Fig. 1: Breast cancer patients exhibit subtype-specific alternative splicing (AS) events.

A Schematic representation of the strategy for identifying alternatively spliced (AS) events in breast cancer subtypes (TCGA-BRCA dataset). B Number of AS events caused by differential usage of cassette exons (CE) or by intron retention (IR) for Luminal A, Luminal B, HER2⁺, and Basal breast cancer subtypes, and total number of genes that they correspond to. Statistical test Irwin–Hall p-value summarization was used on individual splicing events. Details of samples for each subtype are in Data set 1 in supplementary information. C, D Distribution of number of genes undergoing different number of CE (C) and IR events (D) predicted for Luminal A, Luminal B, HER2⁺, and Basal subtypes. E–H Quantitative real-time-PCR (qRT-PCR) validation in MCF-10A (untransformed mammary epithelial-derived), and representative subtype-specific cancer cell lines like BT-474 (Luminal B), MDA-MB-231 (Basal), and MDA-MB-453 (HER2⁺) for CE event in TOP1 (E, F) predicted for Luminal B and HER2⁺ subtypes; and for CE event in RHOA (G, H) predicted for Basal subtype. Normalized transcript level for protein-coding (PC) and alternatively spliced (AS) isoforms of TOP1 and RHOA gene for each cell line (mean ± SD, n = 4) show differential expression of the isoforms. A pictorial representation of exon/intron positions and primer sites are also shown. Data in (E–H) were analyzed by ANOVA.