Bioinformatic evidences and analysis of putative biomarkers in pancreatic ductal adenocarcinoma

Yuan Gu; Qijin Feng; Han Liu; Qi Zhou; Ailing Hu; Takuji Yamaguchi; Shilin Xia; Hiroyuki Kobayashi

doi:10.1016/j.heliyon.2019.e02378

Bioinformatic evidences and analysis of putative biomarkers in pancreatic ductal adenocarcinoma

Heliyon. 2019 Aug 26;5(8):e02378. doi: 10.1016/j.heliyon.2019.e02378. eCollection 2019 Aug.

Authors

Yuan Gu¹, Qijin Feng¹, Han Liu², Qi Zhou³, Ailing Hu⁴, Takuji Yamaguchi⁴, Shilin Xia^{4

5}, Hiroyuki Kobayashi¹

Affiliations

¹ Center for Advanced Kampo Medicine and Clinical Research, Graduate School of Medicine, Juntendo University, Tokyo, Japan.
² Department of Oral Pathology, Dalian Medical University, Dalian, PR China.
³ Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, PR China.
⁴ Department of Palliative Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan.
⁵ Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, PR China.

Abstract

Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal human cancers. Aberrant expression of genes plays important role in the procession of PDAC. The analysis of gene expression profile will contribute to the research of carcinoma mechanism.

Objective: This present study is focused to investigate the differentially expressed genes (DEGs) from 3 PDAC microarray datasets, which would provide candidate genes for putative biomarkers to understand the mechanism of PDAC and potential targets of treatment.

Method: Based on the overlap genes obtained from 3 GEO datasets, the hub genes were identified using STRING and Cytoscape plugin MCODE. The enrichment and function analysis were applied using DAVID. The protein-protein interaction network was performed using cBioPortal and UCSC Xena. The Oncomine was finally used to determine the candidate gene by analyzing their expression between pancreas sample and PDAC sample.

Results: 25 hub genes were selected from a total of 1006 DEGs from 3 GEO datasets, consisting of 14 upregulated genes and 11 downregulated genes. The overall decline of hub gene expression enriched in G1 phase of cell cycle in other subtypes of pancreatic cancer. Oncomine database was ultimately performed to determine the 8 candidate genes, including CXCL5, CCL20, NMU, F2R, ANXA1, EDNRA, LPAR6, and GNA15.

Conclusions: Conclusively, 8 candidate genes would become the potential PDAC combined biomarkers for diagnosis and therapeutic strategies.

Keywords: Bioinformatic analysis; Bioinformatics; Biomarkers; Cancer research; Diagnostics; Differentially expressed genes; Oncology; Pancreatic ductal adenocarcinoma; Protein-protein interaction.