Identification of candidate biomarkers and pathways associated with psoriasis using bioinformatics analysis.

Abstract

BACKGROUND:

The aim of this study was to identify the candidate biomarkers and pathways associated with psoriasis. GSE13355 and GSE14905 were extracted from the Gene Expression Omnibus (GEO) database. Then the differentially expressed genes (DEGs) with |logFC| > 2 and adjusted P < 0.05 were chosen. In addition, the Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses for DEGs were performed. Then, the GO terms with P < 0.05 and overlap coefficient greater than 0.5 were integrated by EnrichmentMap. Additionally, risk subpathways analysis for DEGs was also conducted by using the iSubpathwayMiner package to obtain more psoriasis-related DEGs and pathways. Finally, protein-protein interaction (PPI) network analysis was performed to identify the hub genes, and the DGIdb database was utilized to search for the candidate drugs for psoriasis.

RESULTS:

A total of 127 DEGs which were mostly associated with keratinization, keratinocyte differentiation, and epidermal cell differentiation biological processes were identified. Based on these GO terms, 3 modules (human skin, epidermis and cuticle differentiation, and enzyme activity) were constructed. Moreover, 9 risk subpathways such as steroid hormone biosynthesis, folate biosynthesis, and pyrimidine metabolism were screened. Finally, PPI network analysis demonstrated that CXCL10 was the hub gene with the highest degree, and CXCR2, CXCL10, IVL, OASL, and ISG15 were the potential gene targets of the drugs for treating psoriasis.

CONCLUSION:

Psoriasis may be mostly caused by keratinization, keratinocyte differentiation, and epidermal cell differentiation; the pathogeneses were more related with pathways such as steroid hormone biosynthesis, folate biosynthesis, and pyrimidine metabolism. Besides, some psoriasis-related genes such as SPRR genes, HSD11B1, GGH, CXCR2, IVL, OASL, ISG15, and CXCL10 may be important targets in psoriatic therapy.

• Authors: Yongqi Luo, Yangyang Luo, Jing Chang, Zhenghui Xiao, Bin Zhou
• Journal: Hereditas (Hereditas) Vol. 157 Issue 1 Pg. 30 (Jul 15 2020) ISSN: 1601-5223 [Electronic] England
• PMID: 32669126 (Publication Type: Journal Article)

Chemical References

• Biomarkers

Topics

• Biomarkers
• Computational Biology (methods)
• Disease Susceptibility
• Gene Expression Profiling
• Gene Expression Regulation
• Gene Ontology
• Gene Regulatory Networks
• Humans
• Protein Interaction Mapping
• Protein Interaction Maps
• Psoriasis (etiology, metabolism, pathology)
• Signal Transduction
• Transcriptome