Table2_RNA Biological Characteristics at the Peak of Cell Death in Different Hereditary Retinal Degeneration Mutants.DOCX

Purpose: The present work investigated changes in the gene expression, molecular mechanisms, and pathogenesis of inherited retinal degeneration (RD) in three different disease models, to identify predictive biomarkers for their varied phenotypes and to provide a better scientific basis for their diagnosis, treatment, and prevention.
Methods: Differentially expressed genes (DEGs) between retinal tissue from RD mouse models obtained during the photoreceptor cell death peak period (Pde6brd1 at post-natal (PN) day 13, Pde6brd10 at PN23, Prphrd2 at PN29) and retinal tissue from C3H wild-type mice were identified using Illumina high-throughput RNA-sequencing. Co-expression gene modules were identified using a combination of GO and KEGG enrichment analyses and gene co-expression network analysis. CircRNA-miRNA-mRNA network interactions were studied by genome-wide circRNA screening.
Results:Pde6brd1, Pde6brd10, and Prphrd2 mice had 1,926, 3,096, and 375 DEGs, respectively. Genes related to ion channels, stress, inflammatory processes, tumor necrosis factor (TNF) production, and microglial cell activation were up-regulated, while genes related to endoplasmic reticulum regulation, metabolism, and homeostasis were down-regulated. Differential expression of transcription factors and non-coding RNAs generally implicated in other human diseases was detected (e.g., glaucoma, diabetic retinopathy, and inherited retinal degeneration). CircRNA-miRNA-mRNA network analysis indicated that these factors may be involved in photoreceptor cell death. Moreover, excessive cGMP accumulation causes photoreceptor cell death, and cGMP-related genes were generally affected by different pathogenic gene mutations.
Conclusion: We screened genes and pathways related to photoreceptor cell death. Additionally, up-stream regulatory factors, such as transcription factors and non-coding RNA and their interaction networks were analyzed. Furthermore, RNAs involved in RD were functionally annotated. Overall, this study lays a foundation for future studies on photoreceptor cell death mechanisms.

研究目的：本研究针对3种不同的遗传性视网膜变性（inherited retinal degeneration, RD）疾病模型，探究其基因表达、分子机制及发病机制的变化，旨在鉴定对应不同表型的预测生物标志物，并为这类疾病的诊断、治疗与预防提供更坚实的科学依据。
研究方法：本研究采用Illumina高通量RNA测序技术，对感光细胞死亡高峰期的RD小鼠模型（Pde6brd1对应出生后（post-natal, PN）第13天，Pde6brd10对应出生后第23天，Prphrd2对应出生后第29天）的视网膜组织，与C3H野生型小鼠的视网膜组织进行差异表达基因（differentially expressed genes, DEGs）筛选。通过GO富集分析、KEGG富集分析与基因共表达网络分析相结合的方式，鉴定共表达基因模块；通过全基因组环状RNA（circRNA）筛选，探究circRNA-miRNA-mRNA的网络互作关系。
研究结果：Pde6brd1、Pde6brd10及Prphrd2型小鼠分别筛选得到1926、3096和375个差异表达基因。其中，与离子通道、应激反应、炎症过程、肿瘤坏死因子（tumor necrosis factor, TNF）生成及小胶质细胞活化相关的基因呈现上调表达；而与内质网调控、代谢及稳态维持相关的基因则呈现下调表达。本研究还检测到在其他人类疾病（如青光眼、糖尿病视网膜病变及遗传性视网膜变性）中普遍涉及的转录因子与非编码RNA存在差异表达。circRNA-miRNA-mRNA网络分析显示，这些因子可能参与感光细胞死亡过程。此外，过量的环磷酸鸟苷（cyclic guanosine monophosphate, cGMP）蓄积可导致感光细胞死亡，且与cGMP相关的基因普遍受不同致病基因突变的影响。
研究结论：本研究筛选出与感光细胞死亡相关的基因及信号通路；此外，对转录因子、非编码RNA等上游调控因子及其互作网络进行了分析；同时对参与RD的RNA进行了功能注释。综上，本研究为后续感光细胞死亡机制的相关研究奠定了基础。