1
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Li R, Zhao Y, Yourick JJ, Sprando RL, Gao X. Phenotypical, functional and transcriptomic comparison of two modified methods of hepatocyte differentiation from human induced pluripotent stem cells. Biomed Rep 2022; 16:43. [PMID: 35371477 PMCID: PMC8972237 DOI: 10.3892/br.2022.1526] [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: 11/23/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
Directed differentiation of human induced pluripotent stem cells (iPSCs) into hepatocytes could provide an unlimited source of liver cells, and therefore holds great promise for regenerative medicine, disease modeling, drug screening and toxicology studies. Various methods have been established during the past decade to differentiate human iPSCs into hepatocyte-like cells (HLCs) using growth factors and/or small molecules. However, direct comparison of the differentiation efficiency and the quality of the final HLCs between different methods has rarely been reported. In the current study, two hepatocyte differentiation methods were devised, termed Method 1 and 2, through modifying existing well-known hepatocyte differentiation strategies, and the resultant cells were compared phenotypically and functionally at different stages of hepatocyte differentiation. Compared to Method 1, higher differentiation efficiency and reproducibility were observed in Method 2, which generated highly homogeneous functional HLCs at the end of the differentiation process. The cells exhibited morphology closely resembling primary human hepatocytes and expressed high levels of hepatic protein markers. More importantly, these HLCs demonstrated several essential characteristics of mature hepatocytes, including major serum protein (albumin, fibronectin and α-1 antitrypsin) secretion, urea release, glycogen storage and inducible cytochrome P450 activity. Further transcriptomic comparison of the HLCs derived from the two methods identified 1,481 differentially expressed genes (DEGs); 290 Gene Ontology terms in the biological process category were enriched by these genes, which were further categorized into 34 functional classes. Pathway analysis of the DEGs identified several signaling pathways closely involved in hepatocyte differentiation of pluripotent stem cells, including 'signaling pathways regulating pluripotency of stem cells', 'Wnt signaling pathway', 'TGF-beta signaling pathway' and 'PI3K-Akt signaling pathway'. These results may provide a molecular basis for the differences observed between the two differentiation methods and suggest ways to further improve hepatocyte differentiation in order to obtain more mature HLCs for biomedical applications.
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Affiliation(s)
- Rong Li
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Yang Zhao
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Jeffrey J Yourick
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Robert L Sprando
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Xiugong Gao
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
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2
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Franek M, Kilar A, Fojtík P, Olšinová M, Benda A, Rotrekl V, Dvořáčková M, Fajkus J. Super-resolution microscopy of chromatin fibers and quantitative DNA methylation analysis of DNA fiber preparations. J Cell Sci 2021; 134:jcs258374. [PMID: 34350964 DOI: 10.1242/jcs.258374] [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: 01/06/2021] [Accepted: 07/05/2021] [Indexed: 11/20/2022] Open
Abstract
Analysis of histone variants and epigenetic marks is dominated by genome-wide approaches in the form of chromatin immunoprecipitation-sequencing (ChIP-seq) and related methods. Although uncontested in their value for single-copy genes, mapping the chromatin of DNA repeats is problematic for biochemical techniques that involve averaging of cell populations or analysis of clusters of tandem repeats in a single-cell analysis. Extending chromatin and DNA fibers allows us to study the epigenetics of individual repeats in their specific chromosomal context, and thus constitutes an important tool for gaining a complete understanding of the epigenetic organization of genomes. We report that using an optimized fiber extension protocol is essential in order to obtain more reproducible data and to minimize the clustering of fibers. We also demonstrate that the use of super-resolution microscopy is important for reliable evaluation of the distribution of histone modifications on individual fibers. Furthermore, we introduce a custom script for the analysis of methylation levels on DNA fibers and apply it to map the methylation of telomeres, ribosomal genes and centromeres.
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Affiliation(s)
- Michal Franek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Agata Kilar
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-61137 Brno, Czech Republic
| | - Petr Fojtík
- International Clinical Research Center (ICRC) at St. Anne's University Hospital, Pekařská 53, CZ-65691 Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Marie Olšinová
- Charles University, Faculty of Science, Biology Section, Imaging methods core facility at BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Aleš Benda
- Charles University, Faculty of Science, Biology Section, Imaging methods core facility at BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Vladimír Rotrekl
- International Clinical Research Center (ICRC) at St. Anne's University Hospital, Pekařská 53, CZ-65691 Brno, Czech Republic
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Martina Dvořáčková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Jíří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-61137 Brno, Czech Republic
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3
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Borys BS, Dang T, So T, Rohani L, Revay T, Walsh T, Thompson M, Argiropoulos B, Rancourt DE, Jung S, Hashimura Y, Lee B, Kallos MS. Overcoming bioprocess bottlenecks in the large-scale expansion of high-quality hiPSC aggregates in vertical-wheel stirred suspension bioreactors. Stem Cell Res Ther 2021; 12:55. [PMID: 33436078 PMCID: PMC7805206 DOI: 10.1186/s13287-020-02109-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Human induced pluripotent stem cells (hiPSCs) hold enormous promise in accelerating breakthroughs in understanding human development, drug screening, disease modeling, and cell and gene therapies. Their potential, however, has been bottlenecked in a mostly laboratory setting due to bioprocess challenges in the scale-up of large quantities of high-quality cells for clinical and manufacturing purposes. While several studies have investigated the production of hiPSCs in bioreactors, the use of conventional horizontal-impeller, paddle, and rocking-wave mixing mechanisms have demonstrated unfavorable hydrodynamic environments for hiPSC growth and quality maintenance. This study focused on using computational fluid dynamics (CFD) modeling to aid in characterizing and optimizing the use of vertical-wheel bioreactors for hiPSC production. METHODS The vertical-wheel bioreactor was modeled with CFD simulation software Fluent at agitation rates between 20 and 100 rpm. These models produced fluid flow patterns that mapped out a hydrodynamic environment to guide in the development of hiPSC inoculation and in-vessel aggregate dissociation protocols. The effect of single-cell inoculation on aggregate formation and growth was tested at select CFD-modeled agitation rates and feeding regimes in the vertical-wheel bioreactor. An in-vessel dissociation protocol was developed through the testing of various proteolytic enzymes and agitation exposure times. RESULTS CFD modeling demonstrated the unique flow pattern and homogeneous distribution of hydrodynamic forces produced in the vertical-wheel bioreactor, making it the opportune environment for systematic bioprocess optimization of hiPSC expansion. We developed a scalable, single-cell inoculation protocol for the culture of hiPSCs as aggregates in vertical-wheel bioreactors, achieving over 30-fold expansion in 6 days without sacrificing cell quality. We have also provided the first published protocol for in-vessel hiPSC aggregate dissociation, permitting the entire bioreactor volume to be harvested into single cells for serial passaging into larger scale reactors. Importantly, the cells harvested and re-inoculated into scaled-up vertical-wheel bioreactors not only maintained consistent growth kinetics, they maintained a normal karyotype and pluripotent characterization and function. CONCLUSIONS Taken together, these protocols provide a feasible solution for the culture of high-quality hiPSCs at a clinical and manufacturing scale by overcoming some of the major documented bioprocess bottlenecks.
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Affiliation(s)
- Breanna S Borys
- Pharmaceutical Production Research Facility, Schulich School of Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
- Biomedical Engineering Graduate Program, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
- Department of Chemical and Petroleum Engineering, Schulich School of Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Tiffany Dang
- Pharmaceutical Production Research Facility, Schulich School of Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
- Biomedical Engineering Graduate Program, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
- Department of Chemical and Petroleum Engineering, Schulich School of Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Tania So
- Pharmaceutical Production Research Facility, Schulich School of Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
- Department of Chemical and Petroleum Engineering, Schulich School of Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Leili Rohani
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary, AB, T2N 4N1, Canada
| | - Tamas Revay
- Department of Medical Genetics, Alberta Health Services, Alberta Children's Hospital, 28 Oki Drive, Calgary, AB, T3B 6A8, Canada
| | - Tylor Walsh
- Pharmaceutical Production Research Facility, Schulich School of Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
- Biomedical Engineering Graduate Program, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
- Department of Chemical and Petroleum Engineering, Schulich School of Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Madalynn Thompson
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary, AB, T2N 4N1, Canada
| | - Bob Argiropoulos
- Department of Medical Genetics, Alberta Health Services, Alberta Children's Hospital, 28 Oki Drive, Calgary, AB, T3B 6A8, Canada
| | - Derrick E Rancourt
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, 3330 Hospital Dr. NW, Calgary, AB, T2N 4N1, Canada
| | - Sunghoon Jung
- PBS Biotech Inc, 1183 Calle Suerte, Camarillo, CA, 93012, USA
| | - Yas Hashimura
- PBS Biotech Inc, 1183 Calle Suerte, Camarillo, CA, 93012, USA
| | - Brian Lee
- PBS Biotech Inc, 1183 Calle Suerte, Camarillo, CA, 93012, USA
| | - Michael S Kallos
- Pharmaceutical Production Research Facility, Schulich School of Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada.
- Biomedical Engineering Graduate Program, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada.
- Department of Chemical and Petroleum Engineering, Schulich School of Engineering, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada.
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4
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Spinal Reflex Recovery after Dorsal Rhizotomy and Repair with Platelet-Rich Plasma (PRP) Gel Combined with Bioengineered Human Embryonic Stem Cells (hESCs). Stem Cells Int 2020; 2020:8834360. [PMID: 33178285 PMCID: PMC7647752 DOI: 10.1155/2020/8834360] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/20/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023] Open
Abstract
Dorsal root rhizotomy (DRZ) is currently considered an untreatable injury, resulting in the loss of sensitive function and usually leading to neuropathic pain. In this context, we recently proposed a new surgical approach to treat DRZ that uses platelet-rich plasma (PRP) gel to restore the spinal reflex. Success was correlated with the reentry of primary afferents into the spinal cord. Here, aiming to enhance previous results, cell therapy with bioengineered human embryonic stem cells (hESCs) to overexpress fibroblast growth factor 2 (FGF2) was combined with PRP. For these experiments, adult female rats were submitted to a unilateral rhizotomy of the lumbar spinal dorsal roots, which was followed by root repair with PRP gel with or without bioengineered hESCs. One week after DRZ, the spinal cords were processed to evaluate changes in the glial response (GFAP and Iba-1) and excitatory synaptic circuits (VGLUT1) by immunofluorescence. Eight weeks postsurgery, the lumbar intumescences were processed for analysis of the repaired microenvironment by transmission electron microscopy. Spinal reflex recovery was evaluated by the electronic Von Frey method for eight weeks. The transcript levels for human FGF2 were over 37-fold higher in the induced hESCs than in the noninduced and the wildtype counterparts. Altogether, the results indicate that the combination of hESCs with PRP gel promoted substantial and prominent axonal regeneration processes after DRZ. Thus, the repair of dorsal roots, if done appropriately, may be considered an approach to regain sensory-motor function after dorsal root axotomy.
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5
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Kohutova A, Raška J, Kruta M, Seneklova M, Barta T, Fojtik P, Jurakova T, Walter CA, Hampl A, Dvorak P, Rotrekl V. Ligase 3–mediated end‐joining maintains genome stability of human embryonic stem cells. FASEB J 2019; 33:6778-6788. [DOI: 10.1096/fj.201801877rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Aneta Kohutova
- Department of BiologyMasaryk UniversityBrnoCzech Republic
- International Clinical Research Center (ICRC)St. Anne's University HospitalBrnoCzech Republic
| | - Jan Raška
- Department of BiologyMasaryk UniversityBrnoCzech Republic
| | - Miriama Kruta
- Department of BiologyMasaryk UniversityBrnoCzech Republic
| | | | - Tomas Barta
- Department of BiologyMasaryk UniversityBrnoCzech Republic
| | - Petr Fojtik
- Department of BiologyMasaryk UniversityBrnoCzech Republic
| | | | - Christi A. Walter
- Department of Cell Systems and AnatomyThe University of Texas Health Science Center at San AntonioSan AntonioTexasUSA
| | - Ales Hampl
- Department of Histology and EmbryologyFaculty of MedicineMasaryk UniversityBrnoCzech Republic
- International Clinical Research Center (ICRC)St. Anne's University HospitalBrnoCzech Republic
| | - Petr Dvorak
- Department of BiologyMasaryk UniversityBrnoCzech Republic
- International Clinical Research Center (ICRC)St. Anne's University HospitalBrnoCzech Republic
| | - Vladimir Rotrekl
- Department of BiologyMasaryk UniversityBrnoCzech Republic
- International Clinical Research Center (ICRC)St. Anne's University HospitalBrnoCzech Republic
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6
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Jelinkova S, Fojtik P, Kohutova A, Vilotic A, Marková L, Pesl M, Jurakova T, Kruta M, Vrbsky J, Gaillyova R, Valášková I, Frák I, Lacampagne A, Forte G, Dvorak P, Meli AC, Rotrekl V. Dystrophin Deficiency Leads to Genomic Instability in Human Pluripotent Stem Cells via NO Synthase-Induced Oxidative Stress. Cells 2019; 8:cells8010053. [PMID: 30650618 PMCID: PMC6356905 DOI: 10.3390/cells8010053] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/29/2018] [Accepted: 01/11/2019] [Indexed: 11/16/2022] Open
Abstract
Recent data on Duchenne muscular dystrophy (DMD) show myocyte progenitor's involvement in the disease pathology often leading to the DMD patient's death. The molecular mechanism underlying stem cell impairment in DMD has not been described. We created dystrophin-deficient human pluripotent stem cell (hPSC) lines by reprogramming cells from two DMD patients, and also by introducing dystrophin mutation into human embryonic stem cells via CRISPR/Cas9. While dystrophin is expressed in healthy hPSC, its deficiency in DMD hPSC lines induces the release of reactive oxygen species (ROS) through dysregulated activity of all three isoforms of nitric oxide synthase (further abrev. as, NOS). NOS-induced ROS release leads to DNA damage and genomic instability in DMD hPSC. We were able to reduce both the ROS release as well as DNA damage to the level of wild-type hPSC by inhibiting NOS activity.
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Affiliation(s)
- Sarka Jelinkova
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
- International Clinical Research Center ICRC, St. Anne's University Hospital Brno, 602 00 Brno, Czech Republic.
| | - Petr Fojtik
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
| | - Aneta Kohutova
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
- International Clinical Research Center ICRC, St. Anne's University Hospital Brno, 602 00 Brno, Czech Republic.
| | - Aleksandra Vilotic
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
| | - Lenka Marková
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
| | - Martin Pesl
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
- International Clinical Research Center ICRC, St. Anne's University Hospital Brno, 602 00 Brno, Czech Republic.
- 1st department of Internal Medicine-Cardioangiology, Faculty of Medicine, Masaryk University, 602 00 Brno, Czech Republic.
| | - Tereza Jurakova
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
| | - Miriama Kruta
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
| | - Jan Vrbsky
- International Clinical Research Center ICRC, St. Anne's University Hospital Brno, 602 00 Brno, Czech Republic.
| | - Renata Gaillyova
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
- Department of Clinical Genetics, University hospital Brno, 613 00 Brno, Czech Republic.
| | - Iveta Valášková
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
- Department of Clinical Genetics, University hospital Brno, 613 00 Brno, Czech Republic.
| | - Ivan Frák
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
| | - Alain Lacampagne
- PhyMedExp, INSERM, University of Montpellier, CNRS, 342 95 Montpellier CEDEX 5, France.
| | - Giancarlo Forte
- International Clinical Research Center ICRC, St. Anne's University Hospital Brno, 602 00 Brno, Czech Republic.
| | - Petr Dvorak
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
- International Clinical Research Center ICRC, St. Anne's University Hospital Brno, 602 00 Brno, Czech Republic.
| | - Albano C Meli
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
- PhyMedExp, INSERM, University of Montpellier, CNRS, 342 95 Montpellier CEDEX 5, France.
| | - Vladimir Rotrekl
- Department of Biology, Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic.
- International Clinical Research Center ICRC, St. Anne's University Hospital Brno, 602 00 Brno, Czech Republic.
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7
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Vanova T, Raska J, Babica P, Sovadinova I, Kunova Bosakova M, Dvorak P, Blaha L, Rotrekl V. Freshwater Cyanotoxin Cylindrospermopsin Has Detrimental Stage-specific Effects on Hepatic Differentiation From Human Embryonic Stem Cells. Toxicol Sci 2018; 168:241-251. [DOI: 10.1093/toxsci/kfy293] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
| | - Jan Raska
- RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Pavel Babica
- RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Iva Sovadinova
- RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | | | | | - Ludek Blaha
- RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Vladimir Rotrekl
- Department of Biology, Faculty of Medicine
- International Clinical Research Center (ICRC), St. Anne’s University Hospital, 62500 Brno, Czech Republic
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8
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Chen KG, Mallon BS, Park K, Robey PG, McKay RDG, Gottesman MM, Zheng W. Pluripotent Stem Cell Platforms for Drug Discovery. Trends Mol Med 2018; 24:805-820. [PMID: 30006147 DOI: 10.1016/j.molmed.2018.06.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 06/13/2018] [Accepted: 06/20/2018] [Indexed: 12/30/2022]
Abstract
Use of human pluripotent stem cells (hPSCs) and their differentiated derivatives have led to recent proof-of-principle drug discoveries, defining a pathway to the implementation of hPSC-based drug discovery (hPDD). Current hPDD strategies, however, have inevitable conceptual biases and technological limitations, including the dimensionality of cell-culture methods, cell maturity and functionality, experimental variability, and data reproducibility. In this review, we dissect representative hPDD systems via analysis of hPSC-based 2D-monolayers, 3D culture, and organoids. We discuss mechanisms of drug discovery and drug repurposing, and roles of membrane drug transporters in tissue maturation and hPDD using the example of drugs that target various mutations of CFTR, the cystic fibrosis transmembrane conductance regulator gene, in patients with cystic fibrosis.
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Affiliation(s)
- Kevin G Chen
- NIH Stem Cell Characterization Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Barbara S Mallon
- NIH Stem Cell Characterization Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kyeyoon Park
- NIH Stem Cell Characterization Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pamela G Robey
- Skeletal Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ronald D G McKay
- The Lieber Institute for Brain Development, Baltimore, MD 21205, USA
| | - Michael M Gottesman
- The Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA
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9
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Bohaciakova D, Renzova T, Fedorova V, Barak M, Kunova Bosakova M, Hampl A, Cajanek L. An Efficient Method for Generation of Knockout Human Embryonic Stem Cells Using CRISPR/Cas9 System. Stem Cells Dev 2017; 26:1521-1527. [PMID: 28835165 DOI: 10.1089/scd.2017.0058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Human embryonic stem cells (hESCs) represent a promising tool to study functions of genes during development, to model diseases, and to even develop therapies when combined with gene editing techniques such as CRISPR/CRISPR-associated protein-9 nuclease (Cas9) system. However, the process of disruption of gene expression by generation of null alleles is often inefficient and tedious. To circumvent these limitations, we developed a simple and efficient protocol to permanently downregulate expression of a gene of interest in hESCs using CRISPR/Cas9. We selected p53 for our proof of concept experiments. The methodology is based on series of hESC transfection, which leads to efficient downregulation of p53 expression even in polyclonal population (p53 Low cells), here proven by a loss of regulation of the expression of p53 target gene, microRNA miR-34a. We demonstrate that our approach achieves over 80% efficiency in generating hESC clonal sublines that do not express p53 protein. Importantly, we document by a set of functional experiments that such genetically modified hESCs do retain typical stem cells characteristics. In summary, we provide a simple and robust protocol to efficiently target expression of gene of interest in hESCs that can be useful for laboratories aiming to employ gene editing in their hESC applications/protocols.
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Affiliation(s)
- Dasa Bohaciakova
- 1 Department of Histology and Embryology, Masaryk University , Brno, Czech Republic
| | - Tereza Renzova
- 1 Department of Histology and Embryology, Masaryk University , Brno, Czech Republic
| | - Veronika Fedorova
- 1 Department of Histology and Embryology, Masaryk University , Brno, Czech Republic
| | - Martin Barak
- 1 Department of Histology and Embryology, Masaryk University , Brno, Czech Republic
| | | | - Ales Hampl
- 1 Department of Histology and Embryology, Masaryk University , Brno, Czech Republic .,3 International Clinical Research Center, St. Anne's University Hospital , Brno, Czech Republic
| | - Lukas Cajanek
- 1 Department of Histology and Embryology, Masaryk University , Brno, Czech Republic
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10
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Vanova T, Konecna Z, Zbonakova Z, La Venuta G, Zoufalova K, Jelinkova S, Varecha M, Rotrekl V, Krejci P, Nickel W, Dvorak P, Kunova Bosakova M. Tyrosine Kinase Expressed in Hepatocellular Carcinoma, TEC, Controls Pluripotency and Early Cell Fate Decisions of Human Pluripotent Stem Cells via Regulation of Fibroblast Growth Factor-2 Secretion. Stem Cells 2017. [PMID: 28631381 DOI: 10.1002/stem.2660] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Human pluripotent stem cells (hPSC) require signaling provided by fibroblast growth factor (FGF) receptors. This can be initiated by the recombinant FGF2 ligand supplied exogenously, but hPSC further support their niche by secretion of endogenous FGF2. In this study, we describe a role of tyrosine kinase expressed in hepatocellular carcinoma (TEC) kinase in this process. We show that TEC-mediated FGF2 secretion is essential for hPSC self-renewal, and its lack mediates specific differentiation. Following both short hairpin RNA- and small interfering RNA-mediated TEC knockdown, hPSC secretes less FGF2. This impairs hPSC proliferation that can be rescued by increasing amounts of recombinant FGF2. TEC downregulation further leads to a lower expression of the pluripotency markers, an improved priming towards neuroectodermal lineage, and a failure to develop cardiac mesoderm. Our data thus demonstrate that TEC is yet another regulator of FGF2-mediated hPSC pluripotency and differentiation. Stem Cells 2017;35:2050-2059.
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Affiliation(s)
- Tereza Vanova
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Zaneta Konecna
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Zuzana Zbonakova
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | | | - Karolina Zoufalova
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Sarka Jelinkova
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Miroslav Varecha
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Vladimir Rotrekl
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Pavel Krejci
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Walter Nickel
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Petr Dvorak
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
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11
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Tesarova L, Simara P, Stejskal S, Koutna I. Hematopoietic Developmental Potential of Human Pluripotent Stem Cell Lines Is Accompanied by the Morphology of Embryoid Bodies and the Expression of Endodermal and Hematopoietic Markers. Cell Reprogram 2017. [PMID: 28632430 DOI: 10.1089/cell.2016.0042] [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: 11/13/2022] Open
Abstract
The potential clinical applications of hematopoietic stem cells (HSCs) derived from human pluripotent stem cells (hPSCs) are limited by the difficulty of recapitulating embryoid hematopoiesis and by the unknown differentiation potential of hPSC lines. To evaluate their hematopoietic developmental potential, available hPSC lines were differentiated by an embryoid body (EB) suspension culture in serum-free medium supplemented with three different cytokine mixes (CMs). The hPSC differentiation status was investigated by the flow cytometry expression profiles of cell surface molecules, and the gene expression of pluripotency and differentiation markers over time was evaluated by real-time reverse transcription polymerase chain reaction (qRT-PCR). hPSC lines differed in several aspects of the differentiation process, including the absolute yield of hematopoietic progenitors, the proportion of hematopoietic progenitor populations, and the effect of various CMs. The ability to generate hematopoietic progenitors was then associated with the morphology of the developing EBs, the expression of the endodermal markers AFP and SOX17, and the hematopoietic transcription factor RUNX1. These findings deepen the knowledge about the hematopoietic propensity of hPSCs and identify its variability as an aspect that must be taken into account before the usage of hPSC-derived HSCs in downstream applications.
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Affiliation(s)
- Lenka Tesarova
- 1 Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University , Brno, Czech Republic .,2 International Clinical Research Center, St. Anne's University Hospital Brno , Brno, Czech Republic
| | - Pavel Simara
- 1 Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University , Brno, Czech Republic .,2 International Clinical Research Center, St. Anne's University Hospital Brno , Brno, Czech Republic
| | - Stanislav Stejskal
- 1 Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University , Brno, Czech Republic
| | - Irena Koutna
- 1 Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University , Brno, Czech Republic .,2 International Clinical Research Center, St. Anne's University Hospital Brno , Brno, Czech Republic
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12
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Araújo MR, Kyrylenko S, Spejo AB, Castro MV, Ferreira Junior RS, Barraviera B, Oliveira ALR. Transgenic human embryonic stem cells overexpressing FGF2 stimulate neuroprotection following spinal cord ventral root avulsion. Exp Neurol 2017; 294:45-57. [PMID: 28450050 DOI: 10.1016/j.expneurol.2017.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 04/19/2017] [Accepted: 04/22/2017] [Indexed: 12/11/2022]
Abstract
Ventral root avulsion (VRA) triggers a strong glial reaction which contributes to neuronal loss, as well as to synaptic detachment. To overcome the degenerative effects of VRA, treatments with neurotrophic factors and stem cells have been proposed. Thus, we investigated neuroprotection elicited by human embryonic stem cells (hESC), modified to overexpress a human fibroblast growth factor 2 (FGF-2), on motoneurons subjected to VRA. Lewis rats were submitted to VRA (L4-L6) and hESC/FGF-2 were applied to the injury site using a fibrin scaffold. The spinal cords were processed to evaluate neuronal survival, synaptic stability, and glial reactivity two weeks post lesion. Then, qRT-PCR was used to assess gene expression of β2-microglobulin (β2m), TNFα, IL1β, IL6 and IL10 in the spinal cord in vivo and FGF2 mRNA levels in hESC in vitro. The results indicate that hESC overexpressing FGF2 significantly rescued avulsed motoneurons, preserving synaptic covering and reducing astroglial reactivity. The cells were also shown to express BDNF and GDNF at the site of injury. Additionally, engraftment of hESC led to a significant reduction in mRNA levels of TNFα at the spinal cord ventral horn, indicating their immunomodulatory properties. Overall, the present data suggest that hESC overexpressing FGF2 are neuroprotective and can shift gene expression towards an anti-inflammatory environment.
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Affiliation(s)
- Marta Rocha Araújo
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, Brazil
| | - Sergiy Kyrylenko
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, Brazil; Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Aline Barroso Spejo
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, Brazil
| | - Mateus Vidigal Castro
- Department of Structural and Functional Biology, Institute of Biology, University of Campinas, Campinas, Sao Paulo, Brazil
| | - Rui Seabra Ferreira Junior
- Department of Tropical Diseases, Botucatu Medical School, São Paulo State University (UNESP-Univ. Estadual Paulista), São Paulo State, Brazil; Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP-Univ. Estadual Paulista), São Paulo State, Brazil
| | - Benedito Barraviera
- Department of Tropical Diseases, Botucatu Medical School, São Paulo State University (UNESP-Univ. Estadual Paulista), São Paulo State, Brazil; Center for the Study of Venoms and Venomous Animals (CEVAP), São Paulo State University (UNESP-Univ. Estadual Paulista), São Paulo State, Brazil
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13
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Jaros J, Petrov M, Tesarova M, Hampl A. Revealing 3D Ultrastructure and Morphology of Stem Cell Spheroids by Electron Microscopy. Methods Mol Biol 2017. [PMID: 28634960 DOI: 10.1007/978-1-4939-7021-6_30] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Cell culture methods have been developed in efforts to produce biologically relevant systems for developmental and disease modeling, and appropriate analytical tools are essential. Knowledge of ultrastructural characteristics represents the basis to reveal in situ the cellular morphology, cell-cell interactions, organelle distribution, niches in which cells reside, and many more. The traditional method for 3D visualization of ultrastructural components, serial sectioning using transmission electron microscopy (TEM), is very labor-intensive due to contentious TEM slice preparation and subsequent image processing of the whole collection. In this chapter, we present serial block-face scanning electron microscopy, together with complex methodology for spheroid formation, contrasting of cellular compartments, image processing, and 3D visualization. The described technique is effective for detailed morphological analysis of stem cell spheroids, organoids, as well as organotypic cell cultures.
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Affiliation(s)
- Josef Jaros
- Faculty of Medicine, Department of Histology and Embryology, Masaryk University, Kamenice 3/A1, 625 00, Brno, Czech Republic. .,Cell and Tissue Regeneration, International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91, Brno, Czech Republic.
| | - Michal Petrov
- TESCAN Brno, s.r.o., Libusina Trida 1, 623 00, Brno, Czech Republic
| | - Marketa Tesarova
- CEITEC BUT, Brno University of Technology, Purkynova 123, 612 00, Brno, Czech Republic
| | - Ales Hampl
- Faculty of Medicine, Department of Histology and Embryology, Masaryk University, Kamenice 3/A1, 625 00, Brno, Czech Republic.,Cell and Tissue Regeneration, International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91, Brno, Czech Republic
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14
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Bagherpoor AJ, Dolezalova D, Barta T, Kučírek M, Sani SA, Ešner M, Kunova Bosakova M, Vinarský V, Peskova L, Hampl A, Štros M. Properties of Human Embryonic Stem Cells and Their Differentiated Derivatives Depend on Nonhistone DNA-Binding HMGB1 and HMGB2 Proteins. Stem Cells Dev 2016; 26:328-340. [PMID: 27863459 DOI: 10.1089/scd.2016.0274] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
HMGB1 and HMGB2 proteins have been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It is unknown whether they are involved in regulating the typical functions of pluripotent human embryonic stem cells (hESCs) and/or those of the differentiated derivatives of hESCs. Using inducible, stably transfected hESCs capable of shRNA-mediated knockdown of HMGB1 and HMGB2, we provide evidence that downregulation of HMGB1 and/or HMGB2 in undifferentiated hESCs does not affect the stemness of cells and induces only minor changes to the proliferation rate, cell-cycle profile, and apoptosis. After differentiation is induced, however, the downregulation of those proteins has important effects on proliferation, apoptosis, telomerase activity, and the efficiency of differentiation toward the neuroectodermal lineage. Furthermore, those processes are affected only when one, but not both, of the two proteins is downregulated; the knockdown of both HMGB1 and HMGB2 results in a normal phenotype. Those results advance our knowledge of regulation of hESC and human neuroectodermal cell differentiation and illustrate the distinct roles of HMGB1 and HMGB2 during early human development.
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Affiliation(s)
- Alireza Jian Bagherpoor
- 1 Laboratory of Analysis of Chromosomal Proteins, Institute of Biophysics , Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Dasa Dolezalova
- 2 Department of Histology and Embryology, Masaryk University , Brno, Czech Republic
| | - Tomas Barta
- 2 Department of Histology and Embryology, Masaryk University , Brno, Czech Republic .,3 International Clinical Research Center, St. Anne's University Hospital , Brno, Czech Republic
| | - Martin Kučírek
- 1 Laboratory of Analysis of Chromosomal Proteins, Institute of Biophysics , Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Soodabeh Abbasi Sani
- 1 Laboratory of Analysis of Chromosomal Proteins, Institute of Biophysics , Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Milan Ešner
- 2 Department of Histology and Embryology, Masaryk University , Brno, Czech Republic
| | | | - Vladimír Vinarský
- 3 International Clinical Research Center, St. Anne's University Hospital , Brno, Czech Republic
| | - Lucie Peskova
- 2 Department of Histology and Embryology, Masaryk University , Brno, Czech Republic
| | - Aleš Hampl
- 2 Department of Histology and Embryology, Masaryk University , Brno, Czech Republic .,3 International Clinical Research Center, St. Anne's University Hospital , Brno, Czech Republic
| | - Michal Štros
- 1 Laboratory of Analysis of Chromosomal Proteins, Institute of Biophysics , Academy of Sciences of the Czech Republic, Brno, Czech Republic
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15
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Brouwer M, Zhou H, Nadif Kasri N. Choices for Induction of Pluripotency: Recent Developments in Human Induced Pluripotent Stem Cell Reprogramming Strategies. Stem Cell Rev Rep 2016; 12:54-72. [PMID: 26424535 PMCID: PMC4720703 DOI: 10.1007/s12015-015-9622-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ability to generate human induced pluripotent stem cells (iPSCs) from somatic cells provides tremendous promises for regenerative medicine and its use has widely increased over recent years. However, reprogramming efficiencies remain low and chromosomal instability and tumorigenic potential are concerns in the use of iPSCs, especially in clinical settings. Therefore, reprogramming methods have been under development to generate safer iPSCs with higher efficiency and better quality. Developments have mainly focused on the somatic cell source, the cocktail of reprogramming factors, the delivery method used to introduce reprogramming factors and culture conditions to maintain the generated iPSCs. This review discusses the developments on these topics and briefly discusses pros and cons of iPSCs in comparison with human embryonic stem cells generated from somatic cell nuclear transfer.
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Affiliation(s)
- Marinka Brouwer
- Department of Cognitive Neuroscience, Radboudumc, Nijmegen, 6500, HB, The Netherlands
| | - Huiqing Zhou
- Department of Human Genetics, Radboudumc, Nijmegen, 6500, HB, The Netherlands. .,Department of Molecular Developmental Biology, Faculty of Science, Radboud University, Nijmegen, 6500, HB, The Netherlands.
| | - Nael Nadif Kasri
- Department of Cognitive Neuroscience, Radboudumc, Nijmegen, 6500, HB, The Netherlands. .,Department of Human Genetics, Radboudumc, Nijmegen, 6500, HB, The Netherlands. .,Donders Institute for Brain, Cognition, and Behaviour , Centre for Neuroscience, Nijmegen, 6525, AJ, The Netherlands.
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16
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Stejskal S, Stepka K, Tesarova L, Stejskal K, Matejkova M, Simara P, Zdrahal Z, Koutna I. Cell cycle-dependent changes in H3K56ac in human cells. Cell Cycle 2016; 14:3851-63. [PMID: 26645646 DOI: 10.1080/15384101.2015.1106760] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The incorporation of histone H3 with an acetylated lysine 56 (H3K56ac) into the nucleosome is important for chromatin remodeling and serves as a marker of new nucleosomes during DNA replication and repair in yeast. However, in human cells, the level of H3K56ac is greatly reduced, and its role during the cell cycle is controversial. Our aim was to determine the potential of H3K56ac to regulate cell cycle progression in different human cell lines. A significant increase in the number of H3K56ac foci, but not in H3K56ac protein levels, was observed during the S and G2 phases in cancer cell lines, but was not observed in embryonic stem cell lines. Despite this increase, the H3K56ac signal was not present in late replication chromatin, and H3K56ac protein levels did not decrease after the inhibition of DNA replication. H3K56ac was not tightly associated with the chromatin and was primarily localized to active chromatin regions. Our results support the role of H3K56ac in transcriptionally active chromatin areas but do not confirm H3K56ac as a marker of newly synthetized nucleosomes in DNA replication.
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Affiliation(s)
- Stanislav Stejskal
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
| | - Karel Stepka
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
| | - Lenka Tesarova
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
| | - Karel Stejskal
- b Research Group - Proteomics; Central European Institute of Technology; Masaryk University ; Brno , Czech Republic.,c National Centre for Biomolecular Research; Faculty of Science; Masaryk University ; Brno , Czech Republic
| | - Martina Matejkova
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
| | - Pavel Simara
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
| | - Zbynek Zdrahal
- b Research Group - Proteomics; Central European Institute of Technology; Masaryk University ; Brno , Czech Republic.,c National Centre for Biomolecular Research; Faculty of Science; Masaryk University ; Brno , Czech Republic
| | - Irena Koutna
- a Centre for Biomedical Image Analysis; Faculty of Informatics; Masaryk University ; Brno , Czech Republic
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17
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Brouwer M, Zhou H, Nadif Kasri N. Choices for Induction of Pluripotency: Recent Developments in Human Induced Pluripotent Stem Cell Reprogramming Strategies. Stem Cell Rev Rep 2015. [PMID: 26424535 DOI: 10.1007/s12015‐015‐9622‐8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ability to generate human induced pluripotent stem cells (iPSCs) from somatic cells provides tremendous promises for regenerative medicine and its use has widely increased over recent years. However, reprogramming efficiencies remain low and chromosomal instability and tumorigenic potential are concerns in the use of iPSCs, especially in clinical settings. Therefore, reprogramming methods have been under development to generate safer iPSCs with higher efficiency and better quality. Developments have mainly focused on the somatic cell source, the cocktail of reprogramming factors, the delivery method used to introduce reprogramming factors and culture conditions to maintain the generated iPSCs. This review discusses the developments on these topics and briefly discusses pros and cons of iPSCs in comparison with human embryonic stem cells generated from somatic cell nuclear transfer.
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Affiliation(s)
- Marinka Brouwer
- Department of Cognitive Neuroscience, Radboudumc, Nijmegen, 6500, HB, The Netherlands
| | - Huiqing Zhou
- Department of Human Genetics, Radboudumc, Nijmegen, 6500, HB, The Netherlands. .,Department of Molecular Developmental Biology, Faculty of Science, Radboud University, Nijmegen, 6500, HB, The Netherlands.
| | - Nael Nadif Kasri
- Department of Cognitive Neuroscience, Radboudumc, Nijmegen, 6500, HB, The Netherlands. .,Department of Human Genetics, Radboudumc, Nijmegen, 6500, HB, The Netherlands. .,Donders Institute for Brain, Cognition, and Behaviour , Centre for Neuroscience, Nijmegen, 6525, AJ, The Netherlands.
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18
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Ireland RG, Simmons CA. Human Pluripotent Stem Cell Mechanobiology: Manipulating the Biophysical Microenvironment for Regenerative Medicine and Tissue Engineering Applications. Stem Cells 2015; 33:3187-96. [DOI: 10.1002/stem.2105] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 06/16/2015] [Accepted: 06/30/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Ronald G. Ireland
- Institute of Biomaterials and Biomedical Engineering, University of Toronto; Toronto Ontario Canada
| | - Craig A. Simmons
- Institute of Biomaterials and Biomedical Engineering, University of Toronto; Toronto Ontario Canada
- Department of Mechanical and Industrial Engineering; University of Toronto; Toronto Ontario Canada
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19
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Guo X, Lian R, Guo Y, Liu Q, Ji Q, Chen J. bFGF and Activin A function to promote survival and proliferation of single iPS cells in conditioned half-exchange mTeSR1 medium. Hum Cell 2015; 28:122-32. [DOI: 10.1007/s13577-015-0113-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 02/24/2015] [Indexed: 01/12/2023]
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20
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Krutá M, Šeneklová M, Raška J, Salykin A, Zerzánková L, Pešl M, Bártová E, Franek M, Baumeisterová A, Košková S, Neelsen KJ, Hampl A, Dvořák P, Rotrekl V. Mutation frequency dynamics in HPRT locus in culture-adapted human embryonic stem cells and induced pluripotent stem cells correspond to their differentiated counterparts. Stem Cells Dev 2014; 23:2443-54. [PMID: 24836366 DOI: 10.1089/scd.2013.0611] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The genomic destabilization associated with the adaptation of human embryonic stem cells (hESCs) to culture conditions or the reprogramming of induced pluripotent stem cells (iPSCs) increases the risk of tumorigenesis upon the clinical use of these cells and decreases their value as a model for cell biology studies. Base excision repair (BER), a major genomic integrity maintenance mechanism, has been shown to fail during hESC adaptation. Here, we show that the increase in the mutation frequency (MF) caused by the inhibition of BER was similar to that caused by the hESC adaptation process. The increase in MF reflected the failure of DNA maintenance mechanisms and the subsequent increase in MF rather than being due solely to the accumulation of mutants over a prolonged period, as was previously suggested. The increase in the ionizing-radiation-induced MF in adapted hESCs exceeded the induced MF in nonadapted hESCs and differentiated cells. Unlike hESCs, the overall DNA maintenance in iPSCs, which was reflected by the MF, was similar to that in differentiated cells regardless of the time spent in culture and despite the upregulation of several genes responsible for genome maintenance during the reprogramming process. Taken together, our results suggest that the changes in BER activity during the long-term cultivation of hESCs increase the mutagenic burden, whereas neither reprogramming nor long-term propagation in culture changes the MF in iPSCs.
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Affiliation(s)
- Miriama Krutá
- 1 Department of Biology, Faculty of Medicine, Masaryk University , Brno, Czech Republic
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21
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Chen KG, Hamilton RS, Robey PG, Mallon BS. Alternative cultures for human pluripotent stem cell production, maintenance, and genetic analysis. J Vis Exp 2014. [PMID: 25077932 DOI: 10.3791/51519] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) hold great promise for regenerative medicine and biopharmaceutical applications. Currently, optimal culture and efficient expansion of large amounts of clinical-grade hPSCs are critical issues in hPSC-based therapies. Conventionally, hPSCs are propagated as colonies on both feeder and feeder-free culture systems. However, these methods have several major limitations, including low cell yields and generation of heterogeneously differentiated cells. To improve current hPSC culture methods, we have recently developed a new method, which is based on non-colony type monolayer (NCM) culture of dissociated single cells. Here, we present detailed NCM protocols based on the Rho-associated kinase (ROCK) inhibitor Y-27632. We also provide new information regarding NCM culture with different small molecules such as Y-39983 (ROCK I inhibitor), phenylbenzodioxane (ROCK II inhibitor), and thiazovivin (a novel ROCK inhibitor). We further extend our basic protocol to cultivate hPSCs on defined extracellular proteins such as the laminin isoform 521 (LN-521) without the use of ROCK inhibitors. Moreover, based on NCM, we have demonstrated efficient transfection or transduction of plasmid DNAs, lentiviral particles, and oligonucleotide-based microRNAs into hPSCs in order to genetically modify these cells for molecular analyses and drug discovery. The NCM-based methods overcome the major shortcomings of colony-type culture, and thus may be suitable for producing large amounts of homogeneous hPSCs for future clinical therapies, stem cell research, and drug discovery.
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Affiliation(s)
- Kevin G Chen
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health;
| | - Rebecca S Hamilton
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health
| | - Pamela G Robey
- Craniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health
| | - Barbara S Mallon
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health
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22
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Salykin A, Kuzmic P, Kyrylenko O, Musilova J, Glatz Z, Dvorak P, Kyrylenko S. Nonlinear regression models for determination of nicotinamide adenine dinucleotide content in human embryonic stem cells. Stem Cell Rev Rep 2014; 9:786-93. [PMID: 23832307 DOI: 10.1007/s12015-013-9454-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent evidence suggests that energy metabolism contributes to molecular mechanisms controlling stem cell identity. For example, human embryonic stem cells (hESCs) receive their metabolic energy mostly via glycolysis rather than mitochondrial oxidative phosphorylation. This suggests a connection of metabolic homeostasis to stemness. Nicotinamide adenine dinucleotide (NAD) is an important cellular redox carrier and a cofactor for various metabolic pathways, including glycolysis. Therefore, accurate determination of NAD cellular levels and dynamics is of growing importance for understanding the physiology of stem cells. Conventional analytic methods for the determination of metabolite levels rely on linear calibration curves. However, in actual practice many two-enzyme cycling assays, such as the assay systems used in this work, display prominently nonlinear behavior. Here we present a diaphorase/lactate dehydrogenase NAD cycling assay optimized for hESCs, together with a mechanism-based, nonlinear regression models for the determination of NAD(+), NADH, and total NAD. We also present experimental data on metabolic homeostasis of hESC under various physiological conditions. We show that NAD(+)/NADH ratio varies considerably with time in culture after routine change of medium, while the total NAD content undergoes relatively minor changes. In addition, we show that the NAD(+)/NADH ratio, as well as the total NAD levels, vary between stem cells and their differentiated counterparts. Importantly, the NAD(+)/NADH ratio was found to be substantially higher in hESC-derived fibroblasts versus hESCs. Overall, our nonlinear mathematical model is applicable to other enzymatic amplification systems.
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Affiliation(s)
- Anton Salykin
- Department of Biology, Faculty of Medicine, Masaryk University, Building A3, Kamenice 735/5, 625 00, Brno-Bohunice, Czech Republic
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23
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Chen KG, Mallon BS, Johnson KR, Hamilton RS, McKay RDG, Robey PG. Developmental insights from early mammalian embryos and core signaling pathways that influence human pluripotent cell growth and differentiation. Stem Cell Res 2014; 12:610-21. [PMID: 24603366 DOI: 10.1016/j.scr.2014.02.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 01/10/2014] [Accepted: 02/04/2014] [Indexed: 12/23/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) have two potentially attractive applications: cell replacement-based therapies and drug discovery. Both require the efficient generation of large quantities of clinical-grade stem cells that are free from harmful genomic alterations. The currently employed colony-type culture methods often result in low cell yields, unavoidably heterogeneous cell populations, and substantial chromosomal abnormalities. Here, we shed light on the structural relationship between hPSC colonies/embryoid bodies and early-stage embryos in order to optimize current culture methods based on the insights from developmental biology. We further highlight core signaling pathways that underlie multiple epithelial-to-mesenchymal transitions (EMTs), cellular heterogeneity, and chromosomal instability in hPSCs. We also analyze emerging methods such as non-colony type monolayer (NCM) and suspension culture, which provide alternative growth models for hPSC expansion and differentiation. Furthermore, based on the influence of cell-cell interactions and signaling pathways, we propose concepts, strategies, and solutions for production of clinical-grade hPSCs, stem cell precursors, and miniorganoids, which are pivotal steps needed for future clinical applications.
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Affiliation(s)
- Kevin G Chen
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Barbara S Mallon
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kory R Johnson
- Information Technology and Bioinformatics Program, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rebecca S Hamilton
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ronald D G McKay
- The Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Pamela G Robey
- Craniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
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24
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Ono T, Suzuki Y, Kato Y, Fujita R, Araki T, Yamashita T, Kato H, Torii R, Sato N. A single-cell and feeder-free culture system for monkey embryonic stem cells. PLoS One 2014; 9:e88346. [PMID: 24505480 PMCID: PMC3915054 DOI: 10.1371/journal.pone.0088346] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 01/11/2014] [Indexed: 12/20/2022] Open
Abstract
Primate pluripotent stem cells (PSCs), including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), hold great potential for research and application in regenerative medicine and drug discovery. To maximize primate PSC potential, a practical system is required for generating desired functional cells and reproducible differentiation techniques. Much progress regarding their culture systems has been reported to date; however, better methods would still be required for their practical use, particularly in industrial and clinical fields. Here we report a new single-cell and feeder-free culture system for primate PSCs, the key feature of which is an originally formulated serum-free medium containing FGF and activin. In this culture system, cynomolgus monkey ESCs can be passaged many times by single-cell dissociation with traditional trypsin treatment and can be propagated with a high proliferation rate as a monolayer without any feeder cells; further, typical PSC properties and genomic stability can be retained. In addition, it has been demonstrated that monkey ESCs maintained in the culture system can be used for various experiments such as in vitro differentiation and gene manipulation. Thus, compared with the conventional culture system, monkey ESCs grown in the aforementioned culture system can serve as a cell source with the following practical advantages: simple, stable, and easy cell maintenance; gene manipulation; cryopreservation; and desired differentiation. We propose that this culture system can serve as a reliable platform to prepare primate PSCs useful for future research and application.
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Affiliation(s)
- Takashi Ono
- Discovery Molecular Pharmacology Department, Discovery Screening Center, Mitsubishi Tanabe Pharma Corporation, Yokohama, Kanagawa, Japan
- * E-mail:
| | - Yutaka Suzuki
- Discovery Molecular Pharmacology Department, Discovery Screening Center, Mitsubishi Tanabe Pharma Corporation, Yokohama, Kanagawa, Japan
| | - Yosuke Kato
- Discovery Molecular Pharmacology Department, Discovery Screening Center, Mitsubishi Tanabe Pharma Corporation, Yokohama, Kanagawa, Japan
| | - Risako Fujita
- Discovery Molecular Pharmacology Department, Discovery Screening Center, Mitsubishi Tanabe Pharma Corporation, Yokohama, Kanagawa, Japan
| | - Toshihiro Araki
- Discovery Molecular Pharmacology Department, Discovery Screening Center, Mitsubishi Tanabe Pharma Corporation, Yokohama, Kanagawa, Japan
| | - Tomoko Yamashita
- Discovery Molecular Pharmacology Department, Discovery Screening Center, Mitsubishi Tanabe Pharma Corporation, Yokohama, Kanagawa, Japan
| | - Hidemasa Kato
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Ryuzo Torii
- Research Center for Animal Life Science, Shiga University of Medical Science, Otsu, Shiga, Japan
| | - Naoya Sato
- Discovery Molecular Pharmacology Department, Discovery Screening Center, Mitsubishi Tanabe Pharma Corporation, Yokohama, Kanagawa, Japan
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Chen KG, Mallon BS, McKay RDG, Robey PG. Human pluripotent stem cell culture: considerations for maintenance, expansion, and therapeutics. Cell Stem Cell 2014; 14:13-26. [PMID: 24388173 PMCID: PMC3915741 DOI: 10.1016/j.stem.2013.12.005] [Citation(s) in RCA: 241] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Human pluripotent stem cells (hPSCs) provide powerful resources for application in regenerative medicine and pharmaceutical development. In the past decade, various methods have been developed for large-scale hPSC culture that rely on combined use of multiple growth components, including media containing various growth factors, extracellular matrices, 3D environmental cues, and modes of multicellular association. In this Protocol Review, we dissect these growth components by comparing cell culture methods and identifying the benefits and pitfalls associated with each one. We further provide criteria, considerations, and suggestions to achieve optimal cell growth for hPSC expansion, differentiation, and use in future therapeutic applications.
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Affiliation(s)
- Kevin G Chen
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Barbara S Mallon
- NIH Stem Cell Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ronald D G McKay
- The Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Pamela G Robey
- Craniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
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26
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Musilová J, Klejdus B, Glatz Z. Simultaneous quantification of energetically important metabolites in various cell types by CZE. J Sep Sci 2013; 36:3807-12. [PMID: 24123860 DOI: 10.1002/jssc.201300926] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 09/19/2013] [Accepted: 09/25/2013] [Indexed: 12/31/2022]
Abstract
A new CZE method was developed for the determination of 12 purine and pyrimidine nucleotides, two adenine coenzymes and their reduced forms, and acetyl coenzyme A in various cell extracts. As the concentration levels of these metabolites in living cells are low; CZE was combined with field-enhanced sample stacking. As a result, the separation conditions were optimised to achieve a suitable resolution at the relatively high sample volume provided by this on-line pre-concentration technique. The optimum BGE was 150 mM glycine buffer (pH 9.5). Samples were introduced hydrodynamically using a pressure of 35 mbar (3.5 kPa) for 25 s, and data were collected at a detection wavelength of 260 nm. An applied voltage of 30 kV (positive polarity) and capillary temperature of 25°C gave the best separation of these compounds. The optimised method was validated by determining the linearity, sensitivity and repeatability and it was successfully applied for the analysis of extracts from Paracoccus denitrificans bacteria and from stem cells.
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Affiliation(s)
- Jindra Musilová
- Department of Biochemistry, Faculty of Science and CEITEC-Central European Institute of Technology, Masaryk University, Czech Republic
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