| 摘要: | 生物網絡，例如代謝路徑的建構，及其隨時間的變化，是瞭解生物的一個主要方法。疾病引起的生化路徑改變，可以用之來開發診斷疾病，甚至治療疾病的方法。基因微晶片的常見應用，例如用叢集分析找出表現量變化相同的基因，被廣泛運用來找尋路徑。但是實際情況要複雜許多，因為表現出來的蛋白質與其他蛋白質之間可能有交互作用，而目前人們無法對這為數龐大的蛋白質一一檢測其交互作用。本計劃的目的是運用本團隊所擁有的特殊技術開發蛋白質晶片，並且利用蛋白質晶片來發展一套整合高通量的蛋白質科技、外碼子基因晶片檢測技術、生物資訊、計算與模型而建構成的蛋白質交互作用以及疾病導致的生物路徑的變異的偵測與研究平台。我們也要利用此平台偵測這些變異在撿體處在不同外加條件下的改變。本計畫的一個特點是使用外碼子微晶片，如此我們可以取得基因多樣性剪接的資訊，在以之與蛋白質晶片的實驗結果結合之後，我們更可以得到生物路徑變異與同位蛋白質之間的關係。本計畫的目標是產生兩件智慧財產。其一是設計及製造蛋白質晶片並建立一套片應用此晶片在研究蛋白質交互作用及蛋白質與DNA 交互作用的標準步驟。此部份大部分屬於化學及硬體類。其二是建立本類跨領域整合型的標準研究平台。此部份涉及資訊、計算、模型、統計、以及系統研發，屬於廣義的物理與軟體類。因為本計畫的性質是研發，我們用我們已經有使用經驗並且已知有高品管性的大腸癌細胞株作為生物模型。本計劃如果成功（我們有信心它會成功），將我們的成果－整合蛋白質晶片、外碼子微晶片、生物資訊、計算與模型以研究疾病導致的生物路徑的變異的研究平台－應用於人類檢體上應該不是一件難事，我們也相信它會被應用於研究人類的癌症及其它疾病上。The construction and a dynamical description of biological pathways are major undertakings of biology. The understanding of disease-induced aberrations in these pathways provides crucial insights for diagnosis and treatment of the disease. A popular method for the study of these topics is based on DNA microarray experiments, where genes are clustered according to their time-course expression profiles. Genes sharing a common time-course are inferred to be taking part in the same function, hence belonging to the same functional pathway. Ideally, since pathways are expression of the interactions among proteins, they could in principle be constructed by the direct detection of such interactions in specific physiological settings. At the moment such detection is very difficult, and impractical when conducted on a large scale, a necessity because of the large number of proteins involved in any pathway. In this project we propose to develop a research and development protocol based on the integration of high-throughput protein chips technology, exon microarrays measurement, bioinformatics, and computational and modeling to construct protein-protein interaction maps (PPIN) and biological pathways and disease induced aberrations in these structures, and the changes in these aberrations when the research model is subjected to a variety of controlled stress conditions. A notable feature of the proposal is the use of exon arrays, from which we expect to obtain information on alternative splicing and, through protein chip technology, to gain insights on relations between isoform and pathway aberration. The proposal aims to generate two intellectual products. One concerns the design and manufacture of a protein chip (or chips) and the development of its high-throughput application, in the detection of PPIN as well as protein-DNA interaction. While it will involve procedural development, this part is mostly chemistry and hardware. The other is the development of the integrated research protocol itself, which will involve informatics, computation, modeling, statistics, and systems development. This part is mostly “physics” and software. Because the nature of the proposal is R&D, we will use (colon) cancer cell lines as our biological model. We use these because of their inherent higher level of quality control over human or animal samples, and because we have acquired reliable expertise dealing with these cell lines over the last several years. If this project is successful, and we have confidence that it will be, our protocol will be transferable to the study of human samples, and we envisage it to be widely applicable in the study of human cancer and other diseases. 研究期間 : 9808 ~ 9907 |
