title: Possible linkages between the inner and outer cellular states of human induced pluripotent stem cells.
abstract: BACKGROUND
  Human iPS cells (hiPSCs) have attracted considerable attention for applications to drug screening and analyses of disease mechanisms, and even as next generation materials for regenerative medicine. Genetic reprogramming of human somatic cells to a pluripotent state was first achieved by the ectopic expression of four factors (Sox2, Oct4, Klf4 and c-Myc), using a retrovirus. Subsequently, this method was applied to various human cells, using different combinations of defined factors. However, the transcription factor-induced acquisition of replication competence and pluripotency raises the question as to how exogenous factors induce changes in the inner and outer cellular states.
  
  
  RESULTS
  We analyzed both the RNA profile, to reveal changes in gene expression, and the glycan profile, to identify changes in glycan structures, between 51 cell samples of four parental somatic cell (SC) lines from amniotic mesodermal, placental artery endothelial, and uterine endometrium sources, fetal lung fibroblast (MRC-5) cells, and nine hiPSC lines that were originally established. The analysis of this information by standard statistical techniques combined with a network approach, named network screening, detected significant expression differences between the iPSCs and the SCs. Subsequent network analysis of the gene expression and glycan signatures revealed that the glycan transfer network is associated with known epitopes for differentiation, e.g., the SSEA epitope family in the glycan biosynthesis pathway, based on the characteristic changes in the cellular surface states of the hiPSCs.
  
  
  CONCLUSIONS
  The present study is the first to reveal the relationships between gene expression patterns and cell surface changes in hiPSCs, and reinforces the importance of the cell surface to identify established iPSCs from SCs. In addition, given the variability of iPSCs, which is related to the characteristics of the parental SCs, a glycosyltransferase expression assay might be established to define hiPSCs more precisely and thus facilitate their standardization, which are important steps towards the eventual therapeutic applications of hiPSCs.
authors.affiliation: Computational Biology Research Center, National Institute of Advanced Industrial Science Technology, 2-4-7 Aomi, Koto-ku, Tokyo, Japan.
authors.forename: Shigeru
authors.initials: S
authors.lastname: Saito
authors.forename: Yasuko
authors.initials: Y
authors.lastname: Onuma
authors.forename: Yuzuru
authors.initials: Y
authors.lastname: Ito
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Tateno
authors.forename: Masashi
authors.initials: M
authors.lastname: Toyoda
authors.forename: Akutsu
authors.initials: A
authors.lastname: Hidenori
authors.forename: Koichiro
authors.initials: K
authors.lastname: Nishino
authors.forename: Emi
authors.initials: E
authors.lastname: Chikazawa
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Fukawatase
authors.forename: Yoshitaka
authors.initials: Y
authors.lastname: Miyagawa
authors.forename: Hajime
authors.initials: H
authors.lastname: Okita
authors.forename: Nobutaka
authors.initials: N
authors.lastname: Kiyokawa
authors.forename: Yohichi
authors.initials: Y
authors.lastname: Shimma
authors.forename: Akihiro
authors.initials: A
authors.lastname: Umezawa
authors.forename: Jun
authors.initials: J
authors.lastname: Hirabayashi
authors.forename: Katsuhisa
authors.initials: K
authors.lastname: Horimoto
authors.forename: Makoto
authors.initials: M
authors.lastname: Asashima
mesh_terms: D002454:Cell Differentiation; D045744:Cell Line, Tumor; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D016695:Glycosyltransferases / Q000378:metabolism; D006801:Humans; D000090062:Kruppel-Like Factor 4; D039904:Pluripotent Stem Cells / Q000166:cytology* / Q000201:enzymology / Q000378:metabolism*; D011134:Polysaccharides / Q000096:biosynthesis / Q000737:chemistry / Q000378:metabolism
chemical_list: C000715467:KLF4 protein, human; D000090062:Kruppel-Like Factor 4; D011134:Polysaccharides; D016695:Glycosyltransferases