Phenotypic signatures of immune selection in HIV-1 reservoir cells

Abstract

Human immunodeficiency virus 1 (HIV-1) reservoir cells persist lifelong despite antiretroviral treatment1,2 but may be vulnerable to host immune responses that could be exploited in strategies to cure HIV-1. Here we used a single-cell, next-generation sequencing approach for the direct ex vivo phenotypic profiling of individual HIV-1-infected memory CD4+ T cells from peripheral blood and lymph nodes of people living with HIV-1 and receiving antiretroviral treatment for approximately 10 years. We demonstrate that in peripheral blood, cells harbouring genome-intact proviruses and large clones of virally infected cells frequently express ensemble signatures of surface markers conferring increased resistance to immune-mediated killing by cytotoxic T and natural killer cells, paired with elevated levels of expression of immune checkpoint markers likely to limit proviral gene transcription; this phenotypic profile might reduce HIV-1 reservoir cell exposure to and killing by cellular host immune responses. Viral reservoir cells harbouring intact HIV-1 from lymph nodes exhibited a phenotypic signature primarily characterized by upregulation of surface markers promoting cell survival, including CD44, CD28, CD127 and the IL-21 receptor. Together, these results suggest compartmentalized phenotypic signatures of immune selection in HIV-1 reservoir cells, implying that only small subsets of infected cells with optimal adaptation to their anatomical immune microenvironment are able to survive during long-term antiretroviral treatment. The identification of phenotypic markers distinguishing viral reservoir cells may inform future approaches for strategies to cure and eradicate HIV-1.

The Dynamic Linkage between Provirus Integration Sites and the Host Functional Genome Property Alongside HIV-1 Infections Associated with Antiretroviral Therapy

“…Conversely, intact provirus-targeted genes were not frequently associated with the signatures of proinflammatory soluble factors (2 genes in pretreatment HIV-1-infected individuals, 1 gene in patients subjected to a short period of ART, 4 genes in patients subjected to a long period of ART, and 4 genes in elite controllers) ( Tables S22–S25 ). A more recent study published by Sun et al (2023) [ 25 ] continued to strengthen this “immune selection hypothesis” proposed by Einkauf and colleagues (the term “immune selection hypothesis” was mentioned in Peer Review File available at (accessed on 25 January 2023)). They observed that HIV-1 reservoir cells harboring intact proviruses frequently express ensemble phenotypic signatures of surface markers (including the checkpoint marker PD-1) that confer resistance to immune-mediated killing by CD8+ T cells and NK cells [ 25 ].…”

“…A more recent study published by Sun et al (2023) [ 25 ] continued to strengthen this “immune selection hypothesis” proposed by Einkauf and colleagues (the term “immune selection hypothesis” was mentioned in Peer Review File available at (accessed on 25 January 2023)). They observed that HIV-1 reservoir cells harboring intact proviruses frequently express ensemble phenotypic signatures of surface markers (including the checkpoint marker PD-1) that confer resistance to immune-mediated killing by CD8+ T cells and NK cells [ 25 ]. In this study, two unique immunologic signatures, GSE26495_NAIVE_VS_PD1LOW_CD8_TCELL_DN [ 26 ] and GSE24026_PD1_LIGATION_VS_CTRL_IN_ACT_TCELL_LINE_DN [ 27 ], enriched in HIV-1-infected individuals subjected to a long period of ART were observed to be associated with PD-1 ( Table S3 ).…”

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

“…Sun et al [55 ▪▪ ] in the Lichterfeld group applied a commercially available platform (Mission Bio) to profile near full-length HIV-1 DNA and surface protein expression at the single cell level (PheP-seq). Briefly, cells were stained with DNA-tagged surface protein antibodies and partitioned into single cells.…”

“…Drop-out of transcripts or stochasticity of expression should be considered [6]. Of note, identification of the short reads of HIV-1 DNA or RNA cannot infer genome intactness, unless targeted DNA amplification [55 ▪▪ ] or long-read RNA sequencing [97 ▪▪ ] identifies all genomic elements [both cis-regulatory element (such as ψ packaging signal) and protein coding regions] to be intact, without hypermutation, internal deletion, or point mutations [6]. Of note, the HIV-1 5’ leader sequence and packaging signal contain secondary RNA elements that are essential for HIV-1 replication competence, such as primer binding site (PBS), dimerization initiation site (DIS), major splice donor (MSD), and packaging stem loops [98,99].…”

Viral and Host Mediators of Non-Suppressible HIV-1 Viremia

“…28 The provirus landscape morphs over time in response to ART and the host immune response to a quasi-homeostatic state marked by cell loss and clonal expansion. [29][30][31][32][33][34][35] A key goal of this study was to assess aspects of host proviruses that contributed to NSV. Longitudinal single-genome sequencing (SGS) of near-full length proviruses and plasma HIV pol and env RNA was performed.…”