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Zaongo SD, Harypursat V, Chen Y. Single-Cell Sequencing Facilitates Elucidation of HIV Immunopathogenesis: A Review of Current Literature. Front Immunol 2022; 13:828860. [PMID: 35185920 PMCID: PMC8850777 DOI: 10.3389/fimmu.2022.828860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/18/2022] [Indexed: 12/18/2022] Open
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.
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Affiliation(s)
- Silvere D Zaongo
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Vijay Harypursat
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Yaokai Chen
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
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Liu R, Yeh YHJ, Varabyou A, Collora JA, Sherrill-Mix S, Talbot CC, Mehta S, Albrecht K, Hao H, Zhang H, Pollack RA, Beg SA, Calvi RM, Hu J, Durand CM, Ambinder RF, Hoh R, Deeks SG, Chiarella J, Spudich S, Douek DC, Bushman FD, Pertea M, Ho YC. Single-cell transcriptional landscapes reveal HIV-1-driven aberrant host gene transcription as a potential therapeutic target. Sci Transl Med 2021; 12:12/543/eaaz0802. [PMID: 32404504 DOI: 10.1126/scitranslmed.aaz0802] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 10/29/2019] [Accepted: 04/17/2020] [Indexed: 12/22/2022]
Abstract
Understanding HIV-1-host interactions can identify the cellular environment supporting HIV-1 reactivation and mechanisms of clonal expansion. We developed HIV-1 SortSeq to isolate rare HIV-1-infected cells from virally suppressed, HIV-1-infected individuals upon early latency reversal. Single-cell transcriptome analysis of HIV-1 SortSeq+ cells revealed enrichment of nonsense-mediated RNA decay and viral transcription pathways. HIV-1 SortSeq+ cells up-regulated cellular factors that can support HIV-1 transcription (IMPDH1 and JAK1) or promote cellular survival (IL2 and IKBKB). HIV-1-host RNA landscape analysis at the integration site revealed that HIV-1 drives high aberrant host gene transcription downstream, but not upstream, of the integration site through HIV-1-to-host aberrant splicing, in which HIV-1 RNA splices into the host RNA and aberrantly drives host RNA transcription. HIV-1-induced aberrant transcription was driven by the HIV-1 promoter as shown by CRISPR-dCas9-mediated HIV-1-specific activation and could be suppressed by CRISPR-dCas9-mediated inhibition of HIV-1 5' long terminal repeat. Overall, we identified cellular factors supporting HIV-1 reactivation and HIV-1-driven aberrant host gene transcription as potential therapeutic targets to disrupt HIV-1 persistence.
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Affiliation(s)
- Runxia Liu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Yang-Hui Jimmy Yeh
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Ales Varabyou
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jack A Collora
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Scott Sherrill-Mix
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - C Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Sameet Mehta
- Yale Center for Genome Analysis, Yale University, New Haven, CT 06519, USA
| | - Kristen Albrecht
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Haiping Hao
- Institute for Basic Biomedical Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Ross A Pollack
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Subul A Beg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rachela M Calvi
- Department of Neurology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Jianfei Hu
- Vaccine Research Center, National Institute of Health, Bethesda, MD 20892, USA
| | - Christine M Durand
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Richard F Ambinder
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, CA 94110, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, CA 94110, USA
| | - Jennifer Chiarella
- Department of Neurology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Serena Spudich
- Department of Neurology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Health, Bethesda, MD 20892, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mihaela Pertea
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.,Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Ya-Chi Ho
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519, USA.
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Abstract
Adult T-cell leukemia (ATL) is one of the most aggressive hematologic malignancies caused by human T-lymphotropic virus type 1 (HTLV-1) infection. The prognosis of ATL is extremely poor; however, effective strategies for diagnosis and treatment have not been established. To identify novel therapeutic targets and diagnostic markers for ATL, we employed focused proteomic profiling of the CD4(+)CD25(+)CCR4(+) T-cell subpopulation in which HTLV-1-infected cells were enriched. Comprehensive quantification of 14 064 peptides and subsequent 2-step statistical analysis using 29 cases (6 uninfected controls, 5 asymptomatic carriers, 9 HTLV-1-associated myelopathy/tropical spastic paraparesis patients, 9 ATL patients) identified 91 peptide determinants that statistically classified 4 clinical groups with an accuracy rate of 92.2% by cross-validation test. Among the identified 17 classifier proteins, α-II spectrin was drastically accumulated in infected T cells derived from ATL patients, whereas its digestive protease calpain-2 (CAN2) was significantly downregulated. Further cell cycle analysis and cell growth assay revealed that rescue of CAN2 activity by overexpressing constitutively active CAN2 (Δ(19)CAN2) could induce remarkable cell death on ATL cells accompanied by reduction of α-II spectrin. These results support that proteomic profiling of HTLV-1-infected T cells could provide potential diagnostic biomarkers and an attractive resource of therapeutic targets for ATL.
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