Frequency and functional characterization of fusion genes in squamous cell carcinoma of the lung

INTRODUCTION

In contrast to lung adenocarcinoma (LUAD), targetable genetic alterations are less frequently detected in squamous cell carcinoma of the lung (LUSC). Over the last years, gene fusions have become promising targets in many solid cancers. Here, we analysed a cohort of LUSC, identified recurrent fusion genes and functionally characterised these tumour genomes.

METHODS

A subset of 1608 squamous cell carcinomas of the lung was analysed by means of the FusionPlex® Lung Panel to identify potentially targetable gene fusions using targeted next-generation sequencing. Cases harbouring recurrent gene fusions were further analysed using FISH, Cytoscan HD arrays and cell culture experiments.

RESULTS

We found both, known and novel gene fusions in about 3 % of the cases. Known fusions occurring in lung cancer included ALK::EML4, EGFRvIII, EZR::ROS1 and FGFR3::TACC. We further identified recurrent gene fusions of currently unknown biological function, involving EGFR::VSTM2A and NSD3::FGFR1 and showed that the occurrence of the EGFR::VSTM2A fusion is accompanied by high-level amplification of EGFR. Our analyses further revealed that the genomes of these LUSC patients are chromosomally unstable, which leads us to believe that such non-actionable genomic rearrangements may be a result of "chromosomal chaos" most probably not representing exclusive cancer-driving genes in this cancer entity.

CONCLUSIONS

We emphasise that caution should be taken when novel fusions are found and that the appearance of new gene fusions should always be interpreted in the molecular context of the respective disease.

[Cytopathology and molecular diagnostics of non-small cell lung cancer (NSCLC)]

Cytological specimens from endobronchial aspirates and pleural effusions are frequently used materials in the diagnostics of non-small cell lung cancer (NSCLC). In the same way as histological samples from endobronchial and transbronchial biopsy material or computed tomography (CT)-guided needle biopsies, cytological specimens are eminently suitable for molecular and immunohistological biomarker diagnostics of NSCLC, provided optimal techniques and clear diagnostic algorithms are employed. This article presents the typical processing techniques and a scheme for biomarker analytics and discusses an optimal approach for comprehensive diagnostics of NSCLC. When cytological specimens are processed and used in this way, the analytics are equivalent to those from histopathological specimens. For a detailed and advanced description of cytological and molecular techniques on cytological specimens the reader is referred to our own review articles.