TY - JOUR
T1 - Application of microRNA and mRNA expression profiling on prognostic biomarker discovery for hepatocellular carcinoma
AU - Wei, Lin
AU - Lian, Baofeng
AU - Zhang, Yuannv
AU - Li, Wei
AU - Gu, Jianren
AU - He, Xianghuo
AU - Xie, Lu
N1 - Funding Information:
Publication of this article was funded by State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine. This article has been published as part of BMC Genomics Volume 15 Supplement 1, 2014: Selected articles from the Twelfth Asia Pacific Bioinformatics Conference (APBC 2014): Genomics. The full contents of the supplement are available online at http://www.biomedcentral.com/ bmcgenomics/supplements/15/S1.
Funding Information:
Written consent was obtained from the patient or their relative for publication for this study. This work was supported by grants from the National 973 Key Basic Research Program (2013CB910500), the National Natural Science Foundation of China (81125016, 81071637, 91029728) and the Key Infectious Disease Project [2012ZX10002012-014].
Publisher Copyright:
© 2014 Wei et al.
PY - 2014/1/24
Y1 - 2014/1/24
N2 - Background: Hepatocellular carcinoma (HCC) is one of the most highly malignant and lethal cancers of the world. Its pathogenesis has been reported to be multi-factorial, and the molecular carcinogenesis of HCC can not be attributed to just a few individual genes. Based on the microRNA and mRNA expression profiling of normal liver tissues, pericancerous hepatocellular tissues and hepatocellular carcinoma tissues, we attempted to find prognosis related gene sets for HCC patients. Results: We identified differentially expressed genes (DEG) from three comparisons: Cancer/Normal, Cancer/ Pericancerous and Pericancerous/Normal. GSEA (gene set enrichment analysis) were performed. Based on the enriched gene sets of GO terms, pathways and transcription factor targets, it was found that the genome instability and cell proliferation increased while the metabolism and differentiation decreased in HCC tissues. The expression profile of DEGs in each enriched gene set was used to correlate to the postoperative survival time of HCC patients. Nine gene sets were found to prognostic correlation. Furthermore, after substituting DEG-targeting-microRNA for DEG members of each gene set, two gene sets with the microRNA expression profiles were obtained that had prognostic potential. Conclusions: The malignancy of HCC could be represented by gene sets, and pericancerous liver exhibits important characteristics of liver cancer. The expression level of gene sets not only in HCC but also in the pericancerous liver showed potential for prognosis implying an option for HCC prognosis at an early stage. Additionally, the gene-targeting-microRNA expression profiles also showed prognostic potential, demonstrating that the multi-factorial molecular pathogenesis of HCC is contributed by various genes and microRNAs.
AB - Background: Hepatocellular carcinoma (HCC) is one of the most highly malignant and lethal cancers of the world. Its pathogenesis has been reported to be multi-factorial, and the molecular carcinogenesis of HCC can not be attributed to just a few individual genes. Based on the microRNA and mRNA expression profiling of normal liver tissues, pericancerous hepatocellular tissues and hepatocellular carcinoma tissues, we attempted to find prognosis related gene sets for HCC patients. Results: We identified differentially expressed genes (DEG) from three comparisons: Cancer/Normal, Cancer/ Pericancerous and Pericancerous/Normal. GSEA (gene set enrichment analysis) were performed. Based on the enriched gene sets of GO terms, pathways and transcription factor targets, it was found that the genome instability and cell proliferation increased while the metabolism and differentiation decreased in HCC tissues. The expression profile of DEGs in each enriched gene set was used to correlate to the postoperative survival time of HCC patients. Nine gene sets were found to prognostic correlation. Furthermore, after substituting DEG-targeting-microRNA for DEG members of each gene set, two gene sets with the microRNA expression profiles were obtained that had prognostic potential. Conclusions: The malignancy of HCC could be represented by gene sets, and pericancerous liver exhibits important characteristics of liver cancer. The expression level of gene sets not only in HCC but also in the pericancerous liver showed potential for prognosis implying an option for HCC prognosis at an early stage. Additionally, the gene-targeting-microRNA expression profiles also showed prognostic potential, demonstrating that the multi-factorial molecular pathogenesis of HCC is contributed by various genes and microRNAs.
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U2 - 10.1186/1471-2164-15-S1-S13
DO - 10.1186/1471-2164-15-S1-S13
M3 - Article
C2 - 24564407
AN - SCOPUS:84904037894
VL - 15
SP - 1
EP - 13
JO - BMC Genomics
JF - BMC Genomics
SN - 1471-2164
ER -