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Yin X, Li Q, Shu Y, Wang H, Thomas B, Maxwell JT, Zhang Y. Exploiting urine-derived induced pluripotent stem cells for advancing precision medicine in cell therapy, disease modeling, and drug testing. J Biomed Sci 2024; 31:47. [PMID: 38724973 PMCID: PMC11084032 DOI: 10.1186/s12929-024-01035-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
The field of regenerative medicine has witnessed remarkable advancements with the emergence of induced pluripotent stem cells (iPSCs) derived from a variety of sources. Among these, urine-derived induced pluripotent stem cells (u-iPSCs) have garnered substantial attention due to their non-invasive and patient-friendly acquisition method. This review manuscript delves into the potential and application of u-iPSCs in advancing precision medicine, particularly in the realms of drug testing, disease modeling, and cell therapy. U-iPSCs are generated through the reprogramming of somatic cells found in urine samples, offering a unique and renewable source of patient-specific pluripotent cells. Their utility in drug testing has revolutionized the pharmaceutical industry by providing personalized platforms for drug screening, toxicity assessment, and efficacy evaluation. The availability of u-iPSCs with diverse genetic backgrounds facilitates the development of tailored therapeutic approaches, minimizing adverse effects and optimizing treatment outcomes. Furthermore, u-iPSCs have demonstrated remarkable efficacy in disease modeling, allowing researchers to recapitulate patient-specific pathologies in vitro. This not only enhances our understanding of disease mechanisms but also serves as a valuable tool for drug discovery and development. In addition, u-iPSC-based disease models offer a platform for studying rare and genetically complex diseases, often underserved by traditional research methods. The versatility of u-iPSCs extends to cell therapy applications, where they hold immense promise for regenerative medicine. Their potential to differentiate into various cell types, including neurons, cardiomyocytes, and hepatocytes, enables the development of patient-specific cell replacement therapies. This personalized approach can revolutionize the treatment of degenerative diseases, organ failure, and tissue damage by minimizing immune rejection and optimizing therapeutic outcomes. However, several challenges and considerations, such as standardization of reprogramming protocols, genomic stability, and scalability, must be addressed to fully exploit u-iPSCs' potential in precision medicine. In conclusion, this review underscores the transformative impact of u-iPSCs on advancing precision medicine and highlights the future prospects and challenges in harnessing this innovative technology for improved healthcare outcomes.
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Affiliation(s)
- Xiya Yin
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Burn and Plastic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Qingfeng Li
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yan Shu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Hongbing Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Biju Thomas
- Keck School of Medicine, Roski Eye Institute, University of Southern California, Los Angeles, CA, 90033, USA
| | - Joshua T Maxwell
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA
| | - Yuanyuan Zhang
- Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, NC, USA.
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2
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Sichani AS, Khoddam S, Shakeri S, Tavakkoli Z, Jafroodi AR, Dabbaghipour R, Sisakht M, Fallahi J. Partial Reprogramming as a Method for Regenerating Neural Tissues in Aged Organisms. Cell Reprogram 2024; 26:10-23. [PMID: 38381402 DOI: 10.1089/cell.2023.0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
Aging causes numerous age-related diseases, leading the human species to death. Nevertheless, rejuvenating strategies based on cell epigenetic modifications are a possible approach to counteract disease progression while getting old. Cell reprogramming of adult somatic cells toward pluripotency ought to be a promising tool for age-related diseases. However, researchers do not have control over this process as cells lose their fate, and cause potential cancerous cells or unexpected cell phenotypes. Direct and partial reprogramming were introduced in recent years with distinctive applications. Although direct reprogramming makes cells lose their identity, it has various applications in regeneration medicine. Temporary and regulated in vivo overexpression of Yamanaka factors has been shown in several experimental contexts to be achievable and is used to rejuvenate mice models. This regeneration can be accomplished by altering the epigenetic adult cell signature to the signature of a younger cell. The greatest advantage of partial reprogramming is that this method does not allow cells to lose their identity when they are resetting their epigenetic clock. It is a regimen of short-term Oct3/4, Sox2, Klf4, and c-Myc expression in vivo that prevents full reprogramming to the pluripotent state and avoids both tumorigenesis and the presence of unwanted undifferentiated cells. We know that many neurological age-related diseases, such as Alzheimer's disease, stroke, dementia, and Parkinson's disease, are the main cause of death in the last decades of life. Therefore, scientists have a special tendency regarding neuroregeneration methods to increase human life expectancy.
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Affiliation(s)
- Ali Saber Sichani
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Somayeh Khoddam
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shayan Shakeri
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Tavakkoli
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Arad Ranji Jafroodi
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Dabbaghipour
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohsen Sisakht
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jafar Fallahi
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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3
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Weng M, Hu H, Graus MS, Tan DS, Gao Y, Ren S, Ho DHH, Langer J, Holzner M, Huang Y, Ling GS, Lai CSW, Francois M, Jauch R. An engineered Sox17 induces somatic to neural stem cell fate transitions independently from pluripotency reprogramming. SCIENCE ADVANCES 2023; 9:eadh2501. [PMID: 37611093 PMCID: PMC10446497 DOI: 10.1126/sciadv.adh2501] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/21/2023] [Indexed: 08/25/2023]
Abstract
Advanced strategies to interconvert cell types provide promising avenues to model cellular pathologies and to develop therapies for neurological disorders. Yet, methods to directly transdifferentiate somatic cells into multipotent induced neural stem cells (iNSCs) are slow and inefficient, and it is unclear whether cells pass through a pluripotent state with full epigenetic reset. We report iNSC reprogramming from embryonic and aged mouse fibroblasts as well as from human blood using an engineered Sox17 (eSox17FNV). eSox17FNV efficiently drives iNSC reprogramming while Sox2 or Sox17 fail. eSox17FNV acquires the capacity to bind different protein partners on regulatory DNA to scan the genome more efficiently and has a more potent transactivation domain than Sox2. Lineage tracing and time-resolved transcriptomics show that emerging iNSCs do not transit through a pluripotent state. Our work distinguishes lineage from pluripotency reprogramming with the potential to generate more authentic cell models for aging-associated neurodegenerative diseases.
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Affiliation(s)
- Mingxi Weng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Center for Translational Stem Cell Biology, Hong Kong SAR, China
| | - Haoqing Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Matthew S. Graus
- The David Richmond Laboratory for Cardiovascular Development: Gene Regulation and Editing Program, The Centenary Institute, Camperdown, NSW 2006, Australia
- Genome Imaging Centre, The Centenary Institute, Camperdown, NSW 2006, Australia
| | - Daisylyn Senna Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ya Gao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Shimiao Ren
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Derek Hoi Hang Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Center for Translational Stem Cell Biology, Hong Kong SAR, China
| | - Jakob Langer
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Markus Holzner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yuhua Huang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Guang Sheng Ling
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Cora Sau Wan Lai
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Cognitive and Brain Research, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mathias Francois
- The David Richmond Laboratory for Cardiovascular Development: Gene Regulation and Editing Program, The Centenary Institute, Camperdown, NSW 2006, Australia
- Genome Imaging Centre, The Centenary Institute, Camperdown, NSW 2006, Australia
- The University of Sydney, School of Medical Sciences, Camperdown, NSW 2006, Australia
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Center for Translational Stem Cell Biology, Hong Kong SAR, China
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4
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Naama M, Buganim Y. Human trophoblast stem cell-state acquisition from pluripotent stem cells and somatic cells. Curr Opin Genet Dev 2023; 81:102084. [PMID: 37451165 DOI: 10.1016/j.gde.2023.102084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 06/10/2023] [Accepted: 06/11/2023] [Indexed: 07/18/2023]
Abstract
For an extended period of time, research on human embryo implantation and early placentation was hindered by ethical limitation and lack of appropriate in vitro models. Recently, an explosion of new research has significantly expanded our knowledge of early human trophoblast development and facilitated the derivation and culture of self-renewing human trophoblast stem cells (hTSCs). Multiple approaches have been undertaken in efforts to derive and understand hTSCs, including from blastocysts, early trophoblast tissue, and, more recently, from human pluripotent stem cells (hPSCs) and somatic cells. In this concise review, we summarize recent advances in derivation of hTSCs, with a focus on derivation from naive and primed hPSCs, as well as via reprogramming of somatic cells into induced hTSCs. Each of these methods harbors distinct advantages and setbacks, which are discussed. Finally, we briefly explore the possibility of the existence of trophectoderm-like hTSCs corresponding to earlier, preimplantation trophoblast cells.
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Affiliation(s)
- Moriyah Naama
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Yosef Buganim
- Department of Developmental Biology and Cancer Research, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
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5
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Gong W, Dsouza N, Garry DJ. SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors. Genome Biol 2023; 24:125. [PMID: 37218013 DOI: 10.1186/s13059-023-02954-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 04/27/2023] [Indexed: 05/24/2023] Open
Abstract
Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) reveals chromatin accessibility across the genome. Currently, no method specifically detects differential chromatin accessibility. Here, SeATAC uses a conditional variational autoencoder model to learn the latent representation of ATAC-seq V-plots and outperforms MACS2 and NucleoATAC on six separate tasks. Applying SeATAC to several pioneer factor-induced differentiation or reprogramming ATAC-seq datasets suggests that induction of these factors not only relaxes the closed chromatin but also decreases chromatin accessibility of 20% to 30% of their target sites. SeATAC is a novel tool to accurately reveal genomic regions with differential chromatin accessibility from ATAC-seq data.
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Affiliation(s)
- Wuming Gong
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.
- Lillehei Heart Institute, University of Minnesota, 2231 6Th St SE, Minneapolis, MN, 55455, USA.
| | - Nikita Dsouza
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Daniel J Garry
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, 55455, USA.
- Lillehei Heart Institute, University of Minnesota, 2231 6Th St SE, Minneapolis, MN, 55455, USA.
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, 55455, USA.
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6
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Abstract
'Age reprogramming' refers to the process by which the molecular and cellular pathways of a cell that are subject to age-related decline are rejuvenated without passage through an embryonic stage. This process differs from the rejuvenation observed in differentiated derivatives of induced pluripotent stem cells, which involves passage through an embryonic stage and loss of cellular identity. Accordingly, the study of age reprogramming can provide an understanding of how ageing can be reversed while retaining cellular identity and the specialised function(s) of a cell, which will be of benefit to regenerative medicine. Here, we highlight recent work that has provided a more nuanced understanding of age reprogramming and point to some open questions in the field that might be explored in the future.
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Affiliation(s)
- Prim B. Singh
- Department of Medicine, Nazarbayev University School of Medicine, 5/1 Kerei Zhanibek Khandar Street, Astana 010000, Republic of Kazakhstan,Author for correspondence ()
| | - Assem Zhakupova
- Department of Medicine, Nazarbayev University School of Medicine, 5/1 Kerei Zhanibek Khandar Street, Astana 010000, Republic of Kazakhstan
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7
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Keniry A, Jansz N, Hickey PF, Breslin KA, Iminitoff M, Beck T, Gouil Q, Ritchie ME, Blewitt ME. A method for stabilising the XX karyotype in female mESC cultures. Development 2022; 149:285125. [PMID: 36355065 PMCID: PMC10112917 DOI: 10.1242/dev.200845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 10/30/2022] [Indexed: 11/12/2022]
Abstract
Female mouse embryonic stem cells (mESCs) present differently from male mESCs in several fundamental ways; however, complications with their in vitro culture have resulted in an under-representation of female mESCs in the literature. Recent studies show that the second X chromosome in female, and more specifically the transcriptional activity from both of these chromosomes due to absent X chromosome inactivation, sets female and male mESCs apart. To avoid this undesirable state, female mESCs in culture preferentially adopt an XO karyotype, with this adaption leading to loss of their unique properties in favour of a state that is near indistinguishable from male mESCs. If female pluripotency is to be studied effectively in this system, it is crucial that high-quality cultures of XX mESCs are available. Here, we report a method for better maintaining XX female mESCs in culture that also stabilises the male karyotype and makes study of female-specific pluripotency more feasible.
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Affiliation(s)
- Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Natasha Jansz
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Peter F Hickey
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Kelsey A Breslin
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Megan Iminitoff
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Tamara Beck
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Quentin Gouil
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Matthew E Ritchie
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia.,The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
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8
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Jung GA, Kim JA, Park HW, Lee H, Chang MS, Cho KO, Song BW, Kim HJ, Kwon YK, Oh IH. Induction of Nanog in neural progenitor cells for adaptive regeneration of ischemic brain. Exp Mol Med 2022; 54:1955-1966. [PMID: 36376495 PMCID: PMC9722910 DOI: 10.1038/s12276-022-00880-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 11/15/2022] Open
Abstract
NANOG plays a key role in cellular plasticity and the acquisition of the stem cell state during reprogramming, but its role in the regenerative process remains unclear. Here, we show that the induction of NANOG in neuronal cells is necessary for the physiological initiation of neuronal regeneration in response to ischemic stress. Specifically, we found that NANOG was preferentially expressed in undifferentiated neuronal cells, and forced expression of Nanog in neural progenitor cells (NPCs) promoted their self-renewing expansion both in ex-vivo slice cultures and in vitro limiting dilution analysis. Notably, the upstream region of the Nanog gene contains sequence motifs for hypoxia-inducible factor-1 alpha (HIF-1α). Therefore, cerebral neurons exposed to hypoxia significantly upregulated NANOG expression selectively in primitive (CD133+) cells, but not in mature cells, leading to the expansion of NPCs. Notably, up to 80% of the neuronal expansion induced by hypoxia was attributed to NANOG-expressing neuronal cells, whereas knockdown during hypoxia abolished this expansion and was accompanied by the downregulation of other pluripotency-related genes. Moreover, the number of NANOG-expressing neuronal cells were transiently increased in response to ischemic insult, predominantly in the infarct area of brain regions undergoing neurogenesis, but not in non-neurogenic loci. Together, these findings reveal a functional effect of NANOG-induction for the initiation of adaptive neuronal regeneration among heterogeneous NPC subsets, pointing to cellular plasticity as a potential link between regeneration and reprogramming processes.
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Affiliation(s)
- Gyung-Ah Jung
- grid.411947.e0000 0004 0470 4224Catholic High-Performance Cell Therapy Center & Department of Medical Life Science, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jin-A Kim
- grid.411947.e0000 0004 0470 4224Catholic High-Performance Cell Therapy Center & Department of Medical Life Science, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hwan-Woo Park
- grid.31501.360000 0004 0470 5905Department of Oral Anatomy, Dental Research Institute & School of Dentistry, Seoul National University, Seoul, Korea ,grid.411143.20000 0000 8674 9741Present Address: Department of Cell Biology, Myunggok Medical Research Institute, Konyang University College of Medicine, Daejeon, Korea
| | - Hyemi Lee
- grid.289247.20000 0001 2171 7818Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Korea
| | - Mi-Sook Chang
- grid.31501.360000 0004 0470 5905Department of Oral Anatomy, Dental Research Institute & School of Dentistry, Seoul National University, Seoul, Korea
| | - Kyung-Ok Cho
- grid.411947.e0000 0004 0470 4224Department of Pharmacology, Department of Biomedicine & Health Sciences, Catholic Neuroscience Institute, Institute of Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Byeong-Wook Song
- grid.411199.50000 0004 0470 5702College of Medicine, Institute for Bio-Medical Convergence, Catholic Kwandong University, Gangneung-si, 25601 Korea
| | - Hyun-Ju Kim
- grid.289247.20000 0001 2171 7818Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Korea
| | - Yunhee Kim Kwon
- grid.289247.20000 0001 2171 7818Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Korea
| | - Il-Hoan Oh
- grid.411947.e0000 0004 0470 4224Catholic High-Performance Cell Therapy Center & Department of Medical Life Science, College of Medicine, The Catholic University of Korea, Seoul, Korea ,Institute for Regenerative Medical Research, StemMeditech Inc., Seoul, Korea
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9
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Ha J, Kim BS, Min B, Nam J, Lee JG, Lee M, Yoon BH, Choi YH, Im I, Park JS, Choi H, Baek A, Cho SM, Lee MO, Nam KH, Mun JY, Kim M, Kim SY, Son MY, Kang YK, Lee JS, Kim JK, Kim J. Intermediate cells of in vitro cellular reprogramming and in vivo tissue regeneration require desmoplakin. SCIENCE ADVANCES 2022; 8:eabk1239. [PMID: 36306352 PMCID: PMC9616504 DOI: 10.1126/sciadv.abk1239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Amphibians and fish show considerable regeneration potential via dedifferentiation of somatic cells into blastemal cells. In terms of dedifferentiation, in vitro cellular reprogramming has been proposed to share common processes with in vivo tissue regeneration, although the details are elusive. Here, we identified the cytoskeletal linker protein desmoplakin (Dsp) as a common factor mediating both reprogramming and regeneration. Our analysis revealed that Dsp expression is elevated in distinct intermediate cells during in vitro reprogramming. Knockdown of Dsp impedes in vitro reprogramming into induced pluripotent stem cells and induced neural stem/progenitor cells as well as in vivo regeneration of zebrafish fins. Notably, reduced Dsp expression impairs formation of the intermediate cells during cellular reprogramming and tissue regeneration. These findings suggest that there is a Dsp-mediated evolutionary link between cellular reprogramming in mammals and tissue regeneration in lower vertebrates and that the intermediate cells may provide alternative approaches for mammalian regenerative therapy.
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Affiliation(s)
- Jeongmin Ha
- Stem Cell Convergence Research Center, Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Bum Suk Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Republic of Korea
| | - Byungkuk Min
- Stem Cell Convergence Research Center, Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Juhyeon Nam
- Stem Cell Convergence Research Center, Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Jae-Geun Lee
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
- Microbiome Convergence Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Minhyung Lee
- Stem Cell Convergence Research Center, Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Byoung-Ha Yoon
- Korea Bioinformation Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Yoon Ha Choi
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Republic of Korea
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Ilkyun Im
- Bio-IT lab, NetTargets Inc., Daejeon 34141, Republic of Korea
| | - Jung Sun Park
- Development and Differentiation Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Hyosun Choi
- Nanobioimaging Center, National Instrumentation Center for Environmental Management (NICEM), Seoul National University, Seoul, Republic of Korea
| | - Areum Baek
- Stem Cell Convergence Research Center, Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Sang Mi Cho
- Laboratory Animal Resource Center, KRIBB, Cheongju 28116, Republic of Korea
| | - Mi-Ok Lee
- Stem Cell Convergence Research Center, Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Ki-Hoan Nam
- Laboratory Animal Resource Center, KRIBB, Cheongju 28116, Republic of Korea
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Mirang Kim
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Seon-Young Kim
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
- Korea Bioinformation Center, KRIBB, Daejeon 34141, Republic of Korea
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Mi Young Son
- Stem Cell Convergence Research Center, Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Yong-Kook Kang
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
- Development and Differentiation Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Jeong-Soo Lee
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
- Microbiome Convergence Research Center, KRIBB, Daejeon 34141, Republic of Korea
- Dementia DTC R&D Convergence Program, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Jong Kyoung Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 42988, Republic of Korea
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Janghwan Kim
- Stem Cell Convergence Research Center, Korea Research Institute Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Republic of Korea
- R&D Center, Regeners Inc., Daejeon 34141, Republic of Korea
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10
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Roux AE, Zhang C, Paw J, Zavala-Solorio J, Malahias E, Vijay T, Kolumam G, Kenyon C, Kimmel JC. Diverse partial reprogramming strategies restore youthful gene expression and transiently suppress cell identity. Cell Syst 2022; 13:574-587.e11. [PMID: 35690067 DOI: 10.1016/j.cels.2022.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 02/15/2022] [Accepted: 05/10/2022] [Indexed: 01/25/2023]
Abstract
Partial pluripotent reprogramming can reverse features of aging in mammalian cells, but the impact on somatic identity and the necessity of individual reprogramming factors remain unknown. Here, we used single-cell genomics to map the identity trajectory induced by partial reprogramming in multiple murine cell types and dissected the influence of each factor by screening all Yamanaka Factor subsets with pooled single-cell screens. We found that partial reprogramming restored youthful expression in adipogenic and mesenchymal stem cells but also temporarily suppressed somatic identity programs. Our pooled screens revealed that many subsets of the Yamanaka Factors both restore youthful expression and suppress somatic identity, but these effects were not tightly entangled. We also found that a multipotent reprogramming strategy inspired by amphibian regeneration restored youthful expression in myogenic cells. Our results suggest that various sets of reprogramming factors can restore youthful expression with varying degrees of somatic identity suppression. A record of this paper's Transparent Peer Review process is included in the supplemental information.
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Affiliation(s)
- Antoine E Roux
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Chunlian Zhang
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Jonathan Paw
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA
| | - José Zavala-Solorio
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Evangelia Malahias
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Twaritha Vijay
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Ganesh Kolumam
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Cynthia Kenyon
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA
| | - Jacob C Kimmel
- Calico Life Sciences, LLC, 1170 Veterans Blvd, South San Francisco, CA 94080, USA.
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11
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Yang Z, Xu X, Gu C, Nielsen AV, Chen G, Guo F, Tang C, Zhao Y. Chemical Pretreatment Activated a Plastic State Amenable to Direct Lineage Reprogramming. Front Cell Dev Biol 2022; 10:865038. [PMID: 35399519 PMCID: PMC8990889 DOI: 10.3389/fcell.2022.865038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 02/21/2022] [Indexed: 11/21/2022] Open
Abstract
Somatic cells can be chemically reprogrammed into a pluripotent stem cell (CiPSC) state, mediated by an extraembryonic endoderm- (XEN-) like state. We found that the chemical cocktail applied in CiPSC generation initially activated a plastic state in mouse fibroblasts before transitioning into XEN-like cells. The plastic state was characterized by broadly activated expression of development-associated transcription factors (TFs), such as Sox17, Ascl1, Tbx3, and Nkx6-1, with a more accessible chromatin state indicating an enhanced capability of cell fate conversion. Intriguingly, introducing such a plastic state remarkably improved the efficiency of chemical reprogramming from fibroblasts to functional neuron-like cells with electrophysiological activity or beating skeletal muscles. Furthermore, the generation of chemically induced neuron-like cells or skeletal muscles from mouse fibroblasts was independent of the intermediate XEN-like state or the pluripotency state. In summary, our findings revealed a plastic chemically activated multi-lineage priming (CaMP) state at the onset of chemical reprogramming. This state enhanced the cells’ potential to adapt to other cell fates. It provides a general approach to empowering chemical reprogramming methods to obtain functional cell types bypassing inducing pluripotent stem cells.
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Affiliation(s)
- Zhenghao Yang
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Xiaochan Xu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Chan Gu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | | | - Guokai Chen
- Centre of Reproduction, Development and Aging, Faculty of Health Sciences, University of Macau, Macau, China
| | - Fan Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chao Tang
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Center for Quantitative Biology, Peking University, Beijing, China
| | - Yang Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, MOE Key Laboratory of Cell Proliferation and Differentiation, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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12
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BAF complex-mediated chromatin relaxation is required for establishment of X chromosome inactivation. Nat Commun 2022; 13:1658. [PMID: 35351876 PMCID: PMC8964718 DOI: 10.1038/s41467-022-29333-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/10/2022] [Indexed: 12/12/2022] Open
Abstract
The process of epigenetic silencing, while fundamentally important, is not yet completely understood. Here we report a replenishable female mouse embryonic stem cell (mESC) system, Xmas, that allows rapid assessment of X chromosome inactivation (XCI), the epigenetic silencing mechanism of one of the two X chromosomes that enables dosage compensation in female mammals. Through a targeted genetic screen in differentiating Xmas mESCs, we reveal that the BAF complex is required to create nucleosome-depleted regions at promoters on the inactive X chromosome during the earliest stages of establishment of XCI. Without this action gene silencing fails. Xmas mESCs provide a tractable model for screen-based approaches that enable the discovery of unknown facets of the female-specific process of XCI and epigenetic silencing more broadly. Female embryonic stem cells (ESCs) are the ideal model to study X chromosome inactivation (XCI) establishment; however, these cells are challenging to keep in culture. Here the authors create fluorescent ‘Xmas’ reporter mice as a renewable source of ESCs and show nucleosome remodelers Smarcc1 and Smarca4 create a nucleosome-free promoter region prior to the establishment of silencing.
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13
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Directly reprogrammed natural killer cells for cancer immunotherapy. Nat Biomed Eng 2021; 5:1360-1376. [PMID: 34341536 DOI: 10.1038/s41551-021-00768-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 06/22/2021] [Indexed: 02/07/2023]
Abstract
Efficacious and accessible sources of natural killer (NK) cells would widen their use as immunotherapeutics, particularly for solid cancers. Here, we show that human somatic cells can be directly reprogrammed into NK cells with a CD56brightCD16bright phenotype using pluripotency transcription factors and an optimized reprogramming medium. The directly reprogrammed NK cells have strong innate-adaptive immunomodulatory activity and are highly potent against a wide range of cancer cells, including difficult-to-treat solid cancers and cancer stem cells. Both directly reprogrammed NK cells bearing a cancer-specific chimeric antigen receptor and reprogrammed NK cells in combination with antibodies competent for antibody-dependent cell-mediated cytotoxicity led to selective anticancer effects with augmented potency. The direct reprogramming of human somatic cells into NK cells is amenable to the production of autologous and allogeneic NK cells, and will facilitate the design and testing of cancer immunotherapies and combination therapies.
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14
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Salman IS, Al-Shammari AM, Haba MK. Direct Reprogramming of Mice Skin Fibroblasts into Insulin-Producing Cells In Vitro. Cell Reprogram 2021; 24:271-282. [PMID: 34637623 DOI: 10.1089/cell.2021.0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Transdifferentiation means mature cell conversion into other mature cells. Ethical issues, epigenetic failure, or teratoma development are found in cellular reprogramming strategies. Thus, new methods are needed. This study aimed to develop a new novel formula of chemical molecules and growth factors that differentiate skin fibroblasts into insulin-producing cells (IPCs). Newborn mice fibroblasts differentiated using four induction methods into IPCs to search for the best method. Fibroblasts, stem cells, and pancreatic markers were identified using an immunocytochemistry (ICC) assay. Insulin was measured using ELISA and dithizone (DTZ) assays. The skin fibroblasts were induced successfully into IPCs. The best method to obtain IPCs was indicated by measuring insulin concentration in differentiated cell supernatant from all induced cells by the four methods. The protein expression of the pancreatic markers of induced cells increased with time, as indicated by the ICC assay. OCT3/4 increased on day 9, after which the expression tended to decrease. DTZ-positive clusters were observed on day 16. Secreted insulin of differentiated cells was injected in streptozotocin-induced diabetic mice, which decreased blood glucose levels after injection. This study indicated an efficient new chemical method for transdifferentiating skin fibroblasts into functional IPCs, which is a promising method for diabetes mellitus therapy.
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Affiliation(s)
- Israa S Salman
- Department of Biology, College of Science for Women, University of Baghdad, Baghdad, Iraq
| | - Ahmed Majeed Al-Shammari
- Experimental Therapy Department, Iraqi Center of Cancer and Medical Genetic Research, Mustansiriyah University, Baghdad, Iraq
| | - Mukhtar Khamis Haba
- Department of Biology, College of Science for Women, University of Baghdad, Baghdad, Iraq
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15
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Recent Advances in Cardiac Tissue Engineering for the Management of Myocardium Infarction. Cells 2021; 10:cells10102538. [PMID: 34685518 PMCID: PMC8533887 DOI: 10.3390/cells10102538] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 12/26/2022] Open
Abstract
Myocardium Infarction (MI) is one of the foremost cardiovascular diseases (CVDs) causing death worldwide, and its case numbers are expected to continuously increase in the coming years. Pharmacological interventions have not been at the forefront in ameliorating MI-related morbidity and mortality. Stem cell-based tissue engineering approaches have been extensively explored for their regenerative potential in the infarcted myocardium. Recent studies on microfluidic devices employing stem cells under laboratory set-up have revealed meticulous events pertaining to the pathophysiology of MI occurring at the infarcted site. This discovery also underpins the appropriate conditions in the niche for differentiating stem cells into mature cardiomyocyte-like cells and leads to engineering of the scaffold via mimicking of native cardiac physiological conditions. However, the mode of stem cell-loaded engineered scaffolds delivered to the site of infarction is still a challenging mission, and yet to be translated to the clinical setting. In this review, we have elucidated the various strategies developed using a hydrogel-based system both as encapsulated stem cells and as biocompatible patches loaded with cells and applied at the site of infarction.
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16
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Taguchi J, Shibata H, Kabata M, Kato M, Fukuda K, Tanaka A, Ohta S, Ukai T, Mitsunaga K, Yamada Y, Nagaoka SI, Yamazawa S, Ohnishi K, Woltjen K, Ushiku T, Ozawa M, Saitou M, Shinkai Y, Yamamoto T, Yamada Y. DMRT1-mediated reprogramming drives development of cancer resembling human germ cell tumors with features of totipotency. Nat Commun 2021; 12:5041. [PMID: 34413299 PMCID: PMC8377058 DOI: 10.1038/s41467-021-25249-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 07/29/2021] [Indexed: 11/23/2022] Open
Abstract
In vivo reprogramming provokes a wide range of cell fate conversion. Here, we discover that in vivo induction of higher levels of OSKM in mouse somatic cells leads to increased expression of primordial germ cell (PGC)-related genes and provokes genome-wide erasure of genomic imprinting, which takes place exclusively in PGCs. Moreover, the in vivo OSKM reprogramming results in development of cancer that resembles human germ cell tumors. Like a subgroup of germ cell tumors, propagated tumor cells can differentiate into trophoblasts. Moreover, these tumor cells give rise to induced pluripotent stem cells (iPSCs) with expanded differentiation potential into trophoblasts. Remarkably, the tumor-derived iPSCs are able to contribute to non-neoplastic somatic cells in adult mice. Mechanistically, DMRT1, which is expressed in PGCs, drives the reprogramming and propagation of the tumor cells in vivo. Furthermore, the DMRT1-related epigenetic landscape is associated with trophoblast competence of the reprogrammed cells and provides a therapeutic target for germ cell tumors. These results reveal an unappreciated route for somatic cell reprogramming and underscore the impact of reprogramming in development of germ cell tumors.
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Affiliation(s)
- Jumpei Taguchi
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Minoto-ku, Tokyo, Japan
| | - Hirofumi Shibata
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
- Department of Otolaryngology, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Mio Kabata
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Masaki Kato
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako-shi, Saitama, Japan
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kei Fukuda
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako-shi, Saitama, Japan
| | - Akito Tanaka
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Sho Ohta
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Minoto-ku, Tokyo, Japan
| | - Tomoyo Ukai
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Minoto-ku, Tokyo, Japan
| | - Kanae Mitsunaga
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yosuke Yamada
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - So I Nagaoka
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
- Department of Embryology, Nara Medical University, Nara, Japan
| | - Sho Yamazawa
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kotaro Ohnishi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
- Department of Gastroenterology/Internal Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Manabu Ozawa
- Laboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Mitinori Saitou
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako-shi, Saitama, Japan
| | - Takuya Yamamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan
- Medical-risk Avoidance Based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto, Japan
- AMED-CREST, AMED 1-7-1 Otemachi, Chiyodaku, Tokyo, Japan
| | - Yasuhiro Yamada
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, The University of Tokyo, Minoto-ku, Tokyo, Japan.
- AMED-CREST, AMED 1-7-1 Otemachi, Chiyodaku, Tokyo, Japan.
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17
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Armstrong JPK, Keane TJ, Roques AC, Patrick PS, Mooney CM, Kuan WL, Pisupati V, Oreffo ROC, Stuckey DJ, Watt FM, Forbes SJ, Barker RA, Stevens MM. A blueprint for translational regenerative medicine. Sci Transl Med 2021; 12:12/572/eaaz2253. [PMID: 33268507 DOI: 10.1126/scitranslmed.aaz2253] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 03/05/2020] [Indexed: 12/11/2022]
Abstract
The past few decades have produced a large number of proof-of-concept studies in regenerative medicine. However, the route to clinical adoption is fraught with technical and translational obstacles that frequently consign promising academic solutions to the so-called "valley of death." Here, we present a proposed blueprint for translational regenerative medicine. We offer principles to help guide the selection of cells and materials, present key in vivo imaging modalities, and argue that the host immune response should be considered throughout design and development. Last, we suggest a pathway to navigate the often complex regulatory and manufacturing landscape of translational regenerative medicine.
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Affiliation(s)
- James P K Armstrong
- Department of Materials, Imperial College London, London SW7 2AZ, UK. .,Department of Bioengineering, Imperial College London, London SW7 2AZ, UK.,Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Timothy J Keane
- Department of Materials, Imperial College London, London SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London SW7 2AZ, UK.,Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Anne C Roques
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
| | - P Stephen Patrick
- Centre for Advanced Biomedical Imaging, University College London, London WC1E 6DD, UK
| | - Claire M Mooney
- Centre for Stem Cells and Regenerative Medicine, King's College London, London SE1 9RT, UK
| | - Wei-Li Kuan
- John van Geest Centre for Brain Repair and Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0PY, UK
| | - Venkat Pisupati
- John van Geest Centre for Brain Repair and Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0PY, UK
| | - Richard O C Oreffo
- Centre for Human Development, Stem Cells and Regeneration, University of Southampton, Southampton SO16 6YD, UK
| | - Daniel J Stuckey
- Centre for Advanced Biomedical Imaging, University College London, London WC1E 6DD, UK
| | - Fiona M Watt
- Centre for Stem Cells and Regenerative Medicine, King's College London, London SE1 9RT, UK
| | - Stuart J Forbes
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Roger A Barker
- John van Geest Centre for Brain Repair and Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0PY, UK
| | - Molly M Stevens
- Department of Materials, Imperial College London, London SW7 2AZ, UK. .,Department of Bioengineering, Imperial College London, London SW7 2AZ, UK.,Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
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18
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Lambert J, Lloret-Fernández C, Laplane L, Poole RJ, Jarriault S. On the origins and conceptual frameworks of natural plasticity-Lessons from single-cell models in C. elegans. Curr Top Dev Biol 2021; 144:111-159. [PMID: 33992151 DOI: 10.1016/bs.ctdb.2021.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
How flexible are cell identities? This problem has fascinated developmental biologists for several centuries and can be traced back to Abraham Trembley's pioneering manipulations of Hydra to test its regeneration abilities in the 1700s. Since the cell theory in the mid-19th century, developmental biology has been dominated by a single framework in which embryonic cells are committed to specific cell fates, progressively and irreversibly acquiring their differentiated identities. This hierarchical, unidirectional and irreversible view of cell identity has been challenged in the past decades through accumulative evidence that many cell types are more plastic than previously thought, even in intact organisms. The paradigm shift introduced by such plasticity calls into question several other key traditional concepts, such as how to define a differentiated cell or more generally cellular identity, and has brought new concepts, such as distinct cellular states. In this review, we want to contribute to this representation by attempting to clarify the conceptual and theoretical frameworks of cell plasticity and identity. In the context of these new frameworks we describe here an atlas of natural plasticity of cell identity in C. elegans, including our current understanding of the cellular and molecular mechanisms at play. The worm further provides interesting cases at the borderlines of cellular plasticity that highlight the conceptual challenges still ahead. We then discuss a set of future questions and perspectives arising from the studies of natural plasticity in the worm that are shared with other reprogramming and plasticity events across phyla.
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Affiliation(s)
- Julien Lambert
- IGBMC, Development and Stem Cells Department, CNRS UMR7104, INSERM U1258, Université de Strasbourg, Strasbourg, France
| | - Carla Lloret-Fernández
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Lucie Laplane
- CNRS UMR 8590, University Paris I Panthéon-Sorbonne, IHPST, Paris, France
| | - Richard J Poole
- Department of Cell and Developmental Biology, University College London, London, United Kingdom.
| | - Sophie Jarriault
- IGBMC, Development and Stem Cells Department, CNRS UMR7104, INSERM U1258, Université de Strasbourg, Strasbourg, France.
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19
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Fan T, Huang Y. Accessible chromatin reveals regulatory mechanisms underlying cell fate decisions during early embryogenesis. Sci Rep 2021; 11:7896. [PMID: 33846424 PMCID: PMC8042068 DOI: 10.1038/s41598-021-86919-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 03/22/2021] [Indexed: 02/01/2023] Open
Abstract
This study was conducted to investigate epigenetic landscape across multiple species and identify transcription factors (TFs) and their roles in controlling cell fate decision events during early embryogenesis. We made a comprehensively joint-research of chromatin accessibility of five species during embryogenesis by integration of ATAC-seq and RNA-seq datasets. Regulatory roles of candidate early embryonic TFs were investigated. Widespread accessible chromatin in early embryos overlapped with putative cis-regulatory sequences. Sets of cell-fate-determining TFs were identified. YOX1, a key cell cycle regulator, were found to homologous to clusters of TFs that are involved in neuron and epidermal cell-fate determination. Our research provides an intriguing insight into evolution of cell-fate decision during early embryogenesis among organisms.
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Affiliation(s)
- Tongqiang Fan
- grid.443483.c0000 0000 9152 7385State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, 311300 People’s Republic of China
| | - Youjun Huang
- grid.443483.c0000 0000 9152 7385State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, 311300 People’s Republic of China
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20
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Iyer AA, Groves AK. Transcription Factor Reprogramming in the Inner Ear: Turning on Cell Fate Switches to Regenerate Sensory Hair Cells. Front Cell Neurosci 2021; 15:660748. [PMID: 33854418 PMCID: PMC8039129 DOI: 10.3389/fncel.2021.660748] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/08/2021] [Indexed: 12/15/2022] Open
Abstract
Non-mammalian vertebrates can restore their auditory and vestibular hair cells naturally by triggering the regeneration of adjacent supporting cells. The transcription factor ATOH1 is a key regulator of hair cell development and regeneration in the inner ear. Following the death of hair cells, supporting cells upregulate ATOH1 and give rise to new hair cells. However, in the mature mammalian cochlea, such natural regeneration of hair cells is largely absent. Transcription factor reprogramming has been used in many tissues to convert one cell type into another, with the long-term hope of achieving tissue regeneration. Reprogramming transcription factors work by altering the transcriptomic and epigenetic landscapes in a target cell, resulting in a fate change to the desired cell type. Several studies have shown that ATOH1 is capable of reprogramming cochlear non-sensory tissue into cells resembling hair cells in young animals. However, the reprogramming ability of ATOH1 is lost with age, implying that the potency of individual hair cell-specific transcription factors may be reduced or lost over time by mechanisms that are still not clear. To circumvent this, combinations of key hair cell transcription factors have been used to promote hair cell regeneration in older animals. In this review, we summarize recent findings that have identified and studied these reprogramming factor combinations for hair cell regeneration. Finally, we discuss the important questions that emerge from these findings, particularly the feasibility of therapeutic strategies using reprogramming factors to restore human hearing in the future.
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Affiliation(s)
- Amrita A. Iyer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Program in Genetics & Genomics, Houston, TX, United States
| | - Andrew K. Groves
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
- Program in Genetics & Genomics, Houston, TX, United States
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States
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21
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Ostrakhovitch EA, Akakura S, Tabibzadeh S. Hydrogen sulfide facilitates reprogramming and trans-differentiation in 3D dermal fibroblast. PLoS One 2020; 15:e0241685. [PMID: 33180827 PMCID: PMC7660576 DOI: 10.1371/journal.pone.0241685] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/19/2020] [Indexed: 12/24/2022] Open
Abstract
The efficiency of cell reprogramming in two-dimensional (2D) cultures is limited. Given that cellular stemness is intimately related to microenvironmental changes, 3D cell cultures have the potential of overcoming this limited capacity by allowing cells to self-organize by aggregation. In 3D space, cells interact more efficiently, modify their cellular topology, gene expression, signaling, and metabolism. It is yet not clear as how 3D culture environments modify the reprogramming potential of fibroblasts. We demonstrate that 3D spheroids from dermal fibroblasts formed under ultra-low attachment conditions showed increased lactate production. This is a requisite for cell reprogramming, increase their expression of pluripotency genes, such as OCT4, NANOG and SOX2, and display upregulated cystathionine-β-synthase (CBS) and hydrogen sulfide (H2S) production. Knockdown of CBS by RNAi suppresses lactic acid and H2S production and concomitantly decreases the expression of OCT4 and NANOG. On the contrary, H2S donors, NaHS and garlic-derived diallyl trisulfide (DATS), promote the expression of OCT4, and support osteogenic trans-differentiation of fibroblasts. These results demonstrate that CBS mediated release of H2S regulates the reprogramming of dermal fibroblasts grown in 3D cultures and supports their trans-differentiation.
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Affiliation(s)
- Elena A. Ostrakhovitch
- Frontiers in Bioscience Research Institute in Aging and Cancer, Irvine, CA, United States of America
| | - Shin Akakura
- Frontiers in Bioscience Research Institute in Aging and Cancer, Irvine, CA, United States of America
| | - Siamak Tabibzadeh
- Frontiers in Bioscience Research Institute in Aging and Cancer, Irvine, CA, United States of America
- * E-mail:
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22
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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: 0.3] [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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23
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The Future of Direct Cardiac Reprogramming: Any GMT Cocktail Variety? Int J Mol Sci 2020; 21:ijms21217950. [PMID: 33114756 PMCID: PMC7663133 DOI: 10.3390/ijms21217950] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/13/2022] Open
Abstract
Direct cardiac reprogramming has emerged as a novel therapeutic approach to treat and regenerate injured hearts through the direct conversion of fibroblasts into cardiac cells. Most studies have focused on the reprogramming of fibroblasts into induced cardiomyocytes (iCMs). The first study in which this technology was described, showed that at least a combination of three transcription factors, GATA4, MEF2C and TBX5 (GMT cocktail), was required for the reprogramming into iCMs in vitro using mouse cells. However, this was later demonstrated to be insufficient for the reprogramming of human cells and additional factors were required. Thereafter, most studies have focused on implementing reprogramming efficiency and obtaining fully reprogrammed and functional iCMs, by the incorporation of other transcription factors, microRNAs or small molecules to the original GMT cocktail. In this respect, great advances have been made in recent years. However, there is still no consensus on which of these GMT-based varieties is best, and robust and highly reproducible protocols are still urgently required, especially in the case of human cells. On the other hand, apart from CMs, other cells such as endothelial and smooth muscle cells to form new blood vessels will be fundamental for the correct reconstruction of damaged cardiac tissue. With this aim, several studies have centered on the direct reprogramming of fibroblasts into induced cardiac progenitor cells (iCPCs) able to give rise to all myocardial cell lineages. Especially interesting are reports in which multipotent and highly expandable mouse iCPCs have been obtained, suggesting that clinically relevant amounts of these cells could be created. However, as of yet, this has not been achieved with human iCPCs, and exactly what stage of maturity is appropriate for a cell therapy product remains an open question. Nonetheless, the major concern in regenerative medicine is the poor retention, survival, and engraftment of transplanted cells in the cardiac tissue. To circumvent this issue, several cell pre-conditioning approaches are currently being explored. As an alternative to cell injection, in vivo reprogramming may face fewer barriers for its translation to the clinic. This approach has achieved better results in terms of efficiency and iCMs maturity in mouse models, indicating that the heart environment can favor this process. In this context, in recent years some studies have focused on the development of safer delivery systems such as Sendai virus, Adenovirus, chemical cocktails or nanoparticles. This article provides an in-depth review of the in vitro and in vivo cardiac reprograming technology used in mouse and human cells to obtain iCMs and iCPCs, and discusses what challenges still lie ahead and what hurdles are to be overcome before results from this field can be transferred to the clinical settings.
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24
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Brovkina O, Dashinimaev E. Advances and complications of regenerative medicine in diabetes therapy. PeerJ 2020; 8:e9746. [PMID: 33194345 PMCID: PMC7485501 DOI: 10.7717/peerj.9746] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/27/2020] [Indexed: 12/23/2022] Open
Abstract
The rapid development of technologies in regenerative medicine indicates clearly that their common application is not a matter of if, but of when. However, the regeneration of beta-cells for diabetes patients remains a complex challenge due to the plurality of related problems. Indeed, the generation of beta-cells masses expressing marker genes is only a first step, with maintaining permanent insulin secretion, their protection from the immune system and avoiding pathological modifications in the genome being the necessary next developments. The prospects of regenerative medicine in diabetes therapy were promoted by the emergence of promising results with embryonic stem cells (ESCs). Their pluripotency and proliferation in an undifferentiated state during culture have ensured the success of ESCs in regenerative medicine. The discovery of induced pluripotent stem cells (iPSCs) derived from the patients’ own mesenchymal cells has provided further hope for diabetes treatment. Nonetheless, the use of stem cells has significant limitations related to the pluripotent stage, such as the risk of development of teratomas. Thus, the direct conversion of mature cells into beta-cells could address this issue. Recent studies have shown the possibility of such transdifferentiation and have set trends for regeneration medicine, directed at minimizing genome modifications and invasive procedures. In this review, we will discuss the published results of beta-cell regeneration and the advantages and disadvantages illustrated by these experiments.
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Affiliation(s)
- Olga Brovkina
- Federal Research Clinical Center for Specialized Types of Health Care and Medical Technologies of Federal Medical and Biology Agency, Moscow, Russia
| | - Erdem Dashinimaev
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
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25
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Kumar A, Mali P. Mapping regulators of cell fate determination: Approaches and challenges. APL Bioeng 2020; 4:031501. [PMID: 32637855 PMCID: PMC7332300 DOI: 10.1063/5.0004611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/01/2020] [Indexed: 12/25/2022] Open
Abstract
Given the limited regenerative capacities of most organs, strategies are needed to efficiently generate large numbers of parenchymal cells capable of integration into the diseased organ. Although it was initially thought that terminally differentiated cells lacked the ability to transdifferentiate, it has since been shown that cellular reprogramming of stromal cells to parenchymal cells through direct lineage conversion holds great potential for the replacement of post-mitotic parenchymal cells lost to disease. To this end, an assortment of genetic, chemical, and mechanical cues have been identified to reprogram cells to different lineages both in vitro and in vivo. However, some key challenges persist that limit broader applications of reprogramming technologies. These include: (1) low reprogramming efficiencies; (2) incomplete functional maturation of derived cells; and (3) difficulty in determining the typically multi-factor combinatorial recipes required for successful transdifferentiation. To improve efficiency by comprehensively identifying factors that regulate cell fate, large scale genetic and chemical screening methods have thus been utilized. Here, we provide an overview of the underlying concept of cell reprogramming as well as the rationale, considerations, and limitations of high throughput screening methods. We next follow with a summary of unique hits that have been identified by high throughput screens to induce reprogramming to various parenchymal lineages. Finally, we discuss future directions of applying this technology toward human disease biology via disease modeling, drug screening, and regenerative medicine.
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Affiliation(s)
- Aditya Kumar
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA
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26
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Lehmann M, Canatelli-Mallat M, Chiavellini P, Cónsole GM, Gallardo MD, Goya RG. Partial Reprogramming As An Emerging Strategy for Safe Induced Cell Generation and Rejuvenation. Curr Gene Ther 2020; 19:248-254. [PMID: 31475896 DOI: 10.2174/1566523219666190902154511] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/05/2019] [Accepted: 08/08/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Conventional cell reprogramming involves converting a somatic cell line into induced pluripotent stem cells (iPSC), which subsequently can be re-differentiated to specific somatic cell types. Alternatively, partial cell reprogramming converts somatic cells into other somatic cell types by transient expression of pluripotency genes thus generating intermediates that retain their original cell identity, but are responsive to appropriate cocktails of specific differentiation factors. Additionally, biological rejuvenation by partial cell reprogramming is an emerging avenue of research. OBJECTIVE Here, we will briefly review the emerging information pointing to partial reprogramming as a suitable strategy to achieve cell reprogramming and rejuvenation, bypassing cell dedifferentiation. METHODS In this context, regulatable pluripotency gene expression systems are the most widely used at present to implement partial cell reprogramming. For instance, we have constructed a regulatable bidirectional adenovector expressing Green Fluorescent Protein and oct4, sox2, klf4 and c-myc genes (known as the Yamanaka genes or OSKM). RESULTS Partial cell reprogramming has been used to reprogram fibroblasts to cardiomyocytes, neural progenitors and neural stem cells. Rejuvenation by cyclic partial reprogramming has been achieved both in vivo and in cell culture using transgenic mice and cells expressing the OSKM genes, respectively, controlled by a regulatable promoter. CONCLUSION Partial reprogramming emerges as a powerful tool for the genesis of iPSC-free induced somatic cells of therapeutic value and for the implementation of in vitro and in vivo rejuvenation keeping cell type identity unchanged.
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Affiliation(s)
- Marianne Lehmann
- INIBIOLP-Pathology B, Faculty of Medicine, UNLP, CC 455 (zip 1900) La Plata, Argentina.,Department of Histology, Cytology and of Embryology B, School of Medicine, University of La Plata, La Plata, Argentina
| | - Martina Canatelli-Mallat
- INIBIOLP-Pathology B, Faculty of Medicine, UNLP, CC 455 (zip 1900) La Plata, Argentina.,Department of Histology, Cytology and of Embryology B, School of Medicine, University of La Plata, La Plata, Argentina
| | - Priscila Chiavellini
- INIBIOLP-Pathology B, Faculty of Medicine, UNLP, CC 455 (zip 1900) La Plata, Argentina.,Department of Histology, Cytology and of Embryology B, School of Medicine, University of La Plata, La Plata, Argentina
| | - Gloria M Cónsole
- Department of Histology, Cytology and of Embryology B, School of Medicine, University of La Plata, La Plata, Argentina
| | - Maria D Gallardo
- INIBIOLP-Pathology B, Faculty of Medicine, UNLP, CC 455 (zip 1900) La Plata, Argentina.,Department of Histology, Cytology and of Embryology B, School of Medicine, University of La Plata, La Plata, Argentina
| | - Rodolfo G Goya
- INIBIOLP-Pathology B, Faculty of Medicine, UNLP, CC 455 (zip 1900) La Plata, Argentina.,Department of Histology, Cytology and of Embryology B, School of Medicine, University of La Plata, La Plata, Argentina
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27
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Abstract
Organ constructs are organ-like structures grown in vitro or in vivo that harbor the components, architecture, and function of in vivo organs, in part or in toto. The convergence of stem cell biology, bioengineering, and gene editing tools have substantially broadened our ability to generate various types of organ constructs for regenerative medicine as well as to address pressing biomedical questions. In this Review, we highlight prevailing approaches for generating organ constructs, from organoids to chimeric organ engineering. We also discuss design principles of different approaches, their utility and limitations, and propose strategies to resolve existing hurdles.
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Affiliation(s)
- Yun Xia
- Lee Kong Chian School of Medicine, Nanyang Technological University, 11 Mandalay Road, Singapore 308232, Singapore.
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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28
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Han MJ, Lee WJ, Choi J, Hong YJ, Uhm SJ, Choi Y, Do JT. Inhibition of neural stem cell aging through the transient induction of reprogramming factors. J Comp Neurol 2020; 529:595-604. [DOI: 10.1002/cne.24967] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/30/2020] [Accepted: 06/02/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Min Ji Han
- Department of Stem Cell and Regenerative Biotechnology KU Institute of Science and Technology, Konkuk University Seoul Republic of Korea
| | - Won Ji Lee
- Department of Stem Cell and Regenerative Biotechnology KU Institute of Science and Technology, Konkuk University Seoul Republic of Korea
| | - Joonhyuk Choi
- Department of Stem Cell and Regenerative Biotechnology KU Institute of Science and Technology, Konkuk University Seoul Republic of Korea
| | - Yean Ju Hong
- Department of Stem Cell and Regenerative Biotechnology KU Institute of Science and Technology, Konkuk University Seoul Republic of Korea
| | - Sang Jun Uhm
- Department of Animal Science Sangji University Wonju Republic of Korea
| | - Youngsok Choi
- Department of Stem Cell and Regenerative Biotechnology KU Institute of Science and Technology, Konkuk University Seoul Republic of Korea
| | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biotechnology KU Institute of Science and Technology, Konkuk University Seoul Republic of Korea
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29
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Direct reprogramming adult fibroblast into cells with partial inner ear hair cell characteristics through cell activation and signal directed approach. Neurosci Lett 2020; 729:135010. [PMID: 32344104 DOI: 10.1016/j.neulet.2020.135010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/22/2020] [Accepted: 04/21/2020] [Indexed: 11/23/2022]
Abstract
Loss of inner ear hair cell (HC) is an irreversible process in mammals and is the most common cause of human hearing and balance disorders especially in the elderly. Cell therapy based on highly scalable generation of HC linage and inner ear transplantation is one of the most promising therapeutic approaches for HC impairment. For fibroblast is quite abundant and readily available in human body, it is an ideal endogenous cell source to generate HC lineage for transplantation purpose. In the present study, by using a cell activation and signaling directed method, we demonstrate that adult fibroblast can be direct reprogrammed into a kind of cell which expresses lots of HC markers. At the same time, an intermediate progenitor stage exists during such a lineage conversion and activation of FGF pathway is critical for its formation. Although these reprogrammed cells still lack some of the key features of HC such as mechanosensitive ion channel hence have not acquired the functional properties of HC, the findings reported here raise the possibility of reprogramming endogenous fibroblasts into functional HC for regenerative purpose.
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30
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Velychko S, Kang K, Kim SM, Kwak TH, Kim KP, Park C, Hong K, Chung C, Hyun JK, MacCarthy CM, Wu G, Schöler HR, Han DW. Fusion of Reprogramming Factors Alters the Trajectory of Somatic Lineage Conversion. Cell Rep 2020; 27:30-39.e4. [PMID: 30943410 DOI: 10.1016/j.celrep.2019.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/23/2019] [Accepted: 03/07/2019] [Indexed: 01/28/2023] Open
Abstract
Simultaneous expression of Oct4, Klf4, Sox2, and cMyc induces pluripotency in somatic cells (iPSCs). Replacing Oct4 with the neuro-specific factor Brn4 leads to transdifferentiation of fibroblasts into induced neural stem cells (iNSCs). However, Brn4 was recently found to induce transient acquisition of pluripotency before establishing the neural fate. We employed genetic lineage tracing and found that induction of iNSCs with individual vectors leads to direct lineage conversion. In contrast, polycistronic expression produces a Brn4-Klf4 fusion protein that enables induction of pluripotency. Our study demonstrates that a combination of pluripotency and tissue-specific factors allows direct somatic cell transdifferentiation, bypassing the acquisition of a pluripotent state. This result has major implications for lineage conversion technologies, which hold potential for providing a safer alternative to iPSCs for clinical application both in vitro and in vivo.
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Affiliation(s)
- Sergiy Velychko
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany
| | - Kyuree Kang
- Department of Stem Cell Biology, School of Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Sung Min Kim
- Department of Stem Cell Biology, School of Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Tae Hwan Kwak
- Department of Stem Cell Biology, School of Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Kee-Pyo Kim
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany
| | - Chanhyeok Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - ChiHye Chung
- Department of Biological Sciences, Konkuk University, Seoul 05029, Republic of Korea
| | - Jung Keun Hyun
- Department of Nanobiomedical Science, Dankook University, Cheonan 330714, Republic of Korea
| | - Caitlin M MacCarthy
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany
| | - Guangming Wu
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany; Department of Stem Cell Biology, School of Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
| | - Dong Wook Han
- Department of Stem Cell Biology, School of Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; KU Open-Innovation Center, Institute of Biomedical Science and Technology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea; Department of Advanced Translational Medicine, School of Medicine, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
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31
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Kremsky I, Corces VG. Protection from DNA re-methylation by transcription factors in primordial germ cells and pre-implantation embryos can explain trans-generational epigenetic inheritance. Genome Biol 2020; 21:118. [PMID: 32423419 PMCID: PMC7236515 DOI: 10.1186/s13059-020-02036-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 05/05/2020] [Indexed: 12/16/2022] Open
Abstract
Background A growing body of evidence suggests that certain epiphenotypes can be passed across generations via both the male and female germlines of mammals. These observations have been difficult to explain owing to a global loss of the majority of known epigenetic marks present in parental chromosomes during primordial germ cell development and after fertilization. Results By integrating previously published BS-seq, DNase-seq, ATAC-seq, and RNA-seq data collected during multiple stages of primordial germ cell and pre-implantation development, we find that the methylation status of the majority of CpGs genome-wide is restored after global de-methylation, despite the fact that global CpG methylation drops to 10% in primordial germ cells and 20% in the inner cell mass of the blastocyst. We estimate the proportion of such CpGs with preserved methylation status to be 78%. Further, we find that CpGs at sites bound by transcription factors during the global re-methylation phases of germline and embryonic development remain hypomethylated across all developmental stages observed. On the other hand, CpGs at sites not bound by transcription factors during the global re-methylation phase have high methylation levels prior to global de-methylation, become de-methylated during global de-methylation, and then become re-methylated. Conclusions The results suggest that transcription factors can act as carriers of epigenetic information during germ cell and pre-implantation development by ensuring that the methylation status of CpGs is maintained. These findings provide the basis for a mechanistic description of trans-generational inheritance of epigenetic information in mammals.
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Affiliation(s)
- Isaac Kremsky
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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32
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Kwak TH, Hali S, Kim S, Kim J, La H, Kim KP, Hong KH, Shin CY, Kim NH, Han DW. Robust and Reproducible Generation of Induced Neural Stem Cells from Human Somatic Cells by Defined Factors. Int J Stem Cells 2020; 13:80-92. [PMID: 32114739 PMCID: PMC7119206 DOI: 10.15283/ijsc19097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 08/16/2019] [Accepted: 08/19/2019] [Indexed: 12/24/2022] Open
Abstract
Background and Objectives Recent studies have described direct reprogramming of mouse and human somatic cells into induced neural stem cells (iNSCs) using various combinations of transcription factors. Although iNSC technology holds a great potential for clinical applications, the low conversion efficiency and limited reproducibility of iNSC generation hinder its further translation into the clinic, strongly suggesting the necessity of highly reproducible method for human iNSCs (hiNSCs). Thus, in orderto develop a highly efficient and reproducible protocol for hiNSC generation, we revisited the reprogramming potentials of previously reported hiNSC reprogramming cocktails by comparing the reprogramming efficiency of distinct factor combinations including ours. Methods We introduced distinct factor combinations, OSKM (OCT4+SOX2+KLF4+C-MYC), OCT4 alone, SOX2 alone, SOX2+HMGA2, BRN4+SKM+SV40LT (BSKMLT), SKLT, SMLT, and SKMLT and performed comparative analysis of reprogramming potentials of distinct factor combinations in hiNSC generation. Results Here we show that ectopic expression of five reprogramming factors, BSKMLT leads the robust hiNSC generation (>80 folds enhanced efficiency) from human somatic cells compared with previously described factor combinations. With our combination, we were able to observe hiNSC conversion within 7 days of transduction. Throughout further optimization steps, we found that both BRN4 and KLF4 are not essential for hiNSC conversion. Conclusions Our factor combination could robustly and reproducibly generate hiNSCs from human somatic cells with distinct origins. Therefore, our novel reprogramming strategy might serve as a useful tool for hiNSC-based clinical application.
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Affiliation(s)
- Tae Hwan Kwak
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, Korea.,Department of Neuroscience, School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul, Korea
| | - Sai Hali
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, Korea.,Department of Neuroscience, School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul, Korea
| | - Sungmin Kim
- School of Cell and Molecular Medicine, University of Bristol, Bristol, UK
| | - Jonghun Kim
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, Korea
| | - Hyeonwoo La
- Department of Stem Cell & Regenerative Biotechnology, Konkuk University, Seoul, Korea
| | - Kee-Pyo Kim
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Kwon Ho Hong
- Department of Stem Cell & Regenerative Biotechnology, Konkuk University, Seoul, Korea
| | - Chan Young Shin
- Department of Neuroscience, School of Medicine and Center for Neuroscience Research, Konkuk University, Seoul, Korea
| | - Nam-Hyung Kim
- Department of Animal Sciences, Chungbuk National University, Cheongju, Korea
| | - Dong Wook Han
- School of Biotechnology and Healthcare, Wuyi University, Jiangmen, China
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33
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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: 0.3] [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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34
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Chuang HM, Huang MH, Chen YS, Harn HJ. SOX2 for Stem Cell Therapy and Medical Use: Pros or Cons? Cell Transplant 2020; 29:963689720907565. [PMID: 32233795 PMCID: PMC7444200 DOI: 10.1177/0963689720907565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/14/2020] [Accepted: 01/27/2020] [Indexed: 11/15/2022] Open
Abstract
Stem cell transplantation is a fast-developing technique, which includes stem cell isolation, purification, and storage, and it is in high demand in the industry. In addition, advanced applications of stem cell transplantation, including differentiation, gene delivery, and reprogramming, are presently being studied in clinical trials. In contrast to somatic cells, stem cells are self-renewing and have the ability to differentiate; however, the molecular mechanisms remain unclear. SOX2 (sex-determining region Y [SRY]-box 2) is one of the well-known reprogramming factors, and it has been recognized as an oncogene associated with cancer induction. The exclusion of SOX2 in reprogramming methodologies has been used as an alternative cancer treatment approach. However, the manner by which SOX2 induces oncogenic effects remains unclear, with most studies demonstrating its regulation of the cell cycle and no insight into the maintenance of cellular stemness. For controlling certain critical pathways, including Shh and Wnt pathways, SOX2 is considered irreplaceable and is required for the normal functioning of stem cells, particularly neural stem cells. In this report, we discussed the functions of SOX2 in both stem and cancer cells, as well as how this powerful regulator can be used to control cell fate.
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Affiliation(s)
- Hong-Meng Chuang
- Buddhist Tzu Chi Bioinnovation Center, Tzu Chi Foundation, Hualien,
Republic of China
- Department of Medical Research, Hualien Tzu Chi Hospital, Hualien,
Republic of China
| | - Mao-Hsuan Huang
- Buddhist Tzu Chi Bioinnovation Center, Tzu Chi Foundation, Hualien,
Republic of China
- Department of Stem Cell Applied Technology, Gwo Xi Stem Cell Applied
Technology, Hsinchu, Republic of China
| | - Yu-Shuan Chen
- Buddhist Tzu Chi Bioinnovation Center, Tzu Chi Foundation, Hualien,
Republic of China
- Department of Medical Research, Hualien Tzu Chi Hospital, Hualien,
Republic of China
| | - Horng-Jyh Harn
- Buddhist Tzu Chi Bioinnovation Center, Tzu Chi Foundation, Hualien,
Republic of China
- Department of Pathology, Hualien Tzu Chi Hospital & Tzu Chi
University, Hualien, Republic of China
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35
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Pires CF, Rosa FF, Kurochkin I, Pereira CF. Understanding and Modulating Immunity With Cell Reprogramming. Front Immunol 2019; 10:2809. [PMID: 31921109 PMCID: PMC6917620 DOI: 10.3389/fimmu.2019.02809] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/15/2019] [Indexed: 12/30/2022] Open
Abstract
Cell reprogramming concepts have been classically developed in the fields of developmental and stem cell biology and are currently being explored for regenerative medicine, given its potential to generate desired cell types for replacement therapy. Cell fate can be experimentally reversed or modified by enforced expression of lineage specific transcription factors leading to pluripotency or attainment of another somatic cell type identity. The possibility to reprogram fibroblasts into induced dendritic cells (DC) competent for antigen presentation creates a paradigm shift for understanding and modulating the immune system with direct cell reprogramming. PU.1, IRF8, and BATF3 were identified as sufficient and necessary to impose DC fate in unrelated cell types, taking advantage of Clec9a, a C-type lectin receptor with restricted expression in conventional DC type 1. The identification of such minimal gene regulatory networks helps to elucidate the molecular mechanisms governing development and lineage heterogeneity along the hematopoietic hierarchy. Furthermore, the generation of patient-tailored reprogrammed immune cells provides new and exciting tools for the expanding field of cancer immunotherapy. Here, we summarize cell reprogramming concepts and experimental approaches, review current knowledge at the intersection of cell reprogramming with hematopoiesis, and propose how cell fate engineering can be merged to immunology, opening new opportunities to understand the immune system in health and disease.
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Affiliation(s)
- Cristiana F. Pires
- Cell Reprogramming in Hematopoiesis and Immunity Laboratory, Lund Stem Cell Center, 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
| | - Fábio F. Rosa
- Cell Reprogramming in Hematopoiesis and Immunity Laboratory, Lund Stem Cell Center, 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
| | - Ilia Kurochkin
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Carlos-Filipe Pereira
- Cell Reprogramming in Hematopoiesis and Immunity Laboratory, Lund Stem Cell Center, 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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36
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Erharter A, Rizzi S, Mertens J, Edenhofer F. Take the shortcut - direct conversion of somatic cells into induced neural stem cells and their biomedical applications. FEBS Lett 2019; 593:3353-3369. [PMID: 31663609 PMCID: PMC6916337 DOI: 10.1002/1873-3468.13656] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 10/12/2019] [Accepted: 10/14/2019] [Indexed: 12/20/2022]
Abstract
Second-generation reprogramming of somatic cells directly into the cell type of interest avoids induction of pluripotency and subsequent cumbersome differentiation procedures. Several recent studies have reported direct conversion of human somatic cells into stably proliferating induced neural stem cells (iNSCs). Importantly, iNSCs are easier, faster, and more cost-efficient to generate than induced pluripotent stem cells (iPSCs), and also have a higher level of clinical safety. Stably, self-renewing iNSCs can be derived from different cellular sources, such as skin fibroblasts and peripheral blood mononuclear cells, and readily differentiate into neuronal and glial lineages that are indistinguishable from their iPSC-derived counterparts or from NSCs isolated from primary tissues. This review focuses on the derivation and characterization of iNSCs and their biomedical applications. We first outline different approaches to generate iNSCs and then discuss the underlying molecular mechanisms. Finally, we summarize the preclinical validation of iNSCs to highlight that these cells are promising targets for disease modeling, autologous cell therapy, and precision medicine.
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Affiliation(s)
- Anita Erharter
- Department of Molecular Biology & CMBI, Genomics, Stem Cell Biology & Regenerative Medicine, Leopold-Franzens-University Innsbruck, Austria
| | - Sandra Rizzi
- Department of Molecular Biology & CMBI, Genomics, Stem Cell Biology & Regenerative Medicine, Leopold-Franzens-University Innsbruck, Austria.,Institute of Pharmacology, Medical University Innsbruck, Austria
| | - Jerome Mertens
- Department of Molecular Biology & CMBI, Genomics, Stem Cell Biology & Regenerative Medicine, Leopold-Franzens-University Innsbruck, Austria
| | - Frank Edenhofer
- Department of Molecular Biology & CMBI, Genomics, Stem Cell Biology & Regenerative Medicine, Leopold-Franzens-University Innsbruck, Austria
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37
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Peskova L, Cerna K, Oppelt J, Mraz M, Barta T. Oct4-mediated reprogramming induces embryonic-like microRNA expression signatures in human fibroblasts. Sci Rep 2019; 9:15759. [PMID: 31673026 PMCID: PMC6823439 DOI: 10.1038/s41598-019-52294-3] [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: 05/02/2019] [Accepted: 10/16/2019] [Indexed: 12/22/2022] Open
Abstract
Oct4-mediated reprogramming has recently become a novel tool for the generation of various cell types from differentiated somatic cells. Although molecular mechanisms underlying this process are unknown, it is well documented that cells over-expressing Oct4 undergo transition from differentiated state into plastic state. This transition is associated with the acquisition of stem cells properties leading to epigenetically “open” state that is permissive to cell fate switch upon external stimuli. In order to contribute to our understanding of molecular mechanisms driving this process, we characterised human fibroblasts over-expressing Oct4 and performed comprehensive small-RNAseq analysis. Our analyses revealed new interesting aspects of Oct4-mediated cell plasticity induction. Cells over-expressing Oct4 lose their cell identity demonstrated by down-regulation of fibroblast-specific genes and up-regulation of epithelial genes. Interestingly, this process is associated with microRNA expression profile that is similar to microRNA profiles typically found in pluripotent stem cells. We also provide extensive network of microRNA families and clusters allowing us to precisely determine the miRNAome associated with the acquisition of Oct4-induced transient plastic state. Our data expands current knowledge of microRNA and their implications in cell fate alterations and contributing to understanding molecular mechanisms underlying it.
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Affiliation(s)
- Lucie Peskova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, 625 00, Czech Republic
| | - Katerina Cerna
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Jan Oppelt
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Marek Mraz
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic.,Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Tomas Barta
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, 625 00, Czech Republic.
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Flitsch LJ, Brüstle O. Evolving principles underlying neural lineage conversion and their relevance for biomedical translation. F1000Res 2019; 8. [PMID: 31559012 PMCID: PMC6743253 DOI: 10.12688/f1000research.18926.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/23/2019] [Indexed: 12/19/2022] Open
Abstract
Scientific and technological advances of the past decade have shed light on the mechanisms underlying cell fate acquisition, including its transcriptional and epigenetic regulation during embryonic development. This knowledge has enabled us to purposefully engineer cell fates
in vitro by manipulating expression levels of lineage-instructing transcription factors. Here, we review the state of the art in the cell programming field with a focus on the derivation of neural cells. We reflect on what we know about the mechanisms underlying fate changes in general and on the degree of epigenetic remodeling conveyed by the distinct reprogramming and direct conversion strategies available. Moreover, we discuss the implications of residual epigenetic memory for biomedical applications such as disease modeling and neuroregeneration. Finally, we cover recent developments approaching cell fate conversion in the living brain and define questions which need to be addressed before cell programming can become an integral part of translational medicine.
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Affiliation(s)
- Lea Jessica Flitsch
- Institute of Reconstructive Neurobiology, University of Bonn School of Medicine & University Hospital Bonn, Bonn, North Rhine Wesphalia, 53127, Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, University of Bonn School of Medicine & University Hospital Bonn, Bonn, North Rhine Wesphalia, 53127, Germany
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39
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Direct Reprogramming of Mouse Fibroblasts into Functional Skeletal Muscle Progenitors. Stem Cell Reports 2019; 10:1505-1521. [PMID: 29742392 PMCID: PMC5995754 DOI: 10.1016/j.stemcr.2018.04.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/13/2018] [Accepted: 04/13/2018] [Indexed: 02/06/2023] Open
Abstract
Skeletal muscle harbors quiescent stem cells termed satellite cells and proliferative progenitors termed myoblasts, which play pivotal roles during muscle regeneration. However, current technology does not allow permanent capture of these cell populations in vitro. Here, we show that ectopic expression of the myogenic transcription factor MyoD, combined with exposure to small molecules, reprograms mouse fibroblasts into expandable induced myogenic progenitor cells (iMPCs). iMPCs express key skeletal muscle stem and progenitor cell markers including Pax7 and Myf5 and give rise to dystrophin-expressing myofibers upon transplantation in vivo. Notably, a subset of transplanted iMPCs maintain Pax7 expression and sustain serial regenerative responses. Similar to satellite cells, iMPCs originate from Pax7+ cells and require Pax7 itself for maintenance. Finally, we show that myogenic progenitor cell lines can be established from muscle tissue following small-molecule exposure alone. This study thus reports on a robust approach to derive expandable myogenic stem/progenitor-like cells from multiple cell types. MyoD and small molecules reprogram fibroblasts to myogenic progenitors termed iMPCs iMPCs self-renew and express key satellite cell and myoblast markers iMPC growth is driven by Pax7+ cells and requires Pax7 gene function Transplanted iMPCs engraft and sustain muscle regeneration in vivo
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40
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Jung YH, Kremsky I, Gold HB, Rowley MJ, Punyawai K, Buonanotte A, Lyu X, Bixler BJ, Chan AWS, Corces VG. Maintenance of CTCF- and Transcription Factor-Mediated Interactions from the Gametes to the Early Mouse Embryo. Mol Cell 2019; 75:154-171.e5. [PMID: 31056445 PMCID: PMC6625867 DOI: 10.1016/j.molcel.2019.04.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/02/2019] [Accepted: 04/09/2019] [Indexed: 12/31/2022]
Abstract
The epigenetic information present in mammalian gametes and whether it is transmitted to the progeny are relatively unknown. We find that many promoters in mouse sperm are occupied by RNA polymerase II (Pol II) and Mediator. The same promoters are accessible in GV and MII oocytes and preimplantation embryos. Sperm distal ATAC-seq sites containing motifs for various transcription factors are conserved in monkeys and humans. ChIP-seq analyses confirm that Foxa1, ERα, and AR occupy distal enhancers in sperm. Accessible sperm enhancers containing H3.3 and H2A.Z are also accessible in oocytes and preimplantation embryos. Furthermore, their interactions with promoters in the gametes persist during early development. Sperm- or oocyte-specific interactions mediated by CTCF and cohesin are only present in the paternal or maternal chromosomes, respectively, in the zygote and 2-cell stages. These interactions converge in both chromosomes by the 8-cell stage. Thus, mammalian gametes contain complex patterns of 3D interactions that can be transmitted to the zygote after fertilization.
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Affiliation(s)
- Yoon Hee Jung
- Department of Biology, Emory University, 1510 Clifton Rd. NE, Atlanta, GA 30322, USA
| | - Isaac Kremsky
- Department of Biology, Emory University, 1510 Clifton Rd. NE, Atlanta, GA 30322, USA
| | - Hannah B Gold
- Department of Biology, Emory University, 1510 Clifton Rd. NE, Atlanta, GA 30322, USA
| | - M Jordan Rowley
- Department of Biology, Emory University, 1510 Clifton Rd. NE, Atlanta, GA 30322, USA
| | - Kanchana Punyawai
- Yerkes National Primate Research Center, 954 Gatewood Rd. NE, Atlanta, GA 39329, USA; Department of Human Genetics, Emory University School of Medicine, 615 Michael St., Atlanta, GA 30322, USA
| | - Alyx Buonanotte
- Yerkes National Primate Research Center, 954 Gatewood Rd. NE, Atlanta, GA 39329, USA; Department of Human Genetics, Emory University School of Medicine, 615 Michael St., Atlanta, GA 30322, USA; Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, 1462 Clifton Rd., Atlanta, GA 30322, USA
| | - Xiaowen Lyu
- Department of Biology, Emory University, 1510 Clifton Rd. NE, Atlanta, GA 30322, USA
| | - Brianna J Bixler
- Department of Biology, Emory University, 1510 Clifton Rd. NE, Atlanta, GA 30322, USA; Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, 1462 Clifton Rd., Atlanta, GA 30322, USA
| | - Anthony W S Chan
- Yerkes National Primate Research Center, 954 Gatewood Rd. NE, Atlanta, GA 39329, USA; Department of Human Genetics, Emory University School of Medicine, 615 Michael St., Atlanta, GA 30322, USA; Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, 1462 Clifton Rd., Atlanta, GA 30322, USA
| | - Victor G Corces
- Department of Biology, Emory University, 1510 Clifton Rd. NE, Atlanta, GA 30322, USA; Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, 1462 Clifton Rd., Atlanta, GA 30322, USA.
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41
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scSLAM-seq reveals core features of transcription dynamics in single cells. Nature 2019; 571:419-423. [DOI: 10.1038/s41586-019-1369-y] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 06/10/2019] [Indexed: 11/08/2022]
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42
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Wong AP, Shojaie S, Liang Q, Xia S, Di Paola M, Ahmadi S, Bilodeau C, Garner J, Post M, Duchesneau P, Waddell TK, Bear CE, Nagy A, Rossant J. Conversion of human and mouse fibroblasts into lung-like epithelial cells. Sci Rep 2019; 9:9027. [PMID: 31227724 PMCID: PMC6588580 DOI: 10.1038/s41598-019-45195-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/31/2019] [Indexed: 01/08/2023] Open
Abstract
Cell lineage conversion of fibroblasts to specialized cell types through transdifferentiation may provide a fast and alternative cell source for regenerative medicine. Here we show that transient transduction of fibroblasts with the four reprogramming factors (Oct4, Sox2, Klf4, and c-Myc) in addition to the early lung transcription factor Nkx2-1 (also known as Ttf1), followed by directed differentiation of the cells, can convert mouse embryonic and human adult dermal fibroblasts into induced lung-like epithelial cells (iLEC). These iLEC differentiate into multiple lung cell types in air liquid interface cultures, repopulate decellularized rat lung scaffolds, and form lung epithelia composed of Ciliated, Goblet, Basal, and Club cells after transplantation into immune-compromised mice. As proof-of-concept, differentiated human iLEC harboring the Cystic Fibrosis mutation dF508 demonstrated pharmacological rescue of CFTR function using the combination of lumacaftor and ivacaftor. Overall, this is a promising alternative approach for generation of patient-specific lung-like progenitors to study lung function, disease and future regeneration strategies.
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Affiliation(s)
- Amy P Wong
- Program in Developmental & Stem Cell Biology, SickKids Research Institute, Hospital for Sick Children, Toronto, ON, Canada.
| | - Sharareh Shojaie
- Program in Translational Medicine, SickKids Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Qin Liang
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Sunny Xia
- Program in Molecular Medicine, SickKids Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Michelle Di Paola
- Program in Molecular Medicine, SickKids Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Saumel Ahmadi
- Program in Molecular Medicine, SickKids Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Claudia Bilodeau
- Program in Translational Medicine, SickKids Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Jodi Garner
- Program in Developmental & Stem Cell Biology, SickKids Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Martin Post
- Program in Translational Medicine, SickKids Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Pascal Duchesneau
- Latner Thoracic Surgery Research Laboratories, Toronto General Research Institute, and the McEwen Centre for Regenerative Medicine, Toronto, Canada
| | - Thomas K Waddell
- Latner Thoracic Surgery Research Laboratories, Toronto General Research Institute, and the McEwen Centre for Regenerative Medicine, Toronto, Canada
| | - Christine E Bear
- Program in Molecular Medicine, SickKids Research Institute, Hospital for Sick Children, Toronto, Canada
| | - Andras Nagy
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Janet Rossant
- Program in Developmental & Stem Cell Biology, SickKids Research Institute, Hospital for Sick Children, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. .,Department of Obstetrics and Gynaecology, University of Toronto, Toronto, Canada.
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43
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Ahlfors JE, Azimi A, El-Ayoubi R, Velumian A, Vonderwalde I, Boscher C, Mihai O, Mani S, Samoilova M, Khazaei M, Fehlings MG, Morshead CM. Examining the fundamental biology of a novel population of directly reprogrammed human neural precursor cells. Stem Cell Res Ther 2019; 10:166. [PMID: 31196173 PMCID: PMC6567617 DOI: 10.1186/s13287-019-1255-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 04/29/2019] [Accepted: 05/06/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Cell reprogramming is a promising avenue for cell-based therapies as it allows for the generation of multipotent, unipotent, or mature somatic cells without going through a pluripotent state. While the use of autologous cells is considered ideal, key challenges for their clinical translation include the ability to reproducibly generate sufficient quantities of cells within a therapeutically relevant time window. METHODS We performed transfection of three distinct human somatic starting populations of cells with a non-integrating synthetic plasmid expressing Musashi 1 (MSI1), Neurogenin 2 (NGN2), and Methyl-CpG-Binding Domain 2 (MBD2). The resulting directly reprogrammed neural precursor cells (drNPCs) were examined in vitro using RT-qPCR, karyotype analysis, immunohistochemistry, and FACS at early and late time post-transfection. Electrophysiology (patch clamp) was performed on drNPC-derived neurons to determine their capacity to generate action potentials. In vivo characterization was performed following transplantation of drNPCs into two animal models (Shiverer and SCID/Beige mice), and the numbers, location, and differentiation profile of the transplanted cells were examined using immunohistochemistry. RESULTS Human somatic cells can be directly reprogrammed within two weeks to neural precursor cells (drNPCs) by transient exposure to Msi1, Ngn2, and MBD2 using non-viral constructs. The drNPCs generate all three neural cell types (astrocytes, oligodendrocytes, and neurons) and can be passaged in vitro to generate large numbers of cells within four weeks. drNPCs can respond to in vivo differentiation and migration cues as demonstrated by their migration to the olfactory bulb and contribution to neurogenesis in vivo. Differentiation profiles of transplanted cells onto the corpus callosum of myelin-deficient mice reveal the production of oligodendrocytes and astrocytes. CONCLUSIONS Human drNPCs can be efficiently and rapidly produced from donor somatic cells and possess all the important characteristics of native neural multipotent cells including differentiation into neurons, astrocytes, and oligodendrocytes, and in vivo neurogenesis and myelination.
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Affiliation(s)
| | - Ashkan Azimi
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario M5S 1A8 Canada
- Division of Anatomy, Department of Surgery, University of Toronto, Ontario, M5S 1A8 Canada
| | | | - Alexander Velumian
- Division of Neurosurgery, Department of Surgery, University of Toronto, Ontario, M5T 1P5 Canada
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8 Canada
| | - Ilan Vonderwalde
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9 Canada
| | | | - Oana Mihai
- New World Laboratories, Laval, Quebec, H7V 5B7 Canada
| | - Sarathi Mani
- New World Laboratories, Laval, Quebec, H7V 5B7 Canada
| | - Marina Samoilova
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8 Canada
| | - Mohamad Khazaei
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8 Canada
| | - Michael G. Fehlings
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario M5S 1A8 Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Ontario, M5T 1P5 Canada
- Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8 Canada
| | - Cindi M Morshead
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario M5S 1A8 Canada
- Division of Anatomy, Department of Surgery, University of Toronto, Ontario, M5S 1A8 Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9 Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S3E1 Canada
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44
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Gancheva MR, Kremer KL, Gronthos S, Koblar SA. Using Dental Pulp Stem Cells for Stroke Therapy. Front Neurol 2019; 10:422. [PMID: 31110489 PMCID: PMC6501465 DOI: 10.3389/fneur.2019.00422] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/08/2019] [Indexed: 12/26/2022] Open
Abstract
Stroke is a leading cause of permanent disability world-wide, but aside from rehabilitation, there is currently no clinically-proven pharmaceutical or biological agent to improve neurological disability. Cell-based therapies using stem cells, such as dental pulp stem cells, are a promising alternative for treatment of neurological diseases, including stroke. The ischaemic environment in stroke affects multiple cell populations, thus stem cells, which act through cellular and molecular mechanisms, are promising candidates. The most common stem cell population studied in the neurological setting has been mesenchymal stem cells due to their accessibility. However, it is believed that neural stem cells, the resident stem cell of the adult brain, would be most appropriate for brain repair. Using reprogramming strategies, alternative sources of neural stem and progenitor cells have been explored. We postulate that a cell of closer origin to the neural lineage would be a promising candidate for reprogramming and modification towards a neural stem or progenitor cell. One such candidate population is dental pulp stem cells, which reside in the root canal of teeth. This review will focus on the neural potential of dental pulp stem cells and their investigations in the stroke setting to date, and include an overview on the use of different sources of neural stem cells in preclinical studies and clinical trials of stroke.
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Affiliation(s)
- Maria R. Gancheva
- Stroke Research Programme Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Karlea L. Kremer
- Stroke Research Programme Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Stan Gronthos
- Mesenchymal Stem Cell Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Simon A. Koblar
- Stroke Research Programme Laboratory, Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Central Adelaide Local Health Network, Adelaide, SA, Australia
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Lehmann M, Canatelli-Mallat M, Chiavellini P, Morel GR, Reggiani PC, Hereñú CB, Goya RG. Regulatable adenovector harboring the GFP and Yamanaka genes for implementing regenerative medicine in the brain. Gene Ther 2019; 26:432-440. [PMID: 30770896 DOI: 10.1038/s41434-019-0063-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/26/2019] [Accepted: 01/31/2019] [Indexed: 02/07/2023]
Abstract
Biological rejuvenation by partial cell reprogramming is an emerging avenue of research. In this context, regulatable pluripotency gene expression systems are the most widely used at present. We have constructed a regulatable bidirectional adenovector expressing the humanized green fluorescent protein (GFP) and oct4, sox2, klf4, and c-myc genes (known as the Yamanaka genes or OSKM). The OSKM genes are arranged as a bicistronic tandem (hSTEMCCA tandem), which is under the control of a Tet-Off bidirectional promoter that also controls the expression of the gFP gene. Separately, a constitutive cassette expresses the regulatory protein tTA. Vector DNA was transfected in HEK293 Cre cells, which were additionally infected with the helper adenovector H14, unable to package its DNA due to the Cre recombinase produced by the HEK293 Cre cells. The newly generated vector was expanded by six iterated coinfections of the above cells which were lysed at the end of the process and the adenovector purified by ultracentrifugation in a CsCl gradient. The titer of the initial preparation was 1.2 × 1012 physical viral particles/ml. As expected, GFP fluorescence in vector-transduced rat fibroblast cultures declined with the dose of doxycycline (DOX) present in the medium. Immunocytochemical analysis of transduced cells confirmed the expression of the four Yamanaka genes. Additionally, 3 days after vector injection in the hypothalamus of rats, a significant level of fluorescence was observed in the region. Addition of 2 mg/ml DOX to the drinking water reduced the GFP expression. This adenovector constitutes a promising tool for implementing nonintegrative partial cell reprogramming.
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Affiliation(s)
- Marianne Lehmann
- Institute for Biochemical Research (INIBIOLP)-Histology B & Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Martina Canatelli-Mallat
- Institute for Biochemical Research (INIBIOLP)-Histology B & Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Priscila Chiavellini
- Institute for Biochemical Research (INIBIOLP)-Histology B & Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Gustavo R Morel
- Institute for Biochemical Research (INIBIOLP)-Histology B & Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Paula C Reggiani
- Institute for Biochemical Research (INIBIOLP)-Histology B & Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Claudia B Hereñú
- Institute for Experimental Pharmacology Cordoba (IFEC), School of Chemical Sciences, National University of Cordoba, Cordoba, Argentina
| | - Rodolfo G Goya
- Institute for Biochemical Research (INIBIOLP)-Histology B & Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina.
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Kanitz A, Syed AP, Kaji K, Zavolan M. Conserved regulation of RNA processing in somatic cell reprogramming. BMC Genomics 2019; 20:100. [PMID: 30704403 PMCID: PMC6357513 DOI: 10.1186/s12864-019-5438-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 01/08/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Along with the reorganization of epigenetic and transcriptional networks, somatic cell reprogramming brings about numerous changes at the level of RNA processing. These include the expression of specific transcript isoforms and 3' untranslated regions. A number of studies have uncovered RNA processing factors that modulate the efficiency of the reprogramming process. However, a comprehensive evaluation of the involvement of RNA processing factors in the reprogramming of somatic mammalian cells is lacking. RESULTS Here, we used data from a large number of studies carried out in three mammalian species, mouse, chimpanzee and human, to uncover consistent changes in gene expression upon reprogramming of somatic cells. We found that a core set of nine splicing factors have consistent changes across the majority of data sets in all three species. Most striking among these are ESRP1 and ESRP2, which accelerate and enhance the efficiency of somatic cell reprogramming by promoting isoform expression changes associated with mesenchymal-to-epithelial transition. We further identify genes and processes in which splicing changes are observed in both human and mouse. CONCLUSIONS Our results provide a general resource for gene expression and splicing changes that take place during somatic cell reprogramming. Furthermore, they support the concept that splicing factors with evolutionarily conserved, cell type-specific expression can modulate the efficiency of the process by reinforcing intermediate states resembling the cell types in which these factors are normally expressed.
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Affiliation(s)
- Alexander Kanitz
- Biozentrum, University of Basel, Basel, Switzerland
- RNA Regulatory Networks, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Afzal Pasha Syed
- Biozentrum, University of Basel, Basel, Switzerland
- RNA Regulatory Networks, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Keisuke Kaji
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Mihaela Zavolan
- Biozentrum, University of Basel, Basel, Switzerland
- RNA Regulatory Networks, Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Sastre-Perona A, Hoang-Phou S, Leitner MC, Okuniewska M, Meehan S, Schober M. De Novo PITX1 Expression Controls Bi-Stable Transcriptional Circuits to Govern Self-Renewal and Differentiation in Squamous Cell Carcinoma. Cell Stem Cell 2019; 24:390-404.e8. [PMID: 30713093 DOI: 10.1016/j.stem.2019.01.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/25/2018] [Accepted: 01/08/2019] [Indexed: 12/21/2022]
Abstract
Basal tumor propagating cells (TPCs) control squamous cell carcinoma (SCC) growth by self-renewing and differentiating into supra-basal SCC cells, which lack proliferative potential. While transcription factors such as SOX2 and KLF4 can drive these behaviors, their molecular roles and regulatory interactions with each other have remained elusive. Here, we show that PITX1 is specifically expressed in TPCs, where it co-localizes with SOX2 and TRP63 and determines cell fate in mouse and human SCC. Combining gene targeting with chromatin immunoprecipitation sequencing (ChIP-seq) and transcriptomic analyses reveals that PITX1 cooperates with SOX2 and TRP63 to sustain an SCC-specific transcriptional feed-forward circuit that maintains TPC-renewal, while inhibiting KLF4 expression and preventing KLF4-dependent differentiation. Conversely, KLF4 represses PITX1, SOX2, and TRP63 expression to prevent TPC expansion. This bi-stable, multi-input network reveals a molecular framework that explains self-renewal, aberrant differentiation, and SCC growth in mice and humans, providing clues for developing differentiation-inducing therapeutic strategies.
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Affiliation(s)
- Ana Sastre-Perona
- The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, NY, USA; New York University School of Medicine, New York, NY, USA
| | - Steven Hoang-Phou
- The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, NY, USA; New York University School of Medicine, New York, NY, USA
| | - Marie-Christin Leitner
- The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, NY, USA; New York University School of Medicine, New York, NY, USA
| | | | - Shane Meehan
- The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, NY, USA; New York University School of Medicine, New York, NY, USA
| | - Markus Schober
- The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, NY, USA; New York University School of Medicine, New York, NY, USA.
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The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome. Nat Commun 2019; 10:30. [PMID: 30604745 PMCID: PMC6318279 DOI: 10.1038/s41467-018-07907-2] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 11/14/2018] [Indexed: 12/16/2022] Open
Abstract
The inactive X chromosome (Xi) in female mammals adopts an atypical higher-order chromatin structure, manifested as a global loss of local topologically associated domains (TADs), A/B compartments and formation of two mega-domains. Here we demonstrate that the non-canonical SMC family protein, SmcHD1, which is important for gene silencing on Xi, contributes to this unique chromosome architecture. Specifically, allelic mapping of the transcriptome and epigenome in SmcHD1 mutant cells reveals the appearance of sub-megabase domains defined by gene activation, CpG hypermethylation and depletion of Polycomb-mediated H3K27me3. These domains, which correlate with sites of SmcHD1 enrichment on Xi in wild-type cells, additionally adopt features of active X chromosome higher-order chromosome architecture, including A/B compartments and partial restoration of TAD boundaries. Xi chromosome architecture changes also occurred following SmcHD1 knockout in a somatic cell model, but in this case, independent of Xi gene derepression. We conclude that SmcHD1 is a key factor in defining the unique chromosome architecture of Xi. The inactive X chromosome (Xi) has an atypical structure, with global loss of TADs, A/B compartments and formation of mega-domains. Here the authors show that the non-canonical SMC family protein, SmcHD1, important for developmental gene silencing on Xi, antagonises TAD formation and compartmentalization on the Xi in a transcription independent way.
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A stably self-renewing adult blood-derived induced neural stem cell exhibiting patternability and epigenetic rejuvenation. Nat Commun 2018; 9:4047. [PMID: 30279449 PMCID: PMC6168501 DOI: 10.1038/s41467-018-06398-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 08/24/2018] [Indexed: 12/20/2022] Open
Abstract
Recent reports suggest that induced neurons (iNs), but not induced pluripotent stem cell (iPSC)-derived neurons, largely preserve age-associated traits. Here, we report on the extent of preserved epigenetic and transcriptional aging signatures in directly converted induced neural stem cells (iNSCs). Employing restricted and integration-free expression of SOX2 and c-MYC, we generated a fully functional, bona fide NSC population from adult blood cells that remains highly responsive to regional patterning cues. Upon conversion, low passage iNSCs display a profound loss of age-related DNA methylation signatures, which further erode across extended passaging, thereby approximating the DNA methylation age of isogenic iPSC-derived neural precursors. This epigenetic rejuvenation is accompanied by a lack of age-associated transcriptional signatures and absence of cellular aging hallmarks. We find iNSCs to be competent for modeling pathological protein aggregation and for neurotransplantation, depicting blood-to-NSC conversion as a rapid alternative route for both disease modeling and neuroregeneration. Induced neurons, but not induced pluripotent stem cell (iPSC)-derived neurons, preserve age-related traits. Here, the authors demonstrate that blood-derived induced neural stem cells (iNSCs), despite lacking a pluripotency transit, lose age-related signatures.
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50
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Durbin MD, Cadar AG, Chun YW, Hong CC. Investigating pediatric disorders with induced pluripotent stem cells. Pediatr Res 2018; 84:499-508. [PMID: 30065271 PMCID: PMC6265074 DOI: 10.1038/s41390-018-0064-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 05/02/2018] [Accepted: 05/07/2018] [Indexed: 12/14/2022]
Abstract
The study of disease pathophysiology has long relied on model systems, including animal models and cultured cells. In 2006, Shinya Yamanaka achieved a breakthrough by reprogramming somatic cells into induced pluripotent stem cells (iPSCs). This revolutionary discovery provided new opportunities for disease modeling and therapeutic intervention. With established protocols, investigators can generate iPSC lines from patient blood, urine, and tissue samples. These iPSCs retain ability to differentiate into every human cell type. Advances in differentiation and organogenesis move cellular in vitro modeling to a multicellular model capable of recapitulating physiology and disease. Here, we discuss limitations of traditional animal and tissue culture models, as well as the application of iPSC models. We highlight various techniques, including reprogramming strategies, directed differentiation, tissue engineering, organoid developments, and genome editing. We extensively summarize current established iPSC disease models that utilize these techniques. Confluence of these technologies will advance our understanding of pediatric diseases and help usher in new personalized therapies for patients.
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Affiliation(s)
- Matthew D. Durbin
- Department of Pediatrics – Division of Neonatal-Perinatal Medicine, Indiana University School of Medicine, Indianapolis, IN 46202
| | - Adrian G. Cadar
- Departments of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Young W. Chun
- Department of Medicine - Cardiovascular Medicine Division University of Maryland School of Medicine, Baltimore, MD 21201
| | - Charles C. Hong
- Department of Medicine - Cardiovascular Medicine Division University of Maryland School of Medicine, Baltimore, MD 21201
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