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Abstract
In mammals, many organs lack robust regenerative abilities. Lost cells in impaired tissue could potentially be compensated by converting nearby cells in situ through in vivo reprogramming. Small molecule-induced cell reprogramming offers a temporally flexible and non-integrative strategy for altering cell fate, which is, in principle, favorable for in vivo reprogramming in organs with notoriously poor regenerative abilities, such as the brain. Here, we demonstrate that in the adult mouse brain, small molecules can reprogram astrocytes into neurons. The in situ chemically induced neurons resemble endogenous neurons in terms of neuron-specific marker expression, electrophysiological properties, and synaptic connectivity. Our study demonstrates the feasibility of in vivo chemical reprogramming in the adult mouse brain and provides a potential approach for developing neuronal replacement therapies.
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102
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Direct cell reprogramming: approaches, mechanisms and progress. Nat Rev Mol Cell Biol 2021; 22:410-424. [PMID: 33619373 DOI: 10.1038/s41580-021-00335-z] [Citation(s) in RCA: 196] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
The reprogramming of somatic cells with defined factors, which converts cells from one lineage into cells of another, has greatly reshaped our traditional views on cell identity and cell fate determination. Direct reprogramming (also known as transdifferentiation) refers to cell fate conversion without transitioning through an intermediary pluripotent state. Given that the number of cell types that can be generated by direct reprogramming is rapidly increasing, it has become a promising strategy to produce functional cells for therapeutic purposes. This Review discusses the evolution of direct reprogramming from a transcription factor-based method to a small-molecule-driven approach, the recent progress in enhancing reprogrammed cell maturation, and the challenges associated with in vivo direct reprogramming for translational applications. It also describes our current understanding of the molecular mechanisms underlying direct reprogramming, including the role of transcription factors, epigenetic modifications, non-coding RNAs, and the function of metabolic reprogramming, and highlights novel insights gained from single-cell omics studies.
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103
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Molecular Mechanisms Underlying Ascl1-Mediated Astrocyte-to-Neuron Conversion. Stem Cell Reports 2021; 16:534-547. [PMID: 33577795 PMCID: PMC7940254 DOI: 10.1016/j.stemcr.2021.01.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 01/12/2021] [Accepted: 01/12/2021] [Indexed: 12/19/2022] Open
Abstract
Direct neuronal reprogramming potentially provides valuable sources for cell-based therapies. Proneural gene Ascl1 converts astrocytes into induced neuronal (iN) cells efficiently both in vitro and in vivo. However, the underlying mechanisms are largely unknown. By combining RNA sequencing and chromatin immunoprecipitation followed by high-throughput sequencing, we found that the expression of 1,501 genes was markedly changed during the early stages of Ascl1-induced astrocyte-to-neuron conversion and that the regulatory regions of 107 differentially expressed genes were directly bound by ASCL1. Among Ascl1's direct targets, Klf10 regulates the neuritogenesis of iN cells at the early stage, Myt1 and Myt1l are critical for the electrophysiological maturation of iN cells, and Neurod4 and Chd7 are required for the efficient conversion of astrocytes into neurons. Together, this study provides more insights into understanding the molecular mechanisms underlying Ascl1-mediated astrocyte-to-neuron conversion and will be of value for the application of direct neuronal reprogramming. RNA-seq and ChIP-seq were used to study Ascl1-induced astrocyte-to-neuron conversion Early Klf10 regulates neuritogenesis and electrophysiological properties of iN cells Myt1 and Myt1l are critical for the electrophysiological maturation of iN cells Neurod4 and Chd7 are required for efficient conversion of astrocytes to neurons
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104
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Soto J, Ding X, Wang A, Li S. Neural crest-like stem cells for tissue regeneration. Stem Cells Transl Med 2021; 10:681-693. [PMID: 33533168 PMCID: PMC8046096 DOI: 10.1002/sctm.20-0361] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 12/13/2022] Open
Abstract
Neural crest stem cells (NCSCs) are a transient population of cells that arise during early vertebrate development and harbor stem cell properties, such as self‐renewal and multipotency. These cells form at the interface of non‐neuronal ectoderm and neural tube and undergo extensive migration whereupon they contribute to a diverse array of cell and tissue derivatives, ranging from craniofacial tissues to cells of the peripheral nervous system. Neural crest‐like stem cells (NCLSCs) can be derived from pluripotent stem cells, placental tissues, adult tissues, and somatic cell reprogramming. NCLSCs have a differentiation capability similar to NCSCs, and possess great potential for regenerative medicine applications. In this review, we present recent developments on the various approaches to derive NCLSCs and the therapeutic application of these cells for tissue regeneration.
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Affiliation(s)
- Jennifer Soto
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, USA
| | - Xili Ding
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, People's Republic of China
| | - Aijun Wang
- Department of Surgery, School of Medicine, University of California Davis, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children, Sacramento, California, USA.,Department of Biomedical Engineering, University of California Davis, Davis, California, USA
| | - Song Li
- Department of Bioengineering, University of California Los Angeles, Los Angeles, California, USA.,Department of Medicine, University of California Los Angeles, Los Angeles, California, USA
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105
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Transcription Factor Programming of Human Pluripotent Stem Cells to Functionally Mature Astrocytes for Monocultures and Cocultures with Neurons. Methods Mol Biol 2021; 2352:133-148. [PMID: 34324185 DOI: 10.1007/978-1-0716-1601-7_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Astrocytes are essential cells for normal brain functionality and have recently emerged as key players in many neurological diseases. However, the limited availability of human primary astrocytes for cell culture studies hinders our understanding of their physiology and precise role in disease development and progression. Here, we describe a detailed step-by-step protocol to rapidly and efficiently generate functionally mature induced astrocytes (iAs) from human embryonic and induced pluripotent stem cells (hES/iPSCs). Astrocyte induction is accomplished by ectopic lentiviral expression of two gliogenic transcription factors, Sox9 and Nfib. iAs exhibit morphology features as well as gene and protein expression similar to human mature astrocytes and display important astrocytic functions, such as glutamate uptake, propagation of calcium waves, expression of various cytokines after stimulation, and support of synapse formation and function, making them suitable models for studying the role of astrocytes in health and disease. Moreover, we describe a procedure for cryopreservation of iAs for long-term storage or shipping. Finally, we provide the required information needed to set up cocultures with human induced neurons (iNs, also described in this book), generated from hES/iPSCs, to generate cocultures, allowing studies on astrocyte-neuron interactions and providing new insights in astrocyte-associated disease mechanisms.
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106
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Roccio M. Directed differentiation and direct reprogramming: Applying stem cell technologies to hearing research. Stem Cells 2020; 39:375-388. [PMID: 33378797 DOI: 10.1002/stem.3315] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/24/2020] [Accepted: 12/01/2020] [Indexed: 12/26/2022]
Abstract
Hearing loss is the most widely spread sensory disorder in our society. In the majority of cases, it is caused by the loss or malfunctioning of cells in the cochlea: the mechanosensory hair cells, which act as primary sound receptors, and the connecting auditory neurons of the spiral ganglion, which relay the signal to upper brain centers. In contrast to other vertebrates, where damage to the hearing organ can be repaired through the activity of resident cells, acting as tissue progenitors, in mammals, sensory cell damage or loss is irreversible. The understanding of gene and cellular functions, through analysis of different animal models, has helped to identify causes of disease and possible targets for hearing restoration. Translation of these findings to novel therapeutics is, however, hindered by the lack of cellular assays, based on human sensory cells, to evaluate the conservation of molecular pathways across species and the efficacy of novel therapeutic strategies. In the last decade, stem cell technologies enabled to generate human sensory cell types in vitro, providing novel tools to study human inner ear biology, model disease, and validate therapeutics. This review focuses specifically on two technologies: directed differentiation of pluripotent stem cells and direct reprogramming of somatic cell types to sensory hair cells and neurons. Recent development in the field are discussed as well as how these tools could be implemented to become routinely adopted experimental models for hearing research.
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Affiliation(s)
- Marta Roccio
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Zurich (USZ), and University of Zurich (UZH), Zurich, Switzerland
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107
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Zhou Y, Wei C, Xiong S, Dong L, Chen Z, Chen SJ, Cheng L. Trajectory of chemical cocktail-induced neutrophil reprogramming. J Hematol Oncol 2020; 13:171. [PMID: 33302977 PMCID: PMC7727137 DOI: 10.1186/s13045-020-01008-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/22/2020] [Indexed: 12/20/2022] Open
Abstract
Hematopoietic reprogramming holds great promise for generating functional target cells and provides new angle for understanding hematopoiesis. We reported before for the first time that diverse differentiated hematopoietic cell lineages could be reprogrammed back into hematopoietic stem/progenitor cell-like cells by chemical cocktail. However, the exact cell types of induced cells and reprogramming trajectory remain elusive. Here, based on genetic tracing method CellTagging and single-cell RNA sequencing, it is found that neutrophils could be reprogrammed into multipotent progenitors, which acquire multi-differentiation potential both in vitro and in vivo, including into lymphoid cells. Construction of trajectory map of the reprogramming procession shows that mature neutrophils follow their canonical developmental route reversely into immature ones, premature ones, granulocyte/monocyte progenitors, common myeloid progenitors, and then the terminal cells, which is stage by stage or skips intermediate stages. Collectively, this study provides a precise dissection of hematopoietic reprogramming procession and sheds light on chemical cocktail-induction of hematopoietic stem cells.
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Affiliation(s)
- Yi Zhou
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chuijin Wei
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Shumin Xiong
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Liaoliao Dong
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhu Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Sai-Juan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Lin Cheng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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108
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Dotson GA, Ryan CW, Chen C, Muir L, Rajapakse I. Cellular reprogramming: Mathematics meets medicine. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2020; 13:e1515. [PMID: 33289324 PMCID: PMC8867497 DOI: 10.1002/wsbm.1515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 11/11/2022]
Abstract
Generating needed cell types using cellular reprogramming is a promising strategy for restoring tissue function in injury or disease. A common method for reprogramming is addition of one or more transcription factors that confer a new function or identity. Advancements in transcription factor selection and delivery have culminated in successful grafting of autologous reprogrammed cells, an early demonstration of their clinical utility. Though cellular reprogramming has been successful in a number of settings, identification of appropriate transcription factors for a particular transformation has been challenging. Computational methods enable more sophisticated prediction of relevant transcription factors for reprogramming by leveraging gene expression data of initial and target cell types, and are built on mathematical frameworks ranging from information theory to control theory. This review highlights the utility and impact of these mathematical frameworks in the field of cellular reprogramming. This article is categorized under: Reproductive System Diseases > Reproductive System Diseases>Genetics/Genomics/Epigenetics Reproductive System Diseases > Reproductive System Diseases>Stem Cells and Development Reproductive System Diseases > Reproductive System Diseases>Computational Models.
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Affiliation(s)
- Gabrielle A. Dotson
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Charles W. Ryan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Medical Scientist Training Program, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Can Chen
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Lindsey Muir
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Indika Rajapakse
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, 48109, USA
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan, 48109, USA
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109
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Black JB, McCutcheon SR, Dube S, Barrera A, Klann TS, Rice GA, Adkar SS, Soderling SH, Reddy TE, Gersbach CA. Master Regulators and Cofactors of Human Neuronal Cell Fate Specification Identified by CRISPR Gene Activation Screens. Cell Rep 2020; 33:108460. [PMID: 33264623 PMCID: PMC7730023 DOI: 10.1016/j.celrep.2020.108460] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 08/02/2020] [Accepted: 11/09/2020] [Indexed: 01/06/2023] Open
Abstract
Technologies to reprogram cell-type specification have revolutionized the fields of regenerative medicine and disease modeling. Currently, the selection of fate-determining factors for cell reprogramming applications is typically a laborious and low-throughput process. Therefore, we use high-throughput pooled CRISPR activation (CRISPRa) screens to systematically map human neuronal cell fate regulators. We utilize deactivated Cas9 (dCas9)-based gene activation to target 1,496 putative transcription factors (TFs) in the human genome. Using a reporter of neuronal commitment, we profile the neurogenic activity of these factors in human pluripotent stem cells (PSCs), leading to a curated set of pro-neuronal factors. Activation of pairs of TFs reveals neuronal cofactors, including E2F7, RUNX3, and LHX8, that improve conversion efficiency, subtype specificity, and maturation of neuronal cell types. Finally, using multiplexed gene regulation with orthogonal CRISPR systems, we demonstrate improved neuronal differentiation with concurrent activation and repression of target genes, underscoring the power of CRISPR-based gene regulation for programming complex cellular phenotypes.
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Affiliation(s)
- Joshua B Black
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Sean R McCutcheon
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Shataakshi Dube
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Alejandro Barrera
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA
| | - Tyler S Klann
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Grayson A Rice
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA
| | - Shaunak S Adkar
- Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Scott H Soderling
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Timothy E Reddy
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA; Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Center for Advanced Genomic Technologies, Duke University, Durham, NC 27708, USA; Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA; Graduate Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA.
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110
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Induced Pluripotency: A Powerful Tool for In Vitro Modeling. Int J Mol Sci 2020; 21:ijms21238910. [PMID: 33255453 PMCID: PMC7727808 DOI: 10.3390/ijms21238910] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
One of the greatest breakthroughs of regenerative medicine in this century was the discovery of induced pluripotent stem cell (iPSC) technology in 2006 by Shinya Yamanaka. iPSCs originate from terminally differentiated somatic cells that have newly acquired the developmental capacity of self-renewal and differentiation into any cells of three germ layers. Before iPSCs can be used routinely in clinical practice, their efficacy and safety need to be rigorously tested; however, iPSCs have already become effective and fully-fledged tools for application under in vitro conditions. They are currently routinely used for disease modeling, preparation of difficult-to-access cell lines, monitoring of cellular mechanisms in micro- or macroscopic scales, drug testing and screening, genetic engineering, and many other applications. This review is a brief summary of the reprogramming process and subsequent differentiation and culture of reprogrammed cells into neural precursor cells (NPCs) in two-dimensional (2D) and three-dimensional (3D) conditions. NPCs can be used as biomedical models for neurodegenerative diseases (NDs), which are currently considered to be one of the major health problems in the human population.
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111
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Zhang Y, Xie X, Hu J, Afreen KS, Zhang CL, Zhuge Q, Yang J. Prospects of Directly Reprogrammed Adult Human Neurons for Neurodegenerative Disease Modeling and Drug Discovery: iN vs. iPSCs Models. Front Neurosci 2020; 14:546484. [PMID: 33328842 PMCID: PMC7710799 DOI: 10.3389/fnins.2020.546484] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 10/12/2020] [Indexed: 12/11/2022] Open
Abstract
A reliable disease model is critical to the study of specific disease mechanisms as well as for the discovery and development of new drugs. Despite providing crucial insights into the mechanisms of neurodegenerative diseases, translation of this information to develop therapeutics in clinical trials have been unsuccessful. Reprogramming technology to convert adult somatic cells to induced Pluripotent Stem Cells (iPSCs) or directly reprogramming adult somatic cells to induced Neurons (iN), has allowed for the creation of better models to understand the molecular mechanisms and design of new drugs. In recent times, iPSC technology has been commonly used for modeling neurodegenerative diseases and drug discovery. However, several technological challenges have limited the application of iN. As evidence suggests, iN for the modeling of neurodegenerative disorders is advantageous compared to those derived from iPSCs. In this review, we will compare iPSCs and iN models for neurodegenerative diseases and their potential applications in the future.
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Affiliation(s)
- Ying Zhang
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xinyang Xie
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,International Department of The Affiliated High School of South China Normal University (HFI), Guangzhou, China
| | - Jiangnan Hu
- Department of Pharmaceutical Sciences, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Kazi Sabrina Afreen
- Department of Microbiology & Immunology, Rosalind Franklin University of Medicine and Science, North Chicago, IL, United States
| | - Chun-Li Zhang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Qichuan Zhuge
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jianjing Yang
- Zhejiang Provincial Key Laboratory of Aging and Neurological Disorder Research, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Department of Neurosurgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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112
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Motohashi T, Kawamura N, Watanabe N, Kitagawa D, Goshima N, Kunisada T. Sox10 Functions as an Inducer of the Direct Conversion of Keratinocytes Into Neural Crest Cells. Stem Cells Dev 2020; 29:1510-1519. [PMID: 33040687 DOI: 10.1089/scd.2020.0106] [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] [Indexed: 12/13/2022] Open
Abstract
Neural crest cells (NCCs) are highly migratory multipotent cells that play critical roles in embryogenesis. The generation of NCCs is controlled by various transcription factors (TFs) that are regulated by each other and combine to form a regulatory network. We previously reported that the conversion of mouse fibroblasts into NCCs was achieved by the overexpression of only one TF, Sox10; therefore, Sox10 may be a powerful inducer of the conversion of NCCs. We herein investigated whether Sox10 functions in the direct conversion of other somatic cells into NCCs. Sox10 directly converted bone marrow-derived mesenchymal cells, but not keratinocytes, into P75+ NCCs. However, by the co-expression of four TFs (Snail1, Snail2, Twist1, and Tcfap2a) that are involved in NCC generation, but unable convert cells into NCCs, Sox10 converted keratinocytes into P75+ NCCs. P75+ NCCs mainly differentiated into glial cells, and to a lesser extent into neuronal cells. On the other hand, when Sox10 was expressed after the four TF expression, which mimicked the expression order in in vivo NCC generation, it converted keratinocytes into multipotent NCCs. These results demonstrate that Sox10 functions as an inducer of direct conversion into NCCs in cooperation with the TFs involved in NCC generation. The sequence of expression of the inducer and cooperative factors is important for the conversion of somatic cells into bona fide target cells.
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Affiliation(s)
- Tsutomu Motohashi
- Department of Tissue and Organ Development, Regeneration, and Advanced Medical Science, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Norito Kawamura
- Department of Tissue and Organ Development, Regeneration, and Advanced Medical Science, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Natsuki Watanabe
- Department of Tissue and Organ Development, Regeneration, and Advanced Medical Science, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Daisuke Kitagawa
- Department of Tissue and Organ Development, Regeneration, and Advanced Medical Science, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Naoki Goshima
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Takahiro Kunisada
- Department of Tissue and Organ Development, Regeneration, and Advanced Medical Science, Gifu University Graduate School of Medicine, Gifu, Japan
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113
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Qin H, Zhao AD, Sun ML, Ma K, Fu XB. Direct conversion of human fibroblasts into dopaminergic neuron-like cells using small molecules and protein factors. Mil Med Res 2020; 7:52. [PMID: 33129359 PMCID: PMC7603706 DOI: 10.1186/s40779-020-00284-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 10/21/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Generation of neurons is essential in cell replacement therapy for neurodegenerative disorders like Parkinson's disease. Several studies have reported the generation of dopaminergic (DA) neurons from mouse and human fibroblasts by ectopic expression of transcription factors, in which genetic manipulation is associated with potential risks. METHODS The small molecules and protein factors were selected based on their function to directly induce human fetal lung IMR-90 fibroblasts into DA neuron-like cells. Microscopical, immunocytochemical, and RT-qPCR analyses were used to characterize the morphology, phenotype, and gene expression features of the induced cells. The whole-cell patch-clamp recordings were exploited to measure the electrophysiological properties. RESULTS Human IMR-90 fibroblasts were rapidly converted into DA neuron-like cells after the chemical induction using small molecules and protein factors, with a yield of approximately 95% positive TUJ1-positive cells. The induced DA neuron-like cells were immunopositive for pan-neuronal markers MAP2, NEUN, and Synapsin 1 and DA markers TH, DDC, DAT, and NURR1. The chemical induction process did not involve a neural progenitor/stem cell intermediate stage. The induced neurons could fire single action potentials, which reflected partially the electrophysiological properties of neurons. CONCLUSION We developed a chemical cocktail of small molecules and protein factors to convert human fibroblasts into DA neuron-like cells without passing through a neural progenitor/stem cell intermediate stage. The induced DA neuron-like cells from human fibroblasts might provide a cellular source for cell-based therapy of Parkinson's disease in the future.
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Affiliation(s)
- Hua Qin
- Research Center for Tissue Repair and Regeneration affiliated to the Medical Innovation Research Division and 4th Medical Center, PLA General Hospital and PLA Medical College, 28 Fu Xing Road, Haidian District, Beijing, 100853, China
| | - An-Dong Zhao
- Research Center for Tissue Repair and Regeneration affiliated to the Medical Innovation Research Division and 4th Medical Center, PLA General Hospital and PLA Medical College, 28 Fu Xing Road, Haidian District, Beijing, 100853, China.,Tianjin Medical University, Tianjin, 300070, China.,PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Beijing, 100048, China
| | - Meng-Li Sun
- Research Center for Tissue Repair and Regeneration affiliated to the Medical Innovation Research Division and 4th Medical Center, PLA General Hospital and PLA Medical College, 28 Fu Xing Road, Haidian District, Beijing, 100853, China.,PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Beijing, 100048, China
| | - Kui Ma
- Research Center for Tissue Repair and Regeneration affiliated to the Medical Innovation Research Division and 4th Medical Center, PLA General Hospital and PLA Medical College, 28 Fu Xing Road, Haidian District, Beijing, 100853, China.,PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Beijing, 100048, China
| | - Xiao-Bing Fu
- Research Center for Tissue Repair and Regeneration affiliated to the Medical Innovation Research Division and 4th Medical Center, PLA General Hospital and PLA Medical College, 28 Fu Xing Road, Haidian District, Beijing, 100853, China. .,PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration, Beijing, 100048, China. .,Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, China.
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114
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Yang DW, Moon JS, Ko HM, Shin YK, Fukumoto S, Kim SH, Kim MS. Direct reprogramming of fibroblasts into diverse lineage cells by DNA demethylation followed by differentiating cultures. THE KOREAN JOURNAL OF PHYSIOLOGY & PHARMACOLOGY : OFFICIAL JOURNAL OF THE KOREAN PHYSIOLOGICAL SOCIETY AND THE KOREAN SOCIETY OF PHARMACOLOGY 2020; 24:463-472. [PMID: 33093268 PMCID: PMC7585590 DOI: 10.4196/kjpp.2020.24.6.463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 09/24/2020] [Accepted: 09/26/2020] [Indexed: 11/15/2022]
Abstract
Direct reprogramming, also known as a trans-differentiation, is a technique to allow mature cells to be converted into other types of cells without inducing a pluripotent stage. It has been suggested as a major strategy to acquire the desired type of cells in cell-based therapies to repair damaged tissues. Studies related to switching the fate of cells through epigenetic modification have been progressing and they can bypass safety issues raised by the virus-based transfection methods. In this study, a protocol was established to directly convert fully differentiated fibroblasts into diverse mesenchymal-lineage cells, such as osteoblasts, adipocytes, chondrocytes, and ectodermal cells, including neurons, by means of DNA demethylation, immediately followed by culturing in various differentiating media. First, 24 h exposure of 5-azacytidine (5-aza-CN), a well-characterized DNA methyl transferase inhibitor, to NIH-3T3 murine fibroblast cells induced the expression of stem-cell markers, that is, increasing cell plasticity. Next, 5-aza-CN treated fibroblasts were cultured in osteogenic, adipogenic, chondrogenic, and neurogenic media with or without bone morphogenetic protein 2 for a designated period. Differentiation of each desired type of cell was verified by quantitative reverse transcriptase-polymerase chain reaction/western blot assays for appropriate marker expression and by various staining methods, such as alkaline phosphatase/alizarin red S/oil red O/alcian blue. These proposed procedures allowed easier acquisition of the desired cells without any transgenic modification, using direct reprogramming technology, and thus may help make it more available in the clinical fields of regenerative medicine.
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Affiliation(s)
- Dong-Wook Yang
- Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju 61186, Korea
| | - Jung-Sun Moon
- Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju 61186, Korea
| | - Hyun-Mi Ko
- Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju 61186, Korea
| | - Yeo-Kyeong Shin
- Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju 61186, Korea
| | - Satoshi Fukumoto
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Sun-Hun Kim
- Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju 61186, Korea
| | - Min-Seok Kim
- Dental Science Research Institute, School of Dentistry, Chonnam National University, Gwangju 61186, Korea
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115
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Takayama Y, Akagi Y, Shibuya Y, Kida YS. Exposure to small molecule cocktails allows induction of neural crest lineage cells from human adipose-derived mesenchymal stem cells. PLoS One 2020; 15:e0241125. [PMID: 33104750 PMCID: PMC7588063 DOI: 10.1371/journal.pone.0241125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/08/2020] [Indexed: 01/22/2023] Open
Abstract
Neural crest cells (NCCs) are a promising source for cell therapy and regenerative medicine owing to their multipotency, self-renewability, and capability to secrete various trophic factors. However, isolating NCCs from adult organs is challenging, because NCCs are broadly distributed throughout the body. Hence, we attempted to directly induce NCCs from human adipose-derived mesenchymal stem cells (ADSCs), which can be isolated easily, using small molecule cocktails. We established a controlled induction protocol with two-step application of small molecule cocktails for 6 days. The induction efficiency was evaluated based on mRNA and protein expression of neural crest markers, such as nerve growth factor receptor (NGFR) and sex-determining region Y-box 10 (SOX10). We also found that various trophic factors were significantly upregulated following treatment with the small molecule cocktails. Therefore, we performed global profiling of cell surface makers and identified distinctly upregulated markers, including the neural crest-specific cell surface markers CD271 and CD57. These results indicate that our chemical treatment can direct human ADSCs to developing into the neural crest lineage. This offers a promising experimental platform to study human NCCs for applications in cell therapy and regenerative medicine.
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Affiliation(s)
- Yuzo Takayama
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- * E-mail: (YT); (YSK)
| | - Yuka Akagi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Advanced Photonics and Biosensing Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yoichiro Shibuya
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Department of Plastic and Reconstructive Surgery, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yasuyuki S. Kida
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Advanced Photonics and Biosensing Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- * E-mail: (YT); (YSK)
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116
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Overcoming Current Dilemma in Cartilage Regeneration: Will Direct Conversion Provide a Breakthrough? Tissue Eng Regen Med 2020; 17:829-834. [PMID: 33098546 DOI: 10.1007/s13770-020-00303-2] [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: 08/18/2020] [Revised: 09/05/2020] [Accepted: 09/16/2020] [Indexed: 12/13/2022] Open
Abstract
Direct reprogramming/direct conversion/transdifferentiation is a process that induces conversion between completely different matured (differentiated) cells in higher organisms. Unlike the process of reprogramming of differentiated cells into induced pluripotent stem cells (iPSCs) and re-differentiation into the desired cell types, differentiated cells undergo the conversion into another type of differentiated cells without going through the iPSCs state. Osteoarthritis (OA) is the most common type of arthritis that causes a significant deterioration in patients' quality of life. The high prevalence of OA as well as the current lack of disease-modifying drugs has led to a rise in regenerative strategy for OA treatment. Regenerative therapy in OA started with the concept of engraftment of the administered cells within the cartilage lesion and differentiation to chondrocytes after the engraftment. However, recent studies show that cells, particularly when injected in suspension, rapidly undergo apoptosis after exerting a transient paracrine effect. In this perspective review, the general overview and current status of direct conversion are introduced along with the conceptual strategy and future directions for possible application of regenerative therapy using stem cells in OA. In vivo direct conversion may open a new stage of regenerative medicine for OA treatment. Recent advances in in vivo gene transfer and smart biomaterials can bring the concept into reality in near future. Direct conversion can be a new type of treatment technology that has the potential to overcome the limitations of current cell therapy.
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117
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Wang J, He Q, Zhang K, Sun H, Zhang G, Liang H, Guo J, Hao L, Ke J, Chen S. Quick Commitment and Efficient Reprogramming Route of Direct Induction of Retinal Ganglion Cell-like Neurons. Stem Cell Reports 2020; 15:1095-1110. [PMID: 33096050 PMCID: PMC7663790 DOI: 10.1016/j.stemcr.2020.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 01/16/2023] Open
Abstract
Direct reprogramming has been widely explored to generate various types of neurons for neurobiological research and translational medicine applications, but there is still no efficient reprogramming method to generate retinal ganglion cell (RGC)-like neurons, which are the sole projection neurons in the retina. Here, we show that three transcription factors, Ascl1, Brn3b, and Isl1, efficiently convert fibroblasts into RGC-like neurons (iRGCs). Furthermore, we show that the competence of cells to enter iRGC reprogramming route is determined by the cell-cycle status at a very early stage of the process. The iRGC reprogramming route involves intermediate states that are characterized by a transient inflammatory-like response followed by active epigenomic and transcriptional modifications. Our study provides an efficient method to generate iRGCs, which would be a valuable cell source for potential glaucoma cell replacement therapy and drug screening studies, and reveals the key cellular events that govern successful neuronal fate reprogramming.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Qinghai He
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Ke Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Hui Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Gong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Huilin Liang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Jingyi Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Lili Hao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Jiangbin Ke
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China
| | - Shuyi Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510623, China.
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118
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Park SJ, Shin H, Won C, Min DH. Non-viral, direct neuronal reprogramming from human fibroblast using a polymer-functionalized nanodot. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2020; 32:102316. [PMID: 33068744 DOI: 10.1016/j.nano.2020.102316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 09/23/2020] [Accepted: 10/06/2020] [Indexed: 01/01/2023]
Abstract
Among various strategies to treat neurodegenerative disorders, cell replacement therapies have drawn much attention recently. Such a trend led to the increase in demand for the rare and specialized cells, followed by the outburst development of various cell reprogramming strategies. However, several limitations on these conventional methods remain to be solved, including the genetic instability of the viral vectors and the high cytotoxicity or poor performance of the non-viral carriers. Therefore, non-viral methods need to be developed to ensure safe and efficient cell reprogramming. Here, we introduce a polymer-modified nano-reagent (Polymer-functionalized Nanodot, PolyN) for the safe and efficient, non-viral direct cell reprogramming. PolyN facilitated the highly efficient contemporary overexpression of the transgene compared to the conventional reagent. With our nano-reagent, we demonstrated the SOX2-mediated cell reprogramming and successfully generated the neuron-like cell from the human fibroblast.
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Affiliation(s)
- Se-Jin Park
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Hojeong Shin
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Cheolhee Won
- Institute of Biotherapeutics Convergence Technology, Lemonex Inc., Seoul, Republic of Korea
| | - Dal-Hee Min
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea; Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Biotherapeutics Convergence Technology, Lemonex Inc., Seoul, Republic of Korea.
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119
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Xu Z, Su S, Zhou S, Yang W, Deng X, Sun Y, Li L, Li Y. How to reprogram human fibroblasts to neurons. Cell Biosci 2020; 10:116. [PMID: 33062254 PMCID: PMC7549215 DOI: 10.1186/s13578-020-00476-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/15/2020] [Indexed: 12/13/2022] Open
Abstract
Destruction and death of neurons can lead to neurodegenerative diseases. One possible way to treat neurodegenerative diseases and damage of the nervous system is replacing damaged and dead neurons by cell transplantation. If new neurons can replace the lost neurons, patients may be able to regain the lost functions of memory, motor, and so on. Therefore, acquiring neurons conveniently and efficiently is vital to treat neurological diseases. In recent years, studies on reprogramming human fibroblasts into neurons have emerged one after another, and this paper summarizes all these studies. Scientists find small molecules and transcription factors playing a crucial role in reprogramming and inducing neuron production. At the same time, both the physiological microenvironment in vivo and the physical and chemical factors in vitro play an essential role in the induction of neurons. Therefore, this paper summarized and analyzed these relevant factors. In addition, due to the unique advantages of physical factors in the process of reprogramming human fibroblasts into neurons, such as safe and minimally invasive, it has a more promising application prospect. Therefore, this paper also summarizes some successful physical mechanisms of utilizing fibroblasts to acquire neurons, which will provide new ideas for somatic cell reprogramming.
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Affiliation(s)
- Ziran Xu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021 People's Republic of China
| | - Shengnan Su
- The Second Hospital of Jilin University, Jilin, Changchun, 130041 China
| | - Siyan Zhou
- Department of Stomatology, The First Hospital of Jilin University, Changchun, 130021 People's Republic of China
| | - Wentao Yang
- Norman Bethune College of Medicine, Jilin University, Changchun, 130021 People's Republic of China
| | - Xin Deng
- Norman Bethune College of Medicine, Jilin University, Changchun, 130021 People's Republic of China
| | - Yingying Sun
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021 People's Republic of China.,Department of Stomatology, The First Hospital of Jilin University, Changchun, 130021 People's Republic of China
| | - Lisha Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021 People's Republic of China
| | - Yulin Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021 People's Republic of China
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120
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Shah R, Del Vecchio D. Reprogramming multistable monotone systems with application to cell fate control. IEEE TRANSACTIONS ON NETWORK SCIENCE AND ENGINEERING 2020; 7:2940-2951. [PMID: 33437845 PMCID: PMC7799369 DOI: 10.1109/tnse.2020.3008135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Multistability is a key property of dynamical systems modeling cellular regulatory networks implicated in cell fate decisions, where, different stable steady states usually represent distinct cell phenotypes. Monotone network motifs are highly represented in these regulatory networks. In this paper, we leverage the properties of monotone dynamical systems to provide theoretical results that guide the selection of inputs that trigger a transition, i.e., reprogram the network, to a desired stable steady state. We first show that monotone dynamical systems with bounded trajectories admit a minimum and a maximum stable steady state. Then, we provide input choices that are guaranteed to reprogram the system to these extreme steady states. For intermediate states, we provide an input space that is guaranteed to contain an input that reprograms the system to the desired state. We then provide implementation guidelines for finite-time procedures that search this space for such an input, along with rules to prune parts of the space during search. We demonstrate these results on simulations of two recurrent regulatory network motifs: self-activation within mutual antagonism and self-activation within mutual cooperation. Our results depend uniquely on the structure of the network and are independent of specific parameter values.
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Affiliation(s)
- Rushina Shah
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Domitilla Del Vecchio
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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121
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Yi B, Dissanayaka WL, Zhang C. Growth Factors and Small-molecule Compounds in Derivation of Endothelial Lineages from Dental Stem Cells. J Endod 2020; 46:S63-S70. [PMID: 32950197 DOI: 10.1016/j.joen.2020.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Incorporating fully assembled microvascular networks into bioengineered dental pulp constructs can significantly enhance functional blood flow and tissue survival upon transplantation. Endothelial cells (ECs), cellular building blocks of vascular tissue, play an essential role in the process of prevascularization. However, obtaining sufficient ECs from a suitable source for translational application is challenging. Dental stem cells (DSCs), which exhibit a robust proliferative ability and immunocompatibility because of their autologous origin, could be a promising alternative cell source for the derivation of endothelial lineages. Under specific culture conditions, DSCs differentiate into osteo/odontogenic, adipogenic, chondrogenic, and neurogenic cell lineages. METHODS Recently, a new approach has been developed to directly reprogram cells using chemical cocktails and growth factors. Compared with the traditional reprogramming approach based on the forced expression of exogenous transcription factors, the chemical strategy avoids the risk associated with lentiviral transduction while offering a more viable methodology to drive cell lineage switch. The aim of this review was to unveil the concept of the use of small-molecule compounds and growth factors modulating key signaling pathways to derive ECs from DSCs. RESULTS In addition, our preliminary study showed that stem cells from the apical papilla could be induced into EC-like cells using small-molecule compounds and growth factors. These EC-like cells expressed endothelial specific genes (CD31 and VEGFR2) and proteins (CD31, VEGF receptor 2, and vascular endothelial cadherin) as well as gave rise to vessel-like tubular structures in vitro. CONCLUSIONS Our preliminary results suggest that chemical reprogramming might offer a novel way to generate EC-like cells from dental stem cells.
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Affiliation(s)
- Baicheng Yi
- Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong, Special Administrative Region, China
| | - Waruna Lakmal Dissanayaka
- Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong, Special Administrative Region, China
| | - Chengfei Zhang
- Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong, Special Administrative Region, China.
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122
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Yu B, Li H, Chen J, He Z, Sun H, Yang G, Shang C, Wang X, Li C, Chen Y, Hu Y. Extensively expanded murine-induced hepatic stem cells maintain high-efficient hepatic differentiation potential for repopulation of injured livers. Liver Int 2020; 40:2293-2304. [PMID: 32394491 DOI: 10.1111/liv.14509] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 04/10/2020] [Accepted: 05/04/2020] [Indexed: 12/28/2022]
Abstract
BACKGROUND & AIM Shortage of donor hepatocytes limits hepatocyte transplantation for clinical application. Induced hepatic stem cells (iHepSCs) have capacities of self-renewal and bipotential differentiations. Here, we investigated whether iHepSCs could be extensively expanded, and whether they could differentiate into sufficient functional hepatocytes as donors for transplantation therapy after their extensive expansions. METHODS Murine extensively expanded iHepSCs (50-55 passages) were induced to differentiate into iHepSC-Heps under a chemically defined condition. iHepSC-Heps were proved for carrying morphological hepatocyte characters and hepatocytic functions including low-density lipoprotein uptake, glycogen storage, CLF secretion, ICG uptake and release, Alb secretion, urea synthesis and metabolism-relative gene expressions respectively. Next, both iHepSCs and iHepSC-Heps were transplanted into Fah-/- mice respectively. Both liver repopulation and alleviation of liver function were compared between two transplantation groups. RESULTS Murine iHepSCs still maintained the capacities of self-renewal and bipotential differentiations after extensive expansion. The efficiency for the functional hepatocyte differentiation from extensively expanded iHepSCs reached to 72.64%. Transplantations of both extensively expanded iHepSCs and iHepSC-Heps resulted in liver engraftment in Fah-/- mice. Survival rate of Fah-/- mice recipients and level of liver repopulation were 50% and 20.32 ± 4.58% respectively in iHepSC-Heps group, while 33% and 10.4 ± 4.3% in iHepSCs group. CONCLUSIONS Extensively expanded iHepSCs can efficiently differentiate into hepatocytes in chemical defined medium. Transplantation of iHepSC-Heps was more effective and more efficient than transplantation of iHepSCs in Fah-/- mice. Our results suggested an innovative system to obtain sufficient hepatocytes through hepatic differentiation of iHepSCs generated by lineage reprogramming.
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Affiliation(s)
- Bing Yu
- Department of Cell Biology, Center for Stem Cell and Medicine, Navy Medical University (Second Military Medical University), Shanghai, P. R. China.,Department of Hepatic Surgery V, Eastern Hepatobiliary Surgery Hospital, Navy Medical University (Second Military Medical University), Shanghai, P.R. China
| | - Hengyu Li
- Department of General Surgery IV, Changhai Hospital, Navy Medical University (Second Military Medical University), Shanghai, P.R. China
| | - Jie Chen
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Zhiying He
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, P.R. China
| | - Haixiang Sun
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion (Fudan University), Ministry of Education, Shanghai, China
| | - Guangshun Yang
- Department of Hepatic Surgery V, Eastern Hepatobiliary Surgery Hospital, Navy Medical University (Second Military Medical University), Shanghai, P.R. China
| | - Changzhen Shang
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Xin Wang
- Research Center for Laboratory Animal Science, Inner Mongolia University, Huhhot, P.R. China.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA.,Hepatoscience Section, Cell Lab Tech Incorporation, Sunnyvale, CA, USA
| | - Chuanjiang Li
- Division of Hepatobiliopancreatic Surgery, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, P. R. China
| | - Yajin Chen
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-sen University, Guangzhou, P.R. China
| | - Yiping Hu
- Department of Cell Biology, Center for Stem Cell and Medicine, Navy Medical University (Second Military Medical University), Shanghai, P. R. China
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Campit SE, Meliki A, Youngson NA, Chandrasekaran S. Nutrient Sensing by Histone Marks: Reading the Metabolic Histone Code Using Tracing, Omics, and Modeling. Bioessays 2020; 42:e2000083. [PMID: 32638413 PMCID: PMC11426192 DOI: 10.1002/bies.202000083] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/23/2020] [Indexed: 12/19/2022]
Abstract
Several metabolites serve as substrates for histone modifications and communicate changes in the metabolic environment to the epigenome. Technologies such as metabolomics and proteomics have allowed us to reconstruct the interactions between metabolic pathways and histones. These technologies have shed light on how nutrient availability can have a dramatic effect on various histone modifications. This metabolism-epigenome cross talk plays a fundamental role in development, immune function, and diseases like cancer. Yet, major challenges remain in understanding the interactions between cellular metabolism and the epigenome. How the levels and fluxes of various metabolites impact epigenetic marks is still unclear. Discussed herein are recent applications and the potential of systems biology methods such as flux tracing and metabolic modeling to address these challenges and to uncover new metabolic-epigenetic interactions. These systems approaches can ultimately help elucidate how nutrients shape the epigenome of microbes and mammalian cells.
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Affiliation(s)
- Scott E. Campit
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA 48109
| | - Alia Meliki
- Center for Bioinformatics and Computational Medicine, Ann Arbor, MI, USA 48109
| | - Neil A. Youngson
- Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences and Medicine, King’s College London, London, UK
- School of Medical Sciences, UNSW Sydney, Sydney, Australia
| | - Sriram Chandrasekaran
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA 48109
- Center for Bioinformatics and Computational Medicine, Ann Arbor, MI, USA 48109
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA 48109
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA 48109
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Li S, Shi Y, Yao X, Wang X, Shen L, Rao Z, Yuan J, Liu Y, Zhou Z, Zhang Z, Liu F, Han S, Geng J, Yang H, Cheng L. Conversion of Astrocytes and Fibroblasts into Functional Noradrenergic Neurons. Cell Rep 2020; 28:682-697.e7. [PMID: 31315047 DOI: 10.1016/j.celrep.2019.06.042] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/25/2019] [Accepted: 06/12/2019] [Indexed: 11/18/2022] Open
Abstract
Dysfunction of noradrenergic (NA) neurons is associated with a number of neuronal disorders. Diverse neuronal subtypes can be generated by direct reprogramming. However, it is still unknown how to convert non-neuronal cells into NA neurons. Here, we show that seven transcription factors (TFs) (Ascl1, Phox2b, AP-2α, Gata3, Hand2, Nurr1, and Phox2a) are able to convert astrocytes and fibroblasts into induced NA (iNA) neurons. These iNA neurons express the genes required for the biosynthesis, release, and re-uptake of noradrenaline. Moreover, iNA neurons fire action potentials, receive synaptic inputs, and control the beating rate of co-cultured ventricular myocytes. Furthermore, iNA neurons survive and integrate into neural circuits after transplantation. Last, human fibroblasts can be converted into functional iNA neurons as well. Together, iNA neurons are generated by direct reprogramming, and they could be potentially useful for disease modeling and cell-based therapies.
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Affiliation(s)
- Sanlan Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuhan Shi
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuan Yao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xing Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Libing Shen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhiping Rao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiacheng Yuan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yueguang Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhenning Zhou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ziheng Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Fei Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Su'e Han
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junlan Geng
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Yang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Leping Cheng
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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125
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Wei C, Yu P, Cheng L. Hematopoietic Reprogramming Entangles with Hematopoiesis. Trends Cell Biol 2020; 30:752-763. [PMID: 32861580 DOI: 10.1016/j.tcb.2020.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023]
Abstract
Hematopoiesis generally refers to hematopoietic development in fetuses and adults, as well as to hematopoietic stem cell differentiation into progeny lineages. The multiple processes that generate diverse hematopoietic cells have been considered to be unidirectional. However, many reports have recently demonstrated that these processes are not only reversible but also interconvertible via cell reprogramming. The cell reprogramming that occurs in hematopoietic cells is termed hematopoietic reprogramming. We focus on both autogenous and artificial hematopoietic reprogramming under physiological and pathological conditions that is mainly directed by the actions of transcription factors (TFs), chemical compounds, or extracellular cytokines. A comprehensive understanding of hematopoietic reprogramming will help us not only to generate desirable cells for cell therapy but also to further analyze normal and malignant hematopoiesis.
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Affiliation(s)
- Chuijin Wei
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Pei Yu
- Department of Orthopaedics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lin Cheng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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126
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Del Sol A, Jung S. The Importance of Computational Modeling in Stem Cell Research. Trends Biotechnol 2020; 39:126-136. [PMID: 32800604 DOI: 10.1016/j.tibtech.2020.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 12/30/2022]
Abstract
The generation of large amounts of omics data is increasingly enabling not only the processing and analysis of large data sets but also the development of computational models in the field of stem cell research. Although computational models have been proposed in recent decades, we believe that the stem cell community is not fully aware of the potentiality of computational modeling in guiding their experimental research. In this regard, we discuss how single-cell technologies provide the right framework for computational modeling at different scales of biological organization in order to address challenges in the stem cell field and to guide experimentalists in the design of new strategies for stem cell therapies and treatment of congenital disorders.
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Affiliation(s)
- Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 6 Avenue du Swing, Esch-sur-Alzette, L-4367 Belvaux, Luxembourg; CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Bizkaia Technology Park, 801 Building, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain.
| | - Sascha Jung
- CIC bioGUNE-BRTA (Basque Research and Technology Alliance), Bizkaia Technology Park, 801 Building, 48160 Derio, Spain
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127
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Habibi S, Khamisipour GH, Obeidi N, Zare Jaliseh S. Direct Differentiation of Human Primary Fibroblast into Hematopoietic-Like Stem Cells; A New Way without Viral Transduction. CELL JOURNAL 2020; 22:141-147. [PMID: 32779444 PMCID: PMC7481898 DOI: 10.22074/cellj.2020.6846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/24/2019] [Indexed: 11/04/2022]
Abstract
Objective The aim of this study was to investigate the possibility of producing safe hematopoietic stem cells without
the use of viral infectious agents that can be used in stem cell transplantation.
Materials and Methods In this experimental study, after single layer cell formation, human primary fibroblast cells were
treated with static electromagnetic fields of 10 and 15 milli Tesla (mT) for 20 minutes each day for seven consecutive
days. On the seventh day and immediately after the last radiation, the cells were added to the wells containing specific
hematopoietic stem cell expansion media. After 21 days and colony formation, the cells belonging to each group were
evaluated in terms of the expression of CD34, CD38, and GATA-1 genes using quantitative real-time polymerase chain
reaction (PCR), as well as surface marker expression of CD34 by flow cytometry.
Results Exposure to 10 mT and 15 mT electromagnetic field increased the expression of CD34 and CD38 genes
(P<0.05). This increase in gene expression levels were 2.85 and 1.84 folds, respectively, in the 10mT group and
6.36 and 3.81 folds, respectively, in the 15 mT group. The expression of the GATA-1 gene in the 10 mT and 15 mT
groups was not significantly different from that of the control group (P<0.05). Electromagnetic waves caused a marked
increase in the expression of the CD34 marker at the surface of reprogrammed cells. The rate of expression was about
42.3% in the 15 mT group and 23.1% in the 10 mT group.
Conclusion The presence of human primary fibroblasts exposed to electromagnetic fields can increase the expression
of specific hematopoietic genes. This method can be suitable for reprogramming cells differentiated into hematopoietic-
like stem cells and does not pose the risks of retroviral use.
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Affiliation(s)
- Sina Habibi
- Department of Hematology, Faculty of Allied Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - G Holamreza Khamisipour
- Department of Hematology, Faculty of Allied Medicine, Bushehr University of Medical Sciences, Bushehr, Iran. Electronic Address:
| | - Narges Obeidi
- Department of Hematology, Faculty of Allied Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Saeedeh Zare Jaliseh
- Department of Anatomy, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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128
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Duan J, Li B, Bhakta M, Xie S, Zhou P, Munshi NV, Hon GC. Rational Reprogramming of Cellular States by Combinatorial Perturbation. Cell Rep 2020; 27:3486-3499.e6. [PMID: 31216470 DOI: 10.1016/j.celrep.2019.05.079] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 04/10/2019] [Accepted: 05/20/2019] [Indexed: 12/11/2022] Open
Abstract
Ectopic expression of transcription factors (TFs) can reprogram cell state. However, because of the large combinatorial space of possible TF cocktails, it remains difficult to identify TFs that reprogram specific cell types. Here, we develop Reprogram-Seq to experimentally screen thousands of TF cocktails for reprogramming performance. Reprogram-Seq leverages organ-specific cell-atlas data with single-cell perturbation and computational analysis to predict, evaluate, and optimize TF combinations that reprogram a cell type of interest. Focusing on the cardiac system, we perform Reprogram-Seq on MEFs using an undirected library of 48 cardiac factors and, separately, a directed library of 10 epicardial-related TFs. We identify a combination of three TFs, which efficiently reprogram MEFs to epicardial-like cells that are transcriptionally, molecularly, morphologically, and functionally similar to primary epicardial cells. Reprogram-Seq holds promise to accelerate the generation of specific cell types for regenerative medicine.
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Affiliation(s)
- Jialei Duan
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Boxun Li
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Minoti Bhakta
- Department of Molecular Biology, Department of Internal Medicine, Division of Cardiology, McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shiqi Xie
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pei Zhou
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nikhil V Munshi
- Department of Molecular Biology, Department of Internal Medicine, Division of Cardiology, McDermott Center for Human Growth and Development, UT Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, Dallas, TX 75390, USA.
| | - Gary C Hon
- Laboratory of Regulatory Genomics, Cecil H. and Ida Green Center for Reproductive Biology Sciences, Division of Basic Reproductive Biology Research, Department of Obstetrics and Gynecology, Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, Dallas, TX 75390, USA.
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129
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Overexpression of early T cell differentiation-specific transcription factors transforms the terminally differentiated effector T cells into less differentiated state. Cell Immunol 2020; 353:104118. [DOI: 10.1016/j.cellimm.2020.104118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 04/02/2020] [Accepted: 04/30/2020] [Indexed: 01/15/2023]
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130
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Ruzittu S, Willnow D, Spagnoli FM. Direct Lineage Reprogramming: Harnessing Cell Plasticity between Liver and Pancreas. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a035626. [PMID: 31767653 DOI: 10.1101/cshperspect.a035626] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Direct lineage reprogramming of abundant and accessible cells into therapeutically useful cell types holds tremendous potential in regenerative medicine. To date, a number of different cell types have been generated by lineage reprogramming methods, including cells from the neural, cardiac, hepatic, and pancreatic lineages. The success of this strategy relies on developmental biology and the knowledge of cell-fate-defining transcriptional networks. Hepatocytes represent a prime target for β cell conversion for numerous reasons, including close developmental origin, accessibility, and regenerative potential. We present here an overview of pancreatic and hepatic development, with a particular focus on the mechanisms underlying the divergence between the two cell lineages. Additionally, we discuss to what extent this lineage relationship can be exploited in efforts to reprogram one cell type into the other and whether such an approach may provide a suitable strategy for regenerative therapies of diabetes.
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Affiliation(s)
- Silvia Ruzittu
- Centre for Stem Cell and Regenerative Medicine, King's College London, London SE1 9RT, United Kingdom.,Max Delbrück Center for Molecular Medicine (MDC), D-13125 Berlin, Germany
| | - David Willnow
- Centre for Stem Cell and Regenerative Medicine, King's College London, London SE1 9RT, United Kingdom
| | - Francesca M Spagnoli
- Centre for Stem Cell and Regenerative Medicine, King's College London, London SE1 9RT, United Kingdom
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131
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Menendez L, Trecek T, Gopalakrishnan S, Tao L, Markowitz AL, Yu HV, Wang X, Llamas J, Huang C, Lee J, Kalluri R, Ichida J, Segil N. Generation of inner ear hair cells by direct lineage conversion of primary somatic cells. eLife 2020; 9:e55249. [PMID: 32602462 PMCID: PMC7326493 DOI: 10.7554/elife.55249] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023] Open
Abstract
The mechanoreceptive sensory hair cells in the inner ear are selectively vulnerable to numerous genetic and environmental insults. In mammals, hair cells lack regenerative capacity, and their death leads to permanent hearing loss and vestibular dysfunction. Their paucity and inaccessibility has limited the search for otoprotective and regenerative strategies. Growing hair cells in vitro would provide a route to overcome this experimental bottleneck. We report a combination of four transcription factors (Six1, Atoh1, Pou4f3, and Gfi1) that can convert mouse embryonic fibroblasts, adult tail-tip fibroblasts and postnatal supporting cells into induced hair cell-like cells (iHCs). iHCs exhibit hair cell-like morphology, transcriptomic and epigenetic profiles, electrophysiological properties, mechanosensory channel expression, and vulnerability to ototoxin in a high-content phenotypic screening system. Thus, direct reprogramming provides a platform to identify causes and treatments for hair cell loss, and may help identify future gene therapy approaches for restoring hearing.
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Affiliation(s)
- Louise Menendez
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesUnited States
| | - Talon Trecek
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
| | - Suhasni Gopalakrishnan
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesUnited States
| | - Litao Tao
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
| | - Alexander L Markowitz
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesUnited States
- USC Caruso Department of Otolaryngology – Head and Neck Surgery, University of Southern CaliforniaLos AngelesUnited States
| | - Haoze V Yu
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
| | - Xizi Wang
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
| | - Juan Llamas
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
| | | | - James Lee
- DRVision TechnologiesBellevueUnited States
| | - Radha Kalluri
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesUnited States
- USC Caruso Department of Otolaryngology – Head and Neck Surgery, University of Southern CaliforniaLos AngelesUnited States
| | - Justin Ichida
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
- Zilkha Neurogenetic Institute, University of Southern CaliforniaLos AngelesUnited States
| | - Neil Segil
- Department of Stem Cell and Regenerative Medicine, University of Southern CaliforniaLos AngelesUnited States
- Eli and Edythe Broad Center, University of Southern CaliforniaLos AngelesUnited States
- USC Caruso Department of Otolaryngology – Head and Neck Surgery, University of Southern CaliforniaLos AngelesUnited States
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132
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3Scover: Identifying Safeguard TF from Cell Type-TF Specificity Network by an Extended Minimum Set Cover Model. iScience 2020; 23:101227. [PMID: 32554189 PMCID: PMC7303665 DOI: 10.1016/j.isci.2020.101227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/27/2020] [Accepted: 05/28/2020] [Indexed: 11/22/2022] Open
Abstract
Transcription factors (TFs) define cellular identity either by activating target cell program or by silencing donor program as demonstrated by intensive cell reprogramming studies. Here, we propose an extended minimum set cover model with stable selection (3Scover) to systematically identify silencing TFs, named safeguard TFs, from omics data. First, a cell type-TF specificity network is constructed to systematically link cell types with their specifically expressed TFs. Then we search the minimum TF set to cover this network with “many but one specificity” characteristic and integrate many subsampling models for a stable solution. 3Scover identified 30 safeguard TFs in human and mouse. These safeguard TFs are significantly enriched in the experimentally discovered reprogramming panel with their protein-protein interactors. In addition, they tend to interact closely with chromatin regulators, negatively regulate transcription, and function earlier in development. Collectively, 3Scover allows us to probe master TFs and combinatorial regulation in controlling cell identity. Cell type-TF specificity networks reveal the relationships among TF and cell identity 3SCover extracts safeguard TFs by “many but one specificity” and parsimony principle Safeguard TFs are enriched in reprogramming panel and interact closely with CR Safeguard TFs are conserved in mouse and human
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133
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Lee H, Lee HY, Lee BE, Gerovska D, Park SY, Zaehres H, Araúzo-Bravo MJ, Kim JI, Ha Y, Schöler HR, Kim JB. Sequentially induced motor neurons from human fibroblasts facilitate locomotor recovery in a rodent spinal cord injury model. eLife 2020; 9:e52069. [PMID: 32571478 PMCID: PMC7311175 DOI: 10.7554/elife.52069] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 05/22/2020] [Indexed: 01/07/2023] Open
Abstract
Generation of autologous human motor neurons holds great promise for cell replacement therapy to treat spinal cord injury (SCI). Direct conversion allows generation of target cells from somatic cells, however, current protocols are not practicable for therapeutic purposes since converted cells are post-mitotic that are not scalable. Therefore, therapeutic effects of directly converted neurons have not been elucidated yet. Here, we show that human fibroblasts can be converted into induced motor neurons (iMNs) by sequentially inducing POU5F1(OCT4) and LHX3. Our strategy enables scalable production of pure iMNs because of the transient acquisition of proliferative iMN-intermediate cell stage which is distinct from neural progenitors. iMNs exhibited hallmarks of spinal motor neurons including transcriptional profiles, electrophysiological property, synaptic activity, and neuromuscular junction formation. Remarkably, transplantation of iMNs showed therapeutic effects, promoting locomotor functional recovery in rodent SCI model. Together, our advanced strategy will provide tools to acquire sufficient human iMNs that may represent a promising cell source for personalized cell therapy.
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Affiliation(s)
- Hyunah Lee
- Hans Schöler Stem Cell Research Center (HSSCRC), Ulsan National Institute of Science and Technology (UNIST)UlsanRepublic of Korea
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST)UlsanRepublic of Korea
| | - Hye Yeong Lee
- Department of Neurosurgery, Spine and Spinal Cord Institute, Severance Hospital, Yonsei University College of MedicineSeoulRepublic of Korea
| | - Byeong Eun Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST)UlsanRepublic of Korea
| | - Daniela Gerovska
- Computational Biology and Systems Biomedicine Group, Computational Biomedicine Data Analysis Platform, Biodonostia Health Research InstituteSan SebastiánSpain
| | - Soo Yong Park
- Hans Schöler Stem Cell Research Center (HSSCRC), Ulsan National Institute of Science and Technology (UNIST)UlsanRepublic of Korea
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST)UlsanRepublic of Korea
| | - Holm Zaehres
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular BiomedicineMünsterGermany
| | - Marcos J Araúzo-Bravo
- Computational Biology and Systems Biomedicine Group, Computational Biomedicine Data Analysis Platform, Biodonostia Health Research InstituteSan SebastiánSpain
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular BiomedicineMünsterGermany
- IKERBASQUE, Basque Foundation for ScienceBilbaoSpain
| | - Jae-Ick Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST)UlsanRepublic of Korea
| | - Yoon Ha
- Department of Neurosurgery, Spine and Spinal Cord Institute, Severance Hospital, Yonsei University College of MedicineSeoulRepublic of Korea
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular BiomedicineMünsterGermany
| | - Jeong Beom Kim
- Hans Schöler Stem Cell Research Center (HSSCRC), Ulsan National Institute of Science and Technology (UNIST)UlsanRepublic of Korea
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST)UlsanRepublic of Korea
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134
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Chiche A, Chen C, Li H. The crosstalk between cellular reprogramming and senescence in aging and regeneration. Exp Gerontol 2020; 138:111005. [PMID: 32561400 DOI: 10.1016/j.exger.2020.111005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/17/2020] [Accepted: 06/10/2020] [Indexed: 02/09/2023]
Abstract
Aging is associated with diminished regenerative capacity and increased risk of chronic diseases. There is now compelling evidence suggests that aging process is reversible. Besides metabolic modification and systematic factors, both senescence elimination and cellular reprogramming showed beneficial effects on tissue regeneration and rejuvenation. Here we review recent studies on the interplay between cellular senescence and reprogramming. We discuss how both strategies could impact aging process and the possibility of combine them for more efficient regeneration and rejuvenation.
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Affiliation(s)
- Aurélie Chiche
- Cellular Plasticity and Disease Modelling, Department of Developmental and Stem Cell Biology, CNRS UMR 3738, Institut Pasteur, 25 Rue du Dr Roux, Paris 75015, France
| | - Cheng Chen
- Cellular Plasticity and Disease Modelling, Department of Developmental and Stem Cell Biology, CNRS UMR 3738, Institut Pasteur, 25 Rue du Dr Roux, Paris 75015, France
| | - Han Li
- Cellular Plasticity and Disease Modelling, Department of Developmental and Stem Cell Biology, CNRS UMR 3738, Institut Pasteur, 25 Rue du Dr Roux, Paris 75015, France.
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135
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Biophysical studies of protein misfolding and aggregation in in vivo models of Alzheimer's and Parkinson's diseases. Q Rev Biophys 2020; 49:e22. [PMID: 32493529 DOI: 10.1017/s0033583520000025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Neurodegenerative disorders, including Alzheimer's (AD) and Parkinson's diseases (PD), are characterised by the formation of aberrant assemblies of misfolded proteins. The discovery of disease-modifying drugs for these disorders is challenging, in part because we still have a limited understanding of their molecular origins. In this review, we discuss how biophysical approaches can help explain the formation of the aberrant conformational states of proteins whose neurotoxic effects underlie these diseases. We discuss in particular models based on the transgenic expression of amyloid-β (Aβ) and tau in AD, and α-synuclein in PD. Because biophysical methods have enabled an accurate quantification and a detailed understanding of the molecular mechanisms underlying protein misfolding and aggregation in vitro, we expect that the further development of these methods to probe directly the corresponding mechanisms in vivo will open effective routes for diagnostic and therapeutic interventions.
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136
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Wu H, Du C, Yang F, Zheng X, Qiu D, Zhang Q, Chen W, Xu Y. Generation of hepatocyte-like cells from human urinary epithelial cells and the role of autophagy during direct reprogramming. Biochem Biophys Res Commun 2020; 527:723-729. [DOI: 10.1016/j.bbrc.2020.03.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 03/20/2020] [Indexed: 12/20/2022]
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137
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Rosa FF, Pires CF, Zimmermannova O, Pereira CF. Direct Reprogramming of Mouse Embryonic Fibroblasts to Conventional Type 1 Dendritic Cells by Enforced Expression of Transcription Factors. Bio Protoc 2020; 10:e3619. [PMID: 33659292 PMCID: PMC7842401 DOI: 10.21769/bioprotoc.3619] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/11/2020] [Accepted: 03/29/2020] [Indexed: 02/02/2023] Open
Abstract
Ectopic expression of transcription factor combinations has been recently demonstrated to reprogram differentiated somatic cells towards the dendritic cell (DC) lineage without reversion to a multipotent state. DCs have the ability to induce potent and long-lasting adaptive immune responses. In particular, conventional type 1 DCs (cDC1s) excel on antigen cross-presentation, a critical step for inducing CD8+ T cell cytotoxic responses. The rarity of naturally occurring cDC1s and lack of in vitro methodologies for the generation of pure cDC1 populations strongly hinders the study of cDC1 lineage specification and function. Here, we describe a protocol for the generation of induced DCs (iDCs) by lentiviral-mediated expression of the transcription factors PU.1, IRF8 and BATF3 in mouse embryonic fibroblasts. iDCs acquire DC morphology, cDC1 phenotype and transcriptional signatures within 9 days. iDCs generated with this protocol acquire functional ability to respond to inflammatory stimuli, engulf dead cells, process and cross-present antigens to CD8+ T cells. DC reprogramming provides a simple and tractable system to generate high numbers of cDC1-like cells for high content screening, opening new avenues to better understand cDC1 specification and function. In the future, faithful induction of cDC1 fate in fibroblasts may lead to the generation of patient-specific DCs for vaccination.
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Affiliation(s)
- Fábio F. Rosa
- Cell Reprogramming in Hematopoiesis and Immunity Laboratory, Lund Stem Cell Center, Department of Molecular Medicine and Gene Therapy, Lund University, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Cristiana F. Pires
- Cell Reprogramming in Hematopoiesis and Immunity Laboratory, Lund Stem Cell Center, Department of Molecular Medicine and Gene Therapy, Lund University, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Olga Zimmermannova
- Cell Reprogramming in Hematopoiesis and Immunity Laboratory, Lund Stem Cell Center, Department of Molecular Medicine and Gene Therapy, Lund University, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
| | - Carlos-Filipe Pereira
- Cell Reprogramming in Hematopoiesis and Immunity Laboratory, Lund Stem Cell Center, Department of Molecular Medicine and Gene Therapy, Lund University, Lund, Sweden
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
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138
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Zheng J, Yun W, Park J, Kang PJ, Lee G, Song G, Kim IY, You S. Long-term expansion of directly reprogrammed keratinocyte-like cells and in vitro reconstitution of human skin. J Biomed Sci 2020; 27:56. [PMID: 32312260 PMCID: PMC7171822 DOI: 10.1186/s12929-020-00642-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/26/2020] [Indexed: 11/29/2022] Open
Abstract
Background Human keratinocytes and derived products are crucial for skin repair and regeneration. Despite substantial advances in engineered skin equivalents, their poor availability and immunorejection remain major challenges in skin grafting. Methods Induced keratinocyte-like cells (iKCs) were directly reprogrammed from human urine cells by retroviral transduction of two lineage-specific transcription factors BMI1 and △NP63α (BN). Expression of keratinocyte stem cell or their differentiation markers were assessed by PCR, immunofluorescence and RNA-Sequencing. Regeneration capacity of iKCs were assessed by reconstitution of a human skin equivalent under air-interface condition. Results BN-driven iKCs were similar to primary keratinocytes (pKCs) in terms of their morphology, protein expression, differentiation potential, and global gene expression. Moreover, BN-iKCs self-assembled to form stratified skin equivalents in vitro. Conclusions This study demonstrated an approach to generate human iKCs that could be directly reprogrammed from human somatic cells and extensively expanded in serum- and feeder cell-free systems, which will facilitate their broad applicability in an efficient and patient-specific manner.
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Affiliation(s)
- Jie Zheng
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.,Institute of Animal Molecular Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Wonjin Yun
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.,Institute of Animal Molecular Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Junghyun Park
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.,Institute of Animal Molecular Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Phil Jun Kang
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.,Institute of Animal Molecular Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Gilju Lee
- Department of Pathology, College of Medicine, Korea University Guro Hospital, Seoul, 08308, Republic of Korea
| | - Gwonhwa Song
- Institute of Animal Molecular Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
| | - In Yong Kim
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
| | - Seungkwon You
- Laboratory of Cell Function Regulation, Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea. .,Institute of Animal Molecular Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
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139
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Pro-neuronal activity of Myod1 due to promiscuous binding to neuronal genes. Nat Cell Biol 2020; 22:401-411. [PMID: 32231311 DOI: 10.1038/s41556-020-0490-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 02/18/2020] [Indexed: 12/25/2022]
Abstract
The on-target pioneer factors Ascl1 and Myod1 are sequence-related but induce two developmentally unrelated lineages-that is, neuronal and muscle identities, respectively. It is unclear how these two basic helix-loop-helix (bHLH) factors mediate such fundamentally different outcomes. The chromatin binding of Ascl1 and Myod1 was surprisingly similar in fibroblasts, yet their transcriptional outputs were drastically different. We found that quantitative binding differences explained differential chromatin remodelling and gene activation. Although strong Ascl1 binding was exclusively associated with bHLH motifs, strong Myod1-binding sites were co-enriched with non-bHLH motifs, possibly explaining why Ascl1 is less context dependent. Finally, we observed that promiscuous binding of Myod1 to neuronal targets results in neuronal reprogramming when the muscle program is inhibited by Myt1l. Our findings suggest that chromatin access of on-target pioneer factors is primarily driven by the protein-DNA interaction, unlike ordinary context-dependent transcription factors, and that promiscuous transcription factor binding requires specific silencing mechanisms to ensure lineage fidelity.
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140
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A developed serum-free medium and an optimized chemical cocktail for direct conversion of human dermal fibroblasts into brown adipocytes. Sci Rep 2020; 10:3775. [PMID: 32111895 PMCID: PMC7048747 DOI: 10.1038/s41598-020-60769-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/17/2020] [Indexed: 01/12/2023] Open
Abstract
Brown adipocytes coordinate systemic energy metabolism associated with the pathogenesis of obesity and related metabolic diseases including type 2 diabetes. We have previously reported chemical compound-induced brown adipocytes (ciBAs) converted from human dermal fibroblasts without using transgenes. In this study, to reveal a precise molecular mechanism underlying the direct conversion and human adipocyte browning, we developed serum-free brown adipogenic medium (SFBAM) with an optimized chemical cocktail consisting of Rosiglitazone, Forskolin, and BMP7. During the direct conversion, treatment with BMP7 enhanced Ucp1 expression rather than the conversion efficiency in the absence of BMP signalling inhibitors. Moreover, treatment with a TGF-β signalling pathway inhibitor was no longer required in the serum-free medium, likely because the TGF-β pathway was already suppressed. SFBAM and the chemical cocktail efficiently converted human dermal fibroblasts into ciBAs within four weeks. The ciBAs exhibited increased mitochondrial levels, elevated oxygen consumption rate, and a response to β-adrenergic receptor agonists. Thus the ciBAs converted by the serum-free medium and the chemical cocktail provide a novel model of human brown (beige) adipocytes applicable for basic research, drug screening, and clinical applications.
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141
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142
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Differentiation of human pluripotent stem cells toward pharyngeal endoderm derivatives: Current status and potential. Curr Top Dev Biol 2020; 138:175-208. [PMID: 32220297 DOI: 10.1016/bs.ctdb.2020.01.004] [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] [Indexed: 12/04/2022]
Abstract
The pharyngeal apparatus, a transient embryological structure, includes diverse cells from all three germ layers that ultimately contribute to a variety of adult tissues. In particular, pharyngeal endoderm produces cells of the inner ear, palatine tonsils, the thymus, parathyroid and thyroid glands, and ultimobranchial bodies. Each of these structures and organs contribute to vital human physiological processes, including central immune tolerance (thymus) and metabolic homeostasis (parathyroid and thyroid glands, and ultimobranchial bodies). Thus, improper development or damage to pharyngeal endoderm derivatives leads to complicated and severe human maladies, such as autoimmunity, immunodeficiency, hypothyroidism, and/or hypoparathyroidism. To study and treat such diseases, we can utilize human pluripotent stem cells (hPSCs), which differentiate into functionally mature cells in vitro given the proper developmental signals. Here, we discuss current efforts regarding the directed differentiation of hPSCs toward pharyngeal endoderm derivatives. We further discuss model system and therapeutic applications of pharyngeal endoderm cell types produced from hPSCs. Finally, we provide suggestions for improving hPSC differentiation approaches to pharyngeal endoderm derivatives with emphasis on current single cell-omics and 3D culture system technologies.
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143
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Fang J, Hsueh YY, Soto J, Sun W, Wang J, Gu Z, Khademhosseini A, Li S. Engineering Biomaterials with Micro/Nanotechnologies for Cell Reprogramming. ACS NANO 2020; 14:1296-1318. [PMID: 32011856 PMCID: PMC10067273 DOI: 10.1021/acsnano.9b04837] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cell reprogramming is a revolutionized biotechnology that offers a powerful tool to engineer cell fate and function for regenerative medicine, disease modeling, drug discovery, and beyond. Leveraging advances in biomaterials and micro/nanotechnologies can enhance the reprogramming performance in vitro and in vivo through the development of delivery strategies and the control of biophysical and biochemical cues. In this review, we present an overview of the state-of-the-art technologies for cell reprogramming and highlight the recent breakthroughs in engineering biomaterials with micro/nanotechnologies to improve reprogramming efficiency and quality. Finally, we discuss future directions and challenges for reprogramming technologies and clinical translation.
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Affiliation(s)
- Jun Fang
- Department of Bioengineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Medicine , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Yuan-Yu Hsueh
- Department of Bioengineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Division of Plastic Surgery, Department of Surgery, College of Medicine , National Cheng Kung University Hospital , Tainan 70456 , Taiwan
| | - Jennifer Soto
- Department of Bioengineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Medicine , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Wujin Sun
- Department of Bioengineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Center for Minimally Invasive Therapeutics (C-MIT), California NanoSystems Institute , University of California, Los Angeles , Los Angles , California 90095 , United States
| | - Jinqiang Wang
- Department of Bioengineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Center for Minimally Invasive Therapeutics (C-MIT), California NanoSystems Institute , University of California, Los Angeles , Los Angles , California 90095 , United States
| | - Zhen Gu
- Department of Bioengineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Center for Minimally Invasive Therapeutics (C-MIT), California NanoSystems Institute , University of California, Los Angeles , Los Angles , California 90095 , United States
- Jonsson Comprehensive Cancer Center , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Ali Khademhosseini
- Department of Bioengineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Center for Minimally Invasive Therapeutics (C-MIT), California NanoSystems Institute , University of California, Los Angeles , Los Angles , California 90095 , United States
- Department of Chemical and Biomolecular Engineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Radiology , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Song Li
- Department of Bioengineering , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Department of Medicine , University of California, Los Angeles , Los Angeles , California 90095 , United States
- Center for Minimally Invasive Therapeutics (C-MIT), California NanoSystems Institute , University of California, Los Angeles , Los Angles , California 90095 , United States
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144
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Kim Y, Jeong J, Choi D. Small-molecule-mediated reprogramming: a silver lining for regenerative medicine. Exp Mol Med 2020; 52:213-226. [PMID: 32080339 PMCID: PMC7062739 DOI: 10.1038/s12276-020-0383-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 12/01/2019] [Accepted: 12/27/2019] [Indexed: 12/25/2022] Open
Abstract
Techniques for reprogramming somatic cells create new opportunities for drug screening, disease modeling, artificial organ development, and cell therapy. The development of reprogramming techniques has grown exponentially since the discovery of induced pluripotent stem cells (iPSCs) by the transduction of four factors (OCT3/4, SOX2, c-MYC, and KLF4) in mouse embryonic fibroblasts. Initial studies on iPSCs led to direct-conversion techniques using transcription factors expressed mainly in target cells. However, reprogramming transcription factors with a virus risks integrating viral DNA and can be complicated by oncogenes. To address these problems, many researchers are developing reprogramming methods that use clinically applicable small molecules and growth factors. This review summarizes research trends in reprogramming cells using small molecules and growth factors, including their modes of action. The reprogramming of cells using small molecules to generate viable, safe stem-cell populations could transform stem-cell therapies, disease modeling and artificial organ development. Existing ways of reprogramming cells to generate stem cells carry risks, because the methods used often involve using viral DNA components or oncogenes, genes with the potential to turn cells into tumour cells. Safer, inexpensive alternatives are sought by scientists, and the efficient reprogramming of cells using small molecules and growth factors shows promise. Dongho Choi and co-workers at Hanyang University College of Medicine in Seoul, South Korea, reviewed recent research highlighting how small molecules including chemical compounds, plant derivatives and certain approved drugs are being used effectively to create different stem-cell populations. Recent successes are also contributing valuable insights into how stem cells differentiate into different cell types.
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Affiliation(s)
- Yohan Kim
- Department of Surgery, Hanyang University College of Medicine, Seoul, 04763, Korea.,HY Indang Center of Regenerative Medicine and Stem Cell Research, Hanyang University, Seoul, 04763, Korea
| | - Jaemin Jeong
- Department of Surgery, Hanyang University College of Medicine, Seoul, 04763, Korea.,HY Indang Center of Regenerative Medicine and Stem Cell Research, Hanyang University, Seoul, 04763, Korea
| | - Dongho Choi
- Department of Surgery, Hanyang University College of Medicine, Seoul, 04763, Korea. .,HY Indang Center of Regenerative Medicine and Stem Cell Research, Hanyang University, Seoul, 04763, Korea.
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145
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Chng SH, Pachnis V. Enteric Nervous System: lessons from neurogenesis for reverse engineering and disease modelling and treatment. Curr Opin Pharmacol 2020; 50:100-106. [DOI: 10.1016/j.coph.2020.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/28/2020] [Accepted: 02/13/2020] [Indexed: 12/18/2022]
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146
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Song B, Lee JM, Park YJ, Kim IK, Kim BS, Shin KS, Jeon I, Koh CH, Bae EA, Seo H, Byun Y, Kang CY. Differentiation of c-Kit + CD24 + natural killer cells into myeloid cells in a GATA-2-dependent manner. FASEB J 2020; 34:4462-4481. [PMID: 31989715 DOI: 10.1096/fj.201902662r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 12/26/2019] [Accepted: 01/14/2020] [Indexed: 01/09/2023]
Abstract
Myeloid progenitor cells have generally been considered the predominant source of myeloid cells under steady-state conditions. Here we show that NK cells contributed to a myeloid cell lineage pool in naïve and tumor-bearing mice. Using fate tracing of NKp46+ cells, we found that myeloid cells could be derived from NK cells. Notably, among mature CD11b+ CD27+ NK cells, c-Kit+ CD24+ NK cells were capable of differentiating into a range of myeloid lineages in vitro and produced neutrophils and monocytes in vivo. The differentiation was completely inhibited by NK-stimulating cytokines. In addition to the potential for differentiation into myeloid cells, c-Kit+ CD24+ NK cells retained NK cell phenotypes and effector functions. Mechanistically, GATA-2 was necessary for the differentiation of c-Kit+ CD24+ NK cells. Therefore, we discovered that GATA-2-dependent differentiation of c-Kit+ CD24+ NK cells contributes to myeloid cell development and identified a novel pathway for myeloid lineage commitment under physiological conditions.
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Affiliation(s)
- Boyeong Song
- Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Jeong-Mi Lee
- Laboratory of Immunology, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Young-Jun Park
- Laboratory of Immune Regulation, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Il-Kyu Kim
- Laboratory of Immunology, Research Institute of Pharmaceutical Science, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Byung-Seok Kim
- Laboratory of Immune Regulation, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Kwang-Soo Shin
- Laboratory of Immunology, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Insu Jeon
- Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Choong-Hyun Koh
- Laboratory of Immunology, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Eun-Ah Bae
- Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Hyungseok Seo
- Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea.,Laboratory of Immunology, Research Institute of Pharmaceutical Science, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Youngro Byun
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Chang-Yuil Kang
- Laboratory of Immunology, Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea.,Laboratory of Immunology, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
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147
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Zhao A, Yang Y, Pan X, Pan Y, Cai S. Generation of keratinocyte stem-like cells from human fibroblasts via a direct reprogramming approach. Biotechnol Prog 2020; 36:e2961. [PMID: 31930712 DOI: 10.1002/btpr.2961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 12/29/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022]
Abstract
Skin repair and reconstruction are important after severe wound and trauma. Keratinocyte stem cells (KSCs) in the basal layer of the epidermis can regrow the stratified epidermis but are almost depleted after skin injury. Thus, generating enough KSCs is indispensable for skin regeneration. Pluripotent stem cells such as ESC and iPSC can differentiate into KSCs, but their applications are challenged by ethical issues and risks of tumor formation. Lineage reprogramming from one cell type into another one makes it feasible to generate the desired cell type. Here, we develop a method to convert human fibroblasts into induced keratinocyte stem-like cells (iKSC) by coupling transient expression of reprogramming factors with a chemically defined culture medium, without the formation of iPSC. iKSC resemble normal KSC in the morphological and phenotypic features and can differentiate in vitro and regenerate stratified epidermis after transplantation in vivo. Therefore, iKSC may provide abundant cellular sources for skin repair and regeneration.
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Affiliation(s)
- Andong Zhao
- Health Science Center, Shenzhen University, Shenzhen, China
| | - Yi Yang
- Health Science Center, Shenzhen University, Shenzhen, China
| | - Xiaohua Pan
- Department of Trauma and Orthopedics, The Affiliated Baoan Hospital of Southern Medical University, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yu Pan
- Department of Trauma and Orthopedics, The Affiliated Baoan Hospital of Southern Medical University, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Sa Cai
- Health Science Center, Shenzhen University, Shenzhen, China
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148
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Abstract
Cardiovascular disease is the leading cause of death worldwide. Cardiomyocytes have limited regenerative capacity; consequently, regenerative therapies are in high demand. There are currently several potential strategies for heart regeneration, with one approach involving in situ generation of new cardiomyocytes from endogenous cell sources. Direct cardiac reprogramming has emerged as a novel therapeutic approach to regenerating the damaged heart by directly converting endogenous cardiac fibroblasts into cardiomyocyte-like cells. Following our first report of direct cardiac reprogramming, significant advances have elucidated the molecular mechanisms associated with cardiac reprogramming. These advances have also improved cardiac-reprogramming efficiency by enabling direct in vivo cardiac reprogramming. Moreover, progress has been made in cardiac reprogramming of human fibroblasts. Although basic research has supported substantial progress in this field, numerous challenges remain in terms of clinical application. Here, we review the current state of cardiac reprogramming as a new technology for understanding and treating cardiovascular diseases.
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149
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Song Y, Soto J, Chen B, Yang L, Li S. Cell engineering: Biophysical regulation of the nucleus. Biomaterials 2020; 234:119743. [PMID: 31962231 DOI: 10.1016/j.biomaterials.2019.119743] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/02/2019] [Accepted: 12/25/2019] [Indexed: 12/12/2022]
Abstract
Cells live in a complex and dynamic microenvironment, and a variety of microenvironmental cues can regulate cell behavior. In addition to biochemical signals, biophysical cues can induce not only immediate intracellular responses, but also long-term effects on phenotypic changes such as stem cell differentiation, immune cell activation and somatic cell reprogramming. Cells respond to mechanical stimuli via an outside-in and inside-out feedback loop, and the cell nucleus plays an important role in this process. The mechanical properties of the nucleus can directly or indirectly modulate mechanotransduction, and the physical coupling of the cell nucleus with the cytoskeleton can affect chromatin structure and regulate the epigenetic state, gene expression and cell function. In this review, we will highlight the recent progress in nuclear biomechanics and mechanobiology in the context of cell engineering, tissue remodeling and disease development.
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Affiliation(s)
- Yang Song
- Department of Bioengineering, University of California, Los Angeles, CA, USA; School of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Jennifer Soto
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Binru Chen
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Li Yang
- School of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Song Li
- Department of Bioengineering, University of California, Los Angeles, CA, USA; Department of Medicine, University of California, Los Angeles, CA, USA.
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150
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Direct Reprogramming Into Corneal Epithelial Cells Using a Transcriptional Network Comprising PAX6, OVOL2, and KLF4. Cornea 2019; 38 Suppl 1:S34-S41. [PMID: 31403532 DOI: 10.1097/ico.0000000000002074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In its early stages, an embryo polarizes to form cell subpopulations that subsequently produce specific organ cell types. These cell subpopulations are defined by transcription factors (TFs) that activate or repress specific genes. Although an embryo comprises thousands of TFs, surprisingly few are needed to determine the fate of a given cell. The ectoderm divides into the neuroectoderm and surface ectoderm, the latter of which gives rise to epidermal keratinocytes and corneal epithelial cells (CECs). Meanwhile, neuroectoderm cells give rise to other parts of the eye such as the corneal endothelium and retina. To investigate the regulatory role of TFs in CECs, we overexpressed the "core TFs" (PAX6, OVOL2, and KLF4) in human fibroblasts and found that the cells adopted a CEC-like quality. OVOL2 overexpression was even able to directly induce cells with a neuroectoderm fate toward a surface ectoderm fate, designated "direct reprogramming." Conversely, suppression of OVOL2 or PAX6 expression induced CECs to show qualities consistent with neural lineage cells or epidermal keratinocytes, respectively. This suggests that these core TFs can maintain the CEC phenotype through reciprocal gene regulation. Direct reprogramming has important implications for cell therapies. The potential benefits of cells derived by direct reprogramming compared with induced pluripotent stem cells include the fact that it requires less time than reprogramming a cell back to the pluripotent state and then to another cell type. Further understanding of the reciprocally repressive mechanism of action for core TFs could lead to alternative treatments for regenerative medicine not requiring cell transplantation.
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