Single-Cell Sequencing Facilitates Elucidation of HIV Immunopathogenesis: A Review of Current Literature.

Silvere D. Zaongo,Yaokai Chen,Vijay Harypursat

doi:10.3389/fimmu.2022.828860

Abstract

Knowledge gaps remain in the understanding of HIV disease establishment and progression. Scientists continue to strive in their endeavor to elucidate the precise underlying immunopathogenic mechanisms of HIV-related disease, in order to identify possible preventive and therapeutic targets. A useful tool in the quest to reveal some of the enigmas related to HIV infection and disease is the single-cell sequencing (scRNA-seq) technique. With its proven capacity to elucidate critical processes in cell formation and differentiation, to decipher critical hematopoietic pathways, and to understand the regulatory gene networks that predict immune function, scRNA-seq is further considered to be a potentially useful tool to explore HIV immunopathogenesis. In this article, we provide an overview of single-cell sequencing platforms, before delving into research findings gleaned from the use of single cell sequencing in HIV research, as published in recent literature. Finally, we describe two important avenues of research that we believe should be further investigated using the single-cell sequencing technique.

Highlights

A broader and deeper knowledge of important immune responses during human immunodeficiency virus (HIV) infection in both the acute and chronic phases of the HIV disease process is likely to assist in the identification of future preventive and therapeutic targets for HIV infection [1]
WTA method; template switching WTA method; in vitro transcription WTA method; poly(A) tagging 5′-end RNA-seq Total RNA-seq Microdroplet-based method Microwell-based method WGA method; isothermal amplification WGA method; PCR-based WGA method; hybrid Whole-genome BS-seq RRBS 5hmC sequencing ATAC-seq ChIP-seq; microdroplet-based Ab-Mnase Ab + protein A-Tn5 transposase Hi-C MDA/PicoPlex (WGA), SMART-seq2 (WTA) No physical separation of DNA and RNA Based on scBS-seq and G&T-seq Based on DamID and cell expression by linear amplification and sequencing (CEL-seq) Based on scATAC-seq and TCR-seq Tn5-DNA/mRNA captured by beads Separation of nucleus and cytoplasm Protein detected by barcode-conjugated antibodies Protein detected by barcode-conjugated antibodies
Single cell RNA sequencing has greatly improved our understanding of HIV immunopathogenesis, especially with respect to its life cycle, the derived-onset of new cell subsets with diverse and/or particular gene signatures, the infected-cell exhaustion profile, and reservoir cell heterogeneity, to list a few

Summary

Introduction

A broader and deeper knowledge of important immune responses during HIV infection in both the acute and chronic phases of the HIV disease process is likely to assist in the identification of future preventive and therapeutic targets for HIV infection [1]. Individual cellular dynamics and cell–cell cooperation in developing and coordinating human immune responses are currently insufficiently understood. In this regard, single-cell sequencing represents an excellent alternative to study these processes, as it has evolved into a valuable tool for the understanding of complex multicellular processes in health and disease [2, 3], as well as to expose testable potential therapeutic targets [4]. ScRNA-seq is commonly used in immunological studies seeking to describe essential processes in cell formation and Explore HIV Immunopathogenesis with scRNA-seq differentiation [9, 10], to decipher critical hematopoietic pathways [11,12,13], and to understand the gene regulatory networks that predict immune function [14,15,16]. We discuss two critical areas of investigation that we believe are worth exploring by utilizing the single-cell sequencing approach

Methods

Results

Conclusion