Simultaneous analysis of gene expression and T cell repertoire in peripheral blood mononuclear cells from patients with cystic fibrosis at the single cell level

Abstract

Abstract Highly sensitive RNA sequencing (RNA-Seq) methods enables gene expression analysis of low-input samples and even single cells. Single-Cell RNA sequencing (scRNA-seq) is a powerful tool for studying the transcriptome and enables discovery of cellular differences usually masked by bulk sampling methods. The Chromium Single Cell Immune Profiling Solution developed by 10X genomics makes it possible to examine gene expression and T cell receptors simultaneously on a cell-by-cell basis. Patients with cystic fibrosis (CF) often suffer inflammatory lung diseases caused by chronic Pseudomonas aeruginosa (PA) colonization. This colonization could also skew the lymphocytes repertoire in peripheral blood mononuclear cells from CF patients. We investigated the use of scRNA-seq to assess the lymphocyte repertoire in CF patients with PA colonization and whether the single-cell transcriptomic changes correlate with preferential T cell receptor (TCR) usage. Our analysis did not find evidence for clonal expansion of T cells in peripheral blood of these CF patients, suggesting that PA colonization mainly elicits local adaptive immune responses in the lungs. However, this dataset did reveal a striking depletion of the population of T cells known as mucosal associated invariant T cells (MAIT cells) in CF patients. Within the MAIT cell population, we found an overrepresentation of certain genes that was observable in healthy but not CF samples. In this study we show the feasibility of simultaneous analysis of gene expression and lymphocytes repertoire in PBMCs. We recapitulate previous findings that implicate a protective role for MAIT cells against PA colonization, and also provide evidence for the involvement of particular genes in this effect.