Fig. 3
From: Defective transcription elongation in a subset of cancers confers immunotherapy resistance
TEdeff is observed in some cancer cell lines and correlates with defects in mRNA transcription, processing, and export. a Left: cell lines are ordered based on the average short/long isoform ratio for the AT genes. Four with the highest scores are highlighted. Middle: correlation of the transcriptional patterns (every gene is z-normalized to the rest of the cell lines) of candidate TEdeff cell lines with the average TEdeff signature (average t-statistic of TEdeff vs. TEprof expression difference for every gene). The p-value of correlation (Spearman) for the cell line with the lowest correlation is shown. Right: quantification of intron–exon junction inclusion ratio in Class I genes (same as in Fig. 1h) in TEprof and TEdeff cell lines. b Three-way correlation of TEdeff-specific transcriptomic signatures (t-values of difference in TEdeff vs. TEprof cells for every gene) obtained for breast cancer cell lines based on RNAseq data from CCLE (y-axis), based on our independent RNAseq (x-axis) and based on RNAseq data from TCGA breast cancer (BRCA) dataset (color-mapped based on the color key). c Differential exon expression heatmap (see Fig. 1c) of TEdeff and TEprof breast cancer lines obtained from our independent RNAseq data. Genes with spurious and overexpressed expression patterns are highlighted (blue and red, respectively). d Enrichment of the spuriously transcribed (blue) and overexpressed (red) genes in c for the Class I genes from the tissue samples. The p-values reflect one-sided hypergeometric distribution, i.e. closer to 0 indicates enrichment, closer to 1 indicates depletion. e Genome-wide distribution plots of total and phospho-Ser5 RNAP II in a TEdeff (UACC-812) and a TEprof (T47D) cell line. f Genome-wide distribution of total and phospho-Ser5 RNAP II around the transcription termination site (TTS) regions of genes in TEdeff and TEprof cells. g Immunoblotting of indicated RNAP II and histone marks in the indicated cell lines. TEdeff cells are highlighted in red. h Ratios of 5′-uncapped to 5′-capped (left) and 3′-non-polyadenylated to 3′-polyadenylated (right) mRNA concentrations after rRNA depletion in the indicated cell lines. P: difference between TEdeff and TEprof cell line values (t-test). Error bars: standard deviation based on four technical replicates
