Transcriptional Profiling of Target CD4+ T-cells that Survive Cytotoxic T Cell Co-culture

To identify candidate mechanisms that may confer CTL resistance to HIV reservoir harboring cells, we studied differential intrinsic sensitivity to CTL killing in primary CD4+ T-cells. Human CD4+ T cells were divided into either a “real” condition, where half of the cells were labeled with CFSE and pulsed with the HIV-Env peptide RLRDLLLIVTR (RR11), while the other half received no peptide and were labeled with CTFR, or a “mock” condition where cells were similarly labeled but received no peptide. Both conditions were then co-cultured with the corresponding HIV-specific CTL clone. Our result showed that the comparison between the ‘real survivors’ to the ‘real bystanders’ identified 1,061 differentially expressed genes (DEGs) by setting a threshold as FDR<0.05: 743 upregulated and 318 downregulated. Among these genes, we observed expression profiles that were consistent with specific selection of over-expression of BCL2, and under-expression of caspase-2 and PARP in the ‘real survivor’ cells that resisted elimination by CTL. Transcriptional profiling for CTL-resistant HIV-peptide-pulsed human CD4+ T cells (real survivors), comparing to HIV-peptide not pulsed bystanders