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Castilho RM, Castilho LS, Palomares BH, Squarize CH. Determinants of Chromatin Organization in Aging and Cancer-Emerging Opportunities for Epigenetic Therapies and AI Technology. Genes (Basel) 2024; 15:710. [PMID: 38927646 PMCID: PMC11202709 DOI: 10.3390/genes15060710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/21/2024] [Accepted: 05/26/2024] [Indexed: 06/28/2024] Open
Abstract
This review article critically examines the pivotal role of chromatin organization in gene regulation, cellular differentiation, disease progression and aging. It explores the dynamic between the euchromatin and heterochromatin, coded by a complex array of histone modifications that orchestrate essential cellular processes. We discuss the pathological impacts of chromatin state misregulation, particularly in cancer and accelerated aging conditions such as progeroid syndromes, and highlight the innovative role of epigenetic therapies and artificial intelligence (AI) in comprehending and harnessing the histone code toward personalized medicine. In the context of aging, this review explores the use of AI and advanced machine learning (ML) algorithms to parse vast biological datasets, leading to the development of predictive models for epigenetic modifications and providing a framework for understanding complex regulatory mechanisms, such as those governing cell identity genes. It supports innovative platforms like CEFCIG for high-accuracy predictions and tools like GridGO for tailored ChIP-Seq analysis, which are vital for deciphering the epigenetic landscape. The review also casts a vision on the prospects of AI and ML in oncology, particularly in the personalization of cancer therapy, including early diagnostics and treatment optimization for diseases like head and neck and colorectal cancers by harnessing computational methods, AI advancements and integrated clinical data for a transformative impact on healthcare outcomes.
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Affiliation(s)
- Rogerio M. Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109-1078, USA
| | - Leonard S. Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
| | - Bruna H. Palomares
- Oral Diagnosis Department, Piracicaba School of Dentistry, State University of Campinas, Piracicaba 13414-903, Sao Paulo, Brazil;
| | - Cristiane H. Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, School of Dentistry, University of Michigan, Ann Arbor, MI 48109-1078, USA; (L.S.C.); (C.H.S.)
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109-1078, USA
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Pennarossa G, Arcuri S, Gandolfi F, Brevini TAL. Generation of Artificial Blastoids Combining miR-200-Mediated Reprogramming and Mechanical Cues. Cells 2024; 13:628. [PMID: 38607067 PMCID: PMC11011911 DOI: 10.3390/cells13070628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/29/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024] Open
Abstract
In vitro-generated blastocyst-like structures are of great importance since they recapitulate specific features or processes of early embryogenesis, thus avoiding ethical concerns as well as increasing scalability and accessibility compared to the use of natural embryos. Here, we combine cell reprogramming and mechanical stimuli to create 3D spherical aggregates that are phenotypically similar to those of natural embryos. Specifically, dermal fibroblasts are reprogrammed, exploiting the miR-200 family property to induce a high plasticity state in somatic cells. Subsequently, miR-200-reprogrammed cells are either driven towards the trophectoderm (TR) lineage using an ad hoc induction protocol or encapsulated into polytetrafluoroethylene micro-bioreactors to maintain and promote pluripotency, generating inner cell mass (ICM)-like spheroids. The obtained TR-like cells and ICM-like spheroids are then co-cultured in the same micro-bioreactor and, subsequently, transferred to microwells to encourage blastoid formation. Notably, the above protocol was applied to fibroblasts obtained from young as well as aged donors, with results that highlighted miR-200's ability to successfully reprogram young and aged cells with comparable blastoid rates, regardless of the donor's cell age. Overall, the approach here described represents a novel strategy for the creation of artificial blastoids to be used in the field of assisted reproduction technologies for the study of peri- and early post-implantation mechanisms.
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Affiliation(s)
- Georgia Pennarossa
- Laboratory of Biomedical Embryology and Tissue Engineering, Department of Health, Animal Science and Food Safety and Center for Stem Cell Research, Università degli Studi di Milano, 20133 Milan, Italy;
| | - Sharon Arcuri
- Laboratory of Biomedical Embryology and Tissue Engineering, Department of Health, Animal Science and Food Safety and Center for Stem Cell Research, Università degli Studi di Milano, 20133 Milan, Italy;
| | - Fulvio Gandolfi
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, Università degli Studi di Milano, 20133 Milan, Italy;
| | - Tiziana A. L. Brevini
- Laboratory of Biomedical Embryology and Tissue Engineering, Department of Health, Animal Science and Food Safety and Center for Stem Cell Research, Università degli Studi di Milano, 20133 Milan, Italy;
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Teale MA, Schneider S, Eibl D, van den Bos C, Neubauer P, Eibl R. Mesenchymal and induced pluripotent stem cell-based therapeutics: a comparison. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12583-4. [PMID: 37246986 DOI: 10.1007/s00253-023-12583-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/07/2023] [Accepted: 05/08/2023] [Indexed: 05/30/2023]
Abstract
Stem cell-based cell therapeutics and especially those based on human mesenchymal stem cells (hMSCs) and induced pluripotent stem cells (hiPSCs) are said to have enormous developmental potential in the coming years. Their applications range from the treatment of orthopedic disorders and cardiovascular diseases to autoimmune diseases and even cancer. However, while more than 27 hMSC-derived therapeutics are currently commercially available, hiPSC-based therapeutics have yet to complete the regulatory approval process. Based on a review of the current commercially available hMSC-derived therapeutic products and upcoming hiPSC-derived products in phase 2 and 3, this paper compares the cell therapy manufacturing process between these two cell types. Moreover, the similarities as well as differences are highlighted and the resulting impact on the production process discussed. Here, emphasis is placed on (i) hMSC and hiPSC characteristics, safety, and ethical aspects, (ii) their morphology and process requirements, as well as (iii) their 2- and 3-dimensional cultivations in dependence of the applied culture medium and process mode. In doing so, also downstream processing aspects are covered and the role of single-use technology is discussed. KEY POINTS: • Mesenchymal and induced pluripotent stem cells exhibit distinct behaviors during cultivation • Single-use stirred bioreactor systems are preferred for the cultivation of both cell types • Future research should adapt and modify downstream processes to available single-use devices.
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Affiliation(s)
- Misha A Teale
- Centre for Biochemical Engineering and Cell Cultivation Techniques, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Grüentalstrasse 14, 8820, Wädenswil, Switzerland.
| | - Samuel Schneider
- Centre for Biochemical Engineering and Cell Cultivation Techniques, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Grüentalstrasse 14, 8820, Wädenswil, Switzerland
| | - Dieter Eibl
- Centre for Biochemical Engineering and Cell Cultivation Techniques, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Grüentalstrasse 14, 8820, Wädenswil, Switzerland
| | | | - Peter Neubauer
- Institute of Biotechnology, Chair of Bioprocess Engineering, Technical University of Berlin, ACK24, Ackerstraße 76, 13355, Berlin, Germany
| | - Regine Eibl
- Centre for Biochemical Engineering and Cell Cultivation Techniques, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Grüentalstrasse 14, 8820, Wädenswil, Switzerland
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4
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Pennarossa G, Arcuri S, De Iorio T, Ledda S, Gandolfi F, Brevini TAL. Combination of epigenetic erasing and mechanical cues to generate human epiBlastoids from adult dermal fibroblasts. J Assist Reprod Genet 2023; 40:1015-1027. [PMID: 36933093 PMCID: PMC10024007 DOI: 10.1007/s10815-023-02773-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/09/2023] [Indexed: 03/19/2023] Open
Abstract
PURPOSE This study is to develop a new protocol that combines the use of epigenetic cues and mechanical stimuli to assemble 3D spherical structures, arbitrarily defined "epiBlastoids," whose phenotype is remarkably similar to natural embryos. METHODS A 3-step approach is used to generate epiBlastoids. In the first step, adult dermal fibroblasts are converted into trophoblast (TR)-like cells, combining the use of 5-azacytidine, to erase the original phenotype, with an ad hoc induction protocol, to drive cells towards TR lineage. In the second step, epigenetic erasing is applied once again, in combination with mechanosensing-related cues, to generate inner cell mass (ICM)-like organoids. Specifically, erased cells are encapsulated into micro-bioreactors to promote 3D cell rearrangement and boost pluripotency. In the third step, TR-like cells are co-cultured with ICM-like spheroids in the same micro-bioreactors. Subsequently, the newly generated embryoids are transferred to microwells to favor epiBlastoid formation. RESULTS Adult dermal fibroblasts are successfully readdressed towards TR lineage. Cells subjected to epigenetic erasing and encapsulated into micro-bioreactors rearrange in 3D ICM-like structures. Co-culture of TR-like cells and ICM-like spheroids into micro-bioreactors and microwells induces the formation of single structures with uniform shape reminiscent in vivo embryos. CDX2+ cells localized in the out layer of the spheroids, while OCT4+ cells in the inner of the structures. TROP2+ cells display YAP nuclear accumulation and actively transcribed for mature TR markers, while TROP2- cells showed YAP cytoplasmic compartmentalization and expressed pluripotency-related genes. CONCLUSION We describe the generation of epiBlastoids that may find useful application in the assisted reproduction field.
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Affiliation(s)
- Georgia Pennarossa
- Department of Veterinary Medicine and Animal Science, Center for Stem Cell Research, Laboratory of Biomedical Embryology and Tissue Engineering, Università Degli Studi Di Milano, 26900, Lodi, Italy
| | - Sharon Arcuri
- Department of Veterinary Medicine and Animal Science, Center for Stem Cell Research, Laboratory of Biomedical Embryology and Tissue Engineering, Università Degli Studi Di Milano, 26900, Lodi, Italy
| | - Teresina De Iorio
- Department of Veterinary Medicine and Animal Science, Center for Stem Cell Research, Laboratory of Biomedical Embryology and Tissue Engineering, Università Degli Studi Di Milano, 26900, Lodi, Italy
| | - Sergio Ledda
- Department of Veterinary Medicine, University of Sassari, 07100, Sassari, Italy
| | - Fulvio Gandolfi
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, 20133, Milan, Italy
| | - Tiziana A L Brevini
- Department of Veterinary Medicine and Animal Science, Center for Stem Cell Research, Laboratory of Biomedical Embryology and Tissue Engineering, Università Degli Studi Di Milano, 26900, Lodi, Italy.
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Synergistic Effect of miR-200 and Young Extracellular Matrix-based Bio-scaffolds to Reduce Signs of Aging in Senescent Fibroblasts. Stem Cell Rev Rep 2023; 19:417-429. [PMID: 36029367 PMCID: PMC9418657 DOI: 10.1007/s12015-022-10438-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2022] [Indexed: 02/07/2023]
Abstract
Aging is defined as a complex, multifaceted degenerative process that causes a gradual decline of physiological functions and a rising mortality risk with time. Stopping senescence or even rejuvenating the body represent one of the long-standing human dreams. Somatic cell nuclear transfer as well as cell reprogramming have suggested the possibility to slow or even reverse signs of aging. We exploited miR-200 family ability to induce a transient high plasticity state in human skin fibroblasts isolated from old individuals and we investigated whether this ameliorates cellular and physiological hallmarks of senescence. In addition, based on the assumption that extracellular matrix (ECM) provides biomechanical stimuli directly influencing cell behavior, we examine whether ECM-based bio-scaffolds, obtained from decellularized ovaries of young swine, stably maintain the rejuvenated phenotype acquired by cells after miR-200 exposure. The results show the existence of multiple factors that cooperate to control a unique program, driving the cell clock. In particular, miR-200 family directly regulates the molecular mechanisms erasing cell senescence. However, this effect is transient, reversible, and quickly lost. On the other hand, the use of an adequate young microenvironment stabilizes the miR-200-mediated rejuvenating effects, suggesting that synergistic interactions occur among molecular effectors and ECM-derived biomechanical stimuli. The model here described is a useful tool to better characterize these complex regulations and to finely dissect the multiple and concurring biochemical and biomechanical cues driving the cell biological clock.
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Coleman JRI. Feasibility and application of polygenic score analysis to the morphology of human-induced pluripotent stem cells. Mol Genet Genomics 2022; 297:1111-1122. [PMID: 35633379 PMCID: PMC9250464 DOI: 10.1007/s00438-022-01905-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 05/04/2022] [Indexed: 11/28/2022]
Abstract
Genome-wide association studies have identified thousands of significant associations between genetic variants and complex traits. Inferring biological insights from these associations has been challenging. One approach attempted has been to examine the effects of individual variants in cellular models. Here, I demonstrate the feasibility of examining the aggregate effect of many variants on cellular phenotypes. I examine the effects of polygenic scores for cross-psychiatric disorder risk, schizophrenia, body mass index and height on cellular morphology, using 1.5 million induced pluripotent stem cells (iPSC) from 60 European-ancestry donors from the Human iPSC Initiative dataset. I show that measuring multiple cells per donor provides sufficient power for polygenic score analyses, and that cross-psychiatric disorder risk is associated with cell area (p = 0.004). Combined with emerging methods of high-throughput iPSC phenotyping, cellular polygenic scoring is a promising method for understanding potential biological effects of the polygenic component of complex traits.
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Affiliation(s)
- Jonathan R I Coleman
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience-PO80, King's College London, DeCrespigny Park, Denmark Hill, London, SE5 8AF, UK. .,National Institute for Health and Care Research Maudsley Biomedical Research Centre, South London and Maudsley NHS Foundation Trust, London, UK.
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Hasaart KA, Manders F, Ubels J, Verheul M, van Roosmalen MJ, Groenen NM, Oka R, Kuijk E, Lopes SMCDS, Boxtel RV. Human induced pluripotent stem cells display a similar mutation burden as embryonic pluripotent cells in vivo. iScience 2022; 25:103736. [PMID: 35118356 PMCID: PMC8792070 DOI: 10.1016/j.isci.2022.103736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/03/2021] [Accepted: 01/02/2022] [Indexed: 11/30/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) hold great promise for regenerative medicine, but genetic instability is a major concern. Embryonic pluripotent cells also accumulate mutations during early development, but how this relates to the mutation burden in iPSCs remains unknown. Here, we directly compared the mutation burden of cultured iPSCs with their isogenic embryonic cells during human embryogenesis. We generated developmental lineage trees of human fetuses by phylogenetic inference from somatic mutations in the genomes of multiple stem cells, which were derived from different germ layers. Using this approach, we characterized the mutations acquired pre-gastrulation and found a rate of 1.65 mutations per cell division. When cultured in hypoxic conditions, iPSCs generated from fetal stem cells of the assessed fetuses displayed a similar mutation rate and spectrum. Our results show that iPSCs maintain a genomic integrity during culture at a similar degree as their pluripotent counterparts do in vivo.
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Affiliation(s)
- Karlijn A.L. Hasaart
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Freek Manders
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Joske Ubels
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Mark Verheul
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Markus J. van Roosmalen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Niels M. Groenen
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Rurika Oka
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Ewart Kuijk
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | | | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands
- Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
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Miniaturized droplet microarray platform enables maintenance of human induced pluripotent stem cell pluripotency. Mater Today Bio 2021; 12:100153. [PMID: 34765963 PMCID: PMC8569722 DOI: 10.1016/j.mtbio.2021.100153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/17/2021] [Accepted: 10/23/2021] [Indexed: 11/29/2022] Open
Abstract
The capacity of human induced pluripotent stem cells (hiPSCs) for indefinite self-renewal warrants their application in disease modeling, drug discovery, toxicity assays and efficacy screening. However, their poor proliferation ability, inability to adhere to surfaces without Matrigel coating and tendency to spontaneously differentiate in vitro hinder the application of hiPSCs in these fields. Here we study the ability to culture hiPSCs inside 200 nL droplets on the droplet microarray (DMA) platform. We demonstrate that (1) hiPSCs can attach to the Matrigel (MG)-free surface of DMA and show good viability after 24 h culture; (2) hiPSC do not spontaneously differentiate when cultured on the MG-free surface of DMAs; (3) culturing of hiPSCs in 200 nL as compared to 2 mL culture leads to higher expression of the Nanog pluripotency marker. Overall, the results demonstrate the possibility to culture undifferentiated hiPSCs in 200 nL droplets on DMA, thereby opening the possibility for high-throughput screenings of hiPSCs with various factors without compromising the results through the involvement of animal-derived materials, such as Matrigel.
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Suldina LA, Sorokina AE, Morozova KN. Ultrastructural heterogeneity of the mitochondrial population in rat embryonic and induced pluripotent stem cells. Cell Biol Int 2021; 45:2238-2250. [PMID: 34288224 DOI: 10.1002/cbin.11672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 06/10/2021] [Accepted: 07/03/2021] [Indexed: 11/10/2022]
Abstract
Even though rats are popular model animals, the ultrastructure of their pluripotent cells, that is, embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), remains unexplored, although fine structure of pluripotent stem cells of mice and humans and its changes during differentiation have been investigated well. In the present study, we carried out ultrastructural and morphometric analyses of three lines of rat ESCs and two lines of rat iPSCs. The rat pluripotent stem cells were found to have the main typical morphological features of pluripotent cells: large nuclei of irregular or nearly round shape, scanty cytoplasm with few membrane organelles, and a poorly developed Golgi apparatus and endoplasmic reticulum. The cytoplasm of the rat pluripotent cells contains clusters of glycogen, previously described in human ESCs. To identify possible differences between rat ESCs and iPSCs, we performed a morphometric analysis of cell parameters. The mean area of cells and nuclei, the nuclear/cytoplasmic ratio, distributions of glycogen and diversity of mitochondria showed marked variations among the lines of rat pluripotent stem cells and were more pronounced than variations between rat ESCs and iPSCs as separate types of pluripotent stem cells. We noted morphological heterogeneity of the mitochondrial population in the rat pluripotent stem cells. The cells contained three types of mitochondria differing in the structure of cristae and in matrix density, and our morphometric analysis revealed differences in cristae structure.
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Affiliation(s)
- Lyubov A Suldina
- Department of Molecular Genetics, Cell Biology, and Bioinformatics, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Anastasiya E Sorokina
- Department of Natural Sciences, Specialized Educational Scientific Center of Novosibirsk State University, Novosibirsk, Russia
| | - Ksenia N Morozova
- Department of Molecular Genetics, Cell Biology, and Bioinformatics, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,Department of Сytology and Genetics, Novosibirsk State University, Novosibirsk, Russia
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Arcuri S, Pennarossa G, Gandolfi F, Brevini TAL. Generation of Trophoblast-Like Cells From Hypomethylated Porcine Adult Dermal Fibroblasts. Front Vet Sci 2021; 8:706106. [PMID: 34350230 PMCID: PMC8326560 DOI: 10.3389/fvets.2021.706106] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/25/2021] [Indexed: 11/13/2022] Open
Abstract
The first differentiation event in mammalian embryos is the formation of the trophectoderm, which is the progenitor of the outer epithelial components of the placenta, and which supports the fetus during the intrauterine life. However, the epigenetic and paracrine controls at work in trophectoderm differentiation are still to be fully elucidated and the creation of dedicated in vitro models is desirable to increase our understanding. Here we propose a novel approach based on the epigenetic conversion of adult dermal fibroblasts into trophoblast-like cells. The method combines the use of epigenetic erasing with an ad hoc differentiation protocol. Dermal fibroblasts are erased with 5-azacytidine (5-aza-CR) that confers cells a transient high plasticity state. They are then readdressed toward the trophoblast (TR) phenotype, using MEF conditioned medium, supplemented with bone morphogenetic protein 4 (BMP4) and inhibitors of the Activin/Nodal and FGF2 signaling pathways in low O2 conditions. The method here described allows the generation of TR-like cells from easily accessible material, such as dermal fibroblasts, that are very simply propagated in vitro. Furthermore, the strategy proposed is free of genetic modifications that make cells prone to instability and transformation. The TR model obtained may also find useful application in order to better characterize embryo implantation mechanisms and developmental disorders based on TR defects.
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Affiliation(s)
- Sharon Arcuri
- Laboratory of Biomedical Embryology, Department of Health, Animal Science and Food Safety and Centre for Stem Cell Research, UniStem, Università Degli Studi di Milano, Milan, Italy
| | - Georgia Pennarossa
- Laboratory of Biomedical Embryology, Department of Health, Animal Science and Food Safety and Centre for Stem Cell Research, UniStem, Università Degli Studi di Milano, Milan, Italy
| | - Fulvio Gandolfi
- Laboratory of Biomedical Embryology, Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy and Centre for Stem Cell Research, UniStem, Università Degli Studi di Milano, Milan, Italy
| | - Tiziana A L Brevini
- Laboratory of Biomedical Embryology, Department of Health, Animal Science and Food Safety and Centre for Stem Cell Research, UniStem, Università Degli Studi di Milano, Milan, Italy
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11
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Solomon E, Davis-Anderson K, Hovde B, Micheva-Viteva S, Harris JF, Twary S, Iyer R. Global transcriptome profile of the developmental principles of in vitro iPSC-to-motor neuron differentiation. BMC Mol Cell Biol 2021; 22:13. [PMID: 33602141 PMCID: PMC7893891 DOI: 10.1186/s12860-021-00343-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/11/2021] [Indexed: 12/30/2022] Open
Abstract
Background Human induced pluripotent stem cells (iPSC) have opened new avenues for regenerative medicine. Consequently, iPSC-derived motor neurons have emerged as potentially viable therapies for spinal cord injuries and neurodegenerative disorders including Amyotrophic Lateral Sclerosis. However, direct clinical application of iPSC bears in itself the risk of tumorigenesis and other unforeseeable genetic or epigenetic abnormalities. Results Employing RNA-seq technology, we identified and characterized gene regulatory networks triggered by in vitro chemical reprogramming of iPSC into cells with the molecular features of motor neurons (MNs) whose function in vivo is to innervate effector organs. We present meta-transcriptome signatures of 5 cell types: iPSCs, neural stem cells, motor neuron progenitors, early motor neurons, and mature motor neurons. In strict response to the chemical stimuli, along the MN differentiation axis we observed temporal downregulation of tumor growth factor-β signaling pathway and consistent activation of sonic hedgehog, Wnt/β-catenin, and Notch signaling. Together with gene networks defining neuronal differentiation (neurogenin 2, microtubule-associated protein 2, Pax6, and neuropilin-1), we observed steady accumulation of motor neuron-specific regulatory genes, including Islet-1 and homeobox protein HB9. Interestingly, transcriptome profiling of the differentiation process showed that Ca2+ signaling through cAMP and LPC was downregulated during the conversion of the iPSC to neural stem cells and key regulatory gene activity of the pathway remained inhibited until later stages of motor neuron formation. Pathways shaping the neuronal development and function were well-represented in the early motor neuron cells including, neuroactive ligand-receptor interactions, axon guidance, and the cholinergic synapse formation. A notable hallmark of our in vitro motor neuron maturation in monoculture was the activation of genes encoding G-coupled muscarinic acetylcholine receptors and downregulation of the ionotropic nicotinic acetylcholine receptors expression. We observed the formation of functional neuronal networks as spontaneous oscillations in the extracellular action potentials recorded on multi-electrode array chip after 20 days of differentiation. Conclusions Detailed transcriptome profile of each developmental step from iPSC to motor neuron driven by chemical induction provides the guidelines to novel therapeutic approaches in the re-construction efforts of muscle innervation. Supplementary Information The online version contains supplementary material available at 10.1186/s12860-021-00343-z.
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Affiliation(s)
- Emilia Solomon
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, USA
| | | | - Blake Hovde
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, USA
| | | | | | - Scott Twary
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, USA
| | - Rashi Iyer
- Los Alamos National Laboratory, Analytics, Intelligence, and Technology Division, Los Alamos, NM, USA.
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12
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El-Habashy SE, Eltaher HM, Gaballah A, Zaki EI, Mehanna RA, El-Kamel AH. Hybrid bioactive hydroxyapatite/polycaprolactone nanoparticles for enhanced osteogenesis. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 119:111599. [PMID: 33321643 DOI: 10.1016/j.msec.2020.111599] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/20/2020] [Accepted: 09/23/2020] [Indexed: 02/05/2023]
Abstract
Hydroxyapatite nanoparticles (HApN) are largely employed as osteogenic inorganic material. Inorganic/polymeric hybrid nanostructures can provide versatile bioactivity for superior osteogenicity, particularly as nanoparticles. Herein, we present hybrid biomaterial-based hydroxyapatite/polycaprolactone nanoparticles (HAp/PCL NPs) realized using simple preparation techniques to augment HApN osteogenicity. Using wet chemical precipitation, we optimized HApN crystalline properties utilizing a 23-factorial design. Optimized HApN exhibited typical Ca/P elemental ratio with high reaction yield. Surface area analysis revealed their mesoporous nature and high surface area. Hybrid HAp/PCL NPs prepared using direct emulsification-solvent evaporation maintained HApN crystallinity with no observed chemical interactions. To the best of our knowledge, we are the first to elaborate the biocompatibility and osteogenicity of nanoparticulate hybrid HAp/PCL. Hybrid HAp/PCL NPs outperformed HApN regarding mesenchymal cell proliferation and osteodifferentiation with reduction of possible cytotoxicity. Unlike HApN, hybrid HAp/PCL NPs presented moderate expression of early osteogenic markers, Runx-2 and osteopontin and significantly elevated expression of the late osteogenic marker, bone sialoprotein after 10-day culture. Our results indicate that hybrid bioactive HAp/PCL NPs could offer a more prominent osteogenic potential than plain HApN for bone regenerative applications as a standalone nanoplatform or as part of complex engineered systems.
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Affiliation(s)
- Salma E El-Habashy
- Department of Pharmaceutics, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Hoda M Eltaher
- Department of Pharmaceutics, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Ahmed Gaballah
- Microbiology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Eiman I Zaki
- Histology and Cell Biology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Radwa A Mehanna
- Medical Physiology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt; Center of Excellence for Research in Regenerative Medicine and Applications CERRMA, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Amal H El-Kamel
- Department of Pharmaceutics, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt.
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13
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Pennarossa G, Manzoni EFM, Ledda S, deEguileor M, Gandolfi F, Brevini TAL. Use of a PTFE Micro-Bioreactor to Promote 3D Cell Rearrangement and Maintain High Plasticity in Epigenetically Erased Fibroblasts. Stem Cell Rev Rep 2020; 15:82-92. [PMID: 30397853 DOI: 10.1007/s12015-018-9862-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Phenotype definition is driven by epigenetic mechanisms as well as directly influenced by the cell microenvironment and by biophysical signals deriving from the extracellular matrix. The possibility to interact with the epigenetic signature of an adult mature cell, reversing its differentiated state and inducing a short transient high plasticity window, was previously demonstrated. In parallel, in vitro studies have shown that 3D culture systems, mimicking cell native tissue, exert significant effects on cell behavior and functions. Here we report the production of "PTFE micro-bioreactors" for long-term culture of epigenetically derived high plasticity cells. The system promotes 3D cell rearrangement, global DNA demethylation and elevated transcription of pluripotency markers, that is dependent on WW domain containing transcription regulator 1 (TAZ) nuclear accumulation and SMAD family member 2 (SMAD2) co-shuttling. Our findings demonstrate that the use of 3D culture strategies greatly improves the induction and maintenance of a high plasticity state.
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Affiliation(s)
- Georgia Pennarossa
- Laboratory of Biomedical Embryology, Department of Health, Animal Science and Food Safety, Università degli Studi di Milano, 20133, Milan, Italy
| | - Elena F M Manzoni
- Laboratory of Biomedical Embryology, Department of Health, Animal Science and Food Safety, Università degli Studi di Milano, 20133, Milan, Italy
| | - Sergio Ledda
- Department of Veterinary Medicine, University of Sassari, 07100, Sassari, Italy
| | - Magda deEguileor
- Department of Biotechnology and Life Sciences, Università degli Studi dell'Insubria, 21100, Varese, Italy
| | - Fulvio Gandolfi
- Laboratory of Biomedical Embryology, Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, 20133, Milan, Italy.,Unistem, Centre for Stem Cell Research, Universita' degli Studi di Milano, 20133, Milan, Italy
| | - Tiziana A L Brevini
- Laboratory of Biomedical Embryology, Department of Health, Animal Science and Food Safety, Università degli Studi di Milano, 20133, Milan, Italy. .,Unistem, Centre for Stem Cell Research, Universita' degli Studi di Milano, 20133, Milan, Italy.
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14
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Yoo J, Kim J, Lee JH, Kim H, Jang SJ, Seo HH, Oh ST, Hyeon SJ, Ryu H, Kim J, Moh SH. Acceleration of somatic cell reprogramming into the induced pluripotent stem cell using a mycosporine-like amino acid, Porphyra 334. Sci Rep 2020; 10:3684. [PMID: 32111890 PMCID: PMC7048830 DOI: 10.1038/s41598-020-60680-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 02/13/2020] [Indexed: 11/16/2022] Open
Abstract
Porphyra 334 (P334), a mycosporine-like amino acid (MAA), is a secondary metabolite found in diverse marine and terrestrial organisms and has several beneficial effects on fibroblast proliferation, wound healing, and antioxidant activity. Here, we report that P334 accelerates the cell reprogramming process of mouse tail-tip fibroblasts (TTFs) and human dermal papilla (HDP) cells into induced pluripotent stem cells (iPSCs). We found that P334 significantly improved the cell reprogramming efficiency by activating the tri-methylation of histone 3 lysine 4 (H3K4me3), which controls mesenchymal to epithelial transition (MET) during the reprogramming process. Thus, we found that P334 directly regulates epigenetic changes, providing an efficient approach for natural compound-based cell reprogramming.
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Affiliation(s)
- Junsang Yoo
- Anti-aging Research Institute, BIO-FD&C Co., Ltd, Inchon, 21990, Korea
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul, 02792, Korea
| | - Junyeop Kim
- Department of Biomedical Engineering, Dongguk University, Seoul, 100-715, Korea
| | - Jeong Hun Lee
- Anti-aging Research Institute, BIO-FD&C Co., Ltd, Inchon, 21990, Korea
| | - Hyein Kim
- Anti-aging Research Institute, BIO-FD&C Co., Ltd, Inchon, 21990, Korea
| | - Sung Joo Jang
- Anti-aging Research Institute, BIO-FD&C Co., Ltd, Inchon, 21990, Korea
| | - Hyo Hyun Seo
- Anti-aging Research Institute, BIO-FD&C Co., Ltd, Inchon, 21990, Korea
| | - Seung Taek Oh
- Anti-aging Research Institute, BIO-FD&C Co., Ltd, Inchon, 21990, Korea
| | - Seung Jae Hyeon
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul, 02792, Korea
| | - Hoon Ryu
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul, 02792, Korea
| | - Jongpil Kim
- Department of Biomedical Engineering, Dongguk University, Seoul, 100-715, Korea
| | - Sang Hyun Moh
- Anti-aging Research Institute, BIO-FD&C Co., Ltd, Inchon, 21990, Korea.
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15
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Gain-of-Function Mutant p53: All the Roads Lead to Tumorigenesis. Int J Mol Sci 2019; 20:ijms20246197. [PMID: 31817996 PMCID: PMC6940767 DOI: 10.3390/ijms20246197] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/25/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
The p53 protein is mutated in about 50% of human cancers. Aside from losing the tumor-suppressive functions of the wild-type form, mutant p53 proteins often acquire inherent, novel oncogenic functions, a phenomenon termed mutant p53 gain-of-function (GOF). A growing body of evidence suggests that these pro-oncogenic functions of mutant p53 proteins are mediated by affecting the transcription of various genes, as well as by protein-protein interactions with transcription factors and other effectors. In the current review, we discuss the various GOF effects of mutant p53, and how it may serve as a central node in a network of genes and proteins, which, altogether, promote the tumorigenic process. Finally, we discuss mechanisms by which "Mother Nature" tries to abrogate the pro-oncogenic functions of mutant p53. Thus, we suggest that targeting mutant p53, via its reactivation to the wild-type form, may serve as a promising therapeutic strategy for many cancers that harbor mutant p53. Not only will this strategy abrogate mutant p53 GOF, but it will also restore WT p53 tumor-suppressive functions.
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16
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Gandolfi F, Arcuri S, Pennarossa G, Brevini TAL. New tools for cell reprogramming and conversion: Possible applications to livestock. Anim Reprod 2019; 16:475-484. [PMID: 32435291 PMCID: PMC7234139 DOI: 10.21451/1984-3143-ar2019-0043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Somatic cell nuclear transfer and iPS are both forms of radical cell reprogramming able to transform a fully differentiated cell type into a totipotent or pluripotent cell. Both processes, however, are hampered by low efficiency and, in the case of iPS, the application to livestock species is uncertain. Epigenetic manipulation has recently emerged as an efficient and robust alternative method for cell reprogramming. It is based upon the use of small molecules that are able to modify the levels of DNA methylation with 5-azacitidyne as one of the most widely used. Among a number of advantages, it includes the fact that it can be applied to domestic species including pig, dog and cat. Treated cells undergo a widespread demethylation which is followed by a renewed methylation pattern induced by specific chemical stimuli that lead to the desired phenotype. A detailed study of the mechanisms of epigenetic manipulation revealed that cell plasticity is achieved through the combined action of a reduced DNA methyl transferase activity with an active demethylation driven by the TET protein family. Surprisingly the same combination of molecular processes leads to the transformation of fibroblasts into iPS and regulate the epigenetic changes that take place during early development and, hence, during reprogramming following SCNT. Finally, it has recently emerged that mechanic stimuli in the form of a 3D cell rearrangement can significantly enhance the efficiency of epigenetic reprogramming as well as of maintenance of pluripotency. Interestingly these mechanic stimuli act on the same mechanisms both in epigenetic cell conversion with 5-Aza-CR and in iPS. We suggest that the balanced combination of epigenetic erasing, 3D cell rearrangement and chemical induction can go a long way to obtain ad hoc cell types that can fully exploit the current exiting development brought by gene editing and animal cloning in livestock production.
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Affiliation(s)
- Fulvio Gandolfi
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, University of Milan, Italy
| | - Sharon Arcuri
- Department of Health, Animal Science and Food Safety, University of Milan, Italy
| | - Georgia Pennarossa
- Department of Health, Animal Science and Food Safety, University of Milan, Italy
| | - Tiziana A L Brevini
- Department of Health, Animal Science and Food Safety, University of Milan, Italy
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17
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Directing differentiation of human induced pluripotent stem cells toward androgen-producing Leydig cells rather than adrenal cells. Proc Natl Acad Sci U S A 2019; 116:23274-23283. [PMID: 31591190 DOI: 10.1073/pnas.1908207116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Reduced serum testosterone (T), or hypogonadism, affects millions of men and is associated with many pathologies, including infertility, cardiovascular diseases, metabolic syndrome, and decreased libido and sexual function. Administering T-replacement therapy (TRT) reverses many of the symptoms associated with low T levels. However, TRT is linked to side effects such as infertility and increased risk of prostate cancer and cardiovascular diseases. Thus, there is a need to obtain T-producing cells that could be used to treat hypogonadism via transplantation and reestablishment of T-producing cell lineages in the body. T is synthesized by Leydig cells (LCs), proposed to derive from mesenchymal cells of mesonephric origin. Although mesenchymal cells have been successfully induced into LCs, the limited source and possible trauma to donors hinders their application to clinical therapies. Alternatively, human induced pluripotent stem cells (hiPSCs), which are expandable in culture and have the potential to differentiate into all somatic cell types, have become the emerging source of autologous cell therapies. We have successfully induced the differentiation of hiPSCs into either human Leydig-like (hLLCs) or adrenal-like cells (hALCs) using chemically defined culture conditions. Factors critical for the development of LCs were added to both culture systems. hLLCs expressed all steroidogenic genes and proteins important for T biosynthesis, synthesized T rather than cortisol, secreted steroid hormones in response to dibutyryl-cAMP and 22(R)-hydroxycholesterol, and displayed ultrastructural features resembling LCs. By contrast, hALCs synthesized cortisol rather than T. The success in generating hiPSC-derived hLLCs with broad human LC (hLC) features supports the potential for hiPSC-based hLC regeneration.
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18
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Harkness L, Chen X, Gillard M, Gray PP, Davies AM. Media composition modulates human embryonic stem cell morphology and may influence preferential lineage differentiation potential. PLoS One 2019; 14:e0213678. [PMID: 30889226 PMCID: PMC6424453 DOI: 10.1371/journal.pone.0213678] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/26/2019] [Indexed: 12/22/2022] Open
Abstract
Undifferentiated human embryonic stem cells have a distinct morphology (hESC). Changes in cell morphology during culture can be indicative of differentiation. hESC, maintained in diverse medias, demonstrated alterations in morphological parameters and subsequent alterations in underlying transcript expression and lineage differentiation. Analysis of morphological parameters showed distinct and significant differences between the undefined, less defined and Xeno-free medias while still maintaining pluripotency markers. This suggested that the less defined media may be creating dynamic instability in the cytoskeleton, with the cytoskeleton becoming more stabilised in the Xeno-free media as demonstrated by smaller and rounder cells. Examination of early lineage markers during undirected differentiation using d5 embryoid bodies demonstrated increased mesodermal lineage preference as compared to endodermal or ectoderm in cells originally cultured in Xeno-free media. Undefined media showed preference for mesoderm and ectoderm lineages, while less defined media (BSA present) demonstrated no preference. These data reveal that culture media may produce fundamental changes in cell morphology which are reflected in early lineage differentiation choice.
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Affiliation(s)
- Linda Harkness
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
- * E-mail:
| | - Xiaoli Chen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Marianne Gillard
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Peter Paul Gray
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Anthony Mitchell Davies
- Translational Cell Imaging Queensland, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
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19
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Yoshida K, Okada M, Nagasaka R, Sasaki H, Okada M, Kanie K, Kato R. Time-course colony tracking analysis for evaluating induced pluripotent stem cell culture processes. J Biosci Bioeng 2019; 128:209-217. [PMID: 30738731 DOI: 10.1016/j.jbiosc.2019.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/11/2019] [Accepted: 01/16/2019] [Indexed: 01/15/2023]
Abstract
Increasing the yield and maintaining a high quality of induced pluripotent stem cells (iPSCs) is necessary for manufacturing iPSCs at the industrial scale. However, because iPSCs are delicate, it is important to evaluate their quality during processing. To examine the status of cultured iPSCs non-invasively, morphology-based iPSC colony evaluation may be an efficient technology for cellular status monitoring and analysis. In this study, we examined the effectiveness of time-course colony tracking analysis for evaluating the iPSC culture process. Particularly, we obtained detailed time-course data to evaluate the effect of the pipetting technique on cell dissociation before seeding. Although the pipetting process causes severe shear stress to cells, which affects their quality, these effects have not been quantitatively analyzed because of their complex and uncontrollable parameters. By analyzing the heterogeneity and time-course responses of individual colonies, our colony tracking analysis revealed a critically damaged population caused by pipetting stress which could not be detected in conventional bulk analysis. Moreover, by comprehensively analyzing colony tracking data, which links the time-course morphology and marker staining results with each colony, we found that colony morphology is only highly correlated with the undifferentiated marker in the final stage, with a lower correlation in the early stages. Thus, colony tracking analysis provides a way to quantify cellular morphological information when evaluating complex iPSC manufacturing processes.
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Affiliation(s)
- Kei Yoshida
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Mika Okada
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Risako Nagasaka
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Hiroto Sasaki
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Mai Okada
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kei Kanie
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Ryuji Kato
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya 464-8602, Japan; Stem Cell Evaluation Technology Research Association (SCA), Hacho-bori, Chuou-ku, Tokyo 104-0032, Japan; Institute of Nano-Life-Systems, Institute of Innovation for Future Society, Nagoya University, Division of Micro-Nano Mechatronics, Furocho, Chikusa-ku, Nagoya 464-8602, Japan.
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20
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Koifman G, Shetzer Y, Eizenberger S, Solomon H, Rotkopf R, Molchadsky A, Lonetto G, Goldfinger N, Rotter V. A Mutant p53-Dependent Embryonic Stem Cell Gene Signature Is Associated with Augmented Tumorigenesis of Stem Cells. Cancer Res 2018; 78:5833-5847. [PMID: 30154152 DOI: 10.1158/0008-5472.can-18-0805] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/10/2018] [Accepted: 08/23/2018] [Indexed: 11/16/2022]
Abstract
Mutations in the tumor suppressor p53 are the most frequent alterations in human cancer. These mutations include p53-inactivating mutations as well as oncogenic gain-of-function (GOF) mutations that endow p53 with capabilities to promote tumor progression. A primary challenge in cancer therapy is targeting stemness features and cancer stem cells (CSC) that account for tumor initiation, metastasis, and cancer relapse. Here we show that in vitro cultivation of tumors derived from mutant p53 murine bone marrow mesenchymal stem cells (MSC) gives rise to aggressive tumor lines (TL). These MSC-TLs exhibited CSC features as displayed by their augmented oncogenicity and high expression of CSC markers. Comparative analyses between MSC-TL with their parental mutant p53 MSC allowed for identification of the molecular events underlying their tumorigenic properties, including an embryonic stem cell (ESC) gene signature specifically expressed in MSC-TLs. Knockout of mutant p53 led to a reduction in tumor development and tumorigenic cell frequency, which was accompanied by reduced expression of CSC markers and the ESC MSC-TL signature. In human cancer, MSC-TL ESC signature-derived genes correlated with poor patient survival and were highly expressed in human tumors harboring p53 hotspot mutations. These data indicate that the ESC gene signature-derived genes may serve as new stemness-based prognostic biomarkers as well as novel cancer therapeutic targets.Significance: Mesenchymal cancer stem cell-like cell lines express a mutant p53-dependent embryonic stem cell gene signature, which can serve as a potential prognostic biomarker and therapeutic target in cancer. Cancer Res; 78(20); 5833-47. ©2018 AACR.
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Affiliation(s)
- Gabriela Koifman
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Shetzer
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Shay Eizenberger
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Hilla Solomon
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Ron Rotkopf
- Bioinformatic unit, Life Sciences Core Facilities, The Weizmann Institute of Science, Rehovot, Israel
| | - Alina Molchadsky
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Giuseppe Lonetto
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Naomi Goldfinger
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel
| | - Varda Rotter
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel.
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21
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Ulmer BM, Stoehr A, Schulze ML, Patel S, Gucek M, Mannhardt I, Funcke S, Murphy E, Eschenhagen T, Hansen A. Contractile Work Contributes to Maturation of Energy Metabolism in hiPSC-Derived Cardiomyocytes. Stem Cell Reports 2018; 10:834-847. [PMID: 29503093 PMCID: PMC5919410 DOI: 10.1016/j.stemcr.2018.01.039] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 02/07/2023] Open
Abstract
Energy metabolism is a key aspect of cardiomyocyte biology. Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) are a promising tool for biomedical application, but they are immature and have not undergone metabolic maturation related to early postnatal development. To assess whether cultivation of hiPSC-CMs in 3D engineered heart tissue format leads to maturation of energy metabolism, we analyzed the mitochondrial and metabolic state of 3D hiPSC-CMs and compared it with 2D culture. 3D hiPSC-CMs showed increased mitochondrial mass, DNA content, and protein abundance (proteome). While hiPSC-CMs exhibited the principal ability to use glucose, lactate, and fatty acids as energy substrates irrespective of culture format, hiPSC-CMs in 3D performed more oxidation of glucose, lactate, and fatty acid and less anaerobic glycolysis. The increase in mitochondrial mass and DNA in 3D was diminished by pharmacological reduction of contractile force. In conclusion, contractile work contributes to metabolic maturation of hiPSC-CMs. Higher mitochondrial mass, protein, and DNA content in 3D versus 2D hiPSC-CMs Similarity of mitochondrial proteomes between 3D hiPSC-CMs and adult human heart Preference for oxidative metabolism in favor of anaerobic glycolysis in 3D hiPSC-CMs
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Affiliation(s)
- Bärbel M Ulmer
- University Medical Center Hamburg Eppendorf, Department of Experimental Pharmacology and Toxicology, 20246 Hamburg, Germany; German Center for Heart Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany.
| | - Andrea Stoehr
- Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mirja L Schulze
- University Medical Center Hamburg Eppendorf, Department of Experimental Pharmacology and Toxicology, 20246 Hamburg, Germany; German Center for Heart Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Sajni Patel
- Proteomics Core Facility, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marjan Gucek
- Proteomics Core Facility, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ingra Mannhardt
- University Medical Center Hamburg Eppendorf, Department of Experimental Pharmacology and Toxicology, 20246 Hamburg, Germany; German Center for Heart Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Sandra Funcke
- University Medical Center Hamburg Eppendorf, Department of Experimental Pharmacology and Toxicology, 20246 Hamburg, Germany; German Center for Heart Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Elizabeth Murphy
- Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas Eschenhagen
- University Medical Center Hamburg Eppendorf, Department of Experimental Pharmacology and Toxicology, 20246 Hamburg, Germany; German Center for Heart Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Arne Hansen
- University Medical Center Hamburg Eppendorf, Department of Experimental Pharmacology and Toxicology, 20246 Hamburg, Germany; German Center for Heart Research (DZHK), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany.
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22
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Osawa Y, Miyamoto T, Ohno S, Ohno E. Morphological Analysis of Live Undifferentiated Cells Derived from Induced Pluripotent Stem Cells. Stem Cells Dev 2018; 27:1-9. [PMID: 28978257 DOI: 10.1089/scd.2017.0112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Induced pluripotent stem (iPS) cells possess pluripotency and self-renewal ability. Therefore, iPS cells are expected to be useful in regenerative medicine. However, iPS cells form malignant immature teratomas after transplantation into animals, even after differentiation induction. It has been suggested that undifferentiated cells expressing Nanog that remain after differentiation induction are responsible for teratoma formation. Various methods of removing these undifferentiated cells have therefore been investigated, but few methods involve morphological approaches, which may induce less cell damage. In addition, for cells derived from iPS cells to be applied in regenerative medicine, they must be alive. However, detailed morphological analysis of live undifferentiated cells has not been performed. For the above reasons, we assessed the morphological features of live undifferentiated cells remaining after differentiation induction as a basic investigation into the clinical application of iPS cells. As a result, live undifferentiated cells remaining after differentiation induction exhibited a round or oval cytoplasm about 12 μm in diameter and a nucleus. They exhibited nucleo-cytoplasmic (N/C) ratio of about 60% and eccentric nuclei, and they possessed partially granule-like structures in the cytoplasm and prominent nucleoli. Although they were similar to iPS cells, they were smaller than live iPS cells. Furthermore, very small cells were present among undifferentiated cells after differentiation induction. These results suggest that the removal of undifferentiated cells may be possible using the morphological features of live iPS cells and undifferentiated cells after differentiation induction. In addition, this study supports safe regenerative medicine using iPS cells.
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Affiliation(s)
- Yukihiko Osawa
- 1 Graduate School of Health Science Studies, Kyushu University of Health and Welfare , Nobeoka, Japan .,2 Cancer Cell Institute, Kyushu University of Health and Welfare , Nobeoka, Japan
| | - Tomoyuki Miyamoto
- 2 Cancer Cell Institute, Kyushu University of Health and Welfare , Nobeoka, Japan .,3 Department of Medical Life Science, Faculty of Medical Bioscience, Kyushu University of Health and Welfare , Nobeoka, Japan
| | - Setsuyo Ohno
- 1 Graduate School of Health Science Studies, Kyushu University of Health and Welfare , Nobeoka, Japan .,2 Cancer Cell Institute, Kyushu University of Health and Welfare , Nobeoka, Japan .,3 Department of Medical Life Science, Faculty of Medical Bioscience, Kyushu University of Health and Welfare , Nobeoka, Japan
| | - Eiji Ohno
- 1 Graduate School of Health Science Studies, Kyushu University of Health and Welfare , Nobeoka, Japan .,2 Cancer Cell Institute, Kyushu University of Health and Welfare , Nobeoka, Japan .,3 Department of Medical Life Science, Faculty of Medical Bioscience, Kyushu University of Health and Welfare , Nobeoka, Japan
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Wakui T, Matsumoto T, Matsubara K, Kawasaki T, Yamaguchi H, Akutsu H. Method for evaluation of human induced pluripotent stem cell quality using image analysis based on the biological morphology of cells. J Med Imaging (Bellingham) 2017; 4:044003. [PMID: 29134187 PMCID: PMC5668125 DOI: 10.1117/1.jmi.4.4.044003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 10/16/2017] [Indexed: 12/24/2022] Open
Abstract
We propose an image analysis method for quality evaluation of human pluripotent stem cells based on biologically interpretable features. It is important to maintain the undifferentiated state of induced pluripotent stem cells (iPSCs) while culturing the cells during propagation. Cell culture experts visually select good quality cells exhibiting the morphological features characteristic of undifferentiated cells. Experts have empirically determined that these features comprise prominent and abundant nucleoli, less intercellular spacing, and fewer differentiating cellular nuclei. We quantified these features based on experts' visual inspection of phase contrast images of iPSCs and found that these features are effective for evaluating iPSC quality. We then developed an iPSC quality evaluation method using an image analysis technique. The method allowed accurate classification, equivalent to visual inspection by experts, of three iPSC cell lines.
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Affiliation(s)
| | | | | | - Tomoyuki Kawasaki
- National Research Institute for Child Health and Development, Tokyo, Japan
| | | | - Hidenori Akutsu
- National Research Institute for Child Health and Development, Tokyo, Japan
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Kallepitis C, Bergholt MS, Mazo MM, Leonardo V, Skaalure SC, Maynard SA, Stevens MM. Quantitative volumetric Raman imaging of three dimensional cell cultures. Nat Commun 2017; 8:14843. [PMID: 28327660 PMCID: PMC5364421 DOI: 10.1038/ncomms14843] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 02/03/2017] [Indexed: 02/07/2023] Open
Abstract
The ability to simultaneously image multiple biomolecules in biologically relevant three-dimensional (3D) cell culture environments would contribute greatly to the understanding of complex cellular mechanisms and cell-material interactions. Here, we present a computational framework for label-free quantitative volumetric Raman imaging (qVRI). We apply qVRI to a selection of biological systems: human pluripotent stem cells with their cardiac derivatives, monocytes and monocyte-derived macrophages in conventional cell culture systems and mesenchymal stem cells inside biomimetic hydrogels that supplied a 3D cell culture environment. We demonstrate visualization and quantification of fine details in cell shape, cytoplasm, nucleus, lipid bodies and cytoskeletal structures in 3D with unprecedented biomolecular specificity for vibrational microspectroscopy.
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Affiliation(s)
- Charalambos Kallepitis
- Department of Materials, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Mads S. Bergholt
- Department of Materials, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Manuel M. Mazo
- Department of Materials, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Vincent Leonardo
- Department of Materials, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Stacey C. Skaalure
- Department of Materials, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Stephanie A. Maynard
- Department of Materials, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Molly M. Stevens
- Department of Materials, Imperial College London, London SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
- Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
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25
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Lin J, Kim D, Tse HT, Tseng P, Peng L, Dhar M, Karumbayaram S, Di Carlo D. High-throughput physical phenotyping of cell differentiation. MICROSYSTEMS & NANOENGINEERING 2017; 3:17013. [PMID: 31057860 PMCID: PMC6445007 DOI: 10.1038/micronano.2017.13] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 11/23/2016] [Accepted: 12/21/2016] [Indexed: 05/08/2023]
Abstract
In this report, we present multiparameter deformability cytometry (m-DC), in which we explore a large set of parameters describing the physical phenotypes of pluripotent cells and their derivatives. m-DC utilizes microfluidic inertial focusing and hydrodynamic stretching of single cells in conjunction with high-speed video recording to realize high-throughput characterization of over 20 different cell motion and morphology-derived parameters. Parameters extracted from videos include size, deformability, deformation kinetics, and morphology. We train support vector machines that provide evidence that these additional physical measurements improve classification of induced pluripotent stem cells, mesenchymal stem cells, neural stem cells, and their derivatives compared to size and deformability alone. In addition, we utilize visual interactive stochastic neighbor embedding to visually map the high-dimensional physical phenotypic spaces occupied by these stem cells and their progeny and the pathways traversed during differentiation. This report demonstrates the potential of m-DC for improving understanding of physical differences that arise as cells differentiate and identifying cell subpopulations in a label-free manner. Ultimately, such approaches could broaden our understanding of subtle changes in cell phenotypes and their roles in human biology.
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Affiliation(s)
- Jonathan Lin
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Donghyuk Kim
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Henry T. Tse
- CytoVale Inc., 384 Oyster Point Boulevard #7 South, San Francisco, CA 94080, USA
| | - Peter Tseng
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Lillian Peng
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Manjima Dhar
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Saravanan Karumbayaram
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Los Angeles, CA 90095, USA
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA
- Department of Mechanical Engineering, University of California, Los Angeles, CA 90095, USA
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26
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5-azacytidine affects TET2 and histone transcription and reshapes morphology of human skin fibroblasts. Sci Rep 2016; 6:37017. [PMID: 27841324 PMCID: PMC5107985 DOI: 10.1038/srep37017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/24/2016] [Indexed: 12/11/2022] Open
Abstract
Phenotype definition is controlled by epigenetic regulations that allow cells to acquire their differentiated state. The process is reversible and attractive for therapeutic intervention and for the reactivation of hypermethylated pluripotency genes that facilitate transition to a higher plasticity state. We report the results obtained in human fibroblasts exposed to the epigenetic modifier 5-azacytidine (5-aza-CR), which increases adult cell plasticity and facilitates phenotype change. Although many aspects controlling its demethylating action have been widely investigated, the mechanisms underlying 5-aza-CR effects on cell plasticity are still poorly understood. Our experiments confirm decreased global methylation, but also demonstrate an increase of both Formylcytosine (5fC) and 5-Carboxylcytosine (5caC), indicating 5-aza-CR ability to activate a direct and active demethylating effect, possibly mediated via TET2 protein increased transcription. This was accompanied by transient upregulation of pluripotency markers and incremented histone expression, paralleled by changes in histone acetylating enzymes. Furthermore, adult fibroblasts reshaped into undifferentiated progenitor-like phenotype, with a sparse and open chromatin structure. Our findings indicate that 5-aza-CR induced somatic cell transition to a higher plasticity state is activated by multiple regulations that accompany the demethylating effect exerted by the modifier.
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Tanabe S. Origin of cells and network information. World J Stem Cells 2015; 7:535-540. [PMID: 25914760 PMCID: PMC4404388 DOI: 10.4252/wjsc.v7.i3.535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 01/20/2015] [Accepted: 02/11/2015] [Indexed: 02/06/2023] Open
Abstract
All cells are derived from one cell, and the origin of different cell types is a subject of curiosity. Cells construct life through appropriately timed networks at each stage of development. Communication among cells and intracellular signaling are essential for cell differentiation and for life processes. Cellular molecular networks establish cell diversity and life. The investigation of the regulation of each gene in the genome within the cellular network is therefore of interest. Stem cells produce various cells that are suitable for specific purposes. The dynamics of the information in the cellular network changes as the status of cells is altered. The components of each cell are subject to investigation.
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