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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] [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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Győrffy B, Stelniec-Klotz I, Sigler C, Kasack K, Redmer T, Qian Y, Schäfer R. Effects of RAL signal transduction in KRAS- and BRAF-mutated cells and prognostic potential of the RAL signature in colorectal cancer. Oncotarget 2016; 6:13334-46. [PMID: 26033452 PMCID: PMC4537018 DOI: 10.18632/oncotarget.3871] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 04/02/2015] [Indexed: 01/16/2023] Open
Abstract
Our understanding of oncogenic signaling pathways has strongly fostered current concepts for targeted therapies in metastatic colorectal cancer. The RALA pathway is novel candidate due to its independent role in controlling expression of genes downstream of RAS. We compared RALA GTPase activities in three colorectal cancer cell lines by GTPase pull-down assay and analyzed the transcriptional and phenotypic effects of transient RALA silencing. Knocking-down RALA expression strongly diminished the active GTP-bound form of the protein. Proliferation of KRAS mutated cell lines was significantly reduced, while BRAF mutated cells were mostly unaffected. By microarray analysis we identified common genes showing altered expression upon RALA silencing in all cell lines. None of these genes were affected when the RAF/MAPK or PI3K pathways were blocked. To investigate the potential clinical relevance of the RALA pathway and its associated transcriptome, we performed a meta-analysis interrogating progression-free survival of colorectal cancer patients of five independent data sets using Cox regression. In each dataset, the RALA-responsive signature correlated with worse outcome. In summary, we uncovered the impact of the RAL signal transduction on genetic program and growth control in KRAS- and BRAF-mutated colorectal cells and demonstrated prognostic potential of the pathway-responsive gene signature in cancer patients.
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Affiliation(s)
- Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Budapest, Hungary.,Semmelweis University, 2nd Department of Pediatrics, Budapest, Hungary.,MTA-SE Pediatrics and Nephrology Research Group, Budapest, Hungary
| | - Iwona Stelniec-Klotz
- Laboratories of Functional Genomics and Molecular Tumor Pathology, Charité Universitätsmedizin Berlin, Germany
| | - Christian Sigler
- Laboratories of Functional Genomics and Molecular Tumor Pathology, Charité Universitätsmedizin Berlin, Germany
| | - Katharina Kasack
- Laboratories of Functional Genomics and Molecular Tumor Pathology, Charité Universitätsmedizin Berlin, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
| | - Torben Redmer
- Laboratories of Functional Genomics and Molecular Tumor Pathology, Charité Universitätsmedizin Berlin, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
| | - Yu Qian
- Laboratories of Functional Genomics and Molecular Tumor Pathology, Charité Universitätsmedizin Berlin, Germany
| | - Reinhold Schäfer
- Laboratories of Functional Genomics and Molecular Tumor Pathology, Charité Universitätsmedizin Berlin, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center, Heidelberg, Germany
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Rodriguez L, de Bruijn HS, Di Venosa G, Mamone L, Robinson DJ, Juarranz A, Batlle A, Casas A. Porphyrin synthesis from aminolevulinic acid esters in endothelial cells and its role in photodynamic therapy. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2009; 96:249-54. [DOI: 10.1016/j.jphotobiol.2009.07.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 06/15/2009] [Accepted: 07/01/2009] [Indexed: 12/22/2022]
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SOCS3 regulates p21 expression and cell cycle arrest in response to DNA damage. Cell Signal 2008; 20:2221-30. [PMID: 18793717 DOI: 10.1016/j.cellsig.2008.08.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 08/09/2008] [Accepted: 08/11/2008] [Indexed: 10/21/2022]
Abstract
Genotoxic agents such as ionizing radiation trigger cell cycle arrest at the G1/S and G2/M checkpoints, allowing cells to repair damaged DNA before entry into mitosis. DNA damage-induced G1 arrest involves p53-dependent expression of p21 (Cip1/Waf-1), which inhibits cyclin-dependent kinases and blocks S phase entry. While much of the core DNA damage response has been well-studied, other signaling proteins that intersect with and modulate this response remain uncharacterized. In this study, we identify Suppressor of Cytokine Signaling (SOCS)-3 as an important regulator of radiation-induced G1 arrest. SOCS3-deficient fibroblasts fail to undergo G1 arrest and accumulate in the G2/M phase of the cell cycle. SOCS3 knockout cells phosphorylate p53 and H2AX normally in response to radiation, but fail to upregulate p21 expression. In addition, STAT3 phosphorylation is elevated in SOCS3-deficient cells compared to WT cells. Normal G1 arrest can be restored in SOCS3 KO cells by retroviral transduction of WT SOCS3 or a dominant-negative mutant of STAT3. Our results suggest a novel function for SOCS3 in the control of genome stability by negatively regulating STAT3-dependent radioresistant DNA synthesis, and promoting p53-dependent p21 expression.
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