The mRNA, miRNA and lncRNA networks in hepatocellular carcinoma: An integrative transcriptomic analysis from Gene Expression Omnibus

Abstract

Research advances and analysis in the non-protein coding part of the human genome have suggested that microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are associated with tumor initiation, growth and metastasis. Accumulating studies have demonstrated that a class of miRNAs and lncRNAs are dysregulated in hepatocellular carcinoma (HCC) and closely associated with tumorigenesis, diagnosis and prognosis. In the present study, integrative analysis of published data on multi-level Gene Expression Omnibus (GEO) and a bioinformatics computational approach were used to predict regulatory mechanism networks among differentially expressed mRNAs, miRNAs, and lncRNAs. Firstly, nine microarray expression data sets of mRNAs, miRNAs, and lncRNAs associated with HCC were collected from GEO datasets. Secondly, a total of 628 mRNAs, 15 miRNAs, and 49 lncRNAs were differentially expressed in this integrative analysis. Following this, mRNA, miRNA and lncRNA regulatory or co-expression networks were constructed. From the construction of the regulatory networks, five miRNAs and ten lncRNAs were identified as key differentially expressed noncoding RNAs associated with HCC progression. Finally, the regulatory effects of ten lncRNAs and miRNAs were validated. The study provides a novel insight into the understanding of the transcriptional regulation of HCC, and differentially expressed lncRNAs targeted and regulated by miRNAs were identified and validated in HCC specimens and cell lines.

Predictive Value of A Novel lncRNA LINC02518 in Evaluating the Prognosis of Patients With Hepatocellular Carcinoma

“…The lncRNA expression pro les of HCC identi ed by microarray analysis have been previously reported (17,18). Zhu et al performed an lncRNA gene expression pro le analysis in 3 pairs of human HCC and adjacent non-tumor tissues using microarray containing 33,045 lncRNAs and 30,215 coding transcripts and identi ed 214 lncRNAs and 338 mRNAs abnormally expressed in all three HCC tissues with the genome-wide lncRNAs and mRNAs expression pro le analysis (17).…”

“…Zhu et al performed an lncRNA gene expression pro le analysis in 3 pairs of human HCC and adjacent non-tumor tissues using microarray containing 33,045 lncRNAs and 30,215 coding transcripts and identi ed 214 lncRNAs and 338 mRNAs abnormally expressed in all three HCC tissues with the genome-wide lncRNAs and mRNAs expression pro le analysis (17). Additionally, Xu et al collected nine microarray expression data sets of mRNAs, miRNAs, and lncRNAs associated with HCC and found that 628 mRNAs, 15 miRNAs, and 49 lncRNAs were differentially expressed using integrative analysis (18). In our study, we analyzed lncRNA expression pro les of 125 HCCs with a custom microarray having a total of 2,412 lncRNA transcripts, which might signi cantly reduce the confounding factors caused by individual sample differences.…”

Current Status Regarding Tumour Progression, Surveillance, Diagnosis, Staging, and Treatment Of HCC: A Literature Review

“…The RISC complex prevents the ribosome subunit from translating into a protein, so the gene is silenced. The tumorigenesis development can happen in the interaction between non-coding RNAs (lncRNAs), mRNAs and miRNAs [1] .…”

“…Hepatocellular carcinoma (HCC) is considered as primary carcinoma in the liver, and the third vital carcinoma in the world after lung cancer and colorectal cancer. It was described as the fifth and seventh most common cancer in men and women, respectively [1]. HCC global distribution differs depending on the country, for example, African or Asian people, the HCC is considered as the most morbidity cancer into these countries.…”

“…HCC global distribution differs depending on the country, for example, African or Asian people, the HCC is considered as the most morbidity cancer into these countries. There are different risk-factors which increases the risk of HCC including hepatic cirrhosis, chronic inflammations such as Hepatitis B-(HBV), Hepatitis C-virus (HCV), alcohol consumption, aflatoxin exposure, non-alcoholic fatty liver disease (NAFLD) and autoimmunity cases [1].…”