Genomic profiling of HIV-1 integration in microglia links viral insertions to TAD organization

Abstract

HIV-1 persists in anatomically distinct cellular and tissue reservoirs as a stably integrated provirus that is a major barrier to HIV-1 cure. Proviral insertions are largely characterized in blood cells, while HIV-1 integration patterns remain unexplored in microglia, the major brain reservoir. Here, we employ genomics approaches to obtain the first HIV-1 integration site (IS) profiling in microglia and perform in-depth analysis of transcriptome, specific histone signatures and chromatin accessibility on different genomic scales. We show that HIV-1 follows genic insertion patterns into introns of actively transcribed genes, characteristic of blood reservoirs. HIV-1 insertional hotspot analysis by non-negative matrix factorization (NMF)-based approach clusters IS signatures with genic- and super-enhancers. Chromatin accessibility transcription factor (TF) footprints reveal that increased CTCF binding marks latently infected microglia compared to productively infected one. We identify CTCF-enriched topologically associated domain (TAD) borders with signatures of active chromatin as a neighborhood for HIV-1 integration in microglia and CD4+ T cells. Our findings further strengthen the notion that HIV-1 follows the patterns of host cell genome organization to integrate and to establish the silent proviral state and reveal that these principles are largely conserved in different anatomical latent reservoirs.

HIV integration in the human brain is linked to microglial activation and 3D genome remodeling

“…S7C-D). A recent work published the first in vitro microglial IS in the C20 microglial cell line and did not observe the same differences in IS patterns as we observed here compared to T-cells (43). However, based on published RNA-seq data, expression of LEDGF and CPSF6 are significantly higher in C20 cells compared to primary microglia (Fig.…”

“…Here, we built an integrative dataset from 77 sequencing files, including snRNA-seq, Hi-C, IS-seq, and ChIP-seq, providing a critically needed neurogenomics resource from postmortem brain of infected donors and controls. By providing genome-scale maps for viral integration sites and their disease-associated chromosomal conformation and single nuclei expression states, our resource greatly extends previous, tissue-homogenate based gene expression profiling and integration site analyses in cell culture models ( 43 ).…”

Dynamics of Viral and Host 3D Genome Structure upon Infection

“…Recent Hi-C analysis of HIV-1-infected cells revealed that genes recurrently targeted by the virus are proximal to super-enhancer genomic elements that tend to cluster spatially in the nuclei of CD4 + T cells [ 80 ]. Because HIV-1 can invade the central nervous system, productively infecting macrophages and microglia therein, the HIV-1 integration pattern in relation to the 3D genomic architecture of microglia cells was also investigated by Hi-C [ 81 ]. The results further strengthened the notion that HIV-1 integration preferentially occurs at active, open chromatin, including CTCF-bound regions with active histone marks positioned proximal to TAD boundaries.…”