Abstract 322: Triple combination array analysis detects the Collagen type1 alpha1 (COL1A1) gene as a new tumor related gene in hepatocellular carcinoma

Abstract Background: Epigenetics is one of the most important mechanisms for inactivating tumor suppressor genes or tumor-related genes in various human cancers. Hepatocellular carcinoma (HCC) is one type of human cancer in which epigenetic gene suppression is frequently found. To effectively detect a tumor-related, we performed triple combination array analysis, which consists of an expression array, a single nucleotide polymorphism (SNP) array, and a methylation array of the same surgical HCC specimen. Methods: Triple array analysis of one HCC sample from a 68-year-old female patient was performed. Gene expression profiles were determined using Affymetrix HGU133A and B Gene-Chips using RNA. The SNP chip array was conducted using the standard protocol for Affymetrix Gene Chip Mapping 500K arrays. Methylation array analysis used an Illumina Infinium HumanMethylation27 Beadchip Kit. The gene encoding Collagen type1 alpha1 (COL1A1) was identified and verified using HCC cell lines and 48 primary HCC tissues from patients who had undergone hepatectomy at our hospital. Results: Expression array analysis revealed that COL1A1 gene expression was decreased in tumor tissues (Log2 Ratio -1.1). In addition, SNP array analysis showed that the COL1A1 locus, 17q21, did not show a chromosomal deletion. Importantly, the methylation value (0-1.0) in the tumor tissue was higher (0.557) than that of the adjacent normal tissue (0.008). We hypothesized that the expression of this gene was suppressed by promoter hypermethylation. The suppressed expression of the COL1A1 gene in HCC cell lines was reactivated after 5-aza-2′-deoxycytidine (5-aza-dC) treatment. Sequence analysis identified hypermethylated CpG sites in the COL1A1 promoter region. In 48 HCC samples, 21 cases (44%) also showed COL1A1 gene promoter hypermethylation. The expression values of methylated cases, examined by real-time RT-PCR, were significantly downregulated (p=0.004) compared with unmethylated cases. Downregulation of the gene's expression was significantly correlated with pathological fc positive (p=0.026) and liver damage scores (p=0.011). Conclusion: Triple combination array analysis successfully revealed that the COL1A1 gene acts as a tumor suppressor gene in HCC via promoter hypermethylation. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 322. doi:10.1158/1538-7445.AM2011-322