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

Abstract

Next‐generation sequencing (NGS) was applied to 148 lung neuroendocrine tumours (LNETs) comprising the four World Health Organization classification categories: 53 typical carcinoid (TCs), 35 atypical carcinoid (ACs), 27 large‐cell neuroendocrine carcinomas, and 33 small‐cell lung carcinomas. A discovery screen was conducted on 46 samples by the use of 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 LNETs by targeted NGS; their prevalence was then evaluated on the whole series. Thirteen of these 88 genes were also evaluated for copy number alterations (CNAs). Carcinoids and carcinomas shared most of the altered genes but with different prevalence rates. When mutations and copy number changes were combined, MEN1 alterations were almost exclusive to carcinoids, whereas 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 those encoding 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. There were fewer CNAs in carcinoids than in carcinomas; however ACs showed a hybrid pattern, whereby gains of TERT, SDHA, RICTOR, PIK3CA, MYCL and SRC were found at rates similar to those in carcinomas, whereas the 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), whereas KMT2D mutation correlated with longer survival in SCLC (p = 0.0022). In conclusion, molecular profiling may complement histology for better diagnostic definition and prognostic stratification of LNETs. © 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

Insights into Novel Prognostic and Possible Predictive Biomarkers of Lung Neuroendocrine Tumors

“…Regarding SCLC in particular, homozygous deletions comprised 39.4% of the cases. Moreover, when loss of heterozygosity was also included, the RB1 alterations prevailed among SCLC cases, at 91% (22). Loss of TP53 was also frequent among highgrade NETs, as it was detected in 48.5% of SCLC and 40.7% of LCNEC cases, whereas fewer than one-third of carcinoids presented with TP53 losses.…”

“…Simbolo et al showed that chromatin-remodeling genes were mutated in carcinoids (45.5%) and carcinomas (55.0%) at similar rates (22). Specifically, the histone-lysine N-methyltransferase 2 (KMT2) family of covalent histone modifiers (KMT2A, KMT2C and KMT2D) was mutated in 13.6% carcinoids versus 26.7% carcinomas and the AT-rich interaction domain (ARID) family, involved in the switch/sucrose nonfermentable (SWI-SNF) complex (ARID1A, ARID1B, and ARID2), had mutations in 9.0% carcinoids versus 10.0% carcinomas (22).…”

“…Simbolo et al showed that chromatin-remodeling genes were mutated in carcinoids (45.5%) and carcinomas (55.0%) at similar rates (22). Specifically, the histone-lysine N-methyltransferase 2 (KMT2) family of covalent histone modifiers (KMT2A, KMT2C and KMT2D) was mutated in 13.6% carcinoids versus 26.7% carcinomas and the AT-rich interaction domain (ARID) family, involved in the switch/sucrose nonfermentable (SWI-SNF) complex (ARID1A, ARID1B, and ARID2), had mutations in 9.0% carcinoids versus 10.0% carcinomas (22). In another study, Fernandez-Cuesta et al performed gene copy-number analysis, and genome/exome and transcriptome sequencing of pulmonary carcinoids, and covalent histone modifiers were found to be mutated in 40% of the cases, whereas mutated members of the SWI-SNF complex were detected in 22.2% of them.…”

“…The expression of tumor protein 53 (TP53) and retinoblastoma protein 1 (RB1) cell-cycle checkpoint genes in lung NETs has been assessed by whole-exome and targeted sequencing, with a significantly higher mutational load detected in carcinomas (70.0%) compared with carcinoids (10.2%) (22). Loss of RB1 was frequently encountered in all lung NET subtypes, mainly in SCLC (69.7%) and LCNEC (55.6%) compared to typical (24.5%) and atypical carcinoids (11.4%).…”

“…Loss of TP53 was also frequent among highgrade NETs, as it was detected in 48.5% of SCLC and 40.7% of LCNEC cases, whereas fewer than one-third of carcinoids presented with TP53 losses. Conversely, loss of heterozygosity of multiple endocrine neoplasia type 1 (MEN1) was more frequently detected in carcinoids (15.1% in typical and 22.9% in atypical) compared to LCNEC (3.7%) and SCLC (0%) (22). Thus, it has been suggested that TP53 and RB1 transcription patterns may help distinguish between SCLC-and NSCLC-like LCNECs (23).…”