Diagnosis, prognosis and bioinformatics analysis of lncRNAs in hepatocellular carcinoma

Abstract

This study aims to comprehensively analyze the diagnosis and prognosis of lncRNAs in hepatocellular carcinoma (HCC). From the Gene Expression Omnibus database, we screened out and analyzed the differently expressed lncRNAs and related mRNAs using bioinformatics methods. The expressions of lncRNAs were validated in tumor tissues, cell lines and the Cancer Genome Atlas database. At the same time, we also conducted an exploratory analysis on the diagnostic and prognostic ability of lncRNAs in HCC. In this study, we found that most of the targeted mRNAs promote the biological process of cell division, cellular component of nucleoplasm, molecular function of protein binding, which were significantly associated with 12 KEGG pathways. LncRNA CRNDE and LINC01419 also had significant diagnostic value in HCC. In particular, the sensitivity, specificity and area under the curve of CRNDE were 71.0%, 87.1% and 0.701 (95% CI: 0.543-0.860), respectively. In addition, the high expression of CRNDE and GBAP1 predicated poor prognosis, while the high expression of LINC01093 suggested the opposite outcome. Through the comprehensive analysis of lncRNAs, it provided an important reference for the early diagnosis, prognosis evaluation, pathogenesis and targeted therapy of HCC.

Genomewide identification of a novel six‐LncRNA signature to improve prognosis prediction in resectable hepatocellular carcinoma

“…LncRNAs are a class of noncoding RNAs with lengths longer than 200 nucleotides, show no capacity of protein coding, but might regulate gene expression at genetic and epigenetic levels . So far, variety of lncRNAs or lncRNA groups have been uncovered might dictate HCC prognosis by multiple studies, most of which are about the functional roles and working mechanisms of single lncRNAs, and totally two (by Wang et al in 2017 and Ma et al in 2018) are found to describe the prognostic significance of multiple‐lncRNA signature in HCC . However, we should be wary of the conclusions of the previous studies for the following reasons.…”

“…First, most previous studies screened out survival related lncRNAs based on the differential profile between cancer and noncancerous samples . The method could miss considerable survival information in The Cancer Genome Atlas (TCGA) datasets including some important prognostic genes, and lncRNAs as well.…”

“…The patients with the diagnosis of non‐HCC liver cancer (cholangiocarcinoma), pathological metastasis, and postsurgical residual carcinoma, the history of neoadjuvant treatment, and too short survival time are considered to have distinct biological procedures and progression mechanisms, and should be excluded from the prognostic analysis . Third, most studies performed the analysis by mixing resectable and unresectable cancers . While resectable and unresectable HCCs are demonstrated to have entirely distinct prognosis and recommended with completely different treatment strategies and staging systems (the Union for International Cancer Control (UICC)/the American Joint Cancer Committee (AJCC) vs the Cancer of the Liver Italian Program (CLIP)/the Barcelona Clinic Liver Cancer (BCLC)), thus should be analyzed distinctively for the development of prognostic models.…”

LncRNA CRNDE is a biomarker for clinical progression and poor prognosis in clear cell renal cell carcinoma

“…31,32 In intrahepatic cholangiocarcinoma cases, Xia et al indicated that CRNDE overexpression was obviously correlated with poor differentiation grade, present lymph node metastasis, advanced tumor-nodes-metastasis (TNM) stage, and large size. 35 The discrepancy between Chen et al's result and Dai et al's result would be most likely due to the different samples and method used. 23 In addition, similar results also were reported in bladder cancer cases.…”

“…34 However, Dai et al showed that there was no statistically association between CRNDE and clinicopathological characteristics in hepatocellular carcinoma. 35 The discrepancy between Chen et al's result and Dai et al's result would be most likely due to the different samples and method used. Thus, more studies would be needed to verify the clinical significance of CRNDE in hepatocellular carcinoma.…”