Integrated bioinformatics analysis of potential biomarkers for pancreatic cancer.

Abstract

BACKGROUND:

Pancreatic cancer, particularly pancreatic ductal adenocarcinoma (PDA), is an aggressive malignancy associated with a low 5-year survival rate. Poor outcomes associated with PDA are attributable to late detection and inoperability. Most patients with PDA are diagnosed with locally advanced and metastatic disease. Such cases are primarily treated with chemotherapy and radiotherapy. Because of the lack of effective molecular targets, early diagnosis and successful therapies are limited. The purpose of this study was to screen key candidate genes for PDA using a bioinformatic approach and to research their potential functional, pathway mechanisms associated with PDA progression. It may help to understand the role of associated genes in the development and progression of PDA and identify relevant molecular markers with value for early diagnosis and targeted therapy.

MATERIALS AND METHODS:

To identify novel genes associated with carcinogenesis and progression of PDA, we analyzed the microarray datasets GSE62165, GSE125158, and GSE71989 from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified, and the Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. A protein-protein interaction (PPI) network was constructed using STRING, and module analysis was performed using Cytoscape. Gene Expression Profiling Interactive Analysis (GEPIA) was used to evaluate the differential expression of hub genes in patients with PDA. In addition, we verified the expression of these genes in PDA cell lines and normal pancreatic epithelial cells.

RESULTS:

A total of 202 DEGs were identified and these were found to be enriched for various functions and pathways, including cell adhesion, leukocyte migration, extracellular matrix organization, extracellular region, collagen trimer, membrane raft, fibronectin-binding, integrin binding, protein digestion, and absorption, and focal adhesion. Among these DEGs, 12 hub genes with high degrees of connectivity were selected. Survival analysis showed that the hub genes (HMMR, CEP55, CDK1, UHRF1, ASPM, RAD51AP1, DLGAP5, KIF11, SHCBP1, PBK, and HMGB2) may be involved in the tumorigenesis and development of PDA, highlighting their potential as diagnostic and therapeutic factors in PDA.

CONCLUSIONS:

In summary, the DEGs and hub genes identified in the present study not only contribute to a better understanding of the molecular mechanisms underlying the carcinogenesis and progression of PDA but may also serve as potential new biomarkers and targets for PDA.

• Authors: Huaqing Shi, Hao Xu, Changpeng Chai, Zishun Qin, Wence Zhou
• Journal: Journal of clinical laboratory analysis (J Clin Lab Anal) Vol. 36 Issue 5 Pg. e24381 (May 2022) ISSN: 1098-2825 [Electronic] United States
• PMID: 35403252 (Publication Type: Journal Article)
• Copyright: © 2022 The Authors. Journal of Clinical Laboratory Analysis published by Wiley Periodicals LLC.

Chemical References

• Biomarkers, Tumor
• CCAAT-Enhancer-Binding Proteins
• Cell Cycle Proteins
• Cep55 protein, human
• SHCBP1 protein, human
• Shc Signaling Adaptor Proteins
• UHRF1 protein, human
• Ubiquitin-Protein Ligases

Topics

• Biomarkers, Tumor (metabolism)
• CCAAT-Enhancer-Binding Proteins (genetics, metabolism)
• Carcinogenesis (genetics)
• Carcinoma, Pancreatic Ductal (diagnosis, genetics)
• Cell Cycle Proteins (genetics)
• Computational Biology
• Gene Expression Profiling
• Gene Expression Regulation, Neoplastic
• Humans
• Pancreatic Neoplasms (diagnosis, genetics)
• Prognosis
• Shc Signaling Adaptor Proteins
• Ubiquitin-Protein Ligases (genetics, metabolism)
• Pancreatic Neoplasms