Single-cell transcriptomic integrated with machine learning reveals human retinal cell-specific biomarkers in diabetic retinopathy

Background: Diabetic retinopathy (DR) is a leading cause of vision impairment worldwide, yet the cell-type-specific molecular alterations associated with disease progression remain incompletely understood. This study aimed to characterize transcriptional changes across retinal cell types in diabetes and DR and identify candidate disease-associated biomarkers using single-cell transcriptomics and machine-learning approaches. Methods: We generated a single-cell RNA sequencing (scRNA-seq) atlas comprising 297 121 high-quality retinal cells from 20 eyes of 13 Chinese donors, including non-diabetic controls (NON), diabetes without retinopathy (DM), and DR samples. Following quality control, batch correction, clustering, and cell-type annotation, differential expression analyses were performed across disease states within each retinal cell type. Candidate biomarkers were further prioritized using a machine-learning framework incorporating L1-regularized logistic regression, recursive feature elimination with cross-validation, and stability selection. Results: We identified 10 major retinal cell populations and characterized extensive cell-type-specific transcriptional alterations associated with diabetes and DR. Pathway enrichment analyses consistently highlighted immune activation, oxidative stress, neurodegeneration, and synaptic dysfunction across multiple retinal cell types. A total of 707 cell-type-specific candidate marker genes were identified, providing a comprehensive resource for investigating disease-associated molecular mechanisms and potential therapeutic targets. Conclusions: This study establishes a single-cell transcriptomic atlas of the Chinese diabetic retina and reveals cell-type-specific molecular signatures associated with DR progression. These findings provide biological insights into retinal disease mechanisms and nominate candidate biomarkers for future functional and translational studies.