Abstract 5130: Phospho-proteomic dynamics reveal DNA damage and repair signatures of drug sensitivity
Authors: Gali Arad, Avital Hay-Koren, Nitzan Simchi, Dimitri Kovalerchik, Dina Daitchman, Amit Manor, Ofer Givton, Elyad Lezmi, Iris Alchanati, Yonatan Katzenelenbogen, Shay Herman, Alon Shtrikman, Galina Otonin, Eran Seger, Kirill Pevzner
Journal: Cancer Research (2024)

Abstract There are numerous drug development efforts of DNA damage response (DDR) targets, such as PARP, ATR, ATM, CHK1, where the ability to accurately identify responsive sub-populations for monotherapies and combinations is a major challenge. Patients are routinely assigned to these drugs based on BRCA mutation, or BRCAness profile, encompassing homologous recombination deficiencies (HRD) which do not always represent the responsive sub-populations. Since DNA replication and DNA repair mechanisms are dominated by signaling events, we hypothesized that HRD extends beyond the genomic status, and is manifested also in the level of protein expression and protein modification. To that end, we created a harmonized data atlas consisting of phenotypic drug sensitivity and basal and dynamic phosphoproteomics of multiple cell lines before and after treatment of multiple DDR drugs. Proteogenomic analysis of cell lines showed that some cell lines are sensitive to DDR drugs despite being DDR-proficient at the genomic level. Proteomic analysis of these cell lines showed that at least a third of them exhibit proteomic DDR deficiency, explaining DDR sensitivity beyond mutation status. We then utilized our proteogenomic atlas and computational platform to address challenging clinical needs, namely discovery of a predictive ATR biomarker and identifying potential combination treatments to overcome ATRi resistance. Using basal state and protein dynamics of ATR coupled with ATRi sensitivity, we developed a novel predictive ATR biomarker, and tested it using two independent validation datasets. Our ATR biomarker exhibited improved precision and recall compared to genomic biomarkers represented by mutations commonly used in the clinic, and was not confounded by mutations. In addition, integrated analysis of basal and dynamic data of multiple cell lines treated with ATRi, highlighted both known (e.g. ATM) and novel resistance mechanisms and suggested potential drug combinations. Altogether, we demonstrate here the benefit of utilizing (phospho)-proteomic data to tackle clinical challenges in DDR drug development, such as predictive biomarkers and combination strategies. We provide a proteomics-based framework that would enable future patient selection in DDR clinical trials. Citation Format: Gali Arad, Avital Hay-Koren, Nitzan Simchi, Dimitri Kovalerchik, Dina Daitchman, Amit Manor, Ofer Givton, Elyad Lezmi, Iris Alchanati, Yonatan Katzenelenbogen, Shay Herman, Alon Shtrikman, Galina Otonin, Eran Seger, Kirill Pevzner. Phospho-proteomic dynamics reveal DNA damage and repair signatures of drug sensitivity [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 5130.