au Array-Comparative Genomic Hybridization Reveals Loss of SOCS 6 Is Associated with Poor Prognosis in Primary Lung Squamous Cell Carcinoma

Background: Primary tumor recurrence commonly occurs after surgical resection of lung squamous cell carcinoma (SCC). Little is known about the genes driving SCC recurrence. Methods: We used array comparative genomic hybridization (aCGH) to identify genes affected by copy number alterations that may be involved in SCC recurrence. Training and test sets of resected primary lung SCC were assembled. aCGH was used to determine genomic copy number in a training set of 62 primary lung SCCs (28 with recurrence and 34 with no evidence of recurrence) and the altered copy number of candidate genes was confirmed by quantitative PCR (qPCR). An independent test set of 72 primary lung SCCs (20 with recurrence and 52 with no evidence of recurrence) was used for biological validation. mRNA expression of candidate genes was studied using qRT-PCR. Candidate gene promoter methylation was evaluated using methylation microarrays and Sequenom EpiTYPER analysis. Results: 18q22.3 loss was identified by aCGH as being significantly associated with recurrence (p = 0.038). Seven genes within 18q22.3 had aCGH copy number loss associated with recurrence but only SOCS6 copy number was both technically replicated by qPCR and biologically validated in the test set. SOCS6 copy number loss correlated with reduced mRNA expression in the study samples and in the samples with copy number loss, there was a trend for increased methylation, albeit non-significant. Overall survival was significantly poorer in patients with SOCS6 loss compared to patients without SOCS6 loss in both the training (30 vs. 43 months, p = 0.023) and test set (27 vs. 43 months, p = 0.010). Conclusion: Reduced copy number and mRNA expression of SOCS6 are associated with disease recurrence in primary lung SCC and may be useful prognostic biomarkers. Citation: Sriram KB, Larsen JE, Savarimuthu Francis SM, Wright CM, Clarke BE, et al. (2012) Array-Comparative Genomic Hybridization Reveals Loss of SOCS6 Is Associated with Poor Prognosis in Primary Lung Squamous Cell Carcinoma. PLoS ONE 7(2): e30398. doi:10.1371/journal.pone. 0030398 Editor: Christophe Nicot, University of Kansas Medical Center, United States of America Received July 11, 2011; Accepted December 15, 2011; Published February 17, 2012 Copyright: 2012 Sriram et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by NH&MRC and Queensland Smart State project grants; UQ Postgraduate Medical Scholarship and NH&MRC Postgraduate Medical Scholarship (to KBS), NH&MRC Practitioner Fellowship (KMF), NH&MRC Career Development Award (IAY), NH&MRC Biomedical Scholarship (SMS, CMW), Cancer Council Queensland Senior Research Fellowship (KMF), Queensland Clinical Research Fellowship (KMF, IAY) and The Prince Charles Hospital Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: bajee.sriram@uqconnect.edu. au