1
|
Patton MH, Thomas KT, Bayazitov IT, Newman KD, Kurtz NB, Robinson CG, Ramirez CA, Trevisan AJ, Bikoff JB, Peters ST, Pruett-Miller SM, Jiang Y, Schild AB, Nityanandam A, Zakharenko SS. Synaptic plasticity in human thalamocortical assembloids. Cell Rep 2024; 43:114503. [PMID: 39018245 DOI: 10.1016/j.celrep.2024.114503] [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: 03/11/2024] [Revised: 04/23/2024] [Accepted: 06/27/2024] [Indexed: 07/19/2024] Open
Abstract
Synaptic plasticities, such as long-term potentiation (LTP) and depression (LTD), tune synaptic efficacy and are essential for learning and memory. Current studies of synaptic plasticity in humans are limited by a lack of adequate human models. Here, we modeled the thalamocortical system by fusing human induced pluripotent stem cell-derived thalamic and cortical organoids. Single-nucleus RNA sequencing revealed that >80% of cells in thalamic organoids were glutamatergic neurons. When fused to form thalamocortical assembloids, thalamic and cortical organoids formed reciprocal long-range axonal projections and reciprocal synapses detectable by light and electron microscopy, respectively. Using whole-cell patch-clamp electrophysiology and two-photon imaging, we characterized glutamatergic synaptic transmission. Thalamocortical and corticothalamic synapses displayed short-term plasticity analogous to that in animal models. LTP and LTD were reliably induced at both synapses; however, their mechanisms differed from those previously described in rodents. Thus, thalamocortical assembloids provide a model system for exploring synaptic plasticity in human circuits.
Collapse
Affiliation(s)
- Mary H Patton
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kristen T Thomas
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ildar T Bayazitov
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kyle D Newman
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Nathaniel B Kurtz
- Cell and Tissue Imaging Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Camenzind G Robinson
- Cell and Tissue Imaging Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cody A Ramirez
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Alexandra J Trevisan
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jay B Bikoff
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Samuel T Peters
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yanbo Jiang
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Andrew B Schild
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Anjana Nityanandam
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stanislav S Zakharenko
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| |
Collapse
|
2
|
Rehman A, Fatima I, Noor F, Qasim M, Wang P, Jia J, Alshabrmi FM, Liao M. Role of small molecules as drug candidates for reprogramming somatic cells into induced pluripotent stem cells: A comprehensive review. Comput Biol Med 2024; 177:108661. [PMID: 38810477 DOI: 10.1016/j.compbiomed.2024.108661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/08/2024] [Accepted: 05/26/2024] [Indexed: 05/31/2024]
Abstract
With the use of specific genetic factors and recent developments in cellular reprogramming, it is now possible to generate lineage-committed cells or induced pluripotent stem cells (iPSCs) from readily available and common somatic cell types. However, there are still significant doubts regarding the safety and effectiveness of the current genetic methods for reprogramming cells, as well as the conventional culture methods for maintaining stem cells. Small molecules that target specific epigenetic processes, signaling pathways, and other cellular processes can be used as a complementary approach to manipulate cell fate to achieve a desired objective. It has been discovered that a growing number of small molecules can support lineage differentiation, maintain stem cell self-renewal potential, and facilitate reprogramming by either increasing the efficiency of reprogramming or acting as a genetic reprogramming factor substitute. However, ongoing challenges include improving reprogramming efficiency, ensuring the safety of small molecules, and addressing issues with incomplete epigenetic resetting. Small molecule iPSCs have significant clinical applications in regenerative medicine and personalized therapies. This review emphasizes the versatility and potential safety benefits of small molecules in overcoming challenges associated with the iPSCs reprogramming process.
Collapse
Affiliation(s)
- Abdur Rehman
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Israr Fatima
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Fatima Noor
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan; Department of Bioinformatics and Biotechnology, Government College University of Faisalabad, 38000, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University of Faisalabad, 38000, Pakistan
| | - Peng Wang
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Jinrui Jia
- Laboratory of Animal Fat Deposition and Muscle Development, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, PR China
| | - Fahad M Alshabrmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, 51452, Saudi Arabia
| | - Mingzhi Liao
- Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, PR China.
| |
Collapse
|
3
|
Patton MH, Thomas KT, Bayazitov IT, Newman KD, Kurtz NB, Robinson CG, Ramirez CA, Trevisan AJ, Bikoff JB, Peters ST, Pruett-Miller SM, Jiang Y, Schild AB, Nityanandam A, Zakharenko SS. Synaptic plasticity in human thalamocortical assembloids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578421. [PMID: 38352415 PMCID: PMC10862901 DOI: 10.1101/2024.02.01.578421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Synaptic plasticities, such as long-term potentiation (LTP) and depression (LTD), tune synaptic efficacy and are essential for learning and memory. Current studies of synaptic plasticity in humans are limited by a lack of adequate human models. Here, we modeled the thalamocortical system by fusing human induced pluripotent stem cell-derived thalamic and cortical organoids. Single-nucleus RNA-sequencing revealed that most cells in mature thalamic organoids were glutamatergic neurons. When fused to form thalamocortical assembloids, thalamic and cortical organoids formed reciprocal long-range axonal projections and reciprocal synapses detectable by light and electron microscopy, respectively. Using whole-cell patch-clamp electrophysiology and two-photon imaging, we characterized glutamatergic synaptic transmission. Thalamocortical and corticothalamic synapses displayed short-term plasticity analogous to that in animal models. LTP and LTD were reliably induced at both synapses; however, their mechanisms differed from those previously described in rodents. Thus, thalamocortical assembloids provide a model system for exploring synaptic plasticity in human circuits.
Collapse
Affiliation(s)
- Mary H. Patton
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Kristen T. Thomas
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Ildar T. Bayazitov
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Kyle D. Newman
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Nathaniel B. Kurtz
- Cell and Tissue Imaging Center, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Camenzind G. Robinson
- Cell and Tissue Imaging Center, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Cody A. Ramirez
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Alexandra J. Trevisan
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Jay B. Bikoff
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Samuel T. Peters
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Shondra M. Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
- Department of Cell & Molecular Biology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Yanbo Jiang
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Andrew B. Schild
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Anjana Nityanandam
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Stanislav S. Zakharenko
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| |
Collapse
|
4
|
Kumar S, Granados J, Aceves M, Peralta J, Leandro AC, Thomas J, Williams-Blangero S, Curran JE, Blangero J. Pre-Infection Innate Immunity Attenuates SARS-CoV-2 Infection and Viral Load in iPSC-Derived Alveolar Epithelial Type 2 Cells. Cells 2024; 13:369. [PMID: 38474333 PMCID: PMC10931100 DOI: 10.3390/cells13050369] [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: 12/17/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
A large portion of the heterogeneity in coronavirus disease 2019 (COVID-19) susceptibility and severity of illness (SOI) remains poorly understood. Recent evidence suggests that SARS-CoV-2 infection-associated damage to alveolar epithelial type 2 cells (AT2s) in the distal lung may directly contribute to disease severity and poor prognosis in COVID-19 patients. Our in vitro modeling of SARS-CoV-2 infection in induced pluripotent stem cell (iPSC)-derived AT2s from 10 different individuals showed interindividual variability in infection susceptibility and the postinfection cellular viral load. To understand the underlying mechanism of the AT2's capacity to regulate SARS-CoV-2 infection and cellular viral load, a genome-wide differential gene expression analysis between the mock and SARS-CoV-2 infection-challenged AT2s was performed. The 1393 genes, which were significantly (one-way ANOVA FDR-corrected p ≤ 0.05; FC abs ≥ 2.0) differentially expressed (DE), suggest significant upregulation of viral infection-related cellular innate immune response pathways (p-value ≤ 0.05; activation z-score ≥ 3.5), and significant downregulation of the cholesterol- and xenobiotic-related metabolic pathways (p-value ≤ 0.05; activation z-score ≤ -3.5). Whilst the effect of post-SARS-CoV-2 infection response on the infection susceptibility and postinfection viral load in AT2s is not clear, interestingly, pre-infection (mock-challenged) expression of 238 DE genes showed a high correlation with the postinfection SARS-CoV-2 viral load (FDR-corrected p-value ≤ 0.05 and r2-absolute ≥ 0.57). The 85 genes whose expression was negatively correlated with the viral load showed significant enrichment in viral recognition and cytokine-mediated innate immune GO biological processes (p-value range: 4.65 × 10-10 to 2.24 × 10-6). The 153 genes whose expression was positively correlated with the viral load showed significant enrichment in cholesterol homeostasis, extracellular matrix, and MAPK/ERK pathway-related GO biological processes (p-value range: 5.06 × 10-5 to 6.53 × 10-4). Overall, our results strongly suggest that AT2s' pre-infection innate immunity and metabolic state affect their susceptibility to SARS-CoV-2 infection and viral load.
Collapse
Affiliation(s)
- Satish Kumar
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA; (J.G.); (M.A.); (J.T.)
| | - Jose Granados
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA; (J.G.); (M.A.); (J.T.)
| | - Miriam Aceves
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA; (J.G.); (M.A.); (J.T.)
| | - Juan Peralta
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.P.); (A.C.L.); (S.W.-B.); (J.E.C.); (J.B.)
| | - Ana C. Leandro
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.P.); (A.C.L.); (S.W.-B.); (J.E.C.); (J.B.)
| | - John Thomas
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, McAllen, TX 78504, USA; (J.G.); (M.A.); (J.T.)
| | - Sarah Williams-Blangero
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.P.); (A.C.L.); (S.W.-B.); (J.E.C.); (J.B.)
| | - Joanne E. Curran
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.P.); (A.C.L.); (S.W.-B.); (J.E.C.); (J.B.)
| | - John Blangero
- Division of Human Genetics and South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA; (J.P.); (A.C.L.); (S.W.-B.); (J.E.C.); (J.B.)
| |
Collapse
|
5
|
Yang Y, Ma B, Chen J, Liu D, Ma J, Li B, Hao J, Zhou X. Epigenetic regulation and factors that influence the effect of iPSCs-derived neural stem/progenitor cells (NS/PCs) in the treatment of spinal cord injury. Clin Epigenetics 2024; 16:30. [PMID: 38383473 PMCID: PMC10880347 DOI: 10.1186/s13148-024-01639-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
Spinal cord injury (SCI) is a severe neurological disorder that causes neurological impairment and disability. Neural stem/progenitor cells (NS/PCs) derived from induced pluripotent stem cells (iPSCs) represent a promising cell therapy strategy for spinal cord regeneration and repair. However, iPSC-derived NS/PCs face many challenges and issues in SCI therapy; one of the most significant challenges is epigenetic regulation and that factors that influence this mechanism. Epigenetics refers to the regulation of gene expression and function by DNA methylation, histone modification, and chromatin structure without changing the DNA sequence. Previous research has shown that epigenetics plays a crucial role in the generation, differentiation, and transplantation of iPSCs, and can influence the quality, safety, and outcome of transplanted cells. In this study, we review the effects of epigenetic regulation and various influencing factors on the role of iPSC-derived NS/PCs in SCI therapy at multiple levels, including epigenetic reprogramming, regulation, and the adaptation of iPSCs during generation, differentiation, and transplantation, as well as the impact of other therapeutic tools (e.g., drugs, electrical stimulation, and scaffolds) on the epigenetic status of transplanted cells. We summarize our main findings and insights in this field and identify future challenges and directions that need to be addressed and explored.
Collapse
Affiliation(s)
- Yubiao Yang
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Boyuan Ma
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, People's Republic of China
| | - Jinyu Chen
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, People's Republic of China
| | - Derong Liu
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Jun Ma
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Bo Li
- Department of Orthopedics, Beijing Luhe Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Jian Hao
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, People's Republic of China.
| | - Xianhu Zhou
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, People's Republic of China.
| |
Collapse
|
6
|
Edwards MM, Wang N, Massey DJ, Bhatele S, Egli D, Koren A. Incomplete reprogramming of DNA replication timing in induced pluripotent stem cells. Cell Rep 2024; 43:113664. [PMID: 38194345 PMCID: PMC11231959 DOI: 10.1016/j.celrep.2023.113664] [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: 06/22/2023] [Revised: 10/27/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024] Open
Abstract
Induced pluripotent stem cells (iPSCs) are the foundation of cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which could affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing, a process linked to both genome regulation and genome stability, is efficiently reprogrammed to the embryonic state. To answer this, we compare genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicate their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibits delayed replication at heterochromatic regions containing genes downregulated in iPSCs with incompletely reprogrammed DNA methylation. DNA replication delays are not the result of gene expression or DNA methylation aberrations and persist after cells differentiate to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and influence the quality of iPSCs.
Collapse
Affiliation(s)
- Matthew M Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Sakshi Bhatele
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA.
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
| |
Collapse
|
7
|
Chen J, Horiuchi S, Kuramochi S, Kawasaki T, Kawasumi H, Akiyama S, Arai T, Morinaga K, Kimura T, Kiyono T, Akutsu H, Ishida S, Umezawa A. Human intestinal organoid-derived PDGFRα + mesenchymal stroma enables proliferation and maintenance of LGR4 + epithelial stem cells. Stem Cell Res Ther 2024; 15:16. [PMID: 38229108 PMCID: PMC10792855 DOI: 10.1186/s13287-023-03629-5] [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: 09/03/2023] [Accepted: 12/27/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Intestinal epithelial cells derived from human pluripotent stem cells (hPSCs) are generally maintained and cultured as organoids in vitro because they do not exhibit adhesion when cultured. However, the three-dimensional structure of organoids makes their use in regenerative medicine and drug discovery difficult. Mesenchymal stromal cells are found near intestinal stem cells in vivo and provide trophic factors to regulate stem cell maintenance and proliferation, such as BMP inhibitors, WNT, and R-spondin. In this study, we aimed to use mesenchymal stromal cells isolated from hPSC-derived intestinal organoids to establish an in vitro culture system that enables stable proliferation and maintenance of hPSC-derived intestinal epithelial cells in adhesion culture. METHODS We established an isolation protocol for intestinal epithelial cells and mesenchymal stromal cells from hPSCs-derived intestinal organoids and a co-culture system for these cells. We then evaluated the intestinal epithelial cells and mesenchymal stromal cells' morphology, proliferative capacity, chromosomal stability, tumorigenicity, and gene expression profiles. We also evaluated the usefulness of the cells for pharmacokinetic and toxicity studies. RESULTS The proliferating intestinal epithelial cells exhibited a columnar form, microvilli and glycocalyx formation, cell polarity, and expression of drug-metabolizing enzymes and transporters. The intestinal epithelial cells also showed barrier function, transporter activity, and drug-metabolizing capacity. Notably, small intestinal epithelial stem cells cannot be cultured in adherent culture without mesenchymal stromal cells and cannot replaced by other feeder cells. Organoid-derived mesenchymal stromal cells resemble the trophocytes essential for maintaining small intestinal epithelial stem cells and play a crucial role in adherent culture. CONCLUSIONS The high proliferative expansion, productivity, and functionality of hPSC-derived intestinal epithelial cells may have potential applications in pharmacokinetic and toxicity studies and regenerative medicine.
Collapse
Affiliation(s)
- JunLong Chen
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
- Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Sendai, Japan
| | - Shinichiro Horiuchi
- Division of Pharmacology, National Institute of Health Sciences, Kawasaki, Japan
| | - So Kuramochi
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Tomoyuki Kawasaki
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Hayato Kawasumi
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Saeko Akiyama
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
- Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Sendai, Japan
| | - Tomoki Arai
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Kenichi Morinaga
- 1st Section, 1st Development Department, Food and Healthcare Business Development Unit, Business Development Division, Research & Business Development Center, Dai Nippon Printing Co., Ltd., Tokyo, Japan
| | - Tohru Kimura
- Laboratory of Stem Cell Biology, Department of BioSciences, Kitasato University School of Science, Kanagawa, Japan
| | - Tohru Kiyono
- Project for Prevention of HPV-Related Cancer, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Hidenori Akutsu
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Seiichi Ishida
- Division of Pharmacology, National Institute of Health Sciences, Kawasaki, Japan
- Graduate School of Engineering, Sojo University, Kumamoto, Japan
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan.
- Department of Advanced Pediatric Medicine, Tohoku University School of Medicine, Sendai, Japan.
| |
Collapse
|
8
|
Horisawa K, Miura S, Araki H, Miura F, Ito T, Suzuki A. Transcription factor-mediated direct cellular reprogramming yields cell-type specific DNA methylation signature. Sci Rep 2023; 13:22317. [PMID: 38102164 PMCID: PMC10724236 DOI: 10.1038/s41598-023-49546-8] [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: 10/27/2023] [Accepted: 12/09/2023] [Indexed: 12/17/2023] Open
Abstract
Direct reprogramming, inducing the conversion of one type of somatic cell into another by the forced expression of defined transcription factors, is a technology with anticipated medical applications. However, due to the many unresolved aspects of the induction mechanisms, it is essential to thoroughly analyze the epigenomic state of the generated cells. Here, we performed comparative genome-wide DNA methylation analyses of mouse embryonic fibroblasts (MEFs) and cells composing organoids formed by intestinal stem cells (ISCs) or induced ISCs (iISCs) that were directly induced from MEFs. We found that the CpG methylation state was similar between cells forming ISC organoids and iISC organoids, while they differed widely from those in MEFs. Moreover, genomic regions that were differentially methylated between ISC organoid- and iISC organoid-forming cells did not significantly affect gene expression. These results demonstrate the accuracy and safety of iISC induction, leading to the medical applications of this technology.
Collapse
Affiliation(s)
- Kenichi Horisawa
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Shizuka Miura
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hiromitsu Araki
- Insect Science and Creative Entomology Center, Kyushu University Graduate School of Agriculture, Fukuoka, 819-0395, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, 812-8582, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, 812-8582, Japan
| | - Atsushi Suzuki
- Division of Organogenesis and Regeneration, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
| |
Collapse
|
9
|
Verma A, Poondi Krishnan V, Cecere F, D’Angelo E, Lullo V, Strazzullo M, Selig S, Angelini C, Matarazzo MR, Riccio A. ICF1-Syndrome-Associated DNMT3B Mutations Prevent De Novo Methylation at a Subset of Imprinted Loci during iPSC Reprogramming. Biomolecules 2023; 13:1717. [PMID: 38136588 PMCID: PMC10741953 DOI: 10.3390/biom13121717] [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: 08/02/2023] [Revised: 11/19/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Parent-of-origin-dependent gene expression of a few hundred human genes is achieved by differential DNA methylation of both parental alleles. This imprinting is required for normal development, and defects in this process lead to human disease. Induced pluripotent stem cells (iPSCs) serve as a valuable tool for in vitro disease modeling. However, a wave of de novo DNA methylation during reprogramming of iPSCs affects DNA methylation, thus limiting their use. The DNA methyltransferase 3B (DNMT3B) gene is highly expressed in human iPSCs; however, whether the hypermethylation of imprinted loci depends on DNMT3B activity has been poorly investigated. To explore the role of DNMT3B in mediating de novo DNA methylation at imprinted DMRs, we utilized iPSCs generated from patients with immunodeficiency, centromeric instability, facial anomalies type I (ICF1) syndrome that harbor biallelic hypomorphic DNMT3B mutations. Using a whole-genome array-based approach, we observed a gain of methylation at several imprinted loci in control iPSCs but not in ICF1 iPSCs compared to their parental fibroblasts. Moreover, in corrected ICF1 iPSCs, which restore DNMT3B enzymatic activity, imprinted DMRs did not acquire control DNA methylation levels, in contrast to the majority of the hypomethylated CpGs in the genome that were rescued in the corrected iPSC clones. Overall, our study indicates that DNMT3B is responsible for de novo methylation of a subset of imprinted DMRs during iPSC reprogramming and suggests that imprinting is unstable during a specific time window of this process, after which the epigenetic state at these regions becomes resistant to perturbation.
Collapse
Affiliation(s)
- Ankit Verma
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Varsha Poondi Krishnan
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
| | - Emilia D’Angelo
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
| | - Vincenzo Lullo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Maria Strazzullo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Sara Selig
- Department of Genetics and Developmental Biology, Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel;
- Laboratory of Molecular Medicine, Rambam Health Care Campus, Haifa 31096, Israel
| | - Claudia Angelini
- Istituto per le Applicazioni del Calcolo “Mauro Picone”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy;
| | - Maria R. Matarazzo
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (A.V.); (F.C.); (E.D.)
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), 80131 Naples, Italy; (V.P.K.); (V.L.); (M.S.)
| |
Collapse
|
10
|
Ng XY, Peh GSL, Yam GHF, Tay HG, Mehta JS. Corneal Endothelial-like Cells Derived from Induced Pluripotent Stem Cells for Cell Therapy. Int J Mol Sci 2023; 24:12433. [PMID: 37569804 PMCID: PMC10418878 DOI: 10.3390/ijms241512433] [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: 06/30/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Corneal endothelial dysfunction is one of the leading causes of corneal blindness, and the current conventional treatment option is corneal transplantation using a cadaveric donor cornea. However, there is a global shortage of suitable donor graft material, necessitating the exploration of novel therapeutic approaches. A stem cell-based regenerative medicine approach using induced pluripotent stem cells (iPSCs) offers a promising solution, as they possess self-renewal capabilities, can be derived from adult somatic cells, and can be differentiated into all cell types including corneal endothelial cells (CECs). This review discusses the progress and challenges in developing protocols to induce iPSCs into CECs, focusing on the different media formulations used to differentiate iPSCs to neural crest cells (NCCs) and subsequently to CECs, as well as the characterization methods and markers that define iPSC-derived CECs. The hurdles and solutions for the clinical application of iPSC-derived cell therapy are also addressed, including the establishment of protocols that adhere to good manufacturing practice (GMP) guidelines. The potential risks of genetic mutations in iPSC-derived CECs associated with long-term in vitro culture and the danger of potential tumorigenicity following transplantation are evaluated. In all, this review provides insights into the advancement and obstacles of using iPSC in the treatment of corneal endothelial dysfunction.
Collapse
Affiliation(s)
- Xiao Yu Ng
- Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore 169856, Singapore; (X.Y.N.); (G.S.L.P.); (G.H.-F.Y.)
| | - Gary S. L. Peh
- Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore 169856, Singapore; (X.Y.N.); (G.S.L.P.); (G.H.-F.Y.)
- Ophthalmology and Visual Sciences Academic Clinical Program, SingHealth and Duke-NUS Medical School, Singapore 169857, Singapore;
| | - Gary Hin-Fai Yam
- Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore 169856, Singapore; (X.Y.N.); (G.S.L.P.); (G.H.-F.Y.)
- Corneal Regeneration Laboratory, Department of Ophthalmology, University of Pittsburgh, 6614, Pittsburgh, PA 15260, USA
| | - Hwee Goon Tay
- Ophthalmology and Visual Sciences Academic Clinical Program, SingHealth and Duke-NUS Medical School, Singapore 169857, Singapore;
- Centre for Vision Research, DUKE-NUS Medical School, Singapore 169857, Singapore
| | - Jodhbir S. Mehta
- Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore 169856, Singapore; (X.Y.N.); (G.S.L.P.); (G.H.-F.Y.)
- Ophthalmology and Visual Sciences Academic Clinical Program, SingHealth and Duke-NUS Medical School, Singapore 169857, Singapore;
- Centre for Vision Research, DUKE-NUS Medical School, Singapore 169857, Singapore
- Department of Cornea and External Eye Disease, Singapore National Eye Centre, Singapore 168751, Singapore
| |
Collapse
|
11
|
Ite K, Toyoda M, Akiyama S, Enosawa S, Yoshioka S, Yukitake T, Yamazaki-Inoue M, Tatsumi K, Akutsu H, Nishina H, Kimura T, Otani N, Nakazawa A, Fukuda A, Kasahara M, Umezawa A. Stem cell challenges and opportunities. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 199:379-395. [PMID: 37678981 DOI: 10.1016/bs.pmbts.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Hepatocyte-like cells (HLCs) generated from human pluripotent stem cells (PSCs) exhibit hepatocytic properties in vitro; however, their engraftment and functionality in vivo remain unsatisfactory. Despite optimization of differentiation protocols, HLCs did not engraft in a mouse model of liver injury. In contrast, organ-derived hepatocytes reproducibly formed colonies in the liver injury mouse model. As an extension of the phenomenon observed in hematopoietic stem cells giving rise to colonies within the spleen, commonly referred to as "colony-forming units in spleen (CFU-s)", we hypothesize that "colony-forming units in liver (CFU-L)" serves as a reliable indicator of stemness, engraftment, and functionality of hepatocytes. The uniform expression of the randomly inactivated gene in a single colony, as reported by Sugahara et al. 2022, suggests that the colonies generated by isolated hepatocytes likely originate from a single cell. We, therefore, propose that CFU-L can be used to quantify the number of "hepatocytes that engraft and proliferate in vivo" as a quantitative assay for stem cells that utilize colony-forming ability, similar to that observed in hematopoietic stem cells.
Collapse
Affiliation(s)
- Kenta Ite
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Tokyo, Japan; Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masashi Toyoda
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Tokyo, Japan; Research team for Aging Science (Vascular Medicine), Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | - Saeko Akiyama
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Tokyo, Japan; Department of Advanced Pediatric Medicine (National Center for Child Health and Development), Tohoku University School of Medicine, Miyagi, Japan
| | - Shin Enosawa
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Tokyo, Japan
| | - Saeko Yoshioka
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Tokyo, Japan
| | - Takaaki Yukitake
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Tokyo, Japan; Department of Applied Biological Science, Tokyo University of Science, Tokyo, Japan
| | - Mayu Yamazaki-Inoue
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Tokyo, Japan
| | - Kuniko Tatsumi
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Tokyo, Japan
| | - Hidenori Akutsu
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Tokyo, Japan
| | - Hiroshi Nishina
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Toru Kimura
- Department of BioSciences, Kitasato University School of Science, Kanagawa, Japan
| | - Naoko Otani
- Department of Applied Biological Science, Tokyo University of Science, Tokyo, Japan
| | - Atsuko Nakazawa
- Department of Pathology, National Center for Child Health and Development Hospital, Tokyo, Japan
| | - Akinari Fukuda
- Department of Pathology, National Center for Child Health and Development Hospital, Tokyo, Japan
| | - Mureo Kasahara
- Department of Pathology, National Center for Child Health and Development Hospital, Tokyo, Japan
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, Tokyo, Japan; Department of Advanced Pediatric Medicine (National Center for Child Health and Development), Tohoku University School of Medicine, Miyagi, Japan.
| |
Collapse
|
12
|
Edwards MM, Wang N, Massey DJ, Egli D, Koren A. Incomplete Reprogramming of DNA Replication Timing in Induced Pluripotent Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544654. [PMID: 37398435 PMCID: PMC10312660 DOI: 10.1101/2023.06.12.544654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Induced pluripotent stem cells (iPSC) are a widely used cell system and a foundation for cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which have the potential to affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing - a process linked to both genome regulation and genome stability - is efficiently reprogrammed to the embryonic state. To answer this, we profiled and compared genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicated their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibit delayed replication at heterochromatic regions containing genes downregulated in iPSC with incompletely reprogrammed DNA methylation. DNA replication delays were not the result of gene expression and DNA methylation aberrations and persisted after differentiating cells to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and lead to undesirable phenotypes in iPSCs, establishing it as an important genomic feature to consider when evaluating iPSC lines.
Collapse
Affiliation(s)
- Matthew M. Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Dashiell J. Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| |
Collapse
|
13
|
Xu Z, Yang J, Xin X, Liu C, Li L, Mei X, Li M. Merits and challenges of iPSC-derived organoids for clinical applications. Front Cell Dev Biol 2023; 11:1188905. [PMID: 37305682 PMCID: PMC10250752 DOI: 10.3389/fcell.2023.1188905] [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: 03/18/2023] [Accepted: 04/18/2023] [Indexed: 06/13/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) have entered an unprecedented state of development since they were first generated. They have played a critical role in disease modeling, drug discovery, and cell replacement therapy, and have contributed to the evolution of disciplines such as cell biology, pathophysiology of diseases, and regenerative medicine. Organoids, the stem cell-derived 3D culture systems that mimic the structure and function of organs in vitro, have been widely used in developmental research, disease modeling, and drug screening. Recent advances in combining iPSCs with 3D organoids are facilitating further applications of iPSCs in disease research. Organoids derived from embryonic stem cells, iPSCs, and multi-tissue stem/progenitor cells can replicate the processes of developmental differentiation, homeostatic self-renewal, and regeneration due to tissue damage, offering the potential to unravel the regulatory mechanisms of development and regeneration, and elucidate the pathophysiological processes involved in disease mechanisms. Herein, we have summarized the latest research on the production scheme of organ-specific iPSC-derived organoids, the contribution of these organoids in the treatment of various organ-related diseases, in particular their contribution to COVID-19 treatment, and have discussed the unresolved challenges and shortcomings of these models.
Collapse
Affiliation(s)
- Ziran Xu
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, Jilin, China
- Department of Clinical Laboratory, Lequn Branch, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Jiaxu Yang
- Department of Neonatology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Xianyi Xin
- Department of Pediatric Cardiovascular Medicine, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Chengrun Liu
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, Jilin, China
| | - Lisha Li
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, Jilin, China
| | - Xianglin Mei
- Department of pathology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Meiying Li
- The Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, Jilin, China
| |
Collapse
|
14
|
Bhatti JS, Khullar N, Mishra J, Kaur S, Sehrawat A, Sharma E, Bhatti GK, Selman A, Reddy PH. Stem cells in the treatment of Alzheimer's disease - Promises and pitfalls. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166712. [PMID: 37030521 DOI: 10.1016/j.bbadis.2023.166712] [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: 02/25/2023] [Accepted: 03/31/2023] [Indexed: 04/10/2023]
Abstract
Alzheimer's disease (AD) is the most widespread form of neurodegenerative disorder that causes memory loss and multiple cognitive issues. The underlying mechanisms of AD include the build-up of amyloid-β and phosphorylated tau, synaptic damage, elevated levels of microglia and astrocytes, abnormal microRNAs, mitochondrial dysfunction, hormonal imbalance, and age-related neuronal loss. However, the etiology of AD is complex and involves a multitude of environmental and genetic factors. Currently, available AD medications only alleviate symptoms and do not provide a permanent cure. Therefore, there is a need for therapies that can prevent or reverse cognitive decline, brain tissue loss, and neural instability. Stem cell therapy is a promising treatment for AD because stem cells possess the unique ability to differentiate into any type of cell and maintain their self-renewal. This article provides an overview of the pathophysiology of AD and existing pharmacological treatments. This review article focuses on the role of various types of stem cells in neuroregeneration, the potential challenges, and the future of stem cell-based therapies for AD, including nano delivery and gaps in stem cell technology.
Collapse
Affiliation(s)
- Jasvinder Singh Bhatti
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India.
| | - Naina Khullar
- Department of Zoology, Mata Gujri College, Fatehgarh Sahib, Punjab, India
| | - Jayapriya Mishra
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Satinder Kaur
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Abhishek Sehrawat
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Eva Sharma
- Laboratory of Translational Medicine and Nanotherapeutics, Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, India
| | - Gurjit Kaur Bhatti
- Department of Medical Lab Technology, University Institute of Applied Health Sciences, Chandigarh University, Mohali, India
| | - Ashley Selman
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Public Health, Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Neurology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Speech, Language, and Hearing Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Nutritional Sciences Department, College of Human Sciences, Texas Tech University, 1301 Akron Ave, Lubbock, TX 79409, USA.
| |
Collapse
|
15
|
Lee H, Price J, Srivastava DP, Thuret S. In vitro characterization on the role of APOE polymorphism in human hippocampal neurogenesis. Hippocampus 2023; 33:322-346. [PMID: 36709412 PMCID: PMC10947111 DOI: 10.1002/hipo.23502] [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: 08/01/2022] [Revised: 12/14/2022] [Accepted: 01/11/2023] [Indexed: 01/30/2023]
Abstract
Hippocampal neurogenesis (HN) is considered an important mechanism underlying lifelong brain plasticity, and alterations in this process have been implicated in early Alzheimer's disease progression. APOE polymorphism is the most common genetic risk factor for late-onset Alzheimer's disease where the ε4 genotype is associated with a significantly earlier disease onset compared to the neutral ε3 allele. Recently, APOE has been shown to play an important role in the regulation of HN. However, the time-dependent impact of its polymorphism in humans remains elusive, partially due to the difficulties of studying human HN in vivo. To bridge this gap of knowledge, we used an in vitro cellular model of human HN and performed a time course characterization on isogenic induced pluripotent stem cells with different genotypes of APOE. We found that APOE itself was more highly expressed in ε4 at the stem cell stage, while the divergence of differential gene expression phenotype between ε4 and ε3 became prominent at the neuronal stage of differentiation. This divergence was not associated with the differential capacity to generate dentate gyrus granule cell-like neurons, as its level was comparable between ε4 and ε3. Transcriptomic profiling across different stages of neurogenesis indicated a clear "maturation of functional neurons" phenotype in ε3 neural progenitors and neurons, while genes differentially expressed only in ε4 neurons suggested potential alterations in "metabolism and mitochondrial function." Taken together, our in vitro investigation suggests that APOE ε4 allele can exert a transcriptome-wide effect at the later stages of HN, without altering the overall level of neurogenesis per se.
Collapse
Affiliation(s)
- Hyunah Lee
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and NeuroscienceKing's College LondonLondonUK
| | - Jack Price
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and NeuroscienceKing's College LondonLondonUK
| | - Deepak P. Srivastava
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and NeuroscienceKing's College LondonLondonUK
- MRC Centre for Neurodevelopmental DisordersKing's College LondonLondonUK
| | - Sandrine Thuret
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and NeuroscienceKing's College LondonLondonUK
| |
Collapse
|
16
|
Al Sammarraie SHA, Aprile D, Meloni I, Alessio N, Mari F, Manata M, Lo Rizzo C, Di Bernardo G, Peluso G, Renieri A, Galderisi U. An Example of Neuro-Glial Commitment and Differentiation of Muse Stem Cells Obtained from Patients with IQSEC2-Related Neural Disorder: A Possible New Cell-Based Disease Model. Cells 2023; 12:cells12070977. [PMID: 37048050 PMCID: PMC10093355 DOI: 10.3390/cells12070977] [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: 03/03/2023] [Revised: 03/13/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Although adult stem cells may be useful for studying tissue-specific diseases, they cannot be used as a general model for investigating human illnesses given their limited differentiation potential. Multilineage-differentiating stress-enduring (Muse) stem cells, a SSEA3(+) cell population isolated from mesenchymal stromal cells, fat, and skin fibroblasts, may be able to overcome that restriction. The Muse cells present in fibroblast cultures obtained from biopsies of patients' skin may be differentiated into cells of interest for analyzing diseases. We isolated Muse stem cells from patients with an intellectual disability (ID) and mutations in the IQSEC2 gene (i.e., BRAG1 gene) and induced in vitro neuroglial differentiation to study cell commitment and the differentiation of neural lineages. The neuroglial differentiation of Muse cells revealed that IQSEC2 mutations may alter the self-renewal and lineage specification of stem cells. We observed a decrease in the percentage of SOX2 (+) neural stem cells and neural progenitors (i.e., SOX2+ and NESTIN+) in cultures obtained from Muse cells with the mutated IQSEC2 gene. The alteration in the number of stem cells and progenitors produced a bias toward the astrocytes' differentiation. Our research demonstrates that Muse stem cells may represent a new cell-based disease model.
Collapse
Affiliation(s)
| | - Domenico Aprile
- Department of Experimental Medicine, Luigi Vanvitelli Campania University, 80138 Naples, Italy
| | - Ilaria Meloni
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | - Nicola Alessio
- Department of Experimental Medicine, Luigi Vanvitelli Campania University, 80138 Naples, Italy
| | - Francesca Mari
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | - Marianna Manata
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | - Caterina Lo Rizzo
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | - Giovanni Di Bernardo
- Department of Experimental Medicine, Luigi Vanvitelli Campania University, 80138 Naples, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Temple University, Philadelphia, PA 19122, USA
| | | | - Alessandra Renieri
- Department of Medical Biotechnology, University of Siena, 53100 Siena, Italy
| | - Umberto Galderisi
- Department of Experimental Medicine, Luigi Vanvitelli Campania University, 80138 Naples, Italy
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, Temple University, Philadelphia, PA 19122, USA
- Genome and Stem Cell Center (GENKÖK), Erciyes University, 38280 Kayseri, Turkey
| |
Collapse
|
17
|
Ji S, Xiong M, Chen H, Liu Y, Zhou L, Hong Y, Wang M, Wang C, Fu X, Sun X. Cellular rejuvenation: molecular mechanisms and potential therapeutic interventions for diseases. Signal Transduct Target Ther 2023; 8:116. [PMID: 36918530 PMCID: PMC10015098 DOI: 10.1038/s41392-023-01343-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/16/2022] [Accepted: 01/19/2023] [Indexed: 03/16/2023] Open
Abstract
The ageing process is a systemic decline from cellular dysfunction to organ degeneration, with more predisposition to deteriorated disorders. Rejuvenation refers to giving aged cells or organisms more youthful characteristics through various techniques, such as cellular reprogramming and epigenetic regulation. The great leaps in cellular rejuvenation prove that ageing is not a one-way street, and many rejuvenative interventions have emerged to delay and even reverse the ageing process. Defining the mechanism by which roadblocks and signaling inputs influence complex ageing programs is essential for understanding and developing rejuvenative strategies. Here, we discuss the intrinsic and extrinsic factors that counteract cell rejuvenation, and the targeted cells and core mechanisms involved in this process. Then, we critically summarize the latest advances in state-of-art strategies of cellular rejuvenation. Various rejuvenation methods also provide insights for treating specific ageing-related diseases, including cellular reprogramming, the removal of senescence cells (SCs) and suppression of senescence-associated secretory phenotype (SASP), metabolic manipulation, stem cells-associated therapy, dietary restriction, immune rejuvenation and heterochronic transplantation, etc. The potential applications of rejuvenation therapy also extend to cancer treatment. Finally, we analyze in detail the therapeutic opportunities and challenges of rejuvenation technology. Deciphering rejuvenation interventions will provide further insights into anti-ageing and ageing-related disease treatment in clinical settings.
Collapse
Affiliation(s)
- Shuaifei Ji
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Mingchen Xiong
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Huating Chen
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Yiqiong Liu
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Laixian Zhou
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Yiyue Hong
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Mengyang Wang
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Chunming Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, 999078, Macau SAR, China.
| | - Xiaobing Fu
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China.
| | - Xiaoyan Sun
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China.
| |
Collapse
|
18
|
Jones RG, Dimet-Wiley A, Haghani A, da Silva FM, Brightwell CR, Lim S, Khadgi S, Wen Y, Dungan CM, Brooke RT, Greene NP, Peterson CA, McCarthy JJ, Horvath S, Watowich SJ, Fry CS, Murach KA. A molecular signature defining exercise adaptation with ageing and in vivo partial reprogramming in skeletal muscle. J Physiol 2023; 601:763-782. [PMID: 36533424 PMCID: PMC9987218 DOI: 10.1113/jp283836] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Exercise promotes functional improvements in aged tissues, but the extent to which it simulates partial molecular reprogramming is unknown. Using transcriptome profiling from (1) a skeletal muscle-specific in vivo Oct3/4, Klf4, Sox2 and Myc (OKSM) reprogramming-factor expression murine model; (2) an in vivo inducible muscle-specific Myc induction murine model; (3) a translatable high-volume hypertrophic exercise training approach in aged mice; and (4) human exercise muscle biopsies, we collectively defined exercise-induced genes that are common to partial reprogramming. Late-life exercise training lowered murine DNA methylation age according to several contemporary muscle-specific clocks. A comparison of the murine soleus transcriptome after late-life exercise training to the soleus transcriptome after OKSM induction revealed an overlapping signature that included higher JunB and Sun1. Also, within this signature, downregulation of specific mitochondrial and muscle-enriched genes was conserved in skeletal muscle of long-term exercise-trained humans; among these was muscle-specific Abra/Stars. Myc is the OKSM factor most induced by exercise in muscle and was elevated following exercise training in aged mice. A pulse of MYC rewired the global soleus muscle methylome, and the transcriptome after a MYC pulse partially recapitulated OKSM induction. A common signature also emerged in the murine MYC-controlled and exercise adaptation transcriptomes, including lower muscle-specific Melusin and reactive oxygen species-associated Romo1. With Myc, OKSM and exercise training in mice, as well habitual exercise in humans, the complex I accessory subunit Ndufb11 was lower; low Ndufb11 is linked to longevity in rodents. Collectively, exercise shares similarities with genetic in vivo partial reprogramming. KEY POINTS: Advances in the last decade related to cellular epigenetic reprogramming (e.g. DNA methylome remodelling) toward a pluripotent state via the Yamanaka transcription factors Oct3/4, Klf4, Sox2 and Myc (OKSM) provide a window into potential mechanisms for combatting the deleterious effects of cellular ageing. Using global gene expression analysis, we compared the effects of in vivo OKSM-mediated partial reprogramming in skeletal muscle fibres of mice to the effects of late-life murine exercise training in muscle. Myc is the Yamanaka factor most induced by exercise in skeletal muscle, and so we compared the MYC-controlled transcriptome in muscle to Yamanaka factor-mediated and exercise adaptation mRNA landscapes in mice and humans. A single pulse of MYC is sufficient to remodel the muscle methylome. We identify partial reprogramming-associated genes that are innately altered by exercise training and conserved in humans, and propose that MYC contributes to some of these responses.
Collapse
Affiliation(s)
- Ronald G. Jones
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | | | - Amin Haghani
- University of California Los Angeles, Department of Human Genetics, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Francielly Morena da Silva
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cachexia Research Laboratory, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | - Camille R. Brightwell
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Athletic Training and Clinical Nutrition, Lexington, KY, USA
| | - Seongkyun Lim
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cachexia Research Laboratory, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | - Sabin Khadgi
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
| | - Yuan Wen
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Physical Therapy, Lexington, KY, USA
| | - Cory M. Dungan
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Physical Therapy, Lexington, KY, USA
| | | | - Nicholas P. Greene
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cachexia Research Laboratory, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cell and Molecular Biology Graduate Program, Fayetteville, AR, USA
| | - Charlotte A. Peterson
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Physical Therapy, Lexington, KY, USA
- University of Kentucky, Department of Physiology, Lexington, KY, USA
| | - John J. McCarthy
- Altos Labs, San Diego, CA, USA
- University of Kentucky, Department of Physiology, Lexington, KY, USA
| | - Steve Horvath
- University of California Los Angeles, Department of Human Genetics, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Stanley J. Watowich
- Ridgeline Therapeutics, Houston, TX, USA
- University of Texas Medical Branch, Department of Biochemistry and Molecular Biology, Galveston, TX, USA
| | - Christopher S. Fry
- University of Kentucky Center for Muscle Biology, Lexington, KY, USA
- University of Kentucky, Department of Athletic Training and Clinical Nutrition, Lexington, KY, USA
| | - Kevin A. Murach
- University of Arkansas, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, Fayetteville, AR, USA
- University of Arkansas, Cell and Molecular Biology Graduate Program, Fayetteville, AR, USA
| |
Collapse
|
19
|
Peng J, Zhang WJ, Zhang Q, Su YH, Tang LP. The dynamics of chromatin states mediated by epigenetic modifications during somatic cell reprogramming. Front Cell Dev Biol 2023; 11:1097780. [PMID: 36727112 PMCID: PMC9884706 DOI: 10.3389/fcell.2023.1097780] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/05/2023] [Indexed: 01/17/2023] Open
Abstract
Somatic cell reprogramming (SCR) is the conversion of differentiated somatic cells into totipotent or pluripotent cells through a variety of methods. Somatic cell reprogramming also provides a platform to investigate the role of chromatin-based factors in establishing and maintaining totipotency or pluripotency, since high expression of totipotency- or pluripotency-related genes usually require an active chromatin state. Several studies in plants or mammals have recently shed light on the molecular mechanisms by which epigenetic modifications regulate the expression of totipotency or pluripotency genes by altering their chromatin states. In this review, we present a comprehensive overview of the dynamic changes in epigenetic modifications and chromatin states during reprogramming from somatic cells to totipotent or pluripotent cells. In addition, we illustrate the potential role of DNA methylation, histone modifications, histone variants, and chromatin remodeling during somatic cell reprogramming, which will pave the way to developing reliable strategies for efficient cellular reprogramming.
Collapse
Affiliation(s)
| | | | | | - Ying Hua Su
- *Correspondence: Ying Hua Su, ; Li Ping Tang,
| | | |
Collapse
|
20
|
Maintenance of methylation profile in imprinting control regions in human induced pluripotent stem cells. Clin Epigenetics 2022; 14:190. [PMID: 36578048 PMCID: PMC9798676 DOI: 10.1186/s13148-022-01410-8] [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: 10/21/2022] [Accepted: 12/14/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Parental imprinting is an epigenetic mechanism that leads to monoallelic expression of a subset of genes depending on their parental origin. Imprinting disorders (IDs), caused by disturbances of imprinted genes, are a set of rare congenital diseases that mainly affect growth, metabolism and development. To date, there is no accurate model to study the physiopathology of IDs or test therapeutic strategies. Human induced pluripotent stem cells (iPSCs) are a promising cellular approach to model human diseases and complex genetic disorders. However, aberrant hypermethylation of imprinting control regions (ICRs) may appear during the reprogramming process and subsequent culture of iPSCs. Therefore, we tested various conditions of reprogramming and culture of iPSCs and performed an extensive analysis of methylation marks at the ICRs to develop a cellular model that can be used to study IDs. RESULTS We assessed the methylation levels at seven imprinted loci in iPSCs before differentiation, at various passages of cell culture, and during chondrogenic differentiation. Abnormal methylation levels were found, with hypermethylation at 11p15 H19/IGF2:IG-DMR and 14q32 MEG3/DLK1:IG-DMR, independently of the reprogramming method and cells of origin. Hypermethylation at these two loci led to the loss of parental imprinting (LOI), with biallelic expression of the imprinted genes IGF2 and DLK1, respectively. The epiPS™ culture medium combined with culturing of the cells under hypoxic conditions prevented hypermethylation at H19/IGF2:IG-DMR (ICR1) and MEG3/DLK1:IG-DMR, as well as at other imprinted loci, while preserving the proliferation and pluripotency qualities of these iPSCs. CONCLUSIONS An extensive and quantitative analysis of methylation levels of ICRs in iPSCs showed hypermethylation of certain ICRs in human iPSCs, especially paternally methylated ICRs, and subsequent LOI of certain imprinted genes. The epiPS™ culture medium and culturing of the cells under hypoxic conditions prevented hypermethylation of ICRs in iPSCs. We demonstrated that the reprogramming and culture in epiPS™ medium allow the generation of control iPSCs lines with a balanced methylation and ID patient iPSCs lines with unbalanced methylation. Human iPSCs are therefore a promising cellular model to study the physiopathology of IDs and test therapies in tissues of interest.
Collapse
|
21
|
Adami R, Bottai D. NSC Physiological Features in Spinal Muscular Atrophy: SMN Deficiency Effects on Neurogenesis. Int J Mol Sci 2022; 23:ijms232315209. [PMID: 36499528 PMCID: PMC9736802 DOI: 10.3390/ijms232315209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/20/2022] [Accepted: 11/30/2022] [Indexed: 12/08/2022] Open
Abstract
While the U.S. Food and Drug Administration and the European Medicines Evaluation Agency have recently approved new drugs to treat spinal muscular atrophy 1 (SMA1) in young patients, they are mostly ineffective in older patients since many motor neurons have already been lost. Therefore, understanding nervous system (NS) physiology in SMA patients is essential. Consequently, studying neural stem cells (NSCs) from SMA patients is of significant interest in searching for new treatment targets that will enable researchers to identify new pharmacological approaches. However, studying NSCs in these patients is challenging since their isolation damages the NS, making it impossible with living patients. Nevertheless, it is possible to study NSCs from animal models or create them by differentiating induced pluripotent stem cells obtained from SMA patient peripheral tissues. On the other hand, therapeutic interventions such as NSCs transplantation could ameliorate SMA condition. This review summarizes current knowledge on the physiological properties of NSCs from animals and human cellular models with an SMA background converging on the molecular and neuronal circuit formation alterations of SMA fetuses and is not focused on the treatment of SMA. By understanding how SMA alters NSC physiology, we can identify new and promising interventions that could help support affected patients.
Collapse
|
22
|
Variation of DNA methylation on the IRX1/2 genes is responsible for the neural differentiation propensity in human induced pluripotent stem cells. Regen Ther 2022; 21:620-630. [PMID: 36514370 PMCID: PMC9719094 DOI: 10.1016/j.reth.2022.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/05/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Introduction Human induced pluripotent stem cells (hiPSCs) are useful tools for reproducing neural development in vitro. However, each hiPSC line has a different ability to differentiate into specific lineages, known as differentiation propensity, resulting in reduced reproducibility and increased time and funding requirements for research. To overcome this issue, we searched for predictive signatures of neural differentiation propensity of hiPSCs focusing on DNA methylation, which is the main modulator of cellular properties. Methods We obtained 32 hiPSC lines and their comprehensive DNA methylation data using the Infinium MethylationEPIC BeadChip. To assess the neural differentiation efficiency of these hiPSCs, we measured the percentage of neural stem cells on day 7 of induction. Using the DNA methylation data of undifferentiated hiPSCs and their measured differentiation efficiency into neural stem cells as the set of data, and HSIC Lasso, a machine learning-based nonlinear feature selection method, we attempted to identify neural differentiation-associated differentially methylated sites. Results Epigenome-wide unsupervised clustering cannot distinguish hiPSCs with varying differentiation efficiencies. In contrast, HSIC Lasso identified 62 CpG sites that could explain the neural differentiation efficiency of hiPSCs. Features selected by HSIC Lasso were particularly enriched within 3 Mbp of chromosome 5, harboring IRX1, IRX2, and C5orf38 genes. Within this region, DNA methylation rates were correlated with neural differentiation efficiency and were negatively correlated with gene expression of the IRX1/2 genes, particularly in female hiPSCs. In addition, forced expression of the IRX1/2 impaired the neural differentiation ability of hiPSCs in both sexes. Conclusion We for the first time showed that the DNA methylation state of the IRX1/2 genes of hiPSCs is a predictive biomarker of their potential for neural differentiation. The predictive markers for neural differentiation efficiency identified in this study may be useful for the selection of suitable undifferentiated hiPSCs prior to differentiation induction.
Collapse
|
23
|
Oun A, Sabogal-Guaqueta AM, Galuh S, Alexander A, Kortholt A, Dolga AM. The multifaceted role of LRRK2 in Parkinson's disease: From human iPSC to organoids. Neurobiol Dis 2022; 173:105837. [PMID: 35963526 DOI: 10.1016/j.nbd.2022.105837] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/21/2022] [Accepted: 08/06/2022] [Indexed: 11/28/2022] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease affecting elderly people. Pathogenic mutations in Leucine-Rich Repeat Kinase 2 (LRRK2) are the most common cause of autosomal dominant PD. LRRK2 activity is enhanced in both familial and idiopathic PD, thereby studies on LRRK2-related PD research are essential for understanding PD pathology. Finding an appropriate model to mimic PD pathology is crucial for revealing the molecular mechanisms underlying disease progression, and aiding drug discovery. In the last few years, the use of human-induced pluripotent stem cells (hiPSCs) grew exponentially, especially in studying neurodegenerative diseases like PD, where working with brain neurons and glial cells was mainly possible using postmortem samples. In this review, we will discuss the use of hiPSCs as a model for PD pathology and research on the LRRK2 function in both neuronal and immune cells, together with reviewing the recent advances in 3D organoid models and microfluidics.
Collapse
Affiliation(s)
- Asmaa Oun
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen, the Netherlands; Department of Cell Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology (GBB), University of Groningen, Groningen, the Netherlands; Department of Biotechnology, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Angelica Maria Sabogal-Guaqueta
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen, the Netherlands
| | - Sekar Galuh
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen, the Netherlands
| | - Anastasia Alexander
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen, the Netherlands
| | - Arjan Kortholt
- Department of Cell Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology (GBB), University of Groningen, Groningen, the Netherlands; YETEM-Innovative Technologies Application and Research Centre Suleyman Demirel University, Isparta, Turkey.
| | - Amalia M Dolga
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, Groningen, the Netherlands.
| |
Collapse
|
24
|
Establishment and characterization of IPS-OGC-C1: a novel induced pluripotent stem cell line from healthy human ovarian granulosa cells. Hum Cell 2022; 35:1612-1620. [PMID: 35876985 DOI: 10.1007/s13577-022-00757-7] [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: 04/08/2022] [Accepted: 07/18/2022] [Indexed: 11/27/2022]
Abstract
Ovarian granulosa cell (OGC) is a critical somatic component of the ovary, which provides physical support and the microenvironment required for the developing oocyte. Human OGCs are easy to obtain and culture as a by-product of follicular aspiration performed during in vitro fertilization (IVF) procedures. Therefore, OGCs offer a potent cell source to generate induced pluripotent stem cells (iPSCs). This study established a novel OGCs-derived iPSC cell line from the follicular fluid of a healthy female donor with a Chinese Han genetic background and named it IPS-OGC-C1. IPS-OGC-C1 was verified for embryonic stem cell morphology, cell marker expression, alkaline phosphatase (AP) activity, transcriptomic profile, and pluripotency capability in developing all three embryonic germ layers in vivo and in vitro.
Collapse
|
25
|
Jiao H, Lee MS, Sivapatham A, Leiferman EM, Li WJ. Epigenetic regulation of BAF60A determines efficiency of miniature swine iPSC generation. Sci Rep 2022; 12:9039. [PMID: 35641537 PMCID: PMC9156668 DOI: 10.1038/s41598-022-12919-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/18/2022] [Indexed: 02/08/2023] Open
Abstract
Miniature pigs are an ideal animal model for translational research to evaluate stem cell therapies and regenerative applications. While the derivation of induced pluripotent stem cells (iPSCs) from miniature pigs has been demonstrated, there is still a lack of a reliable method to generate and maintain miniature pig iPSCs. In this study, we derived iPSCs from fibroblasts of Wisconsin miniature swine (WMS), Yucatan miniature swine (YMS), and Göttingen minipigs (GM) using our culture medium. By comparing cells of the different pig breeds, we found that YMS fibroblasts were more efficiently reprogrammed into iPSCs, forming colonies with well-defined borders, than WMS and GM fibroblasts. We also demonstrated that YMS iPSC lines with a normal pig karyotype gave rise to cells of the three germ layers in vitro and in vivo. Mesenchymal stromal cells expressing phenotypic characteristics were derived from established iPSC lines as an example of potential applications. In addition, we found that the expression level of the switch/sucrose nonfermentable component BAF60A regulated by STAT3 signaling determined the efficiency of pig iPSC generation. The findings of this study provide insight into the underlying mechanism controlling the reprogramming efficiency of miniature pig cells to develop a viable strategy to enhance the generation of iPSCs for biomedical research.
Collapse
Affiliation(s)
- Hongli Jiao
- Laboratory of Musculoskeletal Biology and Regenerative Medicine, Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, 1111 Highland Ave, WIMR 5051, Madison, WI, 53705, USA
| | - Ming-Song Lee
- Laboratory of Musculoskeletal Biology and Regenerative Medicine, Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, 1111 Highland Ave, WIMR 5051, Madison, WI, 53705, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | - Athillesh Sivapatham
- Laboratory of Musculoskeletal Biology and Regenerative Medicine, Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, 1111 Highland Ave, WIMR 5051, Madison, WI, 53705, USA
| | - Ellen M Leiferman
- Laboratory of Musculoskeletal Biology and Regenerative Medicine, Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, 1111 Highland Ave, WIMR 5051, Madison, WI, 53705, USA
| | - Wan-Ju Li
- Laboratory of Musculoskeletal Biology and Regenerative Medicine, Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, 1111 Highland Ave, WIMR 5051, Madison, WI, 53705, USA.
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
26
|
Du S, Li Y, Geng Z, Zhang Q, Buhler LH, Gonelle-Gispert C, Wang Y. Engineering Islets From Stem Cells: The Optimal Solution for the Treatment of Diabetes? Front Immunol 2022; 13:869514. [PMID: 35572568 PMCID: PMC9092457 DOI: 10.3389/fimmu.2022.869514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Diabetes is a metabolic disease characterized by insulin deficiency. Bioengineering of stem cells with the aim to restore insulin production and glucose regulation has the potential to cure diabetic patients. In this review, we focus on the recent developments for bioengineering of induced pluripotent stem cells (iPSCs), mesenchymal stem cells (MSCs), embryonic stem cells (ESCs), and pancreatic progenitor cells in view of generating insulin producing and glucose regulating cells for β-cell replacement therapies. Recent clinical trials using islet cells derived from stem cells have been initiated for the transplantation into diabetic patients, with crucial bottlenecks of tumorigenesis, post-transplant survival, genetic instability, and immunogenicity that should be further optimized. As a new approach given high expectations, bioengineered islets from stem cells occupies considerable potential for the future clinical application and addressing the treatment dilemma of diabetes.
Collapse
Affiliation(s)
- Suya Du
- Department of Clinical Pharmacy, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yanjiao Li
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhen Geng
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Center of Organ Transplantation, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, Chengdu, China.,Institute of Organ Transplantation, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.,Chinese Academy of Sciences, Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Qi Zhang
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Leo H Buhler
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Center of Organ Transplantation, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, Chengdu, China.,Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | | | - Yi Wang
- Clinical Immunology Translational Medicine Key Laboratory of Sichuan Province, Center of Organ Transplantation, Sichuan Academy of Medical Science and Sichuan Provincial People's Hospital, Chengdu, China.,Institute of Organ Transplantation, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.,Chinese Academy of Sciences, Sichuan Translational Medicine Research Hospital, Chengdu, China
| |
Collapse
|
27
|
Miura K, Matsuura K, Yamasaki Itoyama Y, Sasaki D, Takada T, Furutani Y, Hayama E, Ito M, Nomura S, Morita H, Toyoda M, Umezawa A, Onoue K, Saito Y, Aburatani H, Nakanishi T, Hagiwara N, Komuro I, Shimizu T. Functional Evaluation of Human Bioengineered Cardiac Tissue Using iPS Cells Derived from a Patient with Lamin Variant Dilated Cardiomyopathy. Int Heart J 2022; 63:338-346. [PMID: 35354754 DOI: 10.1536/ihj.21-790] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Dilated cardiomyopathy (DCM) is caused by various gene variants and characterized by systolic dysfunction. Lamin variants have been reported to have a poor prognosis. Medical and device therapies are not sufficient to improve the prognosis of DCM with the lamin variants. Recently, induced pluripotent stem (iPS) cells have been used for research on genetic disorders. However, few studies have evaluated the contractile function of cardiac tissue with lamin variants. The aim of this study was to elucidate the function of cardiac cell sheet tissue derived from patients with lamin variant DCM. iPS cells were generated from a patient with lamin A/C (LMNA) -mutant DCM (LMNA p.R225X mutation). After cardiac differentiation and purification, cardiac cell sheets that were fabricated through cultivation on a temperature-responsive culture dish were transferred to the surface of the fibrin gel, and the contractile force was measured. The contractile force and maximum contraction velocity, but not the maximum relaxation velocity, were significantly decreased in cardiac cell sheet tissue with the lamin variant. A qRT-PCR analysis revealed that mRNA expression of some contractile proteins, cardiac transcription factors, Ca2+-handling genes, and ion channels were downregulated in cardiac tissue with the lamin variant.Human iPS-derived bioengineered cardiac tissue with the LMNA p.R225X mutation has the functional properties of systolic dysfunction and may be a promising tissue model for understanding the underlying mechanisms of DCM.
Collapse
Affiliation(s)
- Koichiro Miura
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University.,Department of Cardiology, Tokyo Women's Medical University
| | - Katsuhisa Matsuura
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University.,Department of Cardiology, Tokyo Women's Medical University
| | - Yu Yamasaki Itoyama
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University
| | - Daisuke Sasaki
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University
| | - Takuma Takada
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University.,Department of Cardiology, Tokyo Women's Medical University
| | - Yoshiyuki Furutani
- Department of Pediatric Cardiology and Adult Congenital Cardiology, Tokyo Women's Medical University
| | - Emiko Hayama
- Department of Pediatric Cardiology and Adult Congenital Cardiology, Tokyo Women's Medical University
| | - Masamichi Ito
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo
| | - Seitaro Nomura
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo
| | - Hiroyuki Morita
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo
| | - Masashi Toyoda
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute.,Tokyo Metropolitan Institute of Gerontology
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute
| | - Kenji Onoue
- Department of Cardiovascular Medicine, Nara Medical University
| | - Yoshihiko Saito
- Department of Cardiovascular Medicine, Nara Medical University
| | - Hiroyuki Aburatani
- Research Center for Advanced Science and Technology, The University of Tokyo
| | - Toshio Nakanishi
- Department of Pediatric Cardiology and Adult Congenital Cardiology, Tokyo Women's Medical University
| | | | - Issei Komuro
- Department of Cardiovascular Medicine, Graduate School of Medicine, The University of Tokyo
| | - Tatsuya Shimizu
- Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University
| |
Collapse
|
28
|
Feng J, Zhao D, Lv F, Yuan Z. Epigenetic Inheritance From Normal Origin Cells Can Determine the Aggressive Biology of Tumor-Initiating Cells and Tumor Heterogeneity. Cancer Control 2022; 29:10732748221078160. [PMID: 35213254 PMCID: PMC8891845 DOI: 10.1177/10732748221078160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The acquisition of genetic- and epigenetic-abnormalities during transformation has been recognized as the two fundamental factors that lead to tumorigenesis and determine the aggressive biology of tumor cells. However, there is a regularity that tumors derived from less-differentiated normal origin cells (NOCs) usually have a higher risk of vascular involvement, lymphatic and distant metastasis, which can be observed in both lymphohematopoietic malignancies and somatic cancers. Obviously, the hypothesis of genetic- and epigenetic-abnormalities is not sufficient to explain how the linear relationship between the cellular origin and the biological behavior of tumors is formed, because the cell origin of tumor is an independent factor related to tumor biology. In a given system, tumors can originate from multiple cell types, and tumor-initiating cells (TICs) can be mapped to different differentiation hierarchies of normal stem cells, suggesting that the heterogeneity of the origin of TICs is not completely chaotic. TIC’s epigenome includes not only genetic- and epigenetic-abnormalities, but also established epigenetic status of genes inherited from NOCs. In reviewing previous studies, we found much evidence supporting that the status of many tumor-related “epigenetic abnormalities” in TICs is consistent with that of the corresponding NOC of the same differentiation hierarchy, suggesting that they may not be true epigenetic abnormalities. So, we speculate that the established statuses of genes that control NOC’s migration, adhesion and colonization capabilities, cell-cycle quiescence, expression of drug transporters, induction of mesenchymal formation, overexpression of telomerase, and preference for glycolysis can be inherited to TICs through epigenetic memory and be manifested as their aggressive biology. TICs of different origins can maintain different degrees of innate stemness from NOC, which may explain why malignancies with stem cell phenotypes are usually more aggressive.
Collapse
Affiliation(s)
- Jiliang Feng
- Clinical-Pathology Center, Capital Medical University Affiliated Beijing Youan Hospital, Beijing, China
| | - Dawei Zhao
- Medical Imaging Department, Capital Medical University Affiliated Beijing Youan Hospital, Beijing, China
| | - Fudong Lv
- Clinical-Pathology Center, Capital Medical University Affiliated Beijing Youan Hospital, Beijing, China
| | - Zhongyu Yuan
- Clinical-Pathology Center, Capital Medical University Affiliated Beijing Youan Hospital, Beijing, China
| |
Collapse
|
29
|
Maretina MA, Valetdinova KR, Tsyganova NA, Egorova AA, Ovechkina VS, Schiöth HB, Zakian SM, Baranov VS, Kiselev AV. Identification of specific gene methylation patterns during motor neuron differentiation from spinal muscular atrophy patient-derived iPSC. Gene 2022; 811:146109. [PMID: 34871761 DOI: 10.1016/j.gene.2021.146109] [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: 08/12/2020] [Revised: 05/08/2021] [Accepted: 11/16/2021] [Indexed: 11/04/2022]
Abstract
Spinal muscular atrophy is a progressive motor neuron disorder caused by deletions or point mutations in the SMN1 gene. It is not known why motor neurons are particularly sensitive to a decrease in SMN protein levels and what factors besides SMN2 underlie the high clinical heterogeneity of the disease. Here we studied the methylation patterns of genes on sequential stages of motor neuron differentiation from induced pluripotent stem cells derived from the patients with SMA type I and II. The genes involved in the regulation of pluripotency, neural differentiation as well as those associated with spinal muscular atrophy development were included. The results show that the PAX6, HB9, CHAT, ARHGAP22, and SMN2 genes are differently methylated in cells derived from SMA patients compared to the cells of healthy individuals. This study clarifies the specificities of the disease pathogenesis and extends the knowledge of pathways involved in the SMA progression.
Collapse
Affiliation(s)
- M A Maretina
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 Saint-Petersburg, Russia
| | - K R Valetdinova
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novsibirsk, Russia
| | - N A Tsyganova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 Saint-Petersburg, Russia
| | - A A Egorova
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 Saint-Petersburg, Russia
| | - V S Ovechkina
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novsibirsk, Russia; Novosibirsk State University, 630090 Novosibirsk, Russia
| | - H B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University, S-75124 Uppsala, Sweden; Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - S M Zakian
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novsibirsk, Russia; Meshalkin National Medical Research Center, Ministry of Healthcare of the Russian Federation, 630055 Novosibirsk, Russia
| | - V S Baranov
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 Saint-Petersburg, Russia
| | - A V Kiselev
- D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, 199034 Saint-Petersburg, Russia.
| |
Collapse
|
30
|
Giacomelli E, Vahsen BF, Calder EL, Xu Y, Scaber J, Gray E, Dafinca R, Talbot K, Studer L. Human stem cell models of neurodegeneration: From basic science of amyotrophic lateral sclerosis to clinical translation. Cell Stem Cell 2022; 29:11-35. [PMID: 34995492 PMCID: PMC8785905 DOI: 10.1016/j.stem.2021.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Neurodegenerative diseases are characterized by progressive cell loss leading to disruption of the structure and function of the central nervous system. Amyotrophic lateral sclerosis (ALS) was among the first of these disorders modeled in patient-specific iPSCs, and recent findings have translated into some of the earliest iPSC-inspired clinical trials. Focusing on ALS as an example, we evaluate the status of modeling neurodegenerative diseases using iPSCs, including methods for deriving and using disease-relevant neuronal and glial lineages. We further highlight the remaining challenges in exploiting the full potential of iPSC technology for understanding and potentially treating neurodegenerative diseases such as ALS.
Collapse
Affiliation(s)
- Elisa Giacomelli
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY, USA
| | - Björn F Vahsen
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Elizabeth L Calder
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY, USA
| | - Yinyan Xu
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK; Chinese Academy of Medical Sciences (CAMS), CAMS Oxford Institute (COI), Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Jakub Scaber
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Elizabeth Gray
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Ruxandra Dafinca
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Kevin Talbot
- Oxford Motor Neuron Disease Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
| | - Lorenz Studer
- The Center for Stem Cell Biology, Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY, USA.
| |
Collapse
|
31
|
Edgar RD, Perrone F, Foster AR, Payne F, Lewis S, Nayak KM, Kraiczy J, Cenier A, Torrente F, Salvestrini C, Heuschkel R, Hensel KO, Harris R, Jones DL, Zerbino DR, Zilbauer M. Culture-Associated DNA Methylation Changes Impact on Cellular Function of Human Intestinal Organoids. Cell Mol Gastroenterol Hepatol 2022; 14:1295-1310. [PMID: 36038072 PMCID: PMC9703134 DOI: 10.1016/j.jcmgh.2022.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND & AIMS Human intestinal epithelial organoids (IEOs) are a powerful tool to model major aspects of intestinal development, health, and diseases because patient-derived cultures retain many features found in vivo. A necessary aspect of the organoid model is the requirement to expand cultures in vitro through several rounds of passaging. This is of concern because the passaging of cells has been shown to affect cell morphology, ploidy, and function. METHODS Here, we analyzed 173 human IEO lines derived from the small and large bowel and examined the effect of culture duration on DNA methylation (DNAm). Furthermore, we tested the potential impact of DNAm changes on gene expression and cellular function. RESULTS Our analyses show a reproducible effect of culture duration on DNAm in a large discovery cohort as well as 2 publicly available validation cohorts generated in different laboratories. Although methylation changes were seen in only approximately 8% of tested cytosine-phosphate-guanine dinucleotides (CpGs) and global cellular function remained stable, a subset of methylation changes correlated with altered gene expression at baseline as well as in response to inflammatory cytokine exposure and withdrawal of Wnt agonists. Importantly, epigenetic changes were found to be enriched in genomic regions associated with colonic cancer and distant to the site of replication, indicating similarities to malignant transformation. CONCLUSIONS Our study shows distinct culture-associated epigenetic changes in mucosa-derived human IEOs, some of which appear to impact gene transcriptomic and cellular function. These findings highlight the need for future studies in this area and the importance of considering passage number as a potentially confounding factor.
Collapse
Affiliation(s)
- Rachel D Edgar
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Francesca Perrone
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - April R Foster
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Centre for Pathway Analysis, Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
| | - Felicity Payne
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Sophia Lewis
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California; Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, California
| | - Komal M Nayak
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Judith Kraiczy
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Aurélie Cenier
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Franco Torrente
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Camilla Salvestrini
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Robert Heuschkel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Kai O Hensel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom; Witten/Herdecke University, Department of Paediatrics, Helios Medical Centre Wuppertal, Children's Hospital, Wuppertal, Germany
| | - Rebecca Harris
- Centre for Pathway Analysis, Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom
| | - D Leanne Jones
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California; Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, California; Department of Anatomy and Medicine, Division of Geriatrics, University of California, San Francisco, San Francisco, California; Eli and Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, California
| | - Daniel R Zerbino
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.
| |
Collapse
|
32
|
Induced pluripotency in the context of stem cell expansion bioprocess development, optimization, and manufacturing: a roadmap to the clinic. NPJ Regen Med 2021; 6:72. [PMID: 34725374 PMCID: PMC8560749 DOI: 10.1038/s41536-021-00183-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/07/2021] [Indexed: 11/09/2022] Open
Abstract
The translation of laboratory-scale bioprocess protocols and technologies to industrial scales and the application of human induced pluripotent stem cell (hiPSC) derivatives in clinical trials globally presents optimism for the future of stem-cell products to impact healthcare. However, while many promising therapeutic approaches are being tested in pre-clinical studies, hiPSC-derived products currently account for a small fraction of active clinical trials. The complexity and volatility of hiPSCs present several bioprocessing challenges, where the goal is to generate a sufficiently large, high-quality, homogeneous population for downstream differentiation-the derivatives of which must retain functional efficacy and meet regulatory safety criteria in application. It is argued herein that one of the major challenges currently faced in improving the robustness of routine stem-cell biomanufacturing is in utilizing continuous, meaningful assessments of molecular and cellular characteristics from process to application. This includes integrating process data with biological characteristic and functional assessment data to model the interplay between variables in the search for global optimization strategies. Coupling complete datasets with relevant computational methods will contribute significantly to model development and automation in achieving process robustness. This overarching approach is thus crucially important in realizing the potential of hiPSC biomanufacturing for transformation of regenerative medicine and the healthcare industry.
Collapse
|
33
|
Kim MH, Thanuthanakhun N, Fujimoto S, Kino-Oka M. Effect of initial seeding density on cell behavior-driven epigenetic memory and preferential lineage differentiation of human iPSCs. Stem Cell Res 2021; 56:102534. [PMID: 34530397 DOI: 10.1016/j.scr.2021.102534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/22/2021] [Accepted: 09/03/2021] [Indexed: 10/20/2022] Open
Abstract
Understanding the cellular behavioral mechanisms underlying memory formation and maintenance in human induced pluripotent stem cell (hiPSC) culture provides key strategies for achieving stability and robustness of cell differentiation. Here, we show that changes in cell behavior-driven epigenetic memory of hiPSC cultures alter their pluripotent state and subsequent differentiation. Interestingly, pluripotency-associated genes were activated during the entire cell growth phases along with increased active modifications and decreased repressive modifications. This memory effect can last several days in the long-term stationary phase and was sustained in the aspect of cell behavioral changes after subculture. Further, changes in growth-related cell behavior were found to induce nucleoskeletal reorganization and active versus repressive modifications, thereby enabling hiPSCs to change their differentiation potential. Overall, we discuss the cell behavior-driven epigenetic memory induced by the culture environment, and the effect of previous memory on cell lineage specification in the process of hiPSC differentiation.
Collapse
Affiliation(s)
- Mee-Hae Kim
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Naruchit Thanuthanakhun
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shun Fujimoto
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masahiro Kino-Oka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
34
|
Tanuma-Takahashi A, Inoue M, Kajiwara K, Takagi R, Yamaguchi A, Samura O, Akutsu H, Sago H, Kiyono T, Okamoto A, Umezawa A. Restoration of keratinocytic phenotypes in autonomous trisomy-rescued cells. Stem Cell Res Ther 2021; 12:476. [PMID: 34433490 PMCID: PMC8390253 DOI: 10.1186/s13287-021-02448-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 06/06/2021] [Indexed: 11/10/2022] Open
Abstract
Background An extra copy of chromosome 21 in humans can alter cellular phenotypes as well as immune and metabolic systems. Down syndrome is associated with many health-related problems and age-related disorders including dermatological abnormalities. However, few studies have focused on the impact of trisomy 21 (T21) on epidermal stem cells and progenitor cell dysfunction. Here, we investigated the differences in keratinocytic characteristics between Down syndrome and euploid cells by differentiating cells from trisomy 21-induced pluripotent stem cells (T21-iPSCs) and autonomous rescued disomy 21-iPSCs (D21-iPSCs). Methods Our protocol for keratinocytic differentiation of T21-iPSCs and D21-iPSCs was employed. For propagation of T21- and D21-iPSC-derived keratinocytes and cell sheet formation, the culture medium supplemented with Rho kinase inhibitor on mouse feeder cells was introduced as growth rate decreased. Before passaging, selection of a keratinocytic population with differential dispase reactivity was performed. Three-dimensional (3D) air-liquid interface was performed in order to evaluate the ability of iPSC-derived keratinocytes to differentiate and form stratified squamous epithelium. Results Trisomy-rescued disomy 21-iPSCs were capable of epidermal differentiation and expressed keratinocytic markers such as KRT14 and TP63 upon differentiation compared to trisomy 21-iPSCs. The lifespan of iPSC-derived keratinocytes could successfully be extended on mouse feeder cells in media containing Rho kinase inhibitor, to more than 34 population doublings over a period of 160 days. Dispase-based purification of disomy iPSC-derived keratinocytes contributed epidermal sheet formation. The trisomy-rescued disomy 21-iPSC-derived keratinocytes with an expanded lifespan generated 3D skin in combination with a dermal fibroblast component. Conclusions Keratinocytes derived from autonomous trisomy-rescued iPSC have the ability of stratification for manufacturing 3D skin with restoration of keratinocytic functions. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-021-02448-w.
Collapse
Affiliation(s)
- Akiko Tanuma-Takahashi
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan.,Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo, 105-8471, Japan
| | - Momoko Inoue
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan.,Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo, 105-8471, Japan
| | - Kazuhiro Kajiwara
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan.,Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo, 105-8471, Japan
| | - Ryo Takagi
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan.,Institute of Advanced Biomedical Engineering and Science, Tokyo Women's Medical University, Tokyo, 162-8666, Japan
| | - Ayumi Yamaguchi
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Osamu Samura
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo, 105-8471, Japan
| | - Hidenori Akutsu
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Haruhiko Sago
- Center for Maternal-Fetal, Neonatal and Reproductive Medicine, National Center for Child Health and Development, Tokyo, 157-8535, Japan
| | - Tohru Kiyono
- Project for Prevention of HPV-related Cancer, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, 277-8577, Japan
| | - Aikou Okamoto
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo, 105-8471, Japan
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Center for Child Health and Development Research Institute, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan.
| |
Collapse
|
35
|
Zhang L, Pu K, Liu X, Bae SDW, Nguyen R, Bai S, Li Y, Qiao L. The Application of Induced Pluripotent Stem Cells Against Liver Diseases: An Update and a Review. Front Med (Lausanne) 2021; 8:644594. [PMID: 34277651 PMCID: PMC8280311 DOI: 10.3389/fmed.2021.644594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 06/04/2021] [Indexed: 11/13/2022] Open
Abstract
Liver diseases are a major health concern globally, and are associated with poor survival and prognosis of patients. This creates the need for patients to accept the main alternative treatment of liver transplantation to prevent progression to end-stage liver disease. Investigation of the molecular mechanisms underpinning complex liver diseases and their pathology is an emerging goal of stem cell scope. Human induced pluripotent stem cells (hiPSCs) derived from somatic cells are a promising alternative approach to the treatment of liver disease, and a prospective model for studying complex liver diseases. Here, we review hiPSC technology of cell reprogramming and differentiation, and discuss the potential application of hiPSC-derived liver cells, such as hepatocytes and cholangiocytes, in refractory liver-disease modeling and treatment, and drug screening and toxicity testing. We also consider hiPSC safety in clinical applications, based on genomic and epigenetic alterations, tumorigenicity, and immunogenicity.
Collapse
Affiliation(s)
- Lei Zhang
- The First Clinical Medical College, Lanzhou University, Lanzhou, China.,Department of General Surgery, The First Hospital of Lanzhou University, Lanzhou, China.,Key Laboratory of Biological Therapy and Regenerative Medicine Transformation Gansu Province, Lanzhou, China
| | - Ke Pu
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Key Laboratory for Gastrointestinal Diseases of Gansu Province, Lanzhou University, Lanzhou, China
| | - Xiaojun Liu
- Department of Medical Oncology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Sarah Da Won Bae
- Storr Liver Centre, Westmead Institute for Medical Research, University of Sydney at Westmead Clinical School, Westmead, NSW, Australia
| | - Romario Nguyen
- Storr Liver Centre, Westmead Institute for Medical Research, University of Sydney at Westmead Clinical School, Westmead, NSW, Australia
| | - Suyang Bai
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Key Laboratory for Gastrointestinal Diseases of Gansu Province, Lanzhou University, Lanzhou, China
| | - Yi Li
- Department of Gastroenterology, The First Hospital of Lanzhou University, Lanzhou, China.,Key Laboratory for Gastrointestinal Diseases of Gansu Province, Lanzhou University, Lanzhou, China
| | - Liang Qiao
- Storr Liver Centre, Westmead Institute for Medical Research, University of Sydney at Westmead Clinical School, Westmead, NSW, Australia
| |
Collapse
|
36
|
α-synuclein pathogenesis in hiPSC models of Parkinson's disease. Neuronal Signal 2021; 5:NS20210021. [PMID: 34239711 PMCID: PMC8222967 DOI: 10.1042/ns20210021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 12/17/2022] Open
Abstract
α-synuclein is an increasingly prominent player in the pathology of a variety of neurodegenerative conditions. Parkinson’s disease (PD) is a neurodegenerative disorder that affects mainly the dopaminergic (DA) neurons in the substantia nigra of the brain. Typical of PD pathology is the finding of protein aggregations termed ‘Lewy bodies’ in the brain regions affected. α-synuclein is implicated in many disease states including dementia with Lewy bodies (DLB) and Alzheimer’s disease. However, PD is the most common synucleinopathy and continues to be a significant focus of PD research in terms of the α-synuclein Lewy body pathology. Mutations in several genes are associated with PD development including SNCA, which encodes α-synuclein. A variety of model systems have been employed to study α-synuclein physiology and pathophysiology in an attempt to relate more closely to PD pathology. These models include cellular and animal system exploring transgenic technologies, viral vector expression and knockdown approaches, and models to study the potential prion protein-like effects of α-synuclein. The current review focuses on human induced pluripotent stem cell (iPSC) models with a specific focus on mutations or multiplications of the SNCA gene. iPSCs are a rapidly evolving technology with huge promise in the study of normal physiology and disease modeling in vitro. The ability to maintain a patient’s genetic background and replicate similar cell phenotypes make iPSCs a powerful tool in the study of neurological diseases. This review focuses on the current knowledge about α-synuclein physiological function as well as its role in PD pathogenesis based on human iPSC models.
Collapse
|
37
|
Maali A, Maroufi F, Sadeghi F, Atashi A, Kouchaki R, Moghadami M, Azad M. Induced pluripotent stem cell technology: trends in molecular biology, from genetics to epigenetics. Epigenomics 2021; 13:631-647. [PMID: 33823614 DOI: 10.2217/epi-2020-0409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Induced pluripotent stem cell (iPSC) technology, based on autologous cells' reprogramming to the embryonic state, is a new approach in regenerative medicine. Current advances in iPSC technology have opened up new avenues for multiple applications, from basic research to clinical therapy. Thus, conducting iPSC trials have attracted increasing attention and requires an extensive understanding of the molecular basis of iPSCs. Since iPSC reprogramming is based on the methods inducing the expression of specific genes involved in pluripotency states, it can be concluded that iPSC reprogramming is strongly influenced by epigenetics. In this study, we reviewed the molecular basis of reprogramming, including the reprogramming factors (OCT4, SOX2, KLF4, c-MYC, NANOG, ESRRB, LIN28 as well as their regulatory networks), applied vectors (retroviral vectors, adenoviral vectors, Sendaiviral vectors, episomal plasmids, piggyBac, simple vectors, etc.) and epigenetic modifications (miRNAs, histones and DNA methylation states) to provide a comprehensive guide for reprogramming studies.
Collapse
Affiliation(s)
- Amirhosein Maali
- Student Research Committee, Pasteur Institute of Iran, Tehran, Iran.,Department of Medical Biotechnology, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Faezeh Maroufi
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Farzin Sadeghi
- Cellular & Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Amir Atashi
- Stem Cells & Tissue Engineering Research Center, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Reza Kouchaki
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mona Moghadami
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran
| | - Mehdi Azad
- Department of Medical Laboratory Sciences, Faculty of Allied Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| |
Collapse
|
38
|
Chang S, Hur SK, Naveh NSS, Thorvaldsen JL, French DL, Gagne AL, Jobaliya CD, Anguera MC, Bartolomei MS, Kalish JM. Derivation and investigation of the first human cell-based model of Beckwith-Wiedemann syndrome. Epigenetics 2020; 16:1295-1305. [PMID: 33300436 DOI: 10.1080/15592294.2020.1861172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Genomic imprinting is a rare form of gene expression in mammals in which a small number of genes are expressed in a parent-of-origin-specific manner. The aetiology of human imprinting disorders is diverse and includes chromosomal abnormalities, mutations, and epigenetic dysregulation of imprinted genes. The most common human imprinting disorder is Beckwith-Wiedemann syndrome (BWS), frequently caused by uniparental isodisomy and DNA methylation alterations. Because these lesions cannot be easily engineered, induced pluripotent stem cells (iPSC) are a compelling alternative. Here, we describe the first iPSC model derived from patients with BWS. Due to the mosaic nature of BWS patients, both BWS and non-BWS iPSC lines were derived from the same patient's fibroblasts. Importantly, we determine that DNA methylation and gene expression patterns of the imprinted region in the iPSC lines reflect the parental cells and are stable over time. Additionally, we demonstrate that differential expression in insulin signalling, cell proliferation, and cell cycle pathways was seen in hepatocyte lineages derived from BWS lines compared to controls. Thus, this cell based-model can be used to investigate the role of imprinting in the pathogenesis of BWS in disease-relevant cell types.
Collapse
Affiliation(s)
- Suhee Chang
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stella K Hur
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Natali S Sobel Naveh
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joanne L Thorvaldsen
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Deborah L French
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alyssa L Gagne
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Chintan D Jobaliya
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Montserrat C Anguera
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Marisa S Bartolomei
- Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer M Kalish
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Departments of Genetics and Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
39
|
Ford E, Pearlman J, Ruan T, Manion J, Waller M, Neely GG, Caron L. Human Pluripotent Stem Cells-Based Therapies for Neurodegenerative Diseases: Current Status and Challenges. Cells 2020; 9:E2517. [PMID: 33233861 PMCID: PMC7699962 DOI: 10.3390/cells9112517] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
Neurodegenerative diseases are characterized by irreversible cell damage, loss of neuronal cells and limited regeneration potential of the adult nervous system. Pluripotent stem cells are capable of differentiating into the multitude of cell types that compose the central and peripheral nervous systems and so have become the major focus of cell replacement therapies for the treatment of neurological disorders. Human embryonic stem cell (hESC) and human induced pluripotent stem cell (hiPSC)-derived cells have both been extensively studied as cell therapies in a wide range of neurodegenerative disease models in rodents and non-human primates, including Parkinson's disease, stroke, epilepsy, spinal cord injury, Alzheimer's disease, multiple sclerosis and pain. In this review, we discuss the latest progress made with stem cell therapies targeting these pathologies. We also evaluate the challenges in clinical application of human pluripotent stem cell (hPSC)-based therapies including risk of oncogenesis and tumor formation, immune rejection and difficulty in regeneration of the heterogeneous cell types composing the central nervous system.
Collapse
Affiliation(s)
- Elizabeth Ford
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, Centenary Institute, University of Sydney, Camperdown, NSW 2006, Australia; (E.F.); (J.P.); (T.R.); (J.M.); (M.W.); (G.G.N.)
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Jodie Pearlman
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, Centenary Institute, University of Sydney, Camperdown, NSW 2006, Australia; (E.F.); (J.P.); (T.R.); (J.M.); (M.W.); (G.G.N.)
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Travis Ruan
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, Centenary Institute, University of Sydney, Camperdown, NSW 2006, Australia; (E.F.); (J.P.); (T.R.); (J.M.); (M.W.); (G.G.N.)
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | - John Manion
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, Centenary Institute, University of Sydney, Camperdown, NSW 2006, Australia; (E.F.); (J.P.); (T.R.); (J.M.); (M.W.); (G.G.N.)
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
- Department of Urology, Boston Children’s Hospital, Boston, MA 02115, USA
- Departments of Surgery and Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Waller
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, Centenary Institute, University of Sydney, Camperdown, NSW 2006, Australia; (E.F.); (J.P.); (T.R.); (J.M.); (M.W.); (G.G.N.)
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | - Gregory G. Neely
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, Centenary Institute, University of Sydney, Camperdown, NSW 2006, Australia; (E.F.); (J.P.); (T.R.); (J.M.); (M.W.); (G.G.N.)
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | - Leslie Caron
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, Centenary Institute, University of Sydney, Camperdown, NSW 2006, Australia; (E.F.); (J.P.); (T.R.); (J.M.); (M.W.); (G.G.N.)
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| |
Collapse
|
40
|
Lampert A, Bennett DL, McDermott LA, Neureiter A, Eberhardt E, Winner B, Zenke M. Human sensory neurons derived from pluripotent stem cells for disease modelling and personalized medicine. NEUROBIOLOGY OF PAIN 2020; 8:100055. [PMID: 33364527 PMCID: PMC7750732 DOI: 10.1016/j.ynpai.2020.100055] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 12/26/2022]
Abstract
New techniques emerge to study peripheral sensory neurons in iPS-cell derived models. Genetic pain syndromes, e.g. gain- and loss-of-function mutations in Nav-channels are helpful. Individualized treatment for neuropathic pain can be identified with iPS-cell derived nociceptors.
In this concise Mini-Review we will summarize ongoing developments of new techniques to study physiology and pathophysiology of the peripheral sensory nervous system in human stem cell derived models. We will focus on recent developments of reprogramming somatic cells into induced pluripotent stem cells, neural differentiation towards neuronal progenitors and human sensory neurons. We will sum up the high potential of this new technique for disease modelling of human neuropathies with a focus on genetic pain syndromes, such as gain- and loss-of-function mutations in voltage-gated sodium channels. The stem cell derived human sensory neurons are used for drug testing and we will summarize their usefulness for individualized treatment identification in patients with neuropathic pain. The review will give an outlook on potential application of this technique as companion diagnostics and for personalized medicine.
Collapse
Affiliation(s)
| | - David L Bennett
- Nuffield Department of Clinical Neurosciences, University of Oxford, UK
| | - Lucy A McDermott
- Nuffield Department of Clinical Neurosciences, University of Oxford, UK.,Wadham College, University of Oxford, UK
| | | | - Esther Eberhardt
- Department of Anesthesiology, FAU Erlangen-Nürnberg, Germany.,Department of Stem Cell Biology, FAU Erlangen-Nürnberg, Germany.,Department of Anesthesiology, RWTH Aachen University, Germany
| | - Beate Winner
- Department of Stem Cell Biology, FAU Erlangen-Nürnberg, Germany
| | | |
Collapse
|
41
|
Nishino K, Takasawa K, Okamura K, Arai Y, Sekiya A, Akutsu H, Umezawa A. Identification of an epigenetic signature in human induced pluripotent stem cells using a linear machine learning model. Hum Cell 2020; 34:99-110. [PMID: 33047283 PMCID: PMC7788050 DOI: 10.1007/s13577-020-00446-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 10/02/2020] [Indexed: 12/14/2022]
Abstract
The use of human induced pluripotent stem cells (iPSCs), used as an alternative to human embryonic stem cells (ESCs), is a potential solution to challenges, such as immune rejection, and does not involve the ethical issues concerning the use of ESCs in regenerative medicine, thereby enabling developments in biological research. However, comparative analyses from previous studies have not indicated any specific feature that distinguishes iPSCs from ESCs. Therefore, in this study, we established a linear classification-based learning model to distinguish among ESCs, iPSCs, embryonal carcinoma cells (ECCs), and somatic cells on the basis of their DNA methylation profiles. The highest accuracy achieved by the learned models in identifying the cell type was 94.23%. In addition, the epigenetic signature of iPSCs, which is distinct from that of ESCs, was identified by component analysis of the learned models. The iPSC-specific regions with methylation fluctuations were abundant on chromosomes 7, 8, 12, and 22. The method developed in this study can be utilized with comprehensive data and widely applied to many aspects of molecular biology research.
Collapse
Affiliation(s)
- Koichiro Nishino
- Laboratory of Veterinary Biochemistry and Molecular Biology, Graduate School of Medicine and Veterinary Medicine/Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan. .,Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan.
| | - Ken Takasawa
- Laboratory of Veterinary Biochemistry and Molecular Biology, Graduate School of Medicine and Veterinary Medicine/Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yoshikazu Arai
- Laboratory of Veterinary Biochemistry and Molecular Biology, Graduate School of Medicine and Veterinary Medicine/Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Asato Sekiya
- Laboratory of Veterinary Biochemistry and Molecular Biology, Graduate School of Medicine and Veterinary Medicine/Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Hidenori Akutsu
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akihiro Umezawa
- Department of Reproductive Biology, Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| |
Collapse
|
42
|
Paniza T, Deshpande M, Wang N, O’Neil R, Zuccaro MV, Smith ME, Madireddy A, James D, Ecker J, Rosenwaks Z, Egli D, Gerhardt J. Pluripotent stem cells with low differentiation potential contain incompletely reprogrammed DNA replication. J Cell Biol 2020; 219:e201909163. [PMID: 32673399 PMCID: PMC7480103 DOI: 10.1083/jcb.201909163] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/26/2020] [Accepted: 05/13/2020] [Indexed: 12/20/2022] Open
Abstract
Reprogrammed pluripotent stem cells (PSCs) are valuable for research and potentially for cell replacement therapy. However, only a fraction of reprogrammed PSCs are developmentally competent. Genomic stability and accurate DNA synthesis are fundamental for cell development and critical for safety. We analyzed whether defects in DNA replication contribute to genomic instability and the diverse differentiation potentials of reprogrammed PSCs. Using a unique single-molecule approach, we visualized DNA replication in isogenic PSCs generated by different reprogramming approaches, either somatic cell nuclear transfer (NT-hESCs) or with defined factors (iPSCs). In PSCs with lower differentiation potential, DNA replication was incompletely reprogrammed, and genomic instability increased during replicative stress. Reprogramming of DNA replication did not correlate with DNA methylation. Instead, fewer replication origins and a higher frequency of DNA breaks in PSCs with incompletely reprogrammed DNA replication were found. Given the impact of error-free DNA synthesis on the genomic integrity and differentiation proficiency of PSCs, analyzing DNA replication may be a useful quality control tool.
Collapse
Affiliation(s)
- Theodore Paniza
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Madhura Deshpande
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Ning Wang
- Department of Pediatrics, Columbia University, New York, NY
| | - Ryan O’Neil
- Plant Molecular and Cellular Biology Laboratory, Salk Institute, La Jolla, CA
| | - Michael V. Zuccaro
- Department of Pediatrics, Columbia University, New York, NY
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | | | - Advaitha Madireddy
- Department of Pediatric Hematology/Oncology, Rutgers University, New Brunswick, NJ
| | - Daylon James
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY
| | - Joseph Ecker
- Plant Molecular and Cellular Biology Laboratory, Salk Institute, La Jolla, CA
| | - Zev Rosenwaks
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Dieter Egli
- Department of Pediatrics, Columbia University, New York, NY
| | - Jeannine Gerhardt
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY
| |
Collapse
|
43
|
Isono W, Kawasaki T, Ichida JK, Ayabe T, Hiraike O, Umezawa A, Akutsu H. The combination of dibenzazepine and a DOT1L inhibitor enables a stable maintenance of human naïve-state pluripotency in non-hypoxic conditions. Regen Ther 2020; 15:161-168. [PMID: 33426214 PMCID: PMC7770342 DOI: 10.1016/j.reth.2020.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/04/2020] [Accepted: 08/12/2020] [Indexed: 10/26/2022] Open
Abstract
Conventional human pluripotent stem cells (hPSCs), known for being in a primed state, are pivotal for both basic research and clinical applications since such cells produce various types of differentiated cells. Recent reports on PSCs shed light on the pluripotent hierarchy of stem cells and have promoted the exploration of new stem cell states along with their culture systems. Human naïve PSCs are expected to provide further knowledge of early developmental mechanisms and improvements for differentiation programmes in the regenerative therapy of conventionally primed PSCs. However, practical challenges exist in using naïve-state PSCs such as determining the conditions for hypoxic culture condition and showing limited stable cellular proliferation. Here, we have developed new leukemia inhibitory factor dependent PSCs by applying our previous work, the combination of dibenzazepine and a DOT1L inhibitor to achieve the stable culture of naïve-state PSCs. The potential of these cells to differentiate into all three germ layers was shown both in vitro and in vivo. Such new naïve-state PSCs formed dome-shaped colonies at a faster rate than conventional, primed-state human induced PSCs and could be maintained for an extended period in the absence of hypoxic culture conditions. We also identified relatively high expression levels of naïve cell markers. Thus, non-hypoxia treated, leukemia inhibitory factor-dependent PSCs are anticipated to have characteristics similar to those of naïve-like PSCs, and to enhance the utility value of PSCs. Such naïve PSCs may allow the molecular characterization of previously undefined naïve human PSCs, and to ultimately contribute to the use of human pluripotent stem cells in regenerative medicine and disease modelling.
Collapse
Affiliation(s)
- Wataru Isono
- Center for Regenerative Medicine, National Center for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan.,Department of Obstetrics and Gynecology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo, 173-8605, Japan
| | - Tomoyuki Kawasaki
- Center for Regenerative Medicine, National Center for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Justin K Ichida
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Takuya Ayabe
- Department of Obstetrics and Gynecology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo, 173-8605, Japan
| | - Osamu Hiraike
- Department of Obstetrics and Gynaecology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-8655, Japan
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Center for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Hidenori Akutsu
- Center for Regenerative Medicine, National Center for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| |
Collapse
|
44
|
Sharma S, Bhonde R. Genetic and epigenetic stability of stem cells: Epigenetic modifiers modulate the fate of mesenchymal stem cells. Genomics 2020; 112:3615-3623. [DOI: 10.1016/j.ygeno.2020.04.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/08/2020] [Accepted: 04/24/2020] [Indexed: 12/11/2022]
|
45
|
Schnichels S, Paquet-Durand F, Löscher M, Tsai T, Hurst J, Joachim SC, Klettner A. Retina in a dish: Cell cultures, retinal explants and animal models for common diseases of the retina. Prog Retin Eye Res 2020; 81:100880. [PMID: 32721458 DOI: 10.1016/j.preteyeres.2020.100880] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 12/11/2022]
Abstract
For many retinal diseases, including age-related macular degeneration (AMD), glaucoma, and diabetic retinopathy (DR), the exact pathogenesis is still unclear. Moreover, the currently available therapeutic options are often unsatisfactory. Research designed to remedy this situation heavily relies on experimental animals. However, animal models often do not faithfully reproduce human disease and, currently, there is strong pressure from society to reduce animal research. Overall, this creates a need for improved disease models to understand pathologies and develop treatment options that, at the same time, require fewer or no experimental animals. Here, we review recent advances in the field of in vitro and ex vivo models for AMD, glaucoma, and DR. We highlight the difficulties associated with studies on complex diseases, in which both the initial trigger and the ensuing pathomechanisms are unclear, and then delineate which model systems are optimal for disease modelling. To this end, we present a variety of model systems, ranging from primary cell cultures, over organotypic cultures and whole eye cultures, to animal models. Specific advantages and disadvantages of such models are discussed, with a special focus on their relevance to putative in vivo disease mechanisms. In many cases, a replacement of in vivo research will mean that several different in vitro models are used in conjunction, for instance to analyze and validate causative molecular pathways. Finally, we argue that the analytical decomposition into appropriate cell and tissue model systems will allow making significant progress in our understanding of complex retinal diseases and may furthermore advance the treatment testing.
Collapse
Affiliation(s)
- Sven Schnichels
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Germany.
| | - François Paquet-Durand
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Germany
| | - Marina Löscher
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Germany
| | - Teresa Tsai
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, Germany
| | - José Hurst
- University Eye Hospital, Centre for Ophthalmology, University of Tübingen, Germany
| | - Stephanie C Joachim
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, Germany
| | - Alexa Klettner
- Department of Ophthalmology, University Medical Center, University of Kiel, Kiel, Germany
| |
Collapse
|
46
|
Conway M, Xu T, Kirkpatrick A, Ripp S, Sayler G, Close D. Real-time tracking of stem cell viability, proliferation, and differentiation with autonomous bioluminescence imaging. BMC Biol 2020; 18:79. [PMID: 32620121 PMCID: PMC7333384 DOI: 10.1186/s12915-020-00815-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 06/18/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Luminescent reporter proteins are vital tools for visualizing cells and cellular activity. Among the current toolbox of bioluminescent systems, only bacterial luciferase has genetically defined luciferase and luciferin synthesis pathways that are functional at the mammalian cell temperature optimum of 37 °C and have the potential for in vivo applications. However, this system is not functional in all cell types, including stem cells, where the ability to monitor continuously and in real-time cellular processes such as differentiation and proliferation would be particularly advantageous. RESULTS We report that artificial subdivision of the bacterial luciferin and luciferase pathway subcomponents enables continuous or inducible bioluminescence in pluripotent and mesenchymal stem cells when the luciferin pathway is overexpressed with a 20-30:1 ratio. Ratio-based expression is demonstrated to have minimal effects on phenotype or differentiation while enabling autonomous bioluminescence without requiring external excitation. We used this method to assay the proliferation, viability, and toxicology responses of iPSCs and showed that these assays are comparable in their performance to established colorimetric assays. Furthermore, we used the continuous luminescence to track stem cell progeny post-differentiation. Finally, we show that tissue-specific promoters can be used to report cell fate with this system. CONCLUSIONS Our findings expand the utility of bacterial luciferase and provide a new tool for stem cell research by providing a method to easily enable continuous, non-invasive bioluminescent monitoring in pluripotent cells.
Collapse
Affiliation(s)
| | - Tingting Xu
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Steven Ripp
- 490 BioTech, Knoxville, TN, 37996, USA
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Gary Sayler
- 490 BioTech, Knoxville, TN, 37996, USA
- Center for Environmental Biotechnology, The University of Tennessee, Knoxville, TN, 37996, USA
| | - Dan Close
- 490 BioTech, Knoxville, TN, 37996, USA.
| |
Collapse
|
47
|
Harnessing targeted DNA methylation and demethylation using dCas9. Essays Biochem 2020; 63:813-825. [PMID: 31724704 DOI: 10.1042/ebc20190029] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022]
Abstract
DNA methylation is an essential DNA modification that plays a crucial role in genome regulation during differentiation and development, and is disrupted in a range of disease states. The recent development of CRISPR/catalytically dead CRISPR/Cas9 (dCas9)-based targeted DNA methylation editing tools has enabled new insights into the roles and functional relevance of this modification, including its importance at regulatory regions and the role of aberrant methylation in various diseases. However, while these tools are advancing our ability to understand and manipulate this regulatory layer of the genome, they still possess a variety of limitations in efficacy, implementation, and targeting specificity. Effective targeted DNA methylation editing will continue to advance our fundamental understanding of the role of this modification in different genomic and cellular contexts, and further improvements may enable more accurate disease modeling and possible future treatments. In this review, we discuss strategies, considerations, and future directions for targeted DNA methylation editing.
Collapse
|
48
|
Sugawara T, Miura T, Kawasaki T, Umezawa A, Akutsu H. The hsa-miR-302 cluster controls ectodermal differentiation of human pluripotent stem cell via repression of DAZAP2. Regen Ther 2020; 15:1-9. [PMID: 32490061 PMCID: PMC7251312 DOI: 10.1016/j.reth.2020.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/03/2020] [Accepted: 03/11/2020] [Indexed: 12/27/2022] Open
Abstract
Introduction Recent studies have revealed that microRNAs (miRNAs, miRs) are important for self-renewal, differentiation, and cellular reprogramming of somatic cells into induced pluripotent stem cells (iPSC); however, their functional roles and target genes that are regulated by human PSC-specific miRs including hsa-miR-302 clusters remain largely unknown. Analysis of their target gene will give us the opportunity to understand the functional roles of such miRs. Methods We analyzed the expression profiles of miRs in 4 somatic cell lines, 8 human iPSC lines derived from 4 different cell types, 3 human ESC lines, and embryoid bodies differentiated from the human ESCs to identify human PSC-specific miRs. We also analyzed the simultaneous expression profiles of miRs and mRNAs to identify candidate targets of human PSC-specific miRs. Then, we constructed a vector for overexpressing one of the target gene to dissect the functions of human PSC-specific miR in maintenance of self-renew and differentiation. Results We focused on hsa-miR-302 cluster as a human PSC-specific miR and identified 22 candidate targets of hsa-miR-302 cluster that were moderately expressed in undifferentiated human PSCs and up-regulated in differentiated cells. Deleted in azoospermia-associated protein 2 (DAZAP2), one such target, was directly repressed by hsa-miR-302a, -302b, -302c and -302d, but not by hsa-miR-367. Overexpression of DAZAP2 caused a decrease in cell proliferation of undifferentiated human iPSCs, although morphology and undifferentiated marker gene expression was not affected. In addition, neural differentiation was suppressed in DAZAP2-overexpressing human iPSCs. Conclusion Our study revealed that hsa-miR-302 cluster controls the cell proliferation of human PSCs and the neural differentiation of human PSCs by repression of DAZAP2, thereby highlighting an additional function of human PSC-specific miRs in maintaining pluripotency.
Collapse
Affiliation(s)
| | | | | | | | - Hidenori Akutsu
- Corresponding author. Department of Reproductive Medicine, National Center for Child Health and Developmen, Okura 2-10-1, Setagaya-ku, Tokyo, 157-8535, Japan. Fax: +81-3-5494-7048.
| |
Collapse
|
49
|
Epigenetic Features of Human Perinatal Stem Cells Redefine Their Stemness Potential. Cells 2020; 9:cells9051304. [PMID: 32456308 PMCID: PMC7290760 DOI: 10.3390/cells9051304] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 02/06/2023] Open
Abstract
Human perinatal stem cells (SCs) can be isolated from fetal annexes without ethical or safety limitations. They are generally considered multipotent; nevertheless, their biological characteristics are still not fully understood. The aim of this study was to investigate the pluripotency potential of human perinatal SCs as compared to human induced pluripotent stem cells (hiPSCs). Despite the low expression of the pluripotent factors NANOG, OCT4, SOX2, and C-KIT in perinatal SC, we observed minor differences in the promoters DNA-methylation profile of these genes with respect to hiPSCs; we also demonstrated that in perinatal SCs miR-145-5p had an inverse trend in comparison to these stemness markers, suggesting that NANOG, OCT4, and SOX2 were regulated at the post-transcriptional level. The reduced expression of stemness markers was also associated with shorter telomere lengths and shift of the oxidative metabolism between hiPSCs and fetal annex-derived cells. Our findings indicate the differentiation ability of perinatal SCs might not be restricted to the mesenchymal lineage due to an epigenetic barrier, but other regulatory mechanisms such as telomere shortening or metabolic changes might impair their differentiation potential and challenge their clinical application.
Collapse
|
50
|
Gorlin syndrome-induced pluripotent stem cells form medulloblastoma with loss of heterozygosity in PTCH1. Aging (Albany NY) 2020; 12:9935-9947. [PMID: 32436863 PMCID: PMC7288908 DOI: 10.18632/aging.103258] [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: 12/28/2019] [Accepted: 03/30/2020] [Indexed: 02/06/2023]
Abstract
Gorlin syndrome is a rare autosomal dominant hereditary disease with a high incidence of tumors such as basal cell carcinoma and medulloblastoma. Disease-specific induced pluripotent stem cells (iPSCs) and an animal model have been used to analyze disease pathogenesis. In this study, we generated iPSCs derived from fibroblasts of four patients with Gorlin syndrome (Gln-iPSCs) with heterozygous mutations of the PTCH1 gene. Gln-iPSCs from the four patients developed into medulloblastoma, a manifestation of Gorlin syndrome, in 100% (four out of four), of teratomas after implantation into immunodeficient mice, but none (0/584) of the other iPSC-teratomas did so. One of the medulloblastomas showed loss of heterozygosity in the PTCH1 gene while the benign teratoma, i.e. the non-medulloblastoma portion, did not, indicating a close clinical correlation between tumorigenesis in Gorlin syndrome patients and Gln-iPSCs.
Collapse
|