The relationship between pluripotency and mitochondrial DNA proliferation during early embryo development and embryonic stem cell differentiation

Mitochondrial proteins and congenital birth defect risk: a mendelian randomization study

BACKGROUND

Mitochondrial dysfunction has been hypothesized to play a role in the etiology of congenital birth defects. However, evidence from observational studies is susceptible to bias and confounding. Mendelian randomization uses genetic variants as instrumental variables to investigate causal relationships. This study aimed to investigate the causal effect of mitochondrial proteins on risk of common congenital defects including orofacial clefts, congenital heart defects, external ear malformations, urinary system malformations, nervous system malformations, and limb malformations.

METHODS

Summary statistics data on congenital birth defects were obtained from the FinnGen consortium. This included 1,994 cases of congenital heart malformations, 258 cases of nervous system malformations, 185 cases of ear malformations, 813 cases of urinary system malformations, 92 cases of limb malformations, and 181 cases of cleft lip and cleft palate, alongside 216,798 to 218,611 controls, depending on the defect type. Data on genetic variants associated with 66 mitochondrial proteins were extracted from the Human Plasma Proteome Atlas (n = 3,301 healthy individuals). The inverse-variance weighted method was applied as the primary analysis, with sensitivity analyses using MR-Egger regression, weighted median estimation, and MR-PRESSO to assess pleiotropy and outliers.

RESULTS

Among the 66 mitochondrial protein traits examined, several displayed significant associations with congenital birth defects. Negative associations were found between pyruvate dehydrogenase kinase isozyme 1 and ATP synthase subunit beta mitochondrial levels and congenital heart malformation risk. GrpE protein homolog 1 mitochondrial was negatively associated with cleft lip/palate risk. 39S ribosomal protein L14 and GrpE protein homolog 1 mitochondrial showed positive and negative links with urinary malformations, respectively. Positive associations were noted between cytochrome c oxidase subunit 4 isoform 2, protein SCO1 homolog, and tRNA pseudouridine synthase A mitochondrial and nervous system malformations, while peptide chain release factor 1-like mitochondrial was negatively related. Cytochrome c oxidase subunit 7 A1 mitochondrial associated positively with ear malformations. Positive relationships were identified between cytochrome c oxidase subunit 7 A1, ADP-ribose pyrophosphatase, coiled-coil-helix-coiled-coil-helix domain-containing protein 10, NFU1 iron-sulfur cluster scaffold homolog mitochondrial, and limb malformation risk. Meanwhile, NADH dehydrogenase [ubiquinone] iron-sulfur protein 4 mitochondrial displayed a negative association.

CONCLUSIONS

This Mendelian randomization study provides evidence that mitochondrial protein levels may be causally implicated in congenital heart, urinary, nervous system, ear, and limb malformations. The findings highlight potential etiological roles for mitochondrial dysfunction in the pathogenesis of structural birth defects. Further large-scale and functional investigations are warranted to corroborate these genetic inference results and elucidate underlying mechanisms that may inform translational applications.

Navigating redox imbalance: the role of oxidative stress in embryonic development and long-term health outcomes

Embryonic development is a complex process of concurrent events comprising cell proliferation, differentiation, morphogenesis, migration, and tissue remodeling. To cope with the demands arising from these developmental processes, cells increase their nutrient uptake, which subsequently increases their metabolic activity. Mitochondria play a key role in the maintenance of metabolism and production of reactive oxygen species (ROS) as a natural byproduct. Regulation of ROS by antioxidants is critical and tightly regulated during embryonic development, as dysregulation results in oxidative stress that damages essential cellular components such as DNA, proteins, and lipids, which are crucial for cellular maintenance and in extension development. However, during development, exposure to certain exogenous factors or damage to cellular components can result in an imbalance between ROS production and its neutralization by antioxidants, leading to detrimental effects on the developmental process. In this review article, we highlight the crucial role of redox homeostasis in normal development and how disruptions in redox balance may result in developmental defects.

A combined proteomic and metabolomic analysis of the early aborted embryonic tissues with maternal COVID-19 infection

COVID-19 still spreads worldwide, and repeated infections are hard to avoid. Maternal infection during pregnancy is associated with adverse maternal and neonatal outcomes. Our study used a multi-omics profiling method to explore the proteome and metabolome alteration in early embryonic development after COVID-19 infection. A total of 30 chorionic tissues after artificial abortion (15 infection and 15 no-infection samples) were collected, and the UHPLC-MS/MS and LC-MS/MS were applied in the present study. As a result, 311 significantly differentially expressed proteins were identified. The function annotations revealed that the thermogenesis pathway is the most significantly enriched signaling pathway; PRKAG2, IGF1R, and RPS6KB2 were identified as the hub proteins. There were 359 metabolites significantly altered after infection. The functional annotations revealed that amino acid metabolism was significantly affected, especially beta-alanine metabolism, glutamate metabolism, and histidine metabolism pathways. The metabolites in ovarian steroidogenesis showed a down-regulating trend in the infection group. Finally, we combined the results of proteins and metabolomics analysis. The biosynthesis of the cofactors pathway was identified as significantly enriched in both proteomics and metabolomics datasets. Our findings provide a network of protein regulation and metabolite perturbation during early embryonic development with COVID-19 infection. Our findings can provide valuable insights for further exploration of the complex mechanism of COVID-19-associated pregnancy complications and outcomes. SIGNIFICANCE: COVID-19 has developed into the most prominent and deadliest pandemic respiratory disease in the world, and repeated infections are complicated to avoid. COVID-19 infection during pregnancy increases the risk of adverse maternal and neonatal outcomes, such as preterm birth and stillbirth. However, previous studies mainly focused on its effect on pregnant women, such as the clinical characteristics and gestation outcomes. There is no relevant report about the effects of virus infection on embryos in early pregnancy. The effects of COVID-19 infection changes of the proteins and metabolites during early embryonic development are undefined. Our findings provide an association between protein regulation, metabolite perturbation, and COVID-19 infection, which can provide valuable insights for further exploration of the complex mechanism COVID-19 COVID-19-associated pregnancy complications and adverse pregnancy outcomes.

Effects of periconceptional ethanol on mitochondrial content and oxidative stress in maternal liver and placentas from male and female fetuses in rats

Alcohol exposure during pregnancy disrupts fetal development and programs lifelong disease. We have shown, in rats, that alcohol exposure during the periconceptional period (PC:EtOH), causes placental dysfunction and cardiometabolic disease in offspring. The process of metabolising alcohol can cause oxidative stress and damage mitochondrial DNA (mtDNA). It is unknown whether alcohol metabolism in a rat model of PC:EtOH impacts oxidative stress markers and mitochondrial content in maternal and placental tissues. We aimed to determine whether PC:EtOH induced oxidative stress and reduced mtDNA in maternal liver and the placental labyrinth and junctional zone. Sprague-Dawley rats were given an ethanol liquid (12.5% v/v) or control (0%) diet for one oestrous cycle before mating to embryonic day (E) 4. Maternal livers were collected at E5 and E20. Placentas were collected at E20 and separated into the junctional zone and labyrinth zone. PC:EtOH reduced Cyp2e1 mRNA levels and mtDNA in the E5 liver with lower mtDNA persisting to E20, at which time mitochondrial proteins were also decreased. PC:EtOH also reduced mitochondrial content in the E20 junctional zone, although mitochondrial protein levels were unaffected. Superoxide dismutase activity was increased in the placental junctional zone and there was no evidence of oxidative stress. The present study demonstrates that alcohol exposure around conception, reduces mitochondrial content within the maternal liver and the junctional zone of the placenta towards the end of pregnancy. These prolonged deficits may have disrupted metabolic processes required for a healthy pregnancy. The study further supports avoiding alcohol when planning a pregnancy. KEY POINTS: Even when alcohol is consumed only around conception (PC:EtOH), it can have profound impacts on the developing baby. Here, we use our established rat model to investigate if PC:EtOH causes oxidative stress and reduces mitochondrial content in the maternal liver immediately after exposure on embryonic day (E) 5. We also investigate these parameters at the end of pregnancy (E20) in maternal liver and the placenta. PC:EtOH reduced mitochondrial DNA content in the maternal liver by 77% at E5 and by 40% at E20. At E20, expression of proteins that form the electron transport chain were also reduced. The placenta had a more subtle reduction in mitochondrial DNA content, but protein levels of mitochondrial complexes were unchanged. There was no evidence of oxidative stress in the maternal liver or placenta in response to PC:EtOH. The lack of oxidative stress in the placenta may be a result of compensatory increases in antioxidants.

Germline ecology: Managed herds, tolerated flocks, and pest control

Multicopy sequences evolve adaptations for increasing their copy number within nuclei. The activities of multicopy sequences under constraints imposed by cellular and organismal selection result in a rich intranuclear ecology in germline cells. Mitochondrial and ribosomal DNA are managed as domestic herds subject to selective breeding by the genes of the single-copy genome. Transposable elements lead a peripatetic existence in which they must continually move to new sites to keep ahead of inactivating mutations at old sites and undergo exponential outbreaks when the production of new copies exceeds the rate of inactivation of old copies. Centromeres become populated by repeats that do little harm. Organisms with late sequestration of germ cells tend to evolve more "junk" in their genomes than organisms with early sequestration of germ cells.

Spinning Disk Confocal Microscopy for Optimized and Quantified Live Imaging of 3D Mitochondrial Network

Mitochondria are the energy factories of a cell, and depending on the metabolic requirements, the mitochondrial morphology, quantity, and membrane potential in a cell change. These changes are frequently assessed using commercially available probes. In this study, we tested the suitability of three commercially available probes-namely 5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazolo-carbocyanine iodide (JC-1), MitoTracker Red CMX Rox (CMXRos), and tetramethylrhodamine methyl ester (TMRM)-for assessing the mitochondrial quantity, morphology, and membrane potential in living human mesoangioblasts in 3D with confocal laser scanning microscope (CLSM) and scanning disk confocal microscope (SDCM). Using CLSM, JC-1, and CMXRos-but not TMRM-uncovered considerable background and variation. Using SDCM, the background signal only remained apparent for the JC-1 monomer. Repetitive imaging of CMXRos and JC-1-but not TMRM-demonstrated a 1.5-2-fold variation in signal intensity between cells using CLSM. The use of SDCM drastically reduced this variation. The slope of the relative signal intensity upon repetitive imaging using CLSM was lowest for TMRM (-0.03) and highest for CMXRos (0.16). Upon repetitive imaging using SDCM, the slope varied from 0 (CMXRos) to a maximum of -0.27 (JC-1 C1). Conclusively, our data show that TMRM staining outperformed JC-1 and CMXRos dyes in a (repetitive) 3D analysis of the entire mitochondrial quantity, morphology, and membrane potential in living cells.

p66Shc signaling and autophagy impact on C2C12 myoblast differentiation during senescence

During aging, muscle regenerative capacities decline, which is concomitant with the loss of satellite cells that enter in a state of irreversible senescence. However, what mechanisms are involved in myogenic senescence and differentiation are largely unknown. Here, we showed that early-passage or "young" C2C12 myoblasts activated the redox-sensitive p66Shc signaling pathway, exhibited a strong antioxidant protection and a bioenergetic profile relying predominantly on OXPHOS, responses that decrease progressively during differentiation. Furthermore, autophagy was increased in myotubes. Otherwise, late-passage or "senescent" myoblasts led to a highly metabolic profile, relying on both OXPHOS and glycolysis, that may be influenced by the loss of SQSTM1/p62 which tightly regulates the metabolic shift from aerobic glycolysis to OXPHOS. Furthermore, during differentiation of late-passage C2C12 cells, both p66Shc signaling and autophagy were impaired and this coincides with reduced myogenic capacity. Our findings recognized that the lack of p66Shc compromises the proliferation and the onset of the differentiation of C2C12 myoblasts. Moreover, the Atg7 silencing favored myoblasts growth, whereas interfered in the viability of differentiated myotubes. Then, our work demonstrates that the p66Shc signaling pathway, which highly influences cellular metabolic status and oxidative environment, is critical for the myogenic commitment and differentiation of C2C12 cells. Our findings also support that autophagy is essential for the metabolic switch observed during the differentiation of C2C12 myoblasts, confirming how its regulation determines cell fate. The regulatory roles of p66Shc and autophagy mechanisms on myogenesis require future attention as possible tools that could predict and measure the aging-related state of frailty and disability.

Significance of quantitative analyses of the impact of heterogeneity in mitochondrial content and shape on cell differentiation

Mitochondria, classically known as the powerhouse of cells, are unique double membrane-bound multifaceted organelles carrying a genome. Mitochondrial content varies between cell types and precisely doubles within cells during each proliferating cycle. Mitochondrial content also increases to a variable degree during cell differentiation triggered after exit from the proliferating cycle. The mitochondrial content is primarily maintained by the regulation of mitochondrial biogenesis, while damaged mitochondria are eliminated from the cells by mitophagy. In any cell with a given mitochondrial content, the steady-state mitochondrial number and shape are determined by a balance between mitochondrial fission and fusion processes. The increase in mitochondrial content and alteration in mitochondrial fission and fusion are causatively linked with the process of differentiation. Here, we critically review the quantitative aspects in the detection methods of mitochondrial content and shape. Thereafter, we quantitatively link these mitochondrial properties in differentiating cells and highlight the implications of such quantitative link on stem cell functionality. Finally, we discuss an example of cell size regulation predicted from quantitative analysis of mitochondrial shape and content. To highlight the significance of quantitative analyses of these mitochondrial properties, we propose three independent rationale based hypotheses and the relevant experimental designs to test them.

Metabolic and proteostatic differences in quiescent and active neural stem cells

Adult neural stem cells are neurogenesis progenitor cells that play an important role in neurogenesis. Therefore, neural regeneration may be a promising target for treatment of many neurological illnesses. The regenerative capacity of adult neural stem cells can be characterized by two states: quiescent and active. Quiescent adult neural stem cells are more stable and guarantee the quantity and quality of the adult neural stem cell pool. Active adult neural stem cells are characterized by rapid proliferation and differentiation into neurons which allow for integration into neural circuits. This review focuses on differences between quiescent and active adult neural stem cells in nutrition metabolism and protein homeostasis. Furthermore, we discuss the physiological significance and underlying advantages of these differences. Due to the limited number of adult neural stem cells studies, we referred to studies of embryonic adult neural stem cells or non-mammalian adult neural stem cells to evaluate specific mechanisms.

Genome-wide methylation profile of mitochondrial DNA across bovine preimplantation development

This study characterized variations in the methylation profile of mitochondrial DNA (mtDNA) during initial bovine embryo development and correlated the presence of methylation with mtDNA transcription. Bovine oocytes were obtained from abattoir ovaries and submitted to in vitro culture procedures. Oocytes and embryos were collected at various stages (immature oocyte, IM; mature oocyte, MII; zygote, ZY; 4-cells, 4C; 16-cells, 16C and blastocysts, BL). Total DNA (including mtDNA) was used for Whole Genome Enzymatic Methyl Sequencing and for quantification of mtDNA copy number. Extracted RNA was used for quantification of mitochondrial transcripts using Droplet Digital PCR. We selected ND6, CYTB, tRNA-Phe and tRNA-Gln based on their location in the mitochondrial genome, functionality and/or previous literature associating these regions with cytosine methylation. The number of mtDNA copies per oocyte/embryo was found to be similar, while methylation levels in mtDNA varied among stages. Higher total methylation levels were found mainly at 4C and 16C. In specific gene regions, higher methylation levels were also observed at 4C and 16C (ND6, CYTB and tRNA-Phe), as well as an inverse correlation with the quantity of transcripts for these regions. This is a first description of epigenetic changes occurring in mtDNA during early embryonic development. Our results indicate that methylation might regulate the mtDNA transcription at a local level, particularly around the time of embryonic genome activation.

Metabolic and cell cycle shift induced by the deletion of Dnm1l attenuates the dissolution of pluripotency in mouse embryonic stem cells

Mitochondria are versatile organelles that continuously change their morphology via fission and fusion. However, the detailed functions of mitochondrial dynamics-related genes in pluripotent stem cells remain largely unclear. Here, we aimed to determine the effects on energy metabolism and differentiation ability of mouse embryonic stem cells (ESCs) following deletion of the mitochondrial fission-related gene Dnml1. Resultant Dnm1l-/- ESCs maintained major pluripotency characteristics. However, Dnm1l-/- ESCs showed several phenotypic changes, including the inhibition of differentiation ability (dissolution of pluripotency). Notably, Dnm1l-/- ESCs maintained the expression of the pluripotency marker Oct4 and undifferentiated colony types upon differentiation induction. RNA sequencing analysis revealed that the most frequently differentially expressed genes were enriched in the glutathione metabolic pathway. Our data suggested that differentiation inhibition of Dnm1l-/- ESCs was primarily due to metabolic shift from glycolysis to OXPHOS, G2/M phase retardation, and high level of Nanog and 2-cell-specific gene expression.

Metabolic protein kinase signalling in neuroblastoma

BACKGROUND

Neuroblastoma is a paediatric malignancy of incredibly complex aetiology. Oncogenic protein kinase signalling in neuroblastoma has conventionally focussed on transduction through the well-characterised PI3K/Akt and MAPK pathways, in which the latter has been implicated in treatment resistance. The discovery of the receptor tyrosine kinase ALK as a target of genetic alterations in cases of familial and sporadic neuroblastoma, was a breakthrough in the understanding of the complex genetic heterogeneity of neuroblastoma. However, despite progress in the development of small-molecule inhibitors of ALK, treatment resistance frequently arises and appears to be a feature of the disease. Moreover, since the identification of ALK, several additional protein kinases, including the PIM and Aurora kinases, have emerged not only as drivers of the disease phenotype, but also as promising druggable targets. This is particularly the case for Aurora-A, given its intimate engagement with MYCN, a driver oncogene of aggressive neuroblastoma previously considered 'undruggable.'

SCOPE OF REVIEW

Aided by significant advances in structural biology and a broader understanding of the mechanisms of protein kinase function and regulation, we comprehensively outline the role of protein kinase signalling, emphasising ALK, PIM and Aurora in neuroblastoma, their respective metabolic outputs, and broader implications for targeted therapies.

MAJOR CONCLUSIONS

Despite massively divergent regulatory mechanisms, ALK, PIM and Aurora kinases all obtain significant roles in cellular glycolytic and mitochondrial metabolism and neuroblastoma progression, and in several instances are implicated in treatment resistance. While metabolism of neuroblastoma tends to display hallmarks of the glycolytic "Warburg effect," aggressive, in particular MYCN-amplified tumours, retain functional mitochondrial metabolism, allowing for survival and proliferation under nutrient stress. Future strategies employing specific kinase inhibitors as part of the treatment regimen should consider combinatorial attempts at interfering with tumour metabolism, either through metabolic pathway inhibitors, or by dietary means, with a view to abolish metabolic flexibility that endows cancerous cells with a survival advantage.

Mitoepigenetics and gliomas: epigenetic alterations to mitochondrial DNA and nuclear DNA alter mtDNA expression and contribute to glioma pathogenicity

Epigenetic mechanisms allow cells to fine-tune gene expression in response to environmental stimuli. For decades, it has been known that mitochondria have genetic material. Still, only recently have studies shown that epigenetic factors regulate mitochondrial DNA (mtDNA) gene expression. Mitochondria regulate cellular proliferation, apoptosis, and energy metabolism, all critical areas of dysfunction in gliomas. Methylation of mtDNA, alterations in mtDNA packaging via mitochondrial transcription factor A (TFAM), and regulation of mtDNA transcription via the micro-RNAs (mir 23-b) and long noncoding RNAs [RNA mitochondrial RNA processing (RMRP)] have all been identified as contributing to glioma pathogenicity. Developing new interventions interfering with these pathways may improve glioma therapy.

Modeling mitochondrial DNA diseases: from base editing to pluripotent stem-cell-derived organoids

Mitochondrial DNA (mtDNA) diseases are multi-systemic disorders caused by mutations affecting a fraction or the entirety of mtDNA copies. Currently, there are no approved therapies for the majority of mtDNA diseases. Challenges associated with engineering mtDNA have in fact hindered the study of mtDNA defects. Despite these difficulties, it has been possible to develop valuable cellular and animal models of mtDNA diseases. Here, we describe recent advances in base editing of mtDNA and the generation of three-dimensional organoids from patient-derived human-induced pluripotent stem cells (iPSCs). Together with already available modeling tools, the combination of these novel technologies could allow determining the impact of specific mtDNA mutations in distinct human cell types and might help uncover how mtDNA mutation load segregates during tissue organization. iPSC-derived organoids could also represent a platform for the identification of treatment strategies and for probing the in vitro effectiveness of mtDNA gene therapies. These studies have the potential to increase our mechanistic understanding of mtDNA diseases and may open the way to highly needed and personalized therapeutic interventions.

BNIP3-dependent mitophagy safeguards ESC genomic integrity via preventing oxidative stress-induced DNA damage and protecting homologous recombination

Embryonic stem cells (ESCs) have a significantly lower mutation load compared to somatic cells, but the mechanisms that guard genomic integrity in ESCs remain largely unknown. Here we show that BNIP3-dependent mitophagy protects genomic integrity in mouse ESCs. Deletion of Bnip3 increases cellular reactive oxygen species (ROS) and decreases ATP generation. Increased ROS in Bnip3^-/- ESCs compromised self-renewal and were partially rescued by either NAC treatment or p53 depletion. The decreased cellular ATP in Bnip3^-/- ESCs induced AMPK activation and deteriorated homologous recombination, leading to elevated mutation load during long-term propagation. Whereas activation of AMPK in X-ray-treated Bnip3^+/+ ESCs dramatically ascended mutation rates, inactivation of AMPK in Bnip3^-/- ESCs under X-ray stress remarkably decreased the mutation load. In addition, enhancement of BNIP3-dependent mitophagy during reprogramming markedly decreased mutation accumulation in established iPSCs. In conclusion, we demonstrated a novel pathway in which BNIP3-dependent mitophagy safeguards ESC genomic stability, and that could potentially be targeted to improve pluripotent stem cell genomic integrity for regenerative medicine.

Insights regarding mitochondrial DNA copy number alterations in human cancer (Review)

Mitochondria are the critical organelles involved in various cellular functions. Mitochondrial biogenesis is activated by multiple cellular mechanisms which require a synchronous regulation between mitochondrial DNA (mtDNA) and nuclear DNA (nDNA). The mitochondrial DNA copy number (mtDNA-CN) is a proxy indicator for mitochondrial activity, and its alteration reflects mitochondrial biogenesis and function. Despite the precise mechanisms that modulate the amount and composition of mtDNA, which have not been fully elucidated, mtDNA-CN is known to influence numerous cellular pathways that are associated with cancer and as well as multiple other diseases. In addition, the utility of current technology in measuring mtDNA-CN contributes to its extensive assessment of diverse traits and tumorigenesis. The present review provides an overview of mtDNA-CN variations across human cancers and an extensive summary of the existing knowledge on the regulation and machinery of mtDNA-CN. The current information on the advanced methods used for mtDNA-CN assessment is also presented.

An Updated View of the Roles of p53 in Embryonic Stem Cells

The TP53 gene is unarguably one of the most studied human genes. Its encoded protein, p53, is a tumor suppressor and is often called the "guardian of the genome" due to its pivotal role in maintaining genome stability. Historically, most studies of p53 have focused on its roles in somatic cells and tissues, but in the last two decades, its functions in embryonic stem cells (ESCs) and induced pluripotent stem cells have attracted increasing attention. Recent studies have identified p53 as a critical regulator of pluripotency, self-renewal, differentiation, proliferation, and genome stability in mouse and human embryonic stem cells. In this article, we systematically review the studies on the functions of p53 in ESCs, provide an updated overview, attempt to reconcile controversial results described in the literature, and discuss the relevance of these cellular functions of p53 to its roles in tumor suppression.

Gene therapy restores mitochondrial function and protects retinal ganglion cells in optic neuropathy induced by a mito-targeted mutant ND1 gene

Therapies for genetic disorders caused by mutated mitochondrial DNA are an unmet need, in large part due barriers in delivering DNA to the organelle and the absence of relevant animal models. We injected into mouse eyes a mitochondrially targeted Adeno-Associated-Virus (MTS-AAV) to deliver the mutant human NADH ubiquinone oxidoreductase subunit I (hND1/m.3460G>A) responsible for Leber’s hereditary optic neuropathy, the most common primary mitochondrial genetic disease. We show that the expression of the mutant hND1 delivered to retinal ganglion cells (RGC) layer colocalizes with the mitochondrial marker PORIN and the assembly of the expressed hND1 protein into host respiration complex I. The hND1 injected eyes exhibit hallmarks of the human disease with progressive loss of RGC function and number, as well as optic nerve degeneration. We also show that gene therapy in the hND1 eyes by means of an injection of a second MTS-AAV vector carrying wild type human ND1 restores mitochondrial respiratory complex I activity, the rate of ATP synthesis and protects RGCs and their axons from dysfunction and degeneration. These results prove that MTS-AAV is a highly efficient gene delivery approach with the ability to create mito-animal models and has the therapeutic potential to treat mitochondrial genetic diseases.

Human embryonic genome activation initiates at the one-cell stage

In human embryos, the initiation of transcription (embryonic genome activation [EGA]) occurs by the eight-cell stage, but its exact timing and profile are unclear. To address this, we profiled gene expression at depth in human metaphase II oocytes and bipronuclear (2PN) one-cell embryos. High-resolution single-cell RNA sequencing revealed previously inaccessible oocyte-to-embryo gene expression changes. This confirmed transcript depletion following fertilization (maternal RNA degradation) but also uncovered low-magnitude upregulation of hundreds of spliced transcripts. Gene expression analysis predicted embryonic processes including cell-cycle progression and chromosome maintenance as well as transcriptional activators that included cancer-associated gene regulators. Transcription was disrupted in abnormal monopronuclear (1PN) and tripronuclear (3PN) one-cell embryos. These findings indicate that human embryonic transcription initiates at the one-cell stage, sooner than previously thought. The pattern of gene upregulation promises to illuminate processes involved at the onset of human development, with implications for epigenetic inheritance, stem-cell-derived embryos, and cancer.

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Gene expression initiates at the one-cell stage in human embryos

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Expression is of low magnitude but remains elevated until the eight-cell stage

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Upregulated transcripts are spliced and correspond to embryonic processes

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Upregulation is disrupted in morphologically abnormal one-cell embryos

Histone Modifications in Stem Cell Development and Their Clinical Implications

Human stem cells bear a great potential for multiple therapeutic applications but at the same time constitute a major threat to human health in the form of cancer stem cells. The molecular processes that govern stem cell maintenance or differentiation have been extensively studied in model organisms or cell culture, but it has been difficult to extrapolate these insights to therapeutic applications. Recent advances in the field suggest that local and global changes in histone modifications that affect chromatin structure could influence the capability of cells to either maintain their stem cell identity or differentiate into specialized cell types. The enzymes that regulate these modifications are therefore among the prime targets for potential drugs that can influence and potentially improve the therapeutic application of stem cells. In this review, we discuss recent findings on the role of histone modifications in stem cell regulation and their potential implications for clinical applications.

Stem cells characterization: OMICS reinforcing analytics

Stem cells hold outstanding potential to model and treat disease and are valuable tools in pharmacology and toxicology. Characterization of stem cells and derivatives still poses many challenges to ensure safe, efficacious, and reliable therapies. Regulatory agencies have defined key mandatory attributes related to identity, purity, sterility, and genomic integrity, however robust analytics to determine cell's potency are still a major challenge, in most cases assessed case-by-case. Importantly, the application of high-throughput 'omic tools is opening new perspectives on stem cell's research and development. Here, analytical methodologies currently employed to characterize stem cells' quality attributes are discussed, with special focus on 'omics as relevant tools for definition of cell's mechanism of action, and for potency assay development and assessment.

Epigenetic Regulation of the Nuclear and Mitochondrial Genomes: Involvement in Metabolism, Development, and Disease

Our understanding of the interactions between the nuclear and mitochondrial genomes is becoming increasingly important as they are extensively involved in establishing early development and developmental progression. Evidence from various biological systems indicates the interdependency between the genomes, which requires a high degree of compatibility and synchrony to ensure effective cellular function throughout development and in the resultant offspring. During development, waves of DNA demethylation, de novo methylation, and maintenance methylation act on the nuclear genome and typify oogenesis and pre- and postimplantation development. At the same time, significant changes in mitochondrial DNA copy number influence the metabolic status of the developing organism in a typically cell-type-specific manner. Collectively, at any given stage in development, these actions establish genomic balance that ensures each developmental milestone is met and that the organism's program for life is established.

Cancer Stem-Like Phenotype of Mitochondria Dysfunctional Hep3B Hepatocellular Carcinoma Cell Line

Mitochondria are major organelles that play various roles in cells, and mitochondrial dysfunction is the main cause of numerous diseases. Mitochondrial dysfunction also occurs in many cancer cells, and these changes are known to affect malignancy. The mitochondria of normal embryonic stem cells (ESCs) exist in an undifferentiated state and do not function properly. We hypothesized that mitochondrial dysfunction in cancer cells caused by the depletion of mitochondrial DNA might be similar to the mitochondrial state of ESCs. We generated mitochondria dysfunctional (ρ0) cells from the Hep3B hepatocellular carcinoma cell line and tested whether these ρ0 cells show cancer stem-like properties, such as self-renewal, chemotherapy resistance, and angiogenesis. Compared with Hep3B cells, the characteristics of each cancer stem-like cell were increased in Hep3B/ρ0 cells. The Hep3B/ρ0 cells formed a continuous and large sphere from a single cell. Additionally, the Hep3B/ρ0 cells showed resistance to the anticancer drug doxorubicin because of the increased expression of ATP-binding cassette Subfamily B Member 1. The Hep3B/ρ0 conditioned medium induced more and thicker blood vessels and increased the mobility and invasiveness of the blood vessel cells. Therefore, our data suggest that mitochondrial dysfunction can transform cancer cells into cancer stem-like cells.

Mitochondrial metabolism is a key regulator of the fibro-inflammatory and adipogenic stromal subpopulations in white adipose tissue

The adipose tissue stroma is a rich source of molecularly distinct stem and progenitor cell populations with diverse functions in metabolic regulation, adipogenesis, and inflammation. The ontology of these populations and the mechanisms that govern their behaviors in response to stimuli, such as overfeeding, however, are unclear. Here, we show that the developmental fates and functional properties of adipose platelet-derived growth factor receptor beta (PDGFRβ)+ progenitor subpopulations are tightly regulated by mitochondrial metabolism. Reducing the mitochondrial β-oxidative capacity of PDGFRβ+ cells via inducible expression of MitoNEET drives a pro-inflammatory phenotype in adipose progenitors and alters lineage commitment. Furthermore, disrupting mitochondrial function in PDGFRβ+ cells rapidly induces alterations in immune cell composition in lean mice and impacts expansion of adipose tissue in diet-induced obesity. The adverse effects on adipose tissue remodeling can be reversed by restoring mitochondrial activity in progenitors, suggesting therapeutic potential for targeting energy metabolism in these cells.

Both quiescent and proliferating cells circulate in the blood of the invasive apple snail Pomacea canaliculata

Gastropod hematopoiesis occurs at specialized tissues in some species, but the evidence also suggests that hemocyte generation is maybe widespread in the connective tissues or the blood system in others. In Ampullariidae (Caenogastropoda), both the kidney and the lung contain putative hematopoietic cells, which react to immune challenges. In the current study, we wanted to explore if hematopoiesis occurs in the blood of Pomacea canaliculata. Thus, we obtained circulating hemocytes from donor animals and tested their ability to proliferate in the blood of conspecific recipients. We tracked cell proliferation by labeling the donors' hemocytes with the fluorescent cell proliferation marker carboxyfluorescein diacetate succinimidyl ester (CFSE). Transferred CFSE-labeled hemocytes survived and proliferated into the recipients' circulation for at least 17 days. We also determined the cell cycle status of circulating hemocytes by using the propidium iodide (PI) and acridine orange (AO) staining methods. Flow cytometry analyses showed that most PI-stained hemocytes were in the G1 phase (~96%), while a lower proportion of cells were through the G2/S-M transition (~4%). When we instead used AO-staining, we further distinguished a subpopulation of cells (~5%) of low size, complexity-granularity, and RNA content. We regarded this subpopulation as quiescent cells. In separate experimental sets, we complemented these findings by assessing in circulating hemocytes two evolutionary conserved features of quiescent, undifferentiated cells. First, we used JC-1 staining to determine the mitochondrial membrane potential (Ψ_m) of circulating hemocytes, which is expected to be low in quiescent cells. Most hemocytes (~87%) showed high aggregation of JC-1, which indicates a high Ψ_m. Besides that, a small hemocyte subpopulation (~11%) showed low aggregation of the dye, thus indicating a low Ψ_m. It is known that the transition from a quiescent to a proliferating state associates with an increase of the Ψ_m. The specificity of these changes was here controlled by membrane depolarization with the Ψ_m disruptor CCCP. Second, we stained hemocytes with Hoechst33342 dye to determine the efflux activity of ABC transporters, which participate in the multixenobiotic resistance system characteristic of undifferentiated cells. Most hemocytes (>99%) showed a low dye-efflux activity, but a small proportion of cells (0.06-0.12%) showed a high dye-efflux activity, which was significantly inhibited by 100 and 500 μM verapamil, and thus is indicative of an undifferentiated subpopulation of circulating hemocytes. Taken together, our results suggest that, among circulating hemocytes, there are cells with the ability to proliferate or to stay in a quiescent state and behave as progenitor cells later, either in the circulation or the hematopoietic tissues/organs.

Low expression of mitofusin 1 is associated with mitochondrial dysfunction and apoptosis in porcine somatic cell nuclear transfer embryos

Mitochondria are necessary for the transition from oocyte to embryo and for early embryonic development. Mitofusin 1 is the main mediator of mitochondrial fusion and homeostasis. We investigated Mitofusin 1 expression levels in porcine somatic cell nuclear transfer (SCNT) embryos. The rate of blastocyst formation in SCNT embryos was reduced significantly compared with that of parthenogenetic activation embryos. SCNT embryos showed significantly decreased Mitofusin 1 expression and mitochondrial membrane potential, while exhibiting increased reactive oxygen species and apoptosis. Mitochondrial functional changes were observed in the SCNT embryos and may be correlated with low levels of Mitofusin 1 to negatively affect development.

Mechanisms of Congenital Malformations in Pregnancies with Pre-existing Diabetes

PURPOSE OF REVIEW

Fetuses of diabetic mothers are at increased risk for congenital malformations. Research in recent decades using animal and embryonic stem cell models has revealed many embryonic developmental processes that are disturbed by maternal diabetes. The aim of this review is to give clinicians a better understanding of the reasons for rigorous glycemic control in early pregnancy, and to provide background to guide future research.

RECENT FINDINGS

Mouse models of diabetic pregnancy have revealed mechanisms for altered expression of tissue-specific genes that lead to malformations that are more common in diabetic pregnancies, such as neural tube defects (NTDs) and congenital heart defects (CHDs), and how altered gene expression causes apoptosis that leads to malformations. Embryos express the glucose transporter, GLUT2, which confers susceptibility to malformation, due to high rates of glucose uptake during maternal hyperglycemia and subsequent oxidative stress; however, the teleological function of GLUT2 for mammalian embryos may be to transport the amino sugar glucosamine (GlcN) from maternal circulation to be used as substrate for glycosylation reactions and to promote embryo cell growth. Malformations in diabetic pregnancy may be not only due to excess glucose uptake but also due to insufficient GlcN uptake. Avoiding maternal hyperglycemia during early pregnancy should prevent excess glucose uptake via GLUT2 into embryo cells, and also permit sufficient GLUT2-mediated GlcN uptake.

Metabolic Changes Accompanying Spermatogonial Stem Cell Differentiation

Male fertility is driven by spermatogonial stem cells (SSCs) that self-renew while also giving rise to differentiating spermatogonia. Spermatogonial transitions are accompanied by a shift in gene expression, however, whether equivalent changes in metabolism occur remains unexplored. In this review, we mined recently published scRNA-seq databases from mouse and human testes to compare expression profiles of spermatogonial subsets, focusing on metabolism. Comparisons revealed a conserved upregulation of genes involved in mitochondrial function, biogenesis, and oxidative phosphorylation in differentiating spermatogonia, while gene expression in SSCs reflected a glycolytic cell. Here, we also discuss the relationship between metabolism and the external microenvironment within which spermatogonia reside.

Diet induced the change of mtDNA copy number and metabolism in Angus cattle

Background

Grass-fed and grain-fed Angus cattle differ in the diet regimes. However, the intricate mechanisms of different beef quality and other phenotypes induced by diet differences are still unclear. Diet affects mitochondrial function and dynamic behavior in response to changes in energy demand and supply. In this study, we examined the mtDNA copy number, mitochondria-related genes expression, and metabolic biomarkers in grass-fed and grain-fed Angus cattle.

Results

We found that the grass-fed group had a higher mtDNA copy number than the grain-fed group. Among different tissues, the mtDNA copy number was the highest in the liver than muscle, rumen, and spleen. Based on the transcriptome of the four tissues, a lower expression of mtDNA-encoded genes in the grass-fed group compared to the grain-fed group was discovered. For the mitochondria-related nuclear genes, however, most of them were significantly down-regulated in the muscle of the grass-fed group and up-regulated in the other three tissues. In which, COX6A2, POLG2, PPIF, DCN, and NDUFA12, involving in ATP synthesis, mitochondrial replication, transcription, and maintenance, might contribute to the alterations of mtDNA copy number and gene expression. Meanwhile, 40 and 23 metabolic biomarkers were identified in the blood and muscle of the grain-fed group compared to a grass-fed group, respectively. Integrated analysis of the altered metabolites and gene expression revealed the high expression level of MDH1 in the grain-fed group might contribute to the mitochondrial NADH oxidation and spermidine metabolism for adapting the deletion mtDNA copy number.

Conclusions

Overall, the study may provide further deep insight into the adaptive and regulatory modulations of the mitochondrial function in response to different feeding systems in Angus cattle.

Metabolic regulation of neurodifferentiation in the adult brain

Understanding the mechanisms behind neurodifferentiation in adults will be an important milestone in our quest to identify treatment strategies for cognitive disorders observed during our natural ageing or disease. It is now clear that the maturation of neural stem cells to neurones, fully integrated into neuronal circuits requires a complete remodelling of cellular metabolism, including switching the cellular energy source. Mitochondria are central for this transition and are increasingly seen as the regulatory hub in defining neural stem cell fate and neurodevelopment. This review explores our current knowledge of metabolism during adult neurodifferentiation.

TGFβ-dependent mitochondrial biogenesis is activated during definitive endoderm differentiation

Whether mitochondrial remodeling and metabolic reprogramming occur during the differentiation of human embryonic stem cells (hESCs) to definitive endoderm (DE) is unknown. We found that fragmented and punctate mitochondria in undifferentiated hESCs progressively fused into an extensive and branched network upon DE differentiation. Mitochondrial mass and mitochondrial DNA (mtDNA) content were significantly increased with the upregulated expression of mitochondrial biogenesis regulator PGC1-A upon DE differentiation, accompanied by the rise of the amount of ATP (2.5-fold) and its by-product reactive oxygen species (2.0-fold). We observed that in contrast to a shutoff of glycolysis, expressions of oxidative phosphorylation (OXPHOS) genes were increased, indicating that a transition from glycolysis to OXPHOS was tightly coupled to DE differentiation. In the meantime, we discovered that inhibition of TGF-β signaling led to impaired mitochondrial biogenesis and disturbed metabolic switch upon DE differentiation. Our work, for the first time, reports that TGF-β signaling-dependent mitochondrial biogenesis and metabolic reprogramming occur during early endodermal differentiation.

miR-379 links glucocorticoid treatment with mitochondrial response in Duchenne muscular dystrophy

Duchenne Muscular Dystrophy (DMD) is a lethal muscle disorder, caused by mutations in the DMD gene and affects approximately 1:5000-6000 male births. In this report, we identified dysregulation of members of the Dlk1-Dio3 miRNA cluster in muscle biopsies of the GRMD dog model. Of these, we selected miR-379 for a detailed investigation because its expression is high in the muscle, and is known to be responsive to glucocorticoid, a class of anti-inflammatory drugs commonly used in DMD patients. Bioinformatics analysis predicts that miR-379 targets EIF4G2, a translational factor, which is involved in the control of mitochondrial metabolic maturation. We confirmed in myoblasts that EIF4G2 is a direct target of miR-379, and identified the DAPIT mitochondrial protein as a translational target of EIF4G2. Knocking down DAPIT in skeletal myotubes resulted in reduced ATP synthesis and myogenic differentiation. We also demonstrated that this pathway is GC-responsive since treating mice with dexamethasone resulted in reduced muscle expression of miR-379 and increased expression of EIF4G2 and DAPIT. Furthermore, miR-379 seric level, which is also elevated in the plasma of DMD patients in comparison with age-matched controls, is reduced by GC treatment. Thus, this newly identified pathway may link GC treatment to a mitochondrial response in DMD.

Energy Metabolism Regulates Stem Cell Pluripotency

Pluripotent stem cells (PSCs) are characterized by their unique capacity for both unlimited self-renewal and their potential to differentiate to all cell lineages contained within the three primary germ layers. While once considered a distinct cellular state, it is becoming clear that pluripotency is in fact a continuum of cellular states, all capable of self-renewal and differentiation, yet with distinct metabolic, mitochondrial and epigenetic features dependent on gestational stage. In this review we focus on two of the most clearly defined states: “naïve” and “primed” PSCs. Like other rapidly dividing cells, PSCs have a high demand for anabolic precursors necessary to replicate their genome, cytoplasm and organelles, while concurrently consuming energy in the form of ATP. This requirement for both anabolic and catabolic processes sufficient to supply a highly adapted cell cycle in the context of reduced oxygen availability, distinguishes PSCs from their differentiated progeny. During early embryogenesis PSCs adapt their substrate preference to match the bioenergetic requirements of each specific developmental stage. This is reflected in different mitochondrial morphologies, membrane potentials, electron transport chain (ETC) compositions, and utilization of glycolysis. Additionally, metabolites produced in PSCs can directly influence epigenetic and transcriptional programs, which in turn can affect self-renewal characteristics. Thus, our understanding of the role of metabolism in PSC fate has expanded from anabolism and catabolism to include governance of the pluripotent epigenetic landscape. Understanding the roles of metabolism and the factors influencing metabolic pathways in naïve and primed pluripotent states provide a platform for understanding the drivers of cell fate during development. This review highlights the roles of the major metabolic pathways in the acquisition and maintenance of the different states of pluripotency.

A connection in life and death: The BCL-2 family coordinates mitochondrial network dynamics and stem cell fate

The B cell CLL/lymphoma-2 (BCL-2) family of proteins control the mitochondrial pathway of apoptosis, also known as intrinsic apoptosis. Direct binding between members of the BCL-2 family regulates mitochondrial outer membrane permeabilization (MOMP) after an apoptotic insult. The ability of the cell to sense stress and translate it into a death signal has been a major theme of research for nearly three decades; however, other mechanisms by which the BCL-2 family coordinates cellular homeostasis beyond its role in initiating apoptosis are emerging. One developing area of research is understanding how the BCL-2 family of proteins regulate development using pluripotent stem cells as a model system. Understanding BCL-2 family-mediated regulation of mitochondrial homeostasis in cell death and beyond would uncover new facets of stem cell maintenance and differentiation potential.

Genomic Balance: Two Genomes Establishing Synchrony to Modulate Cellular Fate and Function

It is becoming increasingly apparent that cells require cooperation between the nuclear and mitochondrial genomes to promote effective function. However, it was long thought that the mitochondrial genome was under the strict control of the nuclear genome and the mitochondrial genome had little influence on cell fate unless it was extensively mutated, as in the case of the mitochondrial DNA diseases. However, as our understanding of the roles that epigenetic regulators, including DNA methylation, and metabolism play in cell fate and function, the role of the mitochondrial genome appears to have a greater influence than previously thought. In this review, I draw on examples from tumorigenesis, stem cells, and oocyte pre- and post-fertilisation events to discuss how modulating one genome affects the other and that this results in a compromise to produce functional mature cells. I propose that, during development, both of the genomes interact with each other through intermediaries to establish genomic balance and that establishing genomic balance is a key facet in determining cell fate and viability.

Differential redox-regulation and mitochondrial dynamics in normal and leukemic hematopoietic stem cells: A potential window for leukemia therapy

The prognosis for many patients with acute myeloid leukemia (AML) is poor, mainly due to disease relapse driven by leukemia stem cells (LSCs). Recent studies have highlighted the unique metabolic properties of LSCs, which might represent opportunities for LSC-selective targeting. LSCs characteristically have low levels of reactive oxygen species (ROS), which apparently result from a combination of low mitochondrial activity and high activity of ROS-removing pathways such as autophagy. Due to this low activity, LSCs are highly dependent on mitochondrial regulatory mechanisms. These include the anti-apoptotic protein BCL-2, which also has crucial roles in regulating the mitochondrial membrane potential, and proteins involved in mitophagy. Here we review the different pathways that impact mitochondrial activity and redox-regulation, and highlight their relevance for the functionality of both HSCs and LSCs. Additionally, novel AML therapy strategies that are based on interference with those pathways, including the promising BCL-2 inhibitor Venetoclax, are summarized.

Effect of PPARGC1A on the development and metabolism of early rabbit embryos in vitro

Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPARGC1A) is a central regulator of mitochondrial biogenesis and metabolism, and its expression is closely related to embryo development. To gain insights into the possible mechanisms of PPARGC1A during early embryogenesis, the development potential, mitochondrial biogenesis, and the culture medium metabolomics of embryos were evaluated when PPARGC1A overexpressed or suppressed in rabbit zygotes. Results showed that different PPARGC1A levels in rabbit zygotes could affect blastocyst percentage, and the expressions of mitochondrial biogenesis and metabolic-related genes, as well as the glutathione and adenosine triphosphate levels during early embryo development. In addition, compared with the controls, 12 and 10 different metabolites involved in carbohydrate, amino acid, and fatty acid metabolism were screened in the 5 day's spent culture medium of PPARGC1A overexpressed and suppressed embryos by gas chromatography-mass spectrometer, respectively. Consistent with these metabolite changes, the transcriptions of genes encoding glucose transporters and fatty acid biosynthetic proteins in the embryos from different groups were regulated by PPARGC1A during rabbit embryo development. Taken together, these data provide evidence that PPARGC1A may regulate early rabbit embryo development through mitochondrial biogenesis and metabolism.

Mitochondria and Female Germline Stem Cells-A Mitochondrial DNA Perspective

Mitochondria and mitochondrial DNA have important roles to play in development. In primordial germ cells, they progress from small numbers to populate the maturing oocyte with high numbers to support post-fertilization events. These processes take place under the control of significant changes in DNA methylation and other epigenetic modifiers, as well as changes to the DNA methylation status of the nuclear-encoded mitochondrial DNA replication factors. Consequently, the differentiating germ cell requires significant synchrony between the two genomes in order to ensure that they are fit for purpose. In this review, I examine these processes in the context of female germline stem cells that are isolated from the ovary and those derived from embryonic stem cells and reprogrammed somatic cells. Although our knowledge is limited in this respect, I provide predictions based on other cellular systems of what is expected and provide insight into how these cells could be used in clinical medicine.

Global DNA methylation synergistically regulates the nuclear and mitochondrial genomes in glioblastoma cells

Replication of mitochondrial DNA is strictly regulated during differentiation and development allowing each cell type to acquire its required mtDNA copy number to meet its specific needs for energy. Undifferentiated cells establish the mtDNA set point, which provides low numbers of mtDNA copy but sufficient template for replication once cells commit to specific lineages. However, cancer cells, such as those from the human glioblastoma multiforme cell line, HSR-GBM1, cannot complete differentiation as they fail to enforce the mtDNA set point and are trapped in a ‘pseudo-differentiated’ state. Global DNA methylation is likely to be a major contributing factor, as DNA demethylation treatments promote differentiation of HSR-GBM1 cells. To determine the relationship between DNA methylation and mtDNA copy number in cancer cells, we applied whole genome MeDIP-Seq and RNA-Seq to HSR-GBM1 cells and following their treatment with the DNA demethylation agents 5-azacytidine and vitamin C. We identified key methylated regions modulated by the DNA demethylation agents that also induced synchronous changes to mtDNA copy number and nuclear gene expression. Our findings highlight the control exerted by DNA methylation on the expression of key genes, the regulation of mtDNA copy number and establishment of the mtDNA set point, which collectively contribute to tumorigenesis.

Remodeling of mitochondrial morphology and function: an emerging hallmark of cellular reprogramming

Research in the stem cell field has traditionally focused on understanding key transcriptional factors that provide pluripotent cell identity. However, much less is known about other critical non-transcriptional signaling networks that govern stem cell identity. Although we continue to gain critical insights into the mechanisms underlying mitochondrial morphology and function during cellular reprogramming – the process of reverting the fate of a differentiated cell into a stem cell, many uncertainties remain. Recent studies suggest an emerging landscape in which mitochondrial morphology and function have an active role in maintaining and regulating changes in cell identity. In this review, we will focus on these emerging concepts as crucial modulators of cellular reprogramming. Recognition of the widespread applicability of these concepts will increase our understanding of the mitochondrial mechanisms involved in cell identity, cell fate and disease.

Mechanisms of the Metabolic Shift during Somatic Cell Reprogramming

Pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), hold a huge promise for regenerative medicine, drug development, and disease modeling. PSCs have unique metabolic features that are akin to those of cancer cells, in which glycolysis predominates to produce energy as well as building blocks for cellular components. Recent studies indicate that the unique metabolism in PSCs is not a mere consequence of their preference for a low oxygen environment, but is an active process for maintaining self-renewal and pluripotency, possibly in preparation for rapid response to the metabolic demands of differentiation. Understanding the regulatory mechanisms of this unique metabolism in PSCs is essential for proper derivation, generation, and maintenance of PSCs. In this review, we discuss the metabolic features of PSCs and describe the current understanding of the mechanisms of the metabolic shift during reprogramming from somatic cells to iPSCs, in which the metabolism switches from oxidative phosphorylation (OxPhos) to glycolysis.

Glioblastoma Stem-Like Cells, Metabolic Strategy to Kill a Challenging Target

Over the years, substantial evidence has definitively confirmed the existence of cancer stem-like cells within tumors such as Glioblastoma (GBM). The importance of Glioblastoma stem-like cells (GSCs) in tumor progression and relapse clearly highlights that cancer eradication requires killing of GSCs that are intrinsically resistant to conventional therapies as well as eradication of the non-GSCs cells since GSCs emergence relies on a dynamic process. The past decade of research highlights that metabolism is a significant player in tumor progression and actually might orchestrate it. The growing interest in cancer metabolism reprogrammation can lead to innovative approaches exploiting metabolic vulnerabilities of cancer cells. These approaches are challenging since they require overcoming the compensatory and adaptive responses of GSCs. In this review, we will summarize the current knowledge on GSCs with a particular focus on their metabolic complexity. We will also discuss potential approaches targeting GSCs metabolism to potentially improve clinical care.

Terminal Uridylyltransferases Execute Programmed Clearance of Maternal Transcriptome in Vertebrate Embryos

During the maternal-to-zygotic transition (MZT), maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However, it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here, through genome-wide profiling of RNA abundance and 3' modification, we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 (TUT4/7) are depleted in zebrafish and Xenopus, maternal mRNA clearance is significantly delayed, leading to developmental defects during gastrulation. Short-tailed mRNAs are selectively uridylated by TUT4/7, with the highly uridylated transcripts degraded faster during the MZT than those with unmodified poly(A) tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation, thereby allowing the progression of early development.

Transmission of Dysfunctional Mitochondrial DNA and Its Implications for Mammalian Reproduction

Mitochondrial DNA (mtDNA) encodes proteins for the electron transport chain which produces the vast majority of cellular energy. MtDNA has its own replication and transcription machinery that relies on nuclear-encoded transcription and replication factors. MtDNA is inherited in a non-Mendelian fashion as maternal-only mtDNA is passed onto the next generation. Mutation to mtDNA can cause mitochondrial dysfunction, which affects energy production and tissue and organ function. In somatic cell nuclear transfer (SCNT), there is an issue with the mixing of two populations of mtDNA, namely from the donor cell and recipient oocyte. This review focuses on the transmission of mtDNA in SCNT embryos and offspring. The transmission of donor cell mtDNA can be prevented by depleting the donor cell of its mtDNA using mtDNA depletion agents prior to SCNT. As a result, SCNT embryos harbour oocyte-only mtDNA. Moreover, culturing SCNT embryos derived from mtDNA depleted cells in media supplemented with a nuclear reprograming agent can increase the levels of expression of genes related to embryo development when compared with non-depleted cell-derived embryos. Furthermore, we have reviewed how mitochondrial supplementation in oocytes can have beneficial effects for SCNT embryos by increasing mtDNA copy number and the levels of expression of genes involved in energy production and decreasing the levels of expression of genes involved in embryonic cell death. Notably, there are beneficial effects of mtDNA supplementation over the use of nuclear reprograming agents in terms of regulating gene expression in embryos. Taken together, manipulating mtDNA in donor cells and/or oocytes prior to SCNT could enhance embryo production efficiency.

The degree of mitochondrial DNA methylation in tumor models of glioblastoma and osteosarcoma

Background

Different cell types possess different copies of mtDNA to support their specific requirements for cellular metabolism. Cell-specific mtDNA copy numbers are established through cell-specific mtDNA replication during cell differentiation. However, cancer cells are trapped in a “pseudo-differentiated” state as they fail to expand mtDNA copy number. Global DNA methylation can regulate this process, as induced DNA demethylation promotes differentiation of cancer cells and expansion of mtDNA copy number.

Results

To determine the role that mtDNA methylation plays in regulating mtDNA replication during tumorigenesis, we have characterized the patterns of mtDNA methylation using glioblastoma and osteosarcoma tumor models that have different combinations of mtDNA genotypes and copy number against common nuclear genome backgrounds at different stages of tumor progression. To ensure the reliability of the findings, we have applied a robust experimental pipeline including three approaches, namely whole-mtDNA bisulfite-sequencing with mtDNA-genotype-specific analysis, pyrosequencing, and methylated immunoprecipitation against 5mC and 5hmC. We have determined genotype-specific methylation profiles, which were modulated through tumor progression. Moreover, a strong influence from the nuclear genome was also observed on mtDNA methylation patterns using the same mtDNA genotype under different nuclear genomes. Furthermore, the numbers of mtDNA copy in tumor-initiating cells affected mtDNA methylation levels in late-stage tumors.

Conclusions

Our findings highlight the influences that the nuclear and mitochondrial genomes have in setting mtDNA methylation patterns to regulate mtDNA copy number in tumorigenesis. They have important implications for assessing global DNA methylation patterns in tumorigenesis and the availability of mtDNA template for mtDNA replication.

Electronic supplementary material

The online version of this article (10.1186/s13148-018-0590-0) contains supplementary material, which is available to authorized users.

New Challenge: Mitochondrial Epigenetics?

Epigenetics can be explored at different levels and can be divided into two major areas: epigenetics of nuclear-encoded DNA and epigenetics of mitochondrial-encoded DNA. In epigenetics of nuclear-encoded DNA, the main roles are played by DNA methylation, changes in histone structure and several types of non-coding RNAs. Mitochondrial epigenetics seems to be similar in the aspect of DNA methylation and to some extent in the role of non-coding RNAs but differs significantly in changes in components coiling DNA. Nuclear DNA is coiled around histones, but mitochondrial DNA, together with associated proteins, is located in mitochondrial pseudocompartments called nucleoids. It has been shown that mitochondrial epigenetic mechanisms influence cell fate, transcription regulation, cell division, cell cycle, physiological homeostasis, bioenergetics and even pathologies, but not all of these mechanisms have been explored in stem cells. The main issue is that most of these mechanisms have only recently been discovered in mitochondria, while improvements in methodology, especially next-generation sequencing, have enabled in-depth studies. Because studies exploring mitochondria from other aspects show that mitochondria are crucial for the normal behavior of stem cells, it is suggested that precise mitochondrial epigenetics in stem cells should be studied more intensively.

Mitochondria in Developmental and Adult Neurogenesis

Generation of new neurons is a tightly regulated process that involves several intrinsic and extrinsic factors. Among them, a metabolic switch from glycolysis to oxidative phosphorylation, together with mitochondrial remodeling, has emerged as crucial actors of neurogenesis. However, although accumulating data raise the importance of mitochondrial morphology and function in neural stem cell proliferation and differentiation during development, information regarding the contribution of mitochondria to adult neurogenesis processes remains limited. In the present review, we discuss recent evidence covering the importance of mitochondrial morphology, function, and energy metabolism in the regulation of neuronal development and adult neurogenesis, and their impact on memory processes.

Modulation of mitochondrial DNA copy number in a model of glioblastoma induces changes to DNA methylation and gene expression of the nuclear genome in tumours

Background

There are multiple copies of mitochondrial DNA (mtDNA) present in each cell type, and they are strictly regulated in a cell-specific manner by a group of nuclear-encoded mtDNA-specific replication factors. This strict regulation of mtDNA copy number is mediated by cell-specific DNA methylation of these replication factors. Glioblastoma multiforme, HSR-GBM1, cells are hyper-methylated and maintain low mtDNA copy number to support their tumorigenic status. We have previously shown that when HSR-GBM1 cells with 50% of their original mtDNA content were inoculated into mice, tumours grew more aggressively than non-depleted cells. However, when the cells possessed only 3% and 0.2% of their original mtDNA content, tumour formation was less frequent and the initiation of tumorigenesis was significantly delayed. Importantly, the process of tumorigenesis was dependent on mtDNA copy number being restored to pre-depletion levels.

Results

By performing whole genome MeDIP-Seq and RNA-Seq on tumours generated from cells possessing 100%, 50%, 0.3% and 0.2% of their original mtDNA content, we determined that restoration of mtDNA copy number caused significant changes to both the nuclear methylome and its transcriptome for each tumour type. The affected genes were specifically associated with gene networks and pathways involving behaviour, nervous system development, cell differentiation and regulation of transcription and cellular processes. The mtDNA-specific replication factors were also modulated.

Conclusions

Our results highlight the bidirectional control of the nuclear and mitochondrial genomes through modulation of DNA methylation to control mtDNA copy number, which, in turn, modulates nuclear gene expression during tumorigenesis.

Electronic supplementary material

The online version of this article (10.1186/s13072-018-0223-z) contains supplementary material, which is available to authorized users.

Bioenergetic Health Assessment of a Single Caenorhabditis elegans from Postembryonic Development to Aging Stages via Monitoring Changes in the Oxygen Consumption Rate within a Microfluidic Device

Monitoring dynamic changes in oxygen consumption rates (OCR) of a living organism in real time provide an indirect method of monitoring changes in mitochondrial function during development, aging, or malfunctioning processes. In this study, we developed a microfluidic device integrated with an optical detection system to measure the OCR of a single developing Caenorhabditis elegans (C. elegans) from postembryonic development to aging stages in real time via phase-based phosphorescence lifetime measurement. The device consists of two components: an acrylic microwell deposited with an oxygen-sensitive luminescent layer for oxygen (O₂) measurement and a microfluidic module with a pneumatically driven acrylic lid to controllably seal the microwell. We successfully measured the basal respiration (basal OCR, in pmol O₂/min/worm) of a single C. elegans inside a microwell from the stages of postembryonic development (larval stages) through adulthood to aged adult. Sequentially adding metabolic inhibitors to block bioenergetic pathways allowed us to measure the metabolic profiles of a single C. elegans at key growth and aging stages, determining the following fundamental parameters: basal OCR, adenosine triphosphate (ATP)-linked OCR, maximal OCR, reserve respiratory capacity, OCR due to proton leak, and non-mitochondrial OCR. The bioenergetic health index (BHI) was calculated from these fundamental parameters to assess the bioenergetic health of a single developing C. elegans from the postembryonic development to aging stages. The changes in BHI are correlated to C. elegans development stage, with the highest BHI = 27.5 for 4-day-old adults, which possess well-developed bioenergetic functionality. Our proposed platform demonstrates for the first time the feasibility of assessing the BHI of a single C. elegans from postembryonic development to aging stages inside a microfluidic device and provides the potential for a wide variety of biomedical applications that relate mitochondrial malfunction and diseases.

Random Mutagenesis, Clonal Events, and Embryonic or Somatic Origin Determine the mtDNA Variant Type and Load in Human Pluripotent Stem Cells

In this study, we deep-sequenced the mtDNA of human embryonic and induced pluripotent stem cells (hESCs and hiPSCs) and their source cells and found that the majority of variants pre-existed in the cells used to establish the lines. Early-passage hESCs carried few and low-load heteroplasmic variants, similar to those identified in oocytes and inner cell masses. The number and heteroplasmic loads of these variants increased with prolonged cell culture. The study of 120 individual cells of early- and late-passage hESCs revealed a significant diversity in mtDNA heteroplasmic variants at the single-cell level and that the variants that increase during time in culture are always passenger to the appearance of chromosomal abnormalities. We found that early-passage hiPSCs carry much higher loads of mtDNA variants than hESCs, which single-fibroblast sequencing proved pre-existed in the source cells. Finally, we show that these variants are stably transmitted during short-term differentiation.