Phan, Z. | Search bioRxiv

bioRxiv2025

Unmatched cell line collections are not optimal for identification of PARP inhibitor response and drug synergies

PurposeWhile PARP inhibitors have shown great efficacy in patients with BRCA1 and BRCA2 mutations, many preclinical studies, including combination therapies, fail to translate into clinical approval, potentially due to the limitations of preclinical models. The goal of this brief report was to identify appropriate cell line models to investigate PARP inhibitor sensitivity and synergies. MethodsAn in-silico study of cell line collections was performed to assess the correlation between BRCA1 or BRCA2 mutations and sensitivity to PARP inhibitor monotherapy or combination therapy with a platinum-based chemotherapy. Subsequently, we characterised an isogenic model with matched cell lines containing Brca1 and Brca2 mutations and investigated the response of cells to PARP inhibitor alone, or in combination with chemotherapy. ResultsUsing cell line collections, cell lines with BRCA1 and BRCA2 alterations are not associated with increased sensitivity to PARP inhibitors. Other factors, such as high PARP1 expression and low-level genome alterations showed correlation with increased sensitivity to a PARP inhibitor. Furthermore, cell line collections did not reflect the synergy observed in patients to combination PARP inhibitor and platinum-based chemotherapy. Subsequently, we demonstrated that the ID8 isogenic model cell lines with specific mutations in Brca1 and Brca2 represent patient response to PARP inhibitor monotherapy, and in combination with chemotherapy. ConclusionsThis study suggests exercising caution when using cell line collections as part of model selection when investigating PARP inhibitor sensitivity and synergy. Our data proposes that using an isogenic preclinical model is more likely to accurately reflect patient response.

cancer biology↗

bioRxiv2025

JNK pathway suppression drives resistance to combination endocrine therapy and CDK4/6 inhibition in ER+ breast cancer

PurposeEndocrine therapy in combination with CDK4/6 inhibition doubles the progression-free survival of patients with advanced ER+ breast cancer, but resistance is inevitable, leaving patients with limited treatment options. Experimental DesignWe performed unbiased genome-wide CRISPR/Cas9 knockout screens using ER+ breast cancer cells to identify novel drivers of resistance to combination endocrine therapy (tamoxifen) and CDK4/6 inhibitor (palbociclib) treatment. Screen hits were validated by CRISPR/Cas9 knockout models, mechanistic analyses and evaluation of patient samples. ResultsOur screens identified the inactivation of JNK signalling, including loss of the kinase MAP2K7, as a key driver of combination resistance. We developed multiple CRISPR/Cas9 knockout ER+ breast cancer cell lines (MCF-7 and T-47D) to investigate the effects of MAP2K7, MAPK8 and MAPK9 loss. MAP2K7 knockout increased metastatic burden in vivo and led to impaired JNK-mediated stress responses, as well as promoting cell survival and reducing senescence entry following endocrine therapy and CDK4/6 inhibitor treatment. Mechanistically, this occurred via loss of the AP-1 transcription factor c-JUN, leading to an attenuated response to combination endocrine therapy plus CDK4/6 inhibition. Furthermore, we analysed ER+ advanced breast cancer patient cohorts and found that inactivation of the JNK pathway was associated with increased metastatic burden, and low pJNKT183/Y185 activity correlated with a poorer response to systemic endocrine and CDK4/6 inhibitor therapies. ConclusionsOverall, we demonstrate that suppression of JNK signalling enables persistent growth during combined endocrine therapy and CDK4/6 inhibition. Furthermore, our data provide a pre-clinical rationale to screen patients tumours for JNK signalling deficiency prior to receiving combined endocrine therapy and CDK4/6 inhibition. STATEMENT OF TRANSLATIONAL RELEVANCEResistance to CDK4/6 inhibitors in the context of endocrine therapy resistance presents an urgent clinical challenge for the management of estrogen receptor positive (ER+) breast cancer. However, the mechanisms driving resistance to this therapeutic combination remain poorly understood. Here, we have identified inactivation of JNK signalling, specifically loss of the JNK kinase MAP2K7, as a major determinant of resistance to combined endocrine therapy and CDK4/6 inhibition in ER+ breast cancer. We uncovered that MAP2K7 loss augments tumour survival in vitro and in vivo. This occurs via disruption of activator protein-1 (AP-1) transcription factors, and thus prevents the induction of therapy-induced senescence and JNK-induced stress response. These findings reveal a critical tumour suppressor role for the JNK pathway in ER+ breast cancer, highlighting the importance of identifying patients with deficient JNK signalling and cautioning against the development of JNK inhibitors for this setting.

cancer biology↗