Lung neuroendocrine tumours: deep sequencing of the four WHO histotypes reveals chromatin remodelling genes as major players and a prognostic role for TERT, RB1, MEN1 and KMT2D

Next-generation sequencing (NGS) was applied to 148 lung neuroendocrine tumours (LNET) comprising the 4 WHO classification categories: 53 typical carcinoid (TC), 35 atypical carcinoid (AC), 27 large cell neuroendocrine carcinoma (LCNEC), and 33 small cell lung carcinoma (SCLC). A discovery screen was conducted on 46 samples using whole-exome sequencing and high-coverage targeted sequencing of 418 genes. Eighty-eight recurrently mutated genes from both the discovery screen and current literature were verified in the 46 cases of the discovery screen and validated on additional 102 LNET by targeted NGS, and their prevalence was evaluated on the whole series. Thirteen of these 88 genes were also evaluated for copy number alterations (CNA). Carcinoids and carcinomas shared most of the altered genes but with different prevalence. Combining mutations and copy number changes, MEN1 alterations were almost exclusive of carcinoids, while alterations of TP53 and RB1 cell cycle regulation genes and PI3K/AKT/mTOR pathway genes were significantly enriched in carcinomas. Conversely, mutations in chromatin-remodelling genes, including histone modifiers and members of SWI/SNF complexes, were found at similar rates in carcinoids (45.5%) and carcinomas (55.0%), suggesting a major role in LNET pathogenesis. One AC and one TC showed a hypermutated profile associated with a POLQ damaging mutation. CNAs were fewer in carcinoids than carcinomas, however ACs showed a hybrid pattern where gains of TERT, SDHA, RICTOR, PIK3CA, MYCL and SRC genes were found at rates similar to carcinomas, while MEN1 loss rate mirrored that of TCs. Multivariate survival analysis revealed RB1 mutation (p=0.0005) and TERT copy gain (p=0.016) as independent predictors of poorer prognosis. MEN1 mutation was associated with poor prognosis in AC (p=0.0045), while KMT2D mutation correlated with longer survival in SCLC (p=0.0022). In conclusion, molecular profiling may complement histology for a better diagnostic definition and prognostic stratification of LNET.