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  4. Vol 2, Issue 1, 2021

Analysis of Lncrna-Mirna Interactions in Esophageal Squamous Cell Carcinoma

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DOI: 10.23977/medsc.2021.020104 | Downloads: 5 | Views: 1076

Author(s)

Ke shun 1, Lu jun 1, Li rui-chao 2, Wang jing 3, Fang ming-hao 1

Affiliation(s)

1 Department of Emergency Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
2 Department of General Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430030, China
3 Department of Clinical Oncology, Remin Hospital of Wuhan University, Wuhan 430071, China

Corresponding Author

Fang ming-hao

ABSTRACT

objective: The study identify hub genes and vital signal pathways by integrated bioinformatics analysis of GEO and TCGA, in order to obtain new prognostic markers for esophageal squamous cell carcinoma. Method: We use R package Limma (chip data) or edgeR[12] (sequencing data) to calculate the differentially expressed mRNA and lncRNA between GEO esophageal squamous cell carcinoma dataset (GSE23400, GSE38129) and TCGA esophageal squamous cell carcinoma dataset. The genes with significant mean difference (ANOVA) (P value =<0.05) in all samples were analyzed by PCA. According to the correlation between lncRNA and mRNA expression, Cytoscape v3.7 was used to construct lncRNA-mRNA network. We construct a PPI network for the most tightly regulated mRNA and lncRNA by the string online tool . Use Cytoscapev3.7 to screen out the hub genes (here, select the top 10 genes with greater connectivity). GO and KEGG enrichment analysis for hub gene. Based on TCGA clinical data, clinical prognostic analysis of the hub genes of the selected COL protein family was performed. Results: We found that lncRNA-RP11-863P13.3,RP11-576I22.2,CTD-2171N6.1 could co-regulate the up-regulation of 16 genes such as MMP11, THY1, and down-regulated lncRNA is the closest to gene regulation is MAMDC2- AS1 interacts with 19 genes including FHL1 and TGFBR3. We determined that COL5A2, COL3A1, COL1A1 and other hub genes are most affected in the lncRNA-mRNA regulatory network of esophageal squamous cell carcinoma. The GO and kegg enrichment analysis of COL family genes showed that extracellular matrix organization, fibrillar collagen trimer, and extracellular matrix structural enrichment scores were the highest. Survival analysis showed that high expression of the four genes COL1A1, COL1A2, COL3A1, COL5A2 can significantly shorten the disease-free survival period of esophageal squamous cell carcinoma, and the prognosis of patients becomes worse. Conclusion: lncRNA-RP11-863P13.3, RP11-576I22.2, CTD-2171N6.1 may promote changes in ECM traits by up-regulating COL1A1,COL1A2,COL3A1,COL5A2, leading to poor prognosis in patients with esophageal squamous cell carcinoma, and could be potential biomarkers for ESCC patients’s prognosis.

KEYWORDS

Esophageal squamous cell carcinoma(escc), Col, Lncrna, Protein-protein interaction network(ppin), Hub gene

CITE THIS PAPER

Ke shun, Lu jun, Li rui-chao, Wang jing, Fang ming-hao. Analysis of Lncrna-Mirna Interactions in Esophageal Squamous Cell Carcinoma. MEDS Clinical Medicine (2021) 2: 15-26. DOI: http://dx.doi.org/10.23977/medsc.2021.020104.

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