Abstract 4684: A comprehensive platform for identification of KRAS-specific synthetic lethal targets using patient-derived cells

Abstract

Abstract Colorectal cancer (CRC) remains a global health concern, constituting a large portion of cancer incidence and mortality. Despite advances in comprehending the genetic and epigenetic landscape of CRC and progress achieved in developing KRAS-specific inhibitors poised for clinical evaluation, a significant unmet medical need persists. This underscores the necessity for innovative therapeutic interventions in this field, as effective therapeutic strategies targeting specific molecular vulnerabilities are currently lacking. Our study aims to address this gap by focusing on the identification of synthetic lethal (SL) inhibitors specific to the KRAS pathway. We have established a platform utilizing human intestinal stem cell (hISC)-derived CRC model cells, patient-derived xenografts (PDXs), and clinical samples for genomic and functional analyses. Employing CRISPR/Cas9 technology, we introduced common CRC mutations into hISCs, generating isogenic CRC model cells with diverse mutational backgrounds including KRAS G12D. Additionally, we developed PDXs from CRC patients and collected biopsy samples from primary and metastatic tumors. Through RNA-seq and whole-exome sequencing (WES), we identified molecular signatures and pathways associated with different mutational variants. Our innovative platform enables high-throughput screening, incorporating both small molecule screening and CRISPR/Cas9 dropout screening with a genome-wide library on CRC model cells. Notably, our focus on KRAS-specific SL inhibitors distinguishes our approach, aiming for targeted therapies tailored to specific CRC subtypes. Validation of driver mutations, such as APC, KRAS, and TP53, in patient-derived material showcased the relevance of our model. High-quality screening results, meeting industry-standard QC criteria, allowed us to identify essential and tumor suppressor genes critical for CRC. Importantly, the use of normal hISCs enabled the identification of genes crucial only for transformed cells. The platform serves as a powerful tool for target discovery and validation in CRC, emphasizing the significance of primary material-derived cells. Beyond CRC, our findings have broader implications for other cancer types and personalized medicine approaches. By focusing on the identification of KRAS-specific SL inhibitors, our research contributes to the development of novel therapies for CRC, addressing the urgent need for targeted interventions in this heterogeneous malignancy. Citation Format: Marcin Dulęba, Eliza Zimoląg, Joanna Szuszkiewicz, Marcin Serocki, Joanna Szklarczyk, Olga Dracz, Zuzanna Kurzejamska, Diego Coelho, Michał Combik, Oleksii Bryzghalov, Joanna Krawczyk, Agata Stachowicz, Michał Mikula, Krzysztof Brzózka, Rafał Dziadziuszko, Tomasz Rzymski, Andrzej Mazan. A comprehensive platform for identification of KRAS-specific synthetic lethal targets using patient-derived cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4684.