Genotypes of cancer stem cells characterized by epithelial-to-mesenchymal transition and proliferation related functions.
Cancer stem cells (CSCs), or cancer cells with stem cell-like properties, generally exhibit drug resistance and have highly potent cancer inducing capabilities. Genome-wide expression data collected at public repositories over the last few years provide excellent material for studies that can lead to insights concerning the molecular and functional characteristics of CSCs. Here, we conducted functional genomic studies of CSC based on fourteen PCA-screened high quality public CSC whole genome gene expression datasets and, as control, four high quality non-stem-like cancer cell and non-cancerous stem cell datasets from the Gene Expression Omnibus database. A total of 6,002 molecular signatures were taken from the Molecular Signatures Database and used to characterize the datasets, which, under two-way hierarchical clustering, formed three genotypes. Type 1, consisting of mainly glia CSCs, had significantly enhanced proliferation, and significantly suppressed epithelial-mesenchymal transition (EMT), related functions. Type 2, mainly breast CSCs, had significantly enhanced EMT, but not proliferation, related functions. Type 3, composed of ovarian, prostate, and colon CSCs, had significantly suppressed proliferation related functions and mixed expressions on EMT related functions.
Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan.
Chueh-Lin
CL
Hsu
Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan.
Feng-Hsiang
FH
Chung
Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan.
Chih-Hao
CH
Chen
Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan.
Tzu-Ting
TT
Hsu
Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan.
Szu-Mam
SM
Liu
Department of Radiation Oncology, Landseed Hospital, Taoyuan, 324, Taiwan.
Dao-Sheng
DS
Chung
Department of Surgery, Landseed Hospital, Taoyuan, 324, Taiwan.
Ya-Fen
YF
Hsu
Department of Nephrology, Landseed Hospital, Taoyuan, 324, Taiwan.
Chien-Lung
CL
Chen
Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan.
Nianhan
N
Ma
Institute of Systems Biology and Bioinformatics, Department of Biomedical Science and Engineering, National Central University, Zhongli, 32001, Taiwan.|Department of Physics, Chung Yuan Christian University, Zhongli, 32023, Taiwan.|Center for Dynamical Biomarkers and Translational Medicine, National Central University, Zhongli, 32001, Taiwan.
Hoong-Chien
HC
Lee
D049109:Cell Proliferation; D016000:Cluster Analysis; D030541:Databases, Genetic; D058750:Epithelial-Mesenchymal Transition / Q000235:genetics*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D063990:Gene Ontology; D005838:Genotype; D006801:Humans; D014411:Neoplastic Stem Cells / Q000378:metabolism* / Q000473:pathology*; D025341:Principal Component Analysis