Comprehensive analysis of a long noncoding RNA-associated competing endogenous RNA network in colorectal cancer

Fan, Qiaowei; Liu, Bing-Rong

doi:10.2147/ott.s158309

Cited by 28 publications

(26 citation statements)

References 43 publications

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“…System-level analysis is widely used to detect diseases. Recently, the ceRNA network has received substantial attention in various diseases, such as gastric cancer, colorectal cancer, and pancreatic cancer (13,35,36). However, research to date on ceRNA in DN is focused on a single lncRNA, a single miRNA, or an lncRNA-miRNA pair; there are no reports on the ceRNA network in DN.…”

Section: Discussionmentioning

confidence: 99%

“…The combination of computational and experimental methods is a useful research approach for predicting and verifying ceRNA interactions (12). In addition, research has shown that changes in topologically critical ceRNAs are associated with the development of lung adenocarcinoma, colorectal cancer, and ovarian cancer (13)(14)(15). Thus, systematic ceRNA network analysis can significantly expand functional understanding of both coding and noncoding RNAs.…”

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confidence: 99%

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The topological key lncRNA H2k2 from the ceRNA network promotes mesangial cell proliferation in diabetic nephropathyviathe miR‐449a/b/Trim11/Mek signaling pathway

et al. 2019

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Evidence has shown that long noncoding RNAs (IncRNAs) in the competing endogenous RNA (ceRNA) network are involved in various diseases. However, there is a lack of studies of the ceRNA network in diabetic nephropathy (DN). In this study, we investigated the effect of IncRNAs on mesangial cell (MC) proliferation in DN‐related ceRNA networks. Differences in IncRNA and mRNA expression between DN and normal mouse kidney tissues were detected with RNA‐seq, and DN‐related IncRNA/mRNA/microRNA (miRNA) ceRNA networks were constructed by R3.4.3. Computational analysis was performed, and expression and interactions between the topological RNAs were detected by bioinformatics methods, real‐time quantitative PCR (qPCR), and luciferase assay. Cell proliferation ability was measured by 5‐ethynyl‐2′‐deoxyuridine (EdU) in MCs cultured under high‐ or low‐glucose conditions. Moreover, the effect of the topological key IncRNA histocompatibility 2 K region locus 2 (H2k2) H2k2 on MC proliferation via the miRNA (miR)‐449a/b/triplet motif 11 (Trim11)/Mek signaling pathway was examined by EdU, flow cytometry analysis, and Western blot. In total, 153 IncRNAs, 428 mRNAs, and 2242 interactions were included in the constructed DN‐related ceRNA network. There were 15 RNAs in the top 5% of degree and betweenness. The expression of IncRNA H2k2 and mRNA Trim11 in MCs was increased in DN, which is consistent with the results of RNA‐seq and real‐time qPCR in vivo and in vitro. miR‐449a and miR‐449b, which were down‐regulated in MCs cultured with high glucose, were selected for further analysis. The results of real‐time qPCR and luciferase assay revealed the IncRNA H2k2‐miR‐449a/b‐Trim11 interaction in MCs. In addition, the data showed that H2k2 regulates MC proliferation via the miR‐449ab/Trim11/Mek signaling pathway. Taken together, these results provide new insight into the association between the topological key IncRNA H2k2 in the DN‐related ceRNA network and the miR‐449a/b/Trim11/Mek signaling pathway during MC proliferation in DN.—Chen, W., Peng, R., Sun, Y., Liu, H., Zhang, L., Peng, H., Zhang, Z. The topological key IncRNA H2k2 from the ceRNA network promotes mesangial cell proliferation in diabetic nephropathy via the miR‐449a/b/Trim11/Mek signaling pathway. FASEB J. 33, 11492–11506 (2019). http://www.fasebj.org

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

The topological key lncRNA H2k2 from the ceRNA network promotes mesangial cell proliferation in diabetic nephropathyviathe miR‐449a/b/Trim11/Mek signaling pathway

et al. 2019

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“…Recently, an lncRNA/miRNA/mRNA interactome was reported based on CRC expression data from the TCGA database. These analyses illustrated a ceRNA network of 25 principal miRNAs and 64 lncRNAs, including CRNDE, H19, HULC and UCA1 [ 17 , 89 ]. As discussed below, UCA1 was reported to interact with 29 miRNAs in several types of cancers.…”

Section: Mechanisms Of Regulation By Long Non-coding Rnas In Cancementioning

confidence: 99%

Epigenetic Regulation by lncRNAs: An Overview Focused on UCA1 in Colorectal Cancer

Neve

Jonckheere

Vincent

et al. 2018

Cancers

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Colorectal cancers have become the second leading cause of cancer-related deaths. In particular, acquired chemoresistance and metastatic lesions occurring in colorectal cancer are a major challenge for chemotherapy treatment. Accumulating evidence shows that long non-coding (lncRNAs) are involved in the initiation, progression, and metastasis of cancer. We here discuss the epigenetic mechanisms through which lncRNAs regulate gene expression in cancer cells. In the second part of this review, we focus on the role of lncRNA Urothelial Cancer Associated 1 (UCA1) to integrate research in different types of cancer in order to decipher its putative function and mechanism of regulation in colorectal cancer cells. UCA1 is highly expressed in cancer cells and mediates transcriptional regulation on an epigenetic level through the interaction with chromatin modifiers, by direct regulation via chromatin looping and/or by sponging the action of a diversity of miRNAs. Furthermore, we discuss the role of UCA1 in the regulation of cell cycle progression and its relation to chemoresistance in colorectal cancer cells.

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“…These studies aimed at some genes including mRNA, miRNA, and lncRNA associated with the cancer and confirmed that some of genes serve important roles in treatment and prognosis. With the development of experimental studies and techniques for lncRNA discovery, lncRNA‐associated ceRNA networks have been constructed and analyzed in colorectal cancer, gastric cancer, and osteosarcoma . However, there existed fewer analysis of ceRNA network in hepatocellular carcinoma (HCC).…”

Section: Introductionmentioning

confidence: 99%

“…With the development of experimental studies and techniques for lncRNA discovery, lncRNA-associated ceRNA networks have been constructed and analyzed in colorectal cancer, gastric cancer, and osteosarcoma. 13,16,17 However, there existed fewer analysis of ceRNA network in hepatocellular carcinoma (HCC).…”

Section: Introductionmentioning

confidence: 99%

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

Lou

Dong

et al. 2019

Cancer Medicine

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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.

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Comprehensive analysis of a long noncoding RNA-associated competing endogenous RNA network in colorectal cancer

Cited by 28 publications

References 43 publications

The topological key lncRNA H2k2 from the ceRNA network promotes mesangial cell proliferation in diabetic nephropathyviathe miR‐449a/b/Trim11/Mek signaling pathway

The topological key lncRNA H2k2 from the ceRNA network promotes mesangial cell proliferation in diabetic nephropathyviathe miR‐449a/b/Trim11/Mek signaling pathway

Epigenetic Regulation by lncRNAs: An Overview Focused on UCA1 in Colorectal Cancer

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

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