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

Research output: Contribution to journalArticle

6 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)163-178
Number of pages16
JournalCancer Informatics
Volume15
DOIs
Publication statusPublished - Aug 16 2016

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Neoplastic Stem Cells
Induced Pluripotent Stem Cells
Gene Expression
Genes
Neoplasms
Primary Cell Culture
Microarray Analysis
Conditioned Culture Medium
Cell Line

Keywords

  • Cancer stem cell
  • HiPSC
  • Spherical self-organizing map

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

Characterization of gene expression patterns among artificially developed cancer stem cells using spherical self-organizing map. / Seno, Akimasa; Kasai, Tomonari; Ikeda, Masashi; Vaidyanath, Arun; Masuda, Junko; Mizutani, Akifumi; Murakami, Hiroshi; Ishikawa, Tetsuya; Seno, Masaharu.

In: Cancer Informatics, Vol. 15, 16.08.2016, p. 163-178.

Research output: Contribution to journalArticle

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