HIV silencing and cell survival signatures in infected T cell reservoirs

Abstract

Rare CD4 T cells that contain HIV under antiretroviral therapy represent an important barrier to HIV cure1–3, but the infeasibility of isolating and characterizing these cells in their natural state has led to uncertainty about whether they possess distinctive attributes that HIV cure-directed therapies might exploit. Here we address this challenge using a microfluidic technology that isolates the transcriptomes of HIV-infected cells based solely on the detection of HIV DNA. HIV-DNA+ memory CD4 T cells in the blood from people receiving antiretroviral therapy showed inhibition of six transcriptomic pathways, including death receptor signalling, necroptosis signalling and antiproliferative Gα12/13 signalling. Moreover, two groups of genes identified by network co-expression analysis were significantly associated with HIV-DNA+ cells. These genes (n = 145) accounted for just 0.81% of the measured transcriptome and included negative regulators of HIV transcription that were higher in HIV-DNA+ cells, positive regulators of HIV transcription that were lower in HIV-DNA+ cells, and other genes involved in RNA processing, negative regulation of mRNA translation, and regulation of cell state and fate. These findings reveal that HIV-infected memory CD4 T cells under antiretroviral therapy are a distinctive population with host gene expression patterns that favour HIV silencing, cell survival and cell proliferation, with important implications for the development of HIV cure strategies.

Targeting HIV persistence in the tissue

“…Identifying the cellular hallmarks of the HIV reservoir is imperative for developing new strategies to achieve reservoir elimination. In human peripheral blood, recent studies show that HIV-infected memory CD4 + T cells contain gene expression patterns that promote cell survival, proliferation, and HIV silencing [22 ▪ ], and these cells express higher levels of co-inhibitory receptors and ligands compared to uninfected cells [23 ▪ ]. Additionally, multiple cellular subsets besides well established CD4 + T CM , effector memory T cells (T EM ) [24] and circulating follicular helper T cells (Tfh) [25], such as mucosal associated invariant T cells and Th2, may harbor integrated proviral DNA under ART [26 ▪ ].…”

“…Additionally, multiple cellular subsets besides well established CD4 + T CM , effector memory T cells (T EM ) [24] and circulating follicular helper T cells (Tfh) [25], such as mucosal associated invariant T cells and Th2, may harbor integrated proviral DNA under ART [26 ▪ ]. Together with potential resistance of CD4 + T cell reservoir cells to immune-mediated killing [22 ▪ ,27], efforts to eliminate the reservoir may thus be further complicated by cellular and epigenetic heterogeneity of the reservoir between and within individuals [26 ▪ ].…”

Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels

“…Clark et al [54 ▪▪ ] in the Abate group and the Boritz group and designed a PCR-activated sorting microfluidic machinery to sort out HIV-1 DNA+ cells for bulk transcriptome profiling (FIND-seq) [54 ▪▪ ]. Briefly, Clark and Abate built a microfluidic device to encapsulate CD4 + T cells with RT-PCR reagents in hydrogel compartments.…”

Development and future of droplet microfluidics

“…8 Confinement of individual targets within the droplets and independent processing of each of them allow high-precision analyses. 9,10 In the past two decades, there have been significant advances in the design and fabrication of microfluidic devices, which has led to production of ever more sophisticated droplets, and enabled precise control and analysis of their contents. 11 Droplet microfluidics is extensively used to produce new materials: droplets serve as advanced templates to synthesize functional materials that enable high-efficiency encapsulation and controlled release of active ingredients.…”

“…8 Confinement of individual targets within the droplets and independent processing of each of them allow high-precision analyses. 9,10…”