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. Author manuscript; available in PMC: 2020 Jan 15.
Published in final edited form as: Nat Immunol. 2019 Jul 15;20(8):1059–1070. doi: 10.1038/s41590-019-0418-x

Figure 3. An atypical TFH-like transcriptional signature in CXCR5neg HIV-specific CD4+ T cells discriminates chronic progressors from elite controllers.

Figure 3.

(a) Representative flow cytometry plots from a CP illustrating the enrichment of cTFH (CXCR5+ CD45RA-) in CD69+CD40L+ Gag-specific CD4+ T cells vs. total population in a CP subject, assessed 9h after stimulation with a Gag peptide pool. (b,c) Quantification from (a). Comparison between CPs and ECs of (b) the percentage of Gag-specific CXCR5mem assessed by flow cytometry (two-sided Mann-Whitney test) (n=10 CPs and 10 ECs); and (c) the enrichment score of a TFH tonsil signature (GSE50391) by ssGSEA (two-sided Mann-Whitney test) (nCP=11, nEC=12). Bars represent the median +/−interquartile range. (d) Correlation of single-sample enrichment score for the TFH tonsil signature with viral load by two-tailed Spearman test (n= 11 CPs, 9 VCs, 12 ECs). (e) Volcano plots depicting differential gene expression between CP and EC, amongst their live-sorted Gag-specific CXCR5mem or CXCR5neg subsets, by microarray analysis. Red and pink dots represent DEG with log2|FC|>1 and padj<0.05 or log2|FC| >1, respectively, and the number of DEGs are displayed in the small tables. Two-sided moderated t-test followed by Benjamini-Hochberg correction method (padj) (n= 5 CPs and 3 ECs). (f) CAMERA enrichment analysis of the tonsil TFH signature of CXCR5mem or CXCR5neg Gag-specific CD4 T cells of CPs compared to ECs (n= 5 CPs and 3 ECs). Two sided p-value by CAMERA and FDR by Benjamini-Hochberg method. (g) Comparison of expression of TFH surface markers on CXCR5mem and CXCR5neg HIV-specific CD4+ T cells of CPs and ECs by flow cytometry (n= 10 CPs and 10 ECs). (h) mRNA expression of TFH-related surface markers or (i) transcription factors by qRT-PCR (Fluidigm) (n= 6 CPs and 6 ECs) on sorted CXCR5mem and CXCR5neg HIV-specific CD4+ T cells of CPs and ECs. (g,h,i) Two-tailed Mann-Whitney test or for paired comparisons by two-tailed Wilcoxon matched-pairs signed-ranked test were used to verify significance. Only p˂0.05 are displayed for clarity. Bars represent the median +/− interquartile range.