Abstract 4269: A gene signature defines chromosomal instability (CIN) and poor survival in liver cancer patients

Abstract

Abstract Background The molecular stratification of cancer patients into different subgroups becomes more and more important for clinical treatment. For human hepatocellular carcinoma (HCC), which is the third most common cause of cancer related deaths, molecular classification can be useful to discriminate between patient subgroups with different biological and clinical features. Especially chromosomal instability (CIN) represents one determinant for poor overall survival of HCC patients; however, a respective molecular signature has not been defined so far. In order to stratify HCC patients into groups with CIN we utilized a gene expression signature (termed CIN25 signature) that has been shown to correlate with CIN in other tumor entities such as glioma and breast cancer (Carter et al. 2006). In this study we examined the presence of the CIN25 signature in HCC patients and its correlation with overall survival. Moreover, the most important genes for patient classification were determined. Methods Gene expression data from 242 HCC patients (Roessler et al., 2010) was quantile discretized into ten bins and the patients were clustered into 3 groups using the k-means algorithm. The differential expression between these groups was visualized as a heatmap, while cluster specific changes in overall survival were shown using Kaplan-Meier curves. Statistical significance of survival was assessed using the log-rank-test and cox proportional hazard models. The Boruta method, which makes use of Random Forest classification models, was used to determine the most important genes for patient subgroup clustering. Results for CIN25 gene expression were confirmed in an independent cohort (n = 20) using quantitative real-time PCR. Results Gene expression analysis of HCC patients revealed the presence of the CIN25 signature. Patients could be clustered into three different groups with low (32%), moderate (35%) and high (33%) expression levels of the CIN signature genes. Survival data analysis showed that patients with high expression levels had a significantly worse overall survival in comparison to patients with low expression levels (p = 0.01). Moreover, the elevated expression of 19 out of the 25 CIN genes was significantly correlated to poor survival. The Boruta method identified MAD2L1, TTK, TPX2 and MCM2 as possible risk stratification markers of HCC patients. In an independent cohort the expression levels of selected CIN genes (n = 9) were measured and revealed significant upregulation in 57-82% of HCC patients. Conclusion These data demonstrate that the presence of the CIN25 signature correlates with poor prognosis in HCC patients and could be used to predict overall survival. The determination of genes that classify patients into different subgroups may lead to the establishment of new biomarkers for HCC in the clinics. References Carter SL, et al., Nat Genet. 2006 Sep;38(9):1043-8. Roessler S, et al., Cancer Res. 2010 Dec 15;70(24):10202-12. Citation Format: Sofia Weiler, Thomas Wolf, Federico Pinna, Stephanie Roessler, Teresa Lutz, Shan Wan, Jens Marquardt, Hauke Lang, Peter Schirmacher, Kai Breuhahn. A gene signature defines chromosomal instability (CIN) and poor survival in liver cancer patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4269. doi:10.1158/1538-7445.AM2015-4269