PARP1 catalytic domain mutations drive high-level resistance to saruparib while preserving DNA damage response vulnerabilities

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The study generated five saruparib-resistant cell lines by exposing BRCA1-deficient MDA-MB-436 triple-negative breast cancer cells to high, clinically relevant doses of the PARP1-specific inhibitor saruparib. The resistant models showed over 1,000-fold resistance, and whole-genome sequencing plus mutant reconstitution identified PARP1 catalytic domain mutations present in all resistant lines as the drivers of resistance, with no HR restoration as a resistance mechanism unlike less-selective PARP inhibitors; the mutations also altered saruparib-dependent PARP1 trapping and PARylation inhibition. Although the authors conclude these findings map a “therapeutic path forward,” the work is limited to cell-line models and mechanistic characterization rather than patient or in vivo validation. Relevance to endometriosis: it is included because PARP inhibitors are discussed in the broader biomedical literature for endometriosis-related pelvic pain and DNA damage response pathways, though this specific paper is centered on saruparib resistance in BRCA1-deficient TNBC.

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Abstract

Clinical poly (ADP)-ribose polymerase (PARP) inhibitors (PARPi) are limited by toxicities associated with inhibition of multiple PARP family proteins and acquired resistance. As PARP1-specific inhibitors, like saruparib (AZD5305), move toward standard-of-care status for BRCA and HR-deficient cancers replacing less specific PARPi, defining mechanisms of intrinsic and acquired resistance is essential for developing effective treatment strategies. Here, we established 5 saruparib-resistant (SR) cell lines from BRCA1-deficient MDA-MB-436 triple negative breast cancer (TNBC) cells using a selection strategy of high-level dosing consistent with clinical exposure, yielding models that are >1,000-fold resistant to saruparib. Whole genome sequencing identified PARP1 catalytic domain mutations in all SR cell lines, and in vitro reconstitution of these PARP1 mutants confirmed them as drivers of saruparib resistance, in contrast to HR restoration as observed in the case of less-selective PARPi. PARP1 mutations also induce altered saruparib-dependent PARP1 trapping and PARylation inhibition. While these mutations render cells highly resistant to saruparib, differential sensitivity to other PARPi was observed and SR cell lines retain, and in some cases, increase, sensitivity to alternative clinical PARPi and DNA damage response (DDR)-targeted therapeutics. Our findings demonstrate that high-intensity selection pressure favors target-site mutation over pathway restoration as a primary escape mechanism from PARP1-selective inhibition. This study provides a first-in-class characterization of saruparib resistance and maps a clear therapeutic path forward. By identifying these specific PARP1 mutations and their collateral DDR vulnerabilities, we provide the molecular framework necessary to monitor and treat patients who progress on next-generation PARP1-selective inhibitors.
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Abstract Clinical poly (ADP)-ribose polymerase (PARP) inhibitors (PARPi) are limited by toxicities associated with inhibition of multiple PARP family proteins and acquired resistance. As PARP1-specific inhibitors, like saruparib (AZD5305), move toward standard-of-care status for BRCA and HR-deficient cancers replacing less specific PARPi, defining mechanisms of intrinsic and acquired resistance is essential for developing effective treatment strategies. Here, we established 5 saruparib-resistant (SR) cell lines from BRCA1-deficient MDA-MB-436 triple negative breast cancer (TNBC) cells using a selection strategy of high-level dosing consistent with clinical exposure, yielding models that are >1,000-fold resistant to saruparib. Whole genome sequencing identified PARP1 catalytic domain mutations in all SR cell lines, and in vitro reconstitution of these PARP1 mutants confirmed them as drivers of saruparib resistance, in contrast to HR restoration as observed in the case of less-selective PARPi. PARP1 mutations also induce altered saruparib-dependent PARP1 trapping and PARylation inhibition. While these mutations render cells highly resistant to saruparib, differential sensitivity to other PARPi was observed and SR cell lines retain, and in some cases, increase, sensitivity to alternative clinical PARPi and DNA damage response (DDR)-targeted therapeutics. Our findings demonstrate that high-intensity selection pressure favors target-site mutation over pathway restoration as a primary escape mechanism from PARP1-selective inhibition. This study provides a first-in-class characterization of saruparib resistance and maps a clear therapeutic path forward. By identifying these specific PARP1 mutations and their collateral DDR vulnerabilities, we provide the molecular framework necessary to monitor and treat patients who progress on next-generation PARP1-selective inhibitors. Competing Interest Statement The authors have declared no competing interest.

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