Uncovering Tyrosine Kinase Inhibitor Resistance Mutations In EGFR Mutant Lung Adenocarcinoma Using Whole Exome Sequencing

Abstract

Lung adenocarcinomas (AD) driven by activating mutations of epidermal growth factor receptor (EGFR) is ideally treated with EGFR tyrosine kinase inhibitors (TKI) but 20% show primary resistance and the mechanisms of 30% of acquired resistance remain unexplained. Identifying resistant mutations in metastatic or post-treatment cancers could be difficult due to tumour inaccessibility, sample inadequacy or patient unwillingness. To uncover potential resistant mutations, we analyzed 40 pre-treatment excision specimens of EGFR-mutated lung AD from 21 TKI responding and 19 non-responding/resistant patients using whole exome sequencing. On average, 2.9K variants were present in each sample, and the number or types of mutations were not associated with TKI response patterns. MET and PI3K-AKT-MTOR signaling were among the most enriched pathways in variant genes of the non-responding cohort. Compared to responders, the resistant cohort encompassed more mutations that were known to be actionable or showed cancer prognostic value. Case-wise manual curation showed resistant candidates were present in 14/19 (74%) of the non-responding group. EGFR T790M was not present. The commonest mutated gene was PTEN (3/19) (p.VL317fs, p.Y155C, p.R15S) followed by PIK3CA (2/19) (p.H1047R, p.V344G) and RB1 (1/19), all of which are known to mediate resistance in EGFR – mutant lung cancers. Promising candidates which were well-known cancer genes in other malignancies but uncommonly involved in lung cancers included CTNNB1, TSC1, APC, CDH1, DNMT3A, FBXW7. In the responding cohort, only 4/21 (19%) cases showed possible resistant candidates but the mutations did not involve functional domains or effects were uncertain. Together, this study showed clinically relevant mutations could be identified in excision specimens of pre-treatment EGFR mutant lung AD that subsequently developed primary TKI resistance. The known and promising targets identified could be useful screening targets for primary or acquired TKI resistance.