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Novel diagnostic biomarkers related to immune infiltration in Parkinson's disease by bioinformatics analysis.

作者信息

Zhang Pengfei, Zhao Liwen, Li Hongbin, Shen Jie, Li Hui, Xing Yongguo

机构信息

Department of Neurosurgery, Beichen Traditional Chinese Medical Hospital Tianjin, Tianjin, China.

Department of Neurosurgery, Tianjin Medical University General Hospital Airport Site, Tianjin, China.

出版信息

Front Neurosci. 2023 Jan 26;17:1083928. doi: 10.3389/fnins.2023.1083928. eCollection 2023.


DOI:10.3389/fnins.2023.1083928
PMID:36777638
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9909419/
Abstract

BACKGROUND: Parkinson's disease (PD) is Pengfei Zhang Liwen Zhao Pengfei Zhang Liwen Zhao a common neurological disorder involving a complex relationship with immune infiltration. Therefore, we aimed to explore PD immune infiltration patterns and identify novel immune-related diagnostic biomarkers. MATERIALS AND METHODS: Three substantia nigra expression microarray datasets were integrated with elimination of batch effects. Differentially expressed genes (DEGs) were screened using the "limma" package, and functional enrichment was analyzed. Weighted gene co-expression network analysis (WGCNA) was performed to explore the key module most significantly associated with PD; the intersection of DEGs and the key module in WGCNA were considered common genes (CGs). The CG protein-protein interaction (PPI) network was constructed to identify candidate hub genes by cytoscape. Candidate hub genes were verified by another two datasets. Receiver operating characteristic curve analysis was used to evaluate the hub gene diagnostic ability, with further gene set enrichment analysis (GSEA). The immune infiltration level was evaluated by ssGSEA and CIBERSORT methods. Spearman correlation analysis was used to evaluate the hub genes association with immune cells. Finally, a nomogram model and microRNA-TF-mRNA network were constructed based on immune-related biomarkers. RESULTS: A total of 263 CGs were identified by the intersection of 319 DEGs and 1539 genes in the key turquoise module. Eleven candidate hub genes were screened by the R package "UpSet." We verified the candidate hub genes based on two validation sets and identified six (SYT1, NEFM, NEFL, SNAP25, GAP43, and GRIA1) that distinguish the PD group from healthy controls. Both CIBERSORT and ssGSEA revealed a significantly increased proportion of neutrophils in the PD group. Correlation between immune cells and hub genes showed SYT1, NEFM, GAP43, and GRIA1 to be significantly related to immune cells. Moreover, the microRNA-TFs-mRNA network revealed that the microRNA-92a family targets all four immune-related genes in PD pathogenesis. Finally, a nomogram exhibited a reliable capability of predicting PD based on the four immune-related genes (AUC = 0.905). CONCLUSION: By affecting immune infiltration, SYT1, NEFM, GAP43, and GRIA1, which are regulated by the microRNA-92a family, were identified as diagnostic biomarkers of PD. The correlation of these four genes with neutrophils and the microRNA-92a family in PD needs further investigation.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/fe024080fa7c/fnins-17-1083928-g011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/4e14d4c75676/fnins-17-1083928-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/704b91003563/fnins-17-1083928-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/a624d66fbeaa/fnins-17-1083928-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/20abf331e0f3/fnins-17-1083928-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/486c66493360/fnins-17-1083928-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/a8e4b0489ec8/fnins-17-1083928-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/c22b37ae472b/fnins-17-1083928-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/30d7830920af/fnins-17-1083928-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/63efa2746940/fnins-17-1083928-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/3759fe057926/fnins-17-1083928-g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/fe024080fa7c/fnins-17-1083928-g011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/4e14d4c75676/fnins-17-1083928-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/704b91003563/fnins-17-1083928-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/a624d66fbeaa/fnins-17-1083928-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/20abf331e0f3/fnins-17-1083928-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/486c66493360/fnins-17-1083928-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/a8e4b0489ec8/fnins-17-1083928-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/c22b37ae472b/fnins-17-1083928-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/30d7830920af/fnins-17-1083928-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/63efa2746940/fnins-17-1083928-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/3759fe057926/fnins-17-1083928-g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f717/9909419/fe024080fa7c/fnins-17-1083928-g011.jpg

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引用本文的文献

[1]
Differential gene expression and immune profiling in Parkinson's disease: unveiling potential candidate biomarkers.

BMC Neurol. 2025-8-27

[2]
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[3]
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[4]
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Int J Mol Sci. 2024-5-14

[5]
Integrated bioinformatics analysis for exploring potential biomarkers related to Parkinson's disease progression.

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本文引用的文献

[1]
CSF GAP-43 as a biomarker of synaptic dysfunction is associated with tau pathology in Alzheimer's disease.

Sci Rep. 2022-10-17

[2]
Landscape of immune infiltration in entorhinal cortex of patients with Alzheimer's disease.

Front Pharmacol. 2022-9-28

[3]
The Potential Roles of Extracellular Vesicles as Biomarkers for Parkinson's Disease: A Systematic Review.

Int J Mol Sci. 2022-9-29

[4]
Neurodegeneration Markers in the Cerebrospinal Fluid of 100 Patients with Schizophrenia Spectrum Disorder.

Schizophr Bull. 2023-3-15

[5]
Identification of Immune Hub Genes Associated With Braak Stages in Alzheimer's Disease and Their Correlation of Immune Infiltration.

Front Aging Neurosci. 2022-5-10

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