揭開斑馬魚的再生策略：對心臟、大腦、鰭與視網膜再生的全面性系統生物學研究

Uncover regeneration strategy of zebrafish organs: a comprehensive systems biology study on heart, brain, fin and retina regeneration

劉芳佑(Liu, Fang Yu)

指導教授 ： 林澤

國立清華大學/電機資訊學院/電機工程學系/碩士(2015年)

摘要

背景：
再生是透過不同的生理機制協調來進行傷口愈合的目的，包含發炎與免疫反應來避免感染、細胞增生進行所需細胞的累積與組織的分化與去分化協調等。其中，斑馬魚是重要的脊椎動物模型並且擁有許多優點，包含了心臟、鰭與中央神經系統的再生能力、與人類相似的基因庫、高生產率及低培養成本，因此用斑馬魚進行再生機制研究的模型開始流行。

結果：
根據斑馬魚心臟、腦、魚鰭與視網膜四個器官修復實驗所定續的微陣列資訊，我們建立了四個蛋白互動網路，並透過AIC剔除假陽性的蛋白質互動關係，捕捉了被激活的生物路徑。我們提取了核心蛋白群（交集）與特異性蛋白群（差集）並利用基因本體論中生物過程與路徑分類，在核心蛋白群找到了TGF-β訊號路徑，與分別在心臟、腦、魚鰭與視網膜的特意蛋白群中找到了整合素、Wnt訊號路徑、血管新生與Bdnf這些重要的生物路徑，為了研究器官再生的作用機制，我們提出了一個五步驟的胚再生模型，並應用在這些蛋白與路徑來試著揭開斑馬魚的再生策略，結果上而言我們發現核心蛋白群的TGF-β訊號參與了廣泛的生物功能，並參與了再生胚模型的五個步驟，在心臟則是由整合素、纖維母細胞生長因子與血小板衍生生長因子訊號路徑共同調控了纖維蛋白之間的親和力，以加速心臟受損時的止血能力。而腦部與魚鰭則是由Wnt訊號來調控神經幹細胞的分化成長，而Bdnf則會強化視網膜細胞受損之後的生存能力，避免二次傷害。

結論：
透過四個再生蛋白互動網路的分析，我們探討了斑馬魚的再生策略，有了這些再生策略更進一步的理解後，相信我們有機會可以在再生醫學裡增進藥物治療與設計。

關鍵字

斑馬魚 ； 再生 ； 分化 ； 魚鰭 ； 心臟 ； 腦 ； 視網膜 ； 蛋白質互動網路 ； 系統生物學

並列摘要

Background: Regeneration process orchestrates various bio-physiology mechanisms for wound healing such as inflammation immune response for preventing infection, proliferation for blastema accumulation, differentiation and dedifferentiation of cells for tissue development. Zebrafish is an important vertebrate organism for modeling and has many advantages includes its strong regenerative capability on heart, fins, and central nervous system, genome similarity to human, high productive rate and low maintenance costs. Using zebrafish as the model to study regeneration mechanism becomes popular.
Result: Based on time-course microarray data of four zebrafish-organs wound healing experiments includes heart, brain, fin and retina, we constructed four regenerative PPI networks, which captures activated pathways based on experiment data through applying AIC to select significant PPIs. We extracted core proteins (intersection set) and specific proteins (relatively complement set) and use both GO biological function and pathway classification on these proteins sets including TGF-β signaling for core proteins, integrins for heart specific proteins, Wnt signaling for brain specific proteins, angiogenesis for fin specific proteins, and Bdnf for retina specific proteins. To investigate the underlying mechanism of organ regeneration, we proposed a five-step blastema model and applied our observation from the PPI networks to uncover regeneration strategy of zebrafish. In result, TGF-β signaling in core proteins participates variety biological function and was observed in each step in blastema model. Integrins, FGF and PDGF co-regulate binding affinity for fibrin and fibrinogen for rapid hemostasis through mediation of integrins during heart injury. Wnt signaling mediates growth and differentiation of neuron stem cells for brain and fin in differentiation and pattern formation step. And Bdnf prevents retinal neuron from secondary damage and strengthens the survival ability at the injury response step.
Conclusion: Via our analysis of all four zebrafish regenerative PPI networks, we investigated the underlying strategy of zebrafish organ regeneration. With a better understanding of regeneration strategy for zebrafish, we hope to advance therapeutic and drug design for regenerative medicine.

並列關鍵字

zebrafish ； regeneration ； differentiation ； fin ； heart ； brain ； retina ； PPI network ； systems biology

參考文獻

1. Olson, J.L., A. Atala, and J.J. Yoo, Tissue Engineering: Current Strategies and Future Directions. Chonnam Med J, 2011. 47(1): p. 1-13.

4. Shi, W., et al., Using zebrafish as the model organism to understand organ regeneration. Sci China Life Sci, 2015. 58(4): p. 343-51.

5. Gemberling, M., et al., The zebrafish as a model for complex tissue regeneration. Trends Genet, 2013. 29(11): p. 611-20.

6. Liu, J. and D.Y. Stainier, Zebrafish in the study of early cardiac development. Circ Res, 2012. 110(6): p. 870-4.

7. Bakkers, J., Zebrafish as a model to study cardiac development and human cardiac disease. Cardiovasc Res, 2011. 91(2): p. 279-88.