1
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Perez-Estrada JR, Tangeman JA, Proto-Newton M, Sanaka H, Smucker B, Del Rio-Tsonis K. Metabolic states influence chicken retinal pigment epithelium cell fate decisions. Development 2024; 151:dev202462. [PMID: 39120084 DOI: 10.1242/dev.202462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 07/08/2024] [Indexed: 08/10/2024]
Abstract
During tissue regeneration, proliferation, dedifferentiation and reprogramming are necessary to restore lost structures. However, it is not fully understood how metabolism intersects with these processes. Chicken embryos can regenerate their retina through retinal pigment epithelium (RPE) reprogramming when treated with fibroblast factor 2 (FGF2). Using transcriptome profiling, we uncovered extensive regulation of gene sets pertaining to proliferation, neurogenesis and glycolysis throughout RPE-to-neural retina reprogramming. By manipulating cell media composition, we determined that glucose, glutamine or pyruvate are individually sufficient to support RPE reprogramming, identifying glycolysis as a requisite. Conversely, the activation of pyruvate dehydrogenase by inhibition of pyruvate dehydrogenase kinases, induces epithelial-to-mesenchymal transition, while simultaneously blocking the activation of neural retina fate. We also identified that epithelial-to-mesenchymal transition fate is partially driven by an oxidative environment. Our findings provide evidence that metabolism controls RPE cell fate decisions and provide insights into the metabolic state of RPE cells, which are prone to fate changes in regeneration and pathologies, such as proliferative vitreoretinopathy.
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Affiliation(s)
- J Raúl Perez-Estrada
- Department of Biology, Miami University, Oxford, OH 45056, USA
- Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | - Jared A Tangeman
- Department of Biology, Miami University, Oxford, OH 45056, USA
- Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
| | | | | | - Byran Smucker
- Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
- Department of Statistics, Miami University, Oxford, OH 45056, USA
| | - Katia Del Rio-Tsonis
- Department of Biology, Miami University, Oxford, OH 45056, USA
- Center for Visual Sciences, Miami University, Oxford, OH 45056, USA
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2
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Taniguchi T, Okahashi N, Matsuda F. 13C-metabolic flux analysis reveals metabolic rewiring in HL-60 neutrophil-like cells through differentiation and immune stimulation. Metab Eng Commun 2024; 18:e00239. [PMID: 38883865 PMCID: PMC11176794 DOI: 10.1016/j.mec.2024.e00239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/18/2024] Open
Abstract
Neutrophils are innate immune cells and the first line of defense for the maintenance of homeostasis. However, our knowledge of the metabolic rewiring associated with their differentiation and immune stimulation is limited. Here, quantitative 13C-metabolic flux analysis was performed using HL-60 cells as the neutrophil model. A metabolic model for 13C-metabolic flux analysis of neutrophils was developed based on the accumulation of 13C in intracellular metabolites derived from 13C-labeled extracellular carbon sources and intracellular macromolecules. Aspartate and glutamate in the medium were identified as carbon sources that enter central carbon metabolism. Furthermore, the breakdown of macromolecules, estimated to be fatty acids and nucleic acids, was observed. Based on these results, a modified metabolic model was used for 13C-metabolic flux analysis of undifferentiated, differentiated, and lipopolysaccharide (LPS)-activated HL-60 cells. The glucose uptake rate and glycolytic flux decreased with differentiation, whereas the tricarboxylic acid (TCA) cycle flux remained constant. The addition of LPS to differentiated HL-60 cells activated the glucose uptake rate and pentose phosphate pathway (PPP) flux levels, resulting in an increased rate of total NADPH regeneration, which could be used to generate reactive oxygen species. The flux levels of fatty acid degradation and synthesis were also increased in LPS-activated HL-60 cells. Overall, this study highlights the quantitative metabolic alterations in multiple pathways via the differentiation and activation of HL-60 cells using 13C-metabolic flux analysis.
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Affiliation(s)
- Takeo Taniguchi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Department of Biotechnology, Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Department of Biotechnology, Osaka University Shimadzu Analytical Innovation Research Laboratory, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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Kim HK, Song Y, Kye M, Yu B, Park SB, Kim JH, Moon SH, Choi H, Moon JS, Oh JS, Lee MR. Energy Metabolism in Human Pluripotent Stem and Differentiated Cells Compared Using a Seahorse XF96 Extracellular Flux Analyzer. Int J Stem Cells 2024; 17:194-203. [PMID: 38664993 PMCID: PMC11170120 DOI: 10.15283/ijsc23167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 05/30/2024] Open
Abstract
Evaluating cell metabolism is crucial during pluripotent stem cell (PSC) differentiation and somatic cell reprogramming as it affects cell fate. As cultured stem cells are heterogeneous, a comparative analysis of relative metabolism using existing metabolic analysis methods is difficult, resulting in inaccuracies. In this study, we measured human PSC basal metabolic levels using a Seahorse analyzer. We used fibroblasts, human induced PSCs, and human embryonic stem cells to monitor changes in basal metabolic levels according to cell number and determine the number of cells suitable for analysis. We evaluated normalization methods using glucose and selected the most suitable for the metabolic analysis of heterogeneous PSCs during the reprogramming stage. The response of fibroblasts to glucose increased with starvation time, with oxygen consumption rate and extracellular acidification rate responding most effectively to glucose 4 hours after starvation and declining after 5 hours of starvation. Fibroblasts and PSCs achieved appropriate responses to glucose without damaging their metabolism 2∼4 and 2∼3 hours after starvation, respectively. We developed a novel method for comparing basal metabolic rates of fibroblasts and PSCs, focusing on quantitative analysis of glycolysis and oxidative phosphorylation using glucose without enzyme inhibitors. This protocol enables efficient comparison of energy metabolism among cell types, including undifferentiated PSCs, differentiated cells, and cells undergoing cellular reprogramming, and addresses critical issues, such as differences in basal metabolic levels and sensitivity to normalization, providing valuable insights into cellular energetics.
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Affiliation(s)
- Hyun Kyu Kim
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soon Chun Hyang University, Cheonan, Korea
- Dementia Research Group, Korea Brain Research Institute (KBRI), Daegu, Korea
| | - Yena Song
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soon Chun Hyang University, Cheonan, Korea
| | - Minji Kye
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soon Chun Hyang University, Cheonan, Korea
| | - Byeongho Yu
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soon Chun Hyang University, Cheonan, Korea
| | - Sang Beom Park
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soon Chun Hyang University, Cheonan, Korea
| | - Ji Hyeon Kim
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soon Chun Hyang University, Cheonan, Korea
| | - Sung-Hwan Moon
- Department of Animal Science and Technology College of Biotechnology, Chung-Ang University, Anseong, Korea
| | - Hyungkyu Choi
- Department of Animal Science and Technology College of Biotechnology, Chung-Ang University, Anseong, Korea
| | - Jong-Seok Moon
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soon Chun Hyang University, Cheonan, Korea
| | - Jae Sang Oh
- Department of Neurosurgery, Uijeonbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Man Ryul Lee
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soon Chun Hyang University, Cheonan, Korea
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4
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Ayyamperumal P, Naik HC, Naskar AJ, Bammidi LS, Gayen S. Epigenomic states contribute to coordinated allelic transcriptional bursting in iPSC reprogramming. Life Sci Alliance 2024; 7:e202302337. [PMID: 38320809 PMCID: PMC10847334 DOI: 10.26508/lsa.202302337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Two alleles of a gene can be transcribed independently or coordinatedly, which can lead to temporal expression heterogeneity with potentially distinct impacts on cell fate. Here, we profiled genome-wide allelic transcriptional burst kinetics during the reprogramming of MEF to induced pluripotent stem cells. We show that the degree of coordination of allelic bursting differs among genes, and alleles of many reprogramming-related genes burst in a highly coordinated fashion. Notably, we show that the chromatin accessibility of the two alleles of highly coordinated genes is similar, unlike the semi-coordinated or independent genes, suggesting the degree of coordination of allelic bursting is linked to allelic chromatin accessibility. Consistently, we show that many transcription factors have differential binding affinity between alleles of semi-coordinated or independent genes. We show that highly coordinated genes are enriched with chromatin accessibility regulators such as H3K4me3, H3K4me1, H3K36me3, H3K27ac, histone variant H3.3, and BRD4. Finally, we demonstrate that enhancer elements are highly enriched in highly coordinated genes. Our study demonstrates that epigenomic states contribute to coordinated allelic bursting to fine-tune gene expression during induced pluripotent stem cell reprogramming.
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Affiliation(s)
- Parichitran Ayyamperumal
- https://ror.org/04dese585 Chromatin, RNA and Genome (CRG) Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Hemant Chandru Naik
- https://ror.org/04dese585 Chromatin, RNA and Genome (CRG) Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Amlan Jyoti Naskar
- https://ror.org/04dese585 Chromatin, RNA and Genome (CRG) Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Lakshmi Sowjanya Bammidi
- https://ror.org/04dese585 Chromatin, RNA and Genome (CRG) Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Srimonta Gayen
- https://ror.org/04dese585 Chromatin, RNA and Genome (CRG) Laboratory, Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
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5
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Sendera A, Adamczyk-Grochala J, Pikuła B, Cholewa M, Banaś-Ząbczyk A. Electromagnetic field (50 Hz) enhance metabolic potential and induce adaptive/reprogramming response mediated by the increase of N6-methyladenosine RNA methylation in adipose-derived mesenchymal stem cells in vitro. Toxicol In Vitro 2024; 95:105743. [PMID: 38040129 DOI: 10.1016/j.tiv.2023.105743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 11/08/2023] [Accepted: 11/24/2023] [Indexed: 12/03/2023]
Abstract
BACKGROUND Electromagnetic fields (EMF) have an impact on numerous cellular processes. It can positively and negatively affect adipose-derived stem cells (ASCs) thus their fate through the influence of specific factors and protein secretion. EMF can be a great factor for preconditioning ASCs for regenerative medicine purposes, however, understanding the cell's biological response to its effects in vitro is essential. METHODS ASCs were exposed to the EMF (50 Hz; 1.5 mT) for 24 and 48 h, and then cell biological response was analyzed. RESULTS 24 h exposure of ASCs to EMF, significantly increased N6-methyladenosine (m6A) RNA methylation, indicating epitranscriptomic changes as an important factor in ASCs preconditioning. Furthermore, the expression of stem cell markers such as Nanog, Oct-4, Sox-2, CD44, and CD105 increased after 24 h of EMF exposure. Besides, western blot analysis showed upregulation of p21 and DNMT2/TRDMT1 protein levels compared to control cells with no differences in the p53 profile. Moreover, after 24 h of exposure to EMF, cell membrane flexibility, the metabolic potential of cells as well as the distribution, morphology, and metabolism of mitochondria were altered. CONCLUSION ASCs undergo a process of mobilization and adaptation under the EMF influence through the increased m6A RNA modifications. These conditions may "force" ASCs to redefine their stem cell fate mediated by RNA-modifying enzymes and alter their reprogramming decision of as differentiation begins.
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Affiliation(s)
- Anna Sendera
- Department of Biology, Institute of Medical Sciences, Medical College of Rzeszow University, Rzeszow, Poland
| | - Jagoda Adamczyk-Grochala
- Department of Biotechnology, Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Barbara Pikuła
- Department of Biology, Institute of Medical Sciences, Medical College of Rzeszow University, Rzeszow, Poland
| | - Marian Cholewa
- Institute of Physics, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Agnieszka Banaś-Ząbczyk
- Department of Biology, Institute of Medical Sciences, Medical College of Rzeszow University, Rzeszow, Poland.
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6
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Zhang C, Meng Y, Han J. Emerging roles of mitochondrial functions and epigenetic changes in the modulation of stem cell fate. Cell Mol Life Sci 2024; 81:26. [PMID: 38212548 PMCID: PMC11072137 DOI: 10.1007/s00018-023-05070-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 01/13/2024]
Abstract
Mitochondria serve as essential organelles that play a key role in regulating stem cell fate. Mitochondrial dysfunction and stem cell exhaustion are two of the nine distinct hallmarks of aging. Emerging research suggests that epigenetic modification of mitochondria-encoded genes and the regulation of epigenetics by mitochondrial metabolites have an impact on stem cell aging or differentiation. Here, we review how key mitochondrial metabolites and behaviors regulate stem cell fate through an epigenetic approach. Gaining insight into how mitochondria regulate stem cell fate will help us manufacture and preserve clinical-grade stem cells under strict quality control standards, contributing to the development of aging-associated organ dysfunction and disease.
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Affiliation(s)
- Chensong Zhang
- State Key Laboratory of Biotherapy and Cancer Center, Frontiers Science Center for Disease-Related Molecular Network, and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yang Meng
- State Key Laboratory of Biotherapy and Cancer Center, Frontiers Science Center for Disease-Related Molecular Network, and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Junhong Han
- State Key Laboratory of Biotherapy and Cancer Center, Frontiers Science Center for Disease-Related Molecular Network, and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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7
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Sinenko SA, Tomilin AN. Metabolic control of induced pluripotency. Front Cell Dev Biol 2024; 11:1328522. [PMID: 38274274 PMCID: PMC10808704 DOI: 10.3389/fcell.2023.1328522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/13/2023] [Indexed: 01/27/2024] Open
Abstract
Pluripotent stem cells of the mammalian epiblast and their cultured counterparts-embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs)-have the capacity to differentiate in all cell types of adult organisms. An artificial process of reactivation of the pluripotency program in terminally differentiated cells was established in 2006, which allowed for the generation of induced pluripotent stem cells (iPSCs). This iPSC technology has become an invaluable tool in investigating the molecular mechanisms of human diseases and therapeutic drug development, and it also holds tremendous promise for iPSC applications in regenerative medicine. Since the process of induced reprogramming of differentiated cells to a pluripotent state was discovered, many questions about the molecular mechanisms involved in this process have been clarified. Studies conducted over the past 2 decades have established that metabolic pathways and retrograde mitochondrial signals are involved in the regulation of various aspects of stem cell biology, including differentiation, pluripotency acquisition, and maintenance. During the reprogramming process, cells undergo major transformations, progressing through three distinct stages that are regulated by different signaling pathways, transcription factor networks, and inputs from metabolic pathways. Among the main metabolic features of this process, representing a switch from the dominance of oxidative phosphorylation to aerobic glycolysis and anabolic processes, are many critical stage-specific metabolic signals that control the path of differentiated cells toward a pluripotent state. In this review, we discuss the achievements in the current understanding of the molecular mechanisms of processes controlled by metabolic pathways, and vice versa, during the reprogramming process.
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Affiliation(s)
- Sergey A. Sinenko
- Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
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8
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Hollands P, Ovokaitys T. New Concepts in the Manipulation of the Aging Process. Curr Stem Cell Res Ther 2024; 19:178-184. [PMID: 36752298 DOI: 10.2174/1574888x18666230208102635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 02/09/2023]
Abstract
This review explores the current concepts in aging and then goes on to describe a novel, ground-breaking technology which will change the way we think about and manage aging. The foundation of the review is based on the work carried out on the QiLaser activation of human Very Small Embryonic Like (hVSEL) pluripotent stem cells in autologous Platelet Rich Plasma (PRP), known as the Qigeneration Procedure. The application of this technology in anti-aging technology is discussed with an emphasis on epigenetic changes during aging focusing on DNA methylation.
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Affiliation(s)
- Peter Hollands
- CTO Qigenix, 6125 Paseo Del Norte, Suite 140, Carlsbad, CA 92008, USA
| | - Todd Ovokaitys
- CEO Qigenix, 6125 Paseo Del Norte, Suite 140, Carlsbad, CA 92008, USA
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9
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Rosety I, Zagare A, Saraiva C, Nickels S, Antony P, Almeida C, Glaab E, Halder R, Velychko S, Rauen T, Schöler HR, Bolognin S, Sauter T, Jarazo J, Krüger R, Schwamborn JC. Impaired neuron differentiation in GBA-associated Parkinson's disease is linked to cell cycle defects in organoids. NPJ Parkinsons Dis 2023; 9:166. [PMID: 38110400 PMCID: PMC10728202 DOI: 10.1038/s41531-023-00616-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 12/04/2023] [Indexed: 12/20/2023] Open
Abstract
The mechanisms underlying Parkinson's disease (PD) etiology are only partially understood despite intensive research conducted in the field. Recent evidence suggests that early neurodevelopmental defects might play a role in cellular susceptibility to neurodegeneration. To study the early developmental contribution of GBA mutations in PD we used patient-derived iPSCs carrying a heterozygous N370S mutation in the GBA gene. Patient-specific midbrain organoids displayed GBA-PD relevant phenotypes such as reduction of GCase activity, autophagy impairment, and mitochondrial dysfunction. Genome-scale metabolic (GEM) modeling predicted changes in lipid metabolism which were validated with lipidomics analysis, showing significant differences in the lipidome of GBA-PD. In addition, patient-specific midbrain organoids exhibited a decrease in the number and complexity of dopaminergic neurons. This was accompanied by an increase in the neural progenitor population showing signs of oxidative stress-induced damage and premature cellular senescence. These results provide insights into how GBA mutations may lead to neurodevelopmental defects thereby predisposing to PD pathology.
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Affiliation(s)
- Isabel Rosety
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- OrganoTherapeutics SARL-S, Esch-sur-Alzette, Luxembourg
| | - Alise Zagare
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Claudia Saraiva
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sarah Nickels
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Antony
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Catarina Almeida
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Enrico Glaab
- Biomedical Data Science group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rashi Halder
- Systems Ecology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sergiy Velychko
- Max Planck Institute for Molecular Biomedicine, MPG White Paper Group - Animal Testing in the Max Planck Society, Muenster, Germany
| | - Thomas Rauen
- Max Planck Institute for Molecular Biomedicine, MPG White Paper Group - Animal Testing in the Max Planck Society, Muenster, Germany
| | - Hans R Schöler
- Max Planck Institute for Molecular Biomedicine, MPG White Paper Group - Animal Testing in the Max Planck Society, Muenster, Germany
| | - Silvia Bolognin
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Thomas Sauter
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, 4367, Luxembourg
| | - Javier Jarazo
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- OrganoTherapeutics SARL-S, Esch-sur-Alzette, Luxembourg
| | - Rejko Krüger
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Transversial Translational Medicine, Luxembourg Institute of Health (LIH), 1 A-B rue Thomas Ediison, L-1445, Strassen, Luxembourg
| | - Jens C Schwamborn
- Developmental and Cellular Biology, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.
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10
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Sun G, Liu S, Shi C, Liu X, Guo Q. 3DCNAS: A universal method for predicting the location of fluorescent organelles in living cells in three-dimensional space. Exp Cell Res 2023; 433:113807. [PMID: 37852350 DOI: 10.1016/j.yexcr.2023.113807] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 10/20/2023]
Abstract
Cellular biology research relies on microscopic imaging techniques for studying the complex structures and dynamic processes within cells. Fluorescence microscopy provides high sensitivity and subcellular resolution but has limitations such as photobleaching and sample preparation challenges. Transmission light microscopy offers a label-free alternative but lacks contrast for detailed interpretation. Deep learning methods have shown promise in analyzing cell images and extracting meaningful information. However, accurately learning and simulating diverse subcellular structures remain challenging. In this study, we propose a method named three-dimensional cell neural architecture search (3DCNAS) to predict subcellular structures of fluorescence using unlabeled transmitted light microscope images. By leveraging the automated search capability of differentiable neural architecture search (NAS), our method partially mitigates the issues of overfitting and underfitting caused by the distinct details of various subcellular structures. Furthermore, we apply our method to analyze cell dynamics in genome-edited human induced pluripotent stem cells during mitotic events. This allows us to study the functional roles of organelles and their involvement in cellular processes, contributing to a comprehensive understanding of cell biology and offering insights into disease pathogenesis.
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Affiliation(s)
- Guocheng Sun
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, 102617, China
| | - Shitou Liu
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, 102617, China
| | - Chaojing Shi
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, 102617, China
| | - Xi Liu
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, 102617, China
| | - Qianjin Guo
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, 102617, China.
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11
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Xu H, Li YF, Yi XYL, Zheng XN, Yang Y, Wang Y, Liao DZ, Zhang JP, Tan P, Xiong XY, Jin X, Gong LN, Qiu S, Cao DH, Li H, Wei Q, Yang L, Ai JZ. ADP-dependent glucokinase controls metabolic fitness in prostate cancer progression. Mil Med Res 2023; 10:64. [PMID: 38082365 PMCID: PMC10714548 DOI: 10.1186/s40779-023-00500-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Cell metabolism plays a pivotal role in tumor progression, and targeting cancer metabolism might effectively kill cancer cells. We aimed to investigate the role of hexokinases in prostate cancer (PCa) and identify a crucial target for PCa treatment. METHODS The Cancer Genome Atlas (TCGA) database, online tools and clinical samples were used to assess the expression and prognostic role of ADP-dependent glucokinase (ADPGK) in PCa. The effect of ADPGK expression on PCa cell malignant phenotypes was validated in vitro and in vivo. Quantitative proteomics, metabolomics, and extracellular acidification rate (ECAR) and oxygen consumption rate (OCR) tests were performed to evaluate the impact of ADPGK on PCa metabolism. The underlying mechanisms were explored through ADPGK overexpression and knockdown, co-immunoprecipitation (Co-IP), ECAR analysis and cell counting kit-8 (CCK-8) assays. RESULTS ADPGK was the only glucokinase that was both upregulated and predicted worse overall survival (OS) in prostate adenocarcinoma (PRAD). Clinical sample analysis demonstrated that ADPGK was markedly upregulated in PCa tissues vs. non-PCa tissues. High ADPGK expression indicates worse survival outcomes, and ADPGK serves as an independent factor of biochemical recurrence. In vitro and in vivo experiments showed that ADPGK overexpression promoted PCa cell proliferation and migration, and ADPGK inhibition suppressed malignant phenotypes. Metabolomics, proteomics, and ECAR and OCR tests revealed that ADPGK significantly accelerated glycolysis in PCa. Mechanistically, ADPGK binds aldolase C (ALDOC) to promote glycolysis via AMP-activated protein kinase (AMPK) phosphorylation. ALDOC was positively correlated with ADPGK, and high ALDOC expression was associated with worse survival outcomes in PCa. CONCLUSIONS In summary, ADPGK is a driving factor in PCa progression, and its high expression contributes to a poor prognosis in PCa patients. ADPGK accelerates PCa glycolysis and progression by activating ALDOC-AMPK signaling, suggesting that ADPGK might be an effective target and marker for PCa treatment and prognosis evaluation.
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Affiliation(s)
- Hang Xu
- Department of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yi-Fan Li
- Department of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xian-Yan-Ling Yi
- Department of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiao-Nan Zheng
- Department of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yang Yang
- Animal Experimental Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yan Wang
- Research Core Facility, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Da-Zhou Liao
- Research Core Facility, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jia-Peng Zhang
- Department of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ping Tan
- Department of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xing-Yu Xiong
- Department of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xi Jin
- Department of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Li-Na Gong
- Department of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Shi Qiu
- Department of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - De-Hong Cao
- Department of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Hong Li
- Department of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiang Wei
- Department of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Lu Yang
- Department of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Jian-Zhong Ai
- Department of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China.
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12
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Perez-Estrada JR, Tangeman JA, Proto-Newton M, Sanaka H, Smucker B, Del Rio-Tsonis K. DISTINCT METABOLIC STATES DIRECT RETINAL PIGMENT EPITHELIUM CELL FATE DECISIONS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559631. [PMID: 37808829 PMCID: PMC10557760 DOI: 10.1101/2023.09.26.559631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
During tissue regeneration, proliferation, dedifferentiation, and reprogramming are necessary to restore lost structures. However, it is not fully understood how metabolism intersects with these processes. Chicken embryos can regenerate their retina through retinal pigment epithelium (RPE) reprogramming when treated with fibroblast factor 2 (FGF2). Using transcriptome profiling, we uncovered extensive regulation of gene sets pertaining to proliferation, neurogenesis, and glycolysis throughout RPE-to-neural retina reprogramming. By manipulating cell media composition, we determined that glucose, glutamine, or pyruvate are sufficient to support RPE reprogramming identifying glycolysis as a requisite. Conversely, the induction of oxidative metabolism by activation of pyruvate dehydrogenase induces Epithelial-to-mesenchymal transition (EMT), while simultaneously blocking the activation of neural retina fate. We also identify that EMT is partially driven by an oxidative environment. Our findings provide evidence that metabolism controls RPE cell fate decisions and provide insights into the metabolic state of RPE cells, which are prone to fate changes in regeneration and pathologies, such as proliferative vitreoretinopathy.
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13
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Liorni N, Napoli A, Castellana S, Giallongo S, Řeháková D, Re OL, Koutná I, Mazza T, Vinciguerra M. Integrative CUT&Tag-RNA-Seq analysis of histone variant macroH2A1-dependent orchestration of human induced pluripotent stem cell reprogramming. Epigenomics 2023; 15:863-877. [PMID: 37846557 DOI: 10.2217/epi-2023-0267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023] Open
Abstract
Aim: Human induced pluripotent stem cells (iPSCs) are inefficiently derived from somatic cells by overexpression of defined transcription factors. Overexpression of H2A histone variant macroH2A1.1, but not macroH2A1.2, leads to increased iPSC reprogramming by unclear mechanisms. Materials & methods: Cleavage under targets and tagmentation (CUT&Tag) allows robust epigenomic profiling of a low cell number. We performed an integrative CUT&Tag-RNA-Seq analysis of macroH2A1-dependent orchestration of iPSCs reprogramming using human endothelial cells. Results: We demonstrate wider genome occupancy, predicted transcription factors binding, and gene expression regulated by macroH2A1.1 during reprogramming, compared to macroH2A1.2. MacroH2A1.1, previously associated with neurodegenerative pathologies, specifically activated ectoderm/neural processes. Conclusion: CUT&Tag and RNA-Seq data integration is a powerful tool to investigate the epigenetic mechanisms occurring during cell reprogramming.
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Affiliation(s)
- Niccolò Liorni
- Bioinformatics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza,71013, San Giovanni Rotondo, Italy
| | - Alessandro Napoli
- Bioinformatics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza,71013, San Giovanni Rotondo, Italy
| | - Stefano Castellana
- Bioinformatics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza,71013, San Giovanni Rotondo, Italy
| | - Sebastiano Giallongo
- International Clinical Research Center, St. Anne's University Hospital, 65691, Brno, Czech Republic
- Department of Biomedical & Biotechnological Sciences, University of Catania, 95123, Catania, Italy
| | - Daniela Řeháková
- International Clinical Research Center, St. Anne's University Hospital, 65691, Brno, Czech Republic
- Institute of Experimental Biology, Faculty of Science, Masaryk University, 62500, Brno, Czech Republic
| | - Oriana Lo Re
- International Clinical Research Center, St. Anne's University Hospital, 65691, Brno, Czech Republic
- Department of Translational Stem Cell Biology, Research Institute, Medical University of Varna (RIMUV), 9002, Varna, Bulgaria
| | - Irena Koutná
- International Clinical Research Center, St. Anne's University Hospital, 65691, Brno, Czech Republic
- Department of Histology & Embryology, Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
| | - Tommaso Mazza
- Bioinformatics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza,71013, San Giovanni Rotondo, Italy
| | - Manlio Vinciguerra
- International Clinical Research Center, St. Anne's University Hospital, 65691, Brno, Czech Republic
- Department of Translational Stem Cell Biology, Research Institute, Medical University of Varna (RIMUV), 9002, Varna, Bulgaria
- Faculty of Health, Liverpool John Moores University, L2 2ER, Liverpool, UK
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14
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Amato I, Meurant S, Renard P. The Key Role of Mitochondria in Somatic Stem Cell Differentiation: From Mitochondrial Asymmetric Apportioning to Cell Fate. Int J Mol Sci 2023; 24:12181. [PMID: 37569553 PMCID: PMC10418455 DOI: 10.3390/ijms241512181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
The study of the mechanisms underlying stem cell differentiation is under intensive research and includes the contribution of a metabolic switch from glycolytic to oxidative metabolism. While mitochondrial biogenesis has been previously demonstrated in number of differentiation models, it is only recently that the role of mitochondrial dynamics has started to be explored. The discovery of asymmetric distribution of mitochondria in stem cell progeny has strengthened the interest in the field. This review attempts to summarize the regulation of mitochondrial asymmetric apportioning by the mitochondrial fusion, fission, and mitophagy processes as well as emphasize how asymmetric mitochondrial apportioning in stem cells affects their metabolism, and thus epigenetics, and determines cell fate.
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Affiliation(s)
- Ilario Amato
- Ressearch Unit in Cell Biology (URBC), Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium; (I.A.); (S.M.)
| | - Sébastien Meurant
- Ressearch Unit in Cell Biology (URBC), Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium; (I.A.); (S.M.)
| | - Patricia Renard
- Ressearch Unit in Cell Biology (URBC), Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium; (I.A.); (S.M.)
- Mass Spectrometry Platform (MaSUN), Namur Research Institute for Life Sciences (Narilis), University of Namur (UNamur), 5000 Namur, Belgium
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15
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Fan W, Li X. The SIRT1-c-Myc axis in regulation of stem cells. Front Cell Dev Biol 2023; 11:1236968. [PMID: 37554307 PMCID: PMC10405831 DOI: 10.3389/fcell.2023.1236968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023] Open
Abstract
SIRT1 is the most conserved mammalian NAD+-dependent protein deacetylase. Through deacetylation of transcriptional factors and co-factors, this protein modification enzyme is critically involved in metabolic and epigenetic regulation of stem cells, which is functionally important in maintaining their pluripotency and regulating their differentiation. C-Myc, a key member of Myc proton-oncogene family, is a pivotal factor for transcriptional regulation of genes that control acquisition and maintenance of stemness. Previous cancer research has revealed an intriguing positive feedback loop between SIRT1 and c-Myc that is crucial in tumorigenesis. Recent literature has uncovered important functions of this axis in regulation of maintenance and differentiation of stem cells, including pluripotent stem cells and cancer stem cells. This review highlights recent advances of the SIRT1-c-Myc axis in stem cells.
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Affiliation(s)
- Wei Fan
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, United States
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, United States
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16
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Conte F, Noga MJ, van Scherpenzeel M, Veizaj R, Scharn R, Sam JE, Palumbo C, van den Brandt FCA, Freund C, Soares E, Zhou H, Lefeber DJ. Isotopic Tracing of Nucleotide Sugar Metabolism in Human Pluripotent Stem Cells. Cells 2023; 12:1765. [PMID: 37443799 PMCID: PMC10340731 DOI: 10.3390/cells12131765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/14/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Metabolism not only produces energy necessary for the cell but is also a key regulator of several cellular functions, including pluripotency and self-renewal. Nucleotide sugars (NSs) are activated sugars that link glucose metabolism with cellular functions via protein N-glycosylation and O-GlcNAcylation. Thus, understanding how different metabolic pathways converge in the synthesis of NSs is critical to explore new opportunities for metabolic interference and modulation of stem cell functions. Tracer-based metabolomics is suited for this challenge, however chemically-defined, customizable media for stem cell culture in which nutrients can be replaced with isotopically labeled analogs are scarcely available. Here, we established a customizable flux-conditioned E8 (FC-E8) medium that enables stem cell culture with stable isotopes for metabolic tracing, and a dedicated liquid chromatography mass-spectrometry (LC-MS/MS) method targeting metabolic pathways converging in NS biosynthesis. By 13C6-glucose feeding, we successfully traced the time-course of carbon incorporation into NSs directly via glucose, and indirectly via other pathways, such as glycolysis and pentose phosphate pathways, in induced pluripotent stem cells (hiPSCs) and embryonic stem cells. Then, we applied these tools to investigate the NS biosynthesis in hiPSC lines from a patient affected by deficiency of phosphoglucomutase 1 (PGM1), an enzyme regulating the synthesis of the two most abundant NSs, UDP-glucose and UDP-galactose.
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Affiliation(s)
- Federica Conte
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Marek J. Noga
- Department of Clinical Genetics, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | | | - Raisa Veizaj
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Rik Scharn
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Juda-El Sam
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Chiara Palumbo
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | | | | | - Eduardo Soares
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands
- Department of Neurology, Amsterdam University Medical Centres, Location Academic Medical Center, Amsterdam Neuroscience, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Huiqing Zhou
- Department of Neurology, Amsterdam University Medical Centres, Location Academic Medical Center, Amsterdam Neuroscience, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Dirk J. Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- GlycoMScan B.V., 5349 AB Oss, The Netherlands
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17
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Dottori M, Li WJ, Minchiotti G, Rosa A, Sangiuolo F. Editorial: Reviews in induced pluripotent stem cells. Front Cell Dev Biol 2023; 11:1197891. [PMID: 37215079 PMCID: PMC10193027 DOI: 10.3389/fcell.2023.1197891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/27/2023] [Indexed: 05/24/2023] Open
Affiliation(s)
- Mirella Dottori
- School of Medical, Indigenous and Health Sciences, University of Wollongong, Wollongong, Australia
| | - Wan-Ju Li
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, United States
| | - Gabriella Minchiotti
- Institute of Genetics and Biophysics “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, Naples, Italy
| | - Alessandro Rosa
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Rome, Italy
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Federica Sangiuolo
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
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18
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Safari S, Amiri A, Badiei A. Selective detection of aspartic acid in human serum by a fluorescent probe based on CuInS 2@ZnS quantum dots. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 291:122294. [PMID: 36630810 DOI: 10.1016/j.saa.2022.122294] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
The importance of amino acids identification in biological systems has created expectation to develop a sensitive method for their detection. In this work, an efficient core-shell fluorescent quantum dots (QDs) probe based on CuInS2 (CIS) core and ZnS shell with the formula of CIS@ZnS QDs were synthesised and characterised by FT-IR, UV-Vis, TEM and DLS techniques. The probe was used for detection of Aspartic Acid (Asp) in an aqueous media. The probe shows a remarkable fluorescence response toward Asp over the other amino acids such as valine (Val), glycine (Gly), phenylalanine (Phe), leucine (Leu), alanine (Ala), serine (Ser), isoleucine (Iso), threonine (Thr), methionine (Met), Glutamic acid (Glu), histidine (His), arginine (Arg), cysteine (Cys), asparagine (Asn), glutamine (Gln), citrolline (Cit), sarcosine (Sar) and ornithine (Orn) the fluorescence intensity quenches significantly upon addition of Asp in an aqueous media. The CIS@ZnS QDs probe showed a selective and sensitive response by fluorescence quenching toward Asp in the concentration range of 8.3 × 10-7 M to 3.3 × 10-4 M with the detection limit of 7.8 × 10-8 M. The application of the sensor in determination of Asp in real human serum sample was also investigated. Based on our library search, the all reported fluorescent sensors for detection of Asp, either show a remarkable sensitivity to Glu acid. Luckily, this is the first presented optical probe able to detect just Asp from the solutions containing various amino acids.
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Affiliation(s)
- Sara Safari
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran
| | - Ahmad Amiri
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran.
| | - Alireza Badiei
- School of Chemistry, College of Science, University of Tehran, Tehran, Iran
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19
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Liu Z, Lei J, Wu T, Hu W, Zheng M, Wang Y, Song J, Ruan H, Xu L, Ren T, Xu W, Wen Z. Lipogenesis promotes mitochondrial fusion and maintains cancer stemness in human NSCLC. JCI Insight 2023; 8:158429. [PMID: 36809297 PMCID: PMC10070109 DOI: 10.1172/jci.insight.158429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/15/2023] [Indexed: 02/23/2023] Open
Abstract
Cancer stem-like cells (CSCs) are critically involved in cancer metastasis and chemoresistance, acting as one major obstacle in clinical practice. While accumulating studies have implicated the metabolic reprogramming of CSCs, mitochondrial dynamics in such cells remain poorly understood. Here we pinpointed OPA1hi with mitochondrial fusion as a metabolic feature of human lung CSCs, licensing their stem-like properties. Specifically, human lung CSCs exerted enhanced lipogenesis, inducing OPA1 expression via transcription factor SAM Pointed Domain containing ETS transcription Factor (SPDEF). In consequence, OPA1hi promoted mitochondrial fusion and stemness of CSCs. Such lipogenesishi, SPDEFhi, and OPA1hi metabolic adaptions were verified with primary CSCs from lung cancer patients. Accordingly, blocking lipogenesis and mitochondrial fusion efficiently impeded CSC expansion and growth of organoids derived from patients with lung cancer. Together, lipogenesis regulates mitochondrial dynamics via OPA1 for controlling CSCs in human lung cancer.
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Affiliation(s)
- Zhen Liu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Jiaxin Lei
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Tong Wu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Weijie Hu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Ming Zheng
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Ying Wang
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Jingdong Song
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hang Ruan
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Lin Xu
- Department of Immunology, Zunyi Medical University, Zunyi, Guizhou, China
- Special Key Laboratory of Gene Detection & Therapy of Guizhou Province, Zunyi, Guizhou, China
| | - Tao Ren
- Department of Respiratory Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Xu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Zhenke Wen
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, China
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20
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Cao L, Wang R, Liu G, Zhang Y, Thorne RF, Zhang XD, Li J, Xia Y, Guo L, Shao F, Gu H, Wu M. Glycolytic Pfkp acts as a Lin41 protein kinase to promote endodermal differentiation of embryonic stem cells. EMBO Rep 2023; 24:e55683. [PMID: 36660859 PMCID: PMC9986826 DOI: 10.15252/embr.202255683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 12/21/2022] [Accepted: 01/03/2023] [Indexed: 01/21/2023] Open
Abstract
Unveiling the principles governing embryonic stem cell (ESC) differentiation into specific lineages is critical for understanding embryonic development and for stem cell applications in regenerative medicine. Here, we establish an intersection between LIF-Stat3 signaling that is essential for maintaining murine (m) ESCs pluripotency, and the glycolytic enzyme, the platelet isoform of phosphofructokinase (Pfkp). In the pluripotent state, Stat3 transcriptionally suppresses Pfkp in mESCs while manipulating the cells to lift this repression results in differentiation towards the ectodermal lineage. Pfkp exhibits substrate specificity changes to act as a protein kinase, catalyzing serine phosphorylation of the developmental regulator Lin41. Such phosphorylation stabilizes Lin41 by impeding its autoubiquitination and proteasomal degradation, permitting Lin41-mediated binding and destabilization of mRNAs encoding ectodermal specification markers to favor the expression of endodermal specification genes. This provides new insights into the wiring of pluripotency-differentiation circuitry where Pfkp plays a role in germ layer specification during mESC differentiation.
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Affiliation(s)
- Leixi Cao
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
| | - Ruijie Wang
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
| | - Guangzhi Liu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
| | - Yuwei Zhang
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
| | - Rick Francis Thorne
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
- School of Biomedical Sciences & PharmacyUniversity of NewcastleNewcastleNSWAustralia
| | - Xu Dong Zhang
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
- School of Environmental & Life SciencesUniversity of NewcastleNewcastleNSWAustralia
| | - Jinming Li
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
| | - Yang Xia
- Department of Immunology, School of Basic Medical SciencesAnhui Medical UniversityHefeiChina
| | - Lili Guo
- Department of Immunology, School of Basic Medical SciencesAnhui Medical UniversityHefeiChina
| | - Fengmin Shao
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
| | - Hao Gu
- Department of Immunology, School of Basic Medical SciencesAnhui Medical UniversityHefeiChina
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical ScienceZhengzhou UniversityZhengzhouChina
- School of Clinical MedicineHenan UniversityZhengzhouChina
- CAS Centre for Excellence in Molecular Cell Sciencethe First Affiliated Hospital of University of Science and Technology of ChinaHefeiChina
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21
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Zhou F, Aroua N, Liu Y, Rohde C, Cheng J, Wirth AK, Fijalkowska D, Göllner S, Lotze M, Yun H, Yu X, Pabst C, Sauer T, Oellerich T, Serve H, Röllig C, Bornhäuser M, Thiede C, Baldus C, Frye M, Raffel S, Krijgsveld J, Jeremias I, Beckmann R, Trumpp A, Müller-Tidow C. A Dynamic rRNA Ribomethylome Drives Stemness in Acute Myeloid Leukemia. Cancer Discov 2023; 13:332-347. [PMID: 36259929 PMCID: PMC9900322 DOI: 10.1158/2159-8290.cd-22-0210] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 09/12/2022] [Accepted: 10/14/2022] [Indexed: 02/07/2023]
Abstract
The development and regulation of malignant self-renewal remain unresolved issues. Here, we provide biochemical, genetic, and functional evidence that dynamics in ribosomal RNA (rRNA) 2'-O-methylation regulate leukemia stem cell (LSC) activity in vivo. A comprehensive analysis of the rRNA 2'-O-methylation landscape of 94 patients with acute myeloid leukemia (AML) revealed dynamic 2'-O-methylation specifically at exterior sites of ribosomes. The rRNA 2'-O-methylation pattern is closely associated with AML development stage and LSC gene expression signature. Forced expression of the 2'-O-methyltransferase fibrillarin (FBL) induced an AML stem cell phenotype and enabled engraftment of non-LSC leukemia cells in NSG mice. Enhanced 2'-O-methylation redirected the ribosome translation program toward amino acid transporter mRNAs enriched in optimal codons and subsequently increased intracellular amino acid levels. Methylation at the single site 18S-guanosine 1447 was instrumental for LSC activity. Collectively, our work demonstrates that dynamic 2'-O-methylation at specific sites on rRNAs shifts translational preferences and controls AML LSC self-renewal. SIGNIFICANCE We establish the complete rRNA 2'-O-methylation landscape in human AML. Plasticity of rRNA 2'-O-methylation shifts protein translation toward an LSC phenotype. This dynamic process constitutes a novel concept of how cancers reprogram cell fate and function. This article is highlighted in the In This Issue feature, p. 247.
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Affiliation(s)
- Fengbiao Zhou
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit EMBL-UKHD, Heidelberg, Germany
- Corresponding Authors: Carsten Müller-Tidow, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-2215-68000; E-mail: ; Fengbiao Zhou, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-221-563-7487; E-mail: ; and Andreas Trumpp, Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. Phone: 4906-2214-23901; E-mail:
| | - Nesrine Aroua
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute of Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Yi Liu
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit EMBL-UKHD, Heidelberg, Germany
| | - Christian Rohde
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit EMBL-UKHD, Heidelberg, Germany
| | - Jingdong Cheng
- Gene Center, Department of Biochemistry, University of Munich, Munich, Germany
| | - Anna-Katharina Wirth
- Research Unit Apoptosis in Hematopoietic Stem Cells (AHS), Helmholtz Center Munich, German Center for Environmental Health, Munich, Germany
| | - Daria Fijalkowska
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Göllner
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Michelle Lotze
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Haiyang Yun
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Xiaobing Yu
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Caroline Pabst
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Tim Sauer
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Thomas Oellerich
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt Am Main, Germany
| | - Hubert Serve
- Department of Medicine II, Hematology/Oncology, Goethe University, Frankfurt Am Main, Germany
| | - Christoph Röllig
- Medical Department 1, University Hospital Dresden, Dresden, Germany
| | | | - Christian Thiede
- Medical Department 1, University Hospital Dresden, Dresden, Germany
| | - Claudia Baldus
- Department of Medicine II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Michaela Frye
- Division of Mechanisms Regulating Gene Expression, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simon Raffel
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells (AHS), Helmholtz Center Munich, German Center for Environmental Health, Munich, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany
| | - Roland Beckmann
- Gene Center, Department of Biochemistry, University of Munich, Munich, Germany
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute of Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- National Center for Tumor Diseases, NCT Heidelberg, Heidelberg, Germany
- Corresponding Authors: Carsten Müller-Tidow, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-2215-68000; E-mail: ; Fengbiao Zhou, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-221-563-7487; E-mail: ; and Andreas Trumpp, Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. Phone: 4906-2214-23901; E-mail:
| | - Carsten Müller-Tidow
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
- Molecular Medicine Partnership Unit EMBL-UKHD, Heidelberg, Germany
- National Center for Tumor Diseases, NCT Heidelberg, Heidelberg, Germany
- Corresponding Authors: Carsten Müller-Tidow, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-2215-68000; E-mail: ; Fengbiao Zhou, Department of Internal Medicine V, Heidelberg University Hospital, 69120 Heidelberg, Germany. Phone: 4906-221-563-7487; E-mail: ; and Andreas Trumpp, Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany. Phone: 4906-2214-23901; E-mail:
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22
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Mannully CT, Bruck-Haimson R, Zacharia A, Orih P, Shehadeh A, Saidemberg D, Kogan NM, Alfandary S, Serruya R, Dagan A, Petit I, Moussaieff A. Lipid desaturation regulates the balance between self-renewal and differentiation in mouse blastocyst-derived stem cells. Cell Death Dis 2022; 13:1027. [PMID: 36477438 PMCID: PMC9729213 DOI: 10.1038/s41419-022-05263-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 08/31/2022] [Accepted: 09/13/2022] [Indexed: 12/13/2022]
Abstract
Stem cells are defined by their ability to self-renew and differentiate, both shown in multiple studies to be regulated by metabolic processes. To decipher metabolic signatures of self-renewal in blastocyst-derived stem cells, we compared early differentiating embryonic stem cells (ESCs) and their extra-embryonic counterparts, trophoblast (T)SCs to their self-renewing counterparts. A metabolomics analysis pointed to the desaturation of fatty acyl chains as a metabolic signature of differentiating blastocyst-derived SCs via the upregulation of delta-6 desaturase (D6D; FADS2) and delta-5 desaturase (D5D; FADS1), key enzymes in the biosynthesis of polyunsaturated fatty acids (PUFAs). The inhibition of D6D or D5D by specific inhibitors or SiRNA retained stemness in ESCs and TSCs, and attenuated endoplasmic reticulum (ER) stress-related apoptosis. D6D inhibition in ESCs upregulated stearoyl-CoA desaturase-1 (Scd1), essential to maintain ER homeostasis. In TSCs, however, D6D inhibition downregulated Scd1. TSCs show higher Scd1 mRNA expression and high levels of monounsaturated fatty acyl chain products in comparison to ESCs. The addition of oleic acid, the product of Scd1 (essential for ESCs), to culture medium, was detrimental to TSCs. Interestingly, TSCs express a high molecular mass variant of Scd1 protein, hardly expressed by ESCs. Taken together, our data suggest that lipid desaturation is a metabolic regulator of the balance between differentiation and self-renewal of ESCs and TSCs. They point to lipid polydesaturation as a driver of differentiation in both cell types. Monounsaturated fatty acids (MUFAs), essential for ESCs are detrimental to TSCs.
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Affiliation(s)
- Chanchal Thomas Mannully
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Reut Bruck-Haimson
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anish Zacharia
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Paul Orih
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alaa Shehadeh
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Saidemberg
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Natalya M. Kogan
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sivan Alfandary
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Raphael Serruya
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Arie Dagan
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isabelle Petit
- grid.465261.20000 0004 1793 5929Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Arieh Moussaieff
- grid.9619.70000 0004 1937 0538The Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
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23
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Moiz B, Li A, Padmanabhan S, Sriram G, Clyne AM. Isotope-Assisted Metabolic Flux Analysis: A Powerful Technique to Gain New Insights into the Human Metabolome in Health and Disease. Metabolites 2022; 12:1066. [PMID: 36355149 PMCID: PMC9694183 DOI: 10.3390/metabo12111066] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 04/28/2024] Open
Abstract
Cell metabolism represents the coordinated changes in genes, proteins, and metabolites that occur in health and disease. The metabolic fluxome, which includes both intracellular and extracellular metabolic reaction rates (fluxes), therefore provides a powerful, integrated description of cellular phenotype. However, intracellular fluxes cannot be directly measured. Instead, flux quantification requires sophisticated mathematical and computational analysis of data from isotope labeling experiments. In this review, we describe isotope-assisted metabolic flux analysis (iMFA), a rigorous computational approach to fluxome quantification that integrates metabolic network models and experimental data to generate quantitative metabolic flux maps. We highlight practical considerations for implementing iMFA in mammalian models, as well as iMFA applications in in vitro and in vivo studies of physiology and disease. Finally, we identify promising new frontiers in iMFA which may enable us to fully unlock the potential of iMFA in biomedical research.
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Affiliation(s)
- Bilal Moiz
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Andrew Li
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Surya Padmanabhan
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Ganesh Sriram
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA
| | - Alisa Morss Clyne
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
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24
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Xu Y, Kuppe C, Perales-Patón J, Hayat S, Kranz J, Abdallah AT, Nagai J, Li Z, Peisker F, Saritas T, Halder M, Menzel S, Hoeft K, Kenter A, Kim H, van Roeyen CRC, Lehrke M, Moellmann J, Speer T, Buhl EM, Hoogenboezem R, Boor P, Jansen J, Knopp C, Kurth I, Smeets B, Bindels E, Reinders MEJ, Baan C, Gribnau J, Hoorn EJ, Steffens J, Huber TB, Costa I, Floege J, Schneider RK, Saez-Rodriguez J, Freedman BS, Kramann R. Adult human kidney organoids originate from CD24 + cells and represent an advanced model for adult polycystic kidney disease. Nat Genet 2022; 54:1690-1701. [PMID: 36303074 PMCID: PMC7613830 DOI: 10.1038/s41588-022-01202-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 09/09/2022] [Indexed: 11/09/2022]
Abstract
Adult kidney organoids have been described as strictly tubular epithelia and termed tubuloids. While the cellular origin of tubuloids has remained elusive, here we report that they originate from a distinct CD24+ epithelial subpopulation. Long-term-cultured CD24+ cell-derived tubuloids represent a functional human kidney tubule. We show that kidney tubuloids can be used to model the most common inherited kidney disease, namely autosomal dominant polycystic kidney disease (ADPKD), reconstituting the phenotypic hallmark of this disease with cyst formation. Single-cell RNA sequencing of CRISPR-Cas9 gene-edited PKD1- and PKD2-knockout tubuloids and human ADPKD and control tissue shows similarities in upregulation of disease-driving genes. Furthermore, in a proof of concept, we demonstrate that tolvaptan, the only approved drug for ADPKD, has a significant effect on cyst size in tubuloids but no effect on a pluripotent stem cell-derived model. Thus, tubuloids are derived from a tubular epithelial subpopulation and represent an advanced system for ADPKD disease modeling.
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Affiliation(s)
- Yaoxian Xu
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Christoph Kuppe
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Division of Nephrology and Clinical Immunology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Javier Perales-Patón
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Bioquant, Heidelberg, Germany
| | - Sikander Hayat
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Jennifer Kranz
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Department of Urology and Pediatric Urology, RWTH Aachen University, Aachen, Germany
- Department of Urology and Kidney Transplantation, Martin-Luther-University, Halle, Germany
| | - Ali T Abdallah
- Interdisciplinary Center for Clinical Research, RWTH Aachen University, Aachen, Germany
| | - James Nagai
- Institute of Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Zhijian Li
- Institute of Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Fabian Peisker
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Turgay Saritas
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Division of Nephrology and Clinical Immunology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Maurice Halder
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Sylvia Menzel
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Konrad Hoeft
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Division of Nephrology and Clinical Immunology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Annegien Kenter
- Department of Developmental Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Internal Medicine and Department of Nephrology and Transplantation, Erasmus Medical Center Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Hyojin Kim
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Claudia R C van Roeyen
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Michael Lehrke
- Department of Cardiology, RWTH Aachen University, Aachen, Germany
| | - Julia Moellmann
- Department of Cardiology, RWTH Aachen University, Aachen, Germany
| | - Thimoteus Speer
- Department of Nephrology, University Hospital Homburg, Homburg, Germany
| | - Eva M Buhl
- Institute of Pathology and Electron Microscopy Facility, RWTH Aachen University, Aachen, Germany
| | - Remco Hoogenboezem
- Department of Hematology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Peter Boor
- Division of Nephrology and Clinical Immunology, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Institute of Pathology and Electron Microscopy Facility, RWTH Aachen University, Aachen, Germany
| | - Jitske Jansen
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Department of Pathology, RIMLS, Radboudumc, Nijmegen, the Netherlands
| | - Cordula Knopp
- Institute of Human Genetics, RWTH Aachen University, Aachen, Germany
| | - Ingo Kurth
- Institute of Human Genetics, RWTH Aachen University, Aachen, Germany
| | - Bart Smeets
- Department of Pathology, RIMLS, Radboudumc, Nijmegen, the Netherlands
| | - Eric Bindels
- Department of Hematology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Marlies E J Reinders
- Department of Internal Medicine and Department of Nephrology and Transplantation, Erasmus Medical Center Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Carla Baan
- Department of Internal Medicine and Department of Nephrology and Transplantation, Erasmus Medical Center Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Cell Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ewout J Hoorn
- Department of Internal Medicine and Department of Nephrology and Transplantation, Erasmus Medical Center Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Joachim Steffens
- Department of Urology, St Antonius Hospital, Eschweiler, Germany
| | - Tobias B Huber
- III Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ivan Costa
- Institute of Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Jürgen Floege
- Division of Nephrology and Clinical Immunology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Rebekka K Schneider
- Department of Developmental Biology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Institute of Cell and Tumor Biology, RWTH Aachen University, Aachen, Germany
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Bioquant, Heidelberg, Germany
- Joint Research Center for Computational Biomedicine, RWTH Aachen University, Aachen, Germany
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany
| | - Benjamin S Freedman
- Department of Medicine, Division of Nephrology, Kidney Research Institute and Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Bioengineering (Adjunct), and Department of Laboratory Medicine & Pathology (Adjunct), University of Washington, Seattle, WA, USA
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology, Medical Faculty, RWTH Aachen University, Aachen, Germany.
- Division of Nephrology and Clinical Immunology, Medical Faculty, RWTH Aachen University, Aachen, Germany.
- Department of Internal Medicine and Department of Nephrology and Transplantation, Erasmus Medical Center Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands.
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25
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Pladevall-Morera D, Zylicz JJ. Chromatin as a sensor of metabolic changes during early development. Front Cell Dev Biol 2022; 10:1014498. [PMID: 36299478 PMCID: PMC9588933 DOI: 10.3389/fcell.2022.1014498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Cellular metabolism is a complex network of biochemical reactions fueling development with energy and biomass; however, it can also shape the cellular epigenome. Indeed, some intermediates of metabolic reactions exert a non-canonical function by acting as co-factors, substrates or inhibitors of chromatin modifying enzymes. Therefore, fluctuating availability of such molecules has the potential to regulate the epigenetic landscape. Thanks to this functional coupling, chromatin can act as a sensor of metabolic changes and thus impact cell fate. Growing evidence suggest that both metabolic and epigenetic reprogramming are crucial for ensuring a successful embryo development from the zygote until gastrulation. In this review, we provide an overview of the complex relationship between metabolism and epigenetics in regulating the early stages of mammalian embryo development. We report on recent breakthroughs in uncovering the non-canonical functions of metabolism especially when re-localized to the nucleus. In addition, we identify the challenges and outline future perspectives to advance the novel field of epi-metabolomics especially in the context of early development.
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26
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Navas LE, Carnero A. Nicotinamide Adenine Dinucleotide (NAD) Metabolism as a Relevant Target in Cancer. Cells 2022; 11:cells11172627. [PMID: 36078035 PMCID: PMC9454445 DOI: 10.3390/cells11172627] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/25/2022] [Accepted: 08/16/2022] [Indexed: 11/22/2022] Open
Abstract
NAD+ is an important metabolite in cell homeostasis that acts as an essential cofactor in oxidation–reduction (redox) reactions in various energy production processes, such as the Krebs cycle, fatty acid oxidation, glycolysis and serine biosynthesis. Furthermore, high NAD+ levels are required since they also participate in many other nonredox molecular processes, such as DNA repair, posttranslational modifications, cell signalling, senescence, inflammatory responses and apoptosis. In these nonredox reactions, NAD+ is an ADP-ribose donor for enzymes such as sirtuins (SIRTs), poly-(ADP-ribose) polymerases (PARPs) and cyclic ADP-ribose (cADPRs). Therefore, to meet both redox and nonredox NAD+ demands, tumour cells must maintain high NAD+ levels, enhancing their synthesis mainly through the salvage pathway. NAMPT, the rate-limiting enzyme of this pathway, has been identified as an oncogene in some cancer types. Thus, NAMPT has been proposed as a suitable target for cancer therapy. NAMPT inhibition causes the depletion of NAD+ content in the cell, leading to the inhibition of ATP synthesis. This effect can cause a decrease in tumour cell proliferation and cell death, mainly by apoptosis. Therefore, in recent years, many specific inhibitors of NAMPT have been developed, and some of them are currently in clinical trials. Here we review the NAD metabolism as a cancer therapy target.
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Affiliation(s)
- Lola E. Navas
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, 41013 Sevilla, Spain
- CIBERONC, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Amancio Carnero
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, 41013 Sevilla, Spain
- CIBERONC, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence:
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27
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Zhang Y, Zhong Y, Liu W, Zheng F, Zhao Y, Zou L, Liu X. PFKFB3-mediated glycometabolism reprogramming modulates endothelial differentiation and angiogenic capacity of placenta-derived mesenchymal stem cells. Stem Cell Res Ther 2022; 13:391. [PMID: 35918720 PMCID: PMC9344722 DOI: 10.1186/s13287-022-03089-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/25/2022] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Mesenchymal stem cells (MSCs) have a great potential ability for endothelial differentiation, contributing to an effective means of therapeutic angiogenesis. Placenta-derived mesenchymal stem cells (PMSCs) have gradually attracted attention, while the endothelial differentiation has not been fully evaluated in PMSCs. Metabolism homeostasis plays an important role in stem cell differentiation, but less is known about the glycometabolic reprogramming during the PMSCs endothelial differentiation. Hence, it is critical to investigate the potential role of glycometabolism reprogramming in mediating PMSCs endothelial differentiation. METHODS Dil-Ac-LDL uptake assay, flow cytometry, and immunofluorescence were all to verify the endothelial differentiation in PMSCs. Seahorse XF Extracellular Flux Analyzers, Mito-tracker red staining, Mitochondrial membrane potential (MMP), lactate secretion assay, and transcriptome approach were to assess the variation of mitochondrial respiration and glycolysis during the PMSCs endothelial differentiation. Glycolysis enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3) was considered a potential modulator for endothelial differentiation in PMSCs by small interfering RNA. Furthermore, transwell, in vitro Matrigel tube formation, and in vivo Matrigel plug assays were performed to evaluate the effect of PFKFB3-induced glycolysis on angiogenic capacities in this process. RESULTS PMSCs possessed the superior potential of endothelial differentiation, in which the glycometabolic preference for glycolysis was confirmed. Moreover, PFKFB3-induced glycometabolism reprogramming could modulate the endothelial differentiation and angiogenic abilities of PMSCs. CONCLUSIONS Our results revealed that PFKFB3-mediated glycolysis is important for endothelial differentiation and angiogenesis in PMSCs. Our understanding of cellular glycometabolism and its regulatory effects on endothelial differentiation may propose and improve PMSCs as a putative strategy for clinical therapeutic angiogenesis.
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Affiliation(s)
- Yang Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Yanqi Zhong
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Weifang Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Fanghui Zheng
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Yin Zhao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Li Zou
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan, 430022, China
| | - Xiaoxia Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1277 Jiefang Avenue, Wuhan, 430022, China.
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28
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Haraguchi D, Nakamura T. Pramef12 enhances reprogramming into naïve iPS cells. Biochem Biophys Rep 2022; 30:101267. [PMID: 35592616 PMCID: PMC9111934 DOI: 10.1016/j.bbrep.2022.101267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/07/2022] [Accepted: 04/20/2022] [Indexed: 11/22/2022] Open
Abstract
Somatic cells can be reprogrammed into induced pluripotent stem (iPS) cells by forced expression of the transcription factors Oct3/4, Klf4, Sox2, and c-Myc (OKSM). Somatic cell nuclear transfer can also be utilized to reprogram somatic cells into totipotent embryos, suggesting that factors present in oocytes potentially enhance the efficiency of iPS cell generation. Here, we showed that preferentially expressed antigen of melanoma family member 12 (Pramef12), which is highly expressed in oocytes, enhances the generation of iPS cells from mouse fibroblasts. Overexpression of Pramef12 during the early phase of OKSM-induced reprogramming enhanced the efficiency of iPS cell derivation. In addition, overexpression of Pramef12 also enhanced expression of naïve pluripotency-associated genes, Gtl2 located within the Dlk1–Dio3 imprinted region essential for full pluripotency, glycolysis-associated genes, and oxidative phosphorylation-associated genes, and it promoted mesenchymal-to-epithelial transition during iPS cell generation. Furthermore, Pramef12 greatly activated β-catenin during iPS cell generation. These observations suggested that Pramef12 enhances OKSM-induced reprogramming via activation of the Wnt/β-catenin pathway. Pramef12 enhances OKSM-induced reprogramming into naïve iPS cells. Pramef12 enhances expression of naïve pluripotency-associated genes, essential genes for full pluripotency, glycolysis-associated genes, and oxidative phosphorylation-associated genes. Pramef12 promotes mesenchymal-to-epithelial transition during iPS cell generation. Pramef12 enhances OKSM-induced reprogramming via activation of the Wnt/β-catenin pathway.
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Affiliation(s)
| | - Toshinobu Nakamura
- Gaduate School of Bio-Science, Japan
- Department of Bio-Science, Japan
- Genome Editing Research Institute, Ngahama Institute of Bio-Science and Technology, Shiga, 526-0829, Japan
- Corresponding author. Laboratory for epigenetic regulation, Department of Bio-Science, Nagahama Institute of Bio-Science and Technology, Japan.
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29
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Diamante L, Martello G. Metabolic regulation in pluripotent stem cells. Curr Opin Genet Dev 2022; 75:101923. [PMID: 35691147 DOI: 10.1016/j.gde.2022.101923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/28/2022] [Accepted: 05/05/2022] [Indexed: 11/03/2022]
Abstract
Pluripotent stem cells (PSCs) have the capacity to give rise to all cell types of the adult body and to expand rapidly while retaining genome integrity, representing a perfect tool for regenerative medicine. PSCs are obtained from preimplantation embryos as embryonic stem cells (ESCs), or by reprogramming of somatic cells as induced pluripotent stem cells (iPSCs). Understanding the metabolic requirements of PSCs is instrumental for their efficient generation, expansion and differentiation. PSCs reshape their metabolic profile during developmental progression. Fatty acid oxidation is strictly required for energy production in naive PSCs, but becomes dispensable in more advanced, or primed, PSCs. Other metabolites directly affect proliferation, differentiation or the epigenetic profile of PSCs, showing how metabolism plays an instructive role on PSC behaviour. Developmental progression of pluripotent cells can be paused, both in vitro and in vivo, in response to hormonal and metabolic alterations. Such reversible pausing has been recently linked to mammalian target of rapamycin activity, lipid metabolism and mitochondrial activity. Finally, metabolism is not simply regulated by exogenous stimuli or nutrient availability in PSCs, as key pluripotency regulators, such as Oct4, Stat3 and Tfcp2l1, actively shape the metabolic profile of PSCs.
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Affiliation(s)
- Linda Diamante
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
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30
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Chen A, Kristiansen CK, Høyland LE, Ziegler M, Wang J, Sullivan GJ, Li X, Bindoff LA, Liang KX. POLG mutations lead to abnormal mitochondrial remodeling during neural differentiation of human pluripotent stem cells via SIRT3/AMPK pathway inhibition. Cell Cycle 2022; 21:1178-1193. [PMID: 35298342 PMCID: PMC9103491 DOI: 10.1080/15384101.2022.2044136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We showed previously that POLG mutations cause major changes in mitochondrial function, including loss of mitochondrial respiratory chain (MRC) complex I, mitochondrial DNA (mtDNA) depletion and an abnormal NAD+/NADH ratio in both neural stem cells (NSCs) and astrocytes differentiated from induced pluripotent stem cells (iPSCs). In the current study, we looked at mitochondrial remodeling as stem cells transit pluripotency and during differentiation from NSCs to both dopaminergic (DA) neurons and astrocytes comparing the process in POLG-mutated and control stem cells. We saw that mitochondrial membrane potential (MMP), mitochondrial volume, ATP production and reactive oxygen species (ROS) changed in similar ways in POLG and control NSCs, but mtDNA replication, MRC complex I and NAD+ metabolism failed to remodel normally. In DA neurons differentiated from NSCs, we saw that POLG mutations caused failure to increase MMP and ATP production and blunted the increase in mtDNA and complex I. Interestingly, mitochondrial remodeling during astrocyte differentiation from NSCs was similar in both POLG-mutated and control NSCs. Further, we showed downregulation of the SIRT3/AMPK pathways in POLG-mutated cells, suggesting that POLG mutations lead to abnormal mitochondrial remodeling in early neural development due to the downregulation of these pathways. [Figure: see text].
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Affiliation(s)
- Anbin Chen
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong Province, China,Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway
| | - Cecilie Katrin Kristiansen
- Neuro-SysMed, Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | | | | | - Jian Wang
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong Province, China,Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Gareth John Sullivan
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway,Institute of Immunology, Oslo University Hospital, Oslo, Norway,Hybrid Technology Hub Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway,Department of Pediatric Research, Oslo University Hospital, Oslo, Norway
| | - Xingang Li
- Department of Neurosurgery, Qilu Hospital and Institute of Brain and Brain-Inspired Science, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China,Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong Province, China,CONTACT Kristina Xiao Liang Department of Clinical Medicine (K1, University of Bergen, Jonas Lies vei 87, P. O. Box 7804, Jinan5021 Bergen, Norway
| | - Laurence A. Bindoff
- Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway,Neuro-SysMed, Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital, Bergen, Norway,Laurence A. Bindoff Department of Clinical Medicine, University of Bergen,Norway
| | - Kristina Xiao Liang
- Department of Clinical Medicine (K1), University of Bergen, Bergen, Norway,Neuro-SysMed, Center of Excellence for Clinical Research in Neurological Diseases, Department of Neurology, Haukeland University Hospital, Bergen, Norway,Kristina Xiao Liang Department of Clinical Medicine (K1), University of Bergen, Jonas Lies veg 87, N-5021 Bergen, Norway
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31
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Romero-Morales AI, Gama V. Revealing the Impact of Mitochondrial Fitness During Early Neural Development Using Human Brain Organoids. Front Mol Neurosci 2022; 15:840265. [PMID: 35571368 PMCID: PMC9102998 DOI: 10.3389/fnmol.2022.840265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial homeostasis -including function, morphology, and inter-organelle communication- provides guidance to the intrinsic developmental programs of corticogenesis, while also being responsive to environmental and intercellular signals. Two- and three-dimensional platforms have become useful tools to interrogate the capacity of cells to generate neuronal and glia progeny in a background of metabolic dysregulation, but the mechanistic underpinnings underlying the role of mitochondria during human neurogenesis remain unexplored. Here we provide a concise overview of cortical development and the use of pluripotent stem cell models that have contributed to our understanding of mitochondrial and metabolic regulation of early human brain development. We finally discuss the effects of mitochondrial fitness dysregulation seen under stress conditions such as metabolic dysregulation, absence of developmental apoptosis, and hypoxia; and the avenues of research that can be explored with the use of brain organoids.
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Affiliation(s)
| | - Vivian Gama
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, United States
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32
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Eleftheriadou D, Berg M, Phillips JB, Shipley RJ. A combined experimental and computational framework to evaluate the behavior of therapeutic cells for peripheral nerve regeneration. Biotechnol Bioeng 2022; 119:1980-1996. [PMID: 35445744 PMCID: PMC9323509 DOI: 10.1002/bit.28105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/22/2022] [Accepted: 04/08/2022] [Indexed: 11/08/2022]
Abstract
Recent studies have explored the potential of tissue‐mimetic scaffolds in encouraging nerve regeneration. One of the major determinants of the regenerative success of cellular nerve repair constructs (NRCs) is the local microenvironment, particularly native low oxygen conditions which can affect implanted cell survival and functional performance. In vivo, cells reside in a range of environmental conditions due to the spatial gradients of nutrient concentrations that are established. Here we evaluate in vitro the differences in cellular behavior that such conditions induce, including key biological features such as oxygen metabolism, glucose consumption, cell death, and vascular endothelial growth factor secretion. Experimental measurements are used to devise and parameterize a mathematical model that describes the behavior of the cells. The proposed model effectively describes the interactions between cells and their microenvironment and could in the future be extended, allowing researchers to compare the behavior of different therapeutic cells. Such a combinatorial approach could be used to accelerate the clinical translation of NRCs by identifying which critical design features should be optimized when fabricating engineered nerve repair conduits.
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Affiliation(s)
- D Eleftheriadou
- Centre for Nerve Engineering, University College London, London, WC1E 6B.,Department of Pharmacology, UCL School of Pharmacy, University College London, London, WC1N 1AX.,Department of Mechanical Engineering, University College London, London, WC1E 7JE
| | - M Berg
- Centre for Nerve Engineering, University College London, London, WC1E 6B.,Department of Mechanical Engineering, University College London, London, WC1E 7JE
| | - J B Phillips
- Centre for Nerve Engineering, University College London, London, WC1E 6B.,Department of Pharmacology, UCL School of Pharmacy, University College London, London, WC1N 1AX
| | - R J Shipley
- Centre for Nerve Engineering, University College London, London, WC1E 6B.,Department of Mechanical Engineering, University College London, London, WC1E 7JE
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33
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Rushton MD, Saunderson EA, Patani H, Green MR, Ficz G. An shRNA kinase screen identifies regulators of UHRF1 stability and activity in mouse embryonic stem cells. Epigenetics 2022; 17:1590-1607. [PMID: 35324392 DOI: 10.1080/15592294.2022.2044126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Propagation of DNA methylation through cell division relies on the recognition of methylated cytosines by UHRF1. In reprogramming of mouse embryonic stem cells to naive pluripotency (also known as ground state), despite high levels of Uhrf1 transcript, the protein is targeted for degradation by the proteasome, leading to DNA methylation loss. We have undertaken an shRNA screen to identify the signalling pathways that converge upon UHRF1 and control its degradation, using UHRF1-GFP fluorescence as readout. Many candidates we identified are key enzymes in regulation of glucose metabolism, nucleotide metabolism and Pi3K/AKT/mTOR pathway. Unexpectedly, while downregulation of all candidates we selected for validation rescued UHRF1 protein levels, we found that in some of the cases this was not sufficient to maintain DNA methylation. This has implications for development, ageing and diseased conditions. Our study demonstrates two separate processes that regulate UHRF1 protein abundance and activity.
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Affiliation(s)
- Michael D Rushton
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK.,Horizon Discovery, Cambridge Research Park, 8100 Beach Dr, Waterbeach, Cambridge, CB25 9TL
| | - Emily A Saunderson
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Hemalvi Patani
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK.,Research And Development, CS Genetics Ltd, Cambridge, UK
| | - Michael R Green
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Gabriella Ficz
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, UK
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34
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Sabatier P, Beusch CM, Saei AA, Aoun M, Moruzzi N, Coelho A, Leijten N, Nordenskjöld M, Micke P, Maltseva D, Tonevitsky AG, Millischer V, Carlos Villaescusa J, Kadekar S, Gaetani M, Altynbekova K, Kel A, Berggren PO, Simonson O, Grinnemo KH, Holmdahl R, Rodin S, Zubarev RA. An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation. Nat Commun 2021; 12:6558. [PMID: 34772928 PMCID: PMC8590018 DOI: 10.1038/s41467-021-26879-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 10/25/2021] [Indexed: 12/21/2022] Open
Abstract
Detailed characterization of cell type transitions is essential for cell biology in general and particularly for the development of stem cell-based therapies in regenerative medicine. To systematically study such transitions, we introduce a method that simultaneously measures protein expression and thermal stability changes in cells and provide the web-based visualization tool ProteoTracker. We apply our method to study differences between human pluripotent stem cells and several cell types including their parental cell line and differentiated progeny. We detect alterations of protein properties in numerous cellular pathways and components including ribosome biogenesis and demonstrate that modulation of ribosome maturation through SBDS protein can be helpful for manipulating cell stemness in vitro. Using our integrative proteomics approach and the web-based tool, we uncover a molecular basis for the uncoupling of robust transcription from parsimonious translation in stem cells and propose a method for maintaining pluripotency in vitro.
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Affiliation(s)
- Pierre Sabatier
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
| | - Christian M Beusch
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
| | - Amir A Saei
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Mike Aoun
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
| | - Noah Moruzzi
- The Rolf Luft Research Center for Diabetes and Endocrinology, Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, 17176, Sweden
| | - Ana Coelho
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
| | - Niels Leijten
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Magnus Nordenskjöld
- Center for Molecular Medicine, Karolinska University Hospital, Stockholm, 171 76, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, 17177, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, 171 76, Sweden
| | - Patrick Micke
- Immunology, Genetics and Pathology, Rudbecklaboratoriet, Uppsala University, Uppsala, 751 85, Sweden
| | - Diana Maltseva
- Faculty of biology and biotechnology, National Research University Higher School of Economics, Myasnitskaya Street, 13/4, Moscow, 117997, Russia
| | - Alexander G Tonevitsky
- Faculty of biology and biotechnology, National Research University Higher School of Economics, Myasnitskaya Street, 13/4, Moscow, 117997, Russia
- Scientific Research Center Bioclinicum, Ugreshskaya str. 2/85, Moscow, 115088, Russia
| | - Vincent Millischer
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, 17177, Sweden
- Translational Psychiatry, Center for Molecular Medicine, Karolinska University Hospital, Stockholm, 171 76, Sweden
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, 1090, Austria
| | - J Carlos Villaescusa
- Neurogenetic Unit, Department of Molecular Medicine and Surgery, Karolinska University Hospital, Stockholm, 171 76, Sweden
- Stem Cell R&D-TRU, Novo Nordisk A/S, Måløv, Denmark
| | - Sandeep Kadekar
- Department of Surgical Sciences, Uppsala University, Uppsala, 752 37, Sweden
| | - Massimiliano Gaetani
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
- Chemical Proteomics Core Facility, Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 171 77, Sweden
- Chemical Proteomics, Science for Life Laboratory (SciLifeLab), Stockholm, 17 177, Sweden
| | | | - Alexander Kel
- geneXplain GmbH, Am Exer 19B, 38302, Wolfenbuettel, Germany
| | - Per-Olof Berggren
- The Rolf Luft Research Center for Diabetes and Endocrinology, Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, 17176, Sweden
| | - Oscar Simonson
- Department of Surgical Sciences, Uppsala University, Uppsala, 752 37, Sweden
- Department of Cardio-thoracic Surgery and Anesthesiology, Uppsala University Hospital, Uppsala, 751 85, Sweden
| | - Karl-Henrik Grinnemo
- Department of Surgical Sciences, Uppsala University, Uppsala, 752 37, Sweden
- Department of Cardio-thoracic Surgery and Anesthesiology, Uppsala University Hospital, Uppsala, 751 85, Sweden
| | - Rikard Holmdahl
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden
| | - Sergey Rodin
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden.
- Department of Surgical Sciences, Uppsala University, Uppsala, 752 37, Sweden.
- Department of Cardio-thoracic Surgery and Anesthesiology, Uppsala University Hospital, Uppsala, 751 85, Sweden.
| | - Roman A Zubarev
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, 17177, Sweden.
- Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, 119146, Russia.
- The National Medical Research Center for Endocrinology, Moscow, 115478, Russia.
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35
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Jiang Z, Generoso SF, Badia M, Payer B, Carey LB. A conserved expression signature predicts growth rate and reveals cell & lineage-specific differences. PLoS Comput Biol 2021; 17:e1009582. [PMID: 34762642 PMCID: PMC8610284 DOI: 10.1371/journal.pcbi.1009582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 11/23/2021] [Accepted: 10/21/2021] [Indexed: 12/23/2022] Open
Abstract
Isogenic cells cultured together show heterogeneity in their proliferation rate. To determine the differences between fast and slow-proliferating cells, we developed a method to sort cells by proliferation rate, and performed RNA-seq on slow and fast proliferating subpopulations of pluripotent mouse embryonic stem cells (mESCs) and mouse fibroblasts. We found that slowly proliferating mESCs have a more naïve pluripotent character. We identified an evolutionarily conserved proliferation-correlated transcriptomic signature that is common to all eukaryotes: fast cells have higher expression of genes for protein synthesis and protein degradation. This signature accurately predicted growth rate in yeast and cancer cells, and identified lineage-specific proliferation dynamics during development, using C. elegans scRNA-seq data. In contrast, sorting by mitochondria membrane potential revealed a highly cell-type specific mitochondria-state related transcriptome. mESCs with hyperpolarized mitochondria are fast proliferating, while the opposite is true for fibroblasts. The mitochondrial electron transport chain inhibitor antimycin affected slow and fast subpopulations differently. While a major transcriptional-signature associated with cell-to-cell heterogeneity in proliferation is conserved, the metabolic and energetic dependency of cell proliferation is cell-type specific. By performing RNA sequencing on cells sorted by their proliferation rate, this study identifies a gene expression signature capable of predicting proliferation rates in diverse eukaryotic cell types and species. This signature, applied to single-cell RNA sequencing data from embryos of the roundworm C. elegans, reveals lineage-specific proliferation differences during development. In contrast to the universality of the proliferation signature, mitochondria and metabolism related genes show a high degree of cell-type specificity; mouse pluripotent stem cells (mESCs) and differentiated cells (fibroblasts) exhibit opposite relations between mitochondria state and proliferation. Furthermore, we identified a slow proliferating subpopulation of mESCs with higher expression of pluripotency genes. Finally, we show that fast and slow proliferating subpopulations are differentially sensitive to mitochondria inhibitory drugs in different cell types. Highlights:
A FACS-based method to determine the transcriptomes of fast and slow proliferating subpopulations. A universal proliferation-correlated transcriptional signature indicates high protein synthesis and degradation in fast proliferating cells across cell types and species. Applied to scRNA-seq, the expression signature predicts the global proliferation slowdown during C. elegans development. Mitochondria membrane potential predicts proliferation rate in a cell-type specific manner, with ETC complex III inhibitor having distinct effects on fibroblasts vs mESCs.
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Affiliation(s)
- Zhisheng Jiang
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Serena F. Generoso
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marta Badia
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- * E-mail: (BP); (LBC)
| | - Lucas B. Carey
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- * E-mail: (BP); (LBC)
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36
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Redox Homeostasis and Regulation in Pluripotent Stem Cells: Uniqueness or Versatility? Int J Mol Sci 2021; 22:ijms222010946. [PMID: 34681606 PMCID: PMC8535588 DOI: 10.3390/ijms222010946] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 12/16/2022] Open
Abstract
Pluripotent stem cells (PSCs) hold great potential both in studies on developmental biology and clinical practice. Mitochondrial metabolism that encompasses pathways that generate ATP and produce ROS significantly differs between PSCs and somatic cells. Correspondingly, for quite a long time it was believed that the redox homeostasis in PSCs is also highly specific due to the hypoxic niche of their origin-within the pre-implantation blastocyst. However, recent research showed that redox parameters of cultivated PSCs have much in common with that of their differentiated progeny cells. Moreover, it has been proven that, similar to somatic cells, maintaining the physiological ROS level is critical for the regulation of PSC identity, proliferation, differentiation, and de-differentiation. In this review, we aimed to summarize the studies of redox metabolism and signaling in PSCs to compare the redox profiles of pluripotent and differentiated somatic cells. We collected evidence that PSCs possess metabolic plasticity and are able to adapt to both hypoxia and normoxia, that pluripotency is not strictly associated with anaerobic conditions, and that cellular redox homeostasis is similar in PSCs and many other somatic cells under in vitro conditions that may be explained by the high conservatism of the redox regulation system.
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37
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Zhao J, Yao K, Yu H, Zhang L, Xu Y, Chen L, Sun Z, Zhu Y, Zhang C, Qian Y, Ji S, Pan H, Zhang M, Chen J, Correia C, Weiskittel T, Lin DW, Zhao Y, Chandrasekaran S, Fu X, Zhang D, Fan HY, Xie W, Li H, Hu Z, Zhang J. Metabolic remodelling during early mouse embryo development. Nat Metab 2021; 3:1372-1384. [PMID: 34650276 DOI: 10.1038/s42255-021-00464-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/31/2021] [Indexed: 01/09/2023]
Abstract
During early mammalian embryogenesis, changes in cell growth and proliferation depend on strict genetic and metabolic instructions. However, our understanding of metabolic reprogramming and its influence on epigenetic regulation in early embryo development remains elusive. Here we show a comprehensive metabolomics profiling of key stages in mouse early development and the two-cell and blastocyst embryos, and we reconstructed the metabolic landscape through the transition from totipotency to pluripotency. Our integrated metabolomics and transcriptomics analysis shows that while two-cell embryos favour methionine, polyamine and glutathione metabolism and stay in a more reductive state, blastocyst embryos have higher metabolites related to the mitochondrial tricarboxylic acid cycle, and present a more oxidative state. Moreover, we identify a reciprocal relationship between α-ketoglutarate (α-KG) and the competitive inhibitor of α-KG-dependent dioxygenases, L-2-hydroxyglutarate (L-2-HG), where two-cell embryos inherited from oocytes and one-cell zygotes display higher L-2-HG, whereas blastocysts show higher α-KG. Lastly, increasing 2-HG availability impedes erasure of global histone methylation markers after fertilization. Together, our data demonstrate dynamic and interconnected metabolic, transcriptional and epigenetic network remodelling during early mouse embryo development.
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Affiliation(s)
- Jing Zhao
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Ke Yao
- School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Hua Yu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Ling Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China
| | - Yuyan Xu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Lang Chen
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Zhen Sun
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Yuqing Zhu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Cheng Zhang
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China
| | - Yuli Qian
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Shuyan Ji
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hongru Pan
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Min Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Jie Chen
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
| | - Cristina Correia
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, NY, USA
| | - Taylor Weiskittel
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, NY, USA
| | - Da-Wei Lin
- Center of Computational Medicine and Bioinformatics, Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Research Unit of Chinese Academy of Medical Sciences, East China University of Science and Technology, Shanghai, China
| | - Sriram Chandrasekaran
- Center of Computational Medicine and Bioinformatics, Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Xudong Fu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Heng-Yu Fan
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, NY, USA
| | - Zeping Hu
- School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.
| | - Jin Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou, China.
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou, China.
- Institute of Hematology, Zhejiang University, Hangzhou, China.
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Singh T, Jiao Y, Ferrando LM, Yablonska S, Li F, Horoszko EC, Lacomis D, Friedlander RM, Carlisle DL. Neuronal mitochondrial dysfunction in sporadic amyotrophic lateral sclerosis is developmentally regulated. Sci Rep 2021; 11:18916. [PMID: 34556702 PMCID: PMC8460779 DOI: 10.1038/s41598-021-97928-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 09/01/2021] [Indexed: 02/08/2023] Open
Abstract
Amyotrophic lateral sclerosis is an adult-onset neurodegenerative disorder characterized by loss of motor neurons. Mitochondria are essential for neuronal survival but the developmental timing and mechanistic importance of mitochondrial dysfunction in sporadic ALS (sALS) neurons is not fully understood. We used human induced pluripotent stem cells and generated a developmental timeline by differentiating sALS iPSCs to neural progenitors and to motor neurons and comparing mitochondrial parameters with familial ALS (fALS) and control cells at each developmental stage. We report that sALS and fALS motor neurons have elevated reactive oxygen species levels, depolarized mitochondria, impaired oxidative phosphorylation, ATP loss and defective mitochondrial protein import compared with control motor neurons. This phenotype develops with differentiation into motor neurons, the affected cell type in ALS, and does not occur in the parental undifferentiated sALS cells or sALS neural progenitors. Our work demonstrates a developmentally regulated unifying mitochondrial phenotype between patient derived sALS and fALS motor neurons. The occurrence of a unifying mitochondrial phenotype suggests that mitochondrial etiology known to SOD1-fALS may applicable to sALS. Furthermore, our findings suggest that disease-modifying treatments focused on rescue of mitochondrial function may benefit both sALS and fALS patients.
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Affiliation(s)
- Tanisha Singh
- grid.21925.3d0000 0004 1936 9000Neuroapoptosis Laboratory, Department of Neurological Surgery, University of Pittsburgh, B400 Presbyterian Hospital, 200 Lothrop Street, Pittsburgh, PA 15213 USA
| | - Yuanyuan Jiao
- grid.21925.3d0000 0004 1936 9000Neuroapoptosis Laboratory, Department of Neurological Surgery, University of Pittsburgh, B400 Presbyterian Hospital, 200 Lothrop Street, Pittsburgh, PA 15213 USA
| | - Lisa M. Ferrando
- grid.21925.3d0000 0004 1936 9000Neuroapoptosis Laboratory, Department of Neurological Surgery, University of Pittsburgh, B400 Presbyterian Hospital, 200 Lothrop Street, Pittsburgh, PA 15213 USA
| | - Svitlana Yablonska
- grid.21925.3d0000 0004 1936 9000Neuroapoptosis Laboratory, Department of Neurological Surgery, University of Pittsburgh, B400 Presbyterian Hospital, 200 Lothrop Street, Pittsburgh, PA 15213 USA
| | - Fang Li
- grid.21925.3d0000 0004 1936 9000Neuroapoptosis Laboratory, Department of Neurological Surgery, University of Pittsburgh, B400 Presbyterian Hospital, 200 Lothrop Street, Pittsburgh, PA 15213 USA
| | - Emily C. Horoszko
- grid.21925.3d0000 0004 1936 9000Neuroapoptosis Laboratory, Department of Neurological Surgery, University of Pittsburgh, B400 Presbyterian Hospital, 200 Lothrop Street, Pittsburgh, PA 15213 USA
| | - David Lacomis
- grid.21925.3d0000 0004 1936 9000Departments of Neurology and Pathology, University of Pittsburgh, Pittsburgh, PA 15213 USA
| | - Robert M. Friedlander
- grid.21925.3d0000 0004 1936 9000Neuroapoptosis Laboratory, Department of Neurological Surgery, University of Pittsburgh, B400 Presbyterian Hospital, 200 Lothrop Street, Pittsburgh, PA 15213 USA
| | - Diane L. Carlisle
- grid.21925.3d0000 0004 1936 9000Neuroapoptosis Laboratory, Department of Neurological Surgery, University of Pittsburgh, B400 Presbyterian Hospital, 200 Lothrop Street, Pittsburgh, PA 15213 USA
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Monzón-Nomdedeu MB, Morten KJ, Oltra E. Induced pluripotent stem cells as suitable sensors for fibromyalgia and myalgic encephalomyelitis/chronic fatigue syndrome. World J Stem Cells 2021; 13:1134-1150. [PMID: 34567431 PMCID: PMC8422931 DOI: 10.4252/wjsc.v13.i8.1134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/19/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Fibromyalgia (FM) and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) are devastating metabolic neuroimmune diseases that are difficult to diagnose because of the presence of numerous symptoms and a lack of specific biomarkers. Despite patient heterogeneity linked to patient subgroups and variation in disease severity, anomalies are found in the blood and plasma of these patients when compared with healthy control groups. The seeming specificity of these “plasma factors”, as recently reported by Ron Davis and his group at Stanford University, CA, United States, and observations by our group, have led to the proposal that induced pluripotent stem cells (iPSCs) may be used as metabolic sensors for FM and ME/CFS, a hypothesis that is the basis for this in-depth review.
AIM To identify metabolic signatures in FM and/or ME/CFS supporting the existence of disease-associated plasma factors to be sensed by iPSCs.
METHODS A PRISMA (Preferred Reported Items for Systematic Reviews and Meta-analysis)-based systematic review of the literature was used to select original studies evaluating the metabolite profiles of FM and ME/CFS body fluids. The MeSH terms “metabolomic” or “metabolites” in combination with FM and ME/CFS disease terms were screened against the PubMed database. Only original studies applying omics technologies, published in English, were included. The data obtained were tabulated according to the disease and type of body fluid analyzed. Coincidences across studies were searched and P-values reported by the original studies were gathered to document significant differences found in the disease groups.
RESULTS Eighteen previous studies show that some metabolites are commonly altered in ME/CFS and FM body fluids. In vitro cell-based assays have the potential to be developed as screening platforms, providing evidence for the existence of factors in patient body fluids capable of altering morphology, differentiation state and/or growth patterns. Moreover, they can be further developed using approaches aimed at blocking or reversing the effects of specific plasma/serum factors seen in patients. The documented high sensitivity and effective responses of iPSCs to environmental cues suggests that these pluripotent cells could form robust, reproducible reporter systems of metabolic diseases, including ME/CFS and FM. Furthermore, culturing iPSCs, or their mesenchymal stem cell counterparts, in patient-conditioned medium may provide valuable information to predict individual outcomes to stem-cell therapy in the context of precision medicine studies.
CONCLUSION This opinion review explains our hypothesis that iPSCs could be developed as a screening platform to provide evidence of a metabolic imbalance in FM and ME/CFS.
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Affiliation(s)
- María B Monzón-Nomdedeu
- School of Biotechnology, Universidad Católica de Valencia San Vicente Mártir, Valencia 46001, Spain
| | - Karl J Morten
- Nuffield Department of Women's and Reproductive Health, The Women Centre, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Elisa Oltra
- Department of Pathology, Universidad Católica de Valencia San Vicente Mártir, Valencia 46001, Spain
- Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, Valencia 46001, Spain
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40
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Dudek J, Kutschka I, Maack C. Metabolic and Redox Regulation of Cardiovascular Stem Cell Biology and Pathology. Antioxid Redox Signal 2021; 35:163-181. [PMID: 33121253 DOI: 10.1089/ars.2020.8201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Significance: Cardiovascular stem cells are important for regeneration and repair of damaged tissue. Recent Advances: Pluripotent stem cells have a unique metabolism, which is adopted for their energetic and biosynthetic demand as rapidly proliferating cells. Stem cell differentiation requires an exceptional metabolic flexibility allowing for metabolic remodeling between glycolysis and oxidative phosphorylation. Critical Issues: Respiration is associated with the generation of reactive oxygen species (ROS) by the mitochondrial respiratory chain. But also the membrane-bound protein nicotinamide adenine dinucleotide phosphate oxidase (NADPH oxidase, NOX) contributes to ROS levels. ROS not only play a significant role in stem cell differentiation and tissue renewal but also cause senescence and contribute to tissue aging. Future Directions: For utilization of stem cells in therapeutic approaches, a deep understanding of the molecular mechanisms how metabolism and the cellular redox state regulate stem cell differentiation is required. Modulating the redox state of stem cells using antioxidative agents may be suitable to enhance activity of endothelial progenitor cells. Antioxid. Redox Signal. 35, 163-181.
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Affiliation(s)
- Jan Dudek
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Würzburg, Germany
| | - Ilona Kutschka
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Würzburg, Germany
| | - Christoph Maack
- Department of Translational Research, Comprehensive Heart Failure Center (CHFC), University Clinic Würzburg, Würzburg, Germany.,Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany
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41
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Guo W, Wang S, Zhang X, Shi M, Duan F, Hao J, Gu K, Quan L, Wu Y, Liang Z, Wang Y. Acidic pH transiently prevents the silencing of self-renewal and dampens microRNA function in embryonic stem cells. Sci Bull (Beijing) 2021; 66:1319-1329. [PMID: 36654154 DOI: 10.1016/j.scib.2021.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/18/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023]
Abstract
Enhanced glycolysis is a distinct feature associated with numerous stem cells and cancer cells. However, little is known about its regulatory roles in gene expression and cell fate determination. Here, we confirm that glycolytic metabolism and lactate production decrease during the differentiation of mouse embryonic stem cells (mESCs). Importantly, acidic pH due to lactate accumulation can transiently prevent the silencing of mESC self-renewal in differentiation conditions. Furthermore, acidic pH partially blocks the differentiation of human ESCs (hESCs). Mechanistically, acidic pH downregulates AGO1 protein and de-represses a subset of mRNA targets of miR-290/302 family of microRNAs which facilitate the exit of naive pluripotency state in mESCs. Interestingly, AGO1 protein is also downregulated by acidic pH in cancer cells. Altogether, this study provides insights into the potential function and underlying mechanism of acidic pH in pluripotent stem cells (PSCs).
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Affiliation(s)
- Wenting Guo
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China; Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China.
| | - Shaohua Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Xiaoshan Zhang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Ming Shi
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Feifei Duan
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Jing Hao
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Kaili Gu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Li Quan
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Yixia Wu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Zhiyong Liang
- Department of Pathology, Molecular Pathology Research Centre, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yangming Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China.
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Yuan F, Wang N, Chen Y, Huang X, Yang Z, Xu Y, You K, Zhang J, Wang G, Zhuang Y, Pan T, Xiong Y, Yu X, Yang F, Li Y. Calcitriol promotes the maturation of hepatocyte-like cells derived from human pluripotent stem cells. J Steroid Biochem Mol Biol 2021; 211:105881. [PMID: 33766737 DOI: 10.1016/j.jsbmb.2021.105881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/07/2021] [Accepted: 03/18/2021] [Indexed: 11/23/2022]
Abstract
Human hepatocyte-like cells (HLCs) derived from human pluripotent stem cells (hPSCs) represent a promising cell source for the assessment of hepatotoxicity and pharmaceutical safety testing. However, the hepatic functionality of HLCs remains significantly inferior to primary human hepatocytes. The bioactive vitamin D (VD), calcitriol, promotes the differentiation of many types of cells, and its deficiency is correlated to the severity of liver diseases. Whether calcitriol contributes to the differentiation of HLCs needs to be explored. Here, we found that the supplementation of calcitriol improved the functionalities of hPSCs-derived HLCs in P450 activities, urea production, and albumin secretion. Moreover, calcitriol also enhanced mitochondrial respiratory function with increased protein expression levels of the subunit of respiratory enzyme complexes in HLCs. Further analyses showed that the mitochondrial biogenesis regulators and mitophagy were increased by calcitriol, thus improving the mitochondrial quality. These improvements in functionality and mitochondrial condition were dependent on vitamin D receptor (VDR) because the improvements were abolished under VDR-deficient conditions. Our finding provides a cost-effective chemical process for HLC maturation to meet the demand for basic research and potential clinic applications.
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Affiliation(s)
- Fang Yuan
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese, Academy of Sciences, 510530, Guangzhou, China; School of Life Sciences, University of Science and Technology of China, 230027, Hefei, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell, Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Ning Wang
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese, Academy of Sciences, 510530, Guangzhou, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell, Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Yan Chen
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese, Academy of Sciences, 510530, Guangzhou, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell, Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Xinping Huang
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese, Academy of Sciences, 510530, Guangzhou, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell, Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Zhen Yang
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese, Academy of Sciences, 510530, Guangzhou, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell, Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Yingying Xu
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese, Academy of Sciences, 510530, Guangzhou, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell, Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Kai You
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese, Academy of Sciences, 510530, Guangzhou, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell, Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Jiaye Zhang
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese, Academy of Sciences, 510530, Guangzhou, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell, Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Guodong Wang
- The First Affiliated Hospital of Sun Yat-sen University, 510080, Guangzhou, China
| | - Yuanqi Zhuang
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese, Academy of Sciences, 510530, Guangzhou, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell, Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Tingcai Pan
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese, Academy of Sciences, 510530, Guangzhou, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell, Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Yue Xiong
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese, Academy of Sciences, 510530, Guangzhou, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell, Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Xiaorui Yu
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese, Academy of Sciences, 510530, Guangzhou, China; School of Life Sciences, University of Science and Technology of China, 230027, Hefei, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell, Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Fan Yang
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese, Academy of Sciences, 510530, Guangzhou, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell, Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Yinxiong Li
- Institute of Public Health, Guangzhou Institutes of Biomedicine and Health, Chinese, Academy of Sciences, 510530, Guangzhou, China; Key Laboratory of Regenerative Biology, South China Institute for Stem Cell, Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China; Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China.
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43
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Cui P, Zhang P, Yuan L, Wang L, Guo X, Cui G, Zhang Y, Li M, Zhang X, Li X, Yin Y, Yu Z. HIF-1α Affects the Neural Stem Cell Differentiation of Human Induced Pluripotent Stem Cells via MFN2-Mediated Wnt/β-Catenin Signaling. Front Cell Dev Biol 2021; 9:671704. [PMID: 34235146 PMCID: PMC8256873 DOI: 10.3389/fcell.2021.671704] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/28/2021] [Indexed: 11/20/2022] Open
Abstract
Hypoxia-inducible factor 1α (HIF-1α) plays pivotal roles in maintaining pluripotency, and the developmental potential of pluripotent stem cells (PSCs). However, the mechanisms underlying HIF-1α regulation of neural stem cell (NSC) differentiation of human induced pluripotent stem cells (hiPSCs) remains unclear. In this study, we demonstrated that HIF-1α knockdown significantly inhibits the pluripotency and self-renewal potential of hiPSCs. We further uncovered that the disruption of HIF-1α promotes the NSC differentiation and development potential in vitro and in vivo. Mechanistically, HIF-1α knockdown significantly enhances mitofusin2 (MFN2)-mediated Wnt/β-catenin signaling, and excessive mitochondrial fusion could also promote the NSC differentiation potential of hiPSCs via activating the β-catenin signaling. Additionally, MFN2 significantly reverses the effects of HIF-1α overexpression on the NSC differentiation potential and β-catenin activity of hiPSCs. Furthermore, Wnt/β-catenin signaling inhibition could also reverse the effects of HIF-1α knockdown on the NSC differentiation potential of hiPSCs. This study provided a novel strategy for improving the directed differentiation efficiency of functional NSCs. These findings are important for the development of potential clinical interventions for neurological diseases caused by metabolic disorders.
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Affiliation(s)
- Peng Cui
- Institute of Precision of Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | - Ping Zhang
- Department of Hematology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Lin Yuan
- Institute of Precision of Medicine, Peking University Shenzhen Hospital, Shenzhen, China.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Li Wang
- Department of Oncology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Xin Guo
- Central Laboratory, Peking University Shenzhen Hospital, Shenzhen, China
| | - Guanghui Cui
- Central Laboratory, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yanmin Zhang
- Central Laboratory, Peking University Shenzhen Hospital, Shenzhen, China
| | - Minghua Li
- Central Laboratory, Peking University Shenzhen Hospital, Shenzhen, China
| | - Xiaowei Zhang
- School of Basic Medical Sciences, Peking University, Beijing, China
| | - Xiaoqiang Li
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yuxin Yin
- Institute of Precision of Medicine, Peking University Shenzhen Hospital, Shenzhen, China.,Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing, China
| | - Zhendong Yu
- Central Laboratory, Peking University Shenzhen Hospital, Shenzhen, China
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44
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Xie J, Lou Q, Zeng Y, Liang Y, Xie S, Xu Q, Yuan L, Wang J, Jiang L, Mou L, Lin D, Zhao M. Single-Cell Atlas Reveals Fatty Acid Metabolites Regulate the Functional Heterogeneity of Mesenchymal Stem Cells. Front Cell Dev Biol 2021; 9:653308. [PMID: 33912565 PMCID: PMC8075002 DOI: 10.3389/fcell.2021.653308] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/09/2021] [Indexed: 12/28/2022] Open
Abstract
Bone marrow mesenchymal stem cells (MSCs) are widely used clinically due to their versatile roles in multipotency, immunomodulation, and hematopoietic stem cell (HSC) niche function. However, cellular heterogeneity limits MSCs in the consistency and efficacy of their clinical applications. Metabolism regulates stem cell function and fate decision; however, how metabolites regulate the functional heterogeneity of MSCs remains elusive. Here, using single-cell RNA sequencing, we discovered that fatty acid pathways are involved in the regulation of lineage commitment and functional heterogeneity of MSCs. Functional assays showed that a fatty acid metabolite, butyrate, suppressed the self-renewal, adipogenesis, and osteogenesis differentiation potential of MSCs with increased apoptosis. Conversely, butyrate supplement significantly promoted HSC niche factor expression in MSCs, which suggests that butyrate supplement may provide a therapeutic approach to enhance their HSC niche function. Overall, our work demonstrates that metabolites are essential to regulate the functional heterogeneity of MSCs.
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Affiliation(s)
- Jiayi Xie
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Qi Lou
- Shenzhen Lansi Institute of Artificial Intelligence in Medicine, Shenzhen, China.,The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People's Hospital, Shenzhen, China
| | - Yunxin Zeng
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yingying Liang
- Shenzhen Lansi Institute of Artificial Intelligence in Medicine, Shenzhen, China.,The First Affiliated Hospital of Shenzhen University, Health Science Center, Shenzhen Second People's Hospital, Shenzhen, China
| | - Siyu Xie
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Quanhui Xu
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou, China
| | - Lisha Yuan
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou, China
| | - Jin Wang
- Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou, China
| | - Linjia Jiang
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lisha Mou
- Shenzhen Lansi Institute of Artificial Intelligence in Medicine, Shenzhen, China
| | - Dongjun Lin
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Meng Zhao
- Department of Hematology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.,Shenzhen Lansi Institute of Artificial Intelligence in Medicine, Shenzhen, China.,Key Laboratory of Stem Cells and Tissue Engineering, Zhongshan School of Medicine, Sun Yat-sen University, Ministry of Education, Guangzhou, China
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45
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Li H, Uittenbogaard M, Hao L, Chiaramello A. Clinical Insights into Mitochondrial Neurodevelopmental and Neurodegenerative Disorders: Their Biosignatures from Mass Spectrometry-Based Metabolomics. Metabolites 2021; 11:233. [PMID: 33920115 PMCID: PMC8070181 DOI: 10.3390/metabo11040233] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/01/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are dynamic multitask organelles that function as hubs for many metabolic pathways. They produce most ATP via the oxidative phosphorylation pathway, a critical pathway that the brain relies on its energy need associated with its numerous functions, such as synaptic homeostasis and plasticity. Therefore, mitochondrial dysfunction is a prevalent pathological hallmark of many neurodevelopmental and neurodegenerative disorders resulting in altered neurometabolic coupling. With the advent of mass spectrometry (MS) technology, MS-based metabolomics provides an emerging mechanistic understanding of their global and dynamic metabolic signatures. In this review, we discuss the pathogenetic causes of mitochondrial metabolic disorders and the recent MS-based metabolomic advances on their metabolomic remodeling. We conclude by exploring the MS-based metabolomic functional insights into their biosignatures to improve diagnostic platforms, stratify patients, and design novel targeted therapeutic strategies.
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Affiliation(s)
- Haorong Li
- Department of Chemistry, George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, DC 20052, USA;
| | - Martine Uittenbogaard
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington University, 2300 I Street N.W. Ross Hall 111, Washington, DC 20037, USA;
| | - Ling Hao
- Department of Chemistry, George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, DC 20052, USA;
| | - Anne Chiaramello
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington University, 2300 I Street N.W. Ross Hall 111, Washington, DC 20037, USA;
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46
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Kim HN, Shin JY, Kim DY, Lee JE, Lee PH. Priming mesenchymal stem cells with uric acid enhances neuroprotective properties in parkinsonian models. J Tissue Eng 2021; 12:20417314211004816. [PMID: 33854750 PMCID: PMC8013923 DOI: 10.1177/20417314211004816] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 12/14/2022] Open
Abstract
Mesenchymal stem cells (MSCs) are a potential source of cell-based disease-modifying therapy in Parkinsonian disorders. A promising approach to develop in vitro culture methods that mimic natural MSC niche is cell priming. Uric acid (UA), a powerful antioxidant, scavenges reactive oxygen species, which has a vital role in maintaining self-renewal and differentiation potential of MSCs. Here, we demonstrated that UA treatment in naïve MSCs stimulated glycolysis and upregulated transcriptional factors responsible for regulation of stemness, leading to increase in the expression levels of osteogenesis-, adipogenesis-, and chondrogenesis-related genes. UA-primed MSCs had more enhanced neuroprotective properties in cellular and parkinsonian animal models compared to naïve MSCs by inhibiting apoptotic signaling pathways. Additionally, expression of miR-137 and miR-145 was decreased in UA-treated MSCs. Our data demonstrated that priming MSCs with UA augment neuroprotective properties through enhanced self-renewal and differentiation potential, suggesting a practical strategy for improving the application of MSCs in parkinsonian disorders.
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Affiliation(s)
- Ha Na Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea
| | - Jin Young Shin
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea.,Severance Biomedical Science Institute, Yonsei University, Seoul, Korea
| | - Dong Yeol Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea
| | - Ji Eun Lee
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea
| | - Phil Hyu Lee
- Department of Neurology, Yonsei University College of Medicine, Seoul, Korea.,Severance Biomedical Science Institute, Yonsei University, Seoul, Korea
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47
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Disease-Relevant Single Cell Photonic Signatures Identify S100β Stem Cells and their Myogenic Progeny in Vascular Lesions. Stem Cell Rev Rep 2021; 17:1713-1740. [PMID: 33730327 PMCID: PMC8446106 DOI: 10.1007/s12015-021-10125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2021] [Indexed: 10/31/2022]
Abstract
A hallmark of subclinical atherosclerosis is the accumulation of vascular smooth muscle cell (SMC)-like cells leading to intimal thickening and lesion formation. While medial SMCs contribute to vascular lesions, the involvement of resident vascular stem cells (vSCs) remains unclear. We evaluated single cell photonics as a discriminator of cell phenotype in vitro before the presence of vSC within vascular lesions was assessed ex vivo using supervised machine learning and further validated using lineage tracing analysis. Using a novel lab-on-a-Disk(Load) platform, label-free single cell photonic emissions from normal and injured vessels ex vivo were interrogated and compared to freshly isolated aortic SMCs, cultured Movas SMCs, macrophages, B-cells, S100β+ mVSc, bone marrow derived mesenchymal stem cells (MSC) and their respective myogenic progeny across five broadband light wavelengths (λ465 - λ670 ± 20 nm). We found that profiles were of sufficient coverage, specificity, and quality to clearly distinguish medial SMCs from different vascular beds (carotid vs aorta), discriminate normal carotid medial SMCs from lesional SMC-like cells ex vivo following flow restriction, and identify SMC differentiation of a series of multipotent stem cells following treatment with transforming growth factor beta 1 (TGF- β1), the Notch ligand Jagged1, and Sonic Hedgehog using multivariate analysis, in part, due to photonic emissions from enhanced collagen III and elastin expression. Supervised machine learning supported genetic lineage tracing analysis of S100β+ vSCs and identified the presence of S100β+vSC-derived myogenic progeny within vascular lesions. We conclude disease-relevant photonic signatures may have predictive value for vascular disease.
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48
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Sun L, Fu X, Ma G, Hutchins AP. Chromatin and Epigenetic Rearrangements in Embryonic Stem Cell Fate Transitions. Front Cell Dev Biol 2021; 9:637309. [PMID: 33681220 PMCID: PMC7930395 DOI: 10.3389/fcell.2021.637309] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
A major event in embryonic development is the rearrangement of epigenetic information as the somatic genome is reprogrammed for a new round of organismal development. Epigenetic data are held in chemical modifications on DNA and histones, and there are dramatic and dynamic changes in these marks during embryogenesis. However, the mechanisms behind this intricate process and how it is regulating and responding to embryonic development remain unclear. As embryos develop from totipotency to pluripotency, they pass through several distinct stages that can be captured permanently or transiently in vitro. Pluripotent naïve cells resemble the early epiblast, primed cells resemble the late epiblast, and blastomere-like cells have been isolated, although fully totipotent cells remain elusive. Experiments using these in vitro model systems have led to insights into chromatin changes in embryonic development, which has informed exploration of pre-implantation embryos. Intriguingly, human and mouse cells rely on different signaling and epigenetic pathways, and it remains a mystery why this variation exists. In this review, we will summarize the chromatin rearrangements in early embryonic development, drawing from genomic data from in vitro cell lines, and human and mouse embryos.
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Affiliation(s)
| | | | | | - Andrew P. Hutchins
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
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49
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Wang Q, Xiong Y, Zhang S, Sui Y, Yu C, Liu P, Li H, Guo W, Gao Y, Przepiorski A, Davidson AJ, Guo M, Zhang X. The Dynamics of Metabolic Characterization in iPSC-Derived Kidney Organoid Differentiation via a Comparative Omics Approach. Front Genet 2021; 12:632810. [PMID: 33643392 PMCID: PMC7902935 DOI: 10.3389/fgene.2021.632810] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/20/2021] [Indexed: 12/22/2022] Open
Abstract
The use of differentiating human induced pluripotent stem cells (hiPSCs) in mini-tissue organoids provides an invaluable resource for regenerative medicine applications, particularly in the field of disease modeling. However, most studies using a kidney organoid model, focused solely on the transcriptomics and did not explore mechanisms of regulating kidney organoids related to metabolic effects and maturational phenotype. Here, we applied metabolomics coupled with transcriptomics to investigate the metabolic dynamics and function during kidney organoid differentiation. Not only did we validate the dominant metabolic alteration from glycolysis to oxidative phosphorylation in the iPSC differentiation process but we also showed that glycine, serine, and threonine metabolism had a regulatory role during kidney organoid formation and lineage maturation. Notably, serine had a role in regulating S-adenosylmethionine (SAM) to facilitate kidney organoid formation by altering DNA methylation. Our data revealed that analysis of metabolic characterization broadens our ability to understand phenotype regulation. The utilization of this comparative omics approach, in studying kidney organoid formation, can aid in deciphering unique knowledge about the biological and physiological processes involved in organoid-based disease modeling or drug screening.
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Affiliation(s)
- Qizheng Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Yucui Xiong
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Sheng Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Yufei Sui
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Cunlai Yu
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Peng Liu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Heying Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Wenjing Guo
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Yubo Gao
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Aneta Przepiorski
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Alan J Davidson
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xiao Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.,Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
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50
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Betto RM, Diamante L, Perrera V, Audano M, Rapelli S, Lauria A, Incarnato D, Arboit M, Pedretti S, Rigoni G, Guerineau V, Touboul D, Stirparo GG, Lohoff T, Boroviak T, Grumati P, Soriano ME, Nichols J, Mitro N, Oliviero S, Martello G. Metabolic control of DNA methylation in naive pluripotent cells. Nat Genet 2021; 53:215-229. [PMID: 33526924 PMCID: PMC7116828 DOI: 10.1038/s41588-020-00770-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/17/2020] [Indexed: 12/31/2022]
Abstract
Naive epiblast and embryonic stem cells (ESCs) give rise to all cells of adults. Such developmental plasticity is associated with genome hypomethylation. Here, we show that LIF-Stat3 signaling induces genomic hypomethylation via metabolic reconfiguration. Stat3-/- ESCs show decreased α-ketoglutarate production from glutamine, leading to increased Dnmt3a and Dnmt3b expression and DNA methylation. Notably, genome methylation is dynamically controlled through modulation of α-ketoglutarate availability or Stat3 activation in mitochondria. Alpha-ketoglutarate links metabolism to the epigenome by reducing the expression of Otx2 and its targets Dnmt3a and Dnmt3b. Genetic inactivation of Otx2 or Dnmt3a and Dnmt3b results in genomic hypomethylation even in the absence of active LIF-Stat3. Stat3-/- ESCs show increased methylation at imprinting control regions and altered expression of cognate transcripts. Single-cell analyses of Stat3-/- embryos confirmed the dysregulated expression of Otx2, Dnmt3a and Dnmt3b as well as imprinted genes. Several cancers display Stat3 overactivation and abnormal DNA methylation; therefore, the molecular module that we describe might be exploited under pathological conditions.
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Affiliation(s)
- Riccardo M Betto
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Linda Diamante
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Valentina Perrera
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
- Neuroscience Sector, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Matteo Audano
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy
| | - Stefania Rapelli
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy
| | - Andrea Lauria
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy
| | - Danny Incarnato
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Groningen, the Netherlands
| | - Mattia Arboit
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy
| | - Silvia Pedretti
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy
| | - Giovanni Rigoni
- Department of Biology, University of Padua, Padua, Italy
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Vincent Guerineau
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette, France
| | - David Touboul
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS, Gif-sur-Yvette, France
| | | | - Tim Lohoff
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Thorsten Boroviak
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Paolo Grumati
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | | | - Jennifer Nichols
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Nico Mitro
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, Milan, Italy.
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy.
| | - Graziano Martello
- Department of Molecular Medicine, Medical School, University of Padua, Padua, Italy.
- Department of Biology, University of Padua, Padua, Italy.
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