Abstract 167: Assessment of homologous recombination deficiency cancer signatures with patient-derived tumor organoid models

Abstract BRCA1/2 alterations are commonly used markers to characterize homologous recombination deficiency (HRD) in cancer. Deficiency in the DNA double-strand break repair mechanism can cause tumor vulnerability to platinum and poly (ADP-ribose) polymerase inhibitor (PARPi) through synergistic lethal mechanisms. However, PARPi resistance is observed among some BRCA-mutant cancer patients. Conversely, some wild-type BRCA1/2 cancers are susceptible to these therapies. Hence, there is a need to better characterize HRD cancers and uncover additional treatment options. Patient-derived tumor organoids (PDTOs) are emerging ex vivo cancer models as they harbor the mutational landscape of the original tumor and are shown to accurately replicate drug responses observed in patients. In this project, we used a diverse set of pan-cancer PDTOs to model HRD responses to PARPi and other therapies. A total of n=230 pan-cancer PDTOs were generated and characterized by cytopathology, immunohistochemistry, and NGS platforms, confirming concordance with corresponding tumors. Fifty PDTOs from patients with and without BRCA1/2 mutations and from patients who received platinum or PARPi were selected for this project, including ovary, breast, pancreas, endometrium and gastrointestinal cancers. HRD of the original cancers was determined by their genomic composition and manual curation of single base substitution molecular signatures and structural variants - a novel classifier trained and validated in our pan-cancer whole-genome sequencing (WGS) cohort. Mutational status of genes in HR pathway was recorded only for PDTOs that have whole exome sequencing (WES). We developed an immunofluorescent staining to detect RAD51 foci and support the functional HR status and evaluated the treatment timeline with daily brightfield imaging to record the effect of PARPi. We performed high throughput drug screening (HTDS) on 11 PDTOs with FDA-approved drugs, including DNA synthesis inhibitors, CHEK1 inhibitors, PARPi, and ATM/ATR inhibitors. Four PDTOs (rectum, ovary, and prostate) with BRCA1/2 alterations and 3 wild-type BRCA1/2 (pancreas and ovary) responded to PARPis; while 4 wild-type BRCA1/2 (pancreas and ovary) did not respond. Only 5 PDTOs were sensitive to platinum therapies, but all 11 PDTOs responded to the CHEK1 and ATM/ATR inhibitors. Further HTDS experiments on the rest of the selected PDTOs, including combination therapies, are ongoing. In this project, our combinational approach includes well-characterized pan-cancer PDTOs, a functional assay to determine the effects of genetic variants, and an innovative HTDS pipeline to assess HRD status. These robust and clinically relevant assays will help uncover alternative therapeutic options for patients with HRD cancers. Citation Format: Hui-Hsuan Kuo, Madj Al Assaad, John Nguyen, Jenna Moyer, Hamza Gokozan, Sarah Ackermann, Jared Capuano, Jyothi Manohar, Michael Sigouros, Andrea Sboner, Juan Miguel Mosquera, Olivier Elemento, Maria Laura Martin. Assessment of homologous recombination deficiency cancer signatures with patient-derived tumor organoid models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 167.