Current Progress and Potential Practical Application for Human Pluripotent Stem Cells

International Review of Cell and Molecular Biology

Volumn 292, Issue , 2011, Pages 153-196

  Philonenko, Elena S ^a   Shutova, Maria V ^b   Chestkov, Ilya V ^a,b   Lagarkova, Maria A ^b   Kiselev, Sergey L ^a,b  

^a KURCHATOV INSTITUTE   (Russian Federation)

^b VAVILOV INSTITUTE OF GENERAL GENETICS   (Russian Federation)

Author keywords

Cell therapy; Embryonic stem cells; Epigenetics; Genetic stability; Induced pluripotent stem cells; Reprogramming

Indexed keywords

ARTICLE; BIOMEDICINE; BLASTOCYST; CELL DIFFERENTIATION; CELL TYPE; EMBRYONIC STEM CELL; FERTILIZATION IN VITRO; HUMAN; NONHUMAN; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; SOMATIC CELL; STEM CELL RESEARCH; STEM CELL TRANSPLANTATION; TECHNOLOGY;

EID: 80855156617     PISSN: 19376448     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-386033-0.00004-9     Document Type: Chapter

References (182)

1. Aasen T., Raya A., Barrero M.J., Garreta E., Consiglio A., Gonzalez F., et al. Efficient and rapid generation of induced pluripotent stem cells from human keratinocytes. Nat. Biotechnol. 2008, 26(11):1276-1284.
2. Adewumi O., Aflatoonian B., Ahrlund-Richter L., Amit M., Andrews P.W., Beighton G., et al. Characterization of human embryonic stem cell lines by the International Stem Cell Initiative. Nat. Biotechnol. 2007, 25(7):803-816.
3. Agarwal S., Loh Y.H., McLoughlin E.M., Huang J., Park I.H., Miller J.D., et al. Telomere elongation in induced pluripotent stem cells from dyskeratosis congenita patients. Nature 2010, 464(7286):292-296.
4. Allegrucci C., Young L.E. Differences between human embryonic stem cell lines. Hum. Reprod. Update 2006, 13(2):103-120.
5. Anokye-Danso F., Trivedi C.M., Juhr D., Gupta M., Cui Z., Tian Y., et al. Highly efficient miRNA-mediated reprogramming of mouse and human somatic cells to pluripotency. Cell Stem Cell 2011, 8:376-388.
6. Aoi T., Yae K., Nakagawa M., Ichisaka T., Okita K., Takahashi K., et al. Generation of pluripotent stem cells from adult mouse liver and stomach cells. Science 2008, 321(5889):699-702.
7. Baker D.E., Harrison N.J., Maltby E., Smith K., Moore H.D., Shaw P.J., et al. Adaptation to culture of human embryonic stem cells and oncogenesis in vivo. Nat. Biotechnol. 2007, 25:207-215.
8. Ben-Hur T., Idelson M., Khaner H., Pera M., Reinhartz E., Itzik A., et al. Transplantation of human embryonic stem cell-derived neural progenitors improves behavioral deficit in Parkinsonian rats. Stem Cells 2004, 22:1246-1255.
9. Bernstein B.E., Mikkelsen T.S., Xie X., Kamal M., Huebert D.J., Cuff J., et al. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 2006, 125(2):315-326.
10. Bhutani N., Brady J.J., Damian M., Sacco A., Corbel S.Y., Blau H.M. Reprogramming towards pluripotency requires AID-dependent DNA demethylation. Nature 2010, 463(7284):1042-1047.
11. Boland M.J., Hazen J.L., Nazor K.L., Rodriguez A.R., Gifford W., Martin G., et al. Adult mice generated from induced pluripotent stem cells. Nature 2009, 461(7260):91-94.
12. Boyer L.A., Lee T.I., Cole M.F., Johnstone S.E., Levine S.S., Zucker J.P., et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 2005, 122(6):947-956.
13. Boyer L.A., Plath K., Zeitlinger J., Brambrink T., Medeiros L.A., Lee T.I., et al. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 2006, 441(7091):349-353.
14. Brambrink T., Foreman R., Welstead G.G., Lengner C.J., Wernig M., Suh H., et al. Sequential expression of pluripotency markers during direct reprogramming of mouse somatic cells. Cell Stem Cell 2008, 2(2):151-159.
15. Bresnahan L., Fessler R.G., Natarajan R.N. Evaluation of change in muscle activity as a result of posterior lumbar spine surgery using a dynamic modeling system. Spine (Phila Pa 1976) 2010, 35(16):E761-E767.
16. Bruck T., Benvenisty N. Meta-analysis of the heterogeneity of X chromosome inactivation in human pluripotent stem cells. Stem Cell Res. 2011, 6(2):187-193.
17. Cai J., Yang M., Poremsky E., Kidd S., Schneider J.S., Iacovitti L. Dopaminergic neurons derived from human induced pluripotent stem cells survive and integrate into 6-OHDA-lesioned rats. Stem Cells Dev. 2010, 19(7):1017-1023.
18. Carey B.W., Markoulaki S., Beard C., Hanna J., Jaenisch R. Single-gene transgenic mouse strains for reprogramming adult somatic cells. Nat. Methods 2010, 7(1):56-59.
19. Carvajal-Vergara X., Sevilla A., D'Souza S.L., Ang Y.S., Schaniel C., Lee D.F., et al. Patient-specific induced pluripotent stem-cell-derived models of LEOPARD syndrome. Nature 2010, 465(7299):808-812.
20. Cedar H., Bergman Y. Linking DNA methylation and histone modification: patterns and paradigms. Nat. Rev. Genet. 2009, 10(5):295-304.
21. Chambers I., Colby D., Robertson M., Nichols J., Lee S., Tweedie S., et al. Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell 2003, 113(5):643-655.
22. Chan E.M., Ratanasirintrawoot S., Park I., Manos P.D., Loh Y., Huo H., et al. Live cell imaging distinguishes bona fide human iPS cells from partially reprogrammed cells. Nat. Biotechnol. 2009, 27(11):1033-1037.
23. Chang K.H., Nelson A.M., Cao H., Wang L., Nakamoto B., Ware C.B., et al. Definitive-like erythroid cells derived from human embryonic stem cells coexpress high levels of embryonic and fetal globins with little or no adult globin. Blood 2006, 108(5):1515-1523.
24. Chang C.W., Lai Y.S., Pawlik K.M., Liu K., Sun C.W., Li C., et al. Polycistronic lentiviral vector for hit and run reprogramming of adult skin fibroblasts to induced pluripotent stem cells. Stem Cells 2009, 27(5):1042-1049.
25. Chin M.H., Mason M.J., Xie W., Volinia S., Singer M., Peterson C., et al. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell 2009, 5(1):111-123.
26. Chin M.H., Pellegrini M., Plath K., Lowry W.E. Molecular analyses of human induced pluripotent stem cells and embryonic stem cells. Cell Stem Cell 2010, 7(2):263-269.
27. Choi K., Kennedy M., Kazarov A., Papadimitriou J.C., Keller G. A common precursor for hematopoietic and endothelial cells. Development 1998, 125(4):725-732.
28. Choi K.D., Yu J., Smuga-Otto K., Salvagiotto G., Rehrauer W., Vodyanik M., et al. Hematopoietic and endothelial differentiation of human induced pluripotent stem cells. Stem Cells 2009, 27(3):559-567.
29. Chou B.K., Mali P., Huang X., Ye Z., Dowey S.N., Resar L.M., et al. Efficient human iPS cell derivation by a non-integrating plasmid from blood cells with unique epigenetic and gene expression signatures. Cell Res. 2011, 21(3):518-529.
30. Chow J., Heard E. X inactivation and the complexities of silencing a sex chromosome. Curr. Opin. Cell Biol. 2009, 21(3):359-366.
31. Chung Y.S., Zhang W.J., Arentson E., Kingsley P.D., Palis J., Choi K. Lineage analysis of the hemangioblast as defined by FLK1 and SCL expression. Development 2002, 129:5511-5520.
32. Chung T.L., Turner J.P., Thaker N.Y., Kolle G., Cooper-White J.J., Grimmond S.M., et al. Ascorbate promotes epigenetic activation of CD30 in human embryonic stem cells. Stem Cells 2010, 28(10):1782-1793.
33. Cortés F., Debacker C., Péault B., Labastie M.C. Differential expression of KDR/VEGFR-2 and CD34 during mesoderm development of the early human embryo. Mech. Dev. 1999, 83(1-2):161-164.
34. Cowan C.A., Klimanskaya I., McMahon J., Atienza J., Witmyer J., Zucker J.P., et al. Derivation of embryonic stem-cell lines from human blastocysts. N. Engl. J. Med. 2004, 350:1353-1356.
35. De Felici M., Farini D., Dolci S. In or out stemness: comparing growth factor signalling in mouse embryonic stem cells and primordial germ cells. Curr. Stem Cell Res. Ther. 2009, 4(2):87-97.
36. de la Serna I.L., Ohkawa Y., Imbalzano A.N. Chromatin remodelling in mammalian differentiation: lessons from ATP-dependent remodellers. Nat. Rev. Genet. 2006, 7(6):461-473.
37. Deb K.D., Sarda K. Human embryonic stem cells: preclinical perspectives. J. Transl. Med. 2008, 6:7.
38. Deb-Rinker P., Ly D., Jezierski A., Sikorska M., Walker P.R. Sequential DNA methylation of the Nanog and Oct-4 upstream regions in human NT2 cells during neuronal differentiation. J. Biol. Chem. 2005, 280(8):6257-6260.
39. Duinsbergen D., Eriksson M., 't Hoen P.A., Frisén J., Mikkers H. Induced pluripotency with endogenous and inducible genes. Exp. Cell Res. 2008, 314(17):3255-3263.
40. Dvorák P., Hampl A., Jirmanová L., Pacholíková J., Kusakabe M. Embryoglycan ectodomains regulate biological activity of FGF-2 to embryonic stem cells. J. Cell Sci. 1998, 111:2945-2952.
41. Efroni S., Duttagupta R., Cheng J., Dehghani H., Hoeppner D.J., Dash C., et al. Global transcription in pluripotent embryonic stem cells. Cell Stem Cell 2008, 2(5):437-447.
42. Eiselleova L., Matulka K., Kriz V., Kunova M., Schmidtova Z., Neradil J., et al. A complex role for FGF-2 in self-renewal, survival, and adhesion of human embryonic stem cells. Stem Cells 2009, 27(8):1847-1857.
43. Eminli S., Foudi A., Stadtfeld M., Maherali N., Ahfeldt T., Mostoslavsky G., et al. Differentiation stage determines potential of hematopoietic cells for reprogramming into induced pluripotent stem cells. Nat. Genet. 2009, 41(9):968-976.
44. Eremeev A.V., Svetlakov A.V., Polstianoy A.M., Bogomazova A.N., Philonenko E.S., Sheina Y.I., et al. Derivation of a novel human embryonic stem cell line under serum-free and feeder-free conditions. Dokl. Biol. Sci. 2009, 426:293-295.
45. Esteban M.A., Wang T., Qin B., Yang J., Qin D., Cai J., et al. Vitamin C enhances the generation of mouse and human induced pluripotent stem cells. Cell Stem Cell 2010, 6(1):71-79.
46. Evans P.M., Zhang W., Chen X., Yang J., Bhakat K.K., Liu C. Kruppel-like factor 4 is acetylated by p300 and regulates gene transcription via modulation of histone acetylation. J. Biol. Chem. 2007, 282(47):33994-34002.
47. Feng B., Jiang J., Kraus P., Ng J.H., Heng J.C., Chan Y.S., et al. Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb. Nat. Cell Biol. 2009, 11(2):197-203.
48. Freund C., Davis R.P., Gkatzis K., Ward-van Oostwaard D., Mummery C.L. The first reported generation of human induced pluripotent stem cells (iPS cells) and iPS cell-derived cardiomyocytes in the Netherlands. Neth. Heart J. 2010, 18(1):51-54.
49. Gaspar-Maia A., Alajem A., Polesso F., Sridharan R., Mason M.J., Heidersbach A., et al. Chd1 regulates open chromatin and pluripotency of embryonic stem cells. Nature 2009, 460(7257):863-868.
50. Gore A., Li Z., Fung H.L., Young J.E., Agarwal S., Antosiewicz-Bourget J., et al. Somatic coding mutations in human induced pluripotent stem cells. Nature 2011, 471(7336):63-67.
51. Graichen R., Xu X., Braam S.R., Balakrishnan T., Norfiza S., Sieh S., et al. Enhanced cardiomyogenesis of human embryonic stem cells by a small molecular inhibitor of p38 MAPK. Differentiation 2008, 76(4):357-370.
52. Greber B., Lehrach H., Adjaye J. Silencing of core transcription factors in human EC cells highlights the importance of autocrine FGF signaling for self-renewal. BMC Dev. Biol. 2007, 7:46.
53. Grigoriadis A.E., Kennedy M., Bozec A., Brunton F., Stenbeck G., Park I.H., et al. Directed differentiation of hematopoietic precursors and functional osteoclasts from human ES and iPS cells. Blood 2011, 115(14):2769-2776.
54. Guenther G., Arauz A. Cerebral venous thrombosis: a diagnostic and treatment update. Neurologia 2011, 26(8):488-498.
55. Hajkova P., Jeffries S.J., Lee C., Miller N., Jackson S.P., Surani M.A. Genome-wide reprogramming in the mouse germ line entails the base excision repair pathway. Science 2010, 329(5987):78-82.
56. Hanna J., Markoulaki S., Schorderet P., Carey B.W., Beard C., Wernig M., et al. Direct reprogramming of terminally differentiated mature B lymphocytes to pluripotency. Cell 2008, 133(2):250-264.
57. Hanna J., Saha K., Pando B., van Zon J., Lengner C.J., Creyghton M.P., et al. Direct cell reprogramming is a stochastic process amenable to acceleration. Nature 2009, 462(7273):595-601.
58. Hanna J., Cheng A.W., Saha K., Kim J., Lengner C.J., Soldner F., et al. Human embryonic stem cells with biological and epigenetic characteristics similar to those of mouse ESCs. Proc. Natl. Acad. Sci. USA 2010, 107(20):9222-9227.
59. Harrison N.J., Barnes J., Jones M., Baker D., Gokhale P.J., Andrews P.W. CD30 expression reveals that culture adaptation of human embryonic stem cells can occur through differing routes. Stem Cells 2009, 27(5):1057-1065.
60. Hawkins R.D., Hon G.C., Lee L.K., Ngo Q., Lister R., Pelizzola M., et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 2010, 6(5):479-491.
61. Heintzman N.D., Hon G.C., Hawkins R.D., Kheradpour P., Stark A., Harp L.F., et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 2009, 459(7243):108-112.
62. Heng J.C., Feng B., Han J., Jiang J., Kraus P., Ng J.H., et al. The nuclear receptor Nr5a2 can replace Oct4 in the reprogramming of murine somatic cells to pluripotent cells. Cell Stem Cell 2010, 6(2):167-174.
63. Heng J.C., Orlov Y.L., Ng H.H. Transcription factors for the modulation of pluripotency and reprogramming. Cold Spring Harb. Symp. Quant. Biol. 2010, 75:237-244.
64. Herszfeld D., Wolvetang E., Langton-Bunker E., Chung T.L., Filipczyk A.A., Houssami S., et al. Cd30 is a survival factor and a biomarker for transformed human pluripotent stem cells. Nat. Biotechnol. 2006, 24:351-357.
65. Ho L., Jothi R., Ronan J.L., Cui K., Zhao K., Crabtree G.R. An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proc. Natl. Acad. Sci. USA 2009, 106(13):5187-5191.
66. Holubcová Z., Matula P., Sedláčková M., Vinarský V., Doležalová D., Bárta T., et al. Human embryonic stem cells suffer from centrosomal amplification. Stem Cells 2011, 29(1):46-56.
67. Hong H., Takahashi K., Ichisaka T., Aoi T., Kanagawa O., Nakagawa M., et al. Suppression of induced pluripotent stem cell generation by the p53-p21 pathway. Nature 2009, 460(7259):1132-1135.
68. Howden S.E., Gore A., Li Z., Fung H.L., Nisler B.S., Nie J., et al. Genetic correction and analysis of induced pluripotent stem cells from a patient with gyrate atrophy. Proc. Natl. Acad. Sci. USA 2011, 108(16):6537-6542.
69. Humphrey R.K., Beattie G.M., Lopez A.D., Bucay N., King C.C., Firpo M.T., et al. Maintenance of pluripotency in human embryonic stem cells is STAT3 independent. Stem Cells 2004, 22(4):522-530.
70. Hussein S.M., Batada N.N., Vuoristo S., Ching R.W., Autio R., Närvä E., et al. Copy number variation and selection during reprogramming to pluripotency. Nature 2011, 471(7336):58-62.
71. Ichida J.K., Blanchard J., Lam K., Son E.Y., Chung J.E., Egli D., et al. A small-molecule inhibitor of tgf-Beta signaling replaces sox2 in reprogramming by inducing nanog. Cell Stem Cell 2009, 5(5):491-503.
72. Imreh M.P., Gertow K., Cedervall J., Unger C., Holmberg K., Szöke K., et al. In vitro culture conditions favoring selection of chromosomal abnormalities in human ES cells. J. Cell. Biochem. 2006, 99(2):508-516.
73. Jiang P., Rushing S.N., Kong C.W., Fu J., Lieu D.K., Chan C.W., et al. Electrophysiological properties of human induced pluripotent stem cells. Am. J. Physiol. Cell Physiol. 2010, 298(3):C486-C495.
74. Judson R.L., Babiarz J.E., Venere M., Blelloch R. Embryonic stem cell-specific microRNAs promote induced pluripotency. Nat. Biotechnol. 2009, 27:459-461.
75. Kattman S.J., Huber T.L., Keller G.M. Multipotent flk-1+ cardiovascular progenitor cells give rise to the cardiomyocyte, endothelial, and vascular smooth muscle lineages. Dev. Cell 2006, 11(5):723-732.
76. Kennedy M., D'Souza S.L., Lynch-Kattman M., Schwantz S., Keller G. Development of the hemangioblast defines the onset of hematopoiesis in human ES cell differentiation cultures. Blood 2007, 109:2679-2687.
77. Kim J., Chu J., Shen X., Wang J., Orkin S.H. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 2008, 132(6):1049-1061.
78. Kim J.B., Zaehres H., Wu G., Gentile L., Ko K., Sebastiano V., et al. Pluripotent stem cells induced from adult neural stem cells by reprogramming with two factors. Nature 2008, 454(7204):646-650.
79. Kim D., Kim C.H., Moon J.I., Chung Y.G., Chang M.Y., Han B.S., et al. Generation of human induced pluripotent stem cells by direct delivery of reprogramming proteins. Cell Stem Cell 2009, 4(6):472-476.
80. Kim K., Doi A., Wen B., Ng K., Zhao R., Cahan P., et al. Epigenetic memory in induced pluripotent stem cells. Nature 2010, 467(7313):285-290.
81. Knoepfler P.S. Why myc? An unexpected ingredient in the stem cell cocktail. Cell Stem Cell 2008, 2(1):18-21.
82. Krizhanovsky V., Lowe S.W. Stem cells: the promises and perils of p53. Nature 2009, 460(7259):1085-1086.
83. Krogan N.J., Kim M., Tong A., Golshani A., Cagney G., Canadien V., et al. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol. Cell. Biol. 2003, 23(12):4207-4218.
84. Kuzmenkin A., Liang H., Xu G., Pfannkuche K., Eichhorn H., Fatima A., et al. Functional characterization of cardiomyocytes derived from murine induced pluripotent stem cells in vitro. FASEB J. 2009, 23(12):4168-4180.
85. Lagarkova M.A., Volchkov P.Y., Lyakisheva A.V., Philonenko E.S., Kiselev S.L. Diverse epigenetic profile of novel human embryonic stem cell lines. Cell Cycle 2006, 5(4):416-420.
86. Lagarkova M.A., Volchkov P.Y., Philonenko E.S., Pfannkuche K., Prokhorovich M.A., Zabotina T., et al. CD 30 is a marker of undifferentiated human embryonic stem cells rather than a biomarker of transformed hESCs. Cell Cycle 2008, 7(22):3610-3612.
87. Lagarkova M.A., Volchkov P.Y., Philonenko E.S., Kiselev S.L. Efficient differentiation of hESCs into endothelial cells in vitro is secured by epigenetic changes. Cell Cycle 2008, 7(18):2929-2935.
88. Lagarkova M.A., Shutova M.V., Bogomazova A.N., Vassina E.M., Glazov E.A., Zhang P., et al. Induction of pluripotency in human endothelial cells resets epigenetic profile on genome scale. Cell Cycle 2010, 9(5):937-946.
89. Laurent L.C., Ulitsky I., Slavin I., Tran H., Schork A., Morey R., et al. Dynamic changes in the copy number of pluripotency and cell proliferation genes in human ESCs and iPSCs during reprogramming and time in culture. Cell Stem Cell 2011, 8(1):106-118.
90. Lebedev I. Mosaic aneuploidy in early fetal losses. Cytogenet. Genome Res. 2011, 133(2-4):169-183.
91. Lee T.I., Jenner R.G., Boyer L.A., Guenther M.G., Levine S.S., Kumar R.M., et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 2006, 125(2):301-313.
92. Lee G., Papapetrou E.P., Kim H., Chambers S.M., Tomishima M.J., Fasano C.A., et al. Modelling pathogenesis and treatment of familial dysautonomia using patient-specific iPSCs. Nature 2009, 461(7262):402-406.
93. Lee J.H., Park I.H., Gao Y., Li J.B., Li Z., Daley G.Q., et al. A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells. PLoS Genet. 2009, 5(11):e1000718.
94. Lengerke C., Grauer M., Niebuhr N.I., Riedt T., Kanz L., Park I.H., et al. Hematopoietic development from human induced pluripotent stem cells. Ann. N. Y. Acad. Sci. 2009, 1176:219-227.
95. Levenberg S., Ferreira L.S., Chen-Konak L., Kraehenbuehl T.P., Langer R. Isolation, differentiation and characterization of vascular cells derived from human embryonic stem cells. Nat. Protoc. 2010, 5(6):1115-1126.
96. Li W., Zhou H., Abujarour R., Zhu S., Young Joo J., Lin T., et al. Generation of human-induced pluripotent stem cells in the absence of exogenous Sox2. Stem Cells 2009, 27(12):2992-3000.
97. Li R., Liang J., Ni S., Zhou T., Qing X., Li H., et al. A mesenchymal-to-epithelial transition initiates and is required for the nuclear reprogramming of mouse fibroblasts. Cell Stem Cell 2010, 7(1):51-63.
98. Lian Q., Zhang Y., Zhang J., Zhang H.K., Wu X., Zhang Y., et al. Functional mesenchymal stem cells derived from human induced pluripotent stem cells attenuate limb ischemia in mice. Circulation 2010, 121(9):1113-1123.
99. Liang J., Wan M., Zhang Y., Gu P., Xin H., Jung S.Y., et al. Nanog and Oct4 associate with unique transcriptional repression complexes in embryonic stem cells. Nat. Cell Biol. 2008, 10(6):731-739.
100. Lin T., Ambasudhan R., Yuan X., Li W., Hilcove S., Abujarour R., et al. A chemical platform for improved induction of human iPSCs. Nat. Methods 2009, 6(11):805-808.
101. Lister R., Pelizzola M., Dowen R.H., Hawkins R.D., Hon G., Tonti-Filippini J., et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 2009, 462(7271):315-322.
102. Lister R., Pelizzola M., Kida Y.S., Hawkins R.D., Nery J.R., Hon G., et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature 2011, 471(7336):68-73.
103. Liu L., Luo G.Z., Yang W., Zhao X., Zheng Q., Lv Z., et al. Activation of the imprinted Dlk1-Dio3 region correlates with pluripotency levels of mouse stem cells. J. Biol. Chem. 2010, 285(25):19483-19490.
104. Loh Y.H., Wu Q., Chew J.L., Vega V.B., Zhang W., Chen X., et al. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat. Genet. 2006, 38(4):431-440.
105. Lu S.J., Feng Q., Caballero S., Chen Y., Moore M.A., Grant M.B., et al. Generation of functional hemangioblasts from human embryonic stem cells. Nat. Methods 2007, 4(6):501-509.
106. Lu S.J., Feng Q., Park J.S., Lanza R. Directed differentiation of red blood cells from human embryonic stem cells. Methods Mol. Biol. 2010, 636:105-121.
107. Ma F., Ebihara Y., Umeda K., Sakai H., Hanada S., Zhang H., et al. Generation of functional erythrocytes from human embryonic stem cell-derived definitive hematopoiesis. Proc. Natl. Acad. Sci. USA 2008, 105(35):13087-13092.
108. Maherali N., Sridharan R., Xie W., Utikal J., Eminli S., Arnold K., et al. Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell 2007, 1(1):55-70.
109. Maitra A., Arking D.E., Shivapurkar N., Ikeda M., Stastny V., Kassauei K., et al. Genomic alterations in cultured human embryonic stem cells. Nat. Genet. 2005, 37(10):1099-1103.
110. Mali P., Chou B.K., Yen J., Ye Z., Zou J., Dowey S., et al. Butyrate greatly enhances derivation of human induced pluripotent stem cells by promoting epigenetic remodeling and the expression of pluripotency-associated genes. Stem Cells 2010, 28(4):713-720.
111. Marchetto M.C., Yeo G.W., Kainohana O., Marsala M., Gage F.H., Muotri A.R. Transcriptional signature and memory retention of human-induced pluripotent stem cells. PLoS One 2009, 4(9):e7076.
112. Marson A., Foreman R., Chevalier B., Bilodeau S., Kahn M., Young R.A., et al. Wnt signaling promotes reprogramming of somatic cells to pluripotency. Cell Stem Cell 2008, 3(2):132-135.
113. Matsui T., Leung D., Miyashita H., Maksakova I.A., Miyachi H., Kimura H., et al. Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET. Nature 2010, 464(7290):927-931.
114. Mattout A., Meshorer E. Chromatin plasticity and genome organization in pluripotent embryonic stem cells. Curr. Opin. Cell Biol. 2010, 22(3):334-341.
115. McDevitt T.C., Laflamme M.A., Murry C.E. Proliferation of cardiomyocytes derived from human embryonic stem cells is mediated via the IGF/PI 3-kinase/Akt signaling pathway. J. Mol. Cell. Cardiol. 2005, 39(6):865-873.
116. Ménard C., Grey C., Méry A., Zeineddine D., Aimond F., Pucéat M. Cardiac specification of embryonic stem cells. J. Cell. Biochem. 2004, 93(4):681-687.
117. Meneghini M.D., Wu M., Madhani H.D. Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell 2003, 112(5):725-736.
118. Meshorer E., Yellajoshula D., George E., Scambler P.J., Brown D.T., Misteli T. Hyperdynamic plasticity of chromatin proteins in pluripotent embryonic stem cells. Dev. Cell 2006, 10(1):105-116.
119. Mikkelsen T.S., Ku M., Jaffe D.B., Issac B., Lieberman E., Giannoukos G., et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448(7153):553-560.
120. Miyabayashi T., Teo J.L., Yamamoto M., McMillan M., Nguyen C., Kahn M. Wnt/beta-catenin/CBP signaling maintains long-term murine embryonic stem cell pluripotency. Proc. Natl. Acad. Sci. USA 2007, 104(13):5668-5673.
121. Miyoshi N., Ishii H., Nagano H., Haraguchi N., Dewi D.L., Kano Y., et al. Reprogramming of mouse and human cells to pluripotency using mature microRNAs. Cell Stem Cell 2011, 8(6):633-638.
122. Moretti A., Bellin M., Welling A., Jung C.B., Lam J.T., Bott-Flügel L., et al. Patient-specific induced pluripotent stem-cell models for long-QT syndrome. N. Engl. J. Med. 2010, 363(15):1397-1409.
123. Mummery C., Ward-van Oostwaard D., Doevendans P., Spijker R., van den Brink S., Hassink R., et al. Differentiation of human embryonic stem cells to cardiomyocytes: role of coculture with visceral endoderm-like cells. Circulation 2003, 107(21):2733-2740.
124. Murry C.E., Keller G. Differentiation of embryonic stem cells to clinically relevant populations: lessons from embryonic development. Cell 2008, 132(4):661-680.
125. Nakagawa M., Koyanagi M., Tanabe K., Takahashi K., Ichisaka T., Aoi T., et al. Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts. Nat. Biotechnol. 2008, 26(1):101-106.
126. Närvä E., Autio R., Rahkonen N., Kong L., Harrison N., Kitsberg D., et al. High-resolution DNA analysis of human embryonic stem cell lines reveals culture-induced copy number changes and loss of heterozygosity. Nat. Biotechnol. 2010, 28(4):371-377.
127. Nichols J., Smith A. Naive and primed pluripotent states. Cell Stem Cell 2009, 4(6):487-492.
128. Nichols J., Zevnik B., Anastassiadis K., Niwa H., Klewe-Nebenius D., Chambers I., et al. Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell 1998, 95(3):379-391.
129. Olivier E.N., Qiu C., Velho M., Hirsch R.E., Bouhassira E.E. Large-scale production of embryonic red blood cells from human embryonic stem cells. Exp. Hematol. 2006, 34(12):1635-1642.
130. Osafune K., Caron L., Borowiak M., Martinez R.J., Fitz-Gerald C.S., Sato Y., et al. Marked differences in differentiation propensity among human embryonic stem cell lines. Nat. Biotechnol. 2008, 26(3):313-315.
131. Osakada F., Jin Z.B., Hirami Y., Ikeda H., Danjyo T., Watanabe K., et al. In vitro differentiation of retinal cells from human pluripotent stem cells by small-molecule induction. J. Cell Sci. 2009, 122:3169-3179.
132. Papapetrou E.P., Sadelain M. Reconstructing blood from induced pluripotent stem cells. F1000 Med Rep. 2010, 2:44.
133. Park I.H., Zhao R., West J.A., Yabuuchi A., Huo H., Ince T.A., et al. Reprogramming of human somatic cells to pluripotency with defined factors. Nature 2008, 451(7175):141-146.
134. Pasi C.E., Dereli-Öz A., Negrini S., Friedli M., Fragola G., Lombardo A., et al. Genomic instability in induced stem cells. Cell Death Differ. 2011, 18(5):745-753.
135. Pereira C.F., Piccolo F.M., Tsubouchi T., Sauer S., Ryan N.K., Bruno L., et al. ESCs require PRC2 to direct the successful reprogramming of differentiated cells toward pluripotency. Cell Stem Cell 2010, 6(6):547-556.
136. Pick M., Azzola L., Mossman A., Stanley E.G., Elefanty A.G. Differentiation of human embryonic stem cells in serum-free medium reveals distinct roles for bone morphogenetic protein 4, vascular endothelial growth factor, stem cell factor, and fibroblast growth factor 2 in hematopoiesis. Stem Cells 2007, 25:2206-2214.
137. Prigione A., Fauler B., Lurz R., Lehrach H., Adjaye J. The senescence-related mitochondrial/oxidative stress pathway is repressed in human induced pluripotent stem cells. Stem Cells 2010, 28(4):721-733.
138. Prowse A.B., McQuade L.R., Bryant K.J., Marcal H., Gray P.P. Identification of potential pluripotency determinants for human embryonic stem cells following proteomic analysis of human and mouse fibroblast conditioned media. J. Proteome Res. 2007, 6(9):3796-3807.
139. Raya A., Rodríguez-Pizà I., Guenechea G., Vassena R., Navarro S., Barrero M.J., et al. Disease-corrected haematopoietic progenitors from Fanconi anaemia induced pluripotent stem cells. Nature 2009, 460(7251):53-59.
140. Rhee Y.H., Ko J.Y., Chang M.Y., Yi S.H., Kim D., Kim C.H., et al. Protein-based human iPS cells efficiently generate functional dopamine neurons and can treat a rat model of Parkinson disease. J. Clin. Invest. 2011, 121(6):2326-2335.
141. Rosler E.S., Fisk G.J., Ares X., Irving J., Miura T., Rao M.S., et al. Long-term culture of human embryonic stem cells in feeder-free conditions. Dev. Dyn. 2004, 229:259-274.
142. Ruiz S., Brennand K., Panopoulos A.D., Herrerías A., Gage F.H., Izpisua-Belmonte J.C. High-efficient generation of induced pluripotent stem cells from human astrocytes. PLoS One 2010, 5(12):e15526.
143. Sato N., Meijer L., Skaltsounis L., Greengard P., Brivanlou A.H. Maintenance of pluripotency in human and mouse embryonic stem cells through activation of Wnt signaling by a pharmacological GSK-3-specific inhibitor. Nat. Med. 2004, 10(1):55-63.
144. Shi Y., Desponts C., Do J.T., Hahm H.S., Schöler H.R., Ding S. Induction of pluripotent stem cells from mouse embryonic fibroblasts by Oct4 and Klf4 with small-molecule compounds. Cell Stem Cell 2008, 3(5):568-574.
145. Silva J., Barrandon O., Nichols J., Kawaguchi J., Theunissen T.W., Smith A. Promotion of reprogramming to ground state pluripotency by signal inhibition. PLoS Biol. 2008, 6(10):e253.
146. Silva S.S., Rowntree R.K., Mekhoubad S., Lee J.T. X-chromosome inactivation and epigenetic fluidity in human embryonic stem cells. Proc. Natl. Acad. Sci. USA 2008, 105(12):4820-4825.
147. Silva J., Nichols J., Theunissen T.W., Guo G., van Oosten A.L., Barrandon O., et al. Nanog is the gateway to the pluripotent ground state. Cell 2009, 138(4):722-737.
148. Simonsson S., Gurdon J. DNA demethylation is necessary for the epigenetic reprogramming of somatic cell nuclei. Nat. Cell Biol. 2004, 6(10):984-990.
149. Singhal N., Graumann J., Wu G., Araúzo-Bravo M.J., Han D.W., Greber B., et al. Chromatin-remodeling components of the BAF complex facilitate reprogramming. Cell 2010, 141(6):943-955.
150. Si-Tayeb K., Noto F.K., Nagaoka M., Li J., Battle M.A., Duris C., et al. Highly efficient generation of human hepatocyte-like cells from induced pluripotent stem cells. Hepatology 2010, 51(1):297-305.
151. Soldner F., Hockemeyer D., Beard C., Gao Q., Bell G.W., Cook E.G., et al. Parkinson's disease patient-derived induced pluripotent stem cells free of viral reprogramming factors. Cell 2009, 136(5):964-977.
152. Sommer C.A., Sommer A.G., Longmire T.A., Christodoulou C., Thomas D.D., Gostissa M., et al. Excision of reprogramming transgenes improves the differentiation potential of iPS cells generated with a single excisable vector. Stem Cells 2010, 28(1):64-74.
153. Sridharan R., Tchieu J., Mason M.J., Yachechko R., Kuoy E., Horvath S., et al. Role of the murine reprogramming factors in the induction of pluripotency. Cell 2009, 136(2):364-377.
154. Stadtfeld M., Brennand K., Hochedlinger K. Reprogramming of pancreatic beta cells into induced pluripotent stem cells. Curr. Biol. 2008, 18(12):890-894.
155. Stadtfeld M., Nagaya M., Utikal J., Weir G., Hochedlinger K. Induced pluripotent stem cells generated without viral integration. Science 2008, 322(5903):945-949.
156. Stadtfeld M., Apostolou E., Akutsu H., Fukuda A., Follett P., Natesan S., et al. Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells. Nature 2010, 465(7295):175-181.
157. Szabo E., Rampalli S., Risueño R.M., Schnerch A., Mitchell R., Fiebig-Comyn A., et al. Direct conversion of human fibroblasts to multilineage blood progenitors. Nature 2010, 468(7323):521-526.
158. Szutorisz H., Dillon N. The epigenetic basis for embryonic stem cell pluripotency. Bioessays 2005, 27(12):1286-1293.
159. Takahashi K., Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 2006, 126(4):663-676.
160. Tchieu J., Kuoy E., Chin M.H., Trinh H., Patterson M., Sherman S.P., et al. Female human iPSCs retain an inactive X chromosome. Cell Stem Cell 2010, 7(3):329-342.
161. Tesar P.J., Chenoweth J.G., Brook F.A., Davies T.J., Evans E.P., Mack D.L., et al. New cell lines from mouse epiblast share defining features with human embryonic stem cells. Nature 2007, 448(7150):196-199.
162. Vallier L., Alexander M., Pedersen R.A. Activin/Nodal and FGF pathways cooperate to maintain pluripotency of human embryonic stem cells. J. Cell Sci. 2005, 118:4495-4509.
163. Vallier L., Touboul T., Brown S., Cho C., Bilican B., Alexander M., et al. Signaling pathways controlling pluripotency and early cell fate decisions of human induced pluripotent stem cells. Stem Cells 2009, 27(11):2655-2666.
164. Wang J., Rao S., Chu J., Shen X., Levasseur D.N., Theunissen T.W., et al. A protein interaction network for pluripotency of embryonic stem cells. Nature 2006, 444(7117):364-368.
165. Wang Z.Z., Au P., Chen T., Shao Y., Daheron L.M., Bai H., et al. Endothelial cells derived from human embryonic stem cells form durable blood vessels in vivo. Nat. Biotechnol. 2007, 25(3):317-318.
166. Warren L., Manos P.D., Ahfeldt T., Loh Y.H., Li H., Lau F., et al. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell 2010, 7(5):618-630.
167. Williams R.R., Azuara V., Perry P., Sauer S., Dvorkina M., Jørgensen H., et al. Neural induction promotes large-scale chromatin reorganisation of the Mash1 locus. J. Cell Sci. 2006, 119:132-140.
168. Woltjen K., Michael I.P., Mohseni P., Desai R., Mileikovsky M., Hämäläinen R., et al. piggyBac transposition reprograms fibroblasts to induced pluripotent stem cells. Nature 2009, 458(7239):766-770.
169. Xu R.H., Sampsell-Barron T.L., Gu F., Root S., Peck R.M., Pan G., et al. NANOG is a direct target of TGFbeta/activin-mediated SMAD signaling in human ESCs. Cell Stem Cell 2008, 3(2):196-206.
170. Yakubov E., Rechavi G., Rozenblatt S., Givol D. Reprogramming of human fibroblasts to pluripotent stem cells using mRNA of four transcription factors. Biochem. Biophys. Res. Commun. 2010, 394(1):189-193.
171. Yamanaka S. Elite and stochastic models for induced pluripotent stem cell generation. Nature 2009, 460(7251):49-52.
172. Ye L., Chang J.C., Lin C., Sun X., Yu J., Kan Y.W. Induced pluripotent stem cells offer new approach to therapy in thalassemia and sickle cell anemia and option in prenatal diagnosis in genetic diseases. Proc. Natl. Acad. Sci. USA 2009, 106(24):9826-9830.
173. Ying Q.L., Wray J., Nichols J., Batlle-Morera L., Doble B., Woodgett J., et al. The ground state of embryonic stem cell self-renewal. Nature 2008, 453(7194):519-523.
174. Yoshida Y., Takahashi K., Okita K., Ichisaka T., Yamanaka S. Hypoxia enhances the generation of induced pluripotent stem cells. Cell Stem Cell 2009, 5(3):237-241.
175. Yu J., Vodyanik M.A., Smuga-Otto K., Antosiewicz-Bourget J., Frane J.L., Tian S., et al. Induced pluripotent stem cell lines derived from human somatic cells. Science 2007, 318(5858):1917-1920.
176. Yu J., Hu K., Smuga-Otto K., Tian S., Stewart R., Slukvin I.I., et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 2009, 324(5928):797-801.
177. Yuan H., Corbi N., Basilico C., Dailey L. Developmental-specific activity of the FGF-4 enhancer requires the synergistic action of Sox2 and Oct-3. Genes Dev. 1995, 9(21):2635-2645.
178. Zambidis E.T., Peault B., Park T.S., Bunz F., Civin C.I. Hematopoietic differentiation of human embryonic stem cells progresses through sequential hematoendothelial, primitive, and definitive stages resembling human yolk sac development. Blood 2005, 106:860-870.
179. Zhang J., Wilson G.F., Soerens A.G., Koonce C.H., Yu J., Palecek S.P., et al. Functional cardiomyocytes derived from human induced pluripotent stem cells. Circ. Res. 2009, 104(4):e30-e41.
180. Zhou W., Freed C.R. Adenoviral gene delivery can reprogram human fibroblasts to induced pluripotent stem cells. Stem Cells 2009, 27(11):2667-2674.
181. Zhou H., Wu S., Joo J.Y., Zhu S., Han D.W., Lin T., et al. Generation of induced pluripotent stem cells using recombinant proteins. Cell Stem Cell 2009, 4(5):381-384.
182. Zweigerdt R., Olmer R., Singh H., Haverich A., Martin U. Scalable expansion of human pluripotent stem cells in suspension culture. Nat. Protoc. 2011, 6(5):689-700.