Identification of Biomarkers Associated With CD4+ T-Cell Infiltration With Gene Coexpression Network in Dermatomyositis

Huang, Peng; Li, Tang; Zhang, Lu; Ren, Yi; Peng, Hong; Xu, Jie; Mao, Ding-An; Liu, Lingjuan; Liu, Liqun

doi:10.3389/fimmu.2022.854848

Cited by 13 publications

(18 citation statements)

References 86 publications

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“… 23 , 24 EVPL has shown association with chronic inflammation and immune responses, notably with CD4 T cell infiltration in the dermatitis studies, 25 indicating its potential role in regulating skin inflammation through immune regulation. 26 A diverse array of cytokines, growth factors, chemokines and inflammatory mediators can be secreted in the tumor microenvironment to promote tumor immunosuppression and accelerate tumor progression. 27 In this study, a correlation was observed between EVPL and the infiltration of Macrophages, Mast cells resting, and Dendritic cells resting.…”

Section: Discussionmentioning

confidence: 99%

Envoplakin Inhibits Macrophage Polarization by Altering the Inflammatory Tumor Microenvironment of Melanoma Through the RAS / ERK Signaling Pathway

Cai,

Chen

2024

JIR

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Purpose Tumor growth induces the tumor margin to become a transition zone rich in immune cells. EVPL is a potential prognostic biomarker for melanoma. Melanoma is difficult to cure because of its high metastasis, so it is urgent to find effective genes to inhibit tumor progression and regulate tumor microenvironment. Methods Firstly, differentially expressed genes (DEGs) among normal skin, nevus and melanoma samples in GSE3189 were screened. Bioinformatics was used to further explore the hub genes and enriched pathways closely related to the inflammatory response of DEGs in melanoma. We selected EVPL, which is associated with the Ras/Raf signaling pathway, for in vitro study. CCK-8, colony formation, wound healing, Transwell and flow cytometry assays were respectively used to evaluate the proliferation, migration, invasion, and apoptosis of cancer cells. Enzyme-linked immunosorbent assay was conducted for the monitoring of changes in the tumor microenvironment. To evaluate the effect of EVPL on macrophage recruitment, we established a co-culture system in a Transwell chamber. The polarization of macrophages was examined after treatment of cells with RAS/ERK signaling inhibitors SCH772984 and sh-EVPL. Additionally, changes in the expression of pathway proteins were measured by Western blot. Results Among the screened hub genes, EVPL was associated with the Ras/Raf pathway, a key signaling pathway in melanoma, and may be involved in regulating the inflammatory microenvironment of melanoma. Oe-EVPL was proved to suppress melanoma cell malignant progression. By inhibiting EVPL expression, the inhibitory effects on melanoma progression induced by the addition of SCH772984 were reversed. Furthermore, EVPL was found to inhibit the expression of chemokines, the recruitment of macrophages, and the polarization of macrophages through the Ras/Raf/ERK signaling pathway. Conclusion EVPL can inhibit the progression of melanoma through the RAS/ERK signaling pathway, change the inflammatory tumor microenvironment of melanoma, and inhibit the recruitment of macrophages.

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Section: Discussionmentioning

confidence: 99%

Envoplakin Inhibits Macrophage Polarization by Altering the Inflammatory Tumor Microenvironment of Melanoma Through the RAS / ERK Signaling Pathway

Cai,

Chen

2024

JIR

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“…WGCNA has been successfully applied to identify gene modules with various biological functions or cellular characteristics (35,36). In our study, we used WGCNA to establish a co-expression network of lncRNAs and obtained multiple modules through co-expression relationships.…”

Section: Discussionmentioning

confidence: 99%

Development and validation of a cancer-associated fibroblast-derived lncRNA signature for predicting clinical outcomes in colorectal cancer

Pan

2022

Front. Immunol.

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Cancer-associated fibroblasts (CAFs) are actively involved in cancer progression through generating extracellular matrix and orchestrating the crosstalk within the tumor microenvironment (TME). This study aimed to develop and validate a CAF-derived lncRNA (long non-coding RNA) (CAFDL) signature for predicting clinical outcomes in colorectal cancer (CRC). Clinical data and transcriptomic profiles of 2,320 patients with CRC from The Cancer Genome Atlas (TCGA)-COAD and TCGA-READ datasets and 16 Gene Expression Omnibus datasets were included in this study. CAFDLs were identified using weighted gene co-expression network analysis. The CAFDL signature was constructed using the least absolute shrinkage and selection operator analysis in the TCGA-CRC training set. Multiple CRC cohorts and pan-cancer cohorts were used to validated the CAFDL signature. Patients with high CAFDL scores had significantly worse overall survival and disease-free survival than patients with low CAFDL scores in all CRC cohorts. In addition, non-responders to fluorouracil, leucovorin, and oxaliplatin (FOLFOX)/fluorouracil, leucovorin, and irinotecan (FOLFIRI) chemotherapy, chemoradiotherapy, bevacizumab, and immune checkpoint inhibitors had significantly higher CAFDL scores compared with responders. Pan-cancer analysis showed that CAFDL had prognostic predictive power in multiple cancers such as lung adenocarcinoma, breast invasive carcinoma, stomach adenocarcinoma, and thyroid carcinoma. The CAFDL signature was positively correlated with transforming growth factor-beta (TGF-β) signaling, epithelial–mesenchymal transition, and angiogenesis pathways but negatively correlated with the expression of immune checkpoints such as PDCD1, CD274, and CTLA4. The CAFDL signature reflects CAF properties from a lncRNA perspective and effectively predicts clinical outcomes in CRC and across pan-cancer. The CAFDL signature can serve as a useful tool for risk stratification and provide new insights into the underlying mechanisms of CAFs in cancer immunity.

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“…The overexpression of each motif in a gene set was estimated by calculating the area under the curve (AUC) for each motif-motif pair. The NES of each motif was calculated from the AUC distribution of all motifs in the gene set [ 14 ].…”

Section: Methodsmentioning

confidence: 99%

Identification of potential biomarkers for ankylosing spondylitis based on bioinformatics analysis

Cao

Dong

et al. 2023

BMC Musculoskelet Disord

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Objective The aim of this study was to search for key genes in ankylosing spondylitis (AS) through comprehensive bioinformatics analysis, thus providing some theoretical support for future diagnosis and treatment of AS and further research. Methods Gene expression profiles were collected from Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) by searching for the term "ankylosing spondylitis". Ultimately, two microarray datasets (GSE73754 and GSE11886) were downloaded from the GEO database. A bioinformatic approach was used to screen differentially expressed genes and perform functional enrichment analysis to obtain biological functions and signalling pathways associated with the disease. Weighted correlation network analysis (WGCNA) was used to further obtain key genes. Immune infiltration analysis was performed using the CIBERSORT algorithm to conduct a correlation analysis of key genes with immune cells. The GWAS data of AS were analysed to identify the pathogenic regions of key genes in AS. Finally, potential therapeutic agents for AS were predicted using these key genes. Results A total of 7 potential biomarkers were identified: DYSF, BASP1, PYGL, SPI1, C5AR1, ANPEP and SORL1. ROC curves showed good prediction for each gene. T cell, CD4 naïve cell, and neutrophil levels were significantly higher in the disease group than in the paired normal group, and key gene expression was strongly correlated with immune cells. CMap results showed that the expression profiles of ibuprofen, forskolin, bongkrek-acid, and cimaterol showed the most significant negative correlation with the expression profiles of disease perturbations, suggesting that these drugs may play a role in AS treatment. Conclusion The potential biomarkers of AS screened in this study are closely related to the level of immune cell infiltration and play an important role in the immune microenvironment. This may provide help in the clinical diagnosis and treatment of AS and provide new ideas for further research.

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Identification of Biomarkers Associated With CD4+ T-Cell Infiltration With Gene Coexpression Network in Dermatomyositis

Cited by 13 publications

References 86 publications

Envoplakin Inhibits Macrophage Polarization by Altering the Inflammatory Tumor Microenvironment of Melanoma Through the RAS / ERK Signaling Pathway

Envoplakin Inhibits Macrophage Polarization by Altering the Inflammatory Tumor Microenvironment of Melanoma Through the RAS / ERK Signaling Pathway

Development and validation of a cancer-associated fibroblast-derived lncRNA signature for predicting clinical outcomes in colorectal cancer

Identification of potential biomarkers for ankylosing spondylitis based on bioinformatics analysis

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