Mitochondrial resetting and metabolic reprogramming ...

Biochimica et Biophysica Acta 1860 (2016) 686–693

Contents lists available at ScienceDirect

Biochimica et Biophysica Acta journal homepage: www.elsevier.com/locate/bbagen

Review

Mitochondrial resetting and metabolic reprogramming in induced pluripotent stem cells and mitochondrial disease modeling Yi-Chao Hsu a,1, Chien-Tsun Chen b,1, Yau-Huei Wei a,b,⁎ a b

Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, 252, Taiwan Department of Medicine, Mackay Medical College, New Taipei City, 252, Taiwan

a r t i c l e

i n f o

Article history: Received 5 June 2015 Received in revised form 13 January 2016 Accepted 14 January 2016 Available online 15 January 2016 Keywords: Induced pluripotent stem cells Glycolysis Metabolic reprogramming Mitochondrial disease

a b s t r a c t Background: Nuclear reprogramming with pluripotency factors enables somatic cells to gain the properties of embryonic stem cells. Mitochondrial resetting and metabolic reprogramming are suggested to be key early events in the induction of human skin fibroblasts to induced pluripotent stem cells (iPSCs). Scope of review: We review recent advances in the study of the molecular basis for mitochondrial resetting and metabolic reprogramming in the regulation of the formation of iPSCs. In particular, the recent progress in using iPSCs for mitochondrial disease modeling was discussed. Major conclusions: iPSCs rely on glycolysis rather than oxidative phosphorylation as a major supply of energy. Mitochondrial resetting and metabolic reprogramming thus play crucial roles in the process of generation of iPSCs from somatic cells. General significance: Neurons, myocytes, and cardiomyocytes are cells containing abundant mitochondria in the human body, which can be differentiated from iPSCs or trans-differentiated from fibroblasts. Generating these cells from iPSCs derived from skin fibroblasts of patients with mitochondrial diseases or by trans-differentiation with cell-specific transcription factors will provide valuable insights into the role of mitochondrial DNA heteroplasmy in mitochondrial disease modeling and serves as a novel platform for screening of drugs to treat patients with mitochondrial diseases. © 2016 Elsevier B.V. All rights reserved.

1. Embryonic stem cells and nuclear reprogramming Embryonic stem cells (ESCs) are isolated from the inner cell mass (ICM) of early-stage embryos and can proliferate unlimitedly and remain undifferentiated in vitro [1]. The essential characteristics of ESCs include the ability of self-renewal and pluripotent potential of differentiating into cells of all three germ layers, namely ectoderm, mesoderm, and endoderm [1]. Despite of their great potential in experimental and clinical applications, the ethical concerns have driven researchers to seek for alternatives to bypass the use of abandoned embryos for preparation of ESCs. Remarkably, Dr. Shinya Yamanaka made breakthrough in reprogramming mouse [2] and human fibroblasts [3] to acquire pluripotency using retroviral vectors to introduce 4 genes encoding Yamanaka factors: Oct4, Sox2, Klf4, and c-Myc. The induced pluripotent stem cells (iPSCs) thus obtained have overcome the problems caused by the limited supply and ethical issues of using human ESCs for clinical applications [2,3]. These findings suggest that the processes of cell differentiation and development are reversible. Adult differentiated cells ⁎ Corresponding author at: Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, 252, Taiwan. E-mail address: [email protected] (Y.-H. Wei). 1 These two authors made equal contributions.

http://dx.doi.org/10.1016/j.bbagen.2016.01.009 0304-4165/© 2016 Elsevier B.V. All rights reserved.

can be reprogrammed to regain pluripotency by delivering key pluripotent genes into these cells. Alternatively, direct reprogramming or trans-differentiation has been developed to directly reprogram fibroblasts into induced myoblasts [4], induced neuronal cells (iNs) [5–7], and induced cardiomyocytes [8–10] under defined conditions or by addition of specific factors, suggesting that trans-differentiation is feasible between two differentiated cell types. Thus, trans-differentiation is a dramatic process of lineage conversion as opposed to the generation of a cybrid, which exhibits a chimeric phenotype [7]. Furthermore, utilization of molecules to accelerate reprogramming can enhance the efficiency of trans-differentiation. As a proof of principle, a signaling adaptor protein, SH2B1, can enhance the neurite outgrowth of iNs and increase the efficiency of reprogramming [11]. Remarkably, both iPSC and trans-differentiation technologies are patient-specific without the risk of immune rejection. The iPSCs approach has the advantage of obtaining a larger number of specific differentiated cells. In addition, genetic defects can be corrected at the stage of iPSCs formation, meaning that differentiated cells made from iPSCs of a patient would no longer have the defect [12]. The disadvantage of the approach is its complexity, high cost, and the length of time required to produce iPSCs and to induce differentiation into the specialized cells to be used for transplantation. Furthermore, residual iPSCs in the transplant may cause tumors [13,14]. The advantages of direct reprogramming to desired

Y.-C. Hsu et al. / Biochimica et Biophysica Acta 1860 (2016) 686–693

cell types are the relative simplicity and short time requirement; thus the cost in a clinical setting is reduced. However, the retroviral or lentiviral vectors commonly used to introduce transcription factors are potentially dangerous to cause undesired genetic mutations. Therefore, alternative approaches such as using mRNAs [15], miRNAs [16], or Sendai virus [17] have been developed to overcome this drawback. Regardless of the potential obstacles of these techniques, generating specific lineages of cells from iPSCs or through direct reprogramming is still a promising endeavor which can provide a novel platform for disease modeling and drug screening. 2. Metabolic features of ESCs and iPSCs It has been shown that ESCs and iPSCs display metabolic profiles that are drastically different from their differentiated progenies [18]. The interest to understand the distinct feature of energy metabolism in ESCs and iPSCs has increased with a hope to gain insights of the role of metabolic reprogramming in the regulation of pluripotency. 2.1. Higher dependency on glycolysis for energy supply in ESCs and iPSCs Cells of the ICM have been shown to have a low mitochondrial membrane potential (Δψm) [19]. The Δψm of ESCs was also lower than that of differentiated cells such as neural stem cells (NSCs) and human dermal fibroblasts [20]. Furthermore, upregulation of mitochondrial biogenesis and decreased glycolytic flux were observed during the differentiation of human NSCs into motor neurons [21]. Specifically, peroxisome proliferator-activated receptor gamma coactivator 1-α (PGC1-α) is upregulated during neuronal differentiation of human NSCs. In contrast to differentiated cells, ESCs rely on a high rate of glycolysis for the supply of ATP [22] and exhibit changes in acetyl-CoA level and histone acetylation [23]. It was found that acetate or acetyl-CoA upstream inhibitor could block histone deacetylation and delay the differentiation of ESCs [23]. A switch from oxidative phosphorylation (OXPHOS) to glycolysis has been observed during reprogramming of somatic cells into iPSCs [24–26]. Reprogramming of human and mouse fibroblasts to iPSCs has been found to be accompanied by a decrease in oxygen consumption rate and an increase in lactate production [25]. Therefore, unraveling the metabolic differences between stem cells and differentiated cells may be helpful in the generation of iPSCs [27]. Interestingly, elevation of glycolysis was found to increase the reprogramming efficiency [26, 28], whereas a reduction in the activities of glycolytic enzymes decreased the efficiency of the generation of iPSCs. It was demonstrated that an increase in glycolysis in ESCs is accompanied by upregulation of pentose phosphate pathway. This suggests that ESCs and cancer cells share a common feature of metabolism, the Warburg effect [29,30], which shunts some of the glycolytic intermediates into the biosynthesis of amino acids, lipids, and nucleotides, and provides reducing equivalents for cell proliferation. It was suggested that hypoxia-inducible factor-1α (HIF-1α) facilitated the maintenance of pluripotency of ESCs and reprogramming of iPSCs [31]. However, whole-genome transcriptome analysis of ESCs in stirred-tank bioreactor cultures has provided somewhat different results. Under low-oxygen tension, glycolysis was found to increase to favor an anaerobic Warburg-effectlike phenotype, but hypoxic stress response was not observed, which is different from the observation made in two-dimensional culture of ESCs [32]. 2.2. Decrease of aerobic metabolism during reprogramming of somatic cells to iPSCs The global transcriptome profile of iPSCs is similar to that of ESCs and is very different from that of their parental fibroblasts [33,34]. Although there is no notable difference in the transcripts of nuclear DNA-encoded mitochondrial genes during iPSCs reprogramming, the expression levels of some of the nuclear genes involved in mitochondrial biogenesis are

687

decreased in iPSCs [18]. Glycolytic enzymes have been shown to be upregulated in iPSCs, but the expression levels of some glycolytic enzymes downstream of glucose-6-phosphate are decreased in iPSCs [25,35]. Mitochondrial resetting supports the bioenergetic transition of cells during reprogramming. Up-regulation of a number of glycolytic enzymes and reciprocal down-regulation of respiratory enzyme Complex I subunits were observed in iPSCs [28]. The decrease in the expression of Complex I subunits impaired the coupling between respiration and ATP synthesis, which resulted in a decrease of oxygen consumption rate in iPSCs [35]. By contrast, several subunits of Complexes III and V were reported to be up-regulated, which is thought to be a compensatory response to the decrease of respiratory function in iPSCs [28]. Nuclear reprogramming increases glycolytic flux by the transition of hexokinase from type I to type II. Specifically, hexokinase type II is localized to the mitochondria of iPSCs [25]. In addition, pyruvate dehydrogenase (PDH) activity is regulated by phosphorylation and dephosphorylation through PDH kinase (PDK) and phosphatase, respectively [35,36]. HIF1α facilitates the glycolytic switch and reprogramming of somatic cells through upregulation of glycolysis by activation of PDK and pyruvate kinase (PK) isoform M2 (PKM2). This scenario has been substantiated by the observation of an increase in the levels of PDK1, PDK3, and PKM2, and decrease of PK activity in iPSCs and human ESCs [37]. 2.3. Glycolysis and its metabolic intermediates are required for the formation of iPSCs The efficiency of ATP production by glycolysis is lower than that by OXPHOS; however, this can be compensated by increasing the glycolytic flux [38,39]. Limited nutrients in the culture medium decrease the glycolytic rate [30]. Therefore, the supplement of glutamine, glucose, and pyruvate in the culture medium helps cells utilize glycolysis to supply the majority of ATP. The methylation and expression of genes involved in glycolysis and oxidative phosphorylation are also changed during the formation of iPSCs [26]. In addition, biosynthesis of biomolecules requires ATP and other cofactors including carbon source and NADPH. Therefore, increase of glycolysis is required in proliferating cells [30], which can then synthesize the basic building blocks of fatty acids, amino acids, and nucleotides simultaneously. It has been shown that activation of glycolysis is required for nuclear reprogramming [28]. Moreover, acetyl-CoA is crucial for acetylation, which is involved in the regulation of gene expression and post-translational modification of proteins [40]. As a proof of principle, valproic acid and other inhibitors of histone deacetylases have been shown to increase the efficiency of nuclear reprogramming through histone acetylation, and thereby upregulate the transcription of target genes [35,41,42]. Thus, mitochondrial resetting during the formation of iPSCs may initiate changes in energy metabolism and lead to epigenetic modifications, which ultimately enable somatic cells to acquire the properties of unlimited self-renewal and pluripotency. 2.4. Mitochondrial DNA segregation during nuclear reprogramming It has been reported that nuclear reprogramming reduces the copy number of mtDNA [33,43] and may change the proportions of wildtype and mutated mtDNA, i.e., the degree of heteroplasmy [44], which determines the onset and severity of the symptoms of the mitochondrial disease. The degree of mtDNA heteroplasmy has been suggested to vary among different iPSC clones, indicating uneven mitochondrial segregation during reprogramming. Therefore, it is possible to obtain mtDNA mutation-free clones of iPSCs from patients with a pathogenic mtDNA mutation. Since the mechanism of trans-differentiation is very different from the reprogramming of iPSC, it remains to be elucidated whether the mtDNA heteroplasmy also occurs during the process of trans-differentiation. Further study of mtDNA heteroplasmy using trans-differentiated and iPSCs can simultaneously help elucidate the underlying mechanism of mitochondrial diseases (Fig. 1).

688

Y.-C. Hsu et al. / Biochimica et Biophysica Acta 1860 (2016) 686–693

3. Metabolic reprogramming in pluripotency and nuclear reprogramming 3.1. Mitochondrial biogenesis and ultrastructure in ESCs and iPSCs Mitochondria are responsible for production of the majority of ATP to support various biological functions in mammalian cells [45]. The number and function of mitochondria in different types of cells may vary in response to different energy needs. Mitochondrial biogenesis is regulated by several proteins encoded by nuclear DNA as well as by mtDNA, and is associated with the morphological and structural changes of mitochondria [35,46,47]. Nuclear reprogramming has been demonstrated to be accompanied by extensive remodeling of the structure and function of mitochondria [28]. Mitochondria are elongated, branched, tubular-shaped, and display well-developed profuse cristae in terminally differentiated cells [48,49]. It is worth mentioning that the properties of parental mitochondria have been shown to determine the reprogramming efficiency of both mouse [28,50] and human fibroblasts [25,33,51], suggesting that mitochondrial dynamics is important for the acquirement and maintenance of pluripotency in iPSCs. Mitochondria within iPSCs display features similar to those of mitochondria in ESCs [52–54], which include low copy number of mtDNA and low density of spherical mitochondria without well-developed cristae structure. Immature mitochondria are predominantly found in the perinuclear space in undifferentiated ESCs and iPSCs [35,55,56]. This perinuclear distribution of mitochondria is also observed in human hematopoietic stem cells [57], suggesting a characteristic mitochondrial feature of stem cells [35]. The immature mitochondria of iPSCs result in the down-regulation of mitochondrial function. Hyperpolarization of mitochondrial inner membranes has been demonstrated in iPSCs [28]. ESCs and iPSCs have a low demand for ATP synthesized by OXPHOS as well as a strong antioxidant defense system and low level of oxidative stress [33,43]. In addition, ESCs exhibit metabolic characteristics of a lower mitochondrial content and higher rate of glycolysis compared with mature cells differentiated from ESCs. A switch from OXPHOS to glycolysis as a major source of ATP has also been observed during reprogramming of fibroblasts to iPSCs [25,26,33].

Therefore, the decrease in biogenesis and function of mitochondria is crucial for reprogramming and maintenance of pluripotency in iPSCs [47]. Mitochondria display dynamic changes through fusion and fission [35,58]. In contrast to the abundance of mitochondria in parental fibroblasts, the number and function of mitochondria are decreased in the reprogrammed iPSCs. Furthermore, the mitochondria in the iPSCs exhibit spherical structures with a condensed matrix and loose cristae in comparison with those in their differentiated progenies [51]. These observations suggest that nuclear reprogramming modulates intracellular localization and distribution of mitochondria in cytoskeletal network and thereby resets mitochondrial ultrastructure and function to an ESC-like state. 3.2. Enhancement of nuclear reprogramming through metabolic resetting Overexpression of glycolytic genes and the increase in glycolytic rates have been shown to result in the immortalization of mature mouse fibroblasts [59]. Inhibition of a p53-related pathway can also indirectly stimulate glycolysis and enhance nuclear reprogramming [60]. Furthermore, hypoxia can activate glycolysis and enhance the efficiency of nuclear reprogramming [61,62]. Therefore, direct modulation of metabolism with agents that stimulate glycolysis and inhibit oxidative metabolism can increase the efficiency of reprogramming [63,64]. Specifically, induction of glycolysis by increasing glucose concentration in the medium can also enhance reprogramming efficiency to generate iPSCs. A combination of sodium butyrate, a transforming growth factor β receptor inhibitor (A-8301), and an inhibitor of MAPK and extracellular signal-regulated kinase (ERK) (PD0325901) with the increase of glycolysis by a PDHK1 activator (PS48) could successfully generate iPSCs by transfecting only Oct4 into human fibroblasts [35,65]. These observations suggest that optimizing energy metabolism is a potential approach to manipulate the reprogramming efficiency in the generation of iPSCs. Notably, the replacement of the mitochondria in somatic cells with mitochondria of stem cells may help the metabolic resetting and reprogramming. As a proof of principle, adult cardiomyocytes could be reprogrammed back to the progenitor-like state through partial cell fusion and mitochondrial transfer [66]. Consistently, reprogramming of

Fig. 1. Comparison of iPSCs-derived neurons and direct iNs reprogramming for mitochondrial disease modeling. The cartoon depicts the strategy for reprogramming of the patients' somatic cells containing mtDNA mutations through iPSC reprogramming or direct iNs reprogramming for in vitro generation of neural cells for disease modeling and drug screening. Studies on disease modeling and drug screening should be undertaken in parallel on iPSCs and their neural derivatives containing both heteroplasmic and homoplasmic mtDNA mutations. Due to the mtDNA heteroplasmy that exists among iPSC lines derived from patients' somatic cells with mtDNA mutations, the parallel use of iPSC reprogramming and direct iNs reprogramming are essential for mitochondrial disease modeling.

Y.-C. Hsu et al. / Biochimica et Biophysica Acta 1860 (2016) 686–693

mouse fibroblasts to iPSCs was more efficient when fibroblasts were cultured in a medium containing a higher concentration of glucose [28]. These observations indicate that glycolytic flux plays a critical role in the formation of iPSCs. Whether nuclear reprogramming factors change the metabolic status or the metabolic reprogramming leads to pluripotency of iPSCs remains a controversial issue [27]. Recent studies showed that up-regulation of glycolysis caused reactivation of pluripotency genes [31]. On the other hand, Oct4 alone can reprogram somatic cells into iPSCs [65] through upregulation of glycolytic enzymes, such as HK2 and PKM2, which are crucial for the control of glycolytic influx [67]. Furthermore, Lin28 has been demonstrated to regulate metabolism in different types of stem cells [68,69]. In particular, it was reported that REX1 is essential for Yamanaka factors to complete the reprogramming process by initiating a critical metabolic shift in the process of generation of iPSCs [70]. Moreover, c-Myc was demonstrated to potentiate the glycolytic status of derived iPSCs [71]. 4. Mitochondrial disease modeling through iPSCs Neurons in the central nervous system and cardiomyocytes in the heart are difficult to access in patients. However, establishing iPSCs from the skin fibroblasts of patients with neurological and cardiovascular diseases has made it possible to get patient-specific neurons and cardiomyocytes [72]. Thus, the generation of disease-specific iPSCs is promising for modeling ex vivo phenomena that occur in patients in vivo [73]. In particular, iPSCs derived from patients with cardiovascular and neurological diseases have been established and their applications discussed in recent review articles [74–77]. Mitochondrial defects can range from common diseases to rare genetic disorders [78–80]. Accumulation of mutations in mtDNA is a risk and harmful to vital cellular functions. Moreover, mtDNA suffers from a higher mutation rate than does the nuclear genome partly because of its close proximity to the ROS generated through electron transport chain [81]. Abnormal mitochondria that accumulate mutant mtDNA in affected tissues cause cellular dysfunction. Different degrees of disease severity caused by heteroplasmy of mtDNA have been observed between normal and defective mitochondria in tissue cells. The formation and accumulation of mtDNA mutations are complex processes, including the interplay of DNA replication, DNA damage and repair, purifying and selection of mtDNA, mitochondrial dynamics, mitophagy, and aging. Recently, iPSCs have been established from patients with mitochondrial diseases such as mitochondrial myopathy, encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) [80,82,83]. MELAS syndrome is one of the major clinical subgroups of mitochondrial diseases, which are caused by mutation of a single base pair in mtDNA [84]. Most (N80%) MELAS patients carry an A to G transition at the nucleotide position 3243 of mtDNA, denoted as A3243G mutation [85, 86]. MELAS patients present a broad spectrum of clinical features including seizures, stroke-like episodes, neurological disorders, sensorineural deafness, progressive muscle weakness, cardiomyopathy, and other symptoms. The estimated threshold of A3243G mutation required for impairing mitochondrial respiratory function in MELAS is 80% at the cellular level [87] and 70% in muscle fibers [88]. Fujikura et al. [83] generated iPSCs from two MELAS patients with diabetes. The MELASiPSCs exhibited a bimodal degree of heteroplasmy of mtDNA upon reprogramming, giving rise to iPSC clones free of mutation and with a high mutation load, respectively. They were unable to obtain any mutation-free parental fibroblasts, and iPSCs after long-term passage still maintained a constant proportion of mutated mtDNA, which indicate that the dramatic change of mtDNA mutation load must have occurred during the process of reprogramming. Hämäläinen et al. [89] demonstrated that neurons that had been differentiated from MELASiPSCs with a high proportion of mtDNA with A3243G mutation showed a predominant Complex I deficiency, indicating that iPSCs with certain proportions of mtDNA mutation may ideally recapitulate the tissuespecific mitochondrial dysfunction. Their findings provided promising

689

incentive for the development of iPSCs in mitochondrial disease modeling. Kodaira et al. [82] successfully established iPSCs from the primary culture of MELAS skin fibroblasts carrying 77.7% of mtDNA with A3243G mutation. They found that the proportions of A3243G mutation in MELAS-iPSC lines ranged from 3.6% to 99.4%. It was found that the fibroblasts derived from iPSCs with high levels of mtDNA heteroplasmy showed a deficiency of Complex I activity, but the fibroblasts derived from iPSCs with low mutation loads showed normal Complex I activity. These findings indicate that MELAS-iPSCs can be models for MELAS but the levels of mtDNA heteroplasmy and respiratory functions should be meticulously assessed. Folmes et al. [80] established MELAS-iPSCs from a MELAS patient with heteroplasmic G13513A mutation of mtDNA, but the mutation load of MELAS-iPSCs was gradually decreased during long-term passage. Ma et al. [90] recently generated several iPSC clones from patients with different mtDNA mutations, including A3243G, G13513A, and T8993G mutations. They further applied the somatic cell nuclear transfer (SCNT) technique to replace mutant mtDNA and create mutation-free iPSCs, and showed that the corrected iPSCs regained normal metabolic function. Furthermore, they utilized the SCNT technique to replace mutant mtDNA from homoplasmic T8993G skin fibroblasts to generate corrected Leigh-NT1 iPSCs [90]. In addition, Cherry et al. [91] generated iPSCs from patients with Pearson's syndrome (PS) who carried mtDNA deletions. PS-derived erythroid cells displayed high levels of large-scale deletions of mtDNA and abnormal iron accumulation, which is one of the key features of Pearson's syndrome. Because the degree of mtDNA heteroplasmy changed with cell passage, Cherry and coworkers further cloned and isolated the PSiPSCs without detectable levels of mtDNA deletions. Furthermore, as compared with the mtDNA deletion-free PS-iPSCs, the iPSCs carrying high proportions of deleted mtDNA showed abnormalities in mitochondrial function, hematopoietic differentiation, and cell growth. In addition to creating iPSCs from patients with pathogenic mtDNA mutations, researchers also tested the effects of mtDNA integrity on reprogramming and differentiation of iPSCs. Wahlestedt et al. [92] used the mutant mouse model with an error-prone DNA polymerase gamma to show that the reprogramming efficiency was not affected by a high level of mtDNA mutation (14.7-fold mutation as compared with the wild-type). However, the growth rate and differentiation capability were compromised in the iPSCs harboring high proportions of mutated mtDNA. These observations indicate that functional mitochondria are essential for the metabolic switch during differentiation of iPSCs, despite that the reprogramming is less affected by the mtDNA integrity. Additionally, iPSCs have been made from cells harboring mutations in nuclear genes that affect mitochondrial structure and/or function. Wang et al. [93] generated iPSCs from a patient with Barth syndrome with a mutation in the gene encoding tafazzin, which is associated with abnormalities of metabolism, structure, and function of mitochondria. Friedreich ataxia is also a mitochondrial disease affecting both the nervous and cardiac systems. This disease is caused by mutations in Frataxin protein, which is encoded by nuclear DNA and functions in mitochondria. Furthermore, only few reports have shown a mitochondrial defect in iPSCs made from Friedreich ataxia patients [94,95] (Table 1). On the basis of these reports, the disease-causing mtDNA mutations have been suggested to be randomly segregated in patient-derived iPSCs. Therefore, by using iPSCs to model mitochondrial diseases with specific features of cellular dysfunction, the degree of mtDNA heteroplasmy should be taken into consideration with special care. It remains unclear as to whether the mtDNA heteroplasmy in each iPSC clone is determined by the proportions of the mutated mtDNA in the parental fibroblasts and whether the mtDNA heteroplasmy is generated de novo during the reprogramming process [96,97]. However, the common observations that mutation-free iPSCs can be obtained at a relatively high frequency is a promising phenomenon for the application of iPSCs in cell therapy for patients harboring mtDNA mutations (Table 1).

690

Table 1 Mitochondrial DNA heteroplasmy in induced pluripotent stem cells and their differentiated progenies. MELAS

MELAS

MELAS

MELAS

MELAS

MELAS

Leigh syndrome

Pearson's syndrome

Non-specific

Barth syndrome

Friedreich ataxia

Mutation type

A3243G

A3243G

A3243G

A3243G

G13513A

G13513A

T8993G

tRNALeu(UUR) tRNALeu(UUR) (m) (m)

tRNALeu(UUR) (m)

tRNALeu(UUR) (m)

ND5 (m)

ND5 (m)

ATP6 (m)

PolG D257A PolG (m)

Frameshift and missense mutation Tafazzin (n)

GAA repeat

Affected gene in mitochondria (m) or the nucleus (n)

Parental cell Mutation load (%)

Fibroblasts 18–24 0, 51–87 Stable

Fibroblasts 21–35 ~0, N80 Stable

Fibroblasts 29 0, 33–100 –

Fibroblasts 77.7 3.6–99.4 Stable or increased

Fibroblasts 50 0, 50 Decreased

Fibroblasts 52 0, 29–87 –

Fibroblasts 84 0, 2–100 –

HSC (mouse) – 14.9-folda –

Fibroblasts – – –

Fibroblasts – – –

– Normal

Normal Increased

– –

– Variable

– Decreased

– –

– –

Deletion (10,949–13,449) ND4, ND5, tRNALeu(CUN), SAGY (m) Fibroblasts (BM) N95 55–70 Stable or decreased Decreased –

Normal Normal

– –

– Decreased

– Decreased – – –

– – – – Complex I deficiency in differentiated neurons

– Decreased – – Impaired CM differentiation

– – – – Complex I deficiency in differentiated fibroblasts

– Normal – – –

– Decreased – – –

– Decreased – – Impaired CM differentiation

Normal – Normal Decreased Reduced EB and teratoma formation

– – – – Lower ATP, lower FoF1 ATPase activity in CM

– – – – Impaired ATP production

Fujikura 2012 (83)

Hämäläinen 2013 (89)

Ma 2015 (90)

Kodaira 2015 (82)

Folmes 2013 (80)

Ma 2015 (90)

Ma 2015 (90)

Wahlestedt 2014 (92)

Wang 2014 (93)

Lee 2014 (94)

Parental cells iPSCs After passage

Reprogramming efficiency Mitochondrial mtDNA copy properties in number iPSCs Membrane potential Respiration ATP ROS Differentiation capacity of iPSCs

References

Decreased – – – Decreased proliferation, impaired hematopoiesis Cherry 2013 (91)

Abbreviations: ATPase, ATP synthase; BM, bone marrow; CM, cardiomyocyte; EB, embryonic body; HSC, hematopoietic stem cell; ND, NADH dehydrogenase; PolG, DNA polymerase γ; ROS, reactive oxygen species. a iPSCs derived from DNA polymerase γ mutant cells had 14.9-fold higher mutation frequency per base of mtDNA compared to the wild-type.

Frataxin (n)

Y.-C. Hsu et al. / Biochimica et Biophysica Acta 1860 (2016) 686–693

Mitochondrial disease

Y.-C. Hsu et al. / Biochimica et Biophysica Acta 1860 (2016) 686–693

5. Future perspectives 5.1. Drug development and testing using iPSCs It has been proposed that iPSC technology could facilitate drug development in different phases of clinical trial. Before phase I clinical trials, iPSC-derived differentiated cells, such as hepatocyte, cardiomyocytes, and neurons could be first tested for the drug-induced toxicity in respective tissue cells to identify the candidate drugs [98]. For the screening of drug-induced cardiotoxicity, high-throughput screening methods must be established to effectively decrease late-stage drug attrition [99]. Human iPSCs-derived cardiomyocytes were seeded in a sensor array to create an iPSCs-derived cardiomyocyte-based biosensor array with a beating pattern of cardiomyocytes [100]. Some arrhythmogenic drugs have been validated by using iPSC-derived cardiomyocytes [101,102]. Furthermore, iPSC technology could also be applied before phase II clinical trial to determine the drug responsiveness and help the stratification of patients with mitochondrial diseases [98]. For example, the generation of disease and control iPSCs from a large cohort of patients may facilitate the selection of responsive and non-responsive groups of patients, thus help initiate a phase II clinical trial only for the responsive subgroup of patients [98]. Therefore, the utilization of iPSC technology in mitochondrial disease modeling might change the rules of clinical trials for drug development in the future. 5.2. Prospects for iPSCs in regenerative mitochondrial medicine Using iPSC technology to create the autologous source for cell therapy is an attractive strategy for regenerative medicine. Currently, most of the iPSC-based cell therapies are still tested in laboratory animal models, such as sickle cell anemia [103], spinal cord injury [104,105], age-related macular degeneration (AMD) [106], Parkinson's disease [107,108], and in non-human primates [109–113]. However, it has been demonstrated that human iPSCs could be used as a source of retinal pigment epithelial (RPE) cells for the treatment of AMD [114–116]. And the first clinical trial is now ongoing in the RIKEN Center of Japan using human iPSC-derived RPE cells to treat AMD [13,109]. The iPSCbased cell therapy thus holds great promise for future treatment of human diseases. Clinically, mitochondrial diseases often involve multiple tissues. Despite mainly affecting the nervous system and skeletal muscles, all of which contain abundant mitochondria. A wide spectrum of mitochondrial diseases is caused by specific pathogenic mtDNA mutations, which can impair mitochondrial respiration and cause various abnormalities at the cellular and tissue levels [81]. The major obstacle in mitochondrial regenerative medicine lies in the nature of mtDNA heterogeneity. Traditionally, it is impossible to deplete mutated mtDNA in patients' mitochondria, unless using cytoplasm transfer technique. Fortunately, many researchers have reported that mtDNA mutation loads may vary dramatically during the process of reprogramming, ranging from mutation-free to more than 80% of mutations. These mutation-free iPSC clones are therefore of great value for clinical applications for patients with mitochondrial diseases. 5.3. The iPSCs consortium in Taiwan Recently, the Ministry of Science and Technology of Taiwan funded a National iPSCs Consortium Project to provide quality service for clinicians and biomedical researchers to establish disease-specific iPSCs. A unique pool of Taiwanese patients with definitive diagnosis will be recruited from major hospitals and medical centers in Taiwan. The iPSCs service consortium will focus on neurodegenerative diseases, mitochondrial diseases, retinal degenerative diseases, cardiomyopathy, anti-hepatitis drug resistance, renal toxicity, premature ovarian failure, infertility, and hematopoietic cell dysfunction. We have been funded to establish the iPSC clones from patients with mitochondrial diseases, which include CPEO,

691

MELAS and MERRF syndromes for the investigation of their differentiation potential towards neural cells and cardiomyocytes. We anticipate that this iPSCs Consortium will facilitate the development of cell models for study of important diseases and promote biomedical research and drug development in the near future. Transparency document The Transparency document associated with this article can be found, in online version. Acknowledgement Part of this review article was prepared on the basis of our studies supported by grants from the Ministry of Science and Technology (MOST) of Taiwan Government (MOST103-2314-B-715-001-MY2, MOST104-2314B-715-003-MY3 and MOST103-2321-B-715-001), intramural research grants from Mackay Medical College (MMC1012A10, MMC1012B13, RD1010061, RD1020021, RD1020088, MMC1031B05, RD1030006, RD1030098, RD1040109), and Mackay Memorial Hospital (MMH-MM10304, MMH-MM-10405, MMH-MM-10505). We thank Ms. Yun-Jun. Lou for her assistance in drawing the scheme in Fig. 1. References [1] J.A. Thomson, J. Itskovitz-Eldor, S.S. Shapiro, M.A. Waknitz, J.J. Swiergiel, V.S. Marshall, J.M. Jones, Embryonic stem cell lines derived from human blastocysts, Science 282 (1998) 1145–1147. [2] K. Takahashi, S. Yamanaka, Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors, Cell 126 (2006) 663–676. [3] K. Takahashi, K. Tanabe, M. Ohnuki, M. Narita, T. Ichisaka, K. Tomoda, S. Yamanaka, Induction of pluripotent stem cells from adult human fibroblasts by defined factors, Cell 131 (2007) 861–872. [4] S.J. Tapscott, R.L. Davis, M.J. Thayer, P.F. Cheng, H. Weintraub, A.B. Lassar, MyoD1: a nuclear phosphoprotein requiring a Myc homology region to convert fibroblasts to myoblasts, Science 242 (1988) 405–411. [5] R. Ambasudhan, M. Talantova, R. Coleman, X. Yuan, S. Zhu, S.A. Lipton, S. Ding, Direct reprogramming of adult human fibroblasts to functional neurons under defined conditions, Cell Stem Cell 9 (2011) 113–118. [6] T. Vierbuchen, A. Ostermeier, Z.P. Pang, Y. Kokubu, T.C. Sudhof, M. Wernig, Direct conversion of fibroblasts to functional neurons by defined factors, Nature 463 (2010) 1035–1041. [7] N. Yang, Y.H. Ng, Z.P. Pang, T.C. Sudhof, M. Wernig, Induced neuronal cells: how to make and define a neuron, Cell Stem Cell 9 (2011) 517–525. [8] M. Ieda, J.D. Fu, P. Delgado-Olguin, V. Vedantham, Y. Hayashi, B.G. Bruneau, D. Srivastava, Direct reprogramming of fibroblasts into functional cardiomyocytes by defined factors, Cell 142 (2010) 375–386. [9] T. Sadahiro, S. Yamanaka, M. Ieda, Direct cardiac reprogramming: progress and challenges in basic biology and clinical applications, Circ. Res. 116 (2015) 1378–1391. [10] J.D. Fu, D. Srivastava, Direct reprogramming of fibroblasts into cardiomyocytes for cardiac regenerative medicine, Circ. J. 79 (2015) 245–254. [11] Y.C. Hsu, S.L. Chen, Y.J. Wang, Y.H. Chen, D.Y. Wang, L. Chen, C.H. Chen, H.H. Chen, I.M. Chiu, Signaling adaptor protein SH2B1 enhances neurite outgrowth and accelerates the maturation of human induced neurons, Stem Cells Transl. Med. 3 (2014) 713–722. [12] C. Smith, L. Abalde-Atristain, C. He, B.R. Brodsky, E.M. Braunstein, P. Chaudhari, Y.Y. Jang, L. Cheng, Z. Ye, Efficient and allele-specific genome editing of disease loci in human iPSCs, Mol. Ther. 23 (2015) 570–577. [13] H. Kamao, M. Mandai, S. Okamoto, N. Sakai, A. Suga, S. Sugita, J. Kiryu, M. Takahashi, Characterization of human induced pluripotent stem cell-derived retinal pigment epithelium cell sheets aiming for clinical application, Stem Cell Rep. 2 (2014) 205–218. [14] H. Kanemura, M.J. Go, M. Shikamura, N. Nishishita, N. Sakai, H. Kamao, M. Mandai, C. Morinaga, M. Takahashi, S. Kawamata, Tumorigenicity studies of induced pluripotent stem cell (iPSC)-derived retinal pigment epithelium (RPE) for the treatment of age-related macular degeneration, PLoS One 9 (2014), e85336. [15] P. Wang, J. Na, Reprogramming to pluripotency and differentiation of cells with synthetic mRNA, Methods Mol. Biol. 969 (2013) 221–233. [16] M.B. Victor, M. Richner, T.O. Hermanstyne, J.L. Ransdell, C. Sobieski, P.Y. Deng, V.A. Klyachko, J.M. Nerbonne, A.S. Yoo, Generation of human striatal neurons by microRNA-dependent direct conversion of fibroblasts, Neuron 84 (2014) 311–323. [17] K. Nishimura, M. Sano, M. Ohtaka, B. Furuta, Y. Umemura, Y. Nakajima, Y. Ikehara, T. Kobayashi, H. Segawa, S. Takayasu, H. Sato, K. Motomura, E. Uchida, T. KanayasuToyoda, M. Asashima, H. Nakauchi, T. Yamaguchi, M. Nakanishi, Development of defective and persistent Sendai virus vector: a unique gene delivery/expression system ideal for cell reprogramming, J. Biol. Chem. 286 (2011) 4760–4771.

692

Y.-C. Hsu et al. / Biochimica et Biophysica Acta 1860 (2016) 686–693

[18] A. Prigione, J. Adjaye, Modulation of mitochondrial biogenesis and bioenergetic metabolism upon in vitro and in vivo differentiation of human ES and iPS cells, Int. J. Dev. Biol. 54 (2010) 1729–1741. [19] F.D. Houghton, Energy metabolism of the inner cell mass and trophectoderm of the mouse blastocyst, Differentiation 74 (2006) 11–18. [20] M.J. Birket, A.L. Orr, A.A. Gerencser, D.T. Madden, C. Vitelli, A. Swistowski, M.D. Brand, X. Zeng, A reduction in ATP demand and mitochondrial activity with neural differentiation of human embryonic stem cells, J. Cell Sci. 124 (2011) 348–358. [21] L.C. O'Brien, P.M. Keeney, J.P. Bennett Jr., Differentiation of human neural stem cells into motor neurons stimulates mitochondrial biogenesis and decreases glycolytic flux, Stem Cells Dev. 24 (2015) 1984–1994. [22] B. Mahato, P. Home, G. Rajendran, A. Paul, B. Saha, A. Ganguly, S. Ray, N. Roy, R.H. Swerdlow, S. Paul, Regulation of mitochondrial function and cellular energy metabolism by protein kinase C-lambda/iota: a novel mode of balancing pluripotency, Stem Cells 32 (2014) 2880–2892. [23] A. Moussaieff, M. Rouleau, D. Kitsberg, M. Cohen, G. Levy, D. Barasch, A. Nemirovski, S. Shen-Orr, I. Laevsky, M. Amit, D. Bomze, B. Elena-Herrmann, T. Scherf, M. Nissim-Rafinia, S. Kempa, J. Itskovitz-Eldor, E. Meshorer, D. Aberdam, Y. Nahmias, Glycolysis-mediated changes in acetyl-CoA and histone acetylation control the early differentiation of embryonic stem cells, Cell Metab. 21 (2015) 392–402. [24] N. Shyh-Chang, G.Q. Daley, L.C. Cantley, Stem cell metabolism in tissue development and aging, Development 140 (2013) 2535–2547. [25] S. Varum, A.S. Rodrigues, M.B. Moura, O. Momcilovic, C.A.t. Easley, J. RamalhoSantos, B. Van Houten, G. Schatten, Energy metabolism in human pluripotent stem cells and their differentiated counterparts, PLoS One 6 (2011), e20914. [26] A.D. Panopoulos, O. Yanes, S. Ruiz, Y.S. Kida, D. Diep, R. Tautenhahn, A. Herrerias, E.M. Batchelder, N. Plongthongkum, M. Lutz, W.T. Berggren, K. Zhang, R.M. Evans, G. Siuzdak, J.C. Izpisua Belmonte, The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming, Cell Res. 22 (2012) 168–177. [27] V.A. Rafalski, E. Mancini, A. Brunet, Energy metabolism and energy-sensing pathways in mammalian embryonic and adult stem cell fate, J. Cell Sci. 125 (2012) 5597–5608. [28] C.D. Folmes, T.J. Nelson, A. Martinez-Fernandez, D.K. Arrell, J.Z. Lindor, P.P. Dzeja, Y. Ikeda, C. Perez-Terzic, A. Terzic, Somatic oxidative bioenergetics transitions into pluripotency-dependent glycolysis to facilitate nuclear reprogramming, Cell Metab. 14 (2011) 264–271. [29] R. Abu Dawud, K. Schreiber, D. Schomburg, J. Adjaye, Human embryonic stem cells and embryonal carcinoma cells have overlapping and distinct metabolic signatures, PLoS One 7 (2012), e39896. [30] M.G. Vander Heiden, L.C. Cantley, C.B. Thompson, Understanding the Warburg effect: the metabolic requirements of cell proliferation, Science 324 (2009) 1029–1033. [31] J. Mathieu, W. Zhou, Y. Xing, H. Sperber, A. Ferreccio, Z. Agoston, K.T. Kuppusamy, R.T. Moon, H. Ruohola-Baker, Hypoxia-inducible factors have distinct and stagespecific roles during reprogramming of human cells to pluripotency, Cell Stem Cell 14 (2014) 592–605. [32] M.M. Silva, A.F. Rodrigues, C. Correia, M.F. Sousa, C. Brito, A.S. Coroadinha, M. Serra, P.M. Alves, Robust expansion of human pluripotent stem cells: integration of bioprocess design with transcriptomic and metabolomic characterization, Stem Cells Transl. Med. 4 (2015) 731–742. [33] A. Prigione, B. Fauler, R. Lurz, H. Lehrach, J. Adjaye, The senescence-related mitochondrial/oxidative stress pathway is repressed in human induced pluripotent stem cells, Stem Cells 28 (2010) 721–733. [34] M.H. Chin, M.J. Mason, W. Xie, S. Volinia, M. Singer, C. Peterson, G. Ambartsumyan, O. Aimiuwu, L. Richter, J. Zhang, I. Khvorostov, V. Ott, M. Grunstein, N. Lavon, N. Benvenisty, C.M. Croce, A.T. Clark, T. Baxter, A.D. Pyle, M.A. Teitell, M. Pelegrini, K. Plath, W.E. Lowry, Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures, Cell Stem Cell 5 (2009) 111–123. [35] C.D. Folmes, T.J. Nelson, A. Terzic, Energy metabolism in nuclear reprogramming, Biomark. Med 5 (2011) 715–729. [36] M.C. Sugden, M.J. Holness, Mechanisms underlying regulation of the expression and activities of the mammalian pyruvate dehydrogenase kinases, Arch. Physiol. Biochem. 112 (2006) 139–149. [37] A. Prigione, N. Rohwer, S. Hoffmann, B. Mlody, K. Drews, R. Bukowiecki, K. Blumlein, E.E. Wanker, M. Ralser, T. Cramer, J. Adjaye, HIF1alpha modulates cell fate reprogramming through early glycolytic shift and upregulation of PDK1-3 and PKM2, Stem Cells 32 (2014) 364–376. [38] O. Warburg, On the origin of cancer cells, Science 123 (1956) 309–314. [39] M. Guppy, E. Greiner, K. Brand, The role of the Crabtree effect and an endogenous fuel in the energy metabolism of resting and proliferating thymocytes, Eur. J. Biochem. 212 (1993) 95–99. [40] C. Choudhary, C. Kumar, F. Gnad, M.L. Nielsen, M. Rehman, T.C. Walther, J.V. Olsen, M. Mann, Lysine acetylation targets protein complexes and co-regulates major cellular functions, Science 325 (2009) 834–840. [41] D. Huangfu, R. Maehr, W. Guo, A. Eijkelenboom, M. Snitow, A.E. Chen, D.A. Melton, Induction of pluripotent stem cells by defined factors is greatly improved by smallmolecule compounds, Nat. Biotechnol. 26 (2008) 795–797. [42] D. Huangfu, K. Osafune, R. Maehr, W. Guo, A. Eijkelenboom, S. Chen, W. Muhlestein, D.A. Melton, Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2, Nat. Biotechnol. 26 (2008) 1269–1275. [43] L. Armstrong, K. Tilgner, G. Saretzki, S.P. Atkinson, M. Stojkovic, R. Moreno, S. Przyborski, M. Lako, Human induced pluripotent stem cell lines show stress

[44]

[45] [46] [47]

[48]

[49] [50] [51]

[52] [53] [54]

[55]

[56]

[57]

[58] [59]

[60]

[61]

[62]

[63]

[64]

[65]

[66]

[67]

[68] [69] [70] [71]

defense mechanisms and mitochondrial regulation similar to those of human embryonic stem cells, Stem Cells 28 (2010) 661–673. A. Prigione, B. Lichtner, H. Kuhl, E.A. Struys, M. Wamelink, H. Lehrach, M. Ralser, B. Timmermann, J. Adjaye, Human induced pluripotent stem cells harbor homoplasmic and heteroplasmic mitochondrial DNA mutations while maintaining human embryonic stem cell-like metabolic reprogramming, Stem Cells 29 (2011) 1338–1348. L. Scorrano, Keeping mitochondria in shape: a matter of life and death, Eur. J. Clin. Invest. 43 (2013) 886–893. L.J. Wong, Molecular genetics of mitochondrial disorders, Dev Disabil Res. Rev. 16 (2010) 154–162. C.T. Chen, S.H. Hsu, Y.H. Wei, Mitochondrial bioenergetic function and metabolic plasticity in stem cell differentiation and cellular reprogramming, Biochim. Biophys. Acta 1820 (2012) 571–576. J. Bereiter-Hahn, M. Voth, Dynamics of mitochondria in living cells: shape changes, dislocations, fusion, and fission of mitochondria, Microsc. Res. Tech. 27 (1994) 198–219. A.F. da Silva, F.R. Mariotti, V. Maximo, S. Campello, Mitochondria dynamism: of shape, transport and cell migration, Cell. Mol. Life Sci. 71 (2014) 2313–2324. D. Zeuschner, K. Mildner, H. Zaehres, H.R. Scholer, Induced pluripotent stem cells at nanoscale, Stem Cells Dev. 19 (2010) 615–620. S.T. Suhr, E.A. Chang, J. Tjong, N. Alcasid, G.A. Perkins, M.D. Goissis, M.H. Ellisman, G.I. Perez, J.B. Cibelli, Mitochondrial rejuvenation after induced pluripotency, PLoS One 5 (2010), e14095. J. Rehman, Empowering self-renewal and differentiation: the role of mitochondria in stem cells, J. Mol. Med. (Berl.) 88 (2010) 981–986. T. Lonergan, B. Bavister, C. Brenner, Mitochondria in stem cells, Mitochondrion 7 (2007) 289–296. J.M. Facucho-Oliveira, J.C. St John, The relationship between pluripotency and mitochondrial DNA proliferation during early embryo development and embryonic stem cell differentiation, Stem Cell Rev. 5 (2009) 140–158. H. Baharvand, A. Piryaei, R. Rohani, A. Taei, M.H. Heidari, A. Hosseini, Ultrastructural comparison of developing mouse embryonic stem cell- and in vivo-derived cardiomyocytes, Cell Biol. Int. 30 (2006) 800–807. Y.M. Cho, S. Kwon, Y.K. Pak, H.W. Seol, Y.M. Choi, J. Park do, K.S. Park, H.K. Lee, Dynamic changes in mitochondrial biogenesis and antioxidant enzymes during the spontaneous differentiation of human embryonic stem cells, Biochem. Biophys. Res. Commun. 348 (2006) 1472–1478. C. Piccoli, R. Ria, R. Scrima, O. Cela, A. D'Aprile, D. Boffoli, F. Falzetti, A. Tabilio, N. Capitanio, Characterization of mitochondrial and extra-mitochondrial oxygen consuming reactions in human hematopoietic stem cells. Novel evidence of the occurrence of NAD(P)H oxidase activity, J. Biol. Chem. 280 (2005) 26467–26476. B. Westermann, Mitochondrial fusion and fission in cell life and death, Nat. Rev. Mol. Cell Biol. 11 (2010) 872–884. H. Kondoh, M.E. Lleonart, J. Gil, J. Wang, P. Degan, G. Peters, D. Martinez, A. Carnero, D. Beach, Glycolytic enzymes can modulate cellular life span, Cancer Res. 65 (2005) 177–185. T. Kawamura, J. Suzuki, Y.V. Wang, S. Menendez, L.B. Morera, A. Raya, G.M. Wahl, J.C. Izpisua Belmonte, Linking the p53 tumour suppressor pathway to somatic cell reprogramming, Nature 460 (2009) 1140–1144. Y. Yoshida, K. Takahashi, K. Okita, T. Ichisaka, S. Yamanaka, Hypoxia enhances the generation of induced pluripotent stem cells, Cell Stem Cell 5 (2009) 237–241. D. Bae, P. Mondragon-Teran, D. Hernandez, L. Ruban, C. Mason, S.S. Bhattacharya, F.S. Veraitch, Hypoxia enhances the generation of retinal progenitor cells from human induced pluripotent and embryonic stem cells, Stem Cells and Dev. 21 (2012) 1344–1355. W. Liu, Q. Long, K. Chen, S. Li, G. Xiang, S. Chen, X. Liu, Y. Li, L. Yang, D. Dong, C. Jiang, Z. Feng, D. Qin, X. Liu, Mitochondrial metabolism transition cooperates with nuclear reprogramming during induced pluripotent stem cell generation, Biochem. Biophys. Res. Commun. 431 (2013) 767–771. J.A. Menendez, L. Vellon, C. Oliveras-Ferraros, S. Cufi, A. Vazquez-Martin, mTOR-regulated senescence and autophagy during reprogramming of somatic cells to pluripotency: a roadmap from energy metabolism to stem cell renewal and aging, Cell Cycle 10 (2011) 3658–3677. S. Zhu, W. Li, H. Zhou, W. Wei, R. Ambasudhan, T. Lin, J. Kim, K. Zhang, S. Ding, Reprogramming of human primary somatic cells by OCT4 and chemical compounds, Cell Stem Cell 7 (2010) 651–655. A. Acquistapace, T. Bru, P.F. Lesault, F. Figeac, A.E. Coudert, O. le Coz, C. Christov, X. Baudin, F. Auber, R. Yiou, J.L. Dubois-Rande, A.M. Rodriguez, Human mesenchymal stem cells reprogram adult cardiomyocytes toward a progenitor-like state through partial cell fusion and mitochondria transfer, Stem Cells 29 (2011) 812–824. H. Kim, H. Jang, T.W. Kim, B.H. Kang, S.E. Lee, Y.K. Jeon, D.H. Chung, J. Choi, J. Shin, E.J. Cho, H.D. Youn, Core pluripotency factors directly regulate metabolism in embryonic stem cell to maintain pluripotency, Stem Cells 33 (2015) 2699–2711. N. Shyh-Chang, G.Q. Daley, Lin28: primal regulator of growth and metabolism in stem cells, Cell Stem Cell 12 (2013) 395–406. K. Ito, T. Suda, Metabolic requirements for the maintenance of self-renewing stem cells, Nat. Rev. Mol. Cell Biol. 15 (2014) 243–256. M.Y. Son, H. Choi, Y.M. Han, Y.S. Cho, Unveiling the critical role of REX1 in the regulation of human stem cell pluripotency, Stem Cells 31 (2013) 2374–2387. C.D. Folmes, A. Martinez-Fernandez, R.S. Faustino, S. Yamada, C. Perez-Terzic, T.J. Nelson, A. Terzic, Nuclear reprogramming with c-Myc potentiates glycolytic capacity of derived induced pluripotent stem cells, J. Cardiovasc. Transl. Res. 6 (2013) 10–21.

Y.-C. Hsu et al. / Biochimica et Biophysica Acta 1860 (2016) 686–693 [72] I. Velasco, P. Salazar, A. Giorgetti, V. Ramos-Mejia, J. Castano, D. Romero-Moya, P. Menendez, Concise review: generation of neurons from somatic cells of healthy individuals and neurological patients through induced pluripotency or direct conversion, Stem Cells 32 (2014) 2811–2817. [73] T.T. Onder, G.Q. Daley, New lessons learned from disease modeling with induced pluripotent stem cells, Curr. Opin. Genet. Dev. 22 (2012) 500–508. [74] A.D. Ebert, S. Diecke, I.Y. Chen, J.C. Wu, Reprogramming and transdifferentiation for cardiovascular development and regenerative medicine: where do we stand? EMBO Mol. Med. 7 (2015) 1090–1103. [75] A. Tanaka, S. Yuasa, K. Node, K. Fukuda, Cardiovascular disease modeling using patient-specific induced pluripotent stem cells, Int. J. Mol. Sci. 16 (2015) 18894–18922. [76] S. Corti, I. Faravelli, M. Cardano, L. Conti, Human pluripotent stem cells as tools for neurodegenerative and neurodevelopmental disease modeling and drug discovery, Expert Opin. Drug Discov. 10 (2015) 615–629. [77] X. Zeng, J.G. Hunsberger, A. Simeonov, N. Malik, Y. Pei, M. Rao, Concise review: modeling central nervous system diseases using induced pluripotent stem cells, Stem Cells Transl. Med. 3 (2014) 1418–1428. [78] I. Lokody, Disease genetics: mitochondrial variation affects disease risk, Nat. Rev. Genet. 15 (2014) 440. [79] O. Russell, D. Turnbull, Mitochondrial DNA disease-molecular insights and potential routes to a cure, Exp. Cell Res. 325 (2014) 38–43. [80] C.D. Folmes, A. Martinez-Fernandez, E. Perales-Clemente, X. Li, A. McDonald, D. Oglesbee, S.C. Hrstka, C. Perez-Terzic, A. Terzic, T.J. Nelson, Disease-causing mitochondrial heteroplasmy segregated within induced pluripotent stem cell clones derived from a patient with MELAS, Stem Cells 31 (2013) 1298–1308. [81] W.C. Copeland, M.J. Longley, Mitochondrial genome maintenance in health and disease, DNA Repair 19 (2014) 190–198. [82] M. Kodaira, H. Hatakeyama, S. Yuasa, T. Seki, T. Egashira, S. Tohyama, Y. Kuroda, A. Tanaka, S. Okata, H. Hashimoto, D. Kusumoto, A. Kunitomi, M. Takei, S. Kashimura, T. Suzuki, G. Yozu, M. Shimojima, C. Motoda, N. Hayashiji, Y. Saito, Y. Goto, K. Fukuda, Impaired respiratory function in MELAS-induced pluripotent stem cells with high heteroplasmy levels, FEBS Open Bio 5 (2015) 219–225. [83] J. Fujikura, K. Nakao, M. Sone, M. Noguchi, E. Mori, M. Naito, D. Taura, M. HaradaShiba, I. Kishimoto, A. Watanabe, I. Asaka, K. Hosoda, K. Nakao, Induced pluripotent stem cells generated from diabetic patients with mitochondrial DNA A3243G mutation, Diabetologia 55 (2012) 1689–1698. [84] Y. Kobayashi, M.Y. Momoi, K. Tominaga, H. Shimoizumi, K. Nihei, M. Yanagisawa, Y. Kagawa, S. Ohta, Respiration-deficient cells are caused by a single point mutation in the mitochondrial tRNALeu(UUR) gene in mitochondrial myopathy, encephalopathy, lactic acidosis, and strokelike episodes (MELAS), Am. J. Hum. Genet. 49 (1991) 590–599. [85] Y. Goto, I. Nonaka, S. Horai, A mutation in the tRNA(Leu)(UUR) gene associated with the MELAS subgroup of mitochondrial encephalomyopathies, Nature 348 (1990) 651–653. [86] Y. Kirino, T. Yasukawa, S. Ohta, S. Akira, K. Ishihara, K. Watanabe, T. Suzuki, Codonspecific translational defect caused by a wobble modification deficiency in mutant tRNA from a human mitochondrial disease, Proc. Natl. Acad. Sci. USA 101 (2004) 15070–15075. [87] G. Attardi, M. Yoneda, A. Chomyn, Complementation and segregation behavior of disease-causing mitochondrial DNA mutations in cellular model systems, Biochim. Biophys. Acta 1271 (1995) 241–248. [88] T.D. Jeppesen, M. Schwartz, D.B. Olsen, J. Vissing, Oxidative capacity correlates with muscle mutation load in mitochondrial myopathy, Ann. Neurol. 54 (2003) 86–92. [89] R.H. Hämäläinen, T. Manninen, H. Koivumaki, M. Kislin, T. Otonkoski, A. Suomalainen, Tissue- and cell-type-specific manifestations of heteroplasmic mtDNA 3243 A N G mutation in human induced pluripotent stem cell-derived disease model, Proc. Natl. Acad. Sci. USA 110 (2013) E3622–E3630. [90] H. Ma, C.D. Folmes, J. Wu, R. Morey, S. Mora-Castilla, A. Ocampo, L. Ma, J. Poulton, X. Wang, R. Ahmed, E. Kang, Y. Lee, T. Hayama, Y. Li, C. Van Dyken, N.M. Gutierrez, R. Tippner-Hedges, A. Koski, N. Mitalipov, P. Amato, D.P. Wolf, T. Huang, A. Terzic, L.C. Laurent, J.C. Belmonte, S. Mitalipov, Metabolic rescue in pluripotent cells from patients with mtDNA disease, Nature 524 (2015) 234–238. [91] A.B. Cherry, K.E. Gagne, E.M. McLoughlin, A. Baccei, B. Gorman, O. Hartung, J.D. Miller, J. Zhang, R.L. Zon, T.A. Ince, E.J. Neufeld, P.H. Lerou, M.D. Fleming, G.Q. Daley, S. Agarwal, Induced pluripotent stem cells with a mitochondrial DNA deletion, Stem Cells 31 (2013) 1287–1297. [92] M. Wahlestedt, A. Ameur, R. Moraghebi, G.L. Norddahl, G. Sten, N.B. Woods, D. Bryder, Somatic cells with a heavy mitochondrial DNA mutational load render induced pluripotent stem cells with distinct differentiation defects, Stem Cells 32 (2014) 1173–1182. [93] G. Wang, M.L. McCain, L. Yang, A. He, F.S. Pasqualini, A. Agarwal, H. Yuan, D. Jiang, D. Zhang, L. Zangi, J. Geva, A.E. Roberts, Q. Ma, J. Ding, J. Chen, D.Z. Wang, K. Li, J. Wang, R.J. Wanders, W. Kulik, F.M. Vaz, M.A. Laflamme, C.E. Murry, K.R. Chien, R.I. Kelley, G.M. Church, K.K. Parker, W.T. Pu, Modeling the mitochondrial cardiomyopathy of Barth syndrome with induced pluripotent stem cell and heart-onchip technologies, Nat. Med. 20 (2014) 616–623. [94] Y.K. Lee, P.W. Ho, R. Schick, Y.M. Lau, W.H. Lai, T. Zhou, Y. Li, K.M. Ng, S.L. Ho, M.A. Esteban, O. Binah, H.F. Tse, C.W. Siu, Modeling of Friedreich ataxia-related iron overloading cardiomyopathy using patient-specific-induced pluripotent stem cells, Pflugers Arch. 466 (2014) 1831–1844.

693

[95] A. Eigentler, S. Boesch, R. Schneider, G. Dechant, R. Nat, Induced pluripotent stem cells from Friedreich ataxia patients fail to upregulate frataxin during in vitro differentiation to peripheral sensory neurons, Stem Cells Dev. 22 (2013) 3271–3282. [96] X. Xu, S. Duan, F. Yi, A. Ocampo, G.H. Liu, J.C. Izpisua Belmonte, Mitochondrial regulation in pluripotent stem cells, Cell Metab. 18 (2013) 325–332. [97] A. Prigione, Induced pluripotent stem cells (iPSCs) for modeling mitochondrial DNA disorders, Methods Mol. Biol. 1265 (2015) 349–356. [98] H. Inoue, N. Nagata, H. Kurokawa, S. Yamanaka, iPS cells: a game changer for future medicine, EMBO J. 33 (2014) 409–417. [99] N. Hu, T. Wang, Q. Wang, J. Zhou, L. Zou, K. Su, J. Wu, P. Wang, High-performance beating pattern function of human induced pluripotent stem cell-derived cardiomyocyte-based biosensors for hERG inhibition recognition, Biosens. Bioelectron. 67 (2015) 146–153. [100] N. Sun, M. Yazawa, J. Liu, L. Han, V. Sanchez-Freire, O.J. Abilez, E.G. Navarrete, S. Hu, L. Wang, A. Lee, A. Pavlovic, S. Lin, R. Chen, R.J. Hajjar, M.P. Snyder, R.E. Dolmetsch, M.J. Butte, E.A. Ashley, M.T. Longaker, R.C. Robbins, J.C. Wu, Patient-specific induced pluripotent stem cells as a model for familial dilated cardiomyopathy, Sci. Transl. Med. 4 (2012) 130ra147. [101] L. Guo, L. Coyle, R.M. Abrams, R. Kemper, E.T. Chiao, K.L. Kolaja, Refining the human iPSC-cardiomyocyte arrhythmic risk assessment model, Toxicol. Sci. 136 (2013) 581–594. [102] A.L. Lahti, V.J. Kujala, H. Chapman, A.P. Koivisto, M. Pekkanen-Mattila, E. Kerkela, J. Hyttinen, K. Kontula, H. Swan, B.R. Conklin, S. Yamanaka, O. Silvennoinen, K. AaltoSetala, Model for long QT syndrome type 2 using human iPS cells demonstrates arrhythmogenic characteristics in cell culture, Dis. Model. Mech. 5 (2012) 220–230. [103] J. Hanna, M. Wernig, S. Markoulaki, C.W. Sun, A. Meissner, J.P. Cassady, C. Beard, T. Brambrink, L.C. Wu, T.M. Townes, R. Jaenisch, Treatment of sickle cell anemia mouse model with iPS cells generated from autologous skin, Science 318 (2007) 1920–1923. [104] O. Tsuji, K. Miura, K. Fujiyoshi, S. Momoshima, M. Nakamura, H. Okano, Cell therapy for spinal cord injury by neural stem/progenitor cells derived from iPS/ES cells, Neurotherapeutics 8 (2011) 668–676. [105] O. Tsuji, K. Miura, Y. Okada, K. Fujiyoshi, M. Mukaino, N. Nagoshi, K. Kitamura, G. Kumagai, M. Nishino, S. Tomisato, H. Higashi, T. Nagai, H. Katoh, K. Kohda, Y. Matsuzaki, M. Yuzaki, E. Ikeda, Y. Toyama, M. Nakamura, S. Yamanaka, H. Okano, Therapeutic potential of appropriately evaluated safe-induced pluripotent stem cells for spinal cord injury, Proc. Natl. Acad. Sci. USA 107 (2010) 12704–12709. [106] A.J. Carr, A.A. Vugler, S.T. Hikita, J.M. Lawrence, C. Gias, L.L. Chen, D.E. Buchholz, A. Ahmado, M. Semo, M.J. Smart, S. Hasan, L. da Cruz, L.V. Johnson, D.O. Clegg, P.J. Coffey, Protective effects of human iPS-derived retinal pigment epithelium cell transplantation in the retinal dystrophic rat, PLoS One 4 (2009), e8152. [107] A. Sanchez-Danes, Y. Richaud-Patin, I. Carballo-Carbajal, S. Jimenez-Delgado, C. Caig, S. Mora, C. Di Guglielmo, M. Ezquerra, B. Patel, A. Giralt, J.M. Canals, M. Memo, J. Alberch, J. Lopez-Barneo, M. Vila, A.M. Cuervo, E. Tolosa, A. Consiglio, A. Raya, Disease-specific phenotypes in dopamine neurons from human iPS-based models of genetic and sporadic Parkinson's disease, EMBO Mol. Med. 4 (2012) 380–395. [108] M. Wernig, J.P. Zhao, J. Pruszak, E. Hedlund, D. Fu, F. Soldner, V. Broccoli, M. Constantine-Paton, O. Isacson, R. Jaenisch, Neurons derived from reprogrammed fibroblasts functionally integrate into the fetal brain and improve symptoms of rats with Parkinson's disease, Proc. Natl. Acad. Sci. USA 105 (2008) 5856–5861. [109] A.B. Alvarez Palomo, S. McLenachan, F.K. Chen, L. Da Cruz, R.J. Dilley, J. Requena, M. Lucas, A. Lucas, M. Drukker, M.J. Edel, Prospects for clinical use of reprogrammed cells for autologous treatment of macular degeneration, Fibrogenesis Tissue Repair 8 (2015) 9. [110] S.L. Farnsworth, Z. Qiu, A. Mishra, P.J. Hornsby, Directed neural differentiation of induced pluripotent stem cells from non-human primates, Exp. Biol. Med. (Maywood) 238 (2013) 276–284. [111] T. Kikuchi, A. Morizane, D. Doi, H. Onoe, T. Hayashi, T. Kawasaki, H. Saiki, S. Miyamoto, J. Takahashi, Survival of human induced pluripotent stem cell-derived midbrain dopaminergic neurons in the brain of a primate model of Parkinson's disease, J. Parkinsons Dis. 1 (2011) 395–412. [112] A. Morizane, D. Doi, T. Kikuchi, K. Okita, A. Hotta, T. Kawasaki, T. Hayashi, H. Onoe, T. Shiina, S. Yamanaka, J. Takahashi, Direct comparison of autologous and allogeneic transplantation of iPSC-derived neural cells in the brain of a non-human primate, Stem Cell Reports 1 (2013) 283–292. [113] Z. Qiu, S.L. Farnsworth, A. Mishra, P.J. Hornsby, Patient-specific induced pluripotent stem cells in neurological disease modeling: the importance of nonhuman primate models, Stem Cells Cloning 6 (2013) 19–29. [114] T. Maeda, M.J. Lee, G. Palczewska, S. Marsili, P.J. Tesar, K. Palczewski, M. Takahashi, A. Maeda, Retinal pigmented epithelial cells obtained from human induced pluripotent stem cells possess functional visual cycle enzymes in vitro and in vivo, J. Biol. Chem. 288 (2013) 34484–34493. [115] Z.B. Jin, M. Takahashi, Generation of retinal cells from pluripotent stem cells, Prog. Brain Res. 201 (2012) 171–181. [116] Z.B. Jin, S. Okamoto, P. Xiang, M. Takahashi, Integration-free induced pluripotent stem cells derived from retinitis pigmentosa patient for disease modeling, Stem Cells Transl. Med. 1 (2012) 503–509.