Possible linkages between the inner and outer cellular states of human induced pluripotent stem cells

BMC Systems Biology

Volumn 5, Issue SUPPL. 1, 2011, Pages

  Saito, Shigeru ^a,b   Onuma, Yasuko ^a   Ito, Yuzuru ^a   Tateno, Hiroaki ^a   Toyoda, Masashi ^c   Hidenori, Akutsu ^c   Nishino, Koichiro ^c   Chikazawa, Emi ^c   Fukawatase, Yoshihiro ^c   Miyagawa, Yoshitaka ^c   Okita, Hajime ^c   Kiyokawa, Nobutaka ^c   Shimma, Yohichi ^a   Umezawa, Akihiro ^c   Hirabayashi, Jun ^a   Horimoto, Katsuhisa ^a,d   Asashima, Makoto ^a,e  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b INFOCOM Corporation   (Japan)

^c NATIONAL RESEARCH INSTITUTE FOR CHILD HEALTH AND DEVELOPMENT   (Japan)

^d SHANGHAI UNIVERSITY   (China)

^e UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

IPS;

GLYCOSYLTRANSFERASE; POLYSACCHARIDE;

ARTICLE; BIOSYNTHESIS; CELL DIFFERENTIATION; CHEMISTRY; CYTOLOGY; ENZYMOLOGY; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; HUMAN; METABOLISM; PLURIPOTENT STEM CELL; TUMOR CELL LINE;

CELL DIFFERENTIATION; CELL LINE, TUMOR; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; GLYCOSYLTRANSFERASES; HUMANS; PLURIPOTENT STEM CELLS; POLYSACCHARIDES;

EID: 79959199810     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-S1-S17     Document Type: Article

References (45)

1. Takahashi K, et al. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 2007, 131:861-872. 10.1016/j.cell.2007.11.019, 18035408.
2. Muramatsu T, et al. Carbohydrate antigens expressed on stem cells and early embryonic cells. Glycocon J 2004, 21:41-45.
3. Schopperle WM, et al. The Tra-1-60 and Tra-1-81 human pluripotent stem cell markers are expressed on podocaluxin in embryonal carcinoma. Stem Cells 2006, 25:723-730. 10.1634/stemcells.2005-0597, 17124010.
4. Natunen S, et al. The binding specificity of the marker antibodies Tra-1-60 and Tra-1-81 reveals a novel pluripotency associated type 1 lactosamine epitope. Glycobiology 2010,
5. Satomaa T, et al. The N-glycome of human embryonic stem cells. BMC Cell Biol 2009, 2:10.
6. Toyoda M, et al. Lectin microarray analysis of pluripotent and multipotent stem cells. Genes to Cells 2010, 16:1-11. 10.1111/j.1365-2443.2010.01459.x, 21155951.
7. Chen T, et al. E-cadherin-Mediated Cell-Cell Contact is Critical for Induced Pluripotent Stem Cell Generation. Stem Cells 2010, 28:1315-25. 10.1002/stem.456, 20521328.
8. Tchieu J, et al. Female human iPSCs retain an inactive X chromosome. Cell Stem Cell 2010, 7:329-42. 10.1016/j.stem.2010.06.024, 20727844.
9. Chin MH, et al. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell 2009, 5:111-123. 10.1016/j.stem.2009.06.008, 19570518.
10. Guenther MG, et al. Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells. Cell Stem Cell 2010, 7:249-257. 10.1016/j.stem.2010.06.015, 20682450.
11. Newman AM, et al. Lab-specific gene expression signatures in pluripotent stem cells. Cell Stem Cell 2010, 7:258-262. 10.1016/j.stem.2010.06.016, 20682451.
12. Chin MH, et al. Molecular analyses of human induced pluripotent stem cells and embryonic stem cells. Cell Stem Cell 2010, 7:263-9. 10.1016/j.stem.2010.06.019, 20682452.
13. Lowry WE, et al. Generation of human induced pluripotent stem cells from dermal fibroblasts. Proc Natl Acad Sci USA 2008, 105:2883-2888. 10.1073/pnas.0711983105, 2268554, 18287077.
14. Maherali N, et al. A high-efficiency system for the generation and study of human induced pluripotent stem cells. Cell Stem Cell 2008, 3:340-345. 10.1016/j.stem.2008.08.003, 18786420.
15. Yu J, et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 2009, 324:797-801. 10.1126/science.1172482, 2758053, 19325077.
16. Boyer LA, et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 2005, 122:947-56. 10.1016/j.cell.2005.08.020, 3006442, 16153702.
17. Loh YH, et al. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet 2006, 38:431-40. 10.1038/ng1760, 16518401.
18. Chen X, et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008, 133:1106-17. 10.1016/j.cell.2008.04.043, 18555785.
19. Kim J, et al. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 2008, 132:1049-61. 10.1016/j.cell.2008.02.039, 18358816.
20. Sridharan R, et al. Role of the murine reprogramming factors in the induction of pluripotency. Cell 2009, 136:364-77. 10.1016/j.cell.2009.01.001, 19167336.
21. Saito S, Aburatani S, Horimoto K. Network evaluation from the consistency of the graph structure with the measured data. BMC Sys Biol 2008, 2:84.
22. Makino H, et al. Mesenchymal to embryonic incomplete transition of human cells by chimeric OCT4/3 (POU5F1) with physiological co-activator EWS. Exp Cell Res 2009, 288:2727-2740.
23. Nagata S, et al. Efficient reprogramming of human and mouse primary extra-embryonic cells to pluripotent stem cells. Genes Cells 2009, 14:1395-1404. 10.1111/j.1365-2443.2009.01356.x, 19912344.
24. Subramanian A, et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005, 102:15545-15550. 10.1073/pnas.0506580102, 1239896, 16199517.
25. Lin T, et al. A chemical platform for improved induction of human iPSCs. Nat Methods 2009, 6:805-808. 10.1038/nmeth.1393, 19838168.
26. Sumi T, Tsuneyoshi N, Nakatsuji N, Suemori H. Defining early lineage specification of human embryonic stem cells by the orchestrated balance of canonical Wnt/beta-catenin, Activin/Nodal and BMP signaling. Development 2008, 135:2969-2979. 10.1242/dev.021121, 18667462.
27. Eiselleova L, et al. A complex role for FGF-2 in self-renewal, survival, and adhesion of human embryonic stem cells. Stem Cells 2009, 27:1847-1857. 10.1002/stem.128, 2798073, 19544431.
28. Discher DE, Mooney DJ, Zandstra PW. Growth Factors, matrices, and forces combine and control stem cells. Science 2009, 26:1673-1677.
29. Yamanaka S. Elite and stochastic models for induced pluripotent stem cell generation. Nature 2009, 460:49-52. 10.1038/nature08180, 19571877.
30. Sasaki N, et al. Heparan sulfate regulates self-renewal and pluripotency of embryonic stem cells. J Biol Chem 2008, 283:3594-606. 10.1074/jbc.M705621200, 18024963.
31. Kuno A, et al. Evanescent-field fluorescence-assisted lectin microarray: a new strategy for glycan profiling. Nat. Methods 2005, 2:851-856. 10.1038/nmeth803, 16278656.
32. Gabius H-J. Glycans: bioactive signals decoded by lectins. Biochem Soc Trans 2008, 36:1491-1496. 10.1042/BST0361491, 19021582.
33. Hashimoto K, et al. Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans. Carbohydr Res 2009, 12:881-887.
34. Shevinsky L, Knowles BB, Damjanov I, Solter D. Monoclonal antibody to murine embryos defines a stage-specific embryonic antigen expressed on mouse embryos and human teratocarcinoma cells. Cell 1982, 30:697-705. 10.1016/0092-8674(82)90274-4, 6183004.
35. Kannagi R, et al. Stage-specific embryonic antigens (SSEA-3 and -4) are epitopes of a unique globo-series ganglioside isolated from human teratocarcinoma cells. EMBO J 1983, 2:2355-2361. 555457, 6141938.
36. Gooi HC, et al. Stage-specific embryonic antigen involves a1→3 fucosylated type 2 blood group chains. Nature 1981, 292:156-158. 10.1038/292156a0, 6165896.
37. Bert JE, et al. The HB-6, CDw75, and CD76 differentiation antigens are unique cell-surface carbohydrate determinants generated by the ß-galactoside α2,6-sialyltransferase. J Cell Biol 1992, 116:423-435. 10.1083/jcb.116.2.423, 2289289, 1730763.
38. Chin MH, et al. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell 2009, 5:111-123. 10.1016/j.stem.2009.06.008, 19570518.
39. Marchetto MC, et al. Transcriptional signature and memory retention of human-induced pluripotent stem cells. PLoS One 2009, 4(9):e7076. 10.1371/journal.pone.0007076, 2741600, 19763270.
40. Chin MH, Pellegrini M, Plath K, Lowry WE. Molecular Analyses of Human Induced Pluripo-tent Stem Cells and Embryonic Stem Cells. Cell Stem Cell 2010, 7:263-269. 10.1016/j.stem.2010.06.019, 20682452.
41. Newman AM, Cooper JB. Lab-Specific Gene Expression Signatures in Pluripotent Stem Cells. Cell Stem Cell 2010, 7:258-262. 10.1016/j.stem.2010.06.016, 20682451.
42. Guenther MG, et al. Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells. Cell Stem Cell 2010, 7:249-257. 10.1016/j.stem.2010.06.015, 20682450.
43. Ghosh Z, et al. Persistent Donor Cell Gene Expression among Human Induced Pluripotent Stem Cells Contributes to Differences with Human Embryonic Stem Cells. PLoS One 2010, 5(2):e8975. 10.1371/journal.pone.0008975, 2813859, 20126639.
44. MAQC Consortium The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006, 24:1151-1161. 10.1038/nbt1239, 16964229, MAQC Consortium.
45. Boyle EI, et al. GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 2004, 20:3710-3715. 10.1093/bioinformatics/bth456, 3037731, 15297299.