Single-cell RNA sequencing(scRNA-seq)has enabled high-resolution characterization of molecular signatures of tumor-infiltrating lymphocytes.However,analyses at the transcript isoform level are rarely reported.As alter...Single-cell RNA sequencing(scRNA-seq)has enabled high-resolution characterization of molecular signatures of tumor-infiltrating lymphocytes.However,analyses at the transcript isoform level are rarely reported.As alternative splicing is critical to T-cell differentiation and activation,here,we proposed a computational method named IDEA(Issoform Detection.Enrichment,and functional Annotation)to comprehensively detect and annotate differentially used isoforms across cell subtypes.We applied IDEA on a scRNA-seq data set of 12,346 T cells from non-small-cell lung cancer(NSCLC).we found that most genes tend to dominantly express one isoform in single T cells,enabling typing T cells based on the isotypes.given a gene.lsotype analysis suggested that tumor-infiltrating Tcells significantly preferred specific isotypes for 245 genes in CD8t Tcells and 456 genes in CD4^+T cells.Functional annotation suggests that the preferred isoforms involved in coding/noncoding switches,transcription start site changes,gains/losses of domains,and subcellular translocation.Clonal analysis revealed that isoform switching occurred during T-cell activation/differentiation.Our analysis provides precise characterization of the molecular events in tumor-infiltrating T cells and sheds new light on the regulatory mechanisms oftumor-infiltrating T cells.展开更多
基金Beijing Advanced lnnovation Centre for Genomics at Peking University,Key Technologies R&D Program(2016YFCO900100)the National Natural Science Foundation of China(31991171,31530036,91742203,and 9194230046).
文摘Single-cell RNA sequencing(scRNA-seq)has enabled high-resolution characterization of molecular signatures of tumor-infiltrating lymphocytes.However,analyses at the transcript isoform level are rarely reported.As alternative splicing is critical to T-cell differentiation and activation,here,we proposed a computational method named IDEA(Issoform Detection.Enrichment,and functional Annotation)to comprehensively detect and annotate differentially used isoforms across cell subtypes.We applied IDEA on a scRNA-seq data set of 12,346 T cells from non-small-cell lung cancer(NSCLC).we found that most genes tend to dominantly express one isoform in single T cells,enabling typing T cells based on the isotypes.given a gene.lsotype analysis suggested that tumor-infiltrating Tcells significantly preferred specific isotypes for 245 genes in CD8t Tcells and 456 genes in CD4^+T cells.Functional annotation suggests that the preferred isoforms involved in coding/noncoding switches,transcription start site changes,gains/losses of domains,and subcellular translocation.Clonal analysis revealed that isoform switching occurred during T-cell activation/differentiation.Our analysis provides precise characterization of the molecular events in tumor-infiltrating T cells and sheds new light on the regulatory mechanisms oftumor-infiltrating T cells.
