Open Access

Investigating cellular identity and manipulating cell fate using induced pluripotent stem cells

  • Tohru Sugawara1,
  • Koichiro Nishino2,
  • Akihiro Umezawa1 and
  • Hidenori Akutsu1Email author
Stem Cell Research & Therapy20123:8

DOI: 10.1186/scrt99

Published: 8 March 2012

Abstract

Induced pluripotent stem (iPS) cells, obtained from reprogramming somatic cells by ectopic expression of a defined set of transcription factors or chemicals, are expected to be used as differentiated cells for drug screening or evaluations of drug toxicity and cell replacement therapies. As pluripotent stem cells, iPS cells are similar to embryonic stem (ES) cells in morphology and marker expression. Several types of iPS cells have been generated using combinations of reprogramming molecules and/or small chemical compounds from different types of tissues. A comprehensive approach, such as global gene or microRNA expression analysis and whole genomic DNA methylation profiling, has demonstrated that iPS cells are similar to their embryonic counterparts. Considering the substantial variation among iPS cell lines reported to date, the safety and therapeutic implications of these differences should be thoroughly evaluated before they are used in cell therapies. Here, we review recent research defining the concept of standardization for iPS cells, their ability to differentiate and the identity of the differentiated cells.

The potential of stem cells and reprogramming

During mammalian development, cells in the developing fetus gradually become more committed to their specific lineage. The cellular differentiation process specializes to achieve a particular biological function in the adult, and the potential to differentiate is lost. Cellular differentiation has traditionally been thought of as a unidirectional process, during which a totipotent fertilized zygote becomes pluripotent, multipotent, and terminally differentiated, losing phenotypic plasticity (Figure 1). However, recent cloning experiments using nuclear transplantation have demonstrated that the epigenetic constraints imposed upon differentiation in mammalian oocytes can be released and the adult somatic nucleus restored to a totipotent embryonic state [1]. This process, a rewinding of the developmental clock, is termed nuclear reprogramming.
Figure 1

Hierarchical potential of stem cell development. A totipotent cell, such as a zygote and a blastomere of an early pre-implantation embryo, can give rise to all of the cell types in the whole body and the extraembryonic tissues. During mammalian development, pluripotent cells of the inner cell mass differentiate to give rise to lineage-committing stem cells and progenitor cells, and finally terminally differentiated cells by losing differential potential. Embryonic stem (ES) cells are spun off directly from the inner cell mass of blastocysts and induced pluripotent stem (iPS) cells are generated by reprogramming differentiated cells back to the pluripotent state. ES cells and iPS cells seem to have highly similar pluripotential properties.

Embryonic stem (ES) cells derived from the inner cell mass of the mammalian blastocyst, an early-stage embryo, were first established from mice by Evans and Kaufman in 1981 [2]. Approximately two decades later, a human ES (hES) cell line was established by Thomson and colleagues [3]. ES cells possess a nearly unlimited capacity for self-renewal and pluripotency: the ability to differentiate into cells of three germ layers. This unique property might be useful to generate a sufficient amount of any differentiated cell type for drug screening or evaluations of drug toxicity and for cell replacement therapy. In addition, pluripotent stem cells provide us with an opportunity to understand early human embryonic development and cellular differentiation. Pluripotent ES cells are spun off directly from pre-implantation embryos [25]. To induce the somatic cell back to a pluripotent state, a strategy such as nuclear transplantation is fraught with technical complications and ethical issues. Thus, the direct generation of pluripotent cells without the use of embryonic material has been deemed a more suitable approach that lends itself well to mechanistic analysis and has fewer ethical implications [6].

In a breakthrough experiment, Takahashi and Yamanaka [7] identified reprogramming factors normally expressed in ES cells, Oct3/4, Sox2, c-Myc, and Klf4, that were sufficient to reprogram mouse fibroblasts to become pluripotent stem cells closely resembling ES cells. Because they were induced by the expression of defined factors, these cells were termed induced pluripotent stem (iPS) cells [7]. Since this landmark report in 2006, the technology has been rapidly confirmed among a number of species, including humans [8, 9], rhesus monkeys [10], rats [11, 12], rabbits [13], pigs [14] and two endangered primates [15]. In addition, mouse iPS (miPS) cells can be derived from various cell types, including fibroblasts [7, 16], neural cells [17, 18], liver cells [19], pancreatic β cells [20], and terminally differentiated lymphocytes [21, 22]. Subsequently, human iPS (hiPS) cells have been derived from various readily accessible cell types, including skin fibroblasts [8, 9], keratinocytes [23], gingival fibroblasts [24], peripheral blood cells [25, 26], cord blood cells [27, 28] and hair follicle cells [29].

These products and systems for this state-of-the art technology provide useful platforms for disease modeling and drug discovery, and could enable autologous cell transplantation in the future. Given the methodologies for studying disease mechanisms, disease- and patient-specific iPS cells can be derived from patients. For applying novel reprogramming technologies to biomedical fields, we need to determine the essential features of iPS cells. In this review, we summarize the functional and molecular properties of iPS cells in comparison to ES cells in the undifferentiated state and with regard to differentiation efficiency. We also review evaluation for the types of differentiated cells derived from of iPS and ES cells and compare the functions of these.

Reprogramming methods and factors

Although the establishment of iPS cells from somatic cells is technically easier and simpler compared with nuclear transplantation, several variables should be considered due to variations in the reprogramming process, including the reprogramming factors used, the combinations of factors and the types of donor-parent cells. Each method has advantages and disadvantages, such as efficiency of reprogramming, safety, and complexity, with the process used affecting the quality of the resultant iPS cells. Initial generations of miPS and hiPS cells employed retroviral and lentiviral vectors [79] (Table 1), carrying the risk of both insertional mutagenesis and oncogenesis due to misexpression of the exogenous reprogramming factors, Oct3/4, Sox2, c-Myc, and Klf4. In particular, reactivation of c-Myc increases tumorigenicity in the chimeras and progeny mice, hindering clinical applications.
Table 1

Various methods used for reprogramming

Method

Factorsa

Sources

Enhancement factors

Adenovirus

OSKM

Mouse fibroblast and liver cells [77], human embryonic fibroblast cells [78]

 

Bacteriophage

OSKM

Mouse embryonic fibroblasts, human amniocytes [79]

 

Episomal vector

OSKMNL

Human foreskin fibroblasts [36]

SV40LT

  

Human fibroblasts, adipose stem cells, cod blood cells [80]

SV40LT, LIF, MEK/GSK3b/TGFBR inhibitor, HA-100/human

 

OSKM*L

Human dermal fibroblasts [81]

p53 shRNA

Lentivirus

OSKM

Mouse pancreatic b cells [20]

 
  

Human adult fibroblasts [82]

p53 siRNA, UTF1

  

Mouse B lymphocytes [21]

C/EBPa or Pax5 shRNA

 

OSNL

Human newborn foreskin [9]

 
  

Human fibroblasts [83]

SV40LT

 

OSKMNL

Human fibroblasts [84]

 
 

OSN

Gut mesentery-derived cells [85], human amnion-derived cells [86]

 
 

O

Human epidermal keratinocytes [87]

TGFBR/MEK1 inhibitor, PDK1 activator, sodium butyrate

Minicircle vector

OSNL

Human adipose stromal cells [37]

 

microRNA

miR-200c, 302a/b/c/d, 369-3p/5p

Human and mouse adipose stromal cells [64]

 

mRNA

OSNL

Human fibroblasts [88]

 
 

OSKM(L)

Primary human neonatal epidermal keratinocytes [40]

 

piggyBAC

OSKM

Human and mouse embryonic fibroblasts [89, 90]

 

Plasmid

OSKM

Mouse embryonic fibroblasts [35, 91]

 
 

OSNL

Human foreskin fibroblasts [92]

MEK inhibitor

Protein

OSKM

Mouse embryonic fibroblasts [38]

VPA

 

OSKM

Human fibroblasts [39]

 

Retrovirus

OSKM

Human fibroblasts [8], mouse fibroblasts [7], human keratinocytes [23], human peripheral blood cells [25]

 
  

Human fibroblasts, adipose stem cells [93]

Vitamin C, VPA

 

OSK

Adult human dermal fibroblasts [30]

 
  

Mouse embryonic fibroblasts [94]

Wnt3a

  

Rat liver progenitor cells [11]

MEK/ALK5/GSK3b inhibitor

  

Mouse embryonic fibroblasts [93]

Vitamin C

  

Mouse and human fibroblasts [32]

GLIS1

  

Mouse embryonic fibroblasts [95]

mmu-miR-106a/18b/20b/19b/92a/363 or 302a/302b/302c/302d/367

  

Human fibroblasts [96]

hsa-miR-302b or 372

 

OK

Mouse embryonic fibroblasts [97]

BIX01294, BayK8644

  

Neonatal human epidermal keratinocytes [98]

GSK3b inhibitor

 

O

Mouse neural stem cells [99]

 
  

Mouse fibroblasts [100]

GSK3b inhibitor, vitamin C, BMP4

 

hsa-miR-302a/b/c/d

Human skin cancer cells [101]

 

Sendai virus

OSKM

Human fibroblasts [33], human cord blood [102]

 

aO, OCT3/4; S, SOX2; K, KLF4; M, C-MYC; M*, L-MYC; N, NANOG; L, LIN28. ALK, anaplastic lymphoma kinase; BayK8644, L-type calcium channel agonist; BIX01294, histone methyltransferase inhibitor; BMP, bone morphogenetic protein; GSK, glycogen synthase kinase; GLIS, GLI (MIM 165220)-related Kruppel-like zinc finger; LIF, leukemia inhibitory factor; PDK, pyruvate dehydrogenase kinase; shRNA, short hairpin RNA; siRNA, small interfering RNA; TGFBR, transforming growth factor beta receptor; UTF, undifferentiated transcription factor; VPA, valproic acid (histone deacetylase inhibitor).

Since the initial report of iPS cell generation, modifications to the reprogramming process have been made in order to decrease the risk of tumorigenicity and increase reprogramming efficiency [3032]. Several small molecules and additional factors have been reported to enhance the reprogramming process and/or functionally replace the role of some of the transcription factors (Table 1). Small molecules are easy to use and do not result in permanent genome modifications, although iPS generation using only a set of small molecules has not been reported. Combining small molecule compounds with reprogramming factors would enhance reprogramming efficiency. Integration-free hiPS cells have been established using Sendai virus [33, 34], episomal plasmid vectors [35, 36], minicircle vectors [37], and direct protein [38, 39] or mRNA [40] delivery (Table 1). However, direct delivery of proteins or RNA requires multiple transfection steps with reprogramming factors compared to other viral integration methods.

iPS cells appear indistinguishable from ES cells

The key to generating iPS cells is to revert somatic cells to a pluripotent state that is molecularly and functionally equivalent to ES cells derived from blastocysts (Table 2). Reprogrammed iPS cells express endogenous transcription factors that are required for self-renewal and maintenance of pluripotency, such as OCT3/4, SOX2, and NANOG, and for unlimited proliferation potential, such as TERT [8, 9]. Telomeres were elongated in iPS cells compared to the parental differentiated cells in both humans and mice [41, 42]. In addition, cellular organelles such as mitochondria within hiPS cells were morphologically and functionally similar to those within ES cells [43]. The establishment of an ES cell-like epigenetic state is a critical step during the reprogramming of somatic cells to iPS cells and occurs through activation of endogenous pluripotency related genes. Bisulfite genomic sequencing has shown that the promoter regions of the pluripotency markers NANOG and OCT3/4 are significantly demethylated in both hiPS and hES cells [8, 44], and the heterogeneity of × chromosome inactivation in hiPS cells is similar to that in ES cells [45].
Table 2

Characteristics of human induced pluripotent stem cells compared to human embryonic stem cells

Variable factor

Characteristics

Characteristics of hiPS cells

Cell source

 

Without the use of embryonic material Enable autologous cell transplantation

Technique for the generation of iPS cells

 

Simply trans-activating several transcription factors and/or exposure to several chemical components

Variables due to reprogramming methods and/or donor-parental cells

Morphology

 

Flat and tightly packed colony identical to hES cells

Proliferation potency

 

Unlimited self-renewal identical to hES cells

Pluripotency

Genes

OCT3/4, NANOG, SOX2 expression identical to hES cells

 

Gene promoter

OCT3/4, NANOG demethylation identical to hES cells

 

Cell surface antigens

SSEA3, SSEA4, TRA-1-60, TRA-1-81 positive identical to hES cells

 

Teratoma formation

Differentiation into three germ layers similar to hES cells

X chromosome inactivation (XCI)

 

Heterogeneity (complete XCI, partial XCI, pre-XCI) similar to hES cells

Mitochondria

Genome

Accumulated mtDNA mutations transmitted from parental cells Genetic mutations during reprogramming

 

Morphology

Globular shape with only small christae similar to hES cells and ES cell-like distribution

 

Function

Expression of nuclear factors involved in mitochondrial biogenesis

Telomere

 

Telomere elongation and ES cell-like telomerase activity

Epigenetic profile

 

Retention of somatic memory and aberrant methylation during the reprogramming process

microRNAs

 

Up-regulation of miR-302 cluster identical to hES cells

ES, embryonic stem; hES, human embryonic stem; hiPS, human induced pluripotent stem; iPS, induced pluripotent stem; mtDNA, mitochondrial DNA; XCI, × chromosome inactivation.

In terms of multilineage differentiation capacity, miPS cells from various tissue types have been shown to be competent for germline chimeras [19, 32, 46]. It was shown that miPS cells generated viable mice via tetraploid complementation [47, 48]. In the mouse system, iPS cells retain a developmental pluripotency highly similar to that of mouse ES cells according to the most stringent tests. Although it has been generally assumed that autologous cells should be immune-tolerated by the recipient from whom the iPS cells were derived, Zhao and colleagues [49] reported that the transplantation of immature miPS cells induced a T-cell-dependent immune response even in a syngeneic mouse. This is an unexpected result but some issues need to be considered: the influence of the cell type of origin on the immunogenic properties of resultant iPS cells must be explored; undifferentiated iPSCs should never be used for medical applications; and the mechanism of aberrant gene expression should be determined [50].

To functionally assay hiPS cells, teratoma formation and histological analysis to confirm the presence of structures derived from all three germ layers are currently regarded as the most rigorous ways to prove pluripotency of human stem cells. Recently, Müller and colleagues [51] proposed the use of PluriTest, a bioinformatics assay for the prediction of stem cell pluripotency using microarray data. Such microarray-based gene expression and DNA methylation assays are low cost, save time and have been used to evaluate the differentiation efficiency of individual cell lines [52].

ES and iPS cells differ in their epigenetic signatures

Epigenetic modification of the genome ensures proper gene activation for maintaining the pluripotency of stem cells and also differentiation into proper functional cells [1]. It will be important to assess the epigenetic state of hiPS cells compared to donor parent cells and embryoderived hES cells. Analyzing epigenetic states, such as histone modifications and DNA methylation of selected key pluripotency genes, showed the chromatin state of iPS cells to be identical to that of ES cells upon reprogramming (reviewed in [53]).

Genome-wide analyses of histone methylation patterns have demonstrated that iPS cells were clearly distinguished from their origin and similar to ES cells in the mouse [54]. All of these analyses, however, reported some differentially methylated regions (DMRs) between ES and iPS cells. Recent studies found that miPS cell lines retained the residual signatures of DNA methylation of the parental cells [55, 56]. Additionally, some of the hyper-methylated regions in hiPS cells are also hyper-methylated in the original cells, meaning that an epigenetic memory is inherited during the reprogramming process through early passaging [57]. Parental cell-related DMRs and incomplete promoter DNA methylation contributed to aberrant gene expression profiles in iPS cells to some extent [58]. The other remaining DMRs appeared to be aberrantly methylated regions established in iPS cells during reprogramming that differ from both the parental cells and the ES cells. Nishino and colleagues [57] compared methylation profiles of six hiPS cell lines and two hES cell lines and reported that approximately 60% of DMRs were inherited and 40% were iPS-specific. Interestingly, most aberrant DMRs were hyper-methylated in iPS cell lines [57, 59]. Lister and colleagues [60] also compared methylation profiles in five hiPS cell lines and two hES cell lines and found that the hiPS cells shared megabase-scale DMRs proximal to centromeres and telomeres that display incomplete reprogramming of non-CpG methylation, and differences in CpG methylation and histone modifications in over a thousand DMRs between hES and hiPS cells. Although lots of studies have detected several DMRs shared between iPS and ES cells, no DMRs were found in all iPS cell lines.

microRNAs (miRNAs), which are also epigenetically regulated, play critical roles in gene regulation by targeting specific mRNAs for degradation or by suppressing their translation. Several studies recently reported the presence of unique clusters of miRNAs, such as the human and mouse miR-302 cluster in ES and iPS cells [61, 62]. These miRNAs enhance the transcription factor-mediated reprogramming process (Table 1). Furthermore, two independent groups generated human and mouse iPS cells by adding only miRNAs in the absence of any additional protein factors [63, 64]. Two reports have described a small number of differences in miRNA expression patterns between hiPS and hES cells [62, 65], although our preliminary analysis showed that miR-372 and miR-373 are expressed at similar levels in both hiPS and hES cells and they were not detected in parental cells.

Changes of epigenetic profiles in iPS cells during culture

It is possible that iPS cells vary in their epigenetic profiles and degree of pluripotency due to differential levels of reprogramming. Nishino and colleagues [66] investigated the effect of continuous passaging on DNA methylation profiles of seven hiPS cell lines derived from five cell types. Although de novo DMRs that differ between hES and hiPS cells appeared at each passage, their number decreased and they disappeared with passaging; therefore, the total number of DMRs that differ between ES and iPS cells decreased with passaging. Thus, continuous passaging of the iPS cells diminished the epigenetic differences between iPS and ES cells, implying that iPS cells lose the characteristics inherited from the parental cells and develop to very closely resemble ES cells over time [66]. They also confirmed that the transgenes were silenced at each passage examined, indicating that the number of DMRs that differed between ES and iPS cells decreased during the transgene-independent phase. This is consistent with a study by Chin and colleagues [67], who found that the gene expression profile of hiPS cells appeared to become more similar to that of hES cells upon extended passaging. Although comprehensive DNA methylation profiles have recently been generated for hiPS cells, it seems harder to determine common DMR sites during iPS reprogramming. There are three possible explanations for the many inconsistent results regarding iPS cell-specific DMRs: hiPS cells have only been analyzed at a single point of passage in almost all studies; inherited methylation from parental cells is non-synchronous and stochastic, much like aberrant methylation, rather than deterministic [66]; and the aberrant hyper-methylation at DMRs in iPS cells occurs 'stochastically' throughout the genome during passaging [66].

Genetic changes during reprogramming and extended culture

Genomic stability is critical for the clinical use of hiPS cells. The occurrence of genetic changes in hES cells is now well known as well as that the karyotypic changes observed are nonrandom and commonly affect only a few chromosomes [68]. Recent studies revealed that the reprogramming process and subsequent culture of iPS cells in vitro can induce genetic changes. Three types of genomic abnormalities were seen: aberrations of somatic cell origin, aberrations present in early passages but not of apparent somatic cell origin, and aberrations acquired during passaging. Notably, the high incidence of chromosome 12 duplications observed by Mayshar and colleagues [69] caused significant enrichment for cell cycle-related genes, such as NANOG and GDF3. Another study reported that regions close to pluripotency-associated genes were duplicated in multiple samples [70]. Selection during hiPS cell reprogramming, colony picking and subsequent culturing may be factors contributing to the accumulation of mutations.

Impact of epigenetic differences on pluripotency

One of the goals of using hiPS cells is to generate functional target cells for medical screening and therapeutic applications. For these applications, it must be evaluated thoroughly whether small DMRs among ES and iPS cells affect the competency, differentiation propensities, stability and safety of iPS cells. It remains to be elucidated how the degree of these differences contributes to the variance in pluripotency among ES and iPS cells. Analysis of iPS cells obtained from mouse fibroblasts and hematopoietic and myogenic cells demonstrated that cellular origin influences the potential of miPS cells to differentiate into embryoid bodies and different cell types in vitro. In a related study, Kim and colleagues [56] compared the ability to differentiate to blood lineages of iPS cells derived from fibroblasts, neural cells, hematopoietic cells and ES cells in the mouse system, and demonstrated consistent differences in blood-forming ability - that is, blood derivatives showed more robust hematopoiesis in vitro than neural derivatives. Therefore, low-passage iPS cells derived from different tissues harbor residual DNA methylation signatures characteristic of their somatic tissue of origin, which favors their differentiation along lineages related to the parental cell, while restricting alternative cell fates. Similarly, Miura and colleagues [71] demonstrated that differences in gene expression in miPS cells derived from different types of parental cells result in variations in teratoma formation. These studies demonstrate that reprogramming to generate iPS cells is a gradual process that modifies epigenetic profiles beyond the acquisition of a pluripotent state.

Prediction for pluripotency and differentiation preference

Significant variation has been also observed in the differentiation efficiency of various hES cell lines [72]. Incomplete DNA methylation of somatic cells regulates the efficiency of hiPS cell generation [58], and selection of parental cell types influences the propensity for differentiation [73, 74]. Such differences must be better understood before hES and hiPS cell lines can be confidently used for translational research. To predict a cell line's propensity to differentiate into the three germ layers, Bock and colleagues [52] performed DNA methylation mapping by genome-scale bisulfite sequencing and gene expression profiling using microarrays and quantified the propensity to form multiple lineages by utilizing a non-directed embryoid bodies formation assay and high-throughput transcript counting of 500 lineage marker genes in embryoid bodies using 20 hES cells lines and 12 hiPS cell lines over passages 15 to 30. They bioinformatically integrated these genomic assays into a scorecard that measures the quality and utility of any human pluripotent cell line. The resulting lineage scorecard pinpoints quantitative differences among cell-line-specific differentiation propensities. For example, one hES cell line that received a high score for endoderm differentiation performed well in directed endoderm differentiation, and other hES cell lines that received high scores for neural lineage differentiation efficiently differentiated into motor neurons. In addition, two hiPS lines that the scorecard predicted to have a low propensity to differentiate into the neural lineage were impaired in motor neuron-directed differentiation. On the other hand, other hiPS lines that the scorecard predicted to have a high propensity to differentiate into ectodermal and neural lineages were found to differentiate well into motor neurons. Therefore, the scorecard can detect lineage-specific differences in the differentiation propensities of a given cell line [52].

Functional assay for differentiated cells from iPS and ES cells

Although the propensity for differentiation could be predicted, it remains to be elucidated whether iPS cell-derived cells are functionally and molecularly the same as ES cell-derived cells. To address this issue, two studies conducted functional assays comparing differentiated neural cells derived from iPS cells to those derived from ES cells by marker gene expression and action potential measurements [75, 76]. There was some variation in efficiency and quantitative differences in motor neuron generation among the lines, but the treatment of neuroepithelial cells from pluripotent stem cells with retinoic acid and sonic hedgehog resulted in the generation of iPS and ES cell lines with a neuronal morphology that expressed TUJ1. In addition, electrophysiological recordings using whole-cell patch clamping showed inward and outward currents, and it was concluded that ES cell- and iPS cell-derived neurons are similarly functional at a physiological level. These studies demonstrated that the temporal course and gene-expression pattern during neuroepithelial cell differentiation and production of functional neurons were nearly identical between ES and iPS cells, regardless of the reprogramming method, cellular origin, and differences between iPS and ES cells. These findings raise hopes of applying human iPS cells to the modeling of diseases and potential autologous cell transplantation.

It is important to acquire scientific information on pluripotential stem cells for further applications, such as industrial and clinical uses. Pluripotent stem cells, including disease-specific stem cells, could be showcased with useful annotation data and the most appropriate cell lines could be selected (Figure 2).
Figure 2

Workflow for human iPS cell applications. 1. Selection: choosing donor parent tissue considering accessibility, efficiency of reprogramming, and differential propensity. It would be useful to evaluate the expression of somatic memory genes, such as C9orf64, which reduces the efficiency of induced pluripotent stem (iPS) cell generation [58]. 2. Showcasing/evaluation: provides annotated information on reprogramming methods, culture conditions, physical data on stem cells, and global data on DNA methylation, transcription and microRNAs (miRNAs). It is very informative to integrate the genetic and epigenetic and biological data, such as differential propensity [52, 76]. 3. Application: using annotation data, we can select the most appropriate iPS cell lines for our applications. Various hiPS cell lines (shown as differently shaded spheres) would be listed before further processing of the application. Valid cell lines (colored purple and blue) could be functionally and molecularly selected for appropriate applications, such as cell replacement therapy and/or drug screening.

Conclusion

Many issues have yet to be resolved before the results of stem cell research can benefit the public in the form of medical treatments. In this review, we have discussed the substantial variation observed among pluripotent stem cells, including transcriptional and epigenetic profiles in the undifferentiated state, the ability to differentiate into various types of cells, and the functional and molecular nature of embryoid body or stem cell-derived differentiated cells. These results suggest that most, but not all, iPS cell lines are indistinguishable from ES cell lines, even though there is a difference between the average ES cell and the average iPS cell. Thus, ES and iPS cells should not be regarded as one or two well-defined points in the cellular space but rather as two partially overlapping point clouds with inherent variability among both ES and iPS cell lines [52, 76]. Notably, human iPS cells seemed to be more variable than human ES cells. No single stem cell line may be equally powerful for deriving all cell types in vitro, implying that researchers would benefit from identifying the best cell lines for each application. Furthermore, for clinical use in the future, it is important to use both ES and iPS cells in research, and to standardize reprogramming methods, culture equipment and techniques and to optimize differentiation methods and evaluate the functions and tumorigenicity of differentiated cells.

Note

This article is part of a review series on Induced pluripotent stem cells. Other articles in the series can be found online at http://stemcellres.com/series/ipsc

Abbreviations

DMR: 

differentially methylated region

ES: 

embryonic stem

hES: 

human embryonic stem

hips: 

human induced pluripotent stem

iPS: 

induced pluripotent stem

miPS: 

mouse induced pluripotent stem

miRNA: 

microRNA.

Declarations

Acknowledgements

We apologize to those authors whose publications could not be mentioned here owing to space constraints. We are grateful to Dr D Egli for critical reading of this manuscript, Y Suehiro for preparing figures, and other members of our laboratory for stimulating discussion. This work was supported by grants from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan; a grant from the Ministry of Health, Labour and Welfare Sciences (MHLW) to HA, AU; a Grant-in-aid for Scientific Research (21390456) to HA, and (22770233) to TS; a grant from New Energy and Industrial Technology Development Organization (NEDO) in Japan given to HA; and a grant from JST-CREST given to HA.

Authors’ Affiliations

(1)
Department of Reproductive Biology, Center for Regenerative Medicine, National Institute for Child Health and Development
(2)
Faculty of Agriculture, Laboratory of Veterinary Biochemistry and Molecular Biology, University of Miyazaki

References

  1. Rideout WM, Eggan K, Jaenisch R: Nuclear cloning and epigenetic reprogramming of the genome. Science. 2001, 293: 1093-1098. 10.1126/science.1063206.PubMedGoogle Scholar
  2. Evans MJ, Kaufman MH: Establishment in culture of pluripotential cells from mouse embryos. Nature. 1981, 292: 154-156. 10.1038/292154a0.PubMedGoogle Scholar
  3. Thomson JA, Itskovitz-Eldor J, Shapiro SS, Waknitz MA, Swiergiel JJ, Marshall VS, Jones JM: Embryonic stem cell lines derived from human blastocysts. Science. 1998, 282: 1145-1147.PubMedGoogle Scholar
  4. Chung Y, Klimanskaya I, Becker S, Marh J, Lu SJ, Johnson J, Meisner L, Lanza R: Embryonic and extraembryonic stem cell lines derived from single mouse blastomeres. Nature. 2006, 439: 216-219. 10.1038/nature04277.PubMedGoogle Scholar
  5. Chung Y, Klimanskaya I, Becker S, Li T, Maserati M, Lu SJ, Zdravkovic T, Ilic D, Genbacev O, Fisher S, Krtolica A, Lanza R: Human embryonic stem cell lines generated without embryo destruction. Cell Stem Cell. 2008, 2: 113-117. 10.1016/j.stem.2007.12.013.PubMedGoogle Scholar
  6. Maherali N, Hochedlinger K: Guidelines and techniques for the generation of induced pluripotent stem cells. Cell Stem Cell. 2008, 3: 595-605. 10.1016/j.stem.2008.11.008.PubMedGoogle Scholar
  7. Takahashi K, Yamanaka S: Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell. 2006, 126: 663-676. 10.1016/j.cell.2006.07.024.PubMedGoogle Scholar
  8. Takahashi K, Tanabe K, Ohnuki M, Narita M, Ichisaka T, Tomoda K, Yamanaka S: Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell. 2007, 131: 861-872. 10.1016/j.cell.2007.11.019.PubMedGoogle Scholar
  9. Yu J, Vodyanik MA, Smuga-Otto K, Antosiewicz-Bourget J, Frane JL, Tian S, Nie J, Jonsdottir GA, Ruotti V, Stewart R, Slukvin II, Thomson JA: Induced pluripotent stem cell lines derived from human somatic cells. Science. 2007, 318: 1917-1920. 10.1126/science.1151526.PubMedGoogle Scholar
  10. Liu H, Zhu F, Yong J, Zhang P, Hou P, Li H, Jiang W, Cai J, Liu M, Cui K, Qu X, Xiang T, Lu D, Chi X, Gao G, Ji W, Ding M, Deng H: Generation of induced pluripotent stem cells from adult rhesus monkey fibroblasts. Cell Stem Cell. 2008, 3: 587-590. 10.1016/j.stem.2008.10.014.PubMedGoogle Scholar
  11. Li W, Wei W, Zhu S, Zhu J, Shi Y, Lin T, Hao E, Hayek A, Deng H, Ding S: Generation of rat and human induced pluripotent stem cells by combining genetic reprogramming and chemical inhibitors. Cell Stem Cell. 2009, 4: 16-19. 10.1016/j.stem.2008.11.014.PubMedGoogle Scholar
  12. Liao J, Cui C, Chen S, Ren J, Chen J, Gao Y, Li H, Jia N, Cheng L, Xiao H, Xiao L: Generation of induced pluripotent stem cell lines from adult rat cells. Cell Stem Cell. 2009, 4: 11-15. 10.1016/j.stem.2008.11.013.PubMedGoogle Scholar
  13. Honda A, Hirose M, Hatori M, Matoba S, Miyoshi H, Inoue K, Ogura A: Generation of induced pluripotent stem cells in rabbits. J Biol Chem. 2010, 285: 31362-31369. 10.1074/jbc.M110.150540.PubMed CentralPubMedGoogle Scholar
  14. Ezashi T, Telugu BP, Alexenko AP, Sachdev S, Sinha S, Roberts RM: Derivation of induced pluripotent stem cells from pig somatic cells. Proc Natl Acad Sci USA. 2009, 106: 10993-10998. 10.1073/pnas.0905284106.PubMed CentralPubMedGoogle Scholar
  15. Ben-Nun IF, Montague SC, Houck ML, Tran HT, Garitaonandia I, Leonardo TR, Wang YC, Charter SJ, Laurent LC, Ryder OA, Loring JF: Induced pluripotent stem cells from highly endangered species. Nat Methods. 2011, 8: 829-831. 10.1038/nmeth.1706.PubMedGoogle Scholar
  16. Wernig M, Meissner A, Foreman R, Brambrink T, Ku M, Hochedlinger K, Bernstein BE, Jaenisch R: In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature. 2007, 448: 318-324. 10.1038/nature05944.PubMedGoogle Scholar
  17. Eminli S, Utikal J, Arnold K, Jaenisch R, Hochedlinger K: Reprogramming of neural progenitor cells into induced pluripotent stem cells in the absence of exogenous Sox2 expression. Stem Cells. 2008, 26: 2467-2474. 10.1634/stemcells.2008-0317.PubMedGoogle Scholar
  18. Kim JB, Zaehres H, Wu G, Gentile L, Ko K, Sebastiano V, Arauzo-Bravo MJ, Ruau D, Han DW, Zenke M, Schöler HR: Pluripotent stem cells induced from adult neural stem cells by reprogramming with two factors. Nature. 2008, 454: 646-650. 10.1038/nature07061.PubMedGoogle Scholar
  19. Aoi T, Yae K, Nakagawa M, Ichisaka T, Okita K, Takahashi K, Chiba T, Yamanaka S: Generation of pluripotent stem cells from adult mouse liver and stomach cells. Science. 2008, 321: 699-702. 10.1126/science.1154884.PubMedGoogle Scholar
  20. Stadtfeld M, Brennand K, Hochedlinger K: Reprogramming of pancreatic beta cells into induced pluripotent stem cells. Curr Biol. 2008, 18: 890-894. 10.1016/j.cub.2008.05.010.PubMed CentralPubMedGoogle Scholar
  21. Hanna J, Markoulaki S, Schorderet P, Carey BW, Beard C, Wernig M, Creyghton Menno P, Steine EJ, Cassady JP, Foreman R, Lengner CJ, Dausman JA, Jaenisch R: Direct reprogramming of terminally differentiated mature B lymphocytes to pluripotency. Cell. 2008, 133: 250-264. 10.1016/j.cell.2008.03.028.PubMed CentralPubMedGoogle Scholar
  22. Eminli S, Foudi A, Stadtfeld M, Maherali N, T Ahfeldt, G Mostoslavsky, H Hock, K Hochedlinger: Differentiation stage determines potential of hematopoietic cells for reprogramming into induced pluripotent stem cells. Nat Genet. 2009, 41: 968-976. 10.1038/ng.428.PubMed CentralPubMedGoogle Scholar
  23. Aasen T, Raya A, Barrero MJ, Garreta E, Consiglio A, Gonzalez F, Vassena R, Bilic J, Pekarik V, Tiscornia G, Edel M, Boué S, Izpisúa Belmonte JC: Efficient and rapid generation of induced pluripotent stem cells from human keratinocytes. Nat Biotechnol. 2008, 26: 1276-1284. 10.1038/nbt.1503.PubMedGoogle Scholar
  24. Egusa H, Okita K, Kayashima H, Yu G, Fukuyasu S, Saeki M, Matsumoto T, Yamanaka S, Yatani H: Gingival fibroblasts as a promising source of induced pluripotent stem cells. PLoS One. 2010, 5: e12743-10.1371/journal.pone.0012743.PubMed CentralPubMedGoogle Scholar
  25. Loh YH, Agarwal S, Park IH, Urbach A, Huo H, Heffner GC, Kim K, Miller JD, Ng K, Daley GQ: Generation of induced pluripotent stem cells from human blood. Blood. 2009, 113: 5476-5479. 10.1182/blood-2009-02-204800.PubMed CentralPubMedGoogle Scholar
  26. Choi SM, Liu H, Chaudhari P, Kim Y, Cheng L, Feng J, Sharkis S, Ye Z, Jang YY: Reprogramming of EBV-immortalized B-lymphocyte cell lines into induced pluripotent stem cells. Blood. 2011, 118: 1801-1805. 10.1182/blood-2011-03-340620.PubMed CentralPubMedGoogle Scholar
  27. Haase A, Olmer R, Schwanke K, Wunderlich S, Merkert S, Hess C, Zweigerdt R, Gruh I, Meyer J, Wagner S, Maier LS, Han DW, Glage S, Miller K, Fischer P, Schöler HR, Martin U: Generation of induced pluripotent stem cells from human cord blood. Cell Stem Cell. 2009, 5: 434-441. 10.1016/j.stem.2009.08.021.PubMedGoogle Scholar
  28. Hu K, Yu J, Suknuntha K, Tian S, Montgomery K, Choi KD, Stewart R, Thomson JA, Slukvin II: Efficient generation of transgene-free induced pluripotent stem cells from normal and neoplastic bone marrow and cord blood mononuclear cells. Blood. 2011, 117: e109-119. 10.1182/blood-2010-07-298331.PubMed CentralPubMedGoogle Scholar
  29. Tsai SY, Bouwman BA, Ang YS, Kim SJ, Lee DF, Lemischka IR, Rendl M: Single transcription factor reprogramming of hair follicle dermal papilla cells to induced pluripotent stem cells. Stem Cells. 2011, 29: 964-971. 10.1002/stem.649.PubMedGoogle Scholar
  30. Nakagawa M, Koyanagi M, Tanabe K, Takahashi K, Ichisaka T, Aoi T, Okita K, Mochiduki Y, Takizawa N, Yamanaka S: Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts. Nat Biotechnol. 2008, 26: 101-106. 10.1038/nbt1374.PubMedGoogle Scholar
  31. Nakagawa M, Takizawa N, Narita M, Ichisaka T, Yamanaka S: Promotion of direct reprogramming by transformation-deficient Myc. Proc Natl Acad Sci USA. 2010, 107: 14152-14157. 10.1073/pnas.1009374107.PubMed CentralPubMedGoogle Scholar
  32. Maekawa M, Yamaguchi K, Nakamura T, Shibukawa R, Kodanaka I, Ichisaka T, Kawamura Y, Mochizuki H, Goshima N, Yamanaka S: Direct reprogramming of somatic cells is promoted by maternal transcription factor Glis1. Nature. 2011, 474: 225-229. 10.1038/nature10106.PubMedGoogle Scholar
  33. Fusaki N, Ban H, Nishiyama A, Saeki K, Hasegawa M: Efficient induction of transgene-free human pluripotent stem cells using a vector based on Sendai virus, an RNA virus that does not integrate into the host genome. Proc Jpn Acad Ser B Phys Biol Sci. 2009, 85: 348-362. 10.2183/pjab.85.348.PubMed CentralPubMedGoogle Scholar
  34. Nishimura K, Sano M, Ohtaka M, Furuta B, Umemura Y, Nakajima Y, Ikehara Y, Kobayashi T, Segawa H, Takayasu S, Sato H, Motomura K, Uchida E, Kanayasu-Toyoda T, Asashima M, Nakauchi H, Yamaguchi T, Nakanishi M: Development of defective and persistent Sendai virus vector: a unique gene delivery/expression system ideal for cell reprogramming. J Biol Chem. 2011, 286: 4760-4771. 10.1074/jbc.M110.183780.PubMed CentralPubMedGoogle Scholar
  35. Okita K, Nakagawa M, Hyenjong H, Ichisaka T, Yamanaka S: Generation of mouse induced pluripotent stem cells without viral vectors. Science. 2008, 322: 949-953. 10.1126/science.1164270.PubMedGoogle Scholar
  36. Yu J, Hu K, Smuga-Otto K, Tian S, Stewart R, Slukvin II, Thomson JA: Human induced pluripotent stem cells free of vector and transgene sequences. Science. 2009, 324: 797-801. 10.1126/science.1172482.PubMed CentralPubMedGoogle Scholar
  37. Jia F, Wilson KD, Sun N, Gupta DM, Huang M, Li Z, Panetta NJ, Chen ZY, Robbins RC, Kay MA, Longaker MT, Wu JC: A nonviral minicircle vector for deriving human iPS cells. Nat Methods. 2010, 7: 197-199. 10.1038/nmeth.1426.PubMed CentralPubMedGoogle Scholar
  38. Zhou H, Wu S, Joo JY, Zhu S, Han DW, Lin T, Trauger S, Bien G, Yao S, Zhu Y, Siuzdak G, Schöler HR, Duan L, Ding S: Generation of induced pluripotent stem cells using recombinant proteins. Cell Stem Cell. 2009, 4: 381-384. 10.1016/j.stem.2009.04.005.PubMedGoogle Scholar
  39. Kim D, Kim CH, Moon JI, Chung YG, Chang MY, Han BS, Ko S, Yang E, Cha KY, Lanza R, Kim KS: Generation of human induced pluripotent stem cells by direct delivery of reprogramming proteins. Cell Stem Cell. 2009, 4: 472-476. 10.1016/j.stem.2009.05.005.PubMed CentralPubMedGoogle Scholar
  40. Warren L, Manos PD, Ahfeldt T, Loh YH, Li H, Lau F, Ebina W, Mandal PK, Smith ZD, Meissner A, Daley GQ, Brack AS, Collins JJ, Cowan C, Schlaeger TM, Rossi DJ: Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell. 2010, 7: 618-630. 10.1016/j.stem.2010.08.012.PubMed CentralPubMedGoogle Scholar
  41. Marion RM, Strati K, Li H, Tejera A, Schoeftner S, Ortega S, Serrano M, Blasco MA: Telomeres acquire embryonic stem cell characteristics in induced pluripotent stem cells. Cell Stem Cell. 2009, 4: 141-154. 10.1016/j.stem.2008.12.010.PubMedGoogle Scholar
  42. Suhr ST, Chang EA, Rodriguez RM, Wang K, Ross PJ, Beyhan Z, Murthy S, Cibelli JB: Telomere dynamics in human cells reprogrammed to pluripotency. PLoS One. 2009, 4: e8124-10.1371/journal.pone.0008124.PubMed CentralPubMedGoogle Scholar
  43. 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: 721-733. 10.1002/stem.404.PubMedGoogle Scholar
  44. Park IH, Zhao R, West JA, Yabuuchi A, Huo H, Ince TA, Lerou PH, Lensch MW, Daley GQ: Reprogramming of human somatic cells to pluripotency with defined factors. Nature. 2008, 451: 141-146. 10.1038/nature06534.PubMedGoogle Scholar
  45. Bruck T, Benvenisty N: Meta-analysis of the heterogeneity of × chromosome inactivation in human pluripotent stem cells. Stem Cell Res. 2011, 6: 187-193. 10.1016/j.scr.2010.12.001.PubMedGoogle Scholar
  46. Okita K, Ichisaka T, Yamanaka S: Generation of germline-competent induced pluripotent stem cells. Nature. 2007, 448: 313-317. 10.1038/nature05934.PubMedGoogle Scholar
  47. Zhao XY, Li W, Lv Z, Liu L, Tong M, Hai T, Hao J, Guo CL, Ma QW, Wang L, Zeng F, Zhou Q: iPS cells produce viable mice through tetraploid complementation. Nature. 2009, 461: 86-90. 10.1038/nature08267.PubMedGoogle Scholar
  48. Boland MJ, Hazen JL, Nazor KL, Rodriguez AR, Gifford W, Martin G, Kupriyanov S, Baldwin KK: Adult mice generated from induced pluripotent stem cells. Nature. 2009, 461: 91-94. 10.1038/nature08310.PubMedGoogle Scholar
  49. Zhao T, Zhang ZN, Rong Z, Xu Y: Immunogenicity of induced pluripotent stem cells. Nature. 2011, 474: 212-215.PubMedGoogle Scholar
  50. Okita K, Nagata N, Yamanaka S: Immunogenicity of induced pluripotent stem cells. Circ Res. 2011, 109: 720-721. 10.1161/RES.0b013e318232e187.PubMedGoogle Scholar
  51. Müller FJ, Schuldt BM, Williams R, Mason D, Altun G, Papapetrou EP, Danner S, Goldmann JE, Herbst A, Schmidt NO, Aldenhoff JB, Laurent LC, Loring JF: A bioinformatic assay for pluripotency in human cells. Nat Methods. 2011, 8: 315-317. 10.1038/nmeth.1580.PubMed CentralPubMedGoogle Scholar
  52. Bock C, Kiskinis E, Verstappen G, Gu H, Boulting G, Smith ZD, Ziller M, Croft GF, Amoroso MW, Oakley DH, Gnirke A, Eggan K, Meissner A: Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell. 2011, 144: 439-452. 10.1016/j.cell.2010.12.032.PubMed CentralPubMedGoogle Scholar
  53. Meissner A: Epigenetic modifications in pluripotent and differentiated cells. Nat Biotechnol. 2010, 28: 1079-1088. 10.1038/nbt.1684.PubMedGoogle Scholar
  54. Maherali N, Sridharan R, Xie W, Utika J, Eminli S, Arnold K, Stadtfeld M, Yachechko R, Tchieu J, Jaenisch R, Plath K, Hochedlinger K: Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell. 2007, 1: 55-70. 10.1016/j.stem.2007.05.014.PubMedGoogle Scholar
  55. Polo JM, Liu S, Figueroa ME, Kulalert W, Eminli S, Tan KY, Apostolou E, Stadtfeld M, Li Y, Shioda T, Natesan S, Wagers AJ, Melnick A, Evans T, Hochedlinger K: Cell type of origin infl uences the molecular and functional properties of mouse induced pluripotent stem cells. Nat Biotechnol. 2010, 28: 848-855. 10.1038/nbt.1667.PubMed CentralPubMedGoogle Scholar
  56. Kim K, Doi A, Wen B, Ng K, Zhao R, Cahan P, Kim J, Aryee MJ, Ji H, Ehrlich LI, Yabuuchi A, Takeuchi A, Cunniff KC, Hongguang H, McKinney-Freeman S, Naveiras O, Yoon TJ, Irizarry RA, Jung N, Seita J, Hanna J, Murakami P, Jaenisch R, Weissleder R, Orkin SH, Weissman IL, Feinberg AP, Daley GQ: Epigenetic memory in induced pluripotent stem cells. Nature. 2010, 467: 285-290. 10.1038/nature09342.PubMed CentralPubMedGoogle Scholar
  57. Nishino K, Toyoda M, Yamazaki-Inoue M, Makino H, Fukawatase Y, Chikazawa E, Takahashi Y, Miyagawa Y, Okita H, Kiyokawa N, Akutsu H, Umezawa A: Defining hypo-methylated regions of stem cell-specific promoters in human iPS cells derived from extra-embryonic amnions and lung fibroblasts. PLoS ONE. 2010, 5: e13017-10.1371/journal.pone.0013017.PubMed CentralPubMedGoogle Scholar
  58. Ohi Y, Qin H, Hong C, Blouin L, Polo JM, Guo T, Qi Z, Downey SL, Manos PD, Rossi DJ, Yu J, Hebrok M, Hochedlinger K, Costello JF, Song JS, Ramalho-Santos M: Incomplete DNA methylation underlies a transcriptional memory of somatic cells in human iPS cells. Nat Cell Biol. 2011, 13: 541-549. 10.1038/ncb2239.PubMed CentralPubMedGoogle Scholar
  59. Doi A, Park IH, Wen B, Murakami P, Aryee MJ, Irizarry R, Herb B, Ladd-Acosta C, Rho J, Loewer S, Miller J, Schlaeger T, Daley GQ, Feinberg AP: Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet. 2009, 41: 1350-1353. 10.1038/ng.471.PubMed CentralPubMedGoogle Scholar
  60. Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, R O'Malley, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, Evans RM, Ecker JR: Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 2011, 471: 68-73. 10.1038/nature09798.PubMed CentralPubMedGoogle Scholar
  61. Suh MR, Lee Y, Kim JY, Kim SK, Moon SH, Lee JY, Cha KY, Chung HM, Yoon HS, Moon SY, Kim VN, Kim KS: Human embryonic stem cells express a unique set of microRNAs. Dev Biol. 2004, 270: 488-498. 10.1016/j.ydbio.2004.02.019.PubMedGoogle Scholar
  62. Wilson KD, Venkatasubrahmanyam S, Jia F, Sun N, Butte AJ, Wu JC: MicroRNA profiling of human-induced pluripotent stem cells. Stem Cells Dev. 2009, 18: 749-758. 10.1089/scd.2008.0247.PubMed CentralPubMedGoogle Scholar
  63. Anokye-Danso F, Trivedi CM, Juhr D, Gupta M, Cui Z, Tian Y, Zhang Y, Yang W, Gruber PJ, Epstein JA, Morrisey EE: Highly efficient miRNA-mediated reprogramming of mouse and human somatic cells to pluripotency. Cell Stem Cell. 2011, 8: 367-388.Google Scholar
  64. Miyoshi N, Ishii H, Nagano H, Haraguchi N, Dewi DL, Kano Y, Nishikawa S, Tanemura M, Mimori K, Tanaka F, Saito T, Nishimura J, Takemasa I, Mizushima T, Ikeda M, Yamamoto H, Sekimoto M, Doki Y, Mori M: Reprogramming of mouse and human cells to pluripotency using mature microRNAs. Cell Stem Cell. 2011, 8: 633-638. 10.1016/j.stem.2011.05.001.PubMedGoogle Scholar
  65. Chin MH, Mason MJ, Xie W, Volinia S, Singer M, Peterson C, Ambartsumyan G, Aimiuwu O, Richter L, Zhang J, Khvorostov I, Ott V, Grunstein M, Lavon N, Benvenisty N, Croce CM, Clark AT, Baxter T, Pyle AD, Teitell MA, Pelegrini M, Plath K, Lowry WE: Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell. 2009, 5: 111-123. 10.1016/j.stem.2009.06.008.PubMed CentralPubMedGoogle Scholar
  66. Nishino K, Toyoda M, Yamazaki-Inoue M, Fukawatase Y, Chikazawa E, Sakaguchi H, Akutsu H, Umezawa A: DNA methylation dynamics in human induced pluripotent stem cells over time. PLoS Genet. 2011, 7: e1002085-10.1371/journal.pgen.1002085.PubMed CentralPubMedGoogle Scholar
  67. Chin MH, Pellegrini M, Plath K, Lowry WE: Molecular analyses of human induced pluripotent stem cells and embryonic stem cells. Cell Stem Cell. 2010, 7: 263-269. 10.1016/j.stem.2010.06.019.PubMed CentralPubMedGoogle Scholar
  68. Baker DEC, Harrison NJ, Maltby E, Smith K, Moore HD, Shaw PJ, Heath PR, Holden H, Andrews PW: Adaptation to culture of human embryonic stem cells and oncogenesis in vivo. Nat Biotechnol. 2007, 25: 207-215. 10.1038/nbt1285.PubMedGoogle Scholar
  69. Mayshar Y, Ben-David U, Lavon N, Biancotti J-C, Yakir B, Clark AT, Plath K, Lowry WE, Benvenisty N: Identification and classification of chromosomal aberrations in human induced pluripotent stem cells. Cell Stem Cell. 2010, 7: 521-531. 10.1016/j.stem.2010.07.017.PubMedGoogle Scholar
  70. Laurent LC, Ulitsky I, Slavin I, Tran H, Schork A, Morey R, Lynch C, Harness JV, Lee S, Barrero MJ, Ku S, Martynova M, Semechkin R, Galat V, Gottesfeld J, Izpisua Belmonte JC, Murry C, Keirstead HS, Park HS, Schmidt U, Laslett AL, Muller FJ, Nievergelt CM, Shamir R, Loring JF: 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: 106-118. 10.1016/j.stem.2010.12.003.PubMed CentralPubMedGoogle Scholar
  71. Miura K, Okada Y, Aoi T, Okada A, Takahashi K, Okita K, Nakagawa M, Koyanagi M, Tanabe K, Ohnuki M, Ogawa D, Ikeda E, Okano H, Yamanaka S: Variation in the safety of induced pluripotent stem cell lines. Nat Biotechnol. 2009, 27: 743-745. 10.1038/nbt.1554.PubMedGoogle Scholar
  72. Osafune K, Caron L, Borowiak M, Martinez RJ, Fitz-Gerald CS, Sato Y, Cowan CA, Chien KR, Melton DA: Marked differences in differentiation propensity among human embryonic stem cell lines. Nat Biotechnol. 2008, 26: 313-315. 10.1038/nbt1383.PubMedGoogle Scholar
  73. Hu Q, Friedrich AM, Johnson LV, Clegg DO: Memory in induced pluripotent stem cells: reprogrammed human retinal-pigmented epithelial cells show tendency for spontaneous redifferentiation. Stem Cells. 2010, 28: 1981-1991. 10.1002/stem.531.PubMedGoogle Scholar
  74. Bar-Nur O, Russ HA, Efrat S, Benvenisty N: Epigenetic memory and preferential lineage-specific differentiation in induced pluripotent stem cells derived from human pancreatic islet Beta cells. Cell Stem Cell. 2011, 9: 17-23. 10.1016/j.stem.2011.06.007.PubMedGoogle Scholar
  75. Hu BY, Weick JP, Yu J, Ma LX, Zhang XQ, Thomson JA, Zhang SC: Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency. Proc Natl Acad Sci USA. 2010, 107: 4335-4340. 10.1073/pnas.0910012107.PubMed CentralPubMedGoogle Scholar
  76. Boulting GL, Kiskinis E, Croft GF, Amoroso MW, Oakley DH, Wainger BJ, Williams DJ, Kahler DJ, Yamaki M, Davidow L, Rodolfa CT, Dimos JT, Mikkilineni S, MacDermott AB, Woolf CJ, Henderson CE, Wichterle H, Eggan K: A functionally characterized test set of human induced pluripotent stem cells. Nat Biotechnol. 2011, 29: 279-286. 10.1038/nbt.1783.PubMed CentralPubMedGoogle Scholar
  77. Stadtfeld M, Nagaya M, Utikal J, Weir G, Hochedlinger K: Induced pluripotent stem cells generated without viral integration. Science. 2008, 322: 945-959. 10.1126/science.1162494.PubMed CentralPubMedGoogle Scholar
  78. Zhou W, Freed CR: Adenoviral gene delivery can reprogram human fibroblasts to induced pluripotent stem cells. Stem Cells. 2009, 27: 2667-2674. 10.1002/stem.201.PubMedGoogle Scholar
  79. Ye L, Chang JC, Lin C, Qi Z, Yu J, Kan YW: Generation of induced pluripotent stem cells using site-specific integration with phage integrase. Proc Natl Acad Sci USA. 2010, 107: 19467-19472. 10.1073/pnas.1012677107.PubMed CentralPubMedGoogle Scholar
  80. Yu J, Chau KF, Vodyanik MA, Jiang J, Jiang Y: Efficient feeder-free episomal reprogramming with small molecules. PLoS One. 2011, 6: e17557-10.1371/journal.pone.0017557.PubMed CentralPubMedGoogle Scholar
  81. Okita K, Matsumura Y, Sato Y, Okada A, Morizane A, Okamoto S, Hong H, Nakagawa M, Tanabe K, Tezuka K, Shibata T, Kunisada T, Takahashi M, Takahashi J, Saji H, Yamanaka S: A more efficient method to generate integration-free human iPS cells. Nat Methods. 2011, 8: 409-412. 10.1038/nmeth.1591.PubMedGoogle Scholar
  82. Zhao Y, Yin X, Qin H, Zhu F, Liu H, Yang W, Zhang Q, Xiang C, Hou P, Song Z, Liu Y, Yong J, Zhang P, Cai J, Liu M, Li H, Li Y, Qu X, Cui K, Zhang W, Xiang T, Wu Y, Zhao Y, Liu C, Yu C, Yuan K, Lou J, Ding M, Deng H: Two supporting factors greatly improve the efficiency of human iPSC generation. Cell Stem Cell. 2008, 3: 475-479. 10.1016/j.stem.2008.10.002.PubMedGoogle Scholar
  83. Mali P, Ye Z, Hommond HH, Yu X, Lin J, Chen G, Zou J, Cheng L: Improved efficiency and pace of generating induced pluripotent stem cells from human adult and fetal fibroblasts. Stem Cells. 2008, 26: 1998-2005. 10.1634/stemcells.2008-0346.PubMedGoogle Scholar
  84. Liao J, Wu Z, Wang Y, Cheng L, Cui C, Gao Y, Chen T, Rao L, Chen S, Jia N, Dai H, Xin S, Kang J, Pei G, Xiao L: Enhanced efficiency of generating induced pluripotent stem (iPS) cells from human somatic cells by a combination of six transcription factors. Cell Res. 2008, 18: 600-603. 10.1038/cr.2008.51.PubMedGoogle Scholar
  85. Li Y, Zhao H, Lan F, Lee A, Chen L, Lin C, Yao Y, Li L: Generation of human-induced pluripotent stem cells from gut mesentery-derived cells by ectopic expression of OCT4/SOX2/NANOG. Cell Reprogram. 2010, 12: 237-247.PubMedGoogle Scholar
  86. Zhao HX, Li Y, Jin HF, Xie L, Liu C, Jiang F, Luo YN, Yin GW, Li Y, Wang J, Li LS, Yao YQ, Wang XH: Rapid and efficient reprogramming of human amnionderived cells into pluripotency by three factors OCT4/SOX2/NANOG. Differentiation. 2010, 80: 123-129. 10.1016/j.diff.2010.03.002.PubMedGoogle Scholar
  87. Zhu S, Li W, Zhou H, Wei W, Ambasudhan R, Lin T, Kim J, Zhang K, Ding S: Reprogramming of human primary somatic cells by OCT4 and chemical compounds. Cell Stem Cell. 2010, 7: 651-655. 10.1016/j.stem.2010.11.015.PubMedGoogle Scholar
  88. 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: 189-193. 10.1016/j.bbrc.2010.02.150.PubMedGoogle Scholar
  89. Kaji K, Norrby K, Paca A, Mileikovsky M, Mohseni P, Woltjen K: Virus-free induction of pluripotency and subsequent excision of reprogramming factors. Nature. 2009, 458: 771-775. 10.1038/nature07864.PubMed CentralPubMedGoogle Scholar
  90. Woltjen K, Michael IP, Mohseni P, Desai R, Mileikovsky M, Hämäläinen R, Cowling R, Wang W, Liu P, Gertsenstein M, Kaji K, Sung HK, Nagy A: piggyBac transposition reprograms fibroblasts to induced pluripotent stem cells. Nature. 2009, 458: 766-770. 10.1038/nature07863.PubMed CentralPubMedGoogle Scholar
  91. Gonzalez F, Barragan Monasterio M, Tiscornia G, Montserrat Pulido N, Vassena R, Batlle Morera L, Rodriguez Piza I, Izpisua Belmonte JC: Generation of mouse-induced pluripotent stem cells by transient expression of a single nonviral polycistronic vector. Proc Natl Acad Sci USA. 2009, 106: 8918-8922. 10.1073/pnas.0901471106.PubMed CentralPubMedGoogle Scholar
  92. Si-Tayeb K, Noto FK, Sepac A, Sedlic F, Bosnjak ZJ, Lough JW, Duncan SA: Generation of human induced pluripotent stem cells by simple transient transfection of plasmid DNA encoding reprogramming factors. BMC Dev Biol. 2010, 10: 81-10.1186/1471-213X-10-81.PubMed CentralPubMedGoogle Scholar
  93. Esteban MA, Wang T, Qin B, Yang J, Qin D, Cai J, Li W, Weng Z, Chen J, Ni S, Chen K, Li Y, Liu X, Xu J, Zhang S, Li F, He W, Labuda K, Song Y, Peterbauer A, Wolbank S, Redl H, Zhong M, Cai D, Zeng L, Pei D: Vitamin C enhances the generation of mouse and human induced pluripotent stem cells. Cell Stem Cell. 2010, 6: 71-79. 10.1016/j.stem.2009.12.001.PubMedGoogle Scholar
  94. Marson A, Foreman R, Chevalier B, Bilodeau S, Kahn M, Young RA, Jaenisch R: Wnt signaling promotes reprogramming of somatic cells to pluripotency. Cell Stem Cell. 2008, 3: 132-135. 10.1016/j.stem.2008.06.019.PubMed CentralPubMedGoogle Scholar
  95. Liao B, Bao X, Liu L, Feng S, Zovoilis A, Liu W, Xue Y, Cai J, Guo X, Qin B, Zhang R, Wu J, Lai L, Teng M, Niu L, Zhang B, Esteban MA, Pei D: MicroRNA cluster 302-367 enhances somatic cell reprogramming by accelerating a mesenchymal-to-epithelial transition. J Biol Chem. 2011, 286: 17359-17364. 10.1074/jbc.C111.235960.PubMed CentralPubMedGoogle Scholar
  96. Subramanyam D, Lamouille S, Judson RL, Liu JY, Bucay N, Derynck R, Blelloch R: Multiple targets of miR-302 and miR-372 promote reprogramming of human fibroblasts to induced pluripotent stem cells. Nat Biotechnol. 2011, 29: 443-448. 10.1038/nbt.1862.PubMed CentralPubMedGoogle Scholar
  97. Shi Y, Desponts C, Do JT, Hahm HS, Schöler HR, Ding S: Induction of pluripotent stem cells from mouse embryonic fibroblasts by Oct4 and Klf4 with small-molecule compounds. Cell Stem Cell. 2008, 3: 568-574. 10.1016/j.stem.2008.10.004.PubMedGoogle Scholar
  98. Li W, Zhou H, Abujarour R, Zhu S, Young Joo J, Lin T, Hao E, Schöler HR, Hayek A, Ding S: Generation of human-induced pluripotent stem cells in the absence of exogenous Sox2. Stem Cells. 2009, 27: 2992-3000.PubMed CentralPubMedGoogle Scholar
  99. Kim JB, Sebastiano V, Wu G, Araúzo-Bravo MJ, Sasse P, Gentile L, Ko K, Ruau D, Ehrich M, van den Boom D, Meyer J, Hübner K, Bernemann C, Ortmeier C, Zenke M, Fleischmann BK, Zaehres H, Schöler HR: Oct4-induced pluripotency in adult neural stem cells. Cell. 2009, 136: 411-419. 10.1016/j.cell.2009.01.023.PubMedGoogle Scholar
  100. Chen J, Liu J, Yang J, Chen Y, Chen J, Ni S, Song H, Zeng L, Ding K, Pei D: BMPs functionally replace Klf4 and support efficient reprogramming of mouse fibroblasts by Oct4 alone. Cell Res. 2011, 21: 205-212. 10.1038/cr.2010.172.PubMed CentralPubMedGoogle Scholar
  101. Lin SL, Chang DC, Chang-Lin S, Lin CH, Wu DT, Chen DT, Ying SY: Mir-302 reprograms human skin cancer cells into a pluripotent ES-cell-like state. RNA. 2008, 14: 2115-2124. 10.1261/rna.1162708.PubMed CentralPubMedGoogle Scholar
  102. Ban H, Nishishita N, Fusaki N, Tabata T, Saeki K, Shikamura M, Takada N, Inoue M, Hasegawa M, Kawamata S, Nishikawa S: Efficient generation of transgene-free human induced pluripotent stem cells (iPSCs) by temperature-sensitive Sendai virus vectors. Proc Natl Acad Sci USA. 2011, 108: 14234-14239. 10.1073/pnas.1103509108.PubMed CentralPubMedGoogle Scholar

Copyright

© BioMed Central Ltd 2012