Small RNA Sequencing in microRNA Research

Abstract

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. In our lab we applied and developed bioinformatics and systems biology tools for deciphering cancer and stem cell transcriptome data. Cancer stem-like cells were isolated as colonospheres from primary colon cancer tissues and cell lines and characterized their gene expression patterns and genetic networks. Expanded colon cancer spheres had many features of cancer stem cells, including chemoresistance and radioresistance, the ability to initiate tumor formation, and activation of epithelial-mesenchymal transition (EMT). SNAIL, an activator of EMT, was expressed at high levels by CRC colonospheres. smRNA-Seq and genetic network analyses revealed that SNAIL activates genes and microRNAs, such as IL8 and miR-146a, in colonospheres. Blocking IL-8 or miR-146a expression/activity disrupted SNAIL-induced stem cell-like features of colonospheres. Strategies that disrupt the SNAIL-IL8 and SNAIL-miR146a pathways can be developed to block tumor formation by colon cancer stem-like cells. We also applied our systems on brain tumor 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/RT and MB by sequencing their small RNA fractions. Novel as well as known miRNAs were found deregulated in tumor cells. miR-221 and miR-222 are oncomiRs that can target several tumor suppressors. Further challenge will be to integrate RNA-seq information with systems biology and cloud computing tools.