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. 2024 Dec 28;14:30779. doi: 10.1038/s41598-024-80971-5

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

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Fig. 3 — SLAMF7 expressions in virus-specific T cells during aging. (A) SLAMF7 expression in virus-specific CD8 T cells. The expression of SLAMF7 was compared between virus-specific CD8 T cells in HD during aging (n = 8 for young and n = 11 for elderly), in PLWH (n = 17, including 10 non-treated and 7 under HAART), after SARS-CoV-2 vaccination (n = 14, 5 months post dose 2) and after SARS-CoV-2 breakthrough infection (n = 37, 3 weeks post-infection). The statistical analysis was performed on unpaired samples (U Mann–Whitney test) (*, **, ***, **** for p < 0.05, p < 0.01, p < 0.001, and p < 0.0001 respectively). (B) Specific SLAMF7 signature in virus-specific CD8 T cells. CMV- and EBV-specific CD8 T cells were statistically analyzed on unpaired samples (U Mann–Whitney test) (** for p < 0.01). (C) TOX expression in CD8 T cells. A zebra plot according to TOX and PD-1 or pp65-specific tetramer expressions represented CD8 T cells from an old donor. Gates were defined according to PD-1 and TOX expression as PD-1^-TOX^- (grey), PD-1^-TOX⁺ (green), PD-1^dimTOX⁺ (blue), and PD-1⁺TOX⁺ (red). The respective expressions of surface and intracellular markers were overlaid on histograms. (D) Specific TOX expression in CMV-specific CD8 T cells. The representative expression of TOX in CMV- and EBV-specific CD8 T cells from the same donor was overlaid on the histogram and the frequencies of TOX expressing were represented. (E) Quantification of TOX expression in virus-specific CD8 T cells. (F) Transcription factors signature of CMV-specific CD8 T cells during aging. The frequencies of CMV-specific CD8 T cells expressing TOX with and without TCF-1/7, Eomes, and T-bet were evaluated and compared in young (n = 9) and older donors (n = 10) (Mann–Whitney test, with * and ** for p < 0.05 and p < 0.01 respectively). (G) Transcriptional signature of CMV-specific CD8 T cells during aging. Total and subsets of CMV-specific CD8 T cells were sorted from 10 young and 3 old healthy donors. The extracted transcripts were analyzed by RNA sequencing. The differentially expressed genes were clustered and visualized by a cold-to-hot heat map representing the gene expression intensity. Naïve and Terminal effector T cells were used as internal controls. (H) Non-exhaustion T cell signature of CMV-specific CD8 T cells. The enrichment of gene expression detected in CMV-specific CD8 T cells was calculated in comparison to the naïve T cell signature. Enrichment plot of the gene set reported by GSEA as most enriched among PD-1^low gene sets (GO: 26,495). The profile shows the enrichment score (green curve) and positions of gene set members (black vertical bars) rank-ordered list of differential gene expression. (I) Transcriptional pathway analysis of virus-specific CD8 T cells during aging. Ingenuity pathway analysis of bulk RNASeq data from virus-specific CD8 T cells. The enrichment of a specific pathway is proportional to the bubble size and the significance is associated with the different shades of red (from p < 10^–2 to p < 10^–6).