Characterization of Exon 14 Skipping Alterations (in NSCLC) and Identification of Potential Therapeutic Targets Using Whole Transcriptome Sequencing.

INTRODUCTION

Genomic alterations in the juxtamembrane exon 14 splice sites in NSCLC lead to increased MET stability and oncogenesis. We present the largest cohort study of Exon 14 (ex14) using whole transcriptome sequencing.

METHODS

A total of 21,582 NSCLC tumor samples underwent complete genomic profiling with next-generation sequencing of DNA (592 Gene Panel, NextSeq, whole exome sequencing, NovaSeq) and RNA (NovaSeq, whole transcriptome sequencing). Clinicopathologic information including programmed death-ligand 1 and tumor mutational burden were collected and RNA expression for mutation subtypes and amplification were quantified. Immunogenic signatures and potential pathways of invasion were characterized using single-sample gene set enrichment analysis and mRNA gene signatures.

RESULTS

A total of 533tumors (2.47%) with ex14 were identified. The most common alterations were point mutations (49.5%) at donor splice sites. Most alterations translated to increased expression, with co-amplification resulting in synergistic increase in expression (q < 0.05). Common coalterations were amplifications of (19.0% versus 1.8% wild-type [WT]), (13.2% versus 0.98% WT), and (10.0% versus 1.5% WT) (q < 0.05). High programmed death-ligand 1 > 50% (52.5% versus 27.3% WT, q < 0.0001) and lower proportion of high tumor mutational burden (>10 mutations per megabase, 8.3% versus 36.7% WT, < 0.0001) were associated with ex14, which were also enriched in both immunogenic signatures and immunosuppressive checkpoints. Pathways associated with ex14 included angiogenesis and apical junction pathways (q < 0.05).

CONCLUSIONS

ex14 splicing alterations and co-amplification translated to higher and synergistic expression at the transcriptomic level. High frequencies of and co-amplifications and association with multiple immunosuppressive checkpoints and angiogenic pathways provide insight into potential actionable targets for combination strategies in ex14 NSCLC.