The
phosphoinositide 3-kinase (PI3K) pathway regulates proliferation, survival, and metabolism and is frequently activated across human
cancers. A comprehensive elucidation of how this signaling pathway controls transcriptional and cotranscriptional processes could provide new insights into the key functions of PI3K signaling in
cancer. Here, we undertook a transcriptomic approach to investigate genome-wide gene expression and
transcription factor activity changes, as well as splicing and
isoform usage dynamics, downstream of PI3K. These analyses uncovered widespread alternatively spliced
isoforms linked to proliferation, metabolism, and splicing in PIK3CA-mutant cells, which were reversed by inhibition of PI3Kα. Analysis of paired
tumor biopsies from patients with PIK3CA-mutated
breast cancer undergoing treatment with PI3Kα inhibitors identified widespread splicing alterations that affect specific
isoforms in common with the preclinical models, and these alterations, namely PTK2/FRNK and AFMID
isoforms, were validated as functional drivers of
cancer cell growth or migration. Mechanistically,
isoform-specific
splicing factors mediated PI3K-dependent RNA splicing. Treatment with splicing inhibitors rendered
breast cancer cells more sensitive to the PI3Kα inhibitor
alpelisib, resulting in greater growth inhibition than
alpelisib alone. This study provides the first comprehensive analysis of widespread splicing alterations driven by oncogenic PI3K in
breast cancer. The atlas of PI3K-mediated splicing programs establishes a key role for the PI3K pathway in regulating splicing, opening new avenues for exploiting PI3K signaling as a therapeutic vulnerability in
breast cancer.
SIGNIFICANCE: Transcriptomic analysis reveals a key role for the PI3K pathway in regulating RNA splicing, uncovering new mechanisms by which PI3K regulates proliferation and metabolism in
breast cancer. See related commentary by Claridge and Hopkins, p. 2216.