Abstract 543: Identifying drivers of chemoresistance in SQLC using forward and reverse genetic approaches
Authors: Haarmann Mareike , Gadalla Dennis Said , Brägelmann Johannes 
Published: March 2024

Non-small cell lung cancer, mainly lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (SQLC), accounts for about 85 % of all lung cancers. While LUAD treatment options have greatly improved, SQLC remains challenging, as targetable mutations are rare. Immunotherapy provides benefits, nevertheless, chemotherapy remains a backbone of systemic treatment strategies for SQLC patients. Accordingly, a major challenge for SQLC treatment is the development of chemoresistant tumors, oftentimes leading to cross-resistance to multiple drugs and limiting patient survival. Currently, the causal pathways enabling tumor cells to survive therapeutic stress and drivers of chemotherapy resistance are insufficiently known, which impedes the development of novel therapeutic strategies. We therefore leverage forward and reverse genetic approaches including large-scale chemo-genetic perturbations to systematically map the landscape of molecular drivers involved in chemotherapy resistance in SQLC. By integrating the resulting data we derive specific knowledge of the underlying processes, in order to identify druggable targets in chemoresistant tumors and contribute to improved patient care.

To assess genes causally mediating chemotherapy resistance upon overexpression, we performed genome-wide CRISPR activation screens utilizing clinically used cisplatin and taxol. Additionally, we performed CRISPRa screens against four further drugs currently in clinical trials in order to distinguish genes causing cross-resistance to multiple drugs versus drug-specific mechanisms.

In parallel, we generated chemoresistant clones by prolonged low-dose treatment, to analyze transcriptomic adaptions to chemoresistance and validate the CRISPRa screening hits.

Initial findings show a large selection of unique and shared gene sets that were significantly enriched or reduced after treatment in the CRISPRa screen, indicating their involvement in the development of chemoresistance.

Of note, transcriptomic analysis of chemoresistant cells shows an overlap with the CRISPRa screen specifically for the unfolded protein response (UPR) that is transcriptionally enriched in chemoresistant cells and a positive hit in the CRISPRa screen. Chemoresistant clones show increased resistance to tunicamycine induced ER-stress, indicating an increased ability to overcome the accumulation of misfolded protein under cytotoxic treatment through the UPR. Specific inhibition of the UPR during cytotoxic treatment shows promising results in chemoresistant cells.

By combining our CRISPR activation screen and systematic analysis of chemoresistant cells we were able to identify the UPR as a driver and a druggable synthetically lethal dependency of chemoresistance in SQLC. This opens the possibility of studying the UPR as a potential target in the treatment of patients with chemoresistant tumors, improving patient outcome.

Citation Format: Mareike Haarmann, Dennis Said Gadalla, Johannes Brägelmann. Identifying drivers of chemoresistance in SQLC using forward and reverse genetic approaches [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 543.