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Liu S, Medina-Perez P, Ha-Thi MC, Wieland A, Stecklum M, Hoffmann J, Tchernitsa O, Sers C, Schäfer R. Rapid testing of candidate oncogenes and tumour suppressor genes in signal transduction and neoplastic transformation. Adv Biol Regul 2021; 83:100841. [PMID: 34866037 DOI: 10.1016/j.jbior.2021.100841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/17/2021] [Accepted: 11/20/2021] [Indexed: 11/18/2022]
Abstract
The COSMIC database (version 94) lists 576 genes in the Cancer Gene Census which have a defined function as drivers of malignancy (oncogenes) or as tumour suppressors (Tier 1). In addition, there are 147 genes with similar functions, but which are less well characterised (Tier 2). Furthermore, next-generation sequencing projects in the context of precision oncology activities are constantly discovering new ones. Since cancer genes differ from their wild-type precursors in numerous molecular and biochemical properties and exert significant differential effects on downstream processes, simple assays that can uncover oncogenic or anti-oncogenic functionality are desirable and may precede more sophisticated analyses. We describe simple functional assays for PTPN11 (protein-tyrosine phosphatase, non-receptor-type 11)/SHP2 mutants, which are typically found in RASopathies and exhibit potential oncogenic activity. We have also designed a functional test for lysyl oxidase (LOX), a prototypical class II tumour suppressor gene whose loss of function may contribute to neoplastic transformation by RAS oncogenes. Moreover, we applied this test to analyse three co-regulated, RAS-responsive genes for transformation-suppressive activity. The integration of these tests into systems biology studies will contribute to a better understanding of cellular networks in cancer.
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Affiliation(s)
- Sha Liu
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Paula Medina-Perez
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Minh-Cam Ha-Thi
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Anja Wieland
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Maria Stecklum
- Experimental Pharmacology and Oncology GmbH, Robert-Rössle-Str. 10, D-13125, Berlin-Buch, Germany
| | - Jens Hoffmann
- Experimental Pharmacology and Oncology GmbH, Robert-Rössle-Str. 10, D-13125, Berlin-Buch, Germany
| | - Oleg Tchernitsa
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany
| | - Christine Sers
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; German Cancer Consortium (DKTK), German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany
| | - Reinhold Schäfer
- Laboratory of Molecular Tumour Pathology and Cancer Systems Biology, Institute of Pathology, Charité Universitätsmedizin Berlin, Charitéplatz 1, D-10117, Berlin, Germany; German Cancer Consortium (DKTK), German Cancer Research Center, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany; Charité Comprehensive Cancer Center Berlin, Germany.
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