利用生物資訊學方法分析受多訊息控制的基因表現之轉錄調控機制

Abstract

破解細胞用以調控基因表現的機制為解析細胞生理現象的重要拼圖之一。在調控基因表現的機制中，轉錄因子為整體調控網路的樞紐。轉錄因子可受到上游訊息傳遞途徑的活化，並藉由結合至基因中的特定位置以調控特定功能的基因表現。關於轉錄因子如何協調訊息傳遞途徑以調控基因表現的機制仍無一定論。針對此問題，過去已開發很多相關的演算法分析轉錄因子在訊息傳遞途徑中的樞紐位置與其所參與的調控網路。然而，至今尚未有研究系統性地分析轉錄因子與訊息傳遞途徑的交互作用，與其對下游基因表現的調控機制。本論文欲解開轉錄因子如何協調上游訊息傳遞途徑以調控基因表現，乃發展一整合式計算方法，分析免疫細胞的訊息傳遞蛋白質活性與高通量基因體表現資料，主要探討B細胞中IKK與ERK訊息傳遞路徑調控轉錄性反應的調控機制模型。 本研究藉由分析顯著差異表現基因、預測可能的調控轉錄因子，並進而利用親和力迴歸分析方法估計ERK與IKK訊息傳遞途徑對下游轉錄因子的交互作用。進而發現在B細胞早期活化過程中，大部分轉錄因子的活化由ERK所調控。IKK所調控的轉錄因子屬於少數，但卻在轉錄調控機制中扮演了關鍵的角色。並進一步建構轉錄調控機制的動力學模型，利用電腦模擬分析轉錄因子如何調控基因表現。模擬結果顯示ERK所調控與IKK所調控的轉錄因子間的組合調控機制可以調控多樣化的基因表現樣式以控制B細胞活化過程。本研究揭露了在B細胞早期活化過程，整合不同的訊息傳遞途徑控制轉錄因子組合調控網路是達成B細胞功能的關鍵步驟。 藉由整合線性回歸迴歸分析與建模方法，本研究闡明了B細胞活化過程中，受訊息傳遞途徑調控基因表現的調控機制。本研究成果希望能提升對細胞生理現象中，細胞外刺激與基因表現反應調控機制的認識，並強化B細胞相關研究在臨床應用上的研究基礎。本研究架構同時提供ㄧ可行的整合方法，系統性地分析轉錄因子與訊息傳遞途徑的交互作用，與其對下游基因表現的調控機制，期能應用在分析基礎細胞生理現象，並貢獻於免疫疾病，甚或癌症治療的臨床研究中。

Gene expression is the outcome of the hierarchical activation of signaling pathways via a tightly controlled network of interacting elements in the eukaryotic cell. Among the interacting elements, transcription factors (TFs) play an important role in the signaling pathways and often control gene expression in combinatorial fashion. However, how TFs coordinate the signals from different signaling pathways and their combinatorial control remain unclear. A number of algorithms have been developed to study the central role of TFs in the signaling pathways and regulatory networks. However, a systematic study of the interacting relationship between signaling pathways and TFs, and an explicit paradigm of transcriptional regulatory mechanism still lack yet. In this study, the interacting relationships of TFs in ERK and IKK signaling pathways and the transcriptional regulatory mechanism of the primary response of B cells are addressed. I estimated the interacting relationship between ERK and IKK signaling pathways and TFs by using an affinity regression model. To further analyze the regulatory mechanism of TFs, I built up a kinetic model to simulate and predict how the regulating TFs would coordinate ERK and IKK to control gene expression. According to the regression analysis, I found that the majority of the regulating TFs were regulated dominantly by the ERK signaling in B cells. The simulation revealed that the combination of TFs differentially controlled by ERK and IKK contributed to the divergent gene expression patterns in orchestrating the primary B cell response. This study suggests that coordinating the differentially activated signaling proteins to recruit the proper TF combinatorial regulatory network is important to achieve the transcriptional control of the early B cell development. The key finding elucidates the underlying mechanism of the signal-dependent gene expression in the signaling pathways responsible for the B cell activation. The integrative method could be broadly applied in other stimulus-response systems. Solving the transcriptional regulatory mechanism could provide the conceptual basis for interpreting the underlying mechanism behind the cell physiology in basic cell biology studies and clinical researches.