Fig. 3: TEQUILA-seq analysis of actionable cancer genes in 40 breast cancer cell lines.
From: TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing
a Summary for TEQUILA-seq analysis of 468 actionable cancer genes in 40 breast cancer cell lines. (Upper left) TEQUILA probes were synthesized for 468 genes interrogated by the MSK-IMPACT gene panel. (Lower left) TEQUILA-seq was performed on 40 cell lines from the ATCC Breast Cancer Cell Panel. These cell lines represent four distinct intrinsic subtypes: luminal, HER2 enriched, basal A, and basal B. (Right) Computational workflow for processing TEQUILA-seq data. b Comparison of estimated gene abundances in MCF7 cell line using TEQUILA-seq and whole-transcriptome nanopore 1D cDNA sequencing (non-capture control). Main graphs: top 2000 genes with the highest estimated abundance in each method are shown. Insets: percentage of reads mapped to target genes and non-target genes. Blue: target genes. Gray: non-target genes. c UMAP clustering analysis using isoform proportions of all transcript isoforms across 468 genes in 40 cell lines (n = 2 replicates). Each data point represents one replicate of a cell line. d Stacked barplots showing proportions of DNMT3B transcript isoforms discovered by TEQUILA-seq in 40 cell lines. Red bar: isoform of interest (ENST00000348286); navy bar: canonical isoform (ENST00000328111); lighter blue bars: three other most abundant DNMT3B isoforms; gray bars: remaining DNMT3B isoforms. e Structures of DNMT3B protein and transcript isoforms. (Upper) Domain annotations for protein isoforms. PWWP proline-tryptophan-tryptophan-proline domain, ADD ATRX-DNMT3-DNMT3L-type zinc finger domain, MTase methyltransferase domain. (Lower) Transcript structures. Boxes: exons. Line segments: introns. f Violin plots (median, interquartile range) showing the distribution of isoform proportions for the DNMT3B isoform of interest (ENST00000348286) in different breast cancer intrinsic subtypes. Each data point represents the isoform proportion in a given cell line replicate (n = 18 for Luminal, n = 26 for HER2 enriched, n = 22 for Basal A, and n = 14 for Basal B). Source data are provided as a Source Data file.
