Abstract 1613: Systematic screening for genomic vulnerabilities as drug targets for mesothelioma
Authors: Griffiths Gareth J. , James Dominic I. , Dyson Beth , Nalubowa Immaculate M. , Nakas Apostolos , Baas Paul , Tabi Zsuzsanna , Zhang Min , Sun Qianqian , Faulkner Daniel , Nusrat Nada , Baitei Essa Y. , Dzialo Joanna , Dawson Alan , Poile Charlotte , Spicer Jake , Bzura Aleksandra , Luo Jin-Li , Yang Hongji , Richards Cathy , Fennell Dean A. 
Published: June 2022

Abstract
Mesothelioma is a rare, lethal cancer caused by asbestos. Despite recent advances molecularly stratified therapy is lacking, in part due to the challenge of targeting the preponderance of tumor suppressors. Recent efforts to select therapy from our group have focused on poly(ADP-ribose) polymerase (PARP) and cyclin-dependent kinase 4/6 (CDK4/6) however the molecular determinants of response to therapy are unknown. To address this knowledge gap, we have undertaken high-throughput screening of exome sequenced primary mesothelioma cell lines alongside haploid cell lines harboring CRISPR knockouts of key, positively selected drivers BAP1, NF2 and MTAP. This strategy should enable us to identify robust and repeated drug-gene interactions using ensemble machine learning methods across a drug panel of drugs, both novel and in the clinic. Our platform encompasses multiple cross validation with both primary mesothelioma explants and clinical trial drug-response data. Patients were consented for extended pleurectomy decortication (EPD) and tissue sampled, disaggregated and cultured for no more than four passages to establish cell lines. Immunophenotyping and whole exome sequencing was conducted to validate their mesothelioma origins across an initial panel of 20 cell lines comprising primary cell lines established at the NKI (Netherlands) and Cardiff University (United Kingdom). To further characterize these, we investigated the response of the cell lines to 58 clinically approved cancer drugs using Imagen’s 3-day PredictRx assay. In addition, cell lines were treated with PARP inhibitors, olaparib, rucaparib, niraparib and talazoparib and incubated for 7 days. Cell count and cell death endpoints were captured in addition to phospho-H2AX immunofluorescence. Mesothelioma patient cells displayed differential sensitivity to targeted and non-targeted drugs. There were more nuanced responses amongst the targeted drugs, where for example epithelioid subtypes showed a greater sensitivity to mTOR, VEGFR and HDAC inhibitors in the 3-day assay. Compared with wild type cells, the haploid knockout cells were broadly 3-fold more sensitive to PARP inhibitors; mesothelioma primary cell lines showed exquisite sensitivity to talazoparib (IC50 &lt; 0.1 µM). Multiple cross validation of our results across exome sequenced primary mesothelioma explants and patient tumors (PARP Phase II) is ongoing (data to be presented), leveraging machine learning based prediction of sensitivity, to be further validated in an upcoming PARP randomized trial.
Citation Format: Gareth J. Griffiths, Dominic I. James, Beth Dyson, Immaculate M. Nalubowa, Apostolos Nakas, Paul Baas, Zsuzsanna Tabi, Min Zhang, Qianqian Sun, Daniel Faulkner, Nada Nusrat, Essa Y. Baitei, Joanna Dzialo, Alan Dawson, Charlotte Poile, Jake Spicer, Aleksandra Bzura, Jin-Li Luo, Hongji Yang, Cathy Richards, Dean A. Fennell. Systematic screening for genomic vulnerabilities as drug targets for mesothelioma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1613.