A transcriptome profile in hepatocellular carcinomas based on integrated analysis of microarray studies

Abstract

BackgroundDespite new treatment options for hepatocellular carcinomas (HCC) recently, 5-year survival remains poor, ranging from 50 to 70%, which may attribute to the lack of early diagnostic biomarkers. Thus, developing new biomarkers for early diagnosis of HCC, is extremely urgent, aiming to decrease HCC-related deaths.MethodsIn the study, we conducted a comprehensive characterization of gene expression data of HCC based on a bioinformatics method. The results were confirmed by real time polymerase chain reaction (RT-PCR) and TCGA database to prove the credibility of this integrated analysis.ResultsAfter integrating analysis of seven HCC gene expression datasets, 1167 differential expressed genes (DEGs) were identified. These genes mainly participated in the process of cell cycle, oocyte meiosis, and oocyte maturation mediated by progesterone. The results of experiments and TCGA database validation in 10 genes was in full accordance with findings in integrated analysis, indicating the high credibility of our integrated analysis of different gene expression datasets. ASPM, CCT3, and NEK2 was showed to be significantly associated with overall survival of HCC patients in TCGA database.ConclusionThis method of integrated analysis may be a useful tool to minish the heterogeneity of individual microarray, hopefully outputs more accurate HCC transcriptome profiles based on large sample size, and explores some potential biomarkers and therapy targets for HCC.Electronic supplementary materialThe online version of this article (doi:10.1186/s13000-016-0596-x) contains supplementary material, which is available to authorized users.

Transcriptome Analysis Revealed a Highly Connected Gene Module Associated With Cirrhosis to Hepatocellular Carcinoma Development

“…Except the pathways mentioned above, “oocyte meiosis” and “progesterone-mediated oocyte maturation” are two main KEGG pathways which the identified modular gene were enriched in. Oocyte meiosis and progesterone-mediated oocyte maturation pathways have also been found to be associated with HCC by integrated analysis of microarray studies (Li L. et al, 2017; Wang F. et al, 2017). However, the causal association between oocyte meiosis and HCC onset should be investigated in further study.…”

SOCS1 regulates senescence and ferroptosis by modulating the expression of p53 target genes

“…The correlation between SOCS1 gene expression and that of p53 target genes related to ferroptosis was analysed using The Cancer Genome Atlas (TCGA) [ 51 ] provisional dataset containing 373 hepatocellular carcinoma (HCC) specimens, which was accessed via the cBioportal ( http://www.cbioportal.org ) [ 52 ]. The transcript levels were expressed as RNASeq Ve RESM (RNA-Seq by Expectation Maximization) [ 53 ].…”

CYP3A4 Gene Is a Novel Biomarker for Predicting a Poor Prognosis in Hepatocellular Carcinoma

“…Both RT-PCR and IHC correlated with the findings of the microarray analysis, and we identified CYP3A4 as a novel, potential clinically useful biomarker for the prognosis of HCC. Although many reports have performed comprehensive microarray analyses of the GEP for patients with HCC (10,(17)(18)(19)(20)(21)(22)(23)(24), the frequency of down-regulation and the prognostic impact of the CYP3A4 gene have not yet described in any reports of integrated microarray analyses. Most of these reports have instead focused on genes related to cancer pathways, and few have focused on the frequency of aberrant gene expression and their impact on the prognosis.…”