Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, Australia.
Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia.
Invest Ophthalmol Vis Sci. 2021 Nov 1;62(14):22. doi: 10.1167/iovs.62.14.22.
This study interrogated the transcriptional features and immune cellular landscape of the retinae of rats subjected to oxygen-induced retinopathy (OIR).
Bulk RNA sequencing was performed with retinal RNA isolated from control and OIR rats. Gene set enrichment analysis (GSEA) was undertaken to identify gene sets associated with immune responses in retinal neovascularization. Bulk gene expression deconvolution analysis by CIBERSORTx was performed to identify immune cell types involved in retinal neovascularization, followed by functional enrichment analysis of differentially expressed genes (DEGs). Protein-protein interaction analysis was performed to predict the hub genes relevant to identified immune cell types. CIBERSORTx was applied to profile immune cell types in the macula of patients with both proliferative diabetic retinopathy (PDR) and diabetic macular edema using a public RNA-seq dataset.
Transcriptome analysis by GSEA revealed that the retina of OIR rats and patients with PDR is characterized by increased immunoregulatory interactions and complement cascade. Deconvolution analysis demonstrated that M2 macrophages infiltrate the retinae of OIR rats and patients with PDR. Functional enrichment analysis of DEGs in OIR rats showed that the dysregulated genes are related to leukocyte-mediated immunity and myeloid leukocyte activation. Downstream protein-protein interaction analysis revealed that several potential hub genes, including Ccl2, Itgam, and Tlr2, contribute to M2 macrophage infiltration in the ischemic retina.
This study highlights application of the gene expression deconvolution tool to identify immune cell types in inflammatory ocular diseases with transcriptomes, providing a new approach to assess changes in immune cell types in diseased ocular tissues.
本研究探讨了氧诱导视网膜病变（OIR）大鼠视网膜的转录特征和免疫细胞图谱。
从对照和 OIR 大鼠的视网膜中分离出 RNA，进行批量 RNA 测序。采用基因集富集分析（GSEA）鉴定与视网膜新生血管化中免疫反应相关的基因集。通过 CIBERSORTx 进行批量基因表达去卷积分析，鉴定参与视网膜新生血管化的免疫细胞类型，然后对差异表达基因（DEGs）进行功能富集分析。进行蛋白质-蛋白质相互作用分析，以预测与鉴定的免疫细胞类型相关的关键基因。应用 CIBERSORTx 对一个公共 RNA-seq 数据集进行分析，以分析增生性糖尿病视网膜病变（PDR）和糖尿病性黄斑水肿患者黄斑中的免疫细胞类型。
通过 GSEA 的转录组分析表明，OIR 大鼠和 PDR 患者的视网膜以增强的免疫调节相互作用和补体级联反应为特征。去卷积分析表明 M2 巨噬细胞浸润 OIR 大鼠和 PDR 患者的视网膜。OIR 大鼠中 DEGs 的功能富集分析表明，失调的基因与白细胞介导的免疫和髓样白细胞激活有关。下游蛋白质-蛋白质相互作用分析表明，包括 Ccl2、Itgam 和 Tlr2 在内的几个潜在关键基因，有助于缺血性视网膜中 M2 巨噬细胞的浸润。
本研究强调了应用基因表达去卷积工具来识别炎症性眼病转录组中的免疫细胞类型，为评估患病眼部组织中免疫细胞类型的变化提供了一种新方法。
