Discovering novel hub genes and pathways associated with the pathogenesis of psoriasis

Gao, Lijuan; Shen, Jing; Ren, Yanan; Shi, Junjun; Wang, Deping; Cao, Ji‐Min

doi:10.1111/dth.13993

Cited by 15 publications

(22 citation statements)

References 45 publications

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“…These hue genes and pathways may be vital for the pathogenesis of psoriasis. Some studies reported several genes as hub genes in psoriasis, partly the same with ours [20][21][22].…”

Section: Discussionsupporting

confidence: 83%

“…IFN-inducible oligoadenylate synthetases-like (OASL) protein belongs to atypical oligoadenylate synthetase (OAS) family, possesses antiviral activity, and boosts the innate immunity [34,35]. Gao LJ et al also identi ed OASL as a hub gene [21], but it is rarely studied in psoriasis patients. Additionally, OASL wasn't enriched in the top 5 pathways in our study.…”

Section: Discussionmentioning

confidence: 99%

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Identification of hub genes and pathways in psoriasis through bioinformatics and validation by RT-qPCR

Zou

Jian²

2021

Preprint

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Background Although several studies have attempted to investigate the aetiology and mechanism of psoriasis, the precise molecular mechanism remains unclear. Our study aimed to identify the hub genes and associated pathways that promote its pathogenesis in psoriasis, which would be helpful for the discovery of diagnostic and therapeutic markers. Methods GSE30999, GSE34248, GSE41662, and GSE50790 datasets were extracted from the Gene Expression Omnibus (GEO) database. The GEO profiles were integrated to obtain differentially expressed genes (DEGs) using the affy package in R software, with |logFC|> 1.5 and adjusted P < 0.05. The DEGs were utilised for Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein-protein interaction (PPI) network analyses. Hub genes were identified using Cytoscape and enriched for analysis in www.bioinformatics.com.cn. These hub genes were validated in the four aforementioned datasets and M5-induced HaCaT cells using real-time quantitative polymerase chain reaction (RT-qPCR). Results A total of 359 DEGs were identified, which were mostly associated with responses to bacterium, defence responses to other organism, and antimicrobial humoral response. These DEGs were mostly enriched in the steroid hormone biosynthesis pathway, NOD-like receptor signaling pathway, and cytokine-cytokine receptor interaction. PPI network analysis indicated seven genes (CXCL1, ISG15, CXCL10, STAT1, OASL, IFIT1, and IFIT3) as the probable hub genes of psoriasis; CXCL10 had a positive correlation with the other six hub genes. The chord plot results further supported the GO and KEGG analysis results of the 359 DEGs. Seven predicted hub genes were validated to be upregulated in four datasets and M5-induced HaCaT cells using RT-qPCR. Conclusions The pathogenesis of psoriasis may be associated with seven hub genes (CXCL1, ISG15, CXCL10, STAT1, OASL, IFIT1, and IFIT3) and pathways, such as the NOD-like receptor signaling pathway and cytokine-cytokine receptor interaction. These hub genes, especially CXCL10, can be used as potential biomarkers in psoriasis.

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“…These hue genes and pathways may be vital for the pathogenesis of psoriasis. Some studies reported several genes as hub genes in psoriasis, partly the same with ours [20][21][22].…”

Section: Discussionsupporting

confidence: 83%

Section: Discussionmentioning

confidence: 99%

Identification of hub genes and pathways in psoriasis through bioinformatics and validation by RT-qPCR

Zou

Jian²

2021

Preprint

View full text Add to dashboard Cite

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“…[ 34 ] The interferon-inducible oligoadenylate synthetases-like (OASL) protein belongs to the atypical oligoadenylate synthetase family, possesses anti-viral activity, and boosts innate immunity. [ 35 , 36 ] Gao et al [ 7 ] also identified OASL as a hub gene, but it has been rarely studied in psoriasis patients. Although the expression of OASL was up-regulated in M5-induced HaCaT cells in our study, this needs to be further confirmed.…”

Section: Discussionmentioning

confidence: 99%

CXCL10 and its related key genes as potential biomarkers for psoriasis

Zou

Jian

2021

Medicine

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Although several studies have attempted to investigate the etiology of and mechanism underlying psoriasis, the precise molecular mechanism remains unclear. Our study aimed to explore the molecular mechanism underlying psoriasis based on bioinformatics. GSE30999, GSE34248, GSE41662, and GSE50790 datasets were obtained from the Gene Expression Omnibus database. The Gene Expression Omnibus profiles were integrated to obtain differentially expressed genes in R software. Then a series of analyses was performed, such as Gene Ontology annotation, Kyoto Encyclopedia of Genes and Genomes pathway analysis, protein-protein interaction network analysis, among others. The key genes were obtained by CytoHubba, and validated by real-time quantitative polymerase chain reaction. A total of 359 differentially expressed genes were identified between 270 paired lesional and non-lesional skin groups. The common enriched pathways were nucleotide-binding and oligomerization domain-like receptor signaling pathway, and cytokine-cytokine receptor interaction. Seven key genes were identified, including CXCL1, ISG15, CXCL10, STAT1, OASL, IFIT1, and IFIT3. These key genes were validated as upregulated in the 4 datasets and M5-induced HaCaT cells. Our study identified 7 key genes, namely CXCL1, ISG15, CXCL10, STAT1, OASL, IFIT1, and IFIT3 , and 2 mostly enriched pathways (nucleotide-binding and oligomerization domain-like receptor signaling pathway, and cytokine-cytokine receptor interaction) involved in psoriatic pathogenesis. More importantly, CXCL1, ISG15, STAT1, OASL, IFIT1, IFIT3, and especially CXCL10 may be potential biomarkers. Therefore, our findings may bring a new perspective to the molecular mechanism underlying psoriasis and suggest potential biomarkers.

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“…Although previous studies have separately explored the hub genes associated with psoriasis ( 45 ) and atherosclerosis ( 46 ). However, few studies have explored the common molecular mechanism between them by advanced bioinformatics methods.…”

Section: Discussionmentioning

confidence: 99%

Exploring the Pathogenesis of Psoriasis Complicated With Atherosclerosis via Microarray Data Analysis

Zhao

Wei

et al. 2021

Front. Immunol.

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BackgroundAlthough more and more evidence has supported psoriasis is prone to atherosclerosis, the common mechanism of its occurrence is still not fully elucidated. The purpose of this study is to further explore the molecular mechanism of the occurrence of this complication.MethodsThe gene expression profiles of psoriasis (GSE30999) and atherosclerosis (GSE28829) were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the common differentially expressed genes (DEGs) of psoriasis and atherosclerosis, three kinds of analyses were performed, namely functional annotation, protein‐protein interaction (PPI) network and module construction, and hub gene identification and co-expression analysis.ResultsA total of 94 common DEGs (24 downregulated genes and 70 upregulated genes) was selected for subsequent analyses. Functional analysis emphasizes the important role of chemokines and cytokines in these two diseases. In addition, lipopolysaccharide-mediated signaling pathway is closely related to both. Finally, 16 important hub genes were identified using cytoHubba, including LYN, CSF2RB, IL1RN, RAC2, CCL5, IRF8, C1QB, MMP9, PLEK, PTPRC, FYB, BCL2A1, LCP2, CD53, NCF2 and TLR2.ConclusionsOur study reveals the common pathogenesis of psoriasis and atherosclerosis. These common pathways and hub genes may provide new ideas for further mechanism research.

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Discovering novel hub genes and pathways associated with the pathogenesis of psoriasis

Cited by 15 publications

References 45 publications

Identification of hub genes and pathways in psoriasis through bioinformatics and validation by RT-qPCR

Identification of hub genes and pathways in psoriasis through bioinformatics and validation by RT-qPCR

CXCL10 and its related key genes as potential biomarkers for psoriasis

Exploring the Pathogenesis of Psoriasis Complicated With Atherosclerosis via Microarray Data Analysis

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