Abstract 272: Identification of MicroRNAs unique to cancer stem cells by small RNA deep sequencing.
Authors: Ji Junfang , Forgues Marshonna , Yamashita Taro , Wauthier Eliane , Reid Lola M. , Wen Xinyu , Song Young , Wei Jun , Khan Javed , Thorgeirsson Snorri S. , Wang Xin W. 
Published: August 2014

Abstract
Cancer stem cells (CSCs) are undifferentiated cancer initiating cells with normal stem cell traits and they are responsible for cancer progression, tumor relapse and resistance to chemotherapy. While therapies that target CSCs hold promise in eliminating cancer burden, normal stem cells are likely to be targeted due to their similarities with CSCs. Recently we have demonstrated that EpCAM+ AFP+ hepatocellular carcinoma (HCC) cells are CSCs. EpCAM and AFP are two cellular proteins that are highly expressed in fetal livers and are silenced in adult livers but they are reactivated in a subset of HCC. Since microRNAs play a key role in the maintenance of normal stem cells and CSCs, we hypothesized that abnormal microRNA expression could be a unique feature specific to EpCAM+ AFP+ CSCs but not to normal liver stem cells. In this study, we used the SOLiD-4 system to perform genome-wide measurement of small RNA transcriptome. We constructed 16 small RNA libraries derived from EpCAM+ AFP+ CSCs and corresponding differentiated EpCAM- AFP- tumor cells from primary HCC clinical specimens and HCC cell lines, human embryonic stem cells, primary normal liver stem cells and their lineage restricted hepatoblasts, and differentiated hepatocytes. We generated a total of 290.9 million reads. Using the RNA2MAP (v0.5) computational program, the 35 nucleotide-filtered reads were aligned to the reference human miRBase (v17.0), then to the human genome (hg19). The alignment yielded an average of 10.3 million high-quality mapped reads, of which 59.3% were aligned to miRBase. Further, we developed an in-house bioinformatics analysis pipeline to process mapped reads and identified 83.2% of known microRNA hairpins (n=1426) and 71.0% of known mature microRNAs within the human miRBase (n=1733). Using a stringent comparison criterion between undifferentiated and differentiated cells as well as between normal and cancer cells, we identified 10 microRNAs unique to HCC CSC but not to normal stem cells and 15 microRNAs unique to normal liver stem cells. We also identified several microRNAs that contain candidate somatic mutations. These microRNAs may possess unique functions to HCC CSCs and thus they are strong candidates as therapeutic targets for HCC. Further investigation would allow us to develop novel therapies to specifically eliminate CSC without sacrificing normal stem cells to avoid unwanted side effect.
Citation Format: Junfang Ji, Marshonna Forgues, Taro Yamashita, Eliane Wauthier, Lola M. Reid, Xinyu Wen, Young Song, Jun Wei, Javed Khan, Snorri S. Thorgeirsson, Xin W. Wang. Identification of MicroRNAs unique to cancer stem cells by small RNA deep sequencing. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 272. doi:10.1158/1538-7445.AM2013-272