Transcriptome characterization at the single cell level of viral specific CD8+ T cells

<p>Transcriptome-level characterization of the immune response during viral infection can reveal key mechanisms that underpin the activation and status of cytotoxic CD8+ T Cells (CTL). Once stimulated with antigen CTLs proliferate and differentiate generating a heterogeneous progeny. The advent of single cell analyses, has enabled tracking of the evolving CTLs in human samples during viral infections. We quantified the single cell transcriptome of 81 CTLs identified from a subject with chronic HCV infection. All cells are specific for HLA-I A0201 restricted epitope CINGVCWTV. Single CTLs were obtained from PBMC and from cell line derived from the same patient (unstimulated and following antigen re-stimulation). We analysed the difference between the three groups of single cells using a list of genes previously associated with CTL functions. Genes associated with cytotoxic response (IFN-g, perforin, granzyme B) were highly expressed in cell lines, but not in PBMC derived CTLs. Using unsupervised clustering analysis we identified co-expression clusters within each group. By filtering out the cell-cycle related genes (a major co-founder), we revealed that cells from the restimulated cell line showed a significantly higher level of heterogeneity (p-value <0.0001). The chemokine cell receptors (CCL4, CXCR4) were among the most variable genes.