Single-cell analysis of lymphokine imbalance in asymptomatic HIV-1 infection: evidence for a major alteration within the CD8+
 T cell subset

CD8+ T cells play a key role in mediating protective immunity after immune challenges such as infection or vaccination. Several subsets of differentiated CD8+ T cells have been identified, however, a deeper understanding of the molecular mechanism that underlies T-cell differentiation is lacking. Conventional approaches to the study of immune responses are typically limited to the analysis of bulk groups of cells that mask the cells’ heterogeneity (RNA-seq, microarray) and to the assessment of a relatively limited number of biomarkers that can be evaluated simultaneously at the population level (flow and mass cytometry). Single-cell analysis, on the other hand, represents a possible alternative that enables a deeper characterization of the underlying cellular heterogeneity. In this study, a murine model was used to characterize immunodominant hemagglutinin (HA533-541)-specific CD8+ T-cell responses to nucleic- and protein-based influenza vaccine candidates, using single-cell sorting followed by transcriptomic analysis. Investigation of single-cell gene expression profiles enabled the discovery of unique subsets of CD8+ T cells that co-expressed cytotoxic genes after vaccination. Moreover, this method enabled the characterization of antigen specific CD8+ T cells that were previously undetected. Single-cell transcriptome profiling has the potential to allow for qualitative discrimination of cells, which could lead to novel insights on biological pathways involved in cellular responses. This approach could be further validated and allow for more informed decision making in preclinical and clinical settings.

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A high-throughput single-cell analysis of human CD8+ T cell functions reveals discordance for cytokine secretion and cytolysis

Journal of Clinical Investigation ◽

10.1172/jci58653 ◽

2011 ◽

Vol 121 (11) ◽

pp. 4322-4331 ◽

Cited By ~ 109

Author(s):

Navin Varadarajan ◽

Boris Julg ◽

Yvonne J. Yamanaka ◽

Huabiao Chen ◽

Adebola O. Ogunniyi ◽

...

Keyword(s):

T Cell ◽

Single Cell ◽

High Throughput ◽

Single Cell Analysis ◽

Cd8 T Cell ◽

Cytokine Secretion ◽

Cell Analysis ◽

Cell Functions

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Single Cell RNA-Sequencing-based Analysis of CD4+ T-Cell Subset-Specific Susceptibility to Transcriptional Modulation by HIV-1 Latency-Reversing Agents

10.1101/2020.05.04.075119 ◽

2020 ◽

Author(s):

Julia Kazmierski ◽

Dylan Postmus ◽

Emanuel Wyler ◽

Cornelius Fischer ◽

Jenny Jansen ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

Single Cell ◽

Hdac Inhibitors ◽

Cell Subset ◽

T Cell Subset ◽

Single Cell Rna Sequencing ◽

Hiv 1 ◽

Reversing Agents

AbstractShock-and-kill is one of the conceptually most advanced strategy towards establishment of an HIV-1 cure. Treatment with latency-reversing agents (LRAs), including histone deacetylase inhibitors with chromatin-remodeling capabilities, combined with anti-retroviral therapy, reactivates HIV-1 transcription in vivo. However, LRA treatment fails to significantly reduce the HIV-1 reservoir in HIV-1-positive individuals, indicating that it is probably insufficient to eliminate latently infected cells. The global and T-cell subset-specific impact of individual LRAs on the transcriptome of CD4+ T-cells, the main HIV-1 reservoir containing cell type in vivo, remains understudied. Here, using single cell RNA-sequencing, we characterize LRA treatment-induced alterations of CD4+ T-cell subset composition and of subpopulation-specific transcriptomes, using Vorinostat and Panobinostat as two prototypic HDAC inhibitors. Ex vivo exposure of CD4+ T-cells from an aviremic HIV-1-positive individual to Panobinostat markedly reduced the percentage of TREG cells. Furthermore, it altered expression of a multitude of interferon-regulated genes, resulting in suppression of several well-characterized antiviral genes, and in enhancement of selected interferon-regulated genes with proviral activities. These changes were most pronounced in TN, TCM, TTM and TEM, and less pronounced in TREG. Exposure to Vorinostat resulted in a comparably mild change of cellular transcriptomic profile, regarding both the number of deregulated genes and their fold change of expression. Nevertheless, selected interferon-regulated genes exhibited a subset-specific expression profile upon Vorinostat treatment. Finally, some genes were deregulated by both treatments in a subset-specific manner. We conclude that treatment by both individual HDAC inhibitors induces an overall proviral milieu in CD4+ T-cells subsets. While this proviral state might be favorable for efficient HIV-1 reactivation, we hypothesize that it may impede the instruction of activation of cellular and adaptive immunity required for effective killing of reactivated cells.

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