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Comprehensive analysis of angiogenesis-related genes and pathways in early diabetic retinopathy
BACKGROUND: Angiogenesis is an important parameter in the development of diabetic retinopathy (DR), and it is indicative of an early stage evolving into a late phase. Therefore, examining the role of angiogenic factors in early DR is crucial to understanding the mechanism of neovascularization. METH...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7526206/ https://www.ncbi.nlm.nih.gov/pubmed/32993645 http://dx.doi.org/10.1186/s12920-020-00799-6 |
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author | Gu, Chufeng Lhamo, Thashi Zou, Chen Zhou, Chuandi Su, Tong Draga, Deji Luo, Dawei Zheng, Zhi Yin, Lili Qiu, Qinghua |
author_facet | Gu, Chufeng Lhamo, Thashi Zou, Chen Zhou, Chuandi Su, Tong Draga, Deji Luo, Dawei Zheng, Zhi Yin, Lili Qiu, Qinghua |
author_sort | Gu, Chufeng |
collection | PubMed |
description | BACKGROUND: Angiogenesis is an important parameter in the development of diabetic retinopathy (DR), and it is indicative of an early stage evolving into a late phase. Therefore, examining the role of angiogenic factors in early DR is crucial to understanding the mechanism of neovascularization. METHODS: The present study identified hub genes and pathways associated with angiogenesis in early DR using bioinformatics analysis. Genes from published literature and Gene Expression Omnibus (GEO) were collected and analysed. RESULTS: We collected 73 genes from 70 published studies in PubMed, which were referred to as DR-related gene set 1 (DRgset1). The gene expression profile of GSE12610 was downloaded, and 578 differentially expressed genes (DEGs) between diabetic and normal samples were identified. DEGs and DRgset1 were further combined to create DR-related gene set 2 (DRgset2). After an enrichment analysis, we identified 12 GO terms and 2 pathways associated with neovascularization in DRgset1, and 8 GO terms and 2 pathways in DRgset2. We found 39 new genes associated with angiogenesis and verified 8 candidate angiogenesis-related genes in DR cells using real-time PCR: PIK3CB, ALDH3A1, ITGA7, FGF23, THBS1, COL1A1, MAPK13, and AIF1. We identified 10 hub genes associated with neovascularization by constructing a protein-protein interaction (PPI) network: TNF, VEGFA, PIK3CB, TGFB1, EDN1, MMP9, TLR4, PDGFB, MMP2, and THBS1. CONCLUSIONS: The present study analysed angiogenesis-related genes and pathways in early DR in a comprehensive and systematic manner. PIK3CB, ALDH3A1, ITGA7, FGF23, THBS1, COL1A1, MAPK13, and AIF1 may be the candidate genes to further explore the mechanisms of angiogenesis in early DR. TNF, PIK3CB, TGFB1, EDN1, MMP9, TLR4, PDGFB, MMP2, and THBS1 may be new targets for early neovascularization therapy in the future. |
format | Online Article Text |
id | pubmed-7526206 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-75262062020-09-30 Comprehensive analysis of angiogenesis-related genes and pathways in early diabetic retinopathy Gu, Chufeng Lhamo, Thashi Zou, Chen Zhou, Chuandi Su, Tong Draga, Deji Luo, Dawei Zheng, Zhi Yin, Lili Qiu, Qinghua BMC Med Genomics Research Article BACKGROUND: Angiogenesis is an important parameter in the development of diabetic retinopathy (DR), and it is indicative of an early stage evolving into a late phase. Therefore, examining the role of angiogenic factors in early DR is crucial to understanding the mechanism of neovascularization. METHODS: The present study identified hub genes and pathways associated with angiogenesis in early DR using bioinformatics analysis. Genes from published literature and Gene Expression Omnibus (GEO) were collected and analysed. RESULTS: We collected 73 genes from 70 published studies in PubMed, which were referred to as DR-related gene set 1 (DRgset1). The gene expression profile of GSE12610 was downloaded, and 578 differentially expressed genes (DEGs) between diabetic and normal samples were identified. DEGs and DRgset1 were further combined to create DR-related gene set 2 (DRgset2). After an enrichment analysis, we identified 12 GO terms and 2 pathways associated with neovascularization in DRgset1, and 8 GO terms and 2 pathways in DRgset2. We found 39 new genes associated with angiogenesis and verified 8 candidate angiogenesis-related genes in DR cells using real-time PCR: PIK3CB, ALDH3A1, ITGA7, FGF23, THBS1, COL1A1, MAPK13, and AIF1. We identified 10 hub genes associated with neovascularization by constructing a protein-protein interaction (PPI) network: TNF, VEGFA, PIK3CB, TGFB1, EDN1, MMP9, TLR4, PDGFB, MMP2, and THBS1. CONCLUSIONS: The present study analysed angiogenesis-related genes and pathways in early DR in a comprehensive and systematic manner. PIK3CB, ALDH3A1, ITGA7, FGF23, THBS1, COL1A1, MAPK13, and AIF1 may be the candidate genes to further explore the mechanisms of angiogenesis in early DR. TNF, PIK3CB, TGFB1, EDN1, MMP9, TLR4, PDGFB, MMP2, and THBS1 may be new targets for early neovascularization therapy in the future. BioMed Central 2020-09-29 /pmc/articles/PMC7526206/ /pubmed/32993645 http://dx.doi.org/10.1186/s12920-020-00799-6 Text en © The Author(s) 2020 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Article Gu, Chufeng Lhamo, Thashi Zou, Chen Zhou, Chuandi Su, Tong Draga, Deji Luo, Dawei Zheng, Zhi Yin, Lili Qiu, Qinghua Comprehensive analysis of angiogenesis-related genes and pathways in early diabetic retinopathy |
title | Comprehensive analysis of angiogenesis-related genes and pathways in early diabetic retinopathy |
title_full | Comprehensive analysis of angiogenesis-related genes and pathways in early diabetic retinopathy |
title_fullStr | Comprehensive analysis of angiogenesis-related genes and pathways in early diabetic retinopathy |
title_full_unstemmed | Comprehensive analysis of angiogenesis-related genes and pathways in early diabetic retinopathy |
title_short | Comprehensive analysis of angiogenesis-related genes and pathways in early diabetic retinopathy |
title_sort | comprehensive analysis of angiogenesis-related genes and pathways in early diabetic retinopathy |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7526206/ https://www.ncbi.nlm.nih.gov/pubmed/32993645 http://dx.doi.org/10.1186/s12920-020-00799-6 |
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