Mutational and gene fusion analyses of primary large cell and large cell neuroendocrine lung cancer

Abstract

Large cell carcinoma with or without neuroendocrine features (LCNEC and LC, respectively) constitutes 3–9% of non-small cell lung cancer but is poorly characterized at the molecular level. Herein we analyzed 41 LC and 32 LCNEC (including 15 previously reported cases) tumors using massive parallel sequencing for mutations in 26 cancer-related genes and gene fusions in ALK, RET, and ROS1. LC patients were additionally subdivided into three immunohistochemistry groups based on positive expression of TTF-1/Napsin A (adenocarcinoma-like, n = 24; 59%), CK5/P40 (squamous-like, n = 5; 12%), or no marker expression (marker-negative, n = 12; 29%). Most common alterations were TP53 (83%), KRAS (22%), MET (12%) mutations in LCs, and TP53 (88%), STK11 (16%), and PTEN (13%) mutations in LCNECs. In general, LCs showed more oncogene mutations compared to LCNECs. Immunomarker stratification of LC revealed oncogene mutations in 63% of adenocarcinoma-like cases, but only in 17% of marker-negative cases. Moreover, marker-negative LCs were associated with inferior overall survival compared with adenocarcinoma-like tumors (p = 0.007). No ALK, RET or ROS1 fusions were detected in LCs or LCNECs. Together, our molecular analyses support that LC and LCNEC tumors follow different tumorigenic paths and that LC may be stratified into molecular subgroups with potential implications for diagnosis, prognostics, and therapy decisions.

Clinical framework for next generation sequencing based analysis of treatment predictive mutations and multiplexed gene fusion detection in non-small cell lung cancer

“…Complementary experimental RNA-based NGS analysis (ArcherDX, Boulder, CO, US), performed as previously described [9], identified the suspected fusion to be a TRIM24-RET fusion, confirming the NanoString assay's ability to detect also novel fusions.…”

USP7 inhibitors, downregulating CCDC6, sensitize lung neuroendocrine cancer cells to PARP-inhibitor drugs

“…In addition, in the same samples we observed polymorphic variations in STK11, ALK and MET (data not shown). A recent analyses for a mutational profile in primary lung LCNEC reported alterations in the STK11 gene in addition to PTEN and to p53 mutations, as distinctive feature and promising therapeutic target in neuroendocrine with respect to non-neuroendocrine large cells lung tumors [32]. We intend to further investigate the relevance of the STK11 variations that we identified (Malapelle U, Morra F et al, in preparation).…”

Next-Generation Sequencing of a Cohort of Pulmonary Large Cell Carcinomas Reclassified by World Health Organization 2015 Criteria

“…Antibodies used for whole tissue sections included TTF-1 (8G7G3/1), napsin A (polyclonal), and CK5/6 (D5/16B4), all obtained from Roche Ventana (Tucson, Arizona), and were prediluted. The antibody for p40 (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17) was diluted to 1:3000 and was obtained from EMB Millipore (Billerica, Massachusetts). Immunostaining of whole tissue sections was performed with an automated stainer (BenchMark Ultra; Roche Ventana) and primary antibody incubation times ranging from 20 to 24 minutes.…”

“…Mutation profiles of immunomarker-grouped pulmonary large cell carcinomas have been determined in prior studies with a Sequenom MassARRAY (Sequenom, San Diego, California) that targets hotspots in 8 genes, a variety of sequencing methods targeting 28 genes, and next-generation sequencing (NGS) of whole exomes in 26 genes. [4][5][6] In a pilot study to confirm and expand upon those prior studies, we performed NGS targeting mutation hotspots in 50 genes in NSCLC previously diagnosed as large cell carcinoma and now reclassified by 2015 WHO criteria with particular attention to tumors that now meet 2015 WHO criteria for LCC-N.…”