sites differ in HIV-infected cells by timing of antiretroviral treatment initiation
Jaimy Joy, … , Helen Horton, Lisa M. Frenkel
Jaimy Joy, … , Helen Horton, Lisa M. Frenkel
Published June 4, 2024
Citation Information: J Clin Invest. 2024;134(14):e159569. https://doi.org/10.1172/JCI159569.
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Research Article AIDS/HIV Virology

Antigen specificities and proviral integration sites differ in HIV-infected cells by timing of antiretroviral treatment initiation

Abstract

Despite effective antiretroviral therapy (ART), persons living with HIV harbor reservoirs of persistently infected CD4+ cells, which constitute a barrier to cure. Initiation of ART during acute infection reduces the size of the HIV reservoir, and we hypothesized that in addition, it would favor integration of proviruses in HIV-specific CD4+ T cells, while initiation of ART during chronic HIV infection would favor relatively more proviruses in herpesvirus-specific cells. We further hypothesized that proviruses in acute ART initiators would be integrated into antiviral genes, whereas integration sites (ISs) in chronic ART initiators would favor genes associated with cell proliferation and exhaustion. We found that the HIV DNA distribution across HIV-specific versus herpesvirus-specific CD4+ T cells was as hypothesized. HIV ISs in acute ART initiators were significantly enriched in gene sets controlling lipid metabolism and HIF-1α–mediated hypoxia, both metabolic pathways active in early HIV infection. Persistence of these infected cells during prolonged ART suggests a survival advantage. ISs in chronic ART initiators were enriched in a gene set controlling EZH2 histone methylation, and methylation has been associated with diminished long terminal repeat transcription. These differences that we found in antigen specificities and IS distributions within HIV-infected cells might be leveraged in designing cure strategies tailored to the timing of ART initiation.

Authors

Jaimy Joy, Ana Gervassi, Lennie Chen, Brent Kirshenbaum, Sheila Styrchak, Daisy Ko, Sherry McLaughlin, Danica Shao, Ewelina Kosmider, Paul T. Edlefsen, Janine Maenza, Ann C. Collier, James I. Mullins, Helen Horton, Lisa M. Frenkel

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Figure 1

Peptide antigen stimulation and CD3+CD8–CD137+ cell expansion in vitro.

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Peptide antigen stimulation and CD3+CD8–CD137+ cell expansion in vitro. ...
(A) Experimental schema. CD8+ T cell–depleted PBMCs were incubated with anti-CD3/anti-CD28 Dynabeads (positive control), media alone (negative control), or peptide antigens derived from HIV, CMV, EBV, HSV1, or HSV2 (see Table 2) for 10 days, all with efavirenz, raltegravir, and IL-7 (ART). On day 3, IL-2 was added to the cultures. On days 5, 7, and 10, the media, ART, and growth factors were replenished. On day 10, cells were restimulated with peptide antigens to upregulate activation markers for cell sorting. Following 24 hours of restimulation, cells were harvested for intracellular cytokine staining and flow cytometry to assess reactivity to each antigen, i.e., “antigen discovery.” Cells were stained for CD3, CD8, and CD137 for cell sorting. CD8+ T cell–depleted PBMCs were plated on day 0, cultured as shown in A, and enumerated on day 11. (B) Representative flow cytometry plots for cell sorting based on CD3+CD8–CD137+ cell surface expression. (C) Fold change of total cells on day 11 versus day 0 and (D) fold change of CD3+CD8–CD137+ cells on day 11 versus day 0 are shown for individuals who initiated ART-chronic-HIV in left panels and for individuals who initiated ART-chronic-HIV in right panels. Horizontal lines indicate median of data points.