An atlas of immune cell exhaustion in HIV-infected individuals revealed by single-cell transcriptomics

ABSTRACT

Chronic infection with human immunodeficiency virus (HIV) can cause progressive loss of immune cell function, or exhaustion, which impairs control of virus replication. However, little is known about the development and maintenance, as well as heterogeneity of immune cell exhaustion. Here, we investigated the effects of HIV infection on immune cell exhaustion at the transcriptomic level by analyzing single-cell RNA sequencing of peripheral blood mononuclear cells from four healthy subjects (37,847 cells) and six HIV-infected donors (28,610 cells). We identified nine immune cell clusters and eight T cell subclusters, and three of these (exhausted CD4⁺ and CD8⁺ T cells and interferon-responsive CD8⁺ T cells) were detected only in samples from HIV-infected donors. An inhibitory receptor KLRG1 was identified in a HIV-1 specific exhausted CD8⁺ T cell population expressing KLRG1, TIGIT, and T-bet^dimEomes^hi markers. Ex-vivo antibody blockade of KLRG1 restored the function of HIV-specific exhausted CD8⁺ T cells demonstrating the contribution of KLRG1⁺ population to T cell exhaustion and providing an immunotherapy target to treat HIV chronic infection. These data provide a comprehensive analysis of gene signatures associated with immune cell exhaustion during HIV infection, which could be useful in understanding exhaustion mechanisms and developing new cure therapies.

GRAPHICAL ABSTRACT

KEYWORDS:

• HIV-1
• single-cell RNA-seq
• T cell dysfunction
• immune exhaustion
• KLRG1
• NK cell impairment

Acknowledgments

S.W. and Q.Z. designed and performed the experiments, analyzed the data, and wrote the first manuscript draft; H.H. and K.A. analyzed the data; M.A.Y.K. contributed to obtaining the PBMCs, and data analysis and interpretation; and T.M.R. contributed to the experimental design, data analysis and interpretation, and manuscript writing. All authors contributed to manuscript writing and approved the final version. We thank Drs. Douglas Richman, Jonathan Karn, and Mario Stevenson for helpful discussions, Kristen Jepsen at the IGM Genomics Center for help with scRNA-seq, Celsa Spina of UCSD CFAR for flow analysis and members of the Rana lab for helpful discussions and advice. We also thank Dr. Song Chen for advice and help in sample preparation and data analysis. This work was supported in part by grants from the National Institutes of Health (DA039562, DA046171, DA049524). Access to retrospectively collected blood samples from HIV-1-infected donors was made possible by the University of California, San Diego Center for AIDS Research, an NIH-funded program (P30 AI036214), which is supported by the following NIH Institutes and Centers: NIAID, NCI, NIMH, NIDA, NICHD, NHLBI, NIA, NIGMS, and NIDDK.

Declaration of interest statement

T.M.R. is a founder of ViRx Pharmaceuticals and has an equity interest in the company. The terms of this arrangement have been reviewed and approved by the University of California San Diego in accordance with its conflict of interest policies.

Additional information

Funding

This work was supported by National Institute on Drug Abuse: [Grant Number DA039562,DA046171,DA049524].