Hepatocellular carcinoma (HCC) is the third leading cause of death from cancer in the world. To comprehensively investigate the utility of microRNAs (miRNAs) and protein-encoding transcripts (messenger RNAs [mRNAs]) in HCC as potential biomarkers for early detection and diagnosis, we exhaustively mined genomic data from three available omics datasets (GEO, Oncomine, and TCGA), analyzed the overlaps among gene expression studies from 920 hepatocellular carcinoma samples and 508 healthy (or adjacent normal) liver tissue samples available from six laboratories, and identified 178 differentially expressed genes (DEGs) associated with HCC. Paired with miRNA and lncRNA data, we identified 23 core genes that were targeted by nine differentially expressed miRNAs and 21 HCC-specific lncRNAs. We further demonstrated that alterations in these 23 genes were quite frequent, with five genes altered in over 5% of the population. Patients with high levels of YWHAZ, ENAH, and HMGN4 tended to have high-grade tumors and shorter overall survival, suggesting that these genes could be promising candidate biomarkers for disease and poor prognosis in patients with HCC. Our comprehensive mRNA, miRNA, and lncRNA omics analyses from multiple independent datasets identified robust molecules that may be used as biomarkers for early HCC detection and diagnosis.
[1]Fudan Univ, Shanghai Publ Hlth Clin Ctr, Sci Res Ctr, Shanghai, Peoples R China;
[2]Fudan Univ, Zhong Shan Hosp, Dept Gen Surg, Shanghai, Peoples R China;
[3]Shanghai Univ Med & Hlth Sci, Dept Lab Med, Zhoupu Hosp, Shanghai, Peoples R China;
[4]Natl Ctr Liver Canc, Shanghai, Peoples R China;
[5]Fudan Univ, Shanghai Med Coll, Pancreat Dis Inst, Dept Pancreat Surg,Huashan Hosp, Shanghai, Peoples R China;
[6]Second Mil Med Univ, Eastern Hepatobiliary Surg Hosp, Shanghai, Peoples R China;
[7]Fudan Univ, Shanghai Publ Hlth Clin Ctr, Dept Severe Hepatol, Shanghai, Peoples R China;
[8]Capital Med Univ, Dept Med Oncol, Beijing Chaoyang Hosp, Beijing, Peoples R China;
[9]Anhui Med Univ, Lab Mol Biol, Hefei, Anhui, Peoples R China;
[10]Anhui Med Univ, Dept Biochem, Hefei, Anhui, Peoples R China;
[11]NIDDK, Microarray Core, NIH, Bethesda, MD 20892 USA;
[12]Fudan Univ, Dept Pathol, Shanghai Publ Hlth Clin Ctr, Shanghai, Peoples R China
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