Refined cellular activity expression signatures provide a targeted framework to quantify phenotypic intra-tumour heterogeneity in single-cell data I

Single cell RNA-seq (scRNA-seq) nowadays allows deeper insight into cellular biology at both the individual and population level. Measuring cell-to-cell variations in the population can furthermore help quantify phenotypic heterogeneity in populations in which cell states and identities deviate from healthy expectations. Cellular activities quantifiable using gene set enrichment analyses can provide useful grounds to quantify phenotypic heterogeneity, but the specificity and adequacy of existing molecular signatures scRNA-seq data is still insufficient. Here we induced 6 activities in vitro, for which we refined existing expression signatures to enhance specificity and detection: epithelial-mesenchymal transition (EMT), DNA repair, responses to interferons a and ? (IFNa and IFN?, respectively), glycolysis, oxidative phosphorylation (OxPhos). Overall design: MCF10A cells were cultured in vitro and analyzed in three different conditions: 4 days after EMT induction mediated by TGFb addition to the medium (EMT); 4h post DNA repair induction by irradiation at 4Gy (DNArepair) ; untreated (Control).