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. 2019 Apr 9;8:e44360. doi: 10.7554/eLife.44360

Figure 2. Decreased mRNA levels of several chromosomal three genes in ECr/VCrs.

(A) Decreased ccr2/ccr5 RNA levels in activated CD4 +T cells from EC/VCs with the resistance phenotype, with comparable cxcr4 and cd4 RNA levels in all groups. Shown are individual values with Means ± SD. Pooled results from different experiments are shown with representative samples per group, n = 19 (Ctrl), n = 8 (EC/VC) and n = 21 (ECr/VCr) per group. (B) Positive correlation between ccr2 and ccr5 RNA levels in activated CD4 +T cells. ccr5 RNA levels positively correlated with % of YFP +infected cells by single cycle assay using R5-tropic viruses but not with cd4 or cxcr4 (Figure 2—figure supplement 1A). (C) Decreased RNA levels in multiple chromosomal 3p21 genes in T cells of HIV +infected individuals (Figure 2—figure supplement 1C). Statistical analysis performed using Kruskal-Wallis test and Dunn’s multiple-comparison test. r value calculated using the non-parametric Spearman correlation test. Graphs show individual values with Means ± SD. *p<0.05; **p<0.01; ***p<0.001; ****p<0.0001.

Figure 2.

Figure 2—figure supplement 1. Correlations and fold-change in RNA levels in ECr/VCr.

Figure 2—figure supplement 1.

(A) Correlation between ccr2 and ccr5 with cd4 or cxcr4 RNA levels in activated CD4 +T cells. (B) Positive correlation observed between ccr2/ccr5 RNA and cell surface protein levels and CD69 +cell surface expression, with no correlation versus cxcr4 RNA levels. Values obtained using the non-parametric Spearman correlation test. **p<0.01 (CCR2) and ***p<0.001 or *p<0.05 (CCR5). (C) Fold-change in ECr CD4 +T cell RNA levels, normalized to that of Ctrl, of genes in ~1 Mb region of chr 3p21. Each gene is plotted as the midpoint of the transcriptional unit or TU. RTP3, TDGF1, SLC6A20 and XCR1 are not included because RPKM values were too low for statistical analysis. * indicates statistically significant genes. (D) loc102724291 RNA levels in activated CD4 +T cells from ECr/VCr compared EC/VC and Ctrl, using two different qPCR primer pairs: (i) exon 1–2, centromeric to ccr5, (ii) exon 3, within intron 2 of ccr5. Shown are individual values with Means ± SD. Statistical analysis was performed by using Kruskal-Wallis with Dunn’s multiple-comparison test. **p<0.01.