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Current Stem Cell Research & Therapy

Editor-in-Chief

ISSN (Print): 1574-888X
ISSN (Online): 2212-3946

Review Article

Transcriptional Factors Mediated Reprogramming to Pluripotency

Author(s): Nazira Fatima, Muhammad Saif Ur Rahman, Muhammad Qasim, Usman Ali Ashfaq, Uzair Ahmed and Muhammad Shareef Masoud*

Volume 19, Issue 3, 2024

Published on: 11 May, 2023

Page: [367 - 388] Pages: 22

DOI: 10.2174/1574888X18666230417084518

Price: $65

Open Access Journals Promotions 2
Abstract

A unique kind of pluripotent cell, i.e., Induced pluripotent stem cells (iPSCs), now being targeted for iPSC synthesis, are produced by reprogramming animal and human differentiated cells (with no change in genetic makeup for the sake of high efficacy iPSCs formation). The conversion of specific cells to iPSCs has revolutionized stem cell research by making pluripotent cells more controllable for regenerative therapy. For the past 15 years, somatic cell reprogramming to pluripotency with force expression of specified factors has been a fascinating field of biomedical study. For that technological primary viewpoint reprogramming method, a cocktail of four transcription factors (TF) has required: Kruppel-like factor 4 (KLF4), four-octamer binding protein 34 (OCT3/4), MYC and SOX2 (together referred to as OSKM) and host cells. IPS cells have great potential for future tissue replacement treatments because of their ability to self-renew and specialize in all adult cell types, although factor-mediated reprogramming mechanisms are still poorly understood medically. This technique has dramatically improved performance and efficiency, making it more useful in drug discovery, disease remodeling, and regenerative medicine. Moreover, in these four TF cocktails, more than 30 reprogramming combinations were proposed, but for reprogramming effectiveness, only a few numbers have been demonstrated for the somatic cells of humans and mice. Stoichiometry, a combination of reprogramming agents and chromatin remodeling compounds, impacts kinetics, quality, and efficiency in stem cell research.

Keywords: Stem cells, regenerative medicine, induced pluripotent stem cells (iPSCs), reprogramming, transcription factor, kruppel-like factor 4 (KLF4).

Graphical Abstract
[1]
Briggs R, King TJ. Transplantation of living nuclei from blastula cells into enucleated frogs’ eggs. Proc Natl Acad Sci 1952; 38(5): 455-63.
[http://dx.doi.org/10.1073/pnas.38.5.455] [PMID: 16589125]
[2]
Gurdon JB. The developmental capacity of nuclei taken from intestinal epithelium cells of feeding tadpoles. Development 1962; 10(4): 622-40.
[http://dx.doi.org/10.1242/dev.10.4.622] [PMID: 13951335]
[3]
Hochedlinger K, Jaenisch R. Nuclear reprogramming and pluripotency. Nature 2006; 441(7097): 1061-7.
[http://dx.doi.org/10.1038/nature04955] [PMID: 16810240]
[4]
Warren L, C. Lin. mRNA-based genetic reprogramming. Molecular Therapy 2019; 27: pp. (4)729-34.
[http://dx.doi.org/10.1016/j.ymthe.2018.12.009]
[5]
Feng B, Ng JH, Heng JCD, Ng HH. Molecules that promote or enhance reprogramming of somatic cells to induced pluripotent stem cells. Cell Stem Cell 2009; 4(4): 301-12.
[http://dx.doi.org/10.1016/j.stem.2009.03.005] [PMID: 19341620]
[6]
Kim JS, Choi HW, Choi S, Do JT. Reprogrammed pluripotent stem cells from somatic cells. Int J Stem Cells 2011; 4(1): 1-8.
[http://dx.doi.org/10.15283/ijsc.2011.4.1.1] [PMID: 24298328]
[7]
Edwards JL, Schrick FN, McCracken MD, et al. Cloning adult farm animals: A review of the possibilities and problems associated with somatic cell nuclear transfer. Am J Reprod Immunol 2003; 50(2): 113-23.
[http://dx.doi.org/10.1034/j.1600-0897.2003.00064.x] [PMID: 12846674]
[8]
Vierbuchen T, Wernig M. Direct lineage conversions: Unnatural but useful? Nat Biotechnol 2011; 29(10): 892-907.
[http://dx.doi.org/10.1038/nbt.1946] [PMID: 21997635]
[9]
Blau HM, Chiu CP, Webster C. Cytoplasmic activation of human nuclear genes in stable heterocaryons. Cell 1983; 32(4): 1171-80.
[http://dx.doi.org/10.1016/0092-8674(83)90300-8] [PMID: 6839359]
[10]
Pfannkuche K, Hannes T, Khalil M, et al. Induced pluripotent stem cells: A new approach for physiological research. Cell Physiol Biochem 2010; 26(2): 105-24.
[http://dx.doi.org/10.1159/000320514] [PMID: 20798495]
[11]
Takahashi K, Yamanaka S. A decade of transcription factor-mediated reprogramming to pluripotency. Nat Rev Mol Cell Biol 2016; 17(3): 183-93.
[http://dx.doi.org/10.1038/nrm.2016.8] [PMID: 26883003]
[12]
Zeineddine D, Hammoud AA, Mortada M, Boeuf H. The Oct4 protein: More than a magic stemness marker. Am J Stem Cells 2014; 3(2): 74-82.
[PMID: 25232507]
[13]
Buganim Y, Markoulaki S, van Wietmarschen N, et al. The developmental potential of iPSCs is greatly influenced by reprogramming factor selection. Cell Stem Cell 2014; 15(3): 295-309.
[http://dx.doi.org/10.1016/j.stem.2014.07.003] [PMID: 25192464]
[14]
Limaye A, Hall B, Kulkarni AB. Manipulation of mouse embryonic stem cells for knockout mouse production. Curr Protoc Cell Biol 2009; 44(1): 19.
[http://dx.doi.org/10.1002/0471143030.cb1913s44]
[15]
Saunders A, Faiola F, Wang J. Concise review: Pursuing self-renewal and pluripotency with the stem cell factor Nanog. Stem Cells 2013; 31(7): 1227-36.
[http://dx.doi.org/10.1002/stem.1384] [PMID: 23653415]
[16]
Graf U, Casanova EA, Cinelli P. The role of the leukemia inhibitory factor (LIF)—pathway in derivation and maintenance of murine pluripotent stem cells. Genes 2011; 2(1): 280-97.
[http://dx.doi.org/10.3390/genes2010280] [PMID: 24710148]
[17]
Niwa H, Burdon T, Chambers I, Smith A. Self-renewal of pluripotent embryonic stem cells is mediated via activation of STAT3. Genes Dev 1998; 12(13): 2048-60.
[http://dx.doi.org/10.1101/gad.12.13.2048] [PMID: 9649508]
[18]
Yoshida GJ. Emerging roles of Myc in stem cell biology and novel tumor therapies. J Exp Clin Cancer Res 2018; 37(1): 1-20.
[PMID: 29301578]
[19]
Burdon T, Stracey C, Chambers I, Nichols J, Smith A. Suppression of SHP-2 and ERK signalling promotes self-renewal of mouse embryonic stem cells. Dev Biol 1999; 210(1): 30-43.
[http://dx.doi.org/10.1006/dbio.1999.9265] [PMID: 10364425]
[20]
Cheng AM, Saxton TM, Sakai R, et al. Mammalian Grb2 regulates multiple steps in embryonic development and malignant transformation. Cell 1998; 95(6): 793-803.
[http://dx.doi.org/10.1016/S0092-8674(00)81702-X] [PMID: 9865697]
[21]
Yeo JC, Ng HH. The transcriptional regulation of pluripotency. Cell Res 2013; 23(1): 20-32.
[http://dx.doi.org/10.1038/cr.2012.172] [PMID: 23229513]
[22]
Palmqvist L, Glover CH, Hsu L, et al. Correlation of murine embryonic stem cell gene expression profiles with functional measures of pluripotency. Stem Cells 2005; 23(5): 663-80.
[http://dx.doi.org/10.1634/stemcells.2004-0157] [PMID: 15849174]
[23]
Kitamura T, Koshino Y, Shibata F, et al. Retrovirus-mediated gene transfer and expression cloning: powerful tools in functional genomics. Exp Hematol 2003; 31(11): 1007-14.
[http://dx.doi.org/10.1016/S0301-472X(03)00260-1] [PMID: 14585362]
[24]
Han JW, Yoon Y. Induced pluripotent stem cells: emerging techniques for nuclear reprogramming. Antioxid Redox Signal 2011; 15(7): 1799-820.
[http://dx.doi.org/10.1089/ars.2010.3814] [PMID: 21194386]
[25]
Frisén J, Lendahl U, Perimann T. Mature cells can be reprogrammed to become pluripotent. The 2012 Nobel Prize in Physiology or Medicine–Advanced Information. 2012. Available from: http://Nobelprizeorg
[26]
Wilmut I, Sullivan G, Chambers I. The evolving biology of cell reprogramming. Philos Trans R SocB 2011; 366(1575): 2183-97.
[http://dx.doi.org/10.1098/rstb.2011.0051]
[27]
Ferreira R, Ohneda K, Yamamoto M, Philipsen S. GATA1 function, a paradigm for transcription factors in hematopoiesis. Mol Cell Biol 2005; 25(4): 1215-27.
[http://dx.doi.org/10.1128/MCB.25.4.1215-1227.2005] [PMID: 15684376]
[28]
Di Tullio A, Manh TPV, Schubert A, Castellano G, Månsson R, Graf T. CCAAT/enhancer binding protein α (C/EBPα)-induced transdifferentiation of pre-B cells into macrophages involves no overt retrodifferentiation. Proc Natl Acad Sci 2011; 108(41): 17016-21.
[http://dx.doi.org/10.1073/pnas.1112169108] [PMID: 21969581]
[29]
Shafa M, Krawetz R, Rancourt DE. Returning to the stem state: Epigenetics of recapitulating pre-differentiation chromatin structure. BioEssays 2010; 32(9): 791-9.
[http://dx.doi.org/10.1002/bies.201000033] [PMID: 20652894]
[30]
Robinton DA, Daley GQ. The promise of induced pluripotent stem cells in research and therapy. Nature 2012; 481(7381): 295-305.
[http://dx.doi.org/10.1038/nature10761] [PMID: 22258608]
[31]
García-León JA, Kumar M, Boon R, et al. SOX10 single transcription factor-based fast and efficient generation of oligodendrocytes from human pluripotent stem cells. Stem Cell Reports 2018; 10(2): 655-72.
[http://dx.doi.org/10.1016/j.stemcr.2017.12.014] [PMID: 29337119]
[32]
Tsai SY, Bouwman BA, Ang YS, et al. Single transcription factor reprogramming of hair follicle dermal papilla cells to induced pluripotent stem cells. Stem Cells 2011; 29(6): 964-71.
[http://dx.doi.org/10.1002/stem.649] [PMID: 21563278]
[33]
Fujino S, Miyoshi N. Oct4 gene expression in primary colorectal cancer promotes liver metastasis. Stem Cells Int 2019; 2019: 7896524.
[http://dx.doi.org/10.1155/2019/7896524]
[34]
Kim BE, Choi SW, Shin JH, et al. Single-factor SOX2 mediates direct neural reprogramming of human mesenchymal stem cells via transfection of in vitro transcribed mRNA. Cell Transplant 2018; 27(7): 1154-67.
[http://dx.doi.org/10.1177/0963689718771885] [PMID: 29909688]
[35]
Dhaliwal NK, Abatti LE, Mitchell JA. KLF4 protein stability regulated by interaction with pluripotency transcription factors overrides transcriptional control. Genes Dev 2019; 33(15-16): 1069-82.
[http://dx.doi.org/10.1101/gad.324319.119] [PMID: 31221664]
[36]
González F, Huangfu D. Mechanisms underlying the formation of induced pluripotent stem cells. Wiley Interdiscip Rev Dev Biol 2016; 5(1): 39-65.
[http://dx.doi.org/10.1002/wdev.206] [PMID: 26383234]
[37]
Winkler T, Cantilena A, Métais JY, et al. No evidence for clonal selection due to lentiviral integration sites in human induced pluripotent stem cells. Stem Cells 2010; 28(4): 687-94.
[http://dx.doi.org/10.1002/stem.322] [PMID: 20166152]
[38]
Okita K, Yamakawa T, Matsumura Y, et al. An efficient nonviral method to generate integration-free human-induced pluripotent stem cells from cord blood and peripheral blood cells. Stem Cells 2013; 31(3): 458-66.
[http://dx.doi.org/10.1002/stem.1293] [PMID: 23193063]
[39]
Zhou Q, Liu M, Xia X, et al. A mouse tissue transcription factor atlas. Nat Commun 2017; 8(1): 15089.
[http://dx.doi.org/10.1038/ncomms15089] [PMID: 28429721]
[40]
Kribelbauer JF, Rastogi C, Bussemaker HJ, Mann RS. Low-affinity binding sites and the transcription factor specificity paradox in eukaryotes. Annu Rev Cell Dev Biol 2019; 35(1): 357-79.
[http://dx.doi.org/10.1146/annurev-cellbio-100617-062719] [PMID: 31283382]
[41]
Wang X, Cairns MJ, Yan J. Super-enhancers in transcriptional regulation and genome organization. Nucleic Acids Res 2019; 47(22): gkz1038.
[http://dx.doi.org/10.1093/nar/gkz1038] [PMID: 31724731]
[42]
Tang F, Yang Z, Tan Y, Li Y. Super-enhancer function and its application in cancer targeted therapy. NPJ Precis Oncol 2020; 4(1): 2.
[http://dx.doi.org/10.1038/s41698-020-0108-z] [PMID: 32128448]
[43]
Lee K, Wong W, Feng B. Decoding the pluripotency network: The emergence of new transcription factors. Biomedicines 2013; 1(1): 49-78.
[http://dx.doi.org/10.3390/biomedicines1010049] [PMID: 28548056]
[44]
Bhinge AA. A functional genomics approach to map transcriptional and post-transcriptional gene regulatory network 2009.
[45]
Class I. USPC AN Patent application title: SUPER-ENHANCERS AND METHODS OF USE THEREOF Inventors: Denes Hnisz (Cambridge, MA, US) Brian Abraham (Cambridge, MA, US) Tong Ihn Lee (Somerville, MA, US) Richard A Young (Weston, MA, US). Richard A. Young: Weston, MA, US 2014.
[46]
Schoenfelder S, Fraser P. Long-range enhancer–promoter contacts in gene expression control. Nat Rev Genet 2019; 20(8): 437-55.
[http://dx.doi.org/10.1038/s41576-019-0128-0] [PMID: 31086298]
[47]
Spitz F, Furlong EEM. Transcription factors: From enhancer binding to developmental control. Nat Rev Genet 2012; 13(9): 613-26.
[http://dx.doi.org/10.1038/nrg3207] [PMID: 22868264]
[48]
Heinz S, Romanoski CE, Benner C, Glass CK. The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol 2015; 16(3): 144-54.
[http://dx.doi.org/10.1038/nrm3949] [PMID: 25650801]
[49]
Bi X, Xu Y, Li T, Li X, Li W, Shao W. RNA targets ribogenesis factor WDR43 to chromatin for transcription and pluripotency control. Molecular cell 2019; 75(1): 102-16.e9.
[http://dx.doi.org/10.1016/j.molcel.2019.05.007]
[50]
Kamachi Y, Kondoh H. Sox proteins: Regulators of cell fate specification and differentiation. Development 2013; 140(20): 4129-44.
[http://dx.doi.org/10.1242/dev.091793] [PMID: 24086078]
[51]
Fagnocchi L, Zippo A. Multiple roles of MYC in integrating regulatory networks of pluripotent stem cells. Front Cell Dev Biol 2017; 5: 7.
[http://dx.doi.org/10.3389/fcell.2017.00007] [PMID: 28217689]
[52]
Malik V, Glaser LV, Zimmer D, et al. Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2. Nat Commun 2019; 10(1): 3477.
[http://dx.doi.org/10.1038/s41467-019-11054-7] [PMID: 31375664]
[53]
Niwa H. The principles that govern transcription factor network functions in stem cells. Development 2018; 145(6): dev157420.
[http://dx.doi.org/10.1242/dev.157420]
[54]
Soufi A, Garcia MF, Jaroszewicz A, Osman N, Pellegrini M, Zaret KS. Pioneer transcription factors target partial DNA motifs on nucleosomes to initiate reprogramming. Cell 2015; 161(3): 555-68.
[http://dx.doi.org/10.1016/j.cell.2015.03.017] [PMID: 25892221]
[55]
Aksoy I, Jauch R, Chen J, et al. Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm. EMBO J 2013; 32(7): 938-53.
[http://dx.doi.org/10.1038/emboj.2013.31] [PMID: 23474895]
[56]
Zhang S, Cui W. Sox2, a key factor in the regulation of pluripotency and neural differentiation. World J Stem Cells 2014; 6(3): 305-11.
[http://dx.doi.org/10.4252/wjsc.v6.i3.305] [PMID: 25126380]
[57]
Costa RH, Kalinichenko VV, Lim L. Transcription factors in mouse lung development and function. Am J Physiol Lung Cell Mol Physiol 2001; 280(5): L823-38.
[http://dx.doi.org/10.1152/ajplung.2001.280.5.L823] [PMID: 11290504]
[58]
Kashyap V, Rezende NC, Scotland KB, et al. Regulation of stem cell pluripotency and differentiation involves a mutual regulatory circuit of the NANOG, OCT4, and SOX2 pluripotency transcription factors with polycomb repressive complexes and stem cell microRNAs. Stem Cells Dev 2009; 18(7): 1093-108.
[http://dx.doi.org/10.1089/scd.2009.0113] [PMID: 19480567]
[59]
Rodda DJ, Chew JL, Lim LH, et al. Transcriptional regulation of nanog by OCT4 and SOX2. J Biol Chem 2005; 280(26): 24731-7.
[http://dx.doi.org/10.1074/jbc.M502573200] [PMID: 15860457]
[60]
Niwa H. The principles that govern transcription factor network functions in stem cells. Development 2018; 145(6): dev157420.
[http://dx.doi.org/10.1242/dev.157420] [PMID: 29540464]
[61]
Davies K. Regulation of Stomatal Development Initiation and Cell Fate Transitions by the bHLH Transcription Factor Speechless. PhD Dissertation Stanford University 2014.
[62]
Chen JX, et al. Inefficient reprogramming of fibroblasts into cardiomyocytes using Gata4, Mef2c, and Tbx5 Circulation research 2012; 111(1): 50-5.
[63]
Gökbuget D, Blelloch R. Epigenetic control of transcriptional regulation in pluripotency and early differentiation. Development 2019; 146(19): dev164772.
[http://dx.doi.org/10.1242/dev.164772] [PMID: 31554624]
[64]
Chen AF, Liu AJ, Krishnakumar R, Freimer JW, DeVeale B, Blelloch R. GRHL2-dependent enhancer switching maintains a pluripotent stem cell transcriptional subnetwork after exit from naive pluripotency. Cell Stem Cell 2018; 23(2): 226-38.
[http://dx.doi.org/10.1016/j.stem.2018.06.005]
[65]
Buganim Y, Faddah DA, Jaenisch R. Mechanisms and models of somatic cell reprogramming. Nat Rev Genet 2013; 14(6): 427-39.
[http://dx.doi.org/10.1038/nrg3473] [PMID: 23681063]
[66]
Sterner DE, Berger SL. Acetylation of histones and transcription-related factors. Microbiol Mol Biol Rev 2000; 64(2): 435-59.
[http://dx.doi.org/10.1128/MMBR.64.2.435-459.2000] [PMID: 10839822]
[67]
Schmidt R, Plath K. The roles of the reprogramming factors Oct4, Sox2 and Klf4 in resetting the somatic cell epigenome during induced pluripotent stem cell generation. Genome Biol 2012; 13(10): 251.
[http://dx.doi.org/10.1186/gb-2012-13-10-251] [PMID: 23088445]
[68]
Koche RP, Smith ZD, Adli M, et al. Reprogramming factor expression initiates widespread targeted chromatin remodeling. Cell Stem Cell 2011; 8(1): 96-105.
[http://dx.doi.org/10.1016/j.stem.2010.12.001] [PMID: 21211784]
[69]
Sridharan R, Tchieu J, Mason MJ, et al. Role of the murine reprogramming factors in the induction of pluripotency. Cell 2009; 136(2): 364-77.
[http://dx.doi.org/10.1016/j.cell.2009.01.001] [PMID: 19167336]
[70]
Soufi A, Donahue G, Zaret KS. Facilitators and impediments of the pluripotency reprogramming factors’ initial engagement with the genome. Cell 2012; 151(5): 994-1004.
[http://dx.doi.org/10.1016/j.cell.2012.09.045] [PMID: 23159369]
[71]
Chen J, Liu H, Liu J, et al. H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nat Genet 2013; 45(1): 34-42.
[http://dx.doi.org/10.1038/ng.2491] [PMID: 23202127]
[72]
Liang G, He J, Zhang Y. Kdm2b promotes induced pluripotent stem cell generation by facilitating gene activation early in reprogramming. Nat Cell Biol 2012; 14(5): 457-66.
[http://dx.doi.org/10.1038/ncb2483] [PMID: 22522173]
[73]
Wang T, Chen K, Zeng X, et al. The histone demethylases Jhdm1a/1b enhance somatic cell reprogramming in a vitamin-C-dependent manner. Cell Stem Cell 2011; 9(6): 575-87.
[http://dx.doi.org/10.1016/j.stem.2011.10.005] [PMID: 22100412]
[74]
Onder TT, Kara N, Cherry A, et al. Chromatin-modifying enzymes as modulators of reprogramming. Nature 2012; 483(7391): 598-602.
[http://dx.doi.org/10.1038/nature10953] [PMID: 22388813]
[75]
Zhang B, Day DS, Ho JW, et al. A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity. Genome Res 2013; 23(6): 917-27.
[http://dx.doi.org/10.1101/gr.149674.112] [PMID: 23547170]
[76]
Xie G, Lee JE, McKernan K, et al. (2020) MLL3/MLL4 methyltransferase activities regulate embryonic stem cell differentiation independent of enhancer H3K4me1. bioRxiv 2020; 09
[77]
Seymour T, Twigger AJ, Kakulas F. Pluripotency genes and their functions in the normal and aberrant breast and brain. Int J Mol Sci 2015; 16(11): 27288-301.
[http://dx.doi.org/10.3390/ijms161126024] [PMID: 26580604]
[78]
Cao K, Collings CK, Morgan MA, et al. An Mll4/COMPASS-Lsd1 epigenetic axis governs enhancer function and pluripotency transition in embryonic stem cells. Sci Adv 2018; 4(1): eaap8747.
[http://dx.doi.org/10.1126/sciadv.aap8747] [PMID: 29404406]
[79]
Sze CC, Shilatifard A. MLL3/MLL4/COMPASS family on epigenetic regulation of enhancer function and cancer. Cold Spring Harb Perspect Med 2016; 6(11): a026427.
[http://dx.doi.org/10.1101/cshperspect.a026427] [PMID: 27638352]
[80]
Yan J, Chen SAA, Local A, et al. Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers. Cell Res 2018; 28(2): 204-20.
[http://dx.doi.org/10.1038/cr.2018.1] [PMID: 29313530]
[81]
Bernatavichute YV. Mechanisms of CMT3 activation and histone methylation in Arabidopsis thaliana. PhD Dissertation Los Angeles: University of California 2009.
[82]
Vignali M, Hassan AH, Neely KE, Workman JL. ATP-dependent chromatin-remodeling complexes. Mol Cell Biol 2000; 20(6): 1899-910.
[http://dx.doi.org/10.1128/MCB.20.6.1899-1910.2000] [PMID: 10688638]
[83]
Zhang H, Gayen S, Xiong J, et al. MLL1 inhibition reprograms epiblast stem cells to naive pluripotency. Cell Stem Cell 2016; 18(4): 481-94.
[http://dx.doi.org/10.1016/j.stem.2016.02.004] [PMID: 26996599]
[84]
Prakash K, Fournier D. Evidence for the implication of the histone code in building the genome structure. Biosystems 2018; 164: 49-59.
[http://dx.doi.org/10.1016/j.biosystems.2017.11.005] [PMID: 29158132]
[85]
Hayakawa T, Nakayama J-i. Physiological roles of class I HDAC complex and histone demethylase. J Biomed Biotechnol 2011; 2011: 129383.
[http://dx.doi.org/10.1155/2011/129383]
[86]
Jamaladdin SJ. Investigating the physiological role of HDAC1 and HDAC2 in embryonic stem cells. PhD Dissertation University of Leicester 2016.
[87]
Parbin S, Kar S, Shilpi A, et al. Histone Deacetylases. J Histochem Cytochem 2014; 62(1): 11-33.
[http://dx.doi.org/10.1369/0022155413506582] [PMID: 24051359]
[88]
Yang XJ, Grégoire S. Class II histone deacetylases: From sequence to function, regulation, and clinical implication. Mol Cell Biol 2005; 25(8): 2873-84.
[http://dx.doi.org/10.1128/MCB.25.8.2873-2884.2005] [PMID: 15798178]
[89]
Baas R. Mechanisms controlling SMAD-dependent transcription and chromatin modification. Utrecht University 2017.
[90]
Biddlestone J, Batie M, Bandarra D, Munoz I, Rocha S. SINHCAF/FAM60A and SIN3A specifically repress HIF-2α expression. Biochem J 2018; 475(12): 2073-90.
[http://dx.doi.org/10.1042/BCJ20170945] [PMID: 29784889]
[91]
Ohi Y, Qin H, Hong C, et al. Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat Cell Biol 2011; 13(5): 541-9.
[http://dx.doi.org/10.1038/ncb2239] [PMID: 21499256]
[92]
Nashun B, Hill PWS, Hajkova P. Reprogramming of cell fate: Epigenetic memory and the erasure of memories past. EMBO J 2015; 34(10): 1296-308.
[http://dx.doi.org/10.15252/embj.201490649] [PMID: 25820261]
[93]
Chang G, Gao S, Hou X, et al. High-throughput sequencing reveals the disruption of methylation of imprinted gene in induced pluripotent stem cells. Cell Res 2014; 24(3): 293-306.
[http://dx.doi.org/10.1038/cr.2013.173] [PMID: 24381111]
[94]
Pawlak M, Jaenisch R. De novo DNA methylation by Dnmt3a and Dnmt3b is dispensable for nuclear reprogramming of somatic cells to a pluripotent state. Genes Dev 2011; 25(10): 1035-40.
[http://dx.doi.org/10.1101/gad.2039011] [PMID: 21576263]
[95]
Kallingappa PK, Turner PM, Eichenlaub MP, Green AL, Oback FC, Chibnall AM. Quiescence loosens epigenetic constraints in bovine somatic cells and improves their reprogramming into totipotency. Biol Reprod 2016; 95(1): 16.
[http://dx.doi.org/10.1095/biolreprod.115.137109]
[96]
Hermann A, Gowher H, Jeltsch A. Biochemistry and biology of mammalian DNA methyltransferases. Cell Mol Life Sci 2004; 61(19-20): 2571-87.
[http://dx.doi.org/10.1007/s00018-004-4201-1] [PMID: 15526163]
[97]
Guo H, Zhu P, Yan L, et al. The DNA methylation landscape of human early embryos. Nature 2014; 511(7511): 606-10.
[http://dx.doi.org/10.1038/nature13544] [PMID: 25079557]
[98]
Paniza T, Deshpande M, Wang N, et al. Pluripotent stem cells with low differentiation potential contain incompletely reprogrammed DNA replication. J Cell Biol 2020; 219(9): e201909163.
[http://dx.doi.org/10.1083/jcb.201909163] [PMID: 32673399]
[99]
Parry A, Rulands S, Reik W. (2021); Active turnover of DNA methylation during cell fate decisions. Natture Reviews Genetics 22(1): 59-66.
[100]
Suetake I, Watanebe M, Takeshita K, Takahashi S, Carlton P. The Molecular Basis of DNA Methylation In: Kameda A, Tsukada Yi, Eds DNA and Histone Methylation as Cancer Targets. Cham: Humana Press 2017; pp. 19-51.
[http://dx.doi.org/10.1007/978-3-319-59786-7_2]
[101]
von Meyenn F, Iurlaro M, Habibi E, et al. Impairment of DNA methylation maintenance is the main cause of global demethylation in naive embryonic stem cells. Mol Cell 2016; 62(6): 848-61.
[http://dx.doi.org/10.1016/j.molcel.2016.04.025] [PMID: 27237052]
[102]
Zhang J, Gao Q, Li P, et al. S phase-dependent interaction with DNMT1 dictates the role of UHRF1 but not UHRF2 in DNA methylation maintenance. Cell Res 2011; 21(12): 1723-39.
[http://dx.doi.org/10.1038/cr.2011.176] [PMID: 22064703]
[103]
Kalkan T, Olova N, Roode M, et al. Tracking the embryonic stem cell transition from ground state pluripotency.Development 2017; 144(7): dev.142711.
[http://dx.doi.org/10.1242/dev.142711] [PMID: 28174249]
[104]
Singer ZS, Yong J, Tischler J, et al. Dynamic heterogeneity and DNA methylation in embryonic stem cells. Mol Cell 2014; 55(2): 319-31.
[http://dx.doi.org/10.1016/j.molcel.2014.06.029] [PMID: 25038413]
[105]
Rasmussen KD, Helin K. Role of TET enzymes in DNA methylation, development, and cancer. Genes Dev 2016; 30(7): 733-50.
[http://dx.doi.org/10.1101/gad.276568.115] [PMID: 27036965]
[106]
Dawlaty MM, Breiling A, Le T, et al. Loss of Tet enzymes compromises proper differentiation of embryonic stem cells. Dev Cell 2014; 29(1): 102-11.
[http://dx.doi.org/10.1016/j.devcel.2014.03.003] [PMID: 24735881]
[107]
Pantier R, Tatar T, Colby D, Chambers I. Endogenous epitope-tagging of Tet1, Tet2 and Tet3 identifies TET2 as a naïve pluripotency marker. Life Sci Alliance 2019; 2(5): e201900516.
[http://dx.doi.org/10.26508/lsa.201900516] [PMID: 31582397]
[108]
Fidalgo M, Huang X, Guallar D, et al. Zfp281 coordinates opposing functions of Tet1 and Tet2 in pluripotent states. Cell Stem Cell 2016; 19(3): 355-69.
[http://dx.doi.org/10.1016/j.stem.2016.05.025] [PMID: 27345836]
[109]
Kim K, Zhao R, Doi A, et al. Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nat Biotechnol 2011; 29(12): 1117-9.
[http://dx.doi.org/10.1038/nbt.2052] [PMID: 22119740]
[110]
Liu MY. Deciphering the tetrad of epigenetic cytosine modifications 2016.
[111]
Dahl C, Grønbæk K, Guldberg P. Advances in DNA methylation: 5-hydroxymethylcytosine revisited. Clin Chim Acta 2011; 412(11-12): 831-6.
[http://dx.doi.org/10.1016/j.cca.2011.02.013] [PMID: 21324307]
[112]
Olariu V, Lövkvist C, Sneppen K. Nanog, Oct4 and Tet1 interplay in establishing pluripotency. Sci Rep 2016; 6(1): 25438.
[http://dx.doi.org/10.1038/srep25438] [PMID: 27146218]
[113]
Hu X, Zhang L, Mao SQ, et al. Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming. Cell Stem Cell 2014; 14(4): 512-22.
[http://dx.doi.org/10.1016/j.stem.2014.01.001] [PMID: 24529596]
[114]
Huang Y, Rao A. Connections between TET proteins and aberrant DNA modification in cancer. Trends Genet 2014; 30(10): 464-74.
[http://dx.doi.org/10.1016/j.tig.2014.07.005] [PMID: 25132561]
[115]
De Carvalho DD, You JS, Jones PA. DNA methylation and cellular reprogramming. Trends Cell Biol 2010; 20(10): 609-17.
[http://dx.doi.org/10.1016/j.tcb.2010.08.003] [PMID: 20810283]
[116]
Han C, Deng R, Mao T, et al. Overexpression of Tet3 in donor cells enhances goat somatic cell nuclear transfer efficiency. FEBS J 2018; 285(14): 2708-23.
[http://dx.doi.org/10.1111/febs.14515] [PMID: 29791079]
[117]
Ringrose L. Epigenetics and Systems Biology. Academic Press 2017.
[118]
Kim KP, Wu Y, Yoon J, et al. Reprogramming competence of OCT factors is determined by transactivation domains. Sci Adv 2020; 6(36): eaaz7364.
[http://dx.doi.org/10.1126/sciadv.aaz7364] [PMID: 32917606]
[119]
Spehalski E, Kovalchuk AL, Collins JT, et al. Oncogenic Myc translocations are independent of chromosomal location and orientation of the immunoglobulin heavy chain locus. Proc Natl Acad Sci 2012; 109(34): 13728-32.
[http://dx.doi.org/10.1073/pnas.1202882109] [PMID: 22869734]
[120]
Wuputra K, Ku CC, Wu DC, Lin YC, Saito S, Yokoyama KK. Prevention of tumor risk associated with the reprogramming of human pluripotent stem cells. J Exp Clin Cancer Res 2020; 39(1): 100.
[http://dx.doi.org/10.1186/s13046-020-01584-0] [PMID: 32493501]
[121]
Wang T, Shi S, Sha H. MicroRNAs in regulation of pluripotency and somatic cell reprogramming. RNA Biol 2013; 10(8): 1255-61.
[http://dx.doi.org/10.4161/rna.25828] [PMID: 23921205]
[122]
Choi YJ, Lin CP, Risso D, et al. Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells.Science 2017; 355(6325): eaag1927.
[http://dx.doi.org/10.1126/science.aag1927] [PMID: 28082412]
[123]
Festuccia N, Gonzalez I, Navarro P. The epigenetic paradox of pluripotent ES cells. J Mol Biol 2017; 429(10): 1476-503.
[http://dx.doi.org/10.1016/j.jmb.2016.12.009] [PMID: 27988225]
[124]
Ding H, Blair A, Yang Y, Stuart JM. Biological process activity transformation of single cell gene expression for cross-species alignment. Nat Commun 2019; 10(1): 4899.
[http://dx.doi.org/10.1038/s41467-019-12924-w] [PMID: 31653878]
[125]
Kim H, Lee G, Ganat Y, et al. miR-371-3 expression predicts neural differentiation propensity in human pluripotent stem cells. Cell Stem Cell 2011; 8(6): 695-706.
[http://dx.doi.org/10.1016/j.stem.2011.04.002] [PMID: 21624813]
[126]
Mo CF, Wu FC, Tai KY, et al. Loss of non-coding RNA expression from the DLK1-DIO3 imprinted locus correlates with reduced neural differentiation potential in human embryonic stem cell lines. Stem Cell Res Ther 2015; 6(1): 1-17.
[http://dx.doi.org/10.1186/scrt535] [PMID: 25559585]
[127]
Zhu L, Gomez-Duran A, Saretzki G, et al. The mitochondrial protein CHCHD2 primes the differentiation potential of human induced pluripotent stem cells to neuroectodermal lineages. J Cell Biol 2016; 215(2): 187-202.
[http://dx.doi.org/10.1083/jcb.201601061] [PMID: 27810911]
[128]
Jiang W, Zhang D, Bursac N, Zhang Y. WNT3 is a biomarker capable of predicting the definitive endoderm differentiation potential of hESCs. Stem Cell Reports 2013; 1(1): 46-52.
[http://dx.doi.org/10.1016/j.stemcr.2013.03.003] [PMID: 24052941]
[129]
Butcher LM, Ito M, Brimpari M, et al. Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells. Nat Commun 2016; 7(1): 10458.
[http://dx.doi.org/10.1038/ncomms10458] [PMID: 26822956]
[130]
Yanagihara K, Liu Y, Kanie K, et al. Prediction of differentiation tendency toward hepatocytes from gene expression in undifferentiated human pluripotent stem cells. Stem Cells Dev 2016; 25(24): 1884-97.
[http://dx.doi.org/10.1089/scd.2016.0099] [PMID: 27733097]
[131]
Ran D, Shia WJ, Lo MC, et al. RUNX1a enhances hematopoietic lineage commitment from human embryonic stem cells and inducible pluripotent stem cells. Blood 2013; 121(15): 2882-90.
[http://dx.doi.org/10.1182/blood-2012-08-451641] [PMID: 23372166]
[132]
Ramos-Mejia V, Melen GJ, Sanchez L, et al. Nodal/Activin signaling predicts human pluripotent stem cell lines prone to differentiate toward the hematopoietic lineage. Mol Ther 2010; 18(12): 2173-81.
[http://dx.doi.org/10.1038/mt.2010.179] [PMID: 20736931]
[133]
Bock C, Kiskinis E, Verstappen G, et al. Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell 2011; 144(3): 439-52.
[http://dx.doi.org/10.1016/j.cell.2010.12.032] [PMID: 21295703]
[134]
Nishizawa M, Chonabayashi K, Nomura M, et al. Epigenetic variation between human induced pluripotent stem cell lines is an indicator of differentiation capacity. Cell Stem Cell 2016; 19(3): 341-54.
[http://dx.doi.org/10.1016/j.stem.2016.06.019] [PMID: 27476965]
[135]
Park J, Son Y, Lee NG, et al. DSG2 is a functional cell surface marker for identification and isolation of human pluripotent stem cells. Stem Cell Reports 2018; 11(1): 115-27.
[http://dx.doi.org/10.1016/j.stemcr.2018.05.009] [PMID: 29910125]
[136]
Merkle FT, Ghosh S, Kamitaki N, et al. Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations. Nature 2017; 545(7653): 229-33.
[http://dx.doi.org/10.1038/nature22312] [PMID: 28445466]
[137]
Lin T, Lin Y. p53 switches off pluripotency on differentiation. Stem Cell Res Ther 2017; 8(1): 44.
[http://dx.doi.org/10.1186/s13287-017-0498-1] [PMID: 28241890]
[138]
Alvarez-Palomo AB, Requena-Osete J, Delgado-Morales R, et al. A synthetic mRNA cell reprogramming method using CYCLIN D1 promotes DNA repair, generating improved genetically stable human induced pluripotent stem cells. Stem Cells 2021; 39(7): 866-81.
[http://dx.doi.org/10.1002/stem.3358] [PMID: 33621399]
[139]
Petropoulos S, Edsgärd D, Reinius B, et al. Single-cell RNA-seq reveals lineage and X chromosome dynamics in human preimplantation embryos. Cell 2016; 165(4): 1012-26.
[http://dx.doi.org/10.1016/j.cell.2016.03.023] [PMID: 27062923]
[140]
Liu X, Nefzger CM, Rossello FJ, et al. Comprehensive characterization of distinct states of human naive pluripotency generated by reprogramming. Nat Methods 2017; 14(11): 1055-62.
[http://dx.doi.org/10.1038/nmeth.4436] [PMID: 28945704]
[141]
Davidson KC, Mason EA, Pera MF. The pluripotent state in mouse and human. Development 2015; 142(18): 3090-9.
[http://dx.doi.org/10.1242/dev.116061] [PMID: 26395138]
[142]
Yan L, Yang M, Guo H, et al. Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol 2013; 20(9): 1131-9.
[http://dx.doi.org/10.1038/nsmb.2660] [PMID: 23934149]
[143]
Sahakyan A, Kim R, Chronis C, et al. Human naive pluripotent stem cells model X chromosome dampening and X inactivation. Cell Stem Cell 2017; 20(1): 87-101.
[http://dx.doi.org/10.1016/j.stem.2016.10.006] [PMID: 27989770]
[144]
Xiao L, Shan Y, Ma L, Dunk C, Yu Y, Wei Y. Tuning FOXD3 expression dose-dependently balances human embryonic stem cells between pluripotency and meso-endoderm fates. Biochim Biophys Acta Mol Cell Res 2019; 1866(12): 118531.
[http://dx.doi.org/10.1016/j.bbamcr.2019.118531] [PMID: 31415841]
[145]
Cantone I, Fisher AG. Epigenetic programming and reprogramming during development. Nat Struct Mol Biol 2013; 20(3): 282-9.
[http://dx.doi.org/10.1038/nsmb.2489] [PMID: 23463313]
[146]
Stadhouders R, Filion GJ, Graf T. Transcription factors and 3D genome conformation in cell-fate decisions. Nature 2019; 569(7756): 345-54.
[http://dx.doi.org/10.1038/s41586-019-1182-7] [PMID: 31092938]
[147]
Serrano-Gomez SJ, Maziveyi M, Alahari SK. Regulation of epithelial-mesenchymal transition through epigenetic and post-translational modifications. Mol Cancer 2016; 15(1): 18.
[http://dx.doi.org/10.1186/s12943-016-0502-x] [PMID: 26905733]
[148]
Vacík T, Lađinović D, Raška I. KDM2A/B lysine demethylases and their alternative isoforms in development and disease. Nucleus 2018; 9(1): 431-41.
[http://dx.doi.org/10.1080/19491034.2018.1498707] [PMID: 30059280]
[149]
Shinagawa T, Takagi T, Tsukamoto D, et al. Histone variants enriched in oocytes enhance reprogramming to induced pluripotent stem cells. Cell Stem Cell 2014; 14(2): 217-27.
[http://dx.doi.org/10.1016/j.stem.2013.12.015] [PMID: 24506885]
[150]
Christophorou MA, Castelo-Branco G, Halley-Stott RP, et al. Citrullination regulates pluripotency and histone H1 binding to chromatin. Nature 2014; 507(7490): 104-8.
[http://dx.doi.org/10.1038/nature12942] [PMID: 24463520]
[151]
Gao L, Emperle M, Guo Y, et al. Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms. Nat Commun 2020; 11(1): 3355.
[http://dx.doi.org/10.1038/s41467-020-17109-4] [PMID: 32620778]
[152]
Messerschmidt DM, Knowles BB, Solter D. DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos. Genes Dev 2014; 28(8): 812-28.
[http://dx.doi.org/10.1101/gad.234294.113] [PMID: 24736841]
[153]
Wang G, Weng R, Lan Y, et al. Synergetic effects of DNA methylation and histone modification during mouse induced pluripotent stem cell generation. Sci Rep 2017; 7(1): 39527.
[http://dx.doi.org/10.1038/srep39527] [PMID: 28155862]
[154]
Mao J, Zhang Q, Deng W, et al. Epigenetic modifiers facilitate induction and pluripotency of porcine iPSCs. Stem Cell Reports 2017; 8(1): 11-20.
[http://dx.doi.org/10.1016/j.stemcr.2016.11.013] [PMID: 28041878]
[155]
Tessarz P, Kouzarides T. Histone core modifications regulating nucleosome structure and dynamics. Nat Rev Mol Cell Biol 2014; 15(11): 703-8.
[http://dx.doi.org/10.1038/nrm3890] [PMID: 25315270]
[156]
Federation AJ, Bradner JE, Meissner A. The use of small molecules in somatic-cell reprogramming. Trends Cell Biol 2014; 24(3): 179-87.
[http://dx.doi.org/10.1016/j.tcb.2013.09.011] [PMID: 24183602]
[157]
Fingerman IM, McDaniel L, Zhang X, et al. NCBI Epigenomics: A new public resource for exploring epigenomic data sets. Nucleic Acids Res 2011; 39((Database)): D908-12.
[http://dx.doi.org/10.1093/nar/gkq1146] [PMID: 21075792]
[158]
Banaszynski LA, Wen D, Dewell S, et al. Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells. Cell 2013; 155(1): 107-20.
[http://dx.doi.org/10.1016/j.cell.2013.08.061] [PMID: 24074864]
[159]
Gaspar-Maia A, Alajem A, Meshorer E, Ramalho-Santos M. Open chromatin in pluripotency and reprogramming. Nat Rev Mol Cell Biol 2011; 12(1): 36-47.
[http://dx.doi.org/10.1038/nrm3036] [PMID: 21179060]
[160]
Egli D, Birkhoff G, Eggan K. Mediators of reprogramming: Transcription factors and transitions through mitosis. Nat Rev Mol Cell Biol 2008; 9(7): 505-16.
[http://dx.doi.org/10.1038/nrm2439] [PMID: 18568039]
[161]
Gaspar-Maia A, Qadeer ZA, Hasson D, et al. MacroH2A histone variants act as a barrier upon reprogramming towards pluripotency. Nat Commun 2013; 4(1): 1565.
[http://dx.doi.org/10.1038/ncomms2582] [PMID: 23463008]
[162]
Bortvin A, Eggan K, Skaletsky H, et al. Incomplete reactivation of Oct4 -related genes in mouse embryos cloned from somatic nuclei. Development 2003; 130(8): 1673-80.
[http://dx.doi.org/10.1242/dev.00366] [PMID: 12620990]
[163]
Vallabhaneni H, Lynch PJ, Chen G, et al. High basal levels of γH2AX in human induced pluripotent stem cells are linked to replication-associated DNA damage and repair. Stem Cells 2018; 36(10): 1501-13.
[http://dx.doi.org/10.1002/stem.2861] [PMID: 29873142]
[164]
Ayuningtyas FD, Kim MH, Kino-oka M. Muscle lineage switching by migratory behaviour-driven epigenetic modifications of human mesenchymal stem cells on a dendrimer-immobilized surface. Acta Biomater 2020; 106: 170-80.
[http://dx.doi.org/10.1016/j.actbio.2020.02.026] [PMID: 32092429]
[165]
Mansour AA, Gafni O, Weinberger L, et al. The H3K27 demethylase Utx regulates somatic and germ cell epigenetic reprogramming. Nature 2012; 488(7411): 409-13.
[http://dx.doi.org/10.1038/nature11272] [PMID: 22801502]
[166]
Singhal N, Graumann J, Wu G, et al. Chromatin-remodeling components of the BAF complex facilitate reprogramming. Cell 2010; 141(6): 943-55.
[http://dx.doi.org/10.1016/j.cell.2010.04.037] [PMID: 20550931]
[167]
Doege CA, Inoue K, Yamashita T, et al. Early-stage epigenetic modification during somatic cell reprogramming by Parp1 and Tet2. Nature 2012; 488(7413): 652-5.
[http://dx.doi.org/10.1038/nature11333] [PMID: 22902501]
[168]
Costa Y, Ding J, Theunissen TW, et al. NANOG-dependent function of TET1 and TET2 in establishment of pluripotency. Nature 2013; 495(7441): 370-4.
[http://dx.doi.org/10.1038/nature11925] [PMID: 23395962]
[169]
Gao Y, Chen J, Li K, et al. Replacement of Oct4 by Tet1 during iPSC induction reveals an important role of DNA methylation and hydroxymethylation in reprogramming. Cell Stem Cell 2013; 12(4): 453-69.
[http://dx.doi.org/10.1016/j.stem.2013.02.005] [PMID: 23499384]
[170]
Ang YS, Tsai SY, Lee DF, et al. Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell 2011; 145(2): 183-97.
[http://dx.doi.org/10.1016/j.cell.2011.03.003] [PMID: 21477851]
[171]
Stadtfeld M, Hochedlinger K. Induced pluripotency: History, mechanisms, and applications. Genes Dev 2010; 24(20): 2239-63.
[http://dx.doi.org/10.1101/gad.1963910] [PMID: 20952534]
[172]
Sauer V, Roy-Chowdhury N, Guha C, Roy-Chowdhury J. Induced pluripotent stem cells as a source of hepatocytes. Curr Pathobiol Rep 2014; 2(1): 11-20.
[http://dx.doi.org/10.1007/s40139-013-0039-2] [PMID: 25650171]
[173]
Lai X, Li Q, Wu F, et al. Epithelial-mesenchymal transition and metabolic switching in cancer: Lessons from somatic cell reprogramming. Front Cell Dev Biol 2020; 8: 760.
[http://dx.doi.org/10.3389/fcell.2020.00760] [PMID: 32850862]
[174]
Takaishi M, Tarutani M, Takeda J, Sano S. Mesenchymal to epithelial transition induced by reprogramming factors attenuates the malignancy of cancer cells. PLoS One 2016; 11(6): e0156904.
[http://dx.doi.org/10.1371/journal.pone.0156904] [PMID: 27258152]
[175]
Liu X, Ding J, Meng L. Oncogene-induced senescence: A double edged sword in cancer. Acta Pharmacol Sin 2018; 39(10): 1553-8.
[http://dx.doi.org/10.1038/aps.2017.198] [PMID: 29620049]
[176]
Paranjpe SS, Veenstra GJC. Establishing pluripotency in early development. Biochim Biophys Acta 2015; 1849(6): 626-36.
[http://dx.doi.org/10.1016/j.bbagrm.2015.03.006] [PMID: 25857441]
[177]
Chin MH, Mason MJ, Xie W, et al. Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell 2009; 5(1): 111-23.
[http://dx.doi.org/10.1016/j.stem.2009.06.008] [PMID: 19570518]
[178]
Allshire RC, Madhani HD. Ten principles of heterochromatin formation and function. Nat Rev Mol Cell Biol 2018; 19(4): 229-44.
[http://dx.doi.org/10.1038/nrm.2017.119] [PMID: 29235574]
[179]
Lee JH, Hart SR, Skalnik DG. Histone deacetylase activity is required for embryonic stem cell differentiation. Genesis 2004; 38(1): 32-8.
[http://dx.doi.org/10.1002/gene.10250] [PMID: 14755802]
[180]
Polo JM, Anderssen E, Walsh RM, et al. A molecular roadmap of reprogramming somatic cells into iPS cells. Cell 2012; 151(7): 1617-32.
[http://dx.doi.org/10.1016/j.cell.2012.11.039] [PMID: 23260147]
[181]
Lewandowski J, Kurpisz M. Techniques of human embryonic stem cell and induced pluripotent stem cell derivation. Arch Immunol Ther Exp 2016; 64(5): 349-70.
[http://dx.doi.org/10.1007/s00005-016-0385-y] [PMID: 26939778]
[182]
van Leeuwen J, Berg DK, Pfeffer PL. Morphological and gene expression changes in cattle embryos from hatched blastocyst to early gastrulation stages after transfer of in vitro produced embryos. PLoS One 2015; 10(6): e0129787.
[http://dx.doi.org/10.1371/journal.pone.0129787] [PMID: 26076128]
[183]
Theunissen TW, Jaenisch R. Mechanisms of gene regulation in human embryos and pluripotent stem cells. Development 2017; 144(24): 4496-509.
[http://dx.doi.org/10.1242/dev.157404] [PMID: 29254992]
[184]
Takahashi K, Yamanaka S. A developmental framework for induced pluripotency. Development 2015; 142(19): 3274-85.
[http://dx.doi.org/10.1242/dev.114249] [PMID: 26443632]
[185]
Vierbuchen T, Ostermeier A, Pang ZP, Kokubu Y, Südhof TC, Wernig M. Direct conversion of fibroblasts to functional neurons by defined factors. Nature 2010; 463(7284): 1035-41.
[http://dx.doi.org/10.1038/nature08797] [PMID: 20107439]
[186]
Chen JX, et al. Inefficient reprogramming of fibroblasts into cardiomyocytes using Gata4, Mef2c, and Tbx5. Circulation research 2012; 111(1): 50-5.
[http://dx.doi.org/10.1161/CIRCRESAHA.112.270264]
[187]
Sun S, White RR, Fischer KE, Zhang Z, Austad SN, Vijg J. Inducible aging in Hydra oligactis implicates sexual reproduction, loss of stem cells, and genome maintenance as major pathways. Geroscience 2020; 42(4): 1119-32.
[http://dx.doi.org/10.1007/s11357-020-00214-z] [PMID: 32578072]
[188]
Yang MM, Wang J, Dong L, et al. Lack of association of C3 gene with uveitis: additional insights into the genetic profile of uveitis regarding complement pathway genes. Sci Rep 2017; 7(1): 879.
[http://dx.doi.org/10.1038/s41598-017-00833-1] [PMID: 28408754]
[189]
Yang N, Zuchero JB, Ahlenius H, et al. Generation of oligodendroglial cells by direct lineage conversion. Nat Biotechnol 2013; 31(5): 434-9.
[http://dx.doi.org/10.1038/nbt.2564] [PMID: 23584610]
[190]
Weltner J, Balboa D, Katayama S, et al. Human pluripotent reprogramming with CRISPR activators. Nat Commun 2018; 9(1): 2643.
[http://dx.doi.org/10.1038/s41467-018-05067-x] [PMID: 29980666]
[191]
Aschheim K. Making neurons with microRNAs. Nat Biotechnol 2011; 29(8): 721-2.
[192]
Jayawardena T, Egemnazarov B, Finch E, Zhang L, Payne J, Pandya K. MicroRNA-mediated in vitro and in vivo direct reprogramming of cardiac fibroblasts to cardiomyocytes. Circ Res 2012; 110(11): 1465-73.
[193]
Yamamoto K, Kishida T, Sato Y, et al. Direct conversion of human fibroblasts into functional osteoblasts by defined factors. Proc Natl Acad Sci USA 2015; 112(19): 6152-7.
[http://dx.doi.org/10.1073/pnas.1420713112] [PMID: 25918395]
[194]
Xie H, Ye M, Feng R, Graf T. Stepwise reprogramming of B cells into macrophages. Cell 2004; 117(5): 663-76.
[http://dx.doi.org/10.1016/S0092-8674(04)00419-2] [PMID: 15163413]
[195]
Strumpf D, Mao C-A, Yamanaka Y, Ralston A, Chawengsaksophak K, Beck F. Cdx2 is required for correct cell fate specification and differentiation of trophectoderm in the mouse blastocyst. Development 2005; 132(9): 2093-102.
[http://dx.doi.org/10.1242/dev.01801] [PMID: 15788452]
[196]
Xu H, Tsang KS, Chan JCN, et al. The combined expression of Pdx1 and MafA with either Ngn3 or NeuroD improves the differentiation efficiency of mouse embryonic stem cells into insulin-producing cells. Cell Transplant 2013; 22(1): 147-58.
[http://dx.doi.org/10.3727/096368912X653057] [PMID: 22776709]
[197]
Guo Z, Zhang L, Wu Z, Chen Y, Wang F, Chen G. In vivo direct reprogramming of reactive glial cells into functional neurons after brain injury and in an Alzheimer’s disease model. Cell Stem Cell 2014; 14(2): 188-202.
[http://dx.doi.org/10.1016/j.stem.2013.12.001] [PMID: 24360883]
[198]
Pataskar A, Jung J, Smialowski P, et al. NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program. EMBO J 2016; 35(1): 24-45.
[http://dx.doi.org/10.15252/embj.201591206] [PMID: 26516211]
[199]
Galipeau J, Sensébé L. Mesenchymal stromal cells: Clinical challenges and therapeutic opportunities. Cell Stem Cell 2018; 22(6): 824-33.
[http://dx.doi.org/10.1016/j.stem.2018.05.004] [PMID: 29859173]
[200]
Karow M, Camp JG, Falk S, et al. Direct pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program. Nat Neurosci 2018; 21(7): 932-40.
[http://dx.doi.org/10.1038/s41593-018-0168-3] [PMID: 29915193]
[201]
Ahfeldt T, Schinzel RT, Lee YK, et al. Programming human pluripotent stem cells into white and brown adipocytes. Nat Cell Biol 2012; 14(2): 209-19.
[http://dx.doi.org/10.1038/ncb2411] [PMID: 22246346]
[202]
Liu XS, Wu H, Ji X, Stelzer Y, Wu X, Czauderna S. Editing DNA methylation in the mammalian genome. Cell 2016; 167(1): 233-47.
[http://dx.doi.org/10.1016/j.cell.2016.08.056]
[203]
Baumann V, Wiesbeck M, Breunig CT, et al. Targeted removal of epigenetic barriers during transcriptional reprogramming. Nat Commun 2019; 10(1): 2119.
[http://dx.doi.org/10.1038/s41467-019-10146-8] [PMID: 31073172]
[204]
Black JB, Adler AF, Wang HG, et al. Targeted epigenetic remodeling of endogenous loci by CRISPR/Cas9-based transcriptional activators directly converts fibroblasts to neuronal cells. Cell Stem Cell 2016; 19(3): 406-14.
[http://dx.doi.org/10.1016/j.stem.2016.07.001] [PMID: 27524438]
[205]
Hill PWS, Leitch HG, Requena CE, et al. Epigenetic reprogramming enables the transition from primordial germ cell to gonocyte. Nature 2018; 555(7696): 392-6.
[http://dx.doi.org/10.1038/nature25964] [PMID: 29513657]
[206]
Warren L, Wang J. Feeder‐free reprogramming of human fibroblasts with messenger RNA. Curr Protoc Stem Cell Biol 2013; 27(1): 4A.6.1-4A.6.27.
[http://dx.doi.org/10.1002/9780470151808.sc04a06s27]
[207]
Zhou H. Dissecting transcriptional control by Klf4 in somatic cell reprogramming UCLA Electronic Theses and Dissertations. Los Angeles University of California 2017.
[208]
Tian Z, Guo F, Biswas S, Deng W. Rationale and methodology of reprogramming for generation of induced pluripotent stem cells and induced neural progenitor cells. Int J Mol Sci 2016; 17(4): 594.
[http://dx.doi.org/10.3390/ijms17040594] [PMID: 27104529]
[209]
Rizzino A, Wuebben EL. Sox2/Oct4: A delicately balanced partnership in pluripotent stem cells and embryogenesis. Biochim Biophys Acta Gene Regul Mech 2016; 1859(6): 780-91.
[http://dx.doi.org/10.1016/j.bbagrm.2016.03.006] [PMID: 26992828]
[210]
Rizzino A. Sox2 and Oct‐3/4: A versatile pair of master regulators that orchestrate the self‐renewal and pluripotency of embryonic stem cells. Wiley Interdiscip Rev Syst Biol Med 2009; 1(2): 228-36.
[http://dx.doi.org/10.1002/wsbm.12] [PMID: 20016762]
[211]
Takahashi K, Tanabe K, Ohnuki M, et al. Induction of pluripotency in human somatic cells via a transient state resembling primitive streak-like mesendoderm. Nat Commun 2014; 5(1): 3678.
[http://dx.doi.org/10.1038/ncomms4678] [PMID: 24759836]
[212]
King HW, Klose RJ. The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells. eLife 2017; 6: e22631.
[http://dx.doi.org/10.7554/eLife.22631] [PMID: 28287392]
[213]
Respuela P, Nikolić M, Tan M, et al. Foxd3 promotes exit from naive pluripotency through enhancer decommissioning and inhibits germline specification. Cell Stem Cell 2016; 18(1): 118-33.
[http://dx.doi.org/10.1016/j.stem.2015.09.010] [PMID: 26748758]
[214]
Krishnakumar R, Chen AF, Pantovich MG, et al. FOXD3 regulates pluripotent stem cell potential by simultaneously initiating and repressing enhancer activity. Cell Stem Cell 2016; 18(1): 104-17.
[http://dx.doi.org/10.1016/j.stem.2015.10.003] [PMID: 26748757]
[215]
Iturbide A, Pascual-Reguant L, Fargas L, et al. LOXL2 oxidizes methylated TAF10 and controls TFIID-dependent genes during neural progenitor differentiation. Mol Cell 2015; 58(5): 755-66.
[http://dx.doi.org/10.1016/j.molcel.2015.04.012] [PMID: 25959397]
[216]
Hu K. Quick, coordinated and authentic reprogramming of ribosome biogenesis during iPSC reprogramming. Cells 2020; 9(11): 2484.
[http://dx.doi.org/10.3390/cells9112484] [PMID: 33203179]
[217]
Carey BW, Markoulaki S, Hanna JH, et al. Reprogramming factor stoichiometry influences the epigenetic state and biological properties of induced pluripotent stem cells. Cell Stem Cell 2011; 9(6): 588-98.
[http://dx.doi.org/10.1016/j.stem.2011.11.003] [PMID: 22136932]
[218]
Stadtfeld M, Apostolou E, Akutsu H, et al. Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells. Nature 2010; 465(7295): 175-81.
[http://dx.doi.org/10.1038/nature09017] [PMID: 20418860]
[219]
Han J, Yuan P, Yang H, et al. Tbx3 improves the germ-line competency of induced pluripotent stem cells. Nature 2010; 463(7284): 1096-100.
[http://dx.doi.org/10.1038/nature08735] [PMID: 20139965]
[220]
Jiang J, Lv W, Ye X, et al. Zscan4 promotes genomic stability during reprogramming and dramatically improves the quality of iPS cells as demonstrated by tetraploid complementation. Cell Res 2013; 23(1): 92-106.
[http://dx.doi.org/10.1038/cr.2012.157] [PMID: 23147797]
[221]
Zhao XY, Lv Z, Li W, Zeng F, Zhou Q. Production of mice using iPS cells and tetraploid complementation. Nat Protoc 2010; 5(5): 963-71.
[http://dx.doi.org/10.1038/nprot.2010.61] [PMID: 20431542]
[222]
Lengner CJ, Gimelbrant AA, Erwin JA, et al. Derivation of pre-X inactivation human embryonic stem cells under physiological oxygen concentrations. Cell 2010; 141(5): 872-83.
[http://dx.doi.org/10.1016/j.cell.2010.04.010] [PMID: 20471072]
[223]
Stadtfeld M, Apostolou E, Ferrari F, et al. Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all–iPS cell mice from terminally differentiated B cells. Nat Genet 2012; 44(4): 398-405 S1-S2.
[http://dx.doi.org/10.1038/ng.1110] [PMID: 22387999]
[224]
Yuan X, Wan H, Zhao X, Zhu S, Zhou Q, Ding S. Brief report: Combined chemical treatment enables Oct4-induced reprogramming from mouse embryonic fibroblasts. Stem Cells 2011; 29(3): 549-53.
[http://dx.doi.org/10.1002/stem.594] [PMID: 21425417]
[225]
Omole AE, Fakoya AOJ. Ten years of progress and promise of induced pluripotent stem cells: historical origins, characteristics, mechanisms, limitations, and potential applications. PeerJ 2018; 6: e4370.
[http://dx.doi.org/10.7717/peerj.4370] [PMID: 29770269]
[226]
Ahmadzadeh V, Farajnia S, Baghban R, Rahbarnia L, Zarredar H. CRISPR‐Cas system: Toward a more efficient technology for genome editing and beyond. J Cell Biochem 2019; 120(10): 16379-92.
[http://dx.doi.org/10.1002/jcb.29140] [PMID: 31219653]
[227]
Takahashi S, Kobayashi S, Hiratani I. Epigenetic differences between naïve and primed pluripotent stem cells. Cell Mol Life Sci 2018; 75(7): 1191-203.
[http://dx.doi.org/10.1007/s00018-017-2703-x] [PMID: 29134247]
[228]
Kojima Y, Kaufman-Francis K, Studdert JB, et al. The transcriptional and functional properties of mouse epiblast stem cells resemble the anterior primitive streak. Cell Stem Cell 2014; 14(1): 107-20.
[http://dx.doi.org/10.1016/j.stem.2013.09.014] [PMID: 24139757]
[229]
Graf T, Stadtfeld M. Heterogeneity of embryonic and adult stem cells. Cell Stem Cell 2008; 3(5): 480-3.
[http://dx.doi.org/10.1016/j.stem.2008.10.007] [PMID: 18983963]
[230]
Liu G, David BT, Trawczynski M, Fessler RG. Advances in pluripotent stem cells: history, mechanisms, technologies, and applications. Stem Cell Rev Rep 2020; 16(1): 3-32.
[http://dx.doi.org/10.1007/s12015-019-09935-x] [PMID: 31760627]
[231]
Volpato V, Webber C. Addressing variability in iPSC-derived models of human disease: Guidelines to promote reproducibility. Dis Model Mech 2020; 13(1): dmm042317.
[http://dx.doi.org/10.1242/dmm.042317] [PMID: 31953356]
[232]
Matoba S, Zhang Y. Somatic cell nuclear transfer reprogramming: mechanisms and applications. Cell Stem Cell 2018; 23(4): 471-85.
[http://dx.doi.org/10.1016/j.stem.2018.06.018] [PMID: 30033121]
[233]
Steichen C, Hannoun Z, Luce E, Hauet T, Dubart-Kupperschmitt A. Genomic integrity of human induced pluripotent stem cells: Reprogramming, differentiation and applications. World J Stem Cells 2019; 11(10): 729-47.
[http://dx.doi.org/10.4252/wjsc.v11.i10.729] [PMID: 31692979]
[234]
Schwartz SD, Tan G, Hosseini H, Nagiel A. Subretinal transplantation of embryonic stem cell–derived retinal pigment epithelium for the treatment of macular degeneration: An assessment at 4 years. Invest Ophthalmol Vis Sci 2016; 57(5): ORSFc1-9.
[http://dx.doi.org/10.1167/iovs.15-18681]
[235]
da Cruz L, Fynes K, Georgiadis O, et al. Phase 1 clinical study of an embryonic stem cell–derived retinal pigment epithelium patch in age-related macular degeneration. Nat Biotechnol 2018; 36(4): 328-37.
[http://dx.doi.org/10.1038/nbt.4114] [PMID: 29553577]
[236]
Kudo H, Wada H, Sasaki H, et al. Induction of macrophage-like immunosuppressive cells from mouse ES cells that contribute to prolong allogeneic graft survival. PLoS One 2014; 9(10): e111826.
[http://dx.doi.org/10.1371/journal.pone.0111826] [PMID: 25356669]
[237]
Sasaki H, Wada H, Baghdadi M, et al. New immunosuppressive cell therapy to prolong survival of induced pluripotent stem cell–derived allografts. Transplantation 2015; 99(11): 2301-10.
[http://dx.doi.org/10.1097/TP.0000000000000875] [PMID: 26360665]
[238]
Cai S, Hou J, Fujino M, et al. iPSC-derived regulatory dendritic cells inhibit allograft rejection by generating alloantigen-specific regulatory T cells. Stem Cell Reports 2017; 8(5): 1174-89.
[http://dx.doi.org/10.1016/j.stemcr.2017.03.020] [PMID: 28434942]

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