Characterization of Gene Expression Patterns among Artificially Developed Cancer Stem Cells Using Spherical Self-Organizing Map

Akimasa Seno; Tomonari Kasai; Masashi Ikeda; Arun Vaidyanath; Junko Masuda; Akifumi Mizutani; Hiroshi Murakami; Tetsuya Ishikawa; Masaharu Seno

doi:10.4137/CIN.S39839

Characterization of Gene Expression Patterns among Artificially Developed Cancer Stem Cells Using Spherical Self-Organizing Map

Cancer Inform. 2016 Aug 16:15:163-78. doi: 10.4137/CIN.S39839. eCollection 2016.

Authors

Akimasa Seno¹, Tomonari Kasai¹, Masashi Ikeda¹, Arun Vaidyanath¹, Junko Masuda¹, Akifumi Mizutani¹, Hiroshi Murakami¹, Tetsuya Ishikawa², Masaharu Seno¹

Affiliations

¹ Laboratory of Nano-Biotechnology, Department of Medical Bioengineering Science, Graduate School of Natural Science and Technology, Okayama University, Kita-ku, Okayama, Japan.
² Cell Biology, Core Facilities for Research and Innovative Medicine, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan.; Central Animal Division, Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan.

Abstract

We performed gene expression microarray analysis coupled with spherical self-organizing map (sSOM) for artificially developed cancer stem cells (CSCs). The CSCs were developed from human induced pluripotent stem cells (hiPSCs) with the conditioned media of cancer cell lines, whereas the CSCs were induced from primary cell culture of human cancer tissues with defined factors (OCT3/4, SOX2, and KLF4). These cells commonly expressed human embryonic stem cell (hESC)/hiPSC-specific genes (POU5F1, SOX2, NANOG, LIN28, and SALL4) at a level equivalent to those of control hiPSC 201B7. The sSOM with unsupervised method demonstrated that the CSCs could be divided into three groups based on their culture conditions and original cancer tissues. Furthermore, with supervised method, sSOM nominated TMED9, RNASE1, NGFR, ST3GAL1, TNS4, BTG2, SLC16A3, CD177, CES1, GDF15, STMN2, FAM20A, NPPB, CD99, MYL7, PRSS23, AHNAK, and LOC152573 genes commonly upregulating among the CSCs compared to hiPSC, suggesting the gene signature of the CSCs.

Keywords: cancer stem cell; hiPSC; spherical self-organizing map.