Identification of long non-coding RNA-related and –coexpressed mRNA biomarkers for hepatocellular carcinoma

Abstract

BackgroundWhile changes in mRNA expression during tumorigenesis have been used widely as molecular biomarkers for the diagnosis of a number of cancers, the approach has limitations. For example, traditional methods do not consider the regulatory and positional relationship between mRNA and lncRNA. The latter has been largely shown to possess tumor suppressive or oncogenic properties. The combined analysis of mRNA and lncRNA is likely to facilitate the identification of biomarkers with higher confidence.ResultsTherefore, we have developed an lncRNA-related method to identify traditional mRNA biomarkers. First we identified mRNAs that are differentially expressed in Hepatocellular Carcinoma (HCC) by comparing cancer and matched adjacent non-tumorous liver tissues. Then, we performed mRNA-lncRNA relationship and coexpression analysis and obtained 41 lncRNA-related and -coexpressed mRNA biomarkers. Next, we performed network analysis, gene ontology analysis and pathway analysis to unravel the functional roles and molecular mechanisms of these lncRNA-related and -coexpressed mRNA biomarkers. Finally, we validated the prediction and performance of the 41 lncRNA-related and -coexpressed mRNA biomarkers using Support Vector Machine model with five-fold cross-validation in an independent HCC dataset from RNA-seq.ConclusionsOur results suggested that mRNAs expression profiles coexpressed with positionally related lncRNAs can provide important insights into early diagnosis and specific targeted gene therapy of HCC.

Construction of a genome instability-derived lncRNA-based risk scoring system for the prognosis of hepatocellular carcinoma

“…Transcription and dysfunction of lncRNA is closely involved in tumorigenesis, including HCC [ 22 ]. Moreover, lncRNA with time and tissue specificity shows different expression levels in tumors and healthy states and different tumor stages, which suggests lncRNA has great potential to be a new prognostic biomarker [ 23 ]. For example, a controlled study involving 80 HCC patients and 50 healthy subjects finds that the expression of cancer susceptibility candidate 9 in HCC patients significantly increases with area under the curve (AUC) at 0.933 [ 24 ].…”

Regulation of Tumorigenesis in Hepatocellular Carcinoma via the AKT3 Pathway in Cell Lines

“…The modifications in the condition of the liver all over the formation of hepatocellular carcinoma are supported by altering the tumor microenvironment (TME) form that continues an opportunity advocating malignancy. The modification of the signaling pathways is general in hepatocellular carcinoma and is important for the development of the malignancy [ 10 ].…”

Microtubule-associated protein tau (MAPT) is a promising independent prognostic marker and tumor suppressive protein in clear cell renal cell carcinoma

“…Additionally, in the present study, low expression of MAPT-AS1 was associated with poor prognosis after nephrectomy in silico analysis. Several studies have found that integrated mRNA and lncRNA expression profiling are promising prognostic biomarkers in some cancers [31,32]. Collectively, these results indicate that MAPT and MAPT-AS1 would help to make promising prognostic biomarkers in ccRCC by integrating mRNA and lncRNA expression.…”