Despite recent advances in cancer treatment, lung cancer remains the leading cause of cancer mortality worldwide. Lung adenocarcinoma is the most prevalent subtype of lung cancer. Genomic profiling of lung adenocarcinomas has led to the identification of several targetable oncogenic drivers. Therapies targeting the oncogenic-driver pathway using various tyrosine kinase inhibitors (TKIs), are effective initially but responses are often transient and tumors eventually regrow due to drug resistance. Furthermore, drug resistance can arise via the selection of pre-existing resistant clones or via the de novo acquisition of mutations that are not present before therapy. We set out to understand the mechanism for the de novo acquisition of drug resistance mutations in oncogene-driven lung cancers. To do so, we investigated the gene expression changes that occur upon inhibition of oncogenic pathways. We found that oncoprotein targeted therapy induces adaptations favorable for APOBEC genome mutagenesis. Treatment with small molecule inhibitors against EGFR and ALK promoted transcriptional upregulation of members of APOBEC family of cytidine deaminases and downregulation of the uracil glycosylase UNG, the key protein needed for removal of APOBEC-induced DNA lesions. These changes in mRNA levels resulted in functional effects that can impact nuclear DNA by increasing nuclear APOBEC activity and reducing nuclear uracil excision capacity. Determination of changes in APOBEC mRNA levels and nuclear APOBEC activity over time and depletion studies identified APOBEC3B as a driver of both baseline and targeted therapy-induced nuclear APOBEC activity in pre-clinical lung cancer models. We found that APOBEC3B mediates genetic evolution and emergence of resistance during targeted therapy. We identified NF-kB pathway induction and c-Jun downregulation as key mediators of these treatment-induced molecular changes. Furthermore, we find an upregulation of APOBEC3B in lung cancer patients with progressive disease and a high proportion of APOBEC-associated mutations in patient tumors treated with targeted therapy. Some putative resistance mutations in patient tumors were also in the APOBEC-preferred context. Our study identifies a novel targeted therapy-induced evolutionary process involving an APOBEC DNA deaminase that could serve as an attractive co-target to elicit more durable treatment responses.

Citation Format: Manasi K. Mayekar, Deborah Caswell, Natalie Vokes, Wei Wu, Caroline McCoach, Collin Blakely, Nuri Alpay Temiz, Daniel Lucas Kerr, Julia Rotow, Franziska Haderk, Lauren Cech, Beatrice Gini, Shigeki Nanjo, Lisa Tan, Johnny Yu, Carlos Gomez, Philippe Gui, Elizabeth Yu, Nicholas Thomas, Julian Downward, Reuben Harris, Eliezer Van Allen, Charles Swanton, Trever Bivona. APOBEC3B fuels evolution of resistance during targeted cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB124.