MET Exon 14-altered Lung Cancers and MET Inhibitor Resistance

Abstract

Purpose: MET tyrosine kinase inhibitors (TKIs) can achieve modest clinical outcomes in MET exon 14-altered lung cancers, likely secondary to primary resistance. Mechanisms of primary resistance remain poorly characterized and comprehensive proteomic analyses have not previously been performed.

Experimental design: We performed hybrid capture-based DNA sequencing, targeted RNA sequencing, cell-free DNA sequencing, selected reaction monitoring mass spectrometry (SRM-MS), and immunohistochemistry on patient samples of MET exon 14-altered lung cancers treated with a MET TKI. Associations between overall response rate (ORR), progression-free survival (PFS), and putative genomic alterations and MET protein expression were evaluated.

Results: Seventy-five of 168 MET exon 14-altered lung cancers received a MET TKI. Previously undescribed (zygosity, clonality, whole-genome duplication) and known (copy-number focality, tumor mutational burden, mutation region/type) genomic factors were not associated with ORR/PFS (P > 0.05). In contrast, MET expression was associated with MET TKI benefit. Only cases with detectable MET expression by SRM-MS (N = 15) or immunochemistry (N = 22) responded to MET TKI therapy, and cancers with H-score ≥ 200 had a higher PFS than cancers below this cutoff (10.4 vs. 5.5 months, respectively; HR, 3.87; P = 0.02).

Conclusions: In MET exon 14-altered cancers treated with a MET TKI, a comprehensive analysis of previously unknown and known genomic factors did not identify a genomic mechanism of primary resistance. Instead, MET expression correlated with benefit, suggesting the potential role of interrogating the proteome in addition to the genome in confirmatory prospective trials.

Figure 1.. Landscape of MET exon 14-alterations in lung cancer and sequencing by RNA-based anchored multiple PCR.

For many patients, the likelihood of exon 14 being skipped in their cancer based on DNA-based sequencing was high (light-green). The rest of the cases were nominated for RNA-based confirmation via the MSK-Fusion panel. In patients, with sufficient tissue for MSK-Fusion testing, cases where exon 14 skipping was confirmed are shown in dark green, while those where exon 14 skipping was not observed in RNA are shown in red. Of note, one mutation not confirmed by RNA (c.3028+1221G > A) is deep into intron 14 and is not shown. Patients whose cancers were nominated for MSK-Fusion testing but did not have sufficient tissue for test completion are shown in gray. +, 2 patients; *, 3 patients.

Figure 2.. Pre-treatment genomic features of MET exon 14-altered lung cancers and MET inhibitor activity.

(A) Progression-free survival and best objective response with MET inhibition. Each column is an individual patient/biopsy (N = 75). (B) Splice site region, zygosity, whole genome duplication, copy number changes, focality, and clonality (clonal if > 80%). (C) Tumor mutational burden (TMB). (D) Sample origin, previous exposure to chemotherapy, and concurrent genomic alterations.

Figure 3.. MET expression in MET exon 14-altered lung cancers and acquired resistance.

(a) MET protein expression by mass spectrometry (SRM-MS). (b) MET expression by immunohistochemistry (IHC). (c) Correlation of MET protein expression between SRM-MS and IHC. (d) MET exon 14 skipping detected by RNA-based anchored multiplex PCR (blue – skipping present; open circle– insufficient tissue). (e) Best response to MET inhibition by IHC expression. (f) Best response to MET inhibition by protein expression (SRM-MS). (g) Progression-free survival in cancers stratified by H-score.

Figure 3.. MET expression in MET exon 14-altered lung cancers and acquired resistance.

(a) MET protein expression by mass spectrometry (SRM-MS). (b) MET expression by immunohistochemistry (IHC). (c) Correlation of MET protein expression between SRM-MS and IHC. (d) MET exon 14 skipping detected by RNA-based anchored multiplex PCR (blue – skipping present; open circle– insufficient tissue). (e) Best response to MET inhibition by IHC expression. (f) Best response to MET inhibition by protein expression (SRM-MS). (g) Progression-free survival in cancers stratified by H-score.

Figure 4.

(a) On-/off-target mechanisms of acquired resistance in paired tumor biopsies. (b) Resistance detected in post-progression circulating tumor DNA.