Compartment-Specific Immune, Endothelial, and Fibrotic Programs in Diabetic Retinopathy: An Integrative Multi-Cohort Transcriptomic Study

Proliferative diabetic retinopathy (PDR) is molecularly heterogeneous, but it is unclear whether immune-rich and endothelial-rich transcriptional patterns recur across retinal compartments. We integrated five public human transcriptomic datasets and analyzed PhysioNet CDED separately as the exploratory clinical context. GSE307925 served as the discovery cohort; GSE245561 and GSE165784 provided independent single-cell cross-cohort evaluation; GSE94019 provided CD31-enriched endothelial evaluation; and GSE160306 provided whole-retina disease-spectrum contextualization. In GSE307925, CD31-low and CD31-high samples separated strongly (PC1 61.5%; exact permutation p = 0.0013), with separation retained in all 12 leave-one-out analyses and under TMM normalization. In the two single-cell cohorts, the discovery-derived CD31-low signature localized to myeloid cells and the CD31-high signature to endothelial cells in all nine PDR donors (exact sign-test p = 0.00195 for each); the fibrotic/ECM-remodeling core localized to stromal/pericyte cells in all nine donors. In GSE94019, the fibrotic/ECM-remodeling program was increased in PDR (p = 0.0028; q = 0.0084) and remained associated with PDR after adjustment for an independent pericyte-lineage score (β = 1.473, 95% CI 0.758–2.189; p < 0.001). In GSE160306, the discovery-derived CD31-low program showed a nominal association with advanced DR/DME (β = 0.306, 95% CI 0.026–0.585; p = 0.032; q = 0.085). These findings support compartment-dependent molecular enrichment rather than fixed binary patient subtypes.