1
|
van Dam PA, van Dam PJHH, Rolfo C, Giallombardo M, van Berckelaer C, Trinh XB, Altintas S, Huizing M, Papadimitriou K, Tjalma WAA, van Laere S. In silico pathway analysis in cervical carcinoma reveals potential new targets for treatment. Oncotarget 2016; 7:2780-95. [PMID: 26701206 PMCID: PMC4823071 DOI: 10.18632/oncotarget.6667] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/21/2015] [Indexed: 11/25/2022] Open
Abstract
An in silico pathway analysis was performed in order to improve current knowledge on the molecular drivers of cervical cancer and detect potential targets for treatment. Three publicly available Affymetrix gene expression data-sets (GSE5787, GSE7803, GSE9750) were retrieved, vouching for a total of 9 cervical cancer cell lines (CCCLs), 39 normal cervical samples, 7 CIN3 samples and 111 cervical cancer samples (CCSs). Predication analysis of microarrays was performed in the Affymetrix sets to identify cervical cancer biomarkers. To select cancer cell-specific genes the CCSs were compared to the CCCLs. Validated genes were submitted to a gene set enrichment analysis (GSEA) and Expression2Kinases (E2K). In the CCSs a total of 1,547 probe sets were identified that were overexpressed (FDR < 0.1). Comparing to CCCLs 560 probe sets (481 unique genes) had a cancer cell-specific expression profile, and 315 of these genes (65%) were validated. GSEA identified 5 cancer hallmarks enriched in CCSs (P < 0.01 and FDR < 0.25) showing that deregulation of the cell cycle is a major component of cervical cancer biology. E2K identified a protein-protein interaction (PPI) network of 162 nodes (including 20 drugable kinases) and 1626 edges. This PPI-network consists of 5 signaling modules associated with MYC signaling (Module 1), cell cycle deregulation (Module 2), TGFβ-signaling (Module 3), MAPK signaling (Module 4) and chromatin modeling (Module 5). Potential targets for treatment which could be identified were CDK1, CDK2, ABL1, ATM, AKT1, MAPK1, MAPK3 among others. The present study identified important driver pathways in cervical carcinogenesis which should be assessed for their potential therapeutic drugability.
Collapse
Affiliation(s)
- Peter A van Dam
- Antwerp University Hospital, Centre of Oncologic Research (CORE) Antwerp University, Edegem, Belgium.,Multidisciplinary Oncologic Centre Antwerp (MOCA), Edegem, Belgium
| | - Pieter-Jan H H van Dam
- Antwerp University Hospital, Centre of Oncologic Research (CORE) Antwerp University, Edegem, Belgium
| | - Christian Rolfo
- Antwerp University Hospital, Centre of Oncologic Research (CORE) Antwerp University, Edegem, Belgium.,Multidisciplinary Oncologic Centre Antwerp (MOCA), Edegem, Belgium.,Phase I - Early Clinical Trials Unit, Oncology Department, University Hospital Antwerp UZA, Edegem, Belgium
| | - Marco Giallombardo
- Antwerp University Hospital, Centre of Oncologic Research (CORE) Antwerp University, Edegem, Belgium.,Phase I - Early Clinical Trials Unit, Oncology Department, University Hospital Antwerp UZA, Edegem, Belgium
| | - Christophe van Berckelaer
- Antwerp University Hospital, Centre of Oncologic Research (CORE) Antwerp University, Edegem, Belgium
| | - Xuan Bich Trinh
- Multidisciplinary Oncologic Centre Antwerp (MOCA), Edegem, Belgium
| | - Sevilay Altintas
- Multidisciplinary Oncologic Centre Antwerp (MOCA), Edegem, Belgium
| | - Manon Huizing
- Multidisciplinary Oncologic Centre Antwerp (MOCA), Edegem, Belgium
| | | | - Wiebren A A Tjalma
- Antwerp University Hospital, Centre of Oncologic Research (CORE) Antwerp University, Edegem, Belgium.,Multidisciplinary Oncologic Centre Antwerp (MOCA), Edegem, Belgium
| | - Steven van Laere
- Antwerp University Hospital, Centre of Oncologic Research (CORE) Antwerp University, Edegem, Belgium
| |
Collapse
|