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Martano G, Borroni EM, Lopci E, Cattaneo MG, Mattioli M, Bachi A, Decimo I, Bifari F. Metabolism of Stem and Progenitor Cells: Proper Methods to Answer Specific Questions. Front Mol Neurosci 2019; 12:151. [PMID: 31249511 PMCID: PMC6584756 DOI: 10.3389/fnmol.2019.00151] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/28/2019] [Indexed: 01/01/2023] Open
Abstract
Stem cells can stay quiescent for a long period of time or proliferate and differentiate into multiple lineages. The activity of stage-specific metabolic programs allows stem cells to best adapt their functions in different microenvironments. Specific cellular phenotypes can be, therefore, defined by precise metabolic signatures. Notably, not only cellular metabolism describes a defined cellular phenotype, but experimental evidence now clearly indicate that also rewiring cells towards a particular cellular metabolism can drive their cellular phenotype and function accordingly. Cellular metabolism can be studied by both targeted and untargeted approaches. Targeted analyses focus on a subset of identified metabolites and on their metabolic fluxes. In addition, the overall assessment of the oxygen consumption rate (OCR) gives a measure of the overall cellular oxidative metabolism and mitochondrial function. Untargeted approach provides a large-scale identification and quantification of the whole metabolome with the aim to describe a metabolic fingerprinting. In this review article, we overview the methodologies currently available for the study of invitro stem cell metabolism, including metabolic fluxes, fingerprint analyses, and single-cell metabolomics. Moreover, we summarize available approaches for the study of in vivo stem cell metabolism. For all of the described methods, we highlight their specificities and limitations. In addition, we discuss practical concerns about the most threatening steps, including metabolic quenching, sample preparation and extraction. A better knowledge of the precise metabolic signature defining specific cell population is instrumental to the design of novel therapeutic strategies able to drive undifferentiated stem cells towards a selective and valuable cellular phenotype.
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Affiliation(s)
| | - Elena Monica Borroni
- Humanitas Clinical and Research Center, Rozzano, Italy.,Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Egesta Lopci
- Nuclear Medicine Unit, Humanitas Clinical and Research Hospital-IRCCS, Rozzano, Italy
| | - Maria Grazia Cattaneo
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Milena Mattioli
- Laboratory of Cell Metabolism and Regenerative Medicine, Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Angela Bachi
- IFOM-FIRC Institute of Molecular Oncology, Milan, Italy
| | - Ilaria Decimo
- Laboratory of Pharmacology, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Francesco Bifari
- Laboratory of Cell Metabolism and Regenerative Medicine, Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
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52
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Nishimura K, Fukuda A, Hisatake K. Mechanisms of the Metabolic Shift during Somatic Cell Reprogramming. Int J Mol Sci 2019; 20:ijms20092254. [PMID: 31067778 PMCID: PMC6539623 DOI: 10.3390/ijms20092254] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/25/2019] [Accepted: 05/06/2019] [Indexed: 12/18/2022] Open
Abstract
Pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), hold a huge promise for regenerative medicine, drug development, and disease modeling. PSCs have unique metabolic features that are akin to those of cancer cells, in which glycolysis predominates to produce energy as well as building blocks for cellular components. Recent studies indicate that the unique metabolism in PSCs is not a mere consequence of their preference for a low oxygen environment, but is an active process for maintaining self-renewal and pluripotency, possibly in preparation for rapid response to the metabolic demands of differentiation. Understanding the regulatory mechanisms of this unique metabolism in PSCs is essential for proper derivation, generation, and maintenance of PSCs. In this review, we discuss the metabolic features of PSCs and describe the current understanding of the mechanisms of the metabolic shift during reprogramming from somatic cells to iPSCs, in which the metabolism switches from oxidative phosphorylation (OxPhos) to glycolysis.
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Affiliation(s)
- Ken Nishimura
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan.
| | - Aya Fukuda
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan.
| | - Koji Hisatake
- Laboratory of Gene Regulation, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8577, Japan.
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53
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Maslanka R, Zadrag-Tecza R. Less is more or more is less: Implications of glucose metabolism in the regulation of the reproductive potential and total lifespan of the Saccharomyces cerevisiae yeast. J Cell Physiol 2019; 234:17622-17638. [PMID: 30805924 DOI: 10.1002/jcp.28386] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 01/23/2019] [Accepted: 01/28/2019] [Indexed: 01/10/2023]
Abstract
Carbohydrates are dietary nutrients that have an influence on cells physiology, cell reproductive capacity and, consequently, the lifespan of organisms. They are used in cellular processes after conversion to glucose, which is the primary source of energy and carbon skeleton for biosynthetic processes. Studies of the influence of glucose on cellular parameters and lifespan of organisms are primarily concerned with the effect of low glucose concentration defined as calorie restriction conditions. However, the effect of high glucose concentration on cell physiology is also very important. Thus, a comparative analysis of the effects of low and high glucose concentration conditions on cell efficiency was proposed with regard to reproductive capacity and total lifespan of the cell. Glucose concentration determines the type of metabolism and biosynthetic capabilities, which in turn, through the regulation on the cell size, may affect the reproductive capacity of cells. This study was conducted on yeast cells of wild-type and mutant strains Δgpa2 and Δgpr1 with glucose signalling pathway impairment. Such an experimental model enabled testing both the role of glucose concentration in the regulation of metabolic changes and the extent to which these changes depend on the extracellular or intracellular glucose concentrations. It has been shown here that calorie/glucose excess connected with changes in cell metabolic fluxes increases biosynthetic capabilities of yeast cells. This leads to an increase in cell dry weight accompanied by the increase in cell size and a simultaneous decrease in the reproductive potential and the overall length of cell life.
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Affiliation(s)
- Roman Maslanka
- Department of Biochemistry and Cell Biology, Faculty of Biotechnology, University of Rzeszow, Rzeszow, Poland
| | - Renata Zadrag-Tecza
- Department of Biochemistry and Cell Biology, Faculty of Biotechnology, University of Rzeszow, Rzeszow, Poland
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54
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Increased Cytotoxicity of Herpes Simplex Virus Thymidine Kinase Expression in Human Induced Pluripotent Stem Cells. Int J Mol Sci 2019; 20:ijms20040810. [PMID: 30769780 PMCID: PMC6413063 DOI: 10.3390/ijms20040810] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 02/07/2023] Open
Abstract
Human induced pluripotent stem cells (iPSCs) hold enormous promise for regenerative medicine. The major safety concern is the tumorigenicity of transplanted cells derived from iPSCs. A potential solution would be to introduce a suicide gene into iPSCs as a safety switch. The herpes simplex virus type 1 thymidine kinase (HSV-TK) gene, in combination with ganciclovir, is the most widely used enzyme/prodrug suicide system from basic research to clinical applications. In the present study, we attempted to establish human iPSCs that stably expressed HSV-TK with either lentiviral vectors or CRISPR/Cas9-mediated genome editing. However, this task was difficult to achieve, because high-level and/or constitutive expression of HSV-TK resulted in the induction of cell death or silencing of HSV-TK expression. A nucleotide metabolism analysis suggested that excessive accumulation of thymidine triphosphate, caused by HSV-TK expression, resulted in an imbalance in the dNTP pools. This unbalanced state led to DNA synthesis inhibition and cell death in a process similar to a “thymidine block”, but more severe. We also demonstrated that the Tet-inducible system was a feasible solution for overcoming the cytotoxicity of HSV-TK expression. Our results provided a warning against using the HSV-TK gene in human iPSCs, particularly in clinical applications.
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55
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Targeting glutaminase 1 attenuates stemness properties in hepatocellular carcinoma by increasing reactive oxygen species and suppressing Wnt/beta-catenin pathway. EBioMedicine 2018; 39:239-254. [PMID: 30555042 PMCID: PMC6355660 DOI: 10.1016/j.ebiom.2018.11.063] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/29/2018] [Accepted: 11/29/2018] [Indexed: 12/25/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is an aggressive malignant disease with poor prognosis. Recent advances suggest the existence of cancer stem cells (CSCs) within liver cancer, which are considered to be responsible for tumor relapse, metastasis, and chemoresistance. However, novel therapeutic approaches for eradicating CSCs are yet to be established. Here, we aimed to identify the role of glutaminase 1 (GLS1) in stemness, and the feasibility that GLS1 serves as a therapeutic target for elimination CSCs as well as the possible mechanism. Methods Publicly-available data from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) was mined to unearth the association between GLS1 and stemness phenotype. Using big data, human tissues and multiple cell lines, we gained a general picture of GLS1 expression in HCC progression. We generated stable cell lines by lentiviral-mediated overexpression or CRISPR/Cas9-based knockout. Sphere formation assays and colony formation assays were employed to analyze the relationship between GLS1 and stemness. A series of bioinformatics analyses and molecular experiments including qRT-PCR, immunoblotting, flow cytometry, and immunofluorescence were employed to investigate the role of GLS1 in regulating stemness in vitro and in vivo. Findings We observed GLS1 (both KGA and GAC isoform) is highly expressed in HCC, and that high expression of GAC predicts a poor prognosis. GLS1 is exclusively expressed in the mitochondrial matrix. Upregulation of GLS1 is positively associated with advanced clinicopathological features and stemness phenotype. Targeting GLS1 reduced the expression of stemness-related genes and suppressed CSC properties in vitro. We further found GLS1 regulates stemness properties via ROS/Wnt/β-catenin signaling and that GLS1 knockout inhibits tumorigenicity in vivo. Interpretation Targeting GLS1 attenuates stemness properties in HCC by increasing ROS accumulation and suppressing Wnt/β-catenin pathway, which implied that GLS1 could serve as a therapeutic target for elimination of CSCs.
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56
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Banerjee A, Lindenmair A, Steinborn R, Dumitrescu SD, Hennerbichler S, Kozlov AV, Redl H, Wolbank S, Weidinger A. Oxygen Tension Strongly Influences Metabolic Parameters and the Release of Interleukin-6 of Human Amniotic Mesenchymal Stromal Cells In Vitro. Stem Cells Int 2018; 2018:9502451. [PMID: 30510589 PMCID: PMC6230389 DOI: 10.1155/2018/9502451] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 05/18/2018] [Accepted: 09/06/2018] [Indexed: 12/11/2022] Open
Abstract
The human amniotic membrane (hAM) has been used for tissue regeneration for over a century. In vivo (in utero), cells of the hAM are exposed to low oxygen tension (1-4% oxygen), while the hAM is usually cultured in atmospheric, meaning high, oxygen tension (20% oxygen). We tested the influence of oxygen tensions on mitochondrial and inflammatory parameters of human amniotic mesenchymal stromal cells (hAMSCs). Freshly isolated hAMSCs were incubated for 4 days at 5% and 20% oxygen. We found 20% oxygen to strongly increase mitochondrial oxidative phosphorylation, especially in placental amniotic cells. Oxygen tension did not impact levels of reactive oxygen species (ROS); however, placental amniotic cells showed lower levels of ROS, independent of oxygen tension. In contrast, the release of nitric oxide was independent of the amniotic region but dependent on oxygen tension. Furthermore, IL-6 was significantly increased at 20% oxygen. To conclude, short-time cultivation at 20% oxygen of freshly isolated hAMSCs induced significant changes in mitochondrial function and release of IL-6. Depending on the therapeutic purpose, cultivation conditions of the cells should be chosen carefully for providing the best possible quality of cell therapy.
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Affiliation(s)
- Asmita Banerjee
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, AUVA Research Center, Donaueschingenstraße 13, 1200 Vienna, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Andrea Lindenmair
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, AUVA Research Center, Garnisonstraße 21, 4020 Linz, Austria
| | - Ralf Steinborn
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria
| | - Sergiu Dan Dumitrescu
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, AUVA Research Center, Donaueschingenstraße 13, 1200 Vienna, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Simone Hennerbichler
- Red Cross Blood Transfusion Service for Upper Austria, Krankenhausstraße 7, 4017 Linz, Austria
| | - Andrey V. Kozlov
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, AUVA Research Center, Donaueschingenstraße 13, 1200 Vienna, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Heinz Redl
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, AUVA Research Center, Donaueschingenstraße 13, 1200 Vienna, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Susanne Wolbank
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, AUVA Research Center, Donaueschingenstraße 13, 1200 Vienna, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Adelheid Weidinger
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, AUVA Research Center, Donaueschingenstraße 13, 1200 Vienna, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
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Shi J, Teschendorff AE, Chen W, Chen L, Li T. Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures. Brief Bioinform 2018; 21:248-261. [PMID: 30289442 DOI: 10.1093/bib/bby093] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 01/07/2023] Open
Abstract
MOTIVATION Estimating differentiation potency of single cells is a task of great biological and clinical significance, as it may allow identification of normal and cancer stem cell phenotypes. However, very few single-cell potency models have been proposed, and their robustness and reliability across independent studies have not yet been fully assessed. RESULTS Using nine independent single-cell RNA-Seq experiments, we here compare four different single-cell potency models to each other, in their ability to discriminate cells that ought to differ in terms of differentiation potency. Two of the potency models approximate potency via network entropy measures that integrate the single-cell RNA-Seq profile of a cell with a protein interaction network. The comparison between the four models reveals that integration of RNA-Seq data with a protein interaction network dramatically improves the robustness and reliability of single-cell potency estimates. We demonstrate that underlying this robustness is a correlation relationship, according to which high differentiation potency is positively associated with overexpression of network hubs. We further show that overexpressed network hubs are strongly enriched for ribosomal mitochondrial proteins, suggesting that their mRNA levels may provide a universal marker of a cell's potency. Thus, this study provides novel systems-biological insight into cellular potency and may provide a foundation for improved models of differentiation potency with far-reaching implications for the discovery of novel stem cell or progenitor cell phenotypes.
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Affiliation(s)
- Jifan Shi
- School of Mathematical Sciences, Peking University, Beijing, China
| | | | - Weiyan Chen
- Shanghai Institutes for Biological Sciences, Shanghai, China
| | - Luonan Chen
- Key Lab for Systems Biology, Chinese Academy of Sciences, Shanghai, China
| | - Tiejun Li
- School of Mathematical Sciences, Peking University, Beijing, China
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58
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Knobloch M, Widmann C. Burning fat to keep your stem cells? The role of fatty acid oxidation in various tissue stem cells. Curr Opin Lipidol 2018; 29:426-427. [PMID: 30153135 DOI: 10.1097/mol.0000000000000546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Marlen Knobloch
- Department of Physiology, University of Lausanne, Lausanne, Switzerland
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59
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Biochemical re-programming of human dermal stem cells to neurons by increasing mitochondrial membrane potential. Cell Death Differ 2018; 26:1048-1061. [PMID: 30154448 DOI: 10.1038/s41418-018-0182-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/15/2018] [Accepted: 07/22/2018] [Indexed: 01/07/2023] Open
Abstract
Stem cells are generally believed to contain a small number of mitochondria, thus accounting for their glycolytic phenotype. We demonstrate here, however, that despite an indispensable glucose dependency, human dermal stem cells (hDSCs) contain very numerous mitochondria. Interestingly, these stem cells segregate into two distinct subpopulations. One exhibits high, the other low-mitochondrial membrane potentials (Δψm). We have made the same observations with mouse neural stem cells (mNSCs) which serve here as a complementary model to hDSCs. Strikingly, pharmacologic inhibition of phosphoinositide 3-kinase (PI3K) increased the overall Δψm, decreased the dependency on glycolysis and led to formation of TUJ1 positive, electrophysiologically functional neuron-like cells in both mNSCs and hDSCs, even in the absence of any neuronal growth factors. Furthermore, of the two, it was the Δψm-high subpopulation which produced more mitochondrial reactive oxygen species (ROS) and showed an enhanced neuronal differentiation capacity as compared to the Δψm-low subpopulation. These data suggest that the Δψm-low stem cells may function as the dormant stem cell population to sustain future neuronal differentiation by avoiding excessive ROS production. Thus, chemical modulation of PI3K activity, switching the metabotype of hDSCs to neurons, may have potential as an autologous transplantation strategy for neurodegenerative diseases.
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60
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Dwaraka VB, Smith JJ, Woodcock MR, Voss SR. Comparative transcriptomics of limb regeneration: Identification of conserved expression changes among three species of Ambystoma. Genomics 2018; 111:1216-1225. [PMID: 30092345 DOI: 10.1016/j.ygeno.2018.07.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/23/2018] [Accepted: 07/31/2018] [Indexed: 12/14/2022]
Abstract
Transcriptome studies are revealing the complex gene expression basis of limb regeneration in the primary salamander model - Ambystoma mexicanum (axolotl). To better understand this complexity, there is need to extend analyses to additional salamander species. Using microarray and RNA-Seq, we performed a comparative transcriptomic study using A. mexicanum and two other ambystomatid salamanders: A. andersoni, and A. maculatum. Salamanders were administered forelimb amputations and RNA was isolated and analyzed to identify 405 non-redundant genes that were commonly, differentially expressed 24 h post amputation. Many of the upregulated genes are predicted to function in wound healing and developmental processes, while many of the downregulated genes are typically expressed in muscle. The conserved transcriptional changes identified in this study provide a high-confidence dataset for identifying factors that simultaneous orchestrate wound healing and regeneration processes in response to injury, and more generally for identifying genes that are essential for salamander limb regeneration.
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Affiliation(s)
- Varun B Dwaraka
- Department of Biology, University of Kentucky, Lexington, KY 40506, United States; Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY 40536, United States.
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY 40506, United States
| | - M Ryan Woodcock
- Department of Biology, Keene State College, Keene, NH 03431, United States
| | - S Randal Voss
- Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY 40536, United States; Department of Neuroscience, University of Kentucky, Lexington, KY 40536, United States; Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY 40536, United States
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61
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Vidal RS, Quarti J, Rodrigues MF, Rumjanek FD, Rumjanek VM. Metabolic Reprogramming During Multidrug Resistance in Leukemias. Front Oncol 2018; 8:90. [PMID: 29675398 PMCID: PMC5895924 DOI: 10.3389/fonc.2018.00090] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/15/2018] [Indexed: 02/06/2023] Open
Abstract
Cancer outcome has improved since introduction of target therapy. However, treatment success is still impaired by the same drug resistance mechanism of classical chemotherapy, known as multidrug resistance (MDR) phenotype. This phenotype promotes resistance to drugs with different structures and mechanism of action. Recent reports have shown that resistance acquisition is coupled to metabolic reprogramming. High-gene expression, increase of active transport, and conservation of redox status are one of the few examples that increase energy and substrate demands. It is not clear if the role of this metabolic shift in the MDR phenotype is related to its maintenance or to its induction. Apart from the nature of this relation, the metabolism may represent a new target to avoid or to block the mechanism that has been impairing treatment success. In this mini-review, we discuss the relation between metabolism and MDR resistance focusing on the multiple non-metabolic functions that enzymes of the glycolytic pathway are known to display, with emphasis with the diverse activities of glyceraldehyde-3-phosphate dehydrogenase.
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Affiliation(s)
- Raphael Silveira Vidal
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Julia Quarti
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto de Nutrição Josué de Castro, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Franklin D Rumjanek
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vivian M Rumjanek
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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62
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Osuma EA, Riggs DW, Gibb AA, Hill BG. High throughput measurement of metabolism in planarians reveals activation of glycolysis during regeneration. ACTA ACUST UNITED AC 2018; 5:78-86. [PMID: 29721328 PMCID: PMC5911454 DOI: 10.1002/reg2.95] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 10/30/2017] [Accepted: 10/30/2017] [Indexed: 12/18/2022]
Abstract
Planarians are outstanding models for studying mechanisms of regeneration; however, there are few methods to measure changes in their metabolism. Examining metabolism in planarians is important because the regenerative process is dependent on numerous integrated metabolic pathways, which provide the energy required for tissue repair as well as the ability to synthesize the cellular building blocks needed to form new tissue. Therefore, we standardized an extracellular flux analysis method to measure mitochondrial and glycolytic activity in live planarians during normal growth as well as during regeneration. Small, uninjured planarians showed higher rates of oxygen consumption compared with large planarians, with no difference in glycolytic activity; however, glycolysis increased during planarian regeneration. Exposure of planarians to koningic acid, a specific inhibitor of glyceraldehyde‐3‐phosphate dehydrogenase, completely abolished extracellular acidification with little effect on oxygen consumption, which suggests that the majority of glucose catabolized in planarians is fated for aerobic glycolysis. These studies describe a useful method for measuring respiration and glycolysis in planarians and provide data implicating changes in glucose metabolism in the regenerative response.
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Affiliation(s)
- Edie A Osuma
- Wesleyan College Macon GA USA.,Department of Physiology University of Louisville Louisville KY USA
| | - Daniel W Riggs
- Diabetes and Obesity Center, Department of Medicine University of Louisville Louisville KY USA
| | - Andrew A Gibb
- Diabetes and Obesity Center, Department of Medicine University of Louisville Louisville KY USA.,Department of Physiology University of Louisville Louisville KY USA
| | - Bradford G Hill
- Institute of Molecular Cardiology, Diabetes and Obesity Center, Department of Medicine University of Louisville Louisville KY USA.,Diabetes and Obesity Center, Department of Medicine University of Louisville Louisville KY USA.,Department of Physiology University of Louisville Louisville KY USA
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63
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Hübner D, Jahn K, Pinkert S, Böhnke J, Jung M, Fechner H, Rujescu D, Liebert UG, Claus C. Infection of iPSC Lines with Miscarriage-Associated Coxsackievirus and Measles Virus and Teratogenic Rubella Virus as a Model for Viral Impairment of Early Human Embryogenesis. ACS Infect Dis 2017; 3:886-897. [PMID: 29043768 DOI: 10.1021/acsinfecdis.7b00103] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human induced pluripotent stem cell (iPSC) lines are a promising model for the early phase of human embryonic development. Here, their contribution to the still incompletely understood pathogenesis of congenital virus infections was evaluated. The infection of iPSC lines with miscarriage-associated coxsackievirus B3 (CVB3) and measles virus (MV) was compared to the efficient teratogen rubella virus (RV). While CVB3 and MV were found to be cytopathogenic on iPSC lines, RV replicated without impairment of iPSC colony morphology and integrity. This so far outstanding course of infection enabled maintenance of RV-infected iPSC cultures over several passages and their subsequent differentiation to ectoderm, endoderm, and mesoderm. A modification of the metabolic profile of infected iPSC lines was the only common aspect for all three viruses. This study points toward two important aspects. First, iPSC lines represent a suitable cell culture model for early embryonic virus infection. Second, metabolic activity represents an important means for evaluation of pathogen-associated alterations in iPSC lines.
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Affiliation(s)
- Denise Hübner
- Institute
of Virology, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Kristin Jahn
- Institute
of Virology and Faculty of Life Sciences, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
| | - Sandra Pinkert
- Department
of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Janik Böhnke
- Institute
of Virology and Faculty of Life Sciences, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
| | - Matthias Jung
- Department
of Psychiatry, Psychotherapy, and Psychosomatics, Martin-Luther-University Halle, Julius-Kühn-Str. 7, 06112 Halle, Germany
| | - Henry Fechner
- Department
of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Dan Rujescu
- Department
of Psychiatry, Psychotherapy, and Psychosomatics, Martin-Luther-University Halle, Julius-Kühn-Str. 7, 06112 Halle, Germany
| | - Uwe Gerd Liebert
- Institute
of Virology, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
| | - Claudia Claus
- Institute
of Virology, University of Leipzig, Johannisallee 30, 04103 Leipzig, Germany
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64
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Loffredo LF, Abdala-Valencia H, Anekalla KR, Cuervo-Pardo L, Gottardi CJ, Berdnikovs S. Beyond epithelial-to-mesenchymal transition: Common suppression of differentiation programs underlies epithelial barrier dysfunction in mild, moderate, and severe asthma. Allergy 2017; 72:1988-2004. [PMID: 28599074 DOI: 10.1111/all.13222] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2017] [Indexed: 01/11/2023]
Abstract
BACKGROUND Epithelial barrier dysfunction is a central feature in the pathogenesis of allergic disease. Epithelial-to-mesenchymal transition (EMT) has been proposed as one mechanism afflicting barrier in asthma. However, genes and pathways involved in aberrant epithelial-mesenchymal signaling, and their relationship to asthma severity, are poorly understood. METHODS We used unbiased gene network analysis to evaluate functional convergence in epithelial gene expression signatures across multiple public access transcriptomics datasets of human asthma, followed by text mining to evaluate functional marker relevance of discovered genes. We objectively confirmed these findings in epithelial brushings and primary asthmatic epithelial cells cultured in different biological contexts. RESULTS We found a striking suppression of epithelial differentiation in asthma, overrepresented by insufficiency in insulin and Notch signaling, but with the absence of conventional EMT markers. We identified EFNB2, FGFR1, FGFR2, INSR, IRS2, NOTCH2, TLE1, and NTRK2 as novel markers central to dysregulation of epithelial-mesenchymal signaling, but surprisingly overlooked in asthma research. We found that this "core" signature of asthma is shared by mild, moderate, and severe forms of disease, progressing with severity. Loss of epithelial differentiation induced by insulin deprivation in normal human bronchial epithelial cells cultured in organotypic conditions closely approximated gene expression in asthmatic epithelial brushings. CONCLUSIONS The comparative analysis of publically available transcriptomes demonstrated that epithelial barrier dysfunction in asthma is characterized by persistent underlying de-differentiation program with complex etiology. The lasting alteration of the asthmatic epithelial cell transcriptome implicates regulation involving metabolism and epigenetics, beyond EMT driven by injury and repair in chronic inflammation.
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Affiliation(s)
- L. F. Loffredo
- Division of Allergy and Immunology; Department of Medicine; Northwestern University Feinberg School of Medicine; Chicago IL USA
| | - H. Abdala-Valencia
- Division of Pulmonary and Critical Care; Department of Medicine; Northwestern University Feinberg School of Medicine; Chicago IL USA
| | - K. R. Anekalla
- Division of Pulmonary and Critical Care; Department of Medicine; Northwestern University Feinberg School of Medicine; Chicago IL USA
| | - L. Cuervo-Pardo
- Division of Allergy and Immunology; Department of Medicine; Northwestern University Feinberg School of Medicine; Chicago IL USA
| | - C. J. Gottardi
- Division of Pulmonary and Critical Care; Department of Medicine; Northwestern University Feinberg School of Medicine; Chicago IL USA
| | - S. Berdnikovs
- Division of Allergy and Immunology; Department of Medicine; Northwestern University Feinberg School of Medicine; Chicago IL USA
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65
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Lorenz C, Prigione A. Mitochondrial metabolism in early neural fate and its relevance for neuronal disease modeling. Curr Opin Cell Biol 2017; 49:71-76. [DOI: 10.1016/j.ceb.2017.12.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/12/2017] [Accepted: 12/13/2017] [Indexed: 01/01/2023]
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66
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Beckervordersandforth R. Mitochondrial Metabolism-Mediated Regulation of Adult Neurogenesis. Brain Plast 2017; 3:73-87. [PMID: 29765861 PMCID: PMC5928529 DOI: 10.3233/bpl-170044] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The life-long generation of new neurons from radial glia-like neural stem cells (NSCs) is achieved through a stereotypic developmental sequence that requires precise regulatory mechanisms to prevent exhaustion or uncontrolled growth of the stem cell pool. Cellular metabolism is the new kid on the block of adult neurogenesis research and the identity of stage-specific metabolic programs and their impact on neurogenesis turns out to be an emerging research topic in the field. Mitochondrial metabolism is best known for energy production but it contains a great deal more. Mitochondria are key players in a variety of cellular processes including ATP synthesis through functional coupling of the electron transport chain and oxidative phosphorylation, recycling of hydrogen carriers, biosynthesis of cellular building blocks, and generation of reactive oxygen species that can modulate signaling pathways in a redox-dependent fashion. In this review, I will discuss recent findings describing stage-specific modulations of mitochondrial metabolism within the adult NSC lineage, emphasizing its importance for NSC self-renewal, proliferation of neural stem and progenitor cells (NSPCs), cell fate decisions, and differentiation and maturation of newborn neurons. I will furthermore summarize the important role of mitochondrial dysfunction in tissue regeneration and ageing, suggesting it as a potential therapeutic target for regenerative medicine practice.
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Affiliation(s)
- Ruth Beckervordersandforth
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander Universität Erlangen-Nürnberg, Germany
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67
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Baser A, Skabkin M, Martin-Villalba A. Neural Stem Cell Activation and the Role of Protein Synthesis. Brain Plast 2017; 3:27-41. [PMID: 29765858 PMCID: PMC5928545 DOI: 10.3233/bpl-160038] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Adult neural stem cells are generated at embryonic stages by entering a quiescent state that allows their retention into adulthood and thereby maintenance of life-long brain homeostasis. Thus, a tight balance between the quiescence and activation state is instrumental to meet the brain demands for a specific cell type at the correct numbers, at a given time and position. Protein synthesis is the most energy-consuming process within the cell and, not surprisingly, it occurs at low rates in quiescent stem cells. This way quiescent cells adjust to energy constraints and avoid their premature depletion. Stem cell activation is characterized by upregulation of protein synthesis followed by cell division and differentiation. The role of such upregulation as causative or rather a consequence of the activation remains elusive. Here we summarize recent findings connecting stem cell activation to the regulation of protein synthesis, particularly focusing on embryonic and adult neural stem cells of the ventricular zone.
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Affiliation(s)
- Avni Baser
- Molecular Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Maxim Skabkin
- Molecular Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ana Martin-Villalba
- Molecular Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
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68
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Ko SH, Choi GE, Oh JY, Lee HJ, Kim JS, Chae CW, Choi D, Han HJ. Succinate promotes stem cell migration through the GPR91-dependent regulation of DRP1-mediated mitochondrial fission. Sci Rep 2017; 7:12582. [PMID: 28974722 PMCID: PMC5626702 DOI: 10.1038/s41598-017-12692-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 09/13/2017] [Indexed: 12/24/2022] Open
Abstract
The role of metabolites produced from stem cell metabolism has been emerged as signaling molecules to regulate stem cell behaviors such as migration. The mitochondrial morphology is closely associated with the metabolic balance and stem cell function. However, the physiological role of succinate on human mesenchymal stem cell (hMSC) migration by regulating the mitochondrial morphology remains unclear. Here, we investigate the effect of succinate on hMSC migration via regulation of mitochondrial dynamics and its related signaling pathway. Succinate (50 μM) significantly accelerates hMSC migration. Succinate increases phosphorylation of pan-PKC, especially the atypical PKCζ level which was blocked by the knockdown of Gαq and Gα12. Activated PKCζ subsequently phosphorylates p38 MAPK. Cytosolic DRP1 is phosphorylated by p38 MAPK and results in DRP1 translocation to the mitochondria outer membrane, eventually inducing mitochondrial fragmentation. Mitochondrial fission-induced mitochondrial function elevates mitochondrial ROS (mtROS) levels and activates Rho GTPases, which then induces F-actin formation. Furthermore, in a skin excisional wound model, we found the effects of succinate-pretreated hMSC enhanced wound closure, vascularization and re-epithelialization and confirmed that DRP1 has a vital role in injured tissue regeneration. Overall, succinate promotes DRP1-mediated mitochondrial fission via GPR91, consequently stimulating the hMSC migration through mtROS-induced F-actin formation.
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Affiliation(s)
- So Hee Ko
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS program for Creative Veterinary Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Gee Euhn Choi
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS program for Creative Veterinary Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Ji Young Oh
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute for Agriculture and Life science, Seoul National University, Seoul, 08826, South Korea
| | - Hyun Jik Lee
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS program for Creative Veterinary Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Jun Sung Kim
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS program for Creative Veterinary Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Chang Woo Chae
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS program for Creative Veterinary Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Diana Choi
- Department of Biological Sciences, Mount Holyoke College, South Hadley, Massachusetts, 01075, USA
| | - Ho Jae Han
- Department of Veterinary Physiology, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 PLUS program for Creative Veterinary Research Center, Seoul National University, Seoul, 08826, South Korea.
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69
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She S, Wei Q, Kang B, Wang YJ. Cell cycle and pluripotency: Convergence on octamer‑binding transcription factor 4 (Review). Mol Med Rep 2017; 16:6459-6466. [PMID: 28901500 PMCID: PMC5865814 DOI: 10.3892/mmr.2017.7489] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 07/14/2017] [Indexed: 12/14/2022] Open
Abstract
Embryonic stem cells (ESCs) have unlimited expansion potential and the ability to differentiate into all somatic cell types for regenerative medicine and disease model studies. Octamer-binding transcription factor 4 (OCT4), encoded by the POU domain, class 5, transcription factor 1 gene, is a transcription factor vital for maintaining ESC pluripotency and somatic reprogramming. Many studies have established that the cell cycle of ESCs is featured with an abbreviated G1 phase and a prolonged S phase. Changes in cell cycle dynamics are intimately associated with the state of ESC pluripotency, and manipulating cell-cycle regulators could enable a controlled differentiation of ESCs. The present review focused primarily on the emerging roles of OCT4 in coordinating the cell cycle progression, the maintenance of pluripotency and the glycolytic metabolism in ESCs.
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Affiliation(s)
- Shiqi She
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Qucheng Wei
- Cardiovascular Key Lab of Zhejiang, Department of Cardiology, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310009, P.R. China
| | - Bo Kang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Ying-Jie Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
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70
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Schleimer RP, Berdnikovs S. Etiology of epithelial barrier dysfunction in patients with type 2 inflammatory diseases. J Allergy Clin Immunol 2017; 139:1752-1761. [PMID: 28583447 DOI: 10.1016/j.jaci.2017.04.010] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/21/2017] [Accepted: 04/21/2017] [Indexed: 12/11/2022]
Abstract
Epithelial barriers of the skin, gastrointestinal tract, and airway serve common critical functions, such as maintaining a physical barrier against environmental insults and allergens and providing a tissue interface balancing the communication between the internal and external environments. We now understand that in patients with allergic disease, regardless of tissue location, the homeostatic balance of the epithelial barrier is skewed toward loss of differentiation, reduced junctional integrity, and impaired innate defense. Importantly, epithelial dysfunction characterized by these traits appears to pre-date atopy and development of allergic disease. Despite our growing appreciation of the centrality of barrier dysfunction in initiation of allergic disease, many important questions remain to be answered regarding mechanisms disrupting normal barrier function. Although our external environment (proteases, allergens, and injury) is classically thought of as a principal contributor to barrier disruption associated with allergic sensitization, there is a need to better understand contributions of the internal environment (hormones, diet, and circadian clock). Systemic drivers of disease, such as alterations of the endocrine system, metabolism, and aberrant control of developmental signaling, are emerging as new players in driving epithelial dysfunction and allergic predisposition at various barrier sites. Identifying such central mediators of epithelial dysfunction using both systems biology tools and causality-driven laboratory experimentation will be essential in building new strategic interventions to prevent or reverse the process of barrier loss in allergic patients.
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Affiliation(s)
- Robert P Schleimer
- Division of Allergy and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Sergejs Berdnikovs
- Division of Allergy and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Ill.
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71
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Diehl K, Dinges LA, Helm O, Ammar N, Plundrich D, Arlt A, Röcken C, Sebens S, Schäfer H. Nuclear factor E2-related factor-2 has a differential impact on MCT1 and MCT4 lactate carrier expression in colonic epithelial cells: a condition favoring metabolic symbiosis between colorectal cancer and stromal cells. Oncogene 2017; 37:39-51. [DOI: 10.1038/onc.2017.299] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 07/03/2017] [Accepted: 07/21/2017] [Indexed: 12/28/2022]
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72
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Costa V, Carina V, Fontana S, De Luca A, Monteleone F, Pagani S, Sartori M, Setti S, Faldini C, Alessandro R, Fini M, Giavaresi G. Osteogenic commitment and differentiation of human mesenchymal stem cells by low-intensity pulsed ultrasound stimulation. J Cell Physiol 2017. [PMID: 28621452 DOI: 10.1002/jcp.26058] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Low-intensity pulsed ultrasound (LIPUS) as an adjuvant therapy in in vitro and in vivo bone engineering has proven to be extremely useful. The present study aimed at investigating the effect of 30 mW/cm2 LIPUS stimulation on commercially available human mesenchymal stem cells (hMSCs) cultured in basal or osteogenic medium at different experimental time points (7, 14, 21 days). The hypothesis was that LIPUS would improve the osteogenic differentiation of hMSC and guarantying the maintenance of osteogenic committed fraction, as demonstrated by cell vitality and proteomic analysis. LIPUS stimulation (a) regulated the balance between osteoblast commitment and differentiation by specific networks (activations of RhoA/ROCK signaling and upregulation of Ribosome constituent/Protein metabolic process, Glycolysis/Gluconeogenesis, RNA metabolic process/Splicing and Tubulins); (b) allowed the maintenance of a few percentage of osteoblast precursors (21 days CD73+/CD90+: 6%; OCT-3/4+/NANOG+/SOX2+: 10%); (c) induced the activation of osteogenic specific pathways shown by gene expression (early: ALPL, COL1A1, late: RUNX2, BGLAP, MAPK1/6) and related protein release (COL1a1, OPN, OC), in particular in the presence of osteogenic soluble factors able to mimic bone microenvironment. To summarize, LIPUS might be able to improve the osteogenic commitment of hMSCs in vitro, and, at the same time, enhance their osteogenic differentiation.
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Affiliation(s)
- Viviana Costa
- Rizzoli Orthopedic Institute, Innovative Technological Platforms for Tissue Engineering, Theranostic and Oncology, Palermo, Italy
| | - Valeria Carina
- Rizzoli Orthopedic Institute, Innovative Technological Platforms for Tissue Engineering, Theranostic and Oncology, Palermo, Italy
| | - Simona Fontana
- Biology and Genetics Unit, Department of Biopathology and Medical Biotechnologies, University of Palermo, Italy
| | - Angela De Luca
- Rizzoli Orthopedic Institute, Innovative Technological Platforms for Tissue Engineering, Theranostic and Oncology, Palermo, Italy
| | - Francesca Monteleone
- Biology and Genetics Unit, Department of Biopathology and Medical Biotechnologies, University of Palermo, Italy
| | - Stefania Pagani
- Rizzoli Orthopedic Institute, Laboratory of Preclinical and Surgical Studies, Bologna, Italy
| | - Maria Sartori
- Rizzoli Orthopedic Institute, Laboratory BITTA, Bologna, Italy
| | | | - Cesare Faldini
- Rizzoli Orthopedic Institute, 2nd Orthopaedic and Traumatologic Clinic, Bologna, Italy
| | - Riccardo Alessandro
- Biology and Genetics Unit, Department of Biopathology and Medical Biotechnologies, University of Palermo, Italy
| | - Milena Fini
- Rizzoli Orthopedic Institute, Laboratory of Preclinical and Surgical Studies, Bologna, Italy.,Rizzoli Orthopedic Institute, Laboratory BITTA, Bologna, Italy
| | - Gianluca Giavaresi
- Rizzoli Orthopedic Institute, Innovative Technological Platforms for Tissue Engineering, Theranostic and Oncology, Palermo, Italy.,Rizzoli Orthopedic Institute, Laboratory of Preclinical and Surgical Studies, Bologna, Italy
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73
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Single-cell entropy for accurate estimation of differentiation potency from a cell's transcriptome. Nat Commun 2017; 8:15599. [PMID: 28569836 PMCID: PMC5461595 DOI: 10.1038/ncomms15599] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 04/07/2017] [Indexed: 12/31/2022] Open
Abstract
The ability to quantify differentiation potential of single cells is a task of critical importance. Here we demonstrate, using over 7,000 single-cell RNA-Seq profiles, that differentiation potency of a single cell can be approximated by computing the signalling promiscuity, or entropy, of a cell's transcriptome in the context of an interaction network, without the need for feature selection. We show that signalling entropy provides a more accurate and robust potency estimate than other entropy-based measures, driven in part by a subtle positive correlation between the transcriptome and connectome. Signalling entropy identifies known cell subpopulations of varying potency and drug resistant cancer stem-cell phenotypes, including those derived from circulating tumour cells. It further reveals that expression heterogeneity within single-cell populations is regulated. In summary, signalling entropy allows in silico estimation of the differentiation potency and plasticity of single cells and bulk samples, providing a means to identify normal and cancer stem-cell phenotypes. Robust quantification of the differentiation potential of single cells is a task of great importance. Here the authors integrate single-cell RNA-Seq profiles with a cellular interaction network to compute the signaling entropy, and show that it can identify normal and cancer stem-cell phenotypes.
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74
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Jamaiyar A, Wan W, Ohanyan V, Enrick M, Janota D, Cumpston D, Song H, Stevanov K, Kolz CL, Hakobyan T, Dong F, Newby BMZ, Chilian WM, Yin L. Alignment of inducible vascular progenitor cells on a micro-bundle scaffold improves cardiac repair following myocardial infarction. Basic Res Cardiol 2017; 112:41. [PMID: 28540527 DOI: 10.1007/s00395-017-0631-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/18/2017] [Indexed: 12/26/2022]
Abstract
Ischemic heart disease is still the leading cause of death even with the advancement of pharmaceutical therapies and surgical procedures. Early vascularization in the ischemic heart is critical for a better outcome. Although stem cell therapy has great potential for cardiovascular regeneration, the ideal cell type and delivery method of cells have not been resolved. We tested a new approach of stem cell therapy by delivery of induced vascular progenitor cells (iVPCs) grown on polymer micro-bundle scaffolds in a rat model of myocardial infarction. iVPCs partially reprogrammed from vascular endothelial cells (ECs) had potent angiogenic potential and were able to simultaneously differentiate into vascular smooth muscle cells (SMCs) and ECs in 2D culture. Under hypoxic conditions, iVPCs also secreted angiogenic cytokines such as vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF) as measured by enzyme-linked immunosorbent assay (ELISA). A longitudinal micro-scaffold made from poly(lactic-co-glycolic acid) was sufficient for the growth and delivery of iVPCs. Co-cultured ECs and SMCs aligned well on the micro-bundle scaffold similarly as in the vessels. 3D cell/polymer micro-bundles formed by iVPCs and micro-scaffolds were transplanted into the ischemic myocardium in a rat model of myocardial infarction (MI) with ligation of the left anterior descending artery. Our in vivo data showed that iVPCs on the micro-bundle scaffold had higher survival, and better retention and engraftment in the myocardium than free iVPCs. iVPCs on the micro-bundles promoted better cardiomyocyte survival than free iVPCs. Moreover, iVPCs and iVPC/polymer micro-bundles treatment improved cardiac function (ejection fraction and fractional shortening, endocardial systolic volume) measured by echocardiography, increased vessel density, and decreased infarction size [endocardial and epicardial infarct (scar) length] better than untreated controls at 8 weeks after MI. We conclude that iVPCs grown on a polymer micro-bundle scaffold are new promising approach for cell-based therapy designed for cardiovascular regeneration in ischemic heart disease.
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Affiliation(s)
- Anurag Jamaiyar
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH, 44272, USA.,School of Biomedical Sciences, Kent State University, Kent, OH, USA
| | - Weiguo Wan
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH, 44272, USA
| | - Vahagn Ohanyan
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH, 44272, USA
| | - Molly Enrick
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH, 44272, USA
| | - Danielle Janota
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH, 44272, USA
| | - Devan Cumpston
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH, 44272, USA
| | - Hokyung Song
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Kelly Stevanov
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH, 44272, USA
| | - Christopher L Kolz
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH, 44272, USA
| | - Tatev Hakobyan
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH, 44272, USA
| | - Feng Dong
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH, 44272, USA
| | - Bi-Min Zhang Newby
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - William M Chilian
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH, 44272, USA
| | - Liya Yin
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH, 44272, USA.
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75
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Wang X, Chen L, Yang A, Bu C, He Y. Quantitative Proteomics Analysis of Developmental Reprogramming in Protoplasts of the Moss Physcomitrella patens. PLANT & CELL PHYSIOLOGY 2017; 58:946-961. [PMID: 28398533 DOI: 10.1093/pcp/pcx039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 03/13/2017] [Indexed: 06/07/2023]
Abstract
The moss Physcomitrella patens is a model system for studying Plant developmental processes. To better understand the biochemical and physiological changes involved in developmental reprogramming, we conducted a quantitative proteomics analysis for protonemata, protoplasts made therefrom and protoplasts regenerated for 2 d. Using an iTRAQ peptide labeling strategy and liquid chromatography-tandem mass spectrometry (LC-MS/MS), >3,000 peptides and 1,000 proteins were quantified. Of these, 162 proteins were identified as having differential abundances during developmental reprogramming. These proteins were involved in various biological functions, such as defense, energy production, translation, metabolism, protein destination and storage, transcription, transport, cell growth/division, cell structure and signal transduction. Of these, the proteins involved in energy production and translation increased in abundance, while many of the metabolism and defense proteins decreased in abundance. In addition, most of the cell growth/division, protein stability and cell structure proteins were also down-regulated. This is the first report on the metabolic changes involved in developmental reprogramming in protoplasts. The significance of metabolic networks in developmental programming is beginning to emerge. Our study suggested that stress signals, energy metabolism and ribosomal proteins are pivotal components during developmental programming.
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Affiliation(s)
- Xiaoqin Wang
- Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture, Beijing University of Agriculture, Beijing, China
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit trees, Beijing University of Agriculture, Beijing, China
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Lu Chen
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Aizhen Yang
- Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture, Beijing University of Agriculture, Beijing, China
| | - Chunya Bu
- Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture, Beijing University of Agriculture, Beijing, China
| | - Yikun He
- College of Life Sciences, Capital Normal University, Beijing, China
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76
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Panopoulos AD, Smith EN, Arias AD, Shepard PJ, Hishida Y, Modesto V, Diffenderfer KE, Conner C, Biggs W, Sandoval E, D'Antonio-Chronowska A, Berggren WT, Izpisua Belmonte JC, Frazer KA. Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics. Cell Stem Cell 2017; 20:505-517.e6. [PMID: 28388429 PMCID: PMC5444384 DOI: 10.1016/j.stem.2017.03.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 01/06/2017] [Accepted: 03/15/2017] [Indexed: 01/24/2023]
Abstract
Induced pluripotent stem cells (iPSCs) show variable methylation patterns between lines, some of which reflect aberrant differences relative to embryonic stem cells (ESCs). To examine whether this aberrant methylation results from genetic variation or non-genetic mechanisms, we generated human iPSCs from monozygotic twins to investigate how genetic background, clone, and passage number contribute. We found that aberrantly methylated CpGs are enriched in regulatory regions associated with MYC protein motifs and affect gene expression. We classified differentially methylated CpGs as being associated with genetic and/or non-genetic factors (clone and passage), and we found that aberrant methylation preferentially occurs at CpGs associated with clone-specific effects. We further found that clone-specific effects play a strong role in recurrent aberrant methylation at specific CpG sites across different studies. Our results argue that a non-genetic biological mechanism underlies aberrant methylation in iPSCs and that it is likely based on a probabilistic process involving MYC that takes place during or shortly after reprogramming.
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Affiliation(s)
- Athanasia D Panopoulos
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Erin N Smith
- Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093, USA
| | - Angelo D Arias
- Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093, USA
| | - Peter J Shepard
- Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA; BioSpyder Technologies, Inc., Carlsbad, CA 92008, USA
| | - Yuriko Hishida
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Veronica Modesto
- Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Clay Conner
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | | | | | - W Travis Berggren
- Stem Cell Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | | | - Kelly A Frazer
- Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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Δ133p53 represses p53-inducible senescence genes and enhances the generation of human induced pluripotent stem cells. Cell Death Differ 2017; 24:1017-1028. [PMID: 28362428 DOI: 10.1038/cdd.2017.48] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 12/11/2022] Open
Abstract
p53 functions to induce cellular senescence, which is incompatible with self-renewal of pluripotent stem cells such as induced pluripotent stem cells (iPSC) and embryonic stem cells (ESC). However, p53 also has essential roles in these cells through DNA damage repair for maintaining genomic integrity and high sensitivity to apoptosis for eliminating severely damaged cells. We hypothesized that Δ133p53, a physiological inhibitory p53 isoform, is involved in the balanced regulation of self-renewing capacity, DNA damage repair and apoptosis. We examined 12 lines of human iPSC and their original fibroblasts, as well as three ESC lines, for endogenous protein levels of Δ133p53 and full-length p53 (FL-p53), and mRNA levels of various p53 target genes. While FL-p53 levels in iPSC and ESC widely ranged from below to above those in the fibroblasts, all iPSC and ESC lines expressed elevated levels of Δ133p53. The p53-inducible genes that mediate cellular senescence (p21WAF1, miR-34a, PAI-1 and IGFBP7), but not those for apoptosis (BAX and PUMA) and DNA damage repair (p53R2), were downregulated in iPSC and ESC. Consistent with these endogenous expression profiles, overexpression of Δ133p53 in human fibroblasts preferentially repressed the p53-inducible senescence mediators and significantly enhanced their reprogramming to iPSC. The iPSC lines derived from Δ133p53-overexpressing fibroblasts formed well-differentiated, benign teratomas in immunodeficient mice and had fewer numbers of somatic mutations than an iPSC derived from p53-knocked-down fibroblasts, suggesting that Δ133p53 overexpression is non- or less oncogenic and mutagenic than total inhibition of p53 activities. Overexpressed Δ133p53 prevented FL-p53 from binding to the regulatory regions of p21WAF1 and miR-34a promoters, providing a mechanistic basis for its dominant-negative inhibition of a subset of p53 target genes. This study supports the hypothesis that upregulation of Δ133p53 is an endogenous mechanism that facilitates human somatic cells to become self-renewing pluripotent stem cells with maintained apoptotic and DNA repair activities.
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Kelly GM, Gatie MI. Mechanisms Regulating Stemness and Differentiation in Embryonal Carcinoma Cells. Stem Cells Int 2017; 2017:3684178. [PMID: 28373885 PMCID: PMC5360977 DOI: 10.1155/2017/3684178] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 01/10/2017] [Accepted: 02/08/2017] [Indexed: 02/06/2023] Open
Abstract
Just over ten years have passed since the seminal Takahashi-Yamanaka paper, and while most attention nowadays is on induced, embryonic, and cancer stem cells, much of the pioneering work arose from studies with embryonal carcinoma cells (ECCs) derived from teratocarcinomas. This original work was broad in scope, but eventually led the way for us to focus on the components involved in the gene regulation of stemness and differentiation. As the name implies, ECCs are malignant in nature, yet maintain the ability to differentiate into the 3 germ layers and extraembryonic tissues, as well as behave normally when reintroduced into a healthy blastocyst. Retinoic acid signaling has been thoroughly interrogated in ECCs, especially in the F9 and P19 murine cell models, and while we have touched on this aspect, this review purposely highlights how some key transcription factors regulate pluripotency and cell stemness prior to this signaling. Another major focus is on the epigenetic regulation of ECCs and stem cells, and, towards that end, this review closes on what we see as a new frontier in combating aging and human disease, namely, how cellular metabolism shapes the epigenetic landscape and hence the pluripotency of all stem cells.
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Affiliation(s)
- Gregory M. Kelly
- Department of Biology, Molecular Genetics Unit, Western University, London, ON, Canada
- Collaborative Program in Developmental Biology, Western University, London, ON, Canada
- Department of Paediatrics and Department of Physiology and Pharmacology, Western University, London, ON, Canada
- Child Health Research Institute, London, ON, Canada
- Ontario Institute for Regenerative Medicine, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Mohamed I. Gatie
- Department of Biology, Molecular Genetics Unit, Western University, London, ON, Canada
- Collaborative Program in Developmental Biology, Western University, London, ON, Canada
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Affiliation(s)
- Juan Pablo Muñoz
- a Department of Biochemistry and Molecular Biomedicine , Faculty of Biology, University of Barcelona , Barcelona , Spain.,b Institute for Research in Biomedicine Barcelona, (IRB Barcelona), The Barcelona Institute of Science and Technology , Barcelona , Spain.,c Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III (ISCIII) , Madrid , Spain
| | - Antonio Zorzano
- a Department of Biochemistry and Molecular Biomedicine , Faculty of Biology, University of Barcelona , Barcelona , Spain.,b Institute for Research in Biomedicine Barcelona, (IRB Barcelona), The Barcelona Institute of Science and Technology , Barcelona , Spain.,c Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III (ISCIII) , Madrid , Spain
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80
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Fueling the Cell Division Cycle. Trends Cell Biol 2016; 27:69-81. [PMID: 27746095 DOI: 10.1016/j.tcb.2016.08.009] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 08/08/2016] [Accepted: 08/25/2016] [Indexed: 11/21/2022]
Abstract
Cell division is a complex process with high energy demands. However, how cells regulate the generation of energy required for DNA synthesis and chromosome segregation is not well understood. Recent data suggest that changes in mitochondrial dynamics and metabolic pathways such as oxidative phosphorylation (OXPHOS) and glycolysis crosstalk with, and are tightly regulated by, the cell division machinery. Alterations in energy availability trigger cell-cycle checkpoints, suggesting a bidirectional connection between cell division and general metabolism. Some of these connections are altered in human disease, and their manipulation may help in designing therapeutic strategies for specific diseases including cancer. We review here recent studies describing the control of metabolism by the cell-cycle machinery.
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Izgi K, Canatan H, Iskender B. Current status in cancer cell reprogramming and its clinical implications. J Cancer Res Clin Oncol 2016; 143:371-383. [DOI: 10.1007/s00432-016-2258-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/02/2016] [Indexed: 12/26/2022]
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Masserdotti G, Gascón S, Götz M. Direct neuronal reprogramming: learning from and for development. Development 2016; 143:2494-510. [DOI: 10.1242/dev.092163] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The key signalling pathways and transcriptional programmes that instruct neuronal diversity during development have largely been identified. In this Review, we discuss how this knowledge has been used to successfully reprogramme various cell types into an amazing array of distinct types of functional neurons. We further discuss the extent to which direct neuronal reprogramming recapitulates embryonic development, and examine the particular barriers to reprogramming that may exist given a cell's unique developmental history. We conclude with a recently proposed model for cell specification called the ‘Cook Islands’ model, and consider whether it is a fitting model for cell specification based on recent results from the direct reprogramming field.
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Affiliation(s)
- Giacomo Masserdotti
- Institute of Stem Cell Research, Helmholtz Center Munich, Ingolstädter Landstrasse 1, Neuherberg/Munich D-85764, Germany
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians University Munich, Großhadernerstrasse 9, Martinsried 82154, Germany
| | - Sergio Gascón
- Institute of Stem Cell Research, Helmholtz Center Munich, Ingolstädter Landstrasse 1, Neuherberg/Munich D-85764, Germany
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians University Munich, Großhadernerstrasse 9, Martinsried 82154, Germany
| | - Magdalena Götz
- Institute of Stem Cell Research, Helmholtz Center Munich, Ingolstädter Landstrasse 1, Neuherberg/Munich D-85764, Germany
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians University Munich, Großhadernerstrasse 9, Martinsried 82154, Germany
- Excellence Cluster of Systems Neurology, Großhadernerstrasse 9, Martinsried 82154, Germany
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