建立肝癌中微小核醣核酸與基因間的調控網路

Abstract

肝癌在台灣為第二常見的癌症。近年研究已發現微小核醣核酸（miRNA）與多癌症和疾病有關，包含各種癌症、糖尿病和心血管疾病，而且可能可以當作生物標記和標靶治療。miRNA是長度約為22nts的非編碼小RNA分子，其功能為在轉錄後修飾時藉由抑制基因表現而導致許多疾病和癌症。我們首先開發一個計算工具miTRaCLIP可全面的分析CLIP-seq和PAR-CLIP數據，來解析miRNA所有可能的標靶基因。與現有的工具相比，我們的工具更專注於miRNA的註解與可視化。第二，我們更新了實驗證實的miRNA-標靶基因相互作用（MTIs）的資料庫 - miRTarBase。除了不斷從文獻中將實驗證實的資料整理到資料庫外，此外，使用先前發展的miTRaCLIP，我們系統地分析由21個獨立研究，共138個CLIP-seq資料集的數據。miRTarBase包含4,966篇文獻，7,439筆具有較強的實驗證據MTIs（使用報導基因或西方墨點法驗證）和CLIP-seq 實驗證據MTIs共348,007筆。我們也整合癌症基因組圖譜（TCGA）之miRNA和基因表現資料，以提供對於miRNA的臨床實驗數據更有效概覽。這些重大更新使miRTarBase成為一個最完整且全面的實驗驗證的miRNA標靶相互作用的資料庫，期望對於miRNA的研究能有很大的幫助。為了便於研究miRNA在許多生物體中所扮演的角色，構建一個有系統分析框架是必要的。最後，我們重建肝癌的microRNA基因調控網絡。使用實驗驗證的轉錄因子miRNA（TF-miRNA）的資料庫TransmiR和使用先前構建與更新的miRTarBase 作為miRNA-標靶基因資料庫。利用此分析流程成功利用TCGA肝癌資料建立了肝癌中的miRNA基因調控網絡。此具有高度可信度的計算框架可應用於探索在任何複雜的生物系統的TF-miRNA::標靶基因相互作用。此外，miRTarBase資料庫在對於近年microRNA相關研究具有舉足輕重的角色。

Liver cancer is the 2nd most common cancer in Taiwan. Recent work supports miRNAs down-regulate gene expression during various crucial cell processes such as apoptosis, differentiation and development. Research in various disease processes such as cancer, diabetes, and cardiovascular disease has found that miRNAs play a role in disease pathogenesis and have potential as biomarkers and therapeutic agents. MicroRNAs (miRNAs) are about 22nts small non-coding RNA molecules that negatively regulate the gene expression at the post-transcriptional level cause many disease and cancer. We herein develop the computational tools, miTRaCLIP, to comprehensively identify CLIP-seq and PARCLIP data specifically for decoding miRNA targetome. Comparing with the existing CLIP-seq tools, our results show more visualizing and more functional annotation for miRNA studies. Second, we construct an experimentally validated miRNA-target interactions databases – miRTarBase. We continually manually curated literature. Additionally, using previous develop miRTarCLIP, we systematically identify Argonuate-miRNA-RNA interactions from 138 crosslinking and immunoprecipitation sequencing (CLIP-seq) data sets that were generated by 21 independent studies. The database contains 4,966 articles, 7,439 strongly validated MTIs (using reporter assays or western blots) and 348,007 MTIs from CLIP-seq. The miRNA and gene expression profiles from The Cancer Genome Atlas (TCGA) are integrated to provide an effective overview of this exponential growth in the miRNA experimental data. These improvements make the miRTarBase to be a comprehensively annotated, experimentally validated miRNA-target interactions databases, and motivate additional miRNA research efforts. To facilitate the miRNA study in many physiological processes, it is necessary construct a systematic framework. Finally, we reconstruction of microRNA-mediated gene regulatory networks in liver cancer. The computational framework using publicly available transcription factor-miRNA (TF-miRNA) database, TransmiR, along with miRNA-target databases, using previous construct miRTarBase. We applied the computational framework to elucidate the miRNA-mediated regulatory network in hepatocellular carcinoma. This computational framework can be applied to explore the significant TF-miRNA and miRNA-target gene interactions in any complex biological systems with high degrees of confidence.