Identifying Hub Genes, Key Pathways and Immune Cell Infiltration Characteristics in Pediatric and Adult Ulcerative Colitis by Integrated Bioinformatic Analysis

Xiu, Mengxi; Liu, Yuan-Meng; Chen, Guangyuan; Hu, Cong; Kuang, Bohai

doi:10.1007/s10620-020-06611-w

Cited by 17 publications

(10 citation statements)

References 71 publications

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“…For inflammatory bowel disease (IBD), DEG were identified between UC and Crohn's disease [ 24 ]. Certain key genes and immune cells play a vital role in the difference between the pathology of UC in adults and children [ 25 ], as well as in the progression of UC from normal to colorectal cancer [ 26 , 27 ]. With the assistance of bioinformatics analysis, exploring potential therapeutic agents from functional foods towards UC and unveiling the underlying mechanisms is a promising strategy.…”

Section: Introductionmentioning

confidence: 99%

Protective effect and mechanism insight of purified Antarctic krill phospholipids against mice ulcerative colitis combined with bioinformatics

Huang

Yao

Zhou

et al. 2023

Nat. Prod. Bioprospect.

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Antarctic krill oil is functional oil and has a complex phospholipids composition that poses difficulties in elucidating its effect mechanism on ulcerative colitis (UC). The mechanism of UC action was studied by bioinformatics, and the therapeutic effect of Antarctic krill phospholipids (APL) on dextran sulfate sodium (DSS)-induced colitis mice was verified. GO functional enrichment analysis uncovered an enrichment of these genes in the regulation of cell–cell adhesion, membrane region, signaling receptor activator activity, and cytokine activity. Meanwhile, the KEGG results revealed the genes were enriched in the TNF signaling pathway, pathogenic Escherichia coli infection, inflammatory bowel disease and tight junction. Animal experiments showed that APL treatment alleviated the UC symptoms and reduced inflammatory damage. Meanwhile, the expressions of the tight junction (TJ) proteins, ZO-1 and occludin, were restored, and the levels of IL-6 and TNF-α were reduced. Moreover, Firmicutes/Bacteroidetes ratio in the intestinal microbiota was regulated, and the contents of short-chain fatty acids metabolites were raised. These findings would provide an insight for the beneficial effects of APL and dietary therapy strategies for UC.

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Section: Introductionmentioning

confidence: 99%

Protective effect and mechanism insight of purified Antarctic krill phospholipids against mice ulcerative colitis combined with bioinformatics

Huang

Yao

Zhou

et al. 2023

Nat. Prod. Bioprospect.

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show abstract

“…The gene expression matrix was uploaded to the CIBERSORT online website ( https://cibersort.stanford.edu ), and the default signature matrix was set as 1000 permutations, and the samples with P -value < 0.05 were significant [ 31 ]. The P -value of CIBERSORT reflected the statistical significance of the deconvolution results over all cell subsets and was used to filter out deconvolution with less significant fitting accuracy [ 32 ]. The difference in immune cell infiltration between PAH lung specimens and normal lung specimens was assessed, and the signiﬁcant immune cells between PAH lung specimens and normal lung specimens were screened using the Wilcoxon test at P < 0.05.…”

Section: Methodsmentioning

confidence: 99%

Screening of key biomarkers and immune infiltration in Pulmonary Arterial Hypertension via integrated bioinformatics analysis

Zeng

Zheng

et al. 2021

Bioengineered

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This study aimed to screen key biomarkers and investigate immune infiltration in pulmonary arterial hypertension (PAH) based on integrated bioinformatics analysis. The Gene Expression Omnibus (GEO) database was used to download three mRNA expression profiles comprising 91 PAH lung specimens and 49 normal lung specimens. Three mRNA expression datasets were combined, and differentially expressed genes (DEGs) were obtained. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses and the protein-protein interaction (PPI) network of DEGs were performed using the STRING and DAVID databases, respectively. The diagnostic value of hub gene expression in PAH was also analyzed. Finally, the infiltration of immune cells in PAH was analyzed using the CIBERSORT algorithm. Total 182 DEGs (117 upregulated and 65 downregulated) were identified, and 15 hub genes were screened. These 15 hub genes were significantly associated with immune system functions such as myeloid leukocyte migration, neutrophil migration, cell chemotaxis, Toll-like receptor signaling pathway, and NF-κB signaling pathway. A 7-gene-based model was constructed and had a better diagnostic value in identifying PAH tissues compared with normal controls. The immune infiltration profiles of the PAH and normal control samples were significantly different. High proportions of resting NK cells, activated mast cells, monocytes, and neutrophils were found in PAH samples, while high proportions of resting T cells CD4 memory and Macrophages M1 cell were found in normal control samples. Functional enrichment of DEGs and immune infiltration analysis between PAH and normal control samples might help to understand the pathogenesis of PAH.

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“…The deconvolution approach CIBERSORT has been widely used to study various diseases, including ulcerative colitis, 7 lupus, 8 and rheumatoid arthritis, due to its validity and reliability. 9 The white blood cell gene bio-signature matrix in CIBERSORT comprises 547 genes, known as LM22, which is used to differentiate the 22 immune cell types consisting of regulatory T cells (Tregs), naive CD4 T cells, macrophages M2, activated memory CD4 T cells, plasma cells, follicular helper T cells, gamma delta T cells, CD8 T cells, macrophages M1, memory B cells, activated NK cells, macrophages M0, resting NK cells, monocytes, resting mast cells, resting memory CD4 T cells, activated mast cells, resting dendritic cells, neutrophils, naive B cells, activated dendritic cells, and eosinophils.…”

Section: Immune Infiltration Analysismentioning

confidence: 99%

Identification of Hub Genes and Biological Pathways in Inclusion Body Myositis Using Bioinformatics Analysis

Wu¹,

Zhao²,

Zhang³

et al. 2022

IJGM

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Background: Inclusion body myositis (IBM) is a unique idiopathic inflammatory myopathy with unclear pathogenesis and poor prognosis. Although previous publications have identified some molecular biomarkers, the value of these biomarkers is unknown. Objective: To identify hub genes and signaling pathways related to IBM for understanding the IBM-related mechanisms and providing guidance for therapy development. Methods: Two microarray datasets (GSE3112 and GSE128470) were downloaded from the Gene Expression Omnibus (GEO) database. GEO2R was used to detect differentially expressed genes (DEGs) between IBM and normal muscle tissues. The hub genes were determined using protein-protein interaction (PPI) network in Cytoscape. The specific signaling pathways and biological functions of IBM were identified using GO, KEGG, and GSEA enrichment analyses. Moreover, CIBERSORT was applied to estimate the expression level of 22 immune cell types in IBM and normal muscle tissue. The relationship between the immune cell types and hub genes was then explored. Results: A total of 219 DEGs and 10 hub genes were identified. Enrichment analyses revealed that the chemokine signaling pathway, cellular response to interferon-gamma, and P53 pathway have crucial roles in IBM. Immune infiltration analyses showed that IBM was associated with high level of CD8 T cells, Tregs, and macrophages. Finally, five potential drugs were predicted for IBM patients through CMap (connectivity map) database. Conclusion:In this study, the underlying molecular mechanisms and immunological landscape of IBM were investigated, and thus may provide new directions for future research on IBM pathogenesis.

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Identifying Hub Genes, Key Pathways and Immune Cell Infiltration Characteristics in Pediatric and Adult Ulcerative Colitis by Integrated Bioinformatic Analysis

Cited by 17 publications

References 71 publications

Protective effect and mechanism insight of purified Antarctic krill phospholipids against mice ulcerative colitis combined with bioinformatics

Protective effect and mechanism insight of purified Antarctic krill phospholipids against mice ulcerative colitis combined with bioinformatics

Screening of key biomarkers and immune infiltration in Pulmonary Arterial Hypertension via integrated bioinformatics analysis

Identification of Hub Genes and Biological Pathways in Inclusion Body Myositis Using Bioinformatics Analysis

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