Identification and mechanistic investigation of novel biomarkers for diabetic retinopathy through hypoxia- and cuproptosis-associated gene analysis
Rong Feng , Xia Wang , Xiaodong Li, Zhifang Zhao, Bendan Long, Hui Zhang, Fengjuan Yue
Abstract
Emerging evidence indicates that hypoxia- and cuproptosis-related molecular alterations may contribute to diabetic retinopathy (DR). This study aimed to identify biomarkers associated with these processes and investigate their biological relevance in DR.
Introduction
Diabetes mellitus frequently leads to diabetic retinopathy (DR), a microvascular disorder characterized by progressive degeneration of retinal blood vessels, which can result in visual impairment or complete blindness if untreated .DR progresses through two stages: non-proliferative DR (NPDR) and proliferative DR (PDR). NPDR is marked by microaneurysms, retinal hemorrhages, and hard exudates, while progression to PDR involves altered retinal cellular function and pathological neovascularization, potentially leading to retinal detachment and severe vision loss.
Materials and methods
Data acquisition
Transcriptomic datasets related to DR, specifically GSE189005 and GSE221521, were retrieved from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). GSE189005 comprised 10 DR and 9 control blood samples using the GPL23126 platform, while GSE221521 included 69 DR and 50 control blood samples on the GPL24676 platform. GSE189005 was normalized using the RMA method.
Biomarker identification and validation
For biomarker identification, gene expression analysis of candidate biomarkers was conducted using the “ggplot2” package in GSE189005 and GSE221521. Biomarkers were selected based on significant differential expression between DR and control samples (p < 0.05) with consistent expression trends across both datasets for further analysis.
Results
Identification of 13 candidate genes
First, differential expression analysis identified 36,191 DR-associated genes in GSE189005, including 1,225 upregulated and 34,966 downregulated genes .The large number of initial features arose from the extensive probe coverage of the microarray platform and the use of a relatively permissive nominal p-value threshold, which aimed to maximize screening sensitivity. To address concerns regarding the reliability of the study stemming from the high number of initial DR-associated genes, multiple rounds of intersection analysis and layered machine learning filtering were employed to reduce false positives.
Conclusions
In conclusion, MED19 and CA11 emerge as key diagnostic biomarkers for DR, characterized by marked downregulation and high diagnostic accuracy. Their involvement in critical pathways, such as proteasome function and autophagy, along with correlations with immune infiltration, highlights their roles in DR pathogenesis related to hypoxia and cuproptosis. These findings offer novel insights for developing diagnostic strategies and targeted therapies.
Citation: Feng R, Wang X, Li X, Zhao Z, Long B, Zhang H, et al. (2026) Identification and mechanistic investigation of novel biomarkers for diabetic retinopathy through hypoxia- and cuproptosis-associated gene analysis. PLoS One 21(9): e0358182. https://doi.org/10.1371/journal.pone.0358182
Editor: Kangkang Ji, Huazhong Agriculture University, CHINA
Received: November 19, 2025; Accepted: August 27, 2026; Published: September 25, 2026
Copyright: © 2026 Feng et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: The datasets analysed during the current study are available in the Gene Expression Omnibus (GEO) repository at https://www.ncbi.nlm.nih.gov/geo/, reference numbers GSE189005 and GSE221521.
Funding: This study was financially supported by the Health Commission of Guizhou Province in the form of grants awarded to FY (gzwkj2023-228) and RF (gzwkj2025-191). Additional funding was provided by the Talent Fund of Guizhou Provincial People’s Hospital in the form of a grant awarded to XW ((2026)-13). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
