Institute of Information Science, Academia Sinica

In this post-genomic era it is clear that the sum of the cellular gene expression state determines the cellular phenotypes. The challenge we now face is to keep up the bioinformatics analysis and to understand the genome blueprint. Bearing these in mind, we focus on applying and developing bioinformatics and systems biology tools for deciphering cancer and stem cell transcriptome data. Recently, wesetup analysis pipelines for small RNA sequencing (smRNA-Seq) data and applied them on microRNA research. Atypical teratoid/rhabdoid tumor (AT/RT) is a highly malignant pediatric brain tumor often misdiagnosed as other embryonal brain tumors such as medulloblastoma (MB). AT/RT prognosis is much worse than MB, but the underlying mechanisms are unclear. We deciphered the miRNome patterns of AT/RTs and MBs by sequencing their small RNA fractions. Novel miRNAs as well as known miRNAs were found deregulated in tumor cells. miR-221 and miR-222 are oncomiRs that can target several tumor suppressors. In contrast, miR-221 and miR-222 inhibit tumor angiogenesis by repressing the activity of matured endothelial cells and circulating endothelial progenitor cells (EPCs). Further challenge will be to integrate NGS information with systems biology and cloud computing tools.