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Bioinformatics Tools for Bulk Gene Expression Deconvolution in Diabetic Retinopathy.
Ru Qi Teh1, Guei-Sheung Liu2,3,4, Jiang-Hui Wang5
1Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia.
Methods in Molecular Biology (Clifton, N.J.)
|June 16, 2023
Summary
This study details using CIBERSORTx deconvolution analysis on RNA sequencing data to identify immune cells, like macrophages, involved in retinal neovascularization and proliferative diabetic retinopathy (PDR). This helps understand vision loss causes.
Area of Science:
- Ophthalmology
- Immunology
- Bioinformatics
Background:
- Retinal neovascularization is a major cause of vision loss, characteristic of proliferative diabetic retinopathy (PDR).
- Immune system involvement is recognized in the pathogenesis of diabetic retinopathy (DR).
Purpose of the Study:
- To describe protocols for using CIBERSORTx deconvolution analysis on RNA sequencing (RNA-seq) data.
- To identify specific immune cell types contributing to retinal neovascularization in DR and PDR.
Main Methods:
- Utilizing bioinformatics analysis of RNA sequencing (RNA-seq) data.
- Applying the CIBERSORTx deconvolution algorithm to identify immune cell infiltration.
- Performing downstream analysis of RNA-seq data.
Main Results:
- Previous studies identified macrophage infiltration in hypoxia-induced retinal neovascularization and PDR using CIBERSORTx.
- This work provides a protocol for such analyses.
Conclusions:
- Deconvolution analysis with CIBERSORTx is a viable method for identifying immune cell contributions to retinal neovascularization.
- Understanding these immune cell roles is crucial for addressing vision loss in PDR.
