HSV-2 triggers upregulation of MALAT1 in CD4+ T cells and promotes HIV latency reversal
Carl A. Pierce, … , Kevan C. Herold, Betsy C. Herold
Carl A. Pierce, … , Kevan C. Herold, Betsy C. Herold
Published April 20, 2023
Citation Information: J Clin Invest. 2023;133(11):e164317. https://doi.org/10.1172/JCI164317.
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Research Article AIDS/HIV Virology

HSV-2 triggers upregulation of MALAT1 in CD4+ T cells and promotes HIV latency reversal

Abstract

Herpes simplex virus type 2 (HSV-2) coinfection is associated with increased HIV-1 viral loads and expanded tissue reservoirs, but the mechanisms are not well defined. HSV-2 recurrences result in an influx of activated CD4+ T cells to sites of viral replication and an increase in activated CD4+ T cells in peripheral blood. We hypothesized that HSV-2 induces changes in these cells that facilitate HIV-1 reactivation and replication and tested this hypothesis in human CD4+ T cells and 2D10 cells, a model of HIV-1 latency. HSV-2 promoted latency reversal in HSV-2–infected and bystander 2D10 cells. Bulk and single-cell RNA-Seq studies of activated primary human CD4+ T cells identified decreased expression of HIV-1 restriction factors and increased expression of transcripts including MALAT1 that could drive HIV replication in both the HSV-2–infected and bystander cells. Transfection of 2D10 cells with VP16, an HSV-2 protein that regulates transcription, significantly upregulated MALAT1 expression, decreased trimethylation of lysine 27 on histone H3 protein, and triggered HIV latency reversal. Knockout of MALAT1 from 2D10 cells abrogated the response to VP16 and reduced the response to HSV-2 infection. These results demonstrate that HSV-2 contributes to HIV-1 reactivation through diverse mechanisms, including upregulation of MALAT1 to release epigenetic silencing.

Authors

Carl A. Pierce, Lip Nam Loh, Holly R. Steach, Natalia Cheshenko, Paula Preston-Hurlburt, Fengrui Zhang, Stephanie Stransky, Leah Kravets, Simone Sidoli, William Philbrick, Michel Nassar, Smita Krishnaswamy, Kevan C. Herold, Betsy C. Herold

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Figure 5

Single-cell RNA-Seq identifies features of HSV-2–infected CD4+ T cells.

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Single-cell RNA-Seq identifies features of HSV-2–infected CD4+ T cells. ...
CD4+ T cells isolated from tonsil of an HIV– donor were stimulated with anti-CD3/CD28 cross-linking and then infected with HSV-2(SD90) (MOI = 1) and subjected to single-cell RNA-Seq at 0 (mock), 6, and 24 hpi. (A) Scatterplots show normalized and denoised gene expression (see Methods) of cells within samples collected at different time points. Data points are colored based on upstream gating, where gray represents BCL6– cells and purple, green, and red represent BCL6+ cells from mock, 6 hpi, and 24 hpi, respectively. (B) Pseudotime line plots for all cells showing genes associated with infection (UL15) and Tfh phenotype (BCL6, ICOS, SELPLG, PDCD1, CXCR5). (C) Multiscale PHATE identifies 3 clusters of cells from all time points. Colors denote cluster identity, and the size of a dot in the embedding is proportional to the number of cells represented. Violin plots show expression of select genes organized by Multiscale PHATE cluster. Black horizontal lines represent cluster expression means, and individual points represent single cells. (D) Heatmaps represent expression of select genes involved in response to HSV-2 infection (left) and cell identity (right). Color scheme is based on z score distribution. (E) Mutual information (DREMI) quantified association between expression of UL15 and select genes MALAT1, APOBEC3G, EIF4A2, and DDX5 visualized with DREVI. (F) Histogram shows z score distribution of mutual information between individual genes and UL15 for all measured transcripts, calculated with DREMI. Dashed vertical lines show mean (black) and 95% confidence (red). HSV-2 infection–related genes with z scores above 95% confidence (*P ≥ 0.05) are colored in red.