Landscape of transcript isoforms in single T cells infiltrating in non-small cell lung cancer

Abstract

11Single cell RNA-seq has enabled high-resolution characterization of molecular signatures of tumor-12 infiltrating lymphocytes. However, analyses at the transcript isoform level are rarely reported. As 13 alternative splicing is critical to T cell differentiation and activation, here we proposed a computational 14 method named as IDEA to comprehensively detect and annotate differentially used isoforms across 15 cell subtypes. We applied IDEA on a scRNA-seq dataset of 12,346 T cells from non-small cell lung 16 cancer. We found most genes tend to dominantly express one isoform in single T cells, enabling 17 typing T cells according to the isotypes given a gene. Isotype analysis suggested that tumor-infiltrating 18 T cells significantly preferred specific isotypes for 245 genes in CD8+ T cells and 456 genes in CD4+ 19 T cells. Functional annotation suggests that the preferred isoforms involved in coding/non-coding 20 switches, transcription start site changes, gains/losses of domains and subcellular translocation. 21 Clonal analysis revealed that isoform switching occurred during T cell activation/differentiation. Our 22 analysis provides precise characterization of the molecular events in tumor-infiltrating T cells and 23 sheds new lights into the regulatory mechanisms of tumor-infiltrating T cells. 24 25 65 Altogether, our work provides a comprehensive analysis of the transcript isoform landscape of tumor-66 infiltrating T cells in non-small cell lung cancer at the single-cell resolution. The abundant isoform 67 switching events identified among tumor-infiltrating T cell subtypes may serve as a rich data resource 68for precisely analyzing the mechanisms underlying T cell-based antitumor immunity. Our analysis also 69 highlights the necessity of splicing analysis at the single-cell resolution, which can be applied to a 70 wide range of biological questions.

An Autoimmune Transcriptional Circuit Driving Foxp3+Regulatory T cell Dysfunction

“…One caveat is that we were unable to quantitate PRDM1 isoform expression at single cell resolution in our 10x genomics dataset. Full length mRNA- capturing scRNA-seq has the potential to differentiate between PRDM1 isoforms; thus, this technique could be applied to elucidate further insight at single-cell resolution 83 . This approach will also enable characterization of further differences in T cell transcriptomics between MS and healthy subjects.…”