Targeting ribosome biogenesis sensitizes PARPi-resistant triple-negative breast cancer

Abstract

Poly (ADP-ribose) polymerase inhibitors (PARPi) are the only targeted treatment available for early triple-negative breast cancer (TNBC), an aggressive subtype with limited treatment options. While PARPi are effective in patients with BRCA mutations, resistance to these inhibitors can arise. We previously developed BRCA-mutant cell lines, HCC1395, with acquired resistance to talazoparib and olaparib, and have now developed PARPi-resistant MX1 cell lines in an analogous manner. Ribosomal pathways were upregulated in 3/4 cell lines with acquired PARPi resistance. The resistant cell lines showed high and low basal nucleolar stress based on nucleolar morphology and nucleophosmin delocalization from nucleolus to nucleoplasm. Treatment of these cell lines with the combination of olaparib and a ribosome biogenesis inhibitor, BMH-21, demonstrated synergy in the PARPi-resistant cell lines, but not in the parental cells. Interestingly, HCC1395 cells, which had lower baseline nucleolar stress, showed greater nucleophosmin delocalization with combination treatment than MX1 cells, which had higher baseline nucleolar stress. All four cell lines demonstrated sustained DNA damage with the combination. We extended our investigation to 3 BRCA wild-type TNBC cell lines, BT549, Hs578T, and MDAMB231 and identified synergy in the context of intrinsic PARPi resistance. In MDAMB231 cells, combining olaparib with BMH-21 induced a senescence-like phenotype, increasing gH2AX-positive cells by up to 7.3-fold, senescence-associated B-galactosidase (SA-B-gal) staining by 5.6-fold, and p21 by 3.6-fold. These results were mirrored with a second ribosome biogenesis inhibitor, CX-5461. Finally, we identified distinct patterns of ribosomal pathway activity in a cohort of patients with treatment-resistant TNBC, and found correlations between ribosomal pathways with MYC, proliferation, DNA damage, and senescence. Together, these data identify ribosome biogenesis as a potential therapeutic vulnerability in PARPi-resistant TNBC and support its targeting in combination with PARPi, while demonstrating a broader for ribosome biogenesis in treatment-resistant TNBC.