1
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Albayrak E, Akgol S, Turan RD, Uslu M, Kocabas F. BML-260 promotes the growth of cord blood and mobilized peripheral blood hematopoietic stem and progenitor cells with improved reconstitution ability. J Cell Biochem 2022; 123:2009-2029. [PMID: 36070493 DOI: 10.1002/jcb.30324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/08/2022] [Accepted: 08/22/2022] [Indexed: 12/24/2022]
Abstract
Hematopoietic stem cells (HSCs), which are multipotent and have the ability to self-renew, are frequently used in the treatment of hematological diseases and cancer. Small molecules that target HSC quiescence regulators could be used for ex vivo expansion of both mobilized peripheral blood (mPB) and umbilical cord blood (UCB) hematopoietic stem and progenitor cells (HSPC). We identified and investigated 35 small molecules that target HSC quiescence factors. We looked at how they affected HSC activity, such as expansion, quiescence, multilineage capacity, cycling ability, metabolism, cytotoxicity, and genotoxicity. A transplantation study was carried out on immunocompromised mice to assess the expanded cells' repopulation and engraftment abilities. 4-[(5Z)-5-benzylidene-4-oxo-2-sulfanylidene-1,3-thiazolidin-3-yl]benzoic acid (BML)-260 and tosyl-l-arginine methyl ester (TAME) significantly increased both mPB and UCB-HSPC content and activated HSC re-entry into the cell cycle. The improved multilineage capacity was confirmed by the colony forming unit (CFU) assay. Furthermore, gene expression analysis revealed that BML-260 and TAME molecules aided HSC expansion by modulating cell cycle kinetics, such as p27, SKP2, and CDH1. In addition to these in vitro findings, we discovered that BML-260-expanded HSCs had a high hematopoietic reconstitution capacity with increased immune cell content after xenotransplantation into immunocompromised mice. In addition to the BML-260 molecule, a comparison study of serum-containing and serum-free chemically defined media, including various supplements, was performed. These in vitro and xenotransplantation results show that BML-260 molecules can be used for human HSC expansion and regulation of function. Furthermore, the medium composition discovered may be a novel platform for human HSPC expansion that could be used in clinical trials.
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Affiliation(s)
- Esra Albayrak
- Center of Stem Cell Research and Application, 19 Mayıs University, Samsun, Turkey.,Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Sezer Akgol
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Raife Dilek Turan
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Merve Uslu
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.,Johns Hopkins All Children's Hospital, St. Petersburg, Florida, USA
| | - Fatih Kocabas
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
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2
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Aslan GS, Polat F, Eren SN, Yucel D, Arbatli S, Cumbul A, Kocabas F. Correction to: Identification of Novel and Potent Modulators Involved in Neonatal Cardiac Regeneration. Pediatr Cardiol 2022; 43:709. [PMID: 35107631 DOI: 10.1007/s00246-022-02833-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Galip Servet Aslan
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt, Germany.,Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.,Faculty of Biological Science, Goethe University Frankfurt, Frankfurt, Germany
| | - Feyza Polat
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Seyma Nur Eren
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Dogacan Yucel
- Faculty of Medicine, University of Minnesota, Minnesota, USA
| | | | - Alev Cumbul
- Department of Histology and Embryology, Faculty of Medicine, Yeditepe University, Istanbul, Turkey
| | - Fatih Kocabas
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.
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3
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Alyazici LY, Kocabas F. Identification of Small Molecules That Enhance the Expansion of Mesenchymal Stem Cells Originating from Bone Marrow. Adv Exp Med Biol 2021; 1387:43-55. [PMID: 34845672 DOI: 10.1007/5584_2021_677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Mesenchymal stem cells (MSCs) have been shown to be promising for regenerative medicines with their immunomodulatory characteristics. They may be obtained from a variety of tissue types, including umbilical cord, adipose tissue, dental tissue, and bone marrow (BM). BM-MSCs are challenging in terms of their ex vivo expansion capability. Thus, we aimed to improve the expansion of BM-MSCs with small molecule treatments. We tested about forty small molecules that are potent quiescence modulators, and determined their efficacy by analysis of cell viability, cell cycle, and apoptosis in BM-MSCs. We also examined gene expression for selected small molecules to explore essential molecular pathways. We observed that treatment with SB203580 increased BM-MSCs expansion up to two fold when used for 5 days. SB203580 decreased the proportion of cells in the G1 phase of the cell cycle and substantially increased the ratio of cells in the S-G2-M phase. Enhanced MSC expansion with SB203580 therapy was associated with the lower expression of CDKIs like p15, p18, p19, p21, p27, and p57. In conclusion, we have developed a new approach to facilitate the expansion of BM-MSCs. These results could enhance autologous and immunomodulation therapy involving BM-MSCs.
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Affiliation(s)
- Lamia Yazgi Alyazici
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Fatih Kocabas
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.
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4
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Turgutalp B, Uslu M, Helvacioglu S, Charehsaz M, Gurdal EE, Sippl W, Kocabas F, Yarim M. Lead Optimization and Structure-Activity Relationship Studies on Myeloid Ecotropic Viral Integration Site 1 Inhibitor. J Med Chem 2021; 64:14448-14464. [PMID: 34542289 DOI: 10.1021/acs.jmedchem.1c00972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The pivotal role of the myeloid ecotropic viral integration site 1 (MEIS1) transcriptional factor was reported in cardiac regeneration and hematopoietic stem-cell (HSC) regulation with our previous findings. MEIS1 as a promising target in the context of pharmacological inhibition, we identified a potent myeloid ecotropic viral integration site (MEIS) inhibitor, MEISi-1, to induce murine and human HSC expansion ex vivo and in vivo. In this work, we performed lead optimization on MEISi-1 by synthesizing 45 novel analogues. Structure-activity relationship studies revealed the significance of a para-methoxy group on ring A and a hydrophobic moiety at the meta position of ring B. Obtained biological data were supported by inhibitor docking and molecular dynamics simulation studies. Eleven compounds were depicted as potent inhibitors demonstrating a better inhibitory profile on MEIS1 and target genes Meis1, Hif-1α, and p21. Among those, 4h, 4f, and 4b were the most potent inhibitors. The predicted pharmacokinetics properties fulfill drug-likeness criteria. In addition, compounds exerted neither cytotoxicity on human dermal fibroblasts nor mutagenicity.
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Affiliation(s)
- Bengisu Turgutalp
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Yeditepe University, Istanbul 34755, Turkey.,German Center for Neurodegenerative Diseases (DZNE), Helmholtz Association, Dresden 01307, Germany
| | - Merve Uslu
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul 34755, Turkey
| | - Sinem Helvacioglu
- Department of Toxicology, Faculty of Pharmacy, Yeditepe University, Istanbul 34755, Turkey
| | - Mohammad Charehsaz
- Department of Toxicology, Faculty of Pharmacy, Yeditepe University, Istanbul 34755, Turkey
| | - Enise Ece Gurdal
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Yeditepe University, Istanbul 34755, Turkey.,Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale) 06120, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Halle (Saale) 06120, Germany
| | - Fatih Kocabas
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul 34755, Turkey
| | - Mine Yarim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Yeditepe University, Istanbul 34755, Turkey
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5
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Aslan GS, Polat F, Eren SN, Yucel D, Arbatli S, Cumbul A, Kocabas F. Identification of Novel and Potent Modulators Involved in Neonatal Cardiac Regeneration. Pediatr Cardiol 2021; 42:1554-1566. [PMID: 34046720 DOI: 10.1007/s00246-021-02640-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/18/2021] [Indexed: 12/31/2022]
Abstract
Neonatal mammalian heart has been shown to possess the capacity to regenerate substantially after an injury. This remarkable regenerative capacity is lost in a week. This transition has been marked with cardiomyocyte cell cycle arrest and induction of fibrotic response similar to what occurs after myocardial infarction in adult hearts. Recent studies outlined the function of several cardiogenic factors that play a pivotal role in neonatal cardiac regeneration. However, underlying molecular mechanisms of neonatal cardiac regeneration and other cardiogenic factors remained elusive. Here, we investigated the involvement of novel putative cardiogenic factors in neonatal cardiac regeneration and cardiomyocyte cell cycle withdrawal. We have shown that Cbl, Dnmt3a, and Itch are significantly downregulated during neonatal cardiac regeneration process after cardiac injury in vivo. Intriguingly, several of studied factors are upregulated in non-regenerative period of 7-day-old mice after cardiac injury. Knockdown of Cbl, Dnmt3a and Itch in rat neonatal cardiomyocytes lead to the induction of cardiomyocyte proliferation. Cardiomyocyte proliferation accompanies upregulation of positive regulators of cardiomyocyte division and downregulation of CDKIs. Taken together, our findings suggest that Cbl, Dnmt3a, and Itch may be involved in the regulation of cardiomyocyte cell cycle withdrawal and may represent new targets for the induction of cardiac regeneration.
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Affiliation(s)
- Galip Servet Aslan
- Institute for Cardiovascular Regeneration, Goethe University, Frankfurt, Germany.,Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.,Faculty of Biological Science, Goethe University, Frankfurt, Germany
| | - Feyza Polat
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Seyma Nur Eren
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Dogacan Yucel
- Faculty of Medicine, University of Minnesota, Minnesota, USA
| | | | - Alev Cumbul
- Department of Histology and Embryology, Faculty of Medicine, Yeditepe University, Istanbul, Turkey
| | - Fatih Kocabas
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.
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Akgol S, Kalkan BM, Yucel D, Kocabas F. SC1 limits tube formation, branching, migration, expansion and induce apoptosis of endothelial cells. Vascul Pharmacol 2021; 141:106903. [PMID: 34481979 DOI: 10.1016/j.vph.2021.106903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/02/2021] [Accepted: 08/27/2021] [Indexed: 11/30/2022]
Abstract
Endothelial cells (ECs) are essential in the growth and progression of the tumor cells by supplying nutrition and angiogenesis factors. Targeting ECs emerged as a major strategy to prevent the growth of tumors. Studies suggest that ERK1/2 signaling is important for endothelial cells, which could be specifically targeted by small molecule SC1. We aimed to study the effects of SC1 treatments on endothelial cell proliferation, angiogenesis, and death. To this end, we performed viability, apoptosis, cell cycle, gene expression, wound closure, tube formation, and western blot analysis in endothelial cells post SC1 treatments. Intriguingly, we found that SC1 has an antiangiogenic effect on endothelial cells, which limits the endothelial cell expansion, tube formation, branching, and migration. The proliferation is especially limited in dose dependent manner by SC1. In addition, we found that SC1 elevates the apoptosis of endothelial cells and associated pathways including BAK1, Stat1, Sox4, and Caspase1. We believe that these findings could contribute to the development of improved therapies based on the SC1 as an attractive candidate for anticancer clinical studies targeted to tumor angiogenesis.
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Affiliation(s)
- Sezer Akgol
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | | | - Dogacan Yucel
- Department of Medicine, University of Minnesota, USA
| | - Fatih Kocabas
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.
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7
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Albayrak E, Uslu M, Akgol S, Tuysuz EC, Kocabas F. Small molecule-mediated modulation of ubiquitination and neddylation improves HSC function ex vivo. J Cell Physiol 2021; 236:8122-8136. [PMID: 34101829 DOI: 10.1002/jcp.30466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 05/04/2021] [Accepted: 05/27/2021] [Indexed: 11/07/2022]
Abstract
Hematopoietic stem cells (HSCs) are particularly characterized by their quiescence and self-renewal. Cell cycle regulators tightly control quiescence and self-renewal capacity. Studies suggest that modulation of ubiquitination and neddylation could contribute to HSC function via cyclin-dependent kinase inhibitors (CDKIs). S-phase kinase-associated protein 2 (SKP2) is responsible for ubiquitin-mediated proteolysis of CDKIs. Here, we modulated overall neddylation and SKP2-associated ubiquitination in HSCs by using SKP2-C25, an SKP2 inhibitor, and MLN4924 (Pevonedistat) as an inhibitor of the NEDD8 system. Treatments of SKP2-C25 and MLN4924 increased both murine and human stem and progenitor cell (HSPC) compartments. This is associated with the improved quiescence of murine HSC by upregulation of p27 and p57 CDKIs. A colony-forming unit assay showed an enhanced in vitro self-renewal potential post inhibition of ubiquitination and neddylation. In addition, MLN4924 triggered the mobilization of bone marrow HSPCs to peripheral blood. Intriguingly, MLN4924 treatment could decrease the proliferation of murine bone marrow mesenchymal stem cells or endothelial cells. These findings shed light on the contribution of SKP2, and associated ubiquitination and neddylation in HSC maintenance, self-renewal, and expansion.
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Affiliation(s)
- Esra Albayrak
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Merve Uslu
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Sezer Akgol
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Emre Can Tuysuz
- Department of Medical Genetics, Faculty of Medicine, Yeditepe University, Istanbul, Turkey
| | - Fatih Kocabas
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
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8
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Berber B, Aydin C, Kocabas F, Guney-Esken G, Yilancioglu K, Karadag-Alpaslan M, Caliseki M, Yuce M, Demir S, Tastan C. Gene editing and RNAi approaches for COVID-19 diagnostics and therapeutics. Gene Ther 2021; 28:290-305. [PMID: 33318646 PMCID: PMC7734466 DOI: 10.1038/s41434-020-00209-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 10/20/2020] [Accepted: 10/27/2020] [Indexed: 01/29/2023]
Abstract
The novel coronavirus pneumonia (COVID-19) is a highly infectious acute respiratory disease caused by Severe Acute Respiratory Syndrome-Related Coronavirus (SARS-CoV-2) (Prec Clin Med 2020;3:9-13, Lancet 2020;395:497-506, N. Engl J Med 2020a;382:1199-207, Nature 2020;579:270-3). SARS-CoV-2 surveillance is essential to controlling widespread transmission. However, there are several challenges associated with the diagnostic of the COVID-19 during the current outbreak (Liu and Li (2019), Nature 2020;579:265-9, N. Engl J Med 2020;382:727-33). Firstly, the high number of cases overwhelms diagnostic test capacity and proposes the need for a rapid solution for sample processing (Science 2018;360:444-8). Secondly, SARS-CoV-2 is closely related to other important coronavirus species and subspecies, so detection assays can give false-positive results if they are not efficiently specific to SARS-CoV-2. Thirdly, patients with suspected SARS-CoV-2 infection sometimes have a different respiratory viral infection or co-infections with SARS-CoV-2 and other respiratory viruses (MedRxiv 2020a;1-18). Confirmation of the COVID-19 is performed mainly by virus isolation followed by RT-PCR and sequencing (N. Engl J Med 2020;382:727-33, MedRxiv 2020a, Turkish J Biol 2020;44:192-202). The emergence and outbreak of the novel coronavirus highlighted the urgent need for new therapeutic technologies that are fast, precise, stable, easy to manufacture, and target-specific for surveillance and treatment. Molecular biology tools that include gene-editing approaches such as CRISPR-Cas12/13-based SHERLOCK, DETECTR, CARVER and PAC-MAN, antisense oligonucleotides, antisense peptide nucleic acids, ribozymes, aptamers, and RNAi silencing approaches produced with cutting-edge scientific advances compared to conventional diagnostic or treatment methods could be vital in COVID-19 and other future outbreaks. Thus, in this review, we will discuss potent the molecular biology approaches that can revolutionize diagnostic of viral infections and therapies to fight COVID-19 in a highly specific, stable, and efficient way.
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Affiliation(s)
- Burak Berber
- Department of Biology, Faculty of Science, Eskisehir Technical University, Eskisehir, Turkey
| | - Cihan Aydin
- Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Istanbul Medeniyet University, Istanbul, Turkey
| | - Fatih Kocabas
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Gulen Guney-Esken
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Kaan Yilancioglu
- Institute of Addiction and Forensic Sciences, Uskudar University, Istanbul, Turkey
- Transgenic Cell Technologies and Epigenetics Application and Research Center (TRGENMER), Uskudar University, Istanbul, Turkey
| | - Medine Karadag-Alpaslan
- Department of Medical Genetics, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Mehmet Caliseki
- Department of Molecular Biology, Genetics and Bioengineering, Graduate School of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Melek Yuce
- Center for Stem Cell Research, Ondokuz Mayis University, Samsun, Turkey
| | - Sevda Demir
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Cihan Tastan
- Transgenic Cell Technologies and Epigenetics Application and Research Center (TRGENMER), Uskudar University, Istanbul, Turkey.
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey.
- Faculty of Science and Letters, Department of Molecular Biology and Genetics, Istanbul Kultur University, Istanbul, Turkey.
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9
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Sidal H, Colakoglu Erkan P, Uslu M, Kocabas F. Development of small-molecule-induced fibroblast expansion technologies. J Tissue Eng Regen Med 2020; 14:1476-1487. [PMID: 32770632 DOI: 10.1002/term.3112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 06/25/2020] [Accepted: 07/11/2020] [Indexed: 12/24/2022]
Abstract
Dermal fibroblasts are responsible from the production of extracellular matrix and take role in the closure of skin wounds. Dermal fibroblasts are major cells of origin in the generation of induced pluripotent stem cells (IPSCs) and are historically being used as feeder layer and biofiller in the restorative surgeries. ex vivo expansion of the dermal fibroblasts provides a suitable model to study skin biology and to engineer bioartifical skins. Thus, development of efficient fibroblast expansion technologies gets outmost importance day by day. We sought to identify small molecules that induce ex vivo fibroblast expansion and understand their mechanisms. We analyzed the effect of 35 small molecules, which are expected to target molecular pathways involving cellular quiescence. We have found that small molecules, especially AS1949490 and SKF96365, increase human dermal fibroblast expansion of at least three different fibroblasts. Cell cycle analysis confirms that these small molecules allow cell cycle progression, as evident by increased percentage of cells in S-G2 -M phase of cell cycle. They led to a lower profile of apoptotic or necrotic fibroblasts. Intriguingly, we have found that identified small molecules could also endogenously induce the expression of IPSC generation, collagen synthesis, and aging-related genes. Identified small molecules may contribute to the induction of collagen synthesis in the biofiller products, the development of fibroblast products with better aging profile, and the improvement of IPSC generation.
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Affiliation(s)
- Humeyra Sidal
- Biology Department, Claude Bernard University, Lyon, France.,Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Pinar Colakoglu Erkan
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.,Biotechnology Program, Graduate School of Natural and Applied Sciences, Yeditepe University, Istanbul, Turkey
| | - Merve Uslu
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.,Biotechnology Program, Graduate School of Natural and Applied Sciences, Yeditepe University, Istanbul, Turkey
| | - Fatih Kocabas
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.,Biotechnology Program, Graduate School of Natural and Applied Sciences, Yeditepe University, Istanbul, Turkey
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10
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Turan RD, Albayrak E, Uslu M, Siyah P, Alyazici LY, Kalkan BM, Aslan GS, Yucel D, Aksoz M, Tuysuz EC, Meric N, Durdagi S, Gulbas Z, Kocabas F. Development of Small Molecule MEIS Inhibitors that modulate HSC activity. Sci Rep 2020; 10:7994. [PMID: 32409701 PMCID: PMC7224207 DOI: 10.1038/s41598-020-64888-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 04/20/2020] [Indexed: 12/24/2022] Open
Abstract
Meis1, which belongs to TALE-type class of homeobox gene family, appeared as one of the key regulators of hematopoietic stem cell (HSC) self-renewal and a potential therapeutical target. However, small molecule inhibitors of MEIS1 remained unknown. This led us to develop inhibitors of MEIS1 that could modulate HSC activity. To this end, we have established a library of relevant homeobox family inhibitors and developed a high-throughput in silico screening strategy against homeodomain of MEIS proteins using the AutoDock Vina and PaDEL-ADV platform. We have screened over a million druggable small molecules in silico and selected putative MEIS inhibitors (MEISi) with no predicted cytotoxicity or cardiotoxicity. This was followed by in vitro validation of putative MEIS inhibitors using MEIS dependent luciferase reporter assays and analysis in the ex vivo HSC assays. We have shown that small molecules named MEISi-1 and MEISi-2 significantly inhibit MEIS-luciferase reporters in vitro and induce murine (LSKCD34l°w cells) and human (CD34+, CD133+, and ALDHhi cells) HSC self-renewal ex vivo. In addition, inhibition of MEIS proteins results in downregulation of Meis1 and MEIS1 target gene expression including Hif-1α, Hif-2α and HSC quiescence modulators. MEIS inhibitors are effective in vivo as evident by induced HSC content in the murine bone marrow and downregulation of expression of MEIS target genes. These studies warrant identification of first-in-class MEIS inhibitors as potential pharmaceuticals to be utilized in modulation of HSC activity and bone marrow transplantation studies.
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Affiliation(s)
- Raife Dilek Turan
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.,LabCell, Acibadem University, Istanbul, Turkey
| | - Esra Albayrak
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Merve Uslu
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Pinar Siyah
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Lamia Yazgi Alyazici
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | | | | | - Dogacan Yucel
- Faculty of Medicine, University of Minnesota, Minnesota, USA
| | - Merve Aksoz
- MRC Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Emre Can Tuysuz
- Department of Medical Genetics, Faculty of Medicine, Yeditepe University, Istanbul, Turkey
| | - Neslihan Meric
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.,Bone Marrow Transplantation Center, Anadolu Medical Center, Kocaeli, Turkey
| | - Serdar Durdagi
- Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Zafer Gulbas
- Bone Marrow Transplantation Center, Anadolu Medical Center, Kocaeli, Turkey
| | - Fatih Kocabas
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.
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11
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Kalkan BM, Kala EY, Yuce M, Karadag Alpaslan M, Kocabas F. Development of gene editing strategies for human β-globin (HBB) gene mutations. Gene 2020; 734:144398. [PMID: 31987908 DOI: 10.1016/j.gene.2020.144398] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 01/15/2020] [Accepted: 01/23/2020] [Indexed: 01/19/2023]
Abstract
Recent developments in gene editing technology have enabled scientists to modify DNA sequence by using engineered endonucleases. These gene editing tools are promising candidates for clinical applications, especially for treatment of inherited disorders like sickle cell disease (SCD). SCD is caused by a point mutation in human β-globin gene (HBB). Clinical strategies have demonstrated substantial success, however there is not any permanent cure for SCD available. CRISPR/Cas9 platform uses a single endonuclease and a single guide RNA (gRNA) to induce sequence-specific DNA double strand break (DSB). When this accompanies a repair template, it allows repairing the mutated gene. In this study, it was aimed to target HBB gene via CRISPR/Cas9 genome editing tool to introduce nucleotide alterations for efficient genome editing and correction of point mutations causing SCD in human cell line, by Homology Directed Repair (HDR). We have achieved to induce target specific nucleotide changes on HBB gene in the locus of mutation causing SCD. The effect of on-target activity of bone fide standard gRNA and newly developed longer gRNA were examined. It is observed that longer gRNA has higher affinity to target DNA while having the same performance for targeting and Cas9 induced DSBs. HDR mechanism was triggered by co-delivery of donor DNA repair templates in circular plasmid form. In conclusion, we have suggested methodological pipeline for efficient targeting with higher affinity to target DNA and generating desired modifications on HBB gene.
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Affiliation(s)
- Batuhan Mert Kalkan
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey; Koc University, Istanbul, Turkey
| | - Ezgi Yagmur Kala
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey; Koc University, Istanbul, Turkey
| | - Melek Yuce
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey; Department of Medical Biology and Genetics, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Medine Karadag Alpaslan
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey; Department of Medical Genetics, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Fatih Kocabas
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.
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12
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Kalkan BM, Akgol S, Ak D, Yucel D, Guney Esken G, Kocabas F. CASIN and AMD3100 enhance endothelial cell proliferation, tube formation and sprouting. Microvasc Res 2020; 130:104001. [PMID: 32198058 DOI: 10.1016/j.mvr.2020.104001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/27/2020] [Accepted: 03/14/2020] [Indexed: 01/12/2023]
Abstract
Endothelial dysfunction is prominent in atherosclerosis, hypertension, diabetes, peripheral and cardiovascular diseases, and stroke. Novel therapeutic approaches to these conditions often involve development of tissue-engineered veins with ex vivo expanded endothelial cells. However, high cell number requirements limit these approaches to become applicable to clinical applications and highlight the requirement of technologies that accelerate expansion of vascular-forming cells. We have previously shown that novel small molecules could induce hematopoietic stem cell expansion ex vivo. We hypothesized that various small molecules targeting hematopoietic stem cell quiescence and mobilization could be used to induce endothelial cell expansion and angiogenesis due to common origin and shared characteristics of endothelial and hematopoietic cells. Here, we have screened thirty-five small molecules and found that CASIN and AMD3100 increase endothelial cell expansion up to two-fold and induce tube formation and ex vivo sprouting. In addition, we have studied how CASIN and AMD3100 affect cell migration, apoptosis and cell cycle of endothelial cells. CASIN and AMD3100 upregulate key endothelial marker genes and downregulate a number of cyclin dependent kinase inhibitors. These findings suggest that CASIN and AMD3100 could be further tested in the development of artificial vascular systems and vascular gene editing technologies. Furthermore, these findings may have potential to contribute to the development of alternative treatment methods for diseases that cause endothelial damage.
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Affiliation(s)
- Batuhan Mert Kalkan
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey; Koc University, Istanbul, Turkey
| | - Sezer Akgol
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Deniz Ak
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey; Middle East Technical University, Ankara, Turkey
| | - Dogacan Yucel
- Faculty of Medicine, University of Minnesota, MN, USA
| | - Gulen Guney Esken
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Fatih Kocabas
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey.
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13
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Aksoz M, Albayrak E, Aslan GS, Turan RD, Alyazici LY, Siyah P, Tuysuz EC, Canikyan S, Yucel D, Meric N, Gulbas Z, Sahin F, Kocabas F. c-Myc Inhibitor 10074-G5 Induces Murine and Human Hematopoietic Stem and Progenitor Cell Expansion and HDR Modulator Rad51 Expression. Curr Cancer Drug Targets 2019; 19:479-494. [DOI: 10.2174/1568009618666180905100608] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 04/24/2018] [Accepted: 08/25/2018] [Indexed: 12/29/2022]
Abstract
Background:c-Myc plays a major role in the maintenance of glycolytic metabolism and hematopoietic stem cell (HSC) quiescence.Objective:Targeting modulators of HSC quiescence and metabolism could lead to HSC cell cycle entry with concomitant expansion.Methods and Results:Here we show that c-Myc inhibitor 10074-G5 treatment leads to 2-fold increase in murine LSKCD34low HSC compartment post 7 days. In addition, c-Myc inhibition increases CD34+ and CD133+ human HSC number. c-Myc inhibition leads to downregulation of glycolytic and cyclindependent kinase inhibitor (CDKI) gene expression ex vivo and in vivo. In addition, c-Myc inhibition upregulates major HDR modulator Rad51 expression in hematopoietic cells. Besides, c-Myc inhibition does not alter proliferation kinetics of endothelial cells, fibroblasts or adipose-derived mesenchymal stem cells, however, it limits bone marrow derived mesenchymal stem cell proliferation. We further demonstrate that a cocktail of c-Myc inhibitor 10074-G5 along with tauroursodeoxycholic acid (TUDCA) and i-NOS inhibitor L-NIL provides a robust HSC maintenance and expansion ex vivo as evident by induction of all stem cell antigens analyzed. Intriguingly, the cocktail of c-Myc inhibitor 10074-G5, TUDCA and L-NIL improves HDR related gene expression.Conclusion:These findings provide tools to improve ex vivo HSC maintenance and expansion, autologous HSC transplantation and gene editing through modulation of HSC glycolytic and HDR pathways.
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Affiliation(s)
- Merve Aksoz
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Esra Albayrak
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Galip Servet Aslan
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Raife Dilek Turan
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Lamia Yazgi Alyazici
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Pınar Siyah
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Emre Can Tuysuz
- Biotechnology Program, Graduate School of Natural and Applied Sciences, Yeditepe University, 34755, Istanbul, Turkey
| | - Serli Canikyan
- Onkim Stem Cell Technologies, Istanbul Technical University - KOSGEB, Istanbul, Turkey
| | - Dogacan Yucel
- Faculty of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Neslihan Meric
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Zafer Gulbas
- Bone Marrow Transplantation Center, Anadolu Medical Center, Kocaeli, Turkey
| | - Fikrettin Sahin
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Fatih Kocabas
- Regenerative Biology Research Laboratory, Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
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Kocabas F, Eren SN, Uslu M, Yuksel MY. P69Identification of cardiogenic and hematopoietic MEIS Inhibitors. Cardiovasc Res 2018. [DOI: 10.1093/cvr/cvy060.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- F Kocabas
- Yeditepe University Hospital, Genetics and Bioengineering, Istanbul, Turkey
| | - S N Eren
- Yeditepe University Hospital, Genetics and Bioengineering, Istanbul, Turkey
| | - M Uslu
- Yeditepe University Hospital, Genetics and Bioengineering, Istanbul, Turkey
| | - M Y Yuksel
- Yeditepe University Hospital, Genetics and Bioengineering, Istanbul, Turkey
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15
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Aksoz M, Turan RD, Albayrak E, Kocabas F. Emerging Roles of Meis1 in Cardiac Regeneration, Stem Cells and Cancer. Curr Drug Targets 2018; 19:181-190. [DOI: 10.2174/1389450118666170724165514] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 06/14/2017] [Accepted: 07/13/2017] [Indexed: 11/22/2022]
Affiliation(s)
- Merve Aksoz
- Department of Genetics and Bioengineering, Regenerative Biology Research Laboratory, Faculty of Engineering, Yeditepe University, Istanbul 34755, Turkey
| | - Raife Dilek Turan
- Department of Genetics and Bioengineering, Regenerative Biology Research Laboratory, Faculty of Engineering, Yeditepe University, Istanbul 34755, Turkey
| | - Esra Albayrak
- Department of Genetics and Bioengineering, Regenerative Biology Research Laboratory, Faculty of Engineering, Yeditepe University, Istanbul 34755, Turkey
| | - Fatih Kocabas
- Department of Genetics and Bioengineering, Regenerative Biology Research Laboratory, Faculty of Engineering, Yeditepe University, Istanbul 34755, Turkey
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16
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Yucel D, Kocabas F. Developments in Hematopoietic Stem Cell Expansion and Gene Editing Technologies. Advances in Experimental Medicine and Biology 2017; 1079:103-125. [DOI: 10.1007/5584_2017_114] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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17
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Rimmelé P, Liang R, Bigarella CL, Kocabas F, Xie J, Serasinghe MN, Chipuk J, Sadek H, Zhang CC, Ghaffari S. Mitochondrial metabolism in hematopoietic stem cells requires functional FOXO3. EMBO Rep 2015. [PMID: 26209246 DOI: 10.15252/embr.201439704] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hematopoietic stem cells (HSC) are primarily dormant but have the potential to become highly active on demand to reconstitute blood. This requires a swift metabolic switch from glycolysis to mitochondrial oxidative phosphorylation. Maintenance of low levels of reactive oxygen species (ROS), a by-product of mitochondrial metabolism, is also necessary for sustaining HSC dormancy. Little is known about mechanisms that integrate energy metabolism with hematopoietic stem cell homeostasis. Here, we identify the transcription factor FOXO3 as a new regulator of metabolic adaptation of HSC. ROS are elevated in Foxo3(-/-) HSC that are defective in their activity. We show that Foxo3(-/-) HSC are impaired in mitochondrial metabolism independent of ROS levels. These defects are associated with altered expression of mitochondrial/metabolic genes in Foxo3(-/-) hematopoietic stem and progenitor cells (HSPC). We further show that defects of Foxo3(-/-) HSC long-term repopulation activity are independent of ROS or mTOR signaling. Our results point to FOXO3 as a potential node that couples mitochondrial metabolism with HSC homeostasis. These findings have critical implications for mechanisms that promote malignant transformation and aging of blood stem and progenitor cells.
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Affiliation(s)
- Pauline Rimmelé
- Department of Developmental & Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raymond Liang
- Department of Developmental & Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA Developmental and Stem Cell Biology Multidisciplinary Training Area, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carolina L Bigarella
- Department of Developmental & Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fatih Kocabas
- Division of Cardiology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Jingjing Xie
- Division of Cardiology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Madhavika N Serasinghe
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jerry Chipuk
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hesham Sadek
- Division of Cardiology, UT Southwestern Medical Center, Dallas, TX, USA Department of Physiology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Cheng Cheng Zhang
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Saghi Ghaffari
- Department of Developmental & Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA Developmental and Stem Cell Biology Multidisciplinary Training Area, Icahn School of Medicine at Mount Sinai, New York, NY, USA Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA Division of Hematology, Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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18
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Kocabas F, Xie L, Xie J, Yu Z, DeBerardinis RJ, Kimura W, Thet S, Elshamy AF, Abouellail H, Muralidhar S, Liu X, Chen C, Sadek HA, Zhang CC, Zheng J. Hypoxic metabolism in human hematopoietic stem cells. Cell Biosci 2015. [PMID: 26221532 PMCID: PMC4517642 DOI: 10.1186/s13578-015-0020-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Background Adult hematopoietic stem cells (HSCs) are maintained in a microenvironment, known as niche in the endosteal regions of the bone marrow. This stem cell niche with low oxygen tension requires HSCs to adopt a unique metabolic profile. We have recently demonstrated that mouse long-term hematopoietic stem cells (LT-HSCs) utilize glycolysis instead of mitochondrial oxidative phosphorylation as their main energy source. However, the metabolic phenotype of human hematopoietic progenitor and stem cells (HPSCs) remains unknown. Results We show that HPSCs have a similar metabolic phenotype, as shown by high rates of glycolysis, and low rates of oxygen consumption. Fractionation of human mobilized peripheral blood cells based on their metabolic footprint shows that cells with a low mitochondrial potential are highly enriched for HPSCs. Remarkably, low MP cells had much better repopulation ability as compared to high MP cells. Moreover, similar to their murine counterparts, we show that Hif-1α is upregulated in human HPSCs, where it is transcriptionally regulated by Meis1. Finally, we show that Meis1 and its cofactors Pbx1 and HoxA9 play an important role in transcriptional activation of Hif-1α in a cooperative manner. Conclusions These findings highlight the unique metabolic properties of human HPSCs and the transcriptional network that regulates their metabolic phenotype. Electronic supplementary material The online version of this article (doi:10.1186/s13578-015-0020-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fatih Kocabas
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center at Dallas, Dallas, TX 75390 USA.,Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, 34755 Turkey
| | - Li Xie
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital / Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China.,Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Chongqing South Road 280, Shanghai, 200025 China
| | - Jingjing Xie
- Bingzhou Medical University, Taishan Scholar Program, Yantai, 264003 China
| | - Zhuo Yu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital / Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China.,Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Chongqing South Road 280, Shanghai, 200025 China
| | - Ralph J DeBerardinis
- Departments of Pediatrics and Genetics, UT Southwestern Medical Center at Dallas, Dallas, TX 75390 USA
| | - Wataru Kimura
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center at Dallas, Dallas, TX 75390 USA
| | - SuWannee Thet
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center at Dallas, Dallas, TX 75390 USA
| | - Ahmed F Elshamy
- Department of Clinical Pathology, El Galaa Hospital, Cairo, Egypt
| | | | - Shalini Muralidhar
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center at Dallas, Dallas, TX 75390 USA
| | - Xiaoye Liu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Chongqing South Road 280, Shanghai, 200025 China
| | - Chiqi Chen
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital / Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China
| | - Hesham A Sadek
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center at Dallas, Dallas, TX 75390 USA
| | - Cheng Cheng Zhang
- Departments of Physiology and Developmental Biology, UT Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390 USA
| | - Junke Zheng
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital / Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025 China.,Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Chongqing South Road 280, Shanghai, 200025 China
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19
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Abstract
Crimean-Congo hemorrhagic fever virus (CCHFV) is a deadly virus that has been listed in the Category C as a potential bioterror agent. There are no specific therapies against CCHFV, which urges identification of potential therapeutic targets and development of CCHFV therapies. CCHFV OTU protease takes an important role in viral invasion through antagonizing NF-κB signaling. Inhibition of CCHFV OTU protease by small molecules warrants an exciting potential as antiviral therapeutics. Here we report the expression and purification of a C-His-tagged recombinant CCHFV OTU protease in E. coli BL21 (DE3) host strain. Activity of the refolded purified recombinant viral OTU protease has been validated with a UB-AMC fluorescent assay. In addition, we show a dose-dependent inhibition of the viral OTU protease by two small molecules. This study provides a reliable approach for recombinant expression and purification of CCHFV OTU protease, and demonstrates validation of OTU protease activity and its inhibition based on a UB-AMC florescent assay.
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Affiliation(s)
- Fatih Kocabas
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, 34755, Turkey. .,Department of Education, North American University, Houston, TX, 77038, USA.
| | - Galip S Aslan
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, 34755, Turkey
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20
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Abstract
An important feature of stem cells is their maintenance in their respective hypoxic niche. Survival in this low-oxygen microenvironment requires significant metabolic adaptation. We demonstrated that mouse HSCs utilize glycolysis instead of mitochondrial oxidative phosphorylation to meet their energy demands. We have adapted various tools for characterization of the metabolic properties of hematopoietic stem cells (HSCs). These techniques include flow cytometric profiling of HSCs based on mitochondrial potential and NADH fluorescence as well as measurement of ATP content, oxygen consumption rate, and glycolytic flux in purified HSCs.
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Affiliation(s)
- Fatih Kocabas
- Department of Education, and Texas Institute of Biotechnology, Education and Research, North American University, 3203 N. Sam Houston Pkwy W, Houston, TX, 77038, USA,
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21
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Abstract
There is an outmost need for the identification of specific antiviral compounds. Current antivirals lack specificity, making them susceptible to off-target effects, and highlighting importance of development of assays to discover antivirals targeting viral specific proteins. Previous studies for identification of inhibitors of RNA-dependent RNA polymerase (RdRp) mostly relied on radioactive methods. This study describes a fluorometric approach to assess in vitro activity of viral RdRp for drug screening. Using readily available DNA- and RNA-specific fluorophores, we determined an optimum fluorometric approach that could be used in antiviral discovery specifically for RNA viruses by targeting RdRp. Here, we show that double-stranded RNA could be successfully distinguished from single-stranded RNA. In addition, we provide a strategy based on self-priming RNA to assess RdRp activity.
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Affiliation(s)
- Fatih Kocabas
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, 34755, Istanbul, Turkey,
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22
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Boztas AO, Karakuzu O, Galante G, Ugur Z, Kocabas F, Altuntas CZ, Yazaydin AO. Synergistic Interaction of Paclitaxel and Curcumin with Cyclodextrin Polymer Complexation in Human Cancer Cells. Mol Pharm 2013; 10:2676-83. [DOI: 10.1021/mp400101k] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ali O. Boztas
- Texas Institute of Biotechnology Education and Research, 10555 Stella
Link Road, Houston, Texas, 77025, United States
- Department of Chemical Engineering, University of Surrey, Guildford, GU2 7XH, United Kingdom
| | - Ozgur Karakuzu
- Texas Institute of Biotechnology Education and Research, 10555 Stella
Link Road, Houston, Texas, 77025, United States
| | - Gabriela Galante
- Texas Institute of Biotechnology Education and Research, 10555 Stella
Link Road, Houston, Texas, 77025, United States
| | - Zafer Ugur
- Texas Institute of Biotechnology Education and Research, 10555 Stella
Link Road, Houston, Texas, 77025, United States
| | - Fatih Kocabas
- Texas Institute of Biotechnology Education and Research, 10555 Stella
Link Road, Houston, Texas, 77025, United States
| | - Cengiz Z. Altuntas
- Texas Institute of Biotechnology Education and Research, 10555 Stella
Link Road, Houston, Texas, 77025, United States
| | - A. Ozgur Yazaydin
- Department of Chemical Engineering, University of Surrey, Guildford, GU2 7XH, United Kingdom
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23
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Shih SM, Engel BD, Kocabas F, Bilyard T, Gennerich A, Marshall WF, Yildiz A. Intraflagellar transport drives flagellar surface motility. eLife 2013; 2:e00744. [PMID: 23795295 PMCID: PMC3679542 DOI: 10.7554/elife.00744] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 04/30/2013] [Indexed: 11/23/2022] Open
Abstract
The assembly and maintenance of all cilia and flagella require intraflagellar transport (IFT) along the axoneme. IFT has been implicated in sensory and motile ciliary functions, but the mechanisms of this relationship remain unclear. Here, we used Chlamydomonas flagellar surface motility (FSM) as a model to test whether IFT provides force for gliding of cells across solid surfaces. We show that IFT trains are coupled to flagellar membrane glycoproteins (FMGs) in a Ca2+-dependent manner. IFT trains transiently pause through surface adhesion of their FMG cargos, and dynein-1b motors pull the cell towards the distal tip of the axoneme. Each train is transported by at least four motors, with only one type of motor active at a time. Our results demonstrate the mechanism of Chlamydomonas gliding motility and suggest that IFT plays a major role in adhesion-induced ciliary signaling pathways. DOI:http://dx.doi.org/10.7554/eLife.00744.001 Cilia and flagella protrude like bristles from the cell surface. They share the same basic ‘9+2’ axoneme structure, being made up of nine microtubule doublets that surround a central pair of singlet microtubules. Flagella are generally involved in cell propulsion, whereas motile cilia help to move fluids over cell surfaces. Maintaining cilia and flagella is a challenge for cells, which must find a way to send new proteins all the way along the axoneme to the site of assembly at the flagellar tip. Cells achieve this via a process called intraflagellar transport, in which proteins are carried back and forth by kinesin and dynein motors along the axonemal doublet microtubules. Intraflagellar transport has been proposed to influence other functions of cilia and flagella, including the propulsion of cells over surfaces. However, the details of these interactions are unclear. Through a combination of biophysical and microscopy approaches, Shih et al. describe the mechanism that the green alga Chalmydomonas uses to power flagellar gliding over surfaces. By tracking single fluorescently tagged molecules, Shih et al. observed that flagellar membrane glycoproteins are carried along the axoneme by the intraflagellar transport machinery. During transport, flagellar membrane glycoproteins transiently adhere to the surface, and dynein motors that were previously engaged in carrying these glycoproteins now transmit force that moves the axonemal microtubules. This process, which is dependent on the concentration of calcium ions in the extracellular environment, generates the force that propels the alga's flagella along the surface. Gliding motility is thought to have been one of the initial driving forces for the evolution of cilia and flagella. How the intricate mechanism of flagellar beat motility could have evolved has been the subject of much discussion, as it would require the flagellum to have evolved first. In demonstrating that gliding motility is powered by the same intraflagellar transport mechanism that is required for flagellar assembly, Shih et al. provide strong evidence for the evolution of primitive flagella before the evolution of flagellar beating. Furthermore, since algal flagella have essentially the same structure as the cilia of human cells, these findings could ultimately aid in the development of treatments for diseases that result from defects in intraflagellar transport, including polycystic kidney disease and retinal degeneration. DOI:http://dx.doi.org/10.7554/eLife.00744.002
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Affiliation(s)
- Sheng Min Shih
- Department of Physics , University of California, Berkeley , Berkeley , United States
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24
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Mahmoud AI, Kocabas F, Muralidhar SA, Kimura W, Koura AS, Thet S, Porrello ER, Sadek HA. Meis1 regulates postnatal cardiomyocyte cell cycle arrest. Nature 2013; 497:249-253. [PMID: 23594737 DOI: 10.1038/nature12054] [Citation(s) in RCA: 403] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Accepted: 03/04/2013] [Indexed: 12/11/2022]
Abstract
The neonatal mammalian heart is capable of substantial regeneration following injury through cardiomyocyte proliferation. However, this regenerative capacity is lost by postnatal day 7 and the mechanisms of cardiomyocyte cell cycle arrest remain unclear. The homeodomain transcription factor Meis1 is required for normal cardiac development but its role in cardiomyocytes is unknown. Here we identify Meis1 as a critical regulator of the cardiomyocyte cell cycle. Meis1 deletion in mouse cardiomyocytes was sufficient for extension of the postnatal proliferative window of cardiomyocytes, and for re-activation of cardiomyocyte mitosis in the adult heart with no deleterious effect on cardiac function. In contrast, overexpression of Meis1 in cardiomyocytes decreased neonatal myocyte proliferation and inhibited neonatal heart regeneration. Finally, we show that Meis1 is required for transcriptional activation of the synergistic CDK inhibitors p15, p16 and p21. These results identify Meis1 as a critical transcriptional regulator of cardiomyocyte proliferation and a potential therapeutic target for heart regeneration.
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Affiliation(s)
- Ahmed I Mahmoud
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Fatih Kocabas
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Shalini A Muralidhar
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Wataru Kimura
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Ahmed S Koura
- School of Medicine, Ain Shams University, Cairo, 1156, Egypt
| | - Suwannee Thet
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Enzo R Porrello
- School of Biomedical Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Hesham A Sadek
- Department of Internal Medicine, Division of Cardiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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Kocabas F, Mahmoud AI, Muralidhar S, Porrello E, Olson E, Sadek HA. Abstract 64: Meis1 Is a Key Regulator of Postnatal Cardiomyocyte Cell Cycle Arrest. Circ Res 2012. [DOI: 10.1161/res.111.suppl_1.a64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Heart failure is a costly and deadly disease affecting over 5 million Americans. The inability of the adult mammalian heart to regenerate following injury lies at core of the pathophysiology of heart failure. We recently showed that the neonatal mammalian heart is capable of complete regeneration following resection of the entire ventricular apex. Moreover, our preliminary data indicate that the neonatal mouse heart is also capable of complete regeneration following ischemic myocardial infarction. In both these types of injury, the regenerative response is associated with robust proliferation of cardiomyocytes without significant hypertrophy or fibrosis. Genetic fate mapping studies demonstrated that the majority of newly formed cardiomyocytes originated from pre-existing cardiomyocytes. In an effort to determine the mechanism of cardiomyocytes cell cycle arrest after the first week of life, we performed a gene array after cardiac injury at multiple post-natal timepoints. This enabled us to identify Meis1 as a potential regulator of neonatal cardiomyocyte proliferation. Meis1, which belongs to the TALE family of homeodomain transcription factors, is required for normal hematopoiesis and cardiac development. While Meis1 has been extensively studied in the hematopoietic system, little is known about its role in the heart. Our results indicate that Meis1 expression and nuclear localization in the post-natal cardiomyocytes coincides with cell cycle arrest. To further explore this pattern, we generated a cardiomyocyte-specific Meis1 knockout mouse, and showed that loss of Meis1 results in robust cardiomyocyte proliferation in the adult heart. Moreover, we identified p16 and p21; two synergistic cyclin dependent kinase inhibitors that induce arrest at all three cell cycle checkpoints, as potential targets for transcriptional activation by Meis1. These results identify Meis1 as a key regulator of post-natal cardiomyocyte cell cycle arrest, and a potential therapeutic target for cardiac regeneration.
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Affiliation(s)
| | | | | | | | - Eric Olson
- UT Southwestern Med Cntr at Dallas, Dallas, TX
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Kocabas F, Mahmoud AI, Sosic D, Porrello ER, Chen R, Garcia JA, DeBerardinis RJ, Sadek HA. The hypoxic epicardial and subepicardial microenvironment. J Cardiovasc Transl Res 2012; 5:654-65. [PMID: 22566269 DOI: 10.1007/s12265-012-9366-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 04/12/2012] [Indexed: 12/15/2022]
Abstract
Recent reports indicate that the adult mammalian heart is capable of limited, but measurable, cardiomyocyte turnover. While the lineage origin of the newly formed cardiomyocytes is not entirely understood, mounting evidence suggest that the epicardium and subepicardium may represent an important source of cardiac stem or progenitor cells. Stem cell niches are characterized by low oxygen tension, where stem cells preferentially utilize cytoplasmic glycolysis to meet their energy demands. However, it is unclear if the heart harbors similar hypoxic regions, or whether these regions house metabolically distinct cardiac progenitor populations. Here we identify the epicardium and subepicardium as the cardiac hypoxic niche based on [corrected] capillary density quantification, and localization of Hif-1α in the uninjured heart. We further demonstrate that this hypoxic microenvironment houses a metabolically distinct population of glycolytic progenitor cells. Finally, we show that Hif-1α regulates the glycolytic phenotype and progenitor properties of these cells. These findings highlight important anatomical and functional properties of the epicardial and subepicardial microenvironment, and the potential role of hypoxia signaling in regulation of cardiac progenitors.
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Affiliation(s)
- Fatih Kocabas
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas, TX, USA
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Simsek T, Kocabas F, Zheng J, Deberardinis RJ, Mahmoud AI, Olson EN, Schneider JW, Zhang CC, Sadek HA. The distinct metabolic profile of hematopoietic stem cells reflects their location in a hypoxic niche. Cell Stem Cell 2010; 7:380-90. [PMID: 20804973 DOI: 10.1016/j.stem.2010.07.011] [Citation(s) in RCA: 788] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Revised: 05/24/2010] [Accepted: 07/14/2010] [Indexed: 12/15/2022]
Abstract
Bone marrow transplantation is the primary therapy for numerous hematopoietic disorders. The efficiency of bone marrow transplantation depends on the function of long-term hematopoietic stem cells (LT-HSCs), which is markedly influenced by their hypoxic niche. Survival in this low-oxygen microenvironment requires significant metabolic adaptation. Here, we show that LT-HSCs utilize glycolysis instead of mitochondrial oxidative phosphorylation to meet their energy demands. We used flow cytometry to identify a unique low mitochondrial activity/glycolysis-dependent subpopulation that houses the majority of hematopoietic progenitors and LT-HSCs. Finally, we demonstrate that Meis1 and Hif-1alpha are markedly enriched in LT-HSCs and that Meis1 regulates HSC metabolism through transcriptional activation of Hif-1alpha. These findings reveal an important transcriptional network that regulates HSC metabolism.
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Affiliation(s)
- Tugba Simsek
- Department of Internal Medicine, Division of Cardiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
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Yildiz A, Shih S, Kocabas F. High Precision Tracking of Intracellular Transport with Fluorescent Nanoparticles. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.1084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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