Background:
CD8+ T cells contribute to the antiviral response in simian immunodeficiency virus (SIV) infection in nonhuman primates. CD8+ T cells recognize viral epitopes via the T cell receptor (TCR). In previous studies, we examined the TCR repertoire of CD8+ T cells specific for a single SIV immunodominant epitope, Gag-CM9 (CTPYDINQM), throughout SIV infection. We identified tissue specific TCR sequences and TCRs shared by multiple anatomical sites. We now sought to evaluate if the tissue localization or TCR sequence of a CM9 specific CD8+ T cell corresponds with a transcriptional phenotype.
Methods:
CM9 specific CD8+ T cells were sorted from blood, lymph nodes, spleen, and liver from SIV infected rhesus macaques. The cells were processed through the 10x Genomics single cell sequencing protocol, creating a TCR amplified library and an RNA gene expression library for each cell. The sequenced libraries were demultiplexed and integrated using Cell Ranger and Seurat software. Clonotypes that reside within specific tissue specific and shared across multiple sites and clonotypes shared across multiple individuals (public) were identified.
Results:
Clustering analysis on the transcriptional profiles of CM9 specific CD8+ T cells revealed no obvious clustering by animal, or the presence of a public TCR sequence and minimal clustering was observed by tissue. Cells with tissue specific TCRs were most numerous in the liver. CM9 specific CD8+ T cells with a tissue specific TCR had higher expression of the tissue resident maker gene ITGA1. Multidimensional scaling analysis of CM9 specific CD8+ T cell transcription within the same tissue showed distinct distances between cells with shared and tissue specific TCRs in the blood, lymph nodes and liver. Interestingly, most of the transcriptional variation was captured by the spleen, rather than CM9 specific CD8+ T cells from peripheral blood.
Conclusions:
These data suggest that the tissue of origin of a CM9 specific CD8+ T cell, or the presence of a public TCR sequence does not associate with a distinct transcriptional profile across multiple anatomic sites. However, within the same tissue, whether a cell has a shared or tissue specific TCR sequence does appear to associate with a different transcriptional profile. Importantly, analysis of antigen specific CD8+ T cells from peripheral blood does not capture immunological phenomena occurring within tissues.