Researchers at the University of Alabama at Birmingham have found that ARID1A-deficient bladder cancers are sensitive to combination therapies with an EZH2 inhibitor and inhibitors of PI3K, according to a study published in JCI Insight.
ARID1A is a key part of a chromatin-modifying complex in the cell nucleus. Chromatin is a mix of DNA and proteins that tightly packages the 5-foot-long chromosomal DNA inside each cell and chromatin modifiers act to help turn on or turn off gene expression.
Analysis of existing datasets by the researchers showed that up to 29% of bladder cancers have nonsense or truncating mutations in ARID1A, and these tumors also have high expression of EZH2. Furthermore, several existing bladder cancer cell lines have mutations in ARID1A, while other bladder cancer cell lines did not have ARID1A mutations.
Researchers hypothesized that bladder cancer cells with ARID1A mutation would show sensitivity to EZH2 inhibition, and that could be used to target ARID1A-deficient bladder cancer.
Using cancer cell lines, they showed that ARID1A mutated cancer cells were indeed sensitive to EZH2 inhibition by an EZH2-specific small molecule called GSK-126. In mouse xenograft experiments, using both the bladder cancer cell lines and patient-derived bladder cancer cells, GSK-126 halted growth of cancer cells containing ARID1A mutant, but not wild-type ARID1A.
The researchers than tested if ARID1A-deficient cells become sensitive to GSK-126 due to transcriptional upregulation of specific tumor suppressors that remain transcriptionally repressed in ARID1A wild-type cells. They compared gene expression of GSK-126-treated ARID1A-wild-type bladder cancer cell lines with GSK-126-treated ARID1A knockdown cell lines. The ARID1A knockdown cells have less ARID1A and show a sensitivity to GSK-126 inhibition similar to that of ARID1Amut cells.
Out of about 70 differentially expressed genes, one was notable — the tumor suppressor PIKIP1 that acts by attenuating the cell-signaling pathway PI3K/AKT/mTOR.
Healthy cells with wild-type ARID1A use the MAPK signaling pathway, but the researchers found that cells with ARID1A mutations or ARID1A knockdowns use a different pathway. These cancer cells are dependent on PI3K signaling to activate the PI3K/AKT/mTOR pathway for survival, a signaling that is due to an upregulation of a relatively uncharacterized regulatory subunit of PI3K called PIK3R3.
The researchers confirmed this in clinical lysates of human bladder cancers, showing that tumors deficient in ARID1A protein had elevated levels of PIK3R3 and phosphoAKT, where phosphoAKT is the active form of AKT in the PI3K/AKT/mTOR pathway.
Of potential clinical importance, the researchers showed that ARID1A-deficient bladder cancer was sensitive to combination therapies with the EZH2 inhibitor GSK-126 and several inhibitors of PI3K, acting together in a synergistic manner.