Energy demanding RNA and protein metabolism drive dysfunctionality of HIV-specific T cell changes during chronic HIV infection

Abstract

Antiretroviral treatment of HIV infected individuals cannot eliminate the HIV reservoir and immune control of HIV is rarely seen upon treatment interruption. In long-term non-progressors (LTNP), an effective CD8 T cell response is thought to contribute to be immune control of HIV. Here we studied the transcriptional profile of virus specific CD8 T cells during the asymptomatic phase of disease, to gain molecular insights in CD8 T cell functionality in HIV progressors and different groups of LTNP: HLA-B*57 LTNP, non-HLA-B*57 LTNP and individuals carrying the MAVS minor genotype (rs7262903/rs7269320). Principal component analysis revealed distinct overall transcriptional profiles between the groups. The transcription profile of HIV-specific CD8 T cells of LTNP groups was associated with increased cytokine/IL-12 signaling and protein/RNA metabolism pathways, indicating an increased CD8 T cell functionality. Although the transcription profile of CMV-specific CD8 T cells differed from that of HIV-specific CD8 T cells, with mainly an upregulation of gene expression in progressors, similar affected pathways were identified. Moreover, CMV-specific CD8 T cells from progressors showed increased expression of genes related to effector functions and suggests recent antigen exposure. Our data shows that changes in cytokine signaling and the energy demanding RNA and protein metabolism are related to CD8 T cell dysfunction, which may indicate that mitochondrial dysfunction is an important driver of T cell dysfunctionality during chronic HIV infection. Indeed, improvement of mitochondrial function by IL-12 and mitoTempo treatment, enhanced in vitro IFNγ release by PBMC from PWH upon HIV gag and CMV pp65 peptide stimulation. Our study provides new insights into the molecular pathways associated with CD8 T cell mediated immune control of chronic HIV infection which is important for the design of novel treatment strategies to restore or improve the HIV-specific immune response.

Fig 1. Differentially expressed genes in HIV-specific CD8 T cells and PCA plot.

LogFC expression of the DEGs (logFC >1.5; P-value <0.05) in the HIV-specific CD8 T cells comparing (a) progressors versus B*57 long-term non-progressors (LTNP) and (b) progressors versus non-B*57 LTNP. Negative LogFC: upregulation of DEGs in progressors; Positive LogFC: upregulation of genes in B*57 LTNP, and non-B*57 LTNP as indicated. (c) PCA plot of the HIV-specific CD8 T cell transcription profiles from HIV progressors (red square), B*57 LTNP (purple circle) and non-B*57 LTNP (lilac triangle). Centroids are depicted by the larger symbols.

Fig 2. HIV-specific CD8 T cell transcription profile of MAVS -/- individuals differ from progressors, B*57 long-term non-progressors (LTNP) and non-B*57 LTNP.

(a) LogFC expression of the DEGs comparing progressors versus MAVS -/- in the HIV-specific CD8 T cells (logFC >1.5; P-value <0.05). Negative LogFC: upregulation of DEGs in progressors; Positive LogFC: upregulation of genes in MAVS-/-. (b) PCA plot of the HIV-specific CD8 T cell transcription profiles from HIV progressors (red diamond), B*57 LTNP (purple circle), non-B*57 LTNP (lilac square) and MAVS -/- (orange triangle). Centroids are depicted by the larger symbols.

Fig 3. DEG network plot of the HIV-specific CD8 T cells.

Network analysis of the DEGs in the HIV-specific CD8 T cells of HIV infected individuals reveals 8 different gene clusters.

Fig 4. Differentially expressed genes CMV-specific CD8 T cells.

LogFC of the DEGs (logFC >1.5; P-value <0.05) in the CMV-specific CD8 T cells when comparing progressors versus: (a) B*57 long-term non-progressors (LTNP), (b) non-B*57 LTNP, (c) MAVS-/- and (D) BD. Negative LogFC: upregulation of DEGs in progressors; Positive LogFC: upregulation of genes in B*57 LTNP, non-B*57 LTNP, MAVS-/- and BD as indicated.

Fig 5. CMV-specific CD8 T-cell transcription profile of BD differ from MAVS -/-, progressors, B*57 long-term non-progressors (LTNP) and non-B*57 LTNP.

PCA plot of the CMV-specific CD8 T cell transcription profiles from BD (green asterisk), HIV progressors (red diamond), B*57 LTNP (purple circle), non-B*57 LTNP (lilac square) and MAVS -/- (orange triangle). Centroids are depicted by the larger symbols.

Fig 6. DEG network plot of CMV-specific CD8 T cells.

Network analysis of the DEGs found in the CMV-specific CD8 T cells of HIV infected individuals and BD reveal 13 different gene clusters.

Fig 7. HIV- and CMV-specific CD8 T cells of HIV infected individuals have a different transcriptional profile.

PCA plot of the transcription profile of HIV-specific CD8 T cells (brown triangle) and CMV-specific CD8 T cell (blue circle) from HIV infected individuals. Centroids are depicted by the larger symbols. Each individual is indicated by a number, whereas a letter is given for HIV (H) or CMV (C) specific CD8 cells.

Fig 8. Targeting mitochondrial dysfunction improves cytokine release by HIV- and CMV-specific cells from HIV infected individuals.

A. IFNγ release upon HIV gag (left panel; n = 14) and CMV pp65 (right panel; n = 20) peptide pool stimulation in the presence of MitoTempo or IL-12. Symbols indicate data points from the same individual. Intracellular cytokine staining for IFNγ, IL-2 and TNFα (B and C) and polyfunctionality (D and E) upon HIV gag (B and D) and CMV pp65 (C and E) peptide pool stimulation in the presence of MitoTempo or IL-12 (n = 12). P-value < 0.05 (*), 0.01 (**), 0.001 (***), 0.0001(****).