Identification of differential immune cells and related diagnostic genes in patients with diabetic retinopathy
Copyright © 2023 the Author(s). Published by Wolters Kluwer Health, Inc..
BACKGROUND: Diabetic retinopathy (DR) is a frequent microvascular abnormality associated with diabetes mellitus. The loss of retinal immunity is an important underlying mechanism of the DR pathogenesis, including the change in retinal immunosuppressive characteristics and the blood-retinal barrier disturbances. Therefore, this investigation screens immune-associated biomarkers in the retina of DR patients.
METHODS: In this investigation, the differential expression genes (DEGs) were acquired from Gene Expression Omnibus data GSE102485. The relative expression of 22 immune cell types in each sample was calculated by CIBERSORT analysis based on gene expression profile. The core module closely associated with immune infiltration was also screened by weighted gene co-expression network analysis (WGCNA). The overlapping DEGs and module genes were the differentially expressed immune-related genes (DEIRGs). With the help of the genes/proteins (STRING) database and MCODE plug-in, the protein-protein interaction (PPI) network hub genes were screened. Furthermore, the miRNA-hub genes and transcription factor (TF)-hub gene regulatory network were used to explain the possible signal pathways in DR. The hub genes verification was carried out by Polymerase Chain Reaction. Lastly, select CSF1R and its related pathway factor p-ERK1/2 to verify their expression in RF/6A under normal and high glucose environments.
RESULTS: A total of 3583 principle DEGs, that enriched immune-related GO terms and infection-related pathways were identified. CIBERSORT analysis showed that naive B cells, M2 macrophages, eosinophils, and neutrophil infiltration were significantly different. After intersecting 3583 DEGs, 168 DEIRGs and 181 module genes were identified. Furthermore, 15 hub genes, TYROBP, FCGR3A, CD163, FCGR2A, PTPRC, TLR2, CD14, VSIG4, HCK, CSF1R, LILRB2, ITGAM, CTSS, CD86, and LY86, were identified via PPI network. The identified hub genes were up-regulated in DR and showed a high DR diagnostic value. Regulatory networks of the miRNA- and TF-hub genes can help understand the etiology of disease at the genetic level and optimize treatment strategy. CD14, VSIG4, HCK, and CSF1R were verified to be highly expressed in the vitreous of patients with DR. n RF/6A, CSF1R, and p-ERK1/2 were significantly overexpressed under high glucose conditions, with a statistically significant difference.
CONCLUSION: This investigation identified 15 genes (TYROBP, FCGR3A, CD163, FCGR2A, PTPRC, TLR2, CD14, VSIG4, HCK, CSF1R, LILRB2, ITGAM, CTSS, CD86, and LY86) as hub DR genes, which may serve as a new potential point for the diagnosis and treatment of DR. CSF1R/p-ERK1/2 signaling may promotes the development of retinal neovascularization.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:102 |
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| Enthalten in: |
Medicine - 102(2023), 39 vom: 29. Sept., Seite e35331 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Yuan, LinHui [VerfasserIn] |
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| Links: |
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| Themen: |
EC 2.7.10.1 |
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| Anmerkungen: |
Date Completed 02.10.2023 Date Revised 04.10.2023 published: Print Citation Status MEDLINE |
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| doi: |
10.1097/MD.0000000000035331 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM362699674 |
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| 100 | 1 | |a Yuan, LinHui |e verfasserin |4 aut | |
| 245 | 1 | 0 | |a Identification of differential immune cells and related diagnostic genes in patients with diabetic retinopathy |
| 264 | 1 | |c 2023 | |
| 336 | |a Text |b txt |2 rdacontent | ||
| 337 | |a ƒaComputermedien |b c |2 rdamedia | ||
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| 500 | |a Date Completed 02.10.2023 | ||
| 500 | |a Date Revised 04.10.2023 | ||
| 500 | |a published: Print | ||
| 500 | |a Citation Status MEDLINE | ||
| 520 | |a Copyright © 2023 the Author(s). Published by Wolters Kluwer Health, Inc. | ||
| 520 | |a BACKGROUND: Diabetic retinopathy (DR) is a frequent microvascular abnormality associated with diabetes mellitus. The loss of retinal immunity is an important underlying mechanism of the DR pathogenesis, including the change in retinal immunosuppressive characteristics and the blood-retinal barrier disturbances. Therefore, this investigation screens immune-associated biomarkers in the retina of DR patients | ||
| 520 | |a METHODS: In this investigation, the differential expression genes (DEGs) were acquired from Gene Expression Omnibus data GSE102485. The relative expression of 22 immune cell types in each sample was calculated by CIBERSORT analysis based on gene expression profile. The core module closely associated with immune infiltration was also screened by weighted gene co-expression network analysis (WGCNA). The overlapping DEGs and module genes were the differentially expressed immune-related genes (DEIRGs). With the help of the genes/proteins (STRING) database and MCODE plug-in, the protein-protein interaction (PPI) network hub genes were screened. Furthermore, the miRNA-hub genes and transcription factor (TF)-hub gene regulatory network were used to explain the possible signal pathways in DR. The hub genes verification was carried out by Polymerase Chain Reaction. Lastly, select CSF1R and its related pathway factor p-ERK1/2 to verify their expression in RF/6A under normal and high glucose environments | ||
| 520 | |a RESULTS: A total of 3583 principle DEGs, that enriched immune-related GO terms and infection-related pathways were identified. CIBERSORT analysis showed that naive B cells, M2 macrophages, eosinophils, and neutrophil infiltration were significantly different. After intersecting 3583 DEGs, 168 DEIRGs and 181 module genes were identified. Furthermore, 15 hub genes, TYROBP, FCGR3A, CD163, FCGR2A, PTPRC, TLR2, CD14, VSIG4, HCK, CSF1R, LILRB2, ITGAM, CTSS, CD86, and LY86, were identified via PPI network. The identified hub genes were up-regulated in DR and showed a high DR diagnostic value. Regulatory networks of the miRNA- and TF-hub genes can help understand the etiology of disease at the genetic level and optimize treatment strategy. CD14, VSIG4, HCK, and CSF1R were verified to be highly expressed in the vitreous of patients with DR. n RF/6A, CSF1R, and p-ERK1/2 were significantly overexpressed under high glucose conditions, with a statistically significant difference | ||
| 520 | |a CONCLUSION: This investigation identified 15 genes (TYROBP, FCGR3A, CD163, FCGR2A, PTPRC, TLR2, CD14, VSIG4, HCK, CSF1R, LILRB2, ITGAM, CTSS, CD86, and LY86) as hub DR genes, which may serve as a new potential point for the diagnosis and treatment of DR. CSF1R/p-ERK1/2 signaling may promotes the development of retinal neovascularization | ||
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| 700 | 1 | |a Zou, JiXin |e verfasserin |4 aut | |
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