Exploration of the biomarkers of comorbidity of psoriasis with inflammatory bowel disease and their association with immune infiltration

Multi-omic analysis revealed the immunological patterns and diagnostic value of exhausted T cell-derived PTTG1 in patients with psoriasis

BACKGROUND

Psoriasis, characterized by chronic inflammation, is a persistent skin condition that is notoriously challenging to manage and prone to relapse. Despite significant advancements in its treatment, many adverse reactions still occur. Therefore, exploring the mechanisms behind the occurrence and development of psoriasis is extremely important.

METHODS

The weighted correlation network analysis (WGCNA) algorithm was used to identify phenotype-related genes in patients with psoriasis. We recruited clinical samples of patients with psoriasis, and used single-cell RNA sequencing (scRNA-seq) to visualize divergent genes and metabolisms of varied cells for the psoriasis. Various machine-learning methods were used to identify core genes, and molecular docking was used to analyze the stability of leptomycin B targeting pituitary tumor transforming 1 (PTTG1). Immunofluorescence (IHC) analysis, multiplex immunofluorescence (mIF) analysis, and quantitative reverse transcription polymerase chain reaction (qRT-PCR) were used to validate the results.

RESULTS

Our results identified 1391 genes associated with the phenotype in patients with psoriasis and highlighted the significant alterations in T-cell functionality observed in the disease by WGCNA. There were nine distinct cellular clusters in psoriasis analyzed with the aid of scRNA-seq data. Each subtype of cell exhibited distinct genetic profiles, functional roles, signaling mechanisms, and metabolic characteristics. Machine-learning methods further demonstrated the potential diagnostic value of T cell-derived PTTG1 and its relationship with T-cell exhaustion in psoriasis. Lastly, the leptomycin B was scrutinized and verified had high stability targeting PTTG1.

CONCLUSIONS

This study elucidates the biological basis of psoriasis. At the same time, it was discovered that PTTG1 derived from exhausted T cells serves as a diagnostic biomarker for psoriasis. Leptomycin B could be a potential drug for targeted treatment of psoriasis on PTTG1.

Key genes and immune infiltration patterns and the clinical implications in psoriasis patients

BACKGROUND

Psoriasis is an immune-mediated skin disease, closely related to immune regulation. The aim was to understand the pathogenesis of psoriasis further, reveal potential therapeutic targets, and provide new clues for its diagnosis, treatment, and prevention.

MATERIALS AND METHODS

Expression profiling data were obtained from the Gene Expression Omnibus (GEO) database for skin tissues from healthy population and psoriasis patients. Differentially expressed genes (DEGs) were selected for Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) analysis separately. Machine learning algorithms were used to obtain characteristic genes closely associated with psoriasis. Receiver operating characteristic (ROC) curve was used to assess the diagnostic value of the characteristic genes for psoriasis. The Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm was used to calculate the proportion of immune cell infiltration. Correlation analysis was used to characterize the connection between gene expression and immune cell, Psoriasis Area and Severity Index (PASI).

RESULTS

A total of 254 DEGs were identified in the psoriasis group, including 185 upregulated and 69 downregulated genes. GO was mainly enriched in cytokine-mediated signaling pathway, response to virus, and cytokine activity. KEGG was mainly focused on cytokine-cytokine receptor interaction and IL-17 signaling pathway. GSEA was mainly in chemokine signaling pathway and cytokine-cytokine receptor interaction. The machine learning algorithm screened nine characteristic genes C10orf99, GDA, FCHSD1, C12orf56, S100A7, INA, CHRNA9, IFI44, and CXCL9. In the validation set, the expressions of these nine genes increased in the psoriasis group, and the AUC values were all > 0.9, consistent with those of the training set. The immune infiltration results showed increased proportions of macrophages, T cells, and neutrophils in the psoriasis group. The characteristic genes were positively or negatively correlated to varying degrees with T cells and macrophages. Nine characteristic genes were highly expressed in the moderate to severe psoriasis group and positively correlated with PASI scores.

CONCLUSION

High levels of nine characteristic genes C10orf99, GDA, FCHSD1, C12orf56, S100A7, INA, CHRNA9, IFI44, and CXCL9 were risk factors for psoriasis, the differential expression of which was related to the regulation of immune system activity and PASI scores, affecting the proportions of different immune cells and promoting the occurrence and development of psoriasis.

Identification of common mechanisms and biomarkers for dermatomyositis and atherosclerosis based on bioinformatics analysis

BACKGROUND

Dermatomyositis (DM) manifests as an autoimmune and inflammatory condition, clinically characterized by subacute progressive proximal muscle weakness, rashes or both along with extramuscular manifestations. Literature indicates that DM shares common risk factors with atherosclerosis (AS), and they often co-occur, yet the etiology and pathogenesis remain to be fully elucidated. This investigation aims to utilize bioinformatics methods to clarify the crucial genes and pathways that influence the pathophysiology of both DM and AS.

METHOD

Microarray datasets for DM (GSE128470, GSE1551, GSE143323) and AS (GSE100927, GSE28829, GSE43292) were retrieved from the Gene Expression Omnibus (GEO) database. The weighted gene co-expression network analysis (WGCNA) was used to reveal their co-expressed modules. Differentially expression genes (DEGs) were identified using the "limma" package in R software, and the functions of common DEGs were determined by functional enrichment analysis. A protein-protein interaction (PPI) network was established using the STRING database, with central genes evaluated by the cytoHubba plugin, and validated through external datasets. Immune infiltration analysis of the hub genes was conducted using the CIBERSORT method, along with Gene Set Enrichment Analysis (GSEA). Finally, the NetworkAnalyst platform was employed to examine the transcription factors (TFs) responsible for regulating pivotal crosstalk genes.

RESULTS

Utilizing WGCNA analysis, a total of 271 overlapping genes were pinpointed. Subsequent DEG analysis revealed 34 genes that are commonly found in both DM and AS, including 31 upregulated genes and 3 downregulated genes. The Degree Centrality algorithm was applied separately to the WGCNA and DEG collections to select the 15 genes with the highest connectivity, and crossing the two gene sets yielded 3 hub genes (PTPRC, TYROBP, CXCR4). Validation with external datasets showed their diagnostic value for DM and AS. Analysis of immune infiltration indicates that lymphocytes and macrophages are significantly associated with the pathogenesis of DM and AS. Moreover, GSEA analysis suggested that the shared genes are enriched in various receptor interactions and multiple cytokines and receptor signaling pathways. We coupled the 3 hub genes with their respective predicted genes, identifying a potential key TF, CBFB, which interacts with all 3 hub genes.

CONCLUSION

This research utilized comprehensive bioinformatics techniques to explore the shared pathogenesis of DM and AS. The three key genes, including PTPRC, TYROBP, and CXCR4, are related to the pathogenesis of DM and AS. The central genes and their correlations with immune cells may serve as potential diagnostic and therapeutic targets.

Identification of potential crucial genes shared in psoriasis and ulcerative colitis by machine learning and integrated bioinformatics

BACKGROUND

Mounting evidence suggest that there are an association between psoriasis and ulcerative colitis (UC), although the common pathogeneses are not fully understood. Our study aimed to find potential crucial genes in psoriasis and UC through machine learning and integrated bioinformatics.

METHODS

The overlapping differentially expressed genes (DEGs) of the datasets GSE13355 and GSE87466 were identified. Then the functional enrichment analysis was performed. The overlapping genes in LASSO, SVM-RFE and key module in WGCNA were considered as potential crucial genes. The receiver operator characteristic (ROC) curve was used to estimate their diagnostic confidence. The CIBERSORT was conducted to evaluate immune cell infiltration. Finally, the datasets GSE30999 and GSE107499 were retrieved to validate.

RESULTS

112 overlapping DEGs were identified in psoriasis and UC and the functional enrichment analysis revealed they were closely related to the inflammatory and immune response. Eight genes, including S100A9, PI3, KYNU, WNT5A, SERPINB3, CHI3L2, ARNTL2, and SLAMF7, were ultimately identified as potential crucial genes. ROC curves showed they all had high confidence in the test and validation datasets. CIBERSORT analysis indicated there was a correlation between infiltrating immune cells and potential crucial genes.

CONCLUSION

In our study, we focused on the comprehensive understanding of pathogeneses in psoriasis and UC. The identification of eight potential crucial genes may contribute to not only understanding the common mechanism, but also identifying occult UC in psoriasis patients, even serving as therapeutic targets in the future.