Research Paper Volume 12, Issue 19 pp 19107—19128
Identification of a new pseudogenes/lncRNAs-hsa-miR-26b-5p-COL12A1 competing endogenous RNA network associated with prognosis of pancreatic cancer using bioinformatics analysis
- 1 Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310000, China
- 2 NHFPC Key Laboratory of Combined Multi-Organ Transplantation, Hangzhou 310000, China
- 3 Department of Respiratory, Tianjin Children's Hospital, Tianjin 300134, China
- 4 Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou 310000, China
- 5 Key Laboratory of Organ Transplantation, Zhejiang Province, Hangzhou 310003, China
- 6 Collaborative Innovation Center for Diagnosis Treatment of Infectious Diseases, Hangzhou 310000, China
Received: March 1, 2020 Accepted: June 29, 2020 Published: October 7, 2020
https://doi.org/10.18632/aging.103709How to Cite
Copyright: © 2020 Jing et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Abstract
Background: Pancreatic carcinoma is one of the most malignant cancers globally. However, a systematic mRNA-miRNA-lncRNA/pseudogene network associated with the molecular mechanism of pancreatic cancer progression has not been described.
Results: The significant DEGs identified comprised 159 up-regulated and 92 down-regulated genes. According to the expression and survival analysis, three genes (COL12A1, APOL1, and MMP14) were significantly higher in tumor samples when compared with normal controls and their upregulation indicated a poor prognosis. Subsequently, 28, 17, and 11 miRNAs were predicted to target COL12A1, APOL1, and MMP14, respectively. The hsa-miR-26b-5p-COL12A1 axis showed a potential in suppressing the progression of pancreatic cancer. Moreover, 12 lncRNAs and 92 pseudogenes were predicted to potentially bind to the hsa-miR-26b-5p. Based on the results from expression and correlation analysis, NAMPTP1/HCG11-hsa-miR-26b-5p-COL12A1 competing endogenous RNA (ceRNA) sub-network was associated with the prognosis of pancreatic cancer.
Conclusions: In a word, we elucidate a new NAMPTP1/ HCG11-hsa-miR-26b-5p-COL12A sub-network in the progression of pancreatic cancer, which may serve as a promising diagnostic biomarker or effective therapeutic target for pancreatic cancer.
Materials and methods: Differentially expressed genes (DEGs) were first identified by mining GSE28735, GSE62452 and GSE41368 datasets. Functional enrichment analysis was conducted using the DAVID database. Protein-protein interaction (PPI) network was performed using the STRING database, and hub genes were identified by Cytoscape. Upstream miRNAs and pseudogenes /lncRNAs of mRNAs were forecast using miRTarBase, miRNet, and starBase. Expression, survival, and correlation analysis of genes, miRNAs, and pseudogenes /lncRNAs were validated using GEPIA, Kaplan-Meier, and starBase.
Abbreviations
PDAC: Pancreatic ductal adenocarcinoma; DEGs: differentially expressed genes; GEO: Gene Expression Omnibus; GO: Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; PPI: protein-protein interaction; GEPIA: Gene Expression Profiling Interactive Analysis; BP: Biological process; CC: cellular component; MF: molecular function; STRING: Search Tool for the Retrieval of Interacting Genes; MCODE: Molecular Complex Detection; BiNGO: Biological Networks Gene Oncology; ALB: Albumin; FN1: Fibronectin 1; THBS2: Thrombospondin-2; POSTON: Periostin; VCAN: Versican; MMPs: Metalloproteinases; AJCC: American Joint Committee on Cancer.