Fig. 1

Analysis of pre-mRNA splicing changes in cancer cell lines and xenografts after chemotherapy. a Enrichment analysis of genes with common differential splicing events induced by therapy. Left side: lung adenocarcinoma patient-derived xenografts (PDX) treated with carboplatin, docetaxel, afatinib, BEZ235, BKM120, DAPT, erlotinib, tivantinib, and selumetinib; dataset GSE69405. Right side: A375, A549, H3122, N87, PC9, RT112 cell lines treated with erlotinib, crizotinib, trametinib, lapatinib, vemurafenib, BGJ398; dataset GSE89127. The STRING database was used for Gene Ontology Biological Processes analysis. p value is indicated with a color scale. b Summary of alternative splicing events observed in GSE89127 and GSE69405 datasets (before slash: total number of splicing events; after slash: common splicing events appeared in at least half of the samples). Events: SE—skipped exon, A5SS—alternative 5′ splice site, A3SS—alternative 3′ splice site, RI—retained intron, MXE—mutually exclusive exons. c Scatter plot representing the intron retention (upper panel) and exon skipping (lower panel) events detected in the GSE89127 dataset before and after chemotherapy. Splicing events in spliceosomal genes are illustrated with a dark-blue color. d Sashimi plots for the splicing factor RBM6 in untreated cancer cells (dark blue) and in cancer cells that were treated with different chemotherapeutic drugs (light blue). The inclusion level (IncLevel) indicates the splicing status of the intron. e Heat map demonstrating the changes in the expression of spliceosomal genes (Z-score) after chemotherapy. Clusterization of expression data was made before scaling data (Z-score transformation)