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. 2023 May 18:16:1287-1301.
doi: 10.2147/CCID.S413887. eCollection 2023.

Transcriptome Analysis Identifies Biomarkers for the Diagnosis and Management of Psoriasis Complicated with Depression

Xichun Xia #  1   2 , Hai Yu #  3 , Yanxiang Li  2 , Yunting Liang  1 , Guangqiang Li  2 , Fang Huang  1
Affiliations

Transcriptome Analysis Identifies Biomarkers for the Diagnosis and Management of Psoriasis Complicated with Depression

Xichun Xia et al. Clin Cosmet Investig Dermatol. .

Abstract

Purpose: Psoriasis is a systemic inflammatory disease, and the mechanism that links psoriasis to depression is still elusive. Hence, this study aimed to elucidate the potential pathogenesis of psoriasis and depression comorbidity.

Methods: The gene expression profiles of psoriasis (GSE34248, GSE78097 and GSE161683) and depression (GSE39653) were downloaded from the Gene Expression Omnibus (GEO) DataSets. Functional annotation, protein-protein interaction (PPI) network and module construction, and hub gene identification and co-expression analysis were performed, following identification of the common differentially expressed genes (DEGs) of psoriasis and depression.

Results: A total of 115 common DEGs (55 up-regulated and 60 down-regulated) were identified between psoriasis and depression. Functional analysis indicated that T cell activation and differentiation were predominantly implicated in the potential pathogenesis of these two diseases. In addition, Th17 cell differentiation and cytokines is closely related to both. Finally, 17 hub genes were screened, including CTLA4, LCK, ITK, IL7R, CD3D, SOCS1, IL4R, PRKCQ, SOCS3, IL23A, PDGFB, PAG1, TGFA, FGFR1, RELN, ITGB5 and TNXB, which re-emphasized the importance of the immune system in psoriasis and depression.

Conclusion: Our study reveals the common pathogenesis of psoriasis and depression. These common pathways and hub genes may apply to a molecular screening tool for depression in psoriasis patients, which could help dermatologists optimize patient management in routine care.

Keywords: bioinformatics; depression; differentially expressed genes; hub genes; psoriasis.

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Conflict of interest statement

The authors report no conflicts of interest in this work.

Figures

Figure 1
Figure 1
Research design flow chart.
Figure 2
Figure 2
Volcano diagram and Venn diagram. (A–C) The volcano map of GSE34248 (A), GSE78097 (B) and GSE161683 (C). Up-regulated genes are marked in red; down-regulated genes are marked in blue. (D and E) Venn diagram of the 1515 common up-regulated DEGs (D) and the 1269 common down-regulated DEGs (E) in psoriasis (PS). (F) The volcano map of GSE39653. Up-regulated genes are marked in red; down-regulated genes are marked in blue. (G and H) Venn diagram of the 55 common up-regulated (G) and 60 common down-regulated (H) DEGs between PS and MDD.
Figure 3
Figure 3
The enrichment analysis of common DEGs between PS and MDD. A-C. The GO enrichment analyses of common DEGs with P-value based on the KOBAS 3.0 database. Top 15 BP terms (A), Top 15 CC terms (B) and Top 15 MF terms (C) were shown. (D) The KEGG pathway enrichment analysis of communal DEGs on the ground of KOBAS 3.0 database. The size of the circle represents the number of genes involved, and the abscissa represents the frequency of the genes involved in the term total genes. P-value < 0.05 was considered significant.
Figure 4
Figure 4
The results of PPI network and significant modules. (A) PPI network of common DEGs on the ground of STRING database. (B and C) Two significant gene clustering modules. Significant module 1 (B) and significant module 2 (C) were shown. (D and E) GO and KEGG enrichment analysis of the modular genes. The size of the circle represents the number of genes involved, and the abscissa represents the frequency of the genes involved in the term total genes. P-value < 0.05 was considered significant.
Figure 5
Figure 5
Co-expression network and enrichment analysis of hub genes. (A) 17 hub genes were determined by taking the intersection of the top 20 genes in the seven algorithms of cytoHubba plugin (MCC, DMNC, MNC, Degree, EPC, Closeness and Radiality). (B) PPI network of 17 hub genes. (C) The network of hub genes and their co-expression genes were constructed and analyzed by GeneMANIA. (D and E) GO (D) and KEGG (E) enrichment analysis of the hub genes. The outermost circle is term on the right and the inner circle on the left represents the significant P-value of the corresponding pathway of the gene.
Figure 6
Figure 6
The expression level of hub gene in GSE137218. The comparison between the two sets of data uses the mean T-test. P-value < 0.05 was considered statistically significant. *p < 0.05; **p < 0.01; ***p < 0.001.
Figure 7
Figure 7
The expression level of hub gene in GSE98793. The comparison between the two sets of data uses the mean T-test. P-value < 0.05 was considered statistically significant. **p < 0.01; ***p < 0.001.
Figure 8
Figure 8
TFs regulatory network and its expression in GSE34248 and GSE39653. (A) TFs regulatory network. TFs were marked as square, and the hub genes were marked as circle. (B and C) The expression level of TFs in GSE34248 and GSE39653. The comparison between the two sets of data uses the mean T-test. P-value < 0.05 was considered statistically significant. **p < 0.01; ***p < 0.001.
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