Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapy
Kevin B. Einkauf, … , Xu G. Yu, Mathias Lichterfeld
Kevin B. Einkauf, … , Xu G. Yu, Mathias Lichterfeld
Published July 29, 2019; First published January 28, 2019
Citation Information: J Clin Invest. 2019;129(3):988-998. https://doi.org/10.1172/JCI124291.
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Categories: Research Article AIDS/HIV Infectious disease

Intact HIV-1 proviruses accumulate at distinct chromosomal positions during prolonged antiretroviral therapy

Abstract

Chromosomal integration of genome-intact HIV-1 sequences into the host genome creates a reservoir of virally infected cells that persists throughout life, necessitating indefinite antiretroviral suppression therapy. During effective antiviral treatment, the majority of these proviruses remain transcriptionally silent, but mechanisms responsible for viral latency are insufficiently clear. Here, we used matched integration site and proviral sequencing (MIP-Seq), an experimental approach involving multiple displacement amplification of individual proviral species, followed by near-full-length HIV-1 next-generation sequencing and corresponding chromosomal integration site analysis to selectively map the chromosomal positions of intact and defective proviruses in 3 HIV-1–infected individuals undergoing long-term antiretroviral therapy. Simultaneously, chromatin accessibility and gene expression in autologous CD4+ T cells were analyzed by assays for transposase-accessible chromatin using sequencing (ATAC-Seq) and RNA-Seq. We observed that in comparison to proviruses with defective sequences, intact HIV-1 proviruses were enriched for non-genic chromosomal positions and more frequently showed an opposite orientation relative to host genes. In addition, intact HIV-1 proviruses were preferentially integrated in either relative proximity to or increased distance from active transcriptional start sites and to accessible chromatin regions. These studies strongly suggest selection of intact proviruses with features of deeper viral latency during prolonged antiretroviral therapy, and may be informative for targeting the genome-intact viral reservoir.

Authors

Kevin B. Einkauf, Guinevere Q. Lee, Ce Gao, Radwa Sharaf, Xiaoming Sun, Stephane Hua, Samantha M.Y. Chen, Chenyang Jiang, Xiaodong Lian, Fatema Z. Chowdhury, Eric S. Rosenberg, Tae-Wook Chun, Jonathan Z. Li, Xu G. Yu, Mathias Lichterfeld

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Figure 4

Distinct chromosomal locations of intact HIV-1 proviruses in study participant 1.

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Distinct chromosomal locations of intact HIV-1 proviruses in study parti...
(A and B) Circos plots highlighting ATAC-Seq and RNA-Seq reads in proximity (ATAC-Seq: ±8000 bp; RNA-Seq: ±5000 bp) to integration sites of intact and defective HIV-1 proviruses. (C) Combined individual-value/box-and-whisker plots indicating the chromosomal distance between HIV-1 integration sites and the most proximal TSS listed in Ensembl v86 (databank), or identified through analysis of expressed RNA species located within the boundaries of the host gene, using autologous RNA-Seq data from the indicated cell populations and limiting the analysis to proviruses integrated in expressed genes. (D) Combined individual-value/box-and-whisker plots showing the chromosomal distance between integration sites and the center of the most proximal ATAC-Seq peaks in indicated CD4+ T cell populations. (E) Gene expression intensity of host genes harboring intact or defective proviral integration sites, normalized to the chromosomal distance between integration sites and the most proximal TSSs determined using autologous RNA-Seq data as described in C. In C–E, boxes and whiskers represent median, 25% and 75% percentiles, and minimum/maximum levels. Significance was calculated using 2-tailed Mann Whitney U tests; nominal P values are reported. (F) Distance between each integration site and most proximal TSS, plotted against corresponding distance between each integration site and the center of the nearest ATAC-Seq peak. Spearman’s correlation coefficients are shown for each cell population. In A–F, clonal sequences were shown/counted only once. EM, effector memory; CM, central memory.