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Alidousty C, Becker A, Binot E, Hillmer AM, Merkelbach-Bruse S, Budde B, Bäßmann I, Rappl G, Wolf J, Eich ML, Noh KW, Buettner R, Schultheis AM. Frequency and functional characterization of fusion genes in squamous cell carcinoma of the lung. Gene 2024; 895:148018. [PMID: 37981082 DOI: 10.1016/j.gene.2023.148018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/23/2023] [Accepted: 11/17/2023] [Indexed: 11/21/2023]
Abstract
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.
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Affiliation(s)
- Christina Alidousty
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany; Network Genomic Medicine, Cologne, Germany
| | - Arvid Becker
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany
| | - Elke Binot
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany
| | - Axel M Hillmer
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany; Network Genomic Medicine, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Robert Koch Strasse 21, 50931 Cologne, Germany
| | - Sabine Merkelbach-Bruse
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany; Network Genomic Medicine, Cologne, Germany
| | - Birgit Budde
- Cologne Center for Genomics, Medical Faculty of the University of Cologne, Weyertal 115b, 50931 Cologne, Germany
| | - Ingelore Bäßmann
- Cologne Center for Genomics, Medical Faculty of the University of Cologne, Weyertal 115b, 50931 Cologne, Germany
| | - Gunter Rappl
- Center for Molecular Medicine Cologne, University of Cologne, Robert Koch Strasse 21, 50931 Cologne, Germany
| | - Jürgen Wolf
- Lung Cancer Group Cologne, Department I for Internal Medicine, University Hospital Cologne, Cologne, Germany
| | - Marie-Lisa Eich
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany
| | - Ka-Won Noh
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany
| | - Reinhard Buettner
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany; Network Genomic Medicine, Cologne, Germany; Lung Cancer Group Cologne, Department I for Internal Medicine, University Hospital Cologne, Cologne, Germany
| | - Anne Maria Schultheis
- University Hospital and Medical Faculty, University of Cologne, Institute of Pathology, Kerpener Straße 62, 50937 Cologne, Germany.
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Fassunke J, Engels M, Meemboor S, Buettner R. [Cytopathology and molecular diagnostics of non-small cell lung cancer (NSCLC)]. INNERE MEDIZIN (HEIDELBERG, GERMANY) 2022; 63:694-699. [PMID: 35925269 DOI: 10.1007/s00108-022-01365-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
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.
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Affiliation(s)
- Jana Fassunke
- Institut für Pathologie, Universitätsklinikum Köln und Medizinische Fakultät der Universität zu Köln, Kerpener Str. 62, 50937, Köln, Deutschland
| | - Marianne Engels
- Institut für Pathologie, Universitätsklinikum Köln und Medizinische Fakultät der Universität zu Köln, Kerpener Str. 62, 50937, Köln, Deutschland
| | - Sonja Meemboor
- Institut für Pathologie, Universitätsklinikum Köln und Medizinische Fakultät der Universität zu Köln, Kerpener Str. 62, 50937, Köln, Deutschland
| | - Reinhard Buettner
- Institut für Pathologie, Universitätsklinikum Köln und Medizinische Fakultät der Universität zu Köln, Kerpener Str. 62, 50937, Köln, Deutschland.
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