Identification of novel methylated targets in colorectal cancer by microarray analysis and construction of co-expression network

Abstract

The present study was conducted to investigate novel methylated targets in colorectal cancer (CRC). The mRNA expression profiles of GSE32323 in 17 cancer and non-cancerous tissues from CRC patients, as well as expression profiles of 5 CRC cell lines prior and subsequent to 5-aza-2'-deoxycytidine (5-aza-dC) treatment, were obtained from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) in 5 CRC cell lines prior and subsequent to 5-aza-dC treatment were combined with the CRC-specific gene expression profiling array data. Context likelihood of relatedness algorithm was used to construct the co-expression network of CRC-specific gene expression profile. A sub-network of identified reverse-overlapped DEGs was selected and underwent Kyoto Encyclopedia of Genes and Genomes Pathway Analysis. A total of 6 reverse-overlapped DEGs were identified. This present study verified fibulin 2 (FBLN2) and protein phosphatase 1 regulatory inhibitor subunit 14A (PPP1R14A) to be downregulated in the CRC tissue sample but upregulated in CRC cell lines following 5-aza-dC treatment. The identified reverse-overlapped DEGs were enriched in tumor-associated signaling pathways, including cellular tumor antigen p53, cell cycle and NOD-like receptor (NLR) signaling pathway. A total of 2 silenced genes with abnormal methylation in CRC were identified, including FBLN2 and PPP1R14A. The reverse-overlapped DEGs were enriched in p53, cell cycle and NLR signaling pathways, indicating that reverse-overlapped DEGs, particularly FBLN2 and PPP1R14A, may be important tumor suppressors and that these reverse-overlapped DEGs are inactivated by methylation in CRC.