Research Papers:

Gene identification for risk of relapse in stage I lung adenocarcinoma patients: a combined methodology of gene expression profiling and computational gene network analysis

Vienna Ludovini _, Fortunato Bianconi, Annamaria Siggillino, Danilo Piobbico, Jacopo Vannucci, Giulio Metro, Rita Chiari, Guido Bellezza, Francesco Puma, Maria Agnese Della Fazia, Giuseppe Servillo and Lucio Crinò

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Oncotarget. 2016; 7:30561-30574. https://doi.org/10.18632/oncotarget.8723

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Vienna Ludovini1,*, Fortunato Bianconi2,*, Annamaria Siggillino1, Danilo Piobbico2, Jacopo Vannucci3, Giulio Metro1, Rita Chiari1, Guido Bellezza4, Francesco Puma3, Maria Agnese Della Fazia2, Giuseppe Servillo2, Lucio Crinò1

1Medical Oncology, S. Maria Della Misericordia Hospital, Perugia, Italy

2Department of Experimental Medicine, University of Perugia, Perugia, Italy

3Department of Surgical and Biomedical Science, University of Perugia, Perugia, Italy

4Department of Experimental Medicine, Section of Anatomic Pathology and Histology, Perugia, Italy

*These authors have contributed equally to this work

Correspondence to:

Vienna Ludovini, email: [email protected]

Fortunato Bianconi, email: [email protected]

Keywords: lung adenocarcinoma, gene expression profiling, gene networks, computational biology, cancer systems biology

Received: December 17, 2015    Accepted: March 28, 2016    Published: April 13, 2016


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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