生物信息法推算青光眼小鼠視乳頭及視網膜功能變化

劉靜坤，王霖邦，王　兵，盛亞玲，賀　靜，夢粉鴿

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·實驗研究·

生物信息法推算青光眼小鼠視乳頭及視網膜功能變化

劉靜坤1，王霖邦2，王兵3，盛亞玲1，賀靜1，夢粉鴿1

1Department of Ophthalmology, Xi’an Honghui Hospital, Xi’an 710054, Shaanxi Province, China;2Chongqing Medical University, Chongqing 400016, China;3Department of the Laboratory, Shaanxi Province Health Inspection Institution, Xi’an 710077, Shaanxi Province, China

?METHODS: The data in this study is from Gene Expression Omnibus(GEO) which belong to Nation Center for Biotechnology Information (NCBI), the quality of the raw data CEL files was processed and analyzed by the Expression software which belong to Affymetrix Inc., Santa Clare, CA, USA. Significant analysis method (SAM) which base on the T test was used to identified the significant genes. Based on GRNInfer and Gvedit soft we set up gene networks of optic and retina of mice and further more enriched analysis which based on DAVID and MAS3.0 online software were processed.

?RESULTS: The analysis between the group of the optic nerve heads and retinas in different stage of glaucoma showed that the amount of significant different expressed genes in the optic never head group increased significantly comparing with the group of retina in the early stage of glaucoma, the analysis of the genes network construction show that: the node genes of optic nerve heads included Unc13c、Kif5a、TRPM1、PANX; and the node genes of retina include POU4F1, NEFL, BC03870, CALB2. Metabolic pathways enrichment analysis which based on MAS3.0 online platform show that there was mainly the amyotrophic lateral sclerosis, tyrosine metabolism, melanogenesis, Nitrogen metabolism, Gap junction, Leukocyte transendothelial migration metabolism pathway enriched out in optic nerve head; and there was mainly amyotrophic lateral sclerosis, neurodegenerative disorders, prostate cancer, leukocyte transendothelial migration metabolism pathway enriched out in retina.

?CONCLUSION: By understanding bioinformatics result, it seems optic were more sensitive than the retina to high intraocular pressure, and weather high expression of TYrp1 gene can be as a sensitive diagnostic item require more evidence back up. Functional enrich analysis of node gene showed that cytoskeleton reconstructed，molecular motor and nutrients transport function improve in optic; and in retina, the most prominent finding in retina was enrichment function modules were focus on regeneration, repairing and differentiation of cells, which remind that we should reinforce research on reparation of retina of primary glaucoma. Metabolic pathways enrichment analysis show that inflammatory response plays prominent place in optic and retina of primary glaucoma, because of the optic narrow and crowed anatomic shape, nutrient metabolism and substances transfer enrichment modules play an important role in optics of primary glaucoma.

目的：本研究運用生物信息學軟件，利用數據庫資料，推測青光眼早期小鼠視乳頭及視網膜可能的信號路徑及基因生物功能模塊，為研究青光眼發病機制提供新的途徑。

方法：本研究的數據是從美國生物技術信息中心GEO基因表達數據庫獲得。利用美國昂飛公司Expression Console軟件對原始的CEL數據進行標準化及對數化轉換處理。利用以t檢驗為基礎的基因表達差異顯著性分析方法SAM對基因芯片數據進行顯著性差異分析，分析后篩選顯著性差異表達基因，采用GNRInfer軟件構建了小鼠視乳頭及視網膜前50個有顯著差異表達基因的調控網絡，同時我們利用MAS3.0分子注釋系統軟件及DAVID軟件這兩種在線分析平臺中進一步富集基因信號通路。

結果：青光眼各組視乳頭和視網膜及其相對應組的顯著性差異基因分析表明，在青光眼早期視乳頭組及視網膜組較之正常組相比視乳頭組顯著性差異基因數量明顯增多，青光眼視乳頭及視網膜網絡構建顯示，視乳頭基因網絡中主要調控節點基因包括Unc13c、Kif5a、TRPM1、PANX；視網膜基因網絡中主要調控節點基因包括POU4F1、NEFL、BC03870、CALB2。MAS在線信號通路分析顯示，視乳頭組織中主要的信號代謝通路包括肌萎縮側索硬化代謝通路、神經退行性紊亂、白細胞穿內皮性遷移及前列腺癌信號通路。視網膜組織主要代謝通路包括肌萎縮側索硬化代謝、酪氨酸代謝、黑色素生成、氮代謝、縫隙連接、白細胞穿內皮遷移。……