Concurrent Alterations in EGFR-Mutant Lung Cancers Associated with Resistance to EGFR Kinase Inhibitors and Characterization of MTOR as a Mediator of Resistance

Abstract

To identify molecular factors that determine duration of response to EGFR tyrosine kinase inhibitors and to identify novel mechanisms of drug resistance, we molecularly profiled -mutant tumors prior to treatment and after progression on EGFR TKI using targeted next-generation sequencing. Targeted next-generation sequencing was performed on 374 consecutive patients with metastatic -mutant lung cancer. Clinical data were collected and correlated with somatic mutation data. Erlotinib resistance due to acquired MTOR mutation was functionally evaluated by and studies. In 200 -mutant pretreatment samples, the most frequent concurrent alterations were mutations in, and and focal amplifications in, and Shorter time to progression on EGFR TKI was associated with amplification of (HR = 2.4, = 0.015) or (HR = 3.7, = 0.019), or mutation in (HR = 1.7, = 0.006). In the 136 posttreatment samples, we identified known mechanisms of acquired resistance: EGFR T790M (51%), (7%), and amplifications (5%). In the 38 paired samples, novel acquired alterations representing putative resistance mechanisms included fusion, fusion, amplification, loss, and an MTOR E2419K mutation. Functional studies confirmed the contribution of the latter to reduced sensitivity to EGFR TKI and -mutant lung cancers harbor a spectrum of concurrent alterations that have prognostic and predictive significance. By utilizing paired samples, we identified several novel acquired alterations that may be relevant in mediating resistance, including an activating mutation in MTOR further validated functionally..

Combined targeted DNA and RNA sequencing of advanced NSCLC in routine molecular diagnostics: Analysis of the first 3,000 Heidelberg cases

“…As molecular data accumulate, it becomes evident that multiple other molecular alterations also affect the outcome of patients with oncogenedriven NSCLC, like p16/CDKN2A homozygous deletions, MET and HER2 amplifications for EGFR + NSCLC (present in 8/378 or 2%, 1/378 or 0.3% and 2/378 or 0.1% of patients with TKI-targetable lesions in EGFR in our cohort, respectively), all of which shorten TKI responses. 43,44 On the other hand, KEAP1 and NFE2L2 mutations, present in 11% and 2% of NSCLC in our cohort, appear to predict for chemotherapy resistance, according to the results of a recent study. 45 Only a broad, DNA and RNA-NGS-based diagnostic approach as presented in this work, can facilitate identification of distinct molecular subtypes in NSCLC as well as, in conjunction with a detailed clinical annotation, help to characterize the impact that different combinations of genetic alterations have on clinical outcome.…”

“…42 Of note, although the retrospective outcome analyses exemplary performed in our cohort (Fig. 43,44 On the other hand, KEAP1 and NFE2L2 mutations, present in 11% and 2% of NSCLC in our cohort, appear to predict for chemotherapy resistance, according to the results of a recent study. In our cohort, 18% of cases with TP53 deleterious mutations also carried various targetable genetic alterations (Fig.…”

Targeting Alterations in the RAF–MEK Pathway

“…In these mutants, high ERK activation drives feedback suppression of RAS activation (17), and these mutants do not commonly co-occur with other MAPK pathway alterations. In patients with EGFR-mutant non-small cell lung cancer, class II BRAF mutations have been identified as a mechanism of acquired resistance to EGFR inhibitors (19).…”

Genetic alterations in epidermal growth factor receptor‑tyrosine kinase inhibitor‑na�ve non‑small cell lung carcinoma

“…The following gene alterations were noted: EGFR C797S mutation in 5.2-16.7%, KRAS mutation in 2.6-7.7%, BRAF mutation in 7.7%, PIK3CA mutation in 2.6%, MEK mutation in 2.6%, JAK2 mutation in 2.6%, MET amplification in 2.6-50%, KRAS amplification in 2.6%, ERBB2 insertion in 2.6%, transformation to SCC in 9.1%, and transformation to SqCC in 4.5% of patients (2,3). Furthermore, analysis of matched samples of pre-and post-administration of first-or second-generation EGFR-TKIs showed acquired resistance in addition to T790M mutation in lung adenocarcinoma, MET amplification in 8%, ERBB2 amplification in 5%, and EGFR amplification in 16% of patients (15). Transformation to SCC was noted in 2.6-5.0% of patients (15), and another report demonstrated SqCC rarely occurred (17).…”

“…Several other mechanisms of resistance against all generation EGFR-TKIs have been identified including tertiary gene mutations other than EGFR C797S mutation (9)(10)(11), activation of bypass signaling by gene amplification (e.g., ERBB2 (12) and MET (13,14), driver gene mutations (e.g., RAS, RAF and PIK3CA) (3,15), gene alteration in cell cycle genes (14), and transformation to mesenchyme, small cell carcinoma (SCC), or squamous cell carcinoma (SqCC) (2,16,17). These described EGFR-TKI resistance mechanisms may also be expressed during the pre-TKI NSCLC state (6,15) and can be a challenge for cancer treatment of NSCLC patients with EGFR mutations.…”