The Oncogenic PI3K-Induced Transcriptomic Landscape Reveals Key Functions in Splicing and Gene Expression Regulation

Abstract

The 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 co-transcriptional 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 (TF) activity changes, as well as splicing and isoform usage dynamics, downstream of PI3K. These analyses uncovered widespread alternatively spliced (AS) isoforms linked to proliferation, metabolism, and splicing in PIK3CA mutant cells, which were reversed by inhibition of PI3Kα. Analysis of paired tumor biopsies from PIK3CA-mutated breast cancer patients 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.

Resistance mechanism to Notch inhibition and combination therapy in human T cell acute lymphoblastic leukemia

“…This analysis allowed to establish changes in phosphorylation profiles of splicing factors upon altered PI3K signaling and highlighted a wide spectrum of so far uncharacterized phosphorylation sites. A recent report linked oncogenic PI3K signaling with splicing alterations in breast cancer on the transcriptional level 17 . Thus we reanalyzed our RNA-seq data for differentially expressed transcripts, which were indeed associated with genes involved in cell cycle and regulation of apoptosis signaling pathways (Supplemental Figure 6C-D).…”

“…Recently, oncogenic PI3K signaling was shown to induce expression of alternatively spliced isoforms linked to proliferation and metabolism in breast cancer 17 . The PI3K-AKT pathway has been shown to regulate several proteins of the splicing machinery 28 .…”

“…This was correlated with differential expression levels of transcript isoforms of genes involved in enriched cell cycle and anti-apoptotic pathways as well as with alternative splicing events (Supplemental Figure 6C-E). Recently, oncogenic PI3K signaling was shown to induce expression of alternatively spliced isoforms linked to proliferation and metabolism in breast cancer 17 . The PI3K-AKT pathway has been shown to regulate several proteins of the splicing machinery 28 .…”

Resistance mechanism to Notch inhibition and combination therapy in human T cell acute lymphoblastic leukemia

“…S6C-E). Recently, oncogenic PI3K signaling was shown to induce expression of alternatively spliced isoforms linked to proliferation and metabolism in breast cancer (17). The PI3K-AKT pathway has been shown to regulate several proteins of the splicing machinery(28).…”

“…A recent report linked oncogenic PI3K signaling with splicing alterations in breast cancer on the transcriptional level (17). Thus, we reanalyzed our RNA-seq data for differentially expressed transcripts, which were indeed associated with genes involved in cell cycle and regulation of apoptosis signaling pathways (Fig.…”