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 language | English |
|---|---|
| Pages (from-to) | 163-178 |
| Number of pages | 16 |
| Journal | Cancer Informatics |
| Volume | 15 |
| DOIs | |
| Publication status | Published - Aug 16 2016 |
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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 journal › Article
}
TY - JOUR
T1 - Characterization of gene expression patterns among artificially developed cancer stem cells using spherical self-organizing map
AU - Seno, Akimasa
AU - Kasai, Tomonari
AU - Ikeda, Masashi
AU - Vaidyanath, Arun
AU - Masuda, Junko
AU - Mizutani, Akifumi
AU - Murakami, Hiroshi
AU - Ishikawa, Tetsuya
AU - Seno, Masaharu
PY - 2016/8/16
Y1 - 2016/8/16
N2 - 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.
AB - 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.
KW - Cancer stem cell
KW - HiPSC
KW - Spherical self-organizing map
UR - http://www.scopus.com/inward/record.url?scp=84985995526&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84985995526&partnerID=8YFLogxK
U2 - 10.4137/CIN.S39839
DO - 10.4137/CIN.S39839
M3 - Article
AN - SCOPUS:84985995526
VL - 15
SP - 163
EP - 178
JO - Cancer Informatics
JF - Cancer Informatics
SN - 1176-9351
ER -