Gene Expression and CD4+ T Cell Susceptibility to SIV

Abstract

HIV and its simian counterpart SIV infect CD4+ T cells; however, not all CD4+ T cells are equally vulnerable to infection. Despite decades of research, a complete molecular description of a CD4+ T cell susceptible to infection is still lacking. We hypothesized that the comprehensive expression analysis of a large panel of genes predicted to positively or negatively influence viral replication would provide insights into the molecular mechanisms that underlie differences between subsets of CD4+ T cells in their susceptibility to lentiviral infection. We generated a panel of genes predicted to positively or negatively influence viral replication by mining published data with multiple bioinformatic methods. Using high-throughput microfluidic quantitative real-time PCR, we measured expression of 174 genes in defined subsets of naïve and memory CD4+ T cells from peripheral blood and jejunum. We observed significant modulation of genes in response to memory differentiation, anti-CD3/CD28, and type I interferon stimulation. Despite broad similarities in expression patterns between peripheral blood and jejunum, the highly susceptible CCR5+ transitional memory CD4+ T cells from jejunum had lower total expression of restriction factors relative to the same subset in peripheral blood. Expression of most restriction factors increased during acute SIV infection in all CD4+ T cell subsets. Gene expression in single cells is known to differ from the average expression obtained by bulk methods. We analyzed over 300 single memory CD4+ T cells from rhesus intestinal tissue during acute SIV infection and identified individual infected and uninfected cells. Expression of 96 genes was compared, revealing PD-1 and CXCR5 as the most differentially expressed. Together these genes define T follicular helper cells (Tfh); however, Tfh cells have not been previously described in jejunum tissue. We verified the presence of this population and found many phenotypic, transcriptional, and functional similarities of this novel jejunal cell population to classical Tfh cells from lymph nodes. Finally, we found these cells were highly SIV-infected, at much higher levels than total memory CD4+ T cells. Overall, these studies highlighted determinants of susceptibility, identified a novel Tfh-like cell population, and described a prime target for SIV infection during acute infection.