Comprehensive analysis of five long noncoding RNAs expression as competing endogenous RNAs in regulating hepatoma carcinoma

Abstract

Liver cancer is the most common cancer and is the epitome of a recalcitrant cancer. Increasing evidence shown that long noncoding RNAs (lncRNA) were associated with cancer‐related death and could function as a competing endogenous RNA (ceRNA). To explore regulatory roles and potential prognostic biomarkers of lncRNA for liver cancer, RNA‐sequencing expression data were downloaded from the TCGA database and GEO database. A total of 357 patients were randomly divided into a discovery group and a validation group, of which 313 patients can obtain clinical data. In discovery phrase, 58 lncRNAs, 16 miRNAs, and 34 mRNAs were screened to construct the ceRNA network based on 252 patients employed from discovery group. Univariate and multivariate Cox hazard regression analysis model revealed that five lncRNAs (AATK‐AS1, C10orf91, LINC00162, LINC00200, and LINC00501) from 58 lncRNAs were formulated to predict the overall survival (OS). We used the value of gene expression and regression coefficients to construct a risk score based on the five lncRNAs. Next, we validated our model in the GSE116174 dataset (n = 64) and the validation group (n = 94) from TCGA database. Subgroup analysis suggest that the five lncRNAs played critical parts in early stage in cancer from both discovery and validation groups. The five lncRNAs were also found to be associated with immune cells infiltration including CD4+ memory activated, NK cells activated and mast cells activated, then the results were also validated according to the validation group. Furthermore, KEGG pathway enrichment analysis showed that these nine coexpressed modules using the method of WGCNA, and many of these pathways are associated with the development and progression of disease. At last, the transcription factor binding sites (TFBS) of the five lncRNAs were predicted, which help us to understand the potential mechanism that the TFBS adjusted the ceRNA network. In summary, the ceRNA regulatory network may contribute to a better understanding of liver cancer mechanism and provide potential prognostic biomarkers and therapeutic targets.

Construction of a competing endogenous RNA network using differentially expressed lncRNAs, miRNAs and mRNAs in non‑small cell lung cancer

“…Differentially expressed RNAs were screened from RNA-seq data and miRNA-seq data in TCGA () separately, since lncRNAs and mRNAs were included in the RNA-seq database and miRNAs were included in the miRNA-seq database (21). Then, the data of RNA expression in NSCLC were extracted from these two databases and normalized by ‘DESeq2’ and ‘edgeR’ package.…”

Integrated Analysis of a Competing Endogenous RNA Network Reveals a Prognostic Signature in Kidney Renal Papillary Cell Carcinoma

“…Indeed, in our ceRNA network, GAS6-AS1 and LRRC4 both interacted with miR182; thus, we predicted that GAS6-AS1 could bind miR182 and act as a ceRNA, therefore modulating the levels of the LRRC4 in KIRP. Using PubMed, we found that the only report on the function and mechanism of LINC00200, was from Lou et al (2019) . They reported that LINC00200 played a critical part in early stage hepatocellular carcinoma (HCC) after analyzing RNA-sequencing expression data of liver cancer from the TCGA and GEO database ( Lou et al, 2019 ).…”

“…Using PubMed, we found that the only report on the function and mechanism of LINC00200, was from Lou et al (2019) . They reported that LINC00200 played a critical part in early stage hepatocellular carcinoma (HCC) after analyzing RNA-sequencing expression data of liver cancer from the TCGA and GEO database ( Lou et al, 2019 ). In our study, high expression of LINC00200 was associated with poor survival outcomes in KIRP patients and higher expression of LINC00200 at later tumor stages, which indicated that LINC00200 may have been an oncogene in renal clear cell carcinoma.…”

The Construction and Analysis of ceRNA Network and Patterns of Immune Infiltration in Colon Adenocarcinoma Metastasis

“…In addition, the existence of tumor-infiltrating immune cells, especially leukocytes, is also an essential evident witnesses of the activity of immune system and is supposed to play critical roles in cancer growth, progression and metastasis including the COAD ( Dadabayev et al, 2004 ; Halama et al, 2009 ; Palmqvist et al, 2013 ). However, there are only a few studies focusing on the regulatory mechanism between ceRNA networks and tumor-infiltrating immune cells, not containing COAD ( Lou et al, 2019 ; Yang et al, 2019 ; Zhao R. et al, 2019 ).…”