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Ludovini V, Bianconi F, Siggillino A, Piobbico D, Vannucci J, Metro G, Chiari R, Bellezza G, Puma F, Della Fazia MA, Servillo G, Crinò L. Gene identification for risk of relapse in stage I lung adenocarcinoma patients: a combined methodology of gene expression profiling and computational gene network analysis. Oncotarget 2017; 7:30561-74. [PMID: 27081700 PMCID: PMC5058701 DOI: 10.18632/oncotarget.8723] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/28/2016] [Indexed: 12/30/2022] Open
Abstract
Risk assessment and treatment choice remains a challenge in early non-small-cell lung cancer (NSCLC). The aim of this study was to identify novel genes involved in the risk of early relapse (ER) compared to no relapse (NR) in resected lung adenocarcinoma (AD) patients using a combination of high throughput technology and computational analysis. We identified 18 patients (n.13 NR and n.5 ER) with stage I AD. Frozen samples of patients in ER, NR and corresponding normal lung (NL) were subjected to Microarray technology and quantitative-PCR (Q-PCR). A gene network computational analysis was performed to select predictive genes. An independent set of 79 ADs stage I samples was used to validate selected genes by Q-PCR.From microarray analysis we selected 50 genes, using the fold change ratio of ER versus NR. They were validated both in pool and individually in patient samples (ER and NR) by Q-PCR. Fourteen increased and 25 decreased genes showed a concordance between two methods. They were used to perform a computational gene network analysis that identified 4 increased (HOXA10, CLCA2, AKR1B10, FABP3) and 6 decreased (SCGB1A1, PGC, TFF1, PSCA, SPRR1B and PRSS1) genes. Moreover, in an independent dataset of ADs samples, we showed that both high FABP3 expression and low SCGB1A1 expression was associated with a worse disease-free survival (DFS).Our results indicate that it is possible to define, through gene expression and computational analysis, a characteristic gene profiling of patients with an increased risk of relapse that may become a tool for patient selection for adjuvant therapy.
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Affiliation(s)
- Vienna Ludovini
- Medical Oncology, S. Maria Della Misericordia Hospital, Perugia, Italy
| | - Fortunato Bianconi
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | | | - Danilo Piobbico
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Jacopo Vannucci
- Department of Surgical and Biomedical Science, University of Perugia, Perugia, Italy
| | - Giulio Metro
- Medical Oncology, S. Maria Della Misericordia Hospital, Perugia, Italy
| | - Rita Chiari
- Medical Oncology, S. Maria Della Misericordia Hospital, Perugia, Italy
| | - Guido Bellezza
- Department of Experimental Medicine, Section of Anatomic Pathology and Histology, Perugia, Italy
| | - Francesco Puma
- Department of Surgical and Biomedical Science, University of Perugia, Perugia, Italy
| | | | - Giuseppe Servillo
- Department of Experimental Medicine, University of Perugia, Perugia, Italy
| | - Lucio Crinò
- Medical Oncology, S. Maria Della Misericordia Hospital, Perugia, Italy
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