Biomarker Identification by Proteomic Analysis of Vitreous Humor and Plasma in Diabetic Retinopathy

Huang, Q.; Banks, A.; Stacy, R.; Li, N.; Kim, Y.; Jennings, L.; Finkel, N.; Yao, S.; Wu, A.; Chen, A.; Obeidat, M.; Grosskreutz, C.; Liew, S. H. M.; Prasanna, G.; Yu, H. G.; Loureiro, J.; Zhang, Q.

doi:10.1101/2024.05.18.594835

bioRxiv · 10.1101/2024.05.18.594835

Biomarker Identification by Proteomic Analysis of Vitreous Humor and Plasma in Diabetic Retinopathy

Huang, Q.·Banks, A.·Stacy, R.·Li, N.·Kim, Y.·Jennings, L.·Finkel, N.·Yao, S.·Wu, A.·Chen, A.·Obeidat, M.·Grosskreutz, C.·Liew, S. H. M.·Prasanna, G.·Yu, H. G.·Loureiro, J.·Zhang, Q.

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Abstract

ImportanceIdentify detectable plasma and/or vitreous signals to potentially predict diabetic retinopathy (DR) progression for earlier disease intervention. ObjectiveTo determine the mediators and potential disease progression biomarkers of DR in vitreous humor (VH) and plasma samples using the SomaScan proteome profiling platform. DesignDifferential expression analysis was conducted on VH and plasma samples using the SomaScan Assay. SettingA non-interventional study conducted to collect and analyze VH and plasma samples from patients with diabetic retinopathy. ParticipantsSamples from DR (60 nonproliferative diabetic retinopathy/NPDR, 60 proliferative diabetic retinopathy/PDR) and 60 control patients were collected. Main outcomes and MeasuresDifferentially expressed proteins between disease and control groups were identified. Pathway enrichment analysis was conducted to identify significantly perturbed pathways in DR. Finally, a random forest model was used to identify predictive biomarkers of disease progression. ResultsSomaScan v3 is a pooled aptamer hybridization assay using 5080 SOMAmers to probe over 4100 proteoforms in VH and plasma samples from 3 groups (control, NPDR, and PDR). The most profound protein content change was observed in the VH samples of PDR patients, while minimal changes were measured in plasma samples, highlighting the regionality of PDR pathogenesis. Many key molecules and molecular pathways such as VEGF-A, erythropoietin, and inflammation-associated proteins implicated in DR were significantly affected in the VH of PDR patients. In addition to the classic pathways (hypoxia, immune response, mTORC1 signaling) known to be involved in PDR, novel signaling pathways, including HEME metabolism and adipogenesis, were identified in VH samples. Application of a machine learning algorithm identified a panel of plasma PDR predictive biomarkers and revealed SCARA5 as the top one based on the largest average Gini decrease in the model. ConclusionOur study identified profound alteration of protein expression and molecular pathways in the VH of PDR patients, supporting the key role of local pathogenic changes in DR progression compared to systemic factors. Although the systemic changes related to DR were small, a few disease progression predictive candidate biomarkers (SCARA5, PTK7, FAM3Band FAM3D) were identified, prompting further investigation. Key PointsQuestion: Are plasma/ vitreous humor (VH) proteins predictive of diabetic retinopathy (DR) progression? Findings: This study identifies substantial protein changes in the VH of proliferative diabetic retinopathy (PDR) patients, while early nonproliferative DR (NPDR) patients show minimal change. We identify multiple proteins linked to angiogenesis, inflammation, immune cells (microglia/macrophage/neutrophil), and leukostasis associated with PDR and reveal a potential plasma panel of disease progression (from NPDR to PDR) biomarkers (SCARA5, PTK7, FAM3B, FAM3D). Meaning: Identified disease progression predictive biomarkers permits potential development of prognostic tools to identify individuals most at risk for PDR progression and offering reduced disease burden by earlier intervention.

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Huang, Q., Banks, A., Stacy, R., Li, N., Kim, Y., Jennings, L., Finkel, N., Yao, S., Wu, A., Chen, A., Obeidat, M., Grosskreutz, C., Liew, S. H. M., Prasanna, G., Yu, H. G., Loureiro, J., Zhang, Q.. 2024-05-21. Biomarker Identification by Proteomic Analysis of Vitreous Humor and Plasma in Diabetic Retinopathy. https://doi.org/10.1101/2024.05.18.594835

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