Construction and analysis of dysregulated lncRNA‐associated ceRNA network in colorectal cancer

Zhu, Yiping; Bian, Yinzhu; Zhang, Qun; Hu, Jing; Li, Li; Yang, Mi; Hu, Qian; Yu, Lan; Liu, Baorui; Qian, Xiaoping

doi:10.1002/jcb.28201

Cited by 34 publications

(30 citation statements)

References 62 publications

(103 reference statements)

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“…Previously, LINC00365 expression was reported as 3.12 ± 1.99 in CRC tissues, which was significantly higher than that in the adjacent normal intestinal mucosa (0.98 ± 0.50). 24 In this study, nearly 90% (20/22) of CRC tissues displayed a significant elevation in LINC00365 expression levels ( Figure 1A). LINC00365 expression was also markedly elevated in tumor tissues with lymph node metastasis, vascular invasion, and nerve invasion ( Figure 1B-D).…”

Section: Linc00365 Is Upregulated In Crc Tissues and Cell Linesmentioning

confidence: 50%

LINC00365 promotes colorectal cancer cell progression through the Wnt/β‐catenin signaling pathway

Zhu

Bian

Zhang

et al. 2019

J of Cellular Biochemistry

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In the past decade, substantial evidence established that long noncoding RNAs are serious about mediating the evolution of malignancies. In previous studies, LINC00365, which has not been reported in colorectal cancer (CRC), was selected using the bioinformatics analysis in GSE109454 and GSE41655 data sets. However, the function and mechanism of LINC00365 are still obscure. In our study, LINC00365 was found upregulated in CRC specimens and intimately connected with the prognosis of patients with CRC. In addition, LINC00365 overexpression enhances the cell abilities of proliferation, migration, and invasion in vitro. Meanwhile, mechanistic studies showed that LINC00365 might involve in CRC cell progression by mediating the Wnt/β‐catenin pathway. Furthermore, LINC00365 upregulation increased CDK1 protein expression. In conclusion, this study suggests that LINC00365 acts as a vital part in facilitating CRC progression and might play as a therapeutic target for patients with CRC.

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Section: Linc00365 Is Upregulated In Crc Tissues and Cell Linesmentioning

confidence: 50%

LINC00365 promotes colorectal cancer cell progression through the Wnt/β‐catenin signaling pathway

Zhu

Bian

Zhang

et al. 2019

J of Cellular Biochemistry

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“…Hub genes have been shown to be functionally signi cant and highly interconnected with nodes in a module. In order to screen the top ranked genes with critical role in the protein-protein network (PPI), we construct PPI by uploading all genes in the selected module to the Search Tool for the Retrieval of Interacting Gene (STRING) database (http://www.string-db.org/) [17]. The Cytoscape software was further applied to perform the network analysis and the genes with top 10 degree were identi ed as hub genes [18].…”

Section: Hub Gene Analysis and Validationmentioning

confidence: 99%

Identification of potential prognostic markers for osteosarcoma by integrated analysis

Ding

Bian

et al. 2020

Preprint

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Background: Osteosarcoma (OS) is the most common type of musculoskeletal malignant tumor, accounting for over 30% of primary skeletal sarcomas. Although great efforts have been made, the mechanism of OS still remains largely unknown. In this study, we aim to identify gene modules and representative candidate biomarkers for clinical diagnosis of patients with OS, and reveal the mechanisms of OS progression.Methods: Weighted gene co-expression network analysis (WGCNA) was conducted to construct a co-expression network and investigate the relationship between modules and clinical traits. Functional enrichment analysis was performed on module genes. Protein-protein interaction (PPI) network was constructed to identify the hub gene and the expression level of hub genes was validated based on another dataset.Results: A total of 9854 genes were included in WGCNA, and 17 gene modules were constructed. Gene module related with OS in sacrum was mainly enriched in skeletal system development, bone development and extracellular structure organization. Furthermore, we screened the top 10 hub genes and further validated 5 of the 10 (MMP13, DCN, GNG2, PCOLCE and RUNX2), the expression of which were upregulated as compared with normal tissues.Conclusion: The hub gene we identified show great promise as prognostic markers for the management of OS and our findings also provide new insight for molecular mechanism of OS.

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“…lncRNA-miRNA-mRNA ceRNA network was constructed by "GDCRNATools" (http://bioconductor.org/packages/devel/ bioc/html/GDCRNATools.html) package in R software based on starbase database [13]. The nodes and edges were virtualized by Cytoscape 3.7.2.…”

Section: Lncrna-mirna-mrna Cerna Network Constructionmentioning

confidence: 99%

“…Dysregulation of lncRNA HOTAIR, H19, MALAT1, SNHG7, GAS8-AS, and NEAT1 were extensively well-studied and have been demonstrated to contribute in tumorigenesis and poor prognosis [5,[8][9][10][11][12]. A mounting of investigations have shown that lncRNAs exert their function through competing for endogenous RNA (ceRNA) crosstalk [13]. For instance, it has been shown that lncRNA SCARNA2 was overexpressed in COAD tissues and it remarkably correlated to chemoresistance via targeting miR-342-3p to upregulate EGFR and BCL2 in COAD cells [13].…”

Section: Introductionmentioning

confidence: 99%

“…A mounting of investigations have shown that lncRNAs exert their function through competing for endogenous RNA (ceRNA) crosstalk [13]. For instance, it has been shown that lncRNA SCARNA2 was overexpressed in COAD tissues and it remarkably correlated to chemoresistance via targeting miR-342-3p to upregulate EGFR and BCL2 in COAD cells [13]. Furthermore, overexpression of lncRNA SNHG1 has been shown to modify epithelialmesenchymal transition (EMT) by binding to miR-497/miR-195-5p in COAD cells [14].…”

Section: Introductionmentioning

confidence: 99%

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Comprehensive Analysis of LncRNAs Role in Tumorigenesis of Colon Adenocarcinoma

Poursheikhani¹,

Abbaszadegan²,

Nokhandani³

et al. 2020

Preprint

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Background Colon adenocarcinoma (COAD) is one of the most common gastrointestinal cancers globally. Molecular aberrations of tumor suppressors and/or oncogenes are the main contributors to its tumorigenesis. However, the exact underlying mechanisms of COAD pathogenesis are not clear yet. Thus, there is an urgent need to indicate promising potential diagnostic and prognostic biomarkers in COAD patients. In the current study, level 3 RNA-seq and miR-seq data and corresponding clinical data of colon adenocarcinoma (COAD) were retrieved from the TCGA database.The “limma” package in R software was utilized to indicate the differentially expressed genes. For in silico functional analysis, GO and KEGG signaling pathways were conducted. PPI network was constructed based on the STRING online database by Cytoscape 3.7.2. A ceRNA network was also constructed by “GDCRNATools” package in R software. Kaplan-Meier survival analysis (log-rank test) was used to indicate the relation between RNA expressions with patient’s survival time.Results The differential expression data demonstrated that 1512 mRNAs, 188 lncRNAs, and 329 miRNAs were differentially expressed in COAD. The GO and KEGG pathway analysis indicated that the differentially expressed mRNAs were primarily enriched in canonical processes in cancer. The PPI network showed that the PPARGC1A, ADAMTS5, PTGS2, FGFR2, TBX1, TWIST1, KIT, BDNF and MET proteins were the critical hubs. The Kaplan-Meier analysis revealed that 128 mRNAs, 15 lncRNAs, and 39 miRNAs were associated with overall survival time in the patients. The ceRNA network data demonstrated that three lncRNA including MAGI2-AS3, NEAT1, and SNHG3 genes were involved in the development of COAD.Conclusions Altogether, we integrated differentially expressed mRNAs, lncRNAs, and miRNAs in COAD bioinformatically. Our data suggested promising lncRNAs in the diagnosis and prognosis of patients with COAD.

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Construction and analysis of dysregulated lncRNA‐associated ceRNA network in colorectal cancer

Cited by 34 publications

References 62 publications

LINC00365 promotes colorectal cancer cell progression through the Wnt/β‐catenin signaling pathway

LINC00365 promotes colorectal cancer cell progression through the Wnt/β‐catenin signaling pathway

Identification of potential prognostic markers for osteosarcoma by integrated analysis

Comprehensive Analysis of LncRNAs Role in Tumorigenesis of Colon Adenocarcinoma

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