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Dong W, Liu S, Li S, Wang Z. Cell reprogramming therapy for Parkinson's disease. Neural Regen Res 2024; 19:2444-2455. [PMID: 38526281 PMCID: PMC11090434 DOI: 10.4103/1673-5374.390965] [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: 06/07/2023] [Revised: 07/23/2023] [Accepted: 10/08/2023] [Indexed: 03/26/2024] Open
Abstract
Parkinson's disease is typically characterized by the progressive loss of dopaminergic neurons in the substantia nigra pars compacta. Many studies have been performed based on the supplementation of lost dopaminergic neurons to treat Parkinson's disease. The initial strategy for cell replacement therapy used human fetal ventral midbrain and human embryonic stem cells to treat Parkinson's disease, which could substantially alleviate the symptoms of Parkinson's disease in clinical practice. However, ethical issues and tumor formation were limitations of its clinical application. Induced pluripotent stem cells can be acquired without sacrificing human embryos, which eliminates the huge ethical barriers of human stem cell therapy. Another widely considered neuronal regeneration strategy is to directly reprogram fibroblasts and astrocytes into neurons, without the need for intermediate proliferation states, thus avoiding issues of immune rejection and tumor formation. Both induced pluripotent stem cells and direct reprogramming of lineage cells have shown promising results in the treatment of Parkinson's disease. However, there are also ethical concerns and the risk of tumor formation that need to be addressed. This review highlights the current application status of cell reprogramming in the treatment of Parkinson's disease, focusing on the use of induced pluripotent stem cells in cell replacement therapy, including preclinical animal models and progress in clinical research. The review also discusses the advancements in direct reprogramming of lineage cells in the treatment of Parkinson's disease, as well as the controversy surrounding in vivo reprogramming. These findings suggest that cell reprogramming may hold great promise as a potential strategy for treating Parkinson's disease.
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Affiliation(s)
- Wenjing Dong
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan Province, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan Province, China
| | - Shuyi Liu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan Province, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan Province, China
| | - Shangang Li
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan Province, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan Province, China
| | - Zhengbo Wang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan Province, China
- Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan Province, China
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2
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Escribá R, Beksac M, Bennaceur-Griscelli A, Glover JC, Koskela S, Latsoudis H, Querol S, Alvarez-Palomo B. Submission to Stem Cells Reviews and Reports. Stem Cell Rev Rep 2024:10.1007/s12015-024-10783-7. [PMID: 39276260 DOI: 10.1007/s12015-024-10783-7] [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] [Accepted: 08/20/2024] [Indexed: 09/16/2024]
Abstract
The use of allogeneic induced pluripotent stem cell (iPSC)-derived cell therapies for regenerative medicine offers an affordable and realistic alternative to producing individual iPSC lines for each patient in need. Human Leukocyte Antigens (HLA)-homozygous iPSCs matched in hemi-similarity could provide cell therapies with reduced immune rejection covering a wide range of the population with a few iPSC lines. Several banks of HLA-homozygous iPSCs (haplobanks) have been established worldwide or are underway, to provide clinical grade starting material for cell therapies covering the most frequent HLA haplotypes for certain populations. Harmonizing quality standards among haplobanks and creating a global registry could minimize the collective effort and provide a much wider access to HLA-compatible cell therapies for patients with less frequent haplotypes. In this review we present all the current haplobank initiatives and their potential benefits for the global population.
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Affiliation(s)
- Rubén Escribá
- Cell Therapy Service, Banc de Sang I Teixits, 106 Passeig de Taulat, 08005, Barcelona, Spain
| | - Meral Beksac
- Ankara Liv Hospital Istinye University and Cord Blood Bank, Ankara University, Ankara, Turkey
| | - Annelise Bennaceur-Griscelli
- CiTHERA, Center of iPS Cell Therapy, Infrastructure INGESTEM University Paris Saclay Inserm U1310, 28 Rue Henri Desbruères, 91100, Corbeil-Essonnes, France
| | - Joel C Glover
- Norwegian Center for Stem Cell Research and Norwegian Core Facility for Human Pluripotent Stem Cells, Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Satu Koskela
- Finnish Red Cross Blood Service Biobank, Härkälenkki 13, 01730, Vantaa, Finland
| | - Helen Latsoudis
- Information Systems Laboratory, Institute of Computer Sciences, Foundation for Research and Technology Hellas, 70013, Heraklion, Crete, Greece
- Haemopoiesis Research Laboratory, School of Medicine, University of Crete, 71003, Heraklion, Crete, Greece
| | - Sergi Querol
- Cell Therapy Service, Banc de Sang I Teixits, 106 Passeig de Taulat, 08005, Barcelona, Spain
| | - Belén Alvarez-Palomo
- Cell Therapy Service, Banc de Sang I Teixits, 106 Passeig de Taulat, 08005, Barcelona, Spain.
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3
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Grattoni A, Korbutt G, Tomei AA, García AJ, Pepper AR, Stabler C, Brehm M, Papas K, Citro A, Shirwan H, Millman JR, Melero-Martin J, Graham M, Sefton M, Ma M, Kenyon N, Veiseh O, Desai TA, Nostro MC, Marinac M, Sykes M, Russ HA, Odorico J, Tang Q, Ricordi C, Latres E, Mamrak NE, Giraldo J, Poznansky MC, de Vos P. Harnessing cellular therapeutics for type 1 diabetes mellitus: progress, challenges, and the road ahead. Nat Rev Endocrinol 2024:10.1038/s41574-024-01029-0. [PMID: 39227741 DOI: 10.1038/s41574-024-01029-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/06/2024] [Indexed: 09/05/2024]
Abstract
Type 1 diabetes mellitus (T1DM) is a growing global health concern that affects approximately 8.5 million individuals worldwide. T1DM is characterized by an autoimmune destruction of pancreatic β cells, leading to a disruption in glucose homeostasis. Therapeutic intervention for T1DM requires a complex regimen of glycaemic monitoring and the administration of exogenous insulin to regulate blood glucose levels. Advances in continuous glucose monitoring and algorithm-driven insulin delivery devices have improved the quality of life of patients. Despite this, mimicking islet function and complex physiological feedback remains challenging. Pancreatic islet transplantation represents a potential functional cure for T1DM but is hindered by donor scarcity, variability in harvested cells, aggressive immunosuppressive regimens and suboptimal clinical outcomes. Current research is directed towards generating alternative cell sources, improving transplantation methods, and enhancing cell survival without chronic immunosuppression. This Review maps the progress in cell replacement therapies for T1DM and outlines the remaining challenges and future directions. We explore the state-of-the-art strategies for generating replenishable β cells, cell delivery technologies and local targeted immune modulation. Finally, we highlight relevant animal models and the regulatory aspects for advancing these technologies towards clinical deployment.
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Affiliation(s)
- Alessandro Grattoni
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX, USA.
- Department of Surgery, Houston Methodist Hospital, Houston, TX, USA.
- Department of Radiation Oncology, Houston Methodist Hospital, Houston, TX, USA.
| | - Gregory Korbutt
- Alberta Diabetes Institute, University of Alberta, Edmonton, Alberta, Canada
- Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Alice A Tomei
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Biomedical Engineering, University of Miami, Miami, FL, USA
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Andrés J García
- Woodruff School of Mechanical Engineering and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Andrew R Pepper
- Department of Surgery, University of Alberta, Edmonton, Alberta, Canada
| | - Cherie Stabler
- J. Crayton Pruitt Family Department of Biomedical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA
- Diabetes Institute, University of Florida, Gainesville, FL, USA
| | - Michael Brehm
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Klearchos Papas
- Department of Surgery, The University of Arizona, Tucson, AZ, USA
| | - Antonio Citro
- Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Haval Shirwan
- Department of Pediatrics, Ellis Fischel Cancer Center, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Jeffrey R Millman
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, St. Louis, MO, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Juan Melero-Martin
- Department of Cardiac Surgery, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Melanie Graham
- Department of Surgery, University of Minnesota, Minneapolis, MN, USA
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
| | - Michael Sefton
- Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Minglin Ma
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY, USA
| | - Norma Kenyon
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Omid Veiseh
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Tejal A Desai
- University of California, San Francisco, Department of Bioengineering and Therapeutic Sciences, San Francisco, CA, USA
- Brown University, School of Engineering, Providence, RI, USA
| | - M Cristina Nostro
- McEwen Stem Cell Institute, University Health Network, Toronto, ON, Canada
- Department of Physiology, University of Toronto, Toronto, ON, Canada
| | | | - Megan Sykes
- Department of Medicine, Columbia Center for Translational Immunology, Columbia University, New York, NY, USA
- Department of Microbiology and Immunology, Columbia University, New York, NY, USA
- Department of Surgery, Columbia University, New York, NY, USA
| | - Holger A Russ
- Diabetes Institute, University of Florida, Gainesville, FL, USA
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, USA
| | - Jon Odorico
- UW Health Transplant Center, Madison, WI, USA
- Division of Transplantation, Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Qizhi Tang
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
- Department of Surgery, University of California San Francisco, San Francisco, CA, US
- Gladstone Institute of Genomic Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Camillo Ricordi
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL, USA
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Esther Latres
- Research Department, Breakthrough T1D, New York, NY, USA
| | | | - Jaime Giraldo
- Research Department, Breakthrough T1D, New York, NY, USA.
| | - Mark C Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Paul de Vos
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen and University Medical Center Groningen, Groningen, Netherlands.
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4
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Pierson Smela M, Pepe V, Lubbe S, Kiskinis E, Church GM. SeqVerify: An accessible analysis tool for cell line genomic integrity, contamination, and gene editing outcomes. Stem Cell Reports 2024:S2213-6711(24)00242-X. [PMID: 39270651 DOI: 10.1016/j.stemcr.2024.08.004] [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: 06/19/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 09/15/2024] Open
Abstract
Over the last decade, advances in genome editing and pluripotent stem cell (PSC) culture have let researchers generate edited PSC lines to study a wide variety of biological questions. However, abnormalities in cell lines such as aneuploidy, mutations, on-target and off-target editing errors, and microbial contamination can arise during PSC culture or due to undesired editing outcomes. The ongoing decline of next-generation sequencing prices has made whole-genome sequencing (WGS) a promising option for detecting these abnormalities. However, this approach has been held back by a lack of easily usable data analysis software. Here, we present SeqVerify, a computational pipeline designed to take raw WGS data and a list of intended genome edits, and verify that the edits are present and that there are no abnormalities. We anticipate that SeqVerify will be a useful tool for researchers generating edited PSCs, and more broadly, for cell line quality control in general.
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Affiliation(s)
| | - Valerio Pepe
- Wyss Institute at Harvard University, Boston MA, USA
| | - Steven Lubbe
- The Ken & Ruth Davee Department of Neurology and Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Simpson Querrey Center of Neurogenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology and Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - George M Church
- Wyss Institute at Harvard University, Boston MA, USA; Department of Genetics, Harvard Medical School, Harvard University, Cambridge, MA, USA.
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5
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Al Delbany D, Ghosh MS, Krivec N, Huyghebaert A, Regin M, Duong MC, Lei Y, Sermon K, Olsen C, Spits C. De Novo Cancer Mutations Frequently Associate with Recurrent Chromosomal Abnormalities during Long-Term Human Pluripotent Stem Cell Culture. Cells 2024; 13:1395. [PMID: 39195283 DOI: 10.3390/cells13161395] [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: 07/04/2024] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 08/29/2024] Open
Abstract
Human pluripotent stem cells (hPSCs) are pivotal in regenerative medicine, yet their in vitro expansion often leads to genetic abnormalities, raising concerns about their safety in clinical applications. This study analyzed ten human embryonic stem cell lines across multiple passages to elucidate the dynamics of chromosomal abnormalities and single-nucleotide variants (SNVs) in 380 cancer-related genes. Prolonged in vitro culture resulted in 80% of the lines acquiring gains of chromosome 20q or 1q, both known for conferring an in vitro growth advantage. 70% of lines also acquired other copy number variants (CNVs) outside the recurrent set. Additionally, we detected 122 SNVs in 88 genes, with all lines acquiring at least one de novo SNV during culture. Our findings showed higher loads of both CNVs and SNVs at later passages, which were due to the cumulative acquisition of mutations over a longer time in culture, and not to an increased rate of mutagenesis over time. Importantly, we observed that SNVs and rare CNVs followed the acquisition of chromosomal gains in 1q and 20q, while most of the low-passage and genetically balanced samples were devoid of cancer-associated mutations. This suggests that recurrent chromosomal abnormalities are potential drivers for the acquisition of other mutations.
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Affiliation(s)
- Diana Al Delbany
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | - Manjusha S Ghosh
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | - Nuša Krivec
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | - Anfien Huyghebaert
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | - Marius Regin
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | - Mai Chi Duong
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
- Department of Biochemistry, Military Hospital 175, 786 Nguyen Kiem Street, Ho Chi Minh City 71409, Vietnam
| | - Yingnan Lei
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | - Karen Sermon
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
| | - Catharina Olsen
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
- Brussels Interuniversity Genomics High Throughput Core (BRIGHTcore), Vrije Universiteit Brussel (VUB)-Université Libre de Bruxelles (ULB), Laarbeeklaan 101, 1090 Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles (ULB)-Vrije Universiteit Brussel (VUB), La Plaine Campus Triomflaan, 1050 Brussels, Belgium
| | - Claudia Spits
- Research Group Genetics, Reproduction and Development, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Jette, Belgium
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6
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Li Y, Xu M, Chen J, Huang J, Cao J, Chen H, Zhang J, Luo Y, Wang Y, Sun J. Ameliorating and refining islet organoids to illuminate treatment and pathogenesis of diabetes mellitus. Stem Cell Res Ther 2024; 15:188. [PMID: 38937834 PMCID: PMC11210168 DOI: 10.1186/s13287-024-03780-7] [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: 04/02/2024] [Accepted: 06/01/2024] [Indexed: 06/29/2024] Open
Abstract
Diabetes mellitus, a significant global public health challenge, severely impacts human health worldwide. The organoid, an innovative in vitro three-dimensional (3D) culture model, closely mimics tissues or organs in vivo. Insulin-secreting islet organoid, derived from stem cells induced in vitro with 3D structures, has emerged as a potential alternative for islet transplantation and as a possible disease model that mirrors the human body's in vivo environment, eliminating species difference. This technology has gained considerable attention for its potential in diabetes treatment. Despite advances, the process of stem cell differentiation into islet organoid and its cultivation demonstrates deficiencies, prompting ongoing efforts to develop more efficient differentiation protocols and 3D biomimetic materials. At present, the constructed islet organoid exhibit limitations in their composition, structure, and functionality when compared to natural islets. Consequently, further research is imperative to achieve a multi-tissue system composition and improved insulin secretion functionality in islet organoid, while addressing transplantation-related safety concerns, such as tumorigenicity, immune rejection, infection, and thrombosis. This review delves into the methodologies and strategies for constructing the islet organoid, its application in diabetes treatment, and the pivotal scientific challenges within organoid research, offering fresh perspectives for a deeper understanding of diabetes pathogenesis and the development of therapeutic interventions.
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Affiliation(s)
- Yushan Li
- Department of Endocrinology, Zhujiang Hospital, The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Meiqi Xu
- Department of Biomedical Engineering, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Jiali Chen
- Department of Endocrinology, Zhujiang Hospital, The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jiansong Huang
- Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jiaying Cao
- Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Huajing Chen
- Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jiayi Zhang
- Nanfang Hospital, The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yukun Luo
- Department of Endocrinology, Zhujiang Hospital, The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Yazhuo Wang
- Tsinghua-Peking Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing, China.
| | - Jia Sun
- Department of Endocrinology, Zhujiang Hospital, The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.
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7
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Badja C, Momen S, Koh GCC, Boushaki S, Roumeliotis TI, Kozik Z, Jones I, Bousgouni V, Dias JML, Krokidis MG, Young J, Chen H, Yang M, Docquier F, Memari Y, Valcarcel-Zimenez L, Gupta K, Kong LR, Fawcett H, Robert F, Zhao S, Degasperi A, Kumar Y, Davies H, Harris R, Frezza C, Chatgilialoglu C, Sarkany R, Lehmann A, Bakal C, Choudhary J, Fassihi H, Nik-Zainal S. Insights from multi-omic modeling of neurodegeneration in xeroderma pigmentosum using an induced pluripotent stem cell system. Cell Rep 2024; 43:114243. [PMID: 38805398 DOI: 10.1016/j.celrep.2024.114243] [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: 07/27/2023] [Revised: 04/27/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024] Open
Abstract
Xeroderma pigmentosum (XP) is caused by defective nucleotide excision repair of DNA damage. This results in hypersensitivity to ultraviolet light and increased skin cancer risk, as sunlight-induced photoproducts remain unrepaired. However, many XP patients also display early-onset neurodegeneration, which leads to premature death. The mechanism of neurodegeneration is unknown. Here, we investigate XP neurodegeneration using pluripotent stem cells derived from XP patients and healthy relatives, performing functional multi-omics on samples during neuronal differentiation. We show substantially increased levels of 5',8-cyclopurine and 8-oxopurine in XP neuronal DNA secondary to marked oxidative stress. Furthermore, we find that the endoplasmic reticulum stress response is upregulated and reversal of the mutant genotype is associated with phenotypic rescue. Critically, XP neurons exhibit inappropriate downregulation of the protein clearance ubiquitin-proteasome system (UPS). Chemical enhancement of UPS activity in XP neuronal models improves phenotypes, albeit inadequately. Although more work is required, this study presents insights with intervention potential.
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Affiliation(s)
- Cherif Badja
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK.
| | - Sophie Momen
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Gene Ching Chiek Koh
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Soraya Boushaki
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Theodoros I Roumeliotis
- Functional Proteomics Group, Institute of Cancer Research, Chester Betty Labs, 237 Fulham Road, London SW3 6JB, UK
| | - Zuza Kozik
- Functional Proteomics Group, Institute of Cancer Research, Chester Betty Labs, 237 Fulham Road, London SW3 6JB, UK
| | - Ian Jones
- Dynamical Cell Systems Laboratory, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Vicky Bousgouni
- Dynamical Cell Systems Laboratory, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - João M L Dias
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Marios G Krokidis
- Institute of Nanoscience and Nanotechnology, N.C.S.R. "Demokritos", Agia Paraskevi Attikis, 15310 Athens, Greece; Bioinformatics and Human Electrophysiology Laboratory, Department of Informatics, Ionian University, 49100 Corfu, Greece
| | - Jamie Young
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Hongwei Chen
- Wellcome Sanger Institute, Hinxton CB10 1RQ, UK; Department of Rheumatology and Immunology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Ming Yang
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK; CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - France Docquier
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK
| | - Yasin Memari
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Lorea Valcarcel-Zimenez
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK; CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Komal Gupta
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Li Ren Kong
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK; NUS Centre for Cancer Research, N2CR, Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore; Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Heather Fawcett
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Florian Robert
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Salome Zhao
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Andrea Degasperi
- Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Yogesh Kumar
- Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Helen Davies
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK
| | - Rebecca Harris
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK
| | - Christian Frezza
- Medical Research Council Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK; CECAD Research Center, Faculty of Medicine, University Hospital Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Chryssostomos Chatgilialoglu
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy; Center for Advanced Technologies, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Robert Sarkany
- National Xeroderma Pigmentosum Service, St John's Institute of Dermatology, Guy's and St Thomas' Foundation Trust, London SE1 7EH, UK
| | - Alan Lehmann
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Chris Bakal
- Dynamical Cell Systems Laboratory, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Jyoti Choudhary
- Functional Proteomics Group, Institute of Cancer Research, Chester Betty Labs, 237 Fulham Road, London SW3 6JB, UK
| | - Hiva Fassihi
- National Xeroderma Pigmentosum Service, St John's Institute of Dermatology, Guy's and St Thomas' Foundation Trust, London SE1 7EH, UK
| | - Serena Nik-Zainal
- Department of Medical Genetics, Box 238, Level 6, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0QQ, UK; Early Cancer Institute, Department of Oncology, Box 197, Hutchison Research Centre, Cambridge Biomedical Research Campus, Cambridge CB2 0XZ, UK.
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8
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Gregor A, Zweier C. Modelling phenotypes, variants and pathomechanisms of syndromic diseases in different systems. MED GENET-BERLIN 2024; 36:121-131. [PMID: 38854643 PMCID: PMC11154186 DOI: 10.1515/medgen-2024-2020] [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] [Indexed: 06/11/2024]
Abstract
In this review we describe different model organisms and systems that are commonly used to study syndromic disorders. Different use cases in modeling diseases, underlying pathomechanisms and specific effects of certain variants are elucidated. We also highlight advantages and limitations of different systems. Models discussed include budding yeast, the nematode worm, the fruit fly, the frog, zebrafish, mice and human cell-based systems.
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Affiliation(s)
- Anne Gregor
- University of BernDepartment of Human GeneticsInselspital Bern3010BernSwitzerland
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9
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Bogomiakova ME, Bogomazova AN, Lagarkova MA. Dysregulation of Immune Tolerance to Autologous iPSCs and Their Differentiated Derivatives. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:799-816. [PMID: 38880643 DOI: 10.1134/s0006297924050031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/21/2023] [Accepted: 02/13/2024] [Indexed: 06/18/2024]
Abstract
Induced pluripotent stem cells (iPSCs), capable of differentiating into any cell type, are a promising tool for solving the problem of donor organ shortage. In addition, reprogramming technology makes it possible to obtain a personalized, i.e., patient-specific, cell product transplantation of which should not cause problems related to histocompatibility of the transplanted tissues and organs. At the same time, inconsistent information about the main advantage of autologous iPSC-derivatives - lack of immunogenicity - still casts doubt on the possibility of using such cells beyond immunosuppressive therapy protocols. This review is devoted to immunogenic properties of the syngeneic and autologous iPSCs and their derivatives, as well as to the reasons for dysregulation of their immune tolerance.
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Affiliation(s)
- Margarita E Bogomiakova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, 119435, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Alexandra N Bogomazova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, 119435, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Maria A Lagarkova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, 119435, Russia
- Lomonosov Moscow State University, Moscow, 119991, Russia
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10
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Cerneckis J, Cai H, Shi Y. Induced pluripotent stem cells (iPSCs): molecular mechanisms of induction and applications. Signal Transduct Target Ther 2024; 9:112. [PMID: 38670977 PMCID: PMC11053163 DOI: 10.1038/s41392-024-01809-0] [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: 07/28/2023] [Revised: 03/09/2024] [Accepted: 03/17/2024] [Indexed: 04/28/2024] Open
Abstract
The induced pluripotent stem cell (iPSC) technology has transformed in vitro research and holds great promise to advance regenerative medicine. iPSCs have the capacity for an almost unlimited expansion, are amenable to genetic engineering, and can be differentiated into most somatic cell types. iPSCs have been widely applied to model human development and diseases, perform drug screening, and develop cell therapies. In this review, we outline key developments in the iPSC field and highlight the immense versatility of the iPSC technology for in vitro modeling and therapeutic applications. We begin by discussing the pivotal discoveries that revealed the potential of a somatic cell nucleus for reprogramming and led to successful generation of iPSCs. We consider the molecular mechanisms and dynamics of somatic cell reprogramming as well as the numerous methods available to induce pluripotency. Subsequently, we discuss various iPSC-based cellular models, from mono-cultures of a single cell type to complex three-dimensional organoids, and how these models can be applied to elucidate the mechanisms of human development and diseases. We use examples of neurological disorders, coronavirus disease 2019 (COVID-19), and cancer to highlight the diversity of disease-specific phenotypes that can be modeled using iPSC-derived cells. We also consider how iPSC-derived cellular models can be used in high-throughput drug screening and drug toxicity studies. Finally, we discuss the process of developing autologous and allogeneic iPSC-based cell therapies and their potential to alleviate human diseases.
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Affiliation(s)
- Jonas Cerneckis
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Hongxia Cai
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Yanhong Shi
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
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11
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Yücel AD, Gladyshev VN. The long and winding road of reprogramming-induced rejuvenation. Nat Commun 2024; 15:1941. [PMID: 38431638 PMCID: PMC10908844 DOI: 10.1038/s41467-024-46020-5] [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: 07/22/2023] [Accepted: 02/12/2024] [Indexed: 03/05/2024] Open
Abstract
Organismal aging is inherently connected to the aging of its constituent cells and systems. Reducing the biological age of the organism may be assisted by reducing the age of its cells - an approach exemplified by partial cell reprogramming through the expression of Yamanaka factors or exposure to chemical cocktails. It is crucial to protect cell type identity during partial reprogramming, as cells need to retain or rapidly regain their functions following the treatment. Another critical issue is the ability to quantify biological age as reprogrammed older cells acquire younger states. We discuss recent advances in reprogramming-induced rejuvenation and offer a critical review of this procedure and its relationship to the fundamental nature of aging. We further comparatively analyze partial reprogramming, full reprogramming and transdifferentiation approaches, assess safety concerns and emphasize the importance of distinguishing rejuvenation from dedifferentiation. Finally, we highlight translational opportunities that the reprogramming-induced rejuvenation approach offers.
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Affiliation(s)
- Ali Doğa Yücel
- Department of Molecular Biology and Genetics, Koc University, Istanbul, 34450, Turkey
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Vadim N Gladyshev
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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12
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Lezmi E, Jung J, Benvenisty N. High prevalence of acquired cancer-related mutations in 146 human pluripotent stem cell lines and their differentiated derivatives. Nat Biotechnol 2024:10.1038/s41587-023-02090-2. [PMID: 38195986 DOI: 10.1038/s41587-023-02090-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 12/05/2023] [Indexed: 01/11/2024]
Abstract
To survey cancer-related mutations in human pluripotent stem cells and their derivatives, we analyzed >2,200 transcriptomes from 146 independent lines in the NCBI's Sequence Read Archive. Twenty-two per cent of samples had at least one cancer-related mutation; of these, 64% had TP53 mutations, which conferred a pronounced selective advantage, perturbed target gene expression and altered cellular differentiation. These findings underscore the need for robust surveillance of cancer-related mutations in pluripotent cells, especially in clinical applications.
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Affiliation(s)
- Elyad Lezmi
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Jonathan Jung
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Nissim Benvenisty
- Department of Genetics, The Azrieli Center for Stem Cells and Genetic Research, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel.
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13
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Kuebler B, Alvarez-Palomo B, Aran B, Castaño J, Rodriguez L, Raya A, Querol Giner S, Veiga A. Generation of a bank of clinical-grade, HLA-homozygous iPSC lines with high coverage of the Spanish population. Stem Cell Res Ther 2023; 14:366. [PMID: 38093328 PMCID: PMC10720139 DOI: 10.1186/s13287-023-03576-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Induced pluripotent stem cell (iPSC)-derived cell therapies are an interesting new area in the field of regenerative medicine. One of the approaches to decrease the costs of iPSC-derived therapies is the use of allogenic homozygous human leukocyte antigen (HLA)-matched donors to generate iPSC lines and to build a clinical-grade iPSC bank covering a high percentage of the Spanish population. METHODS The Spanish Stem Cell Transplantation Registry was screened for cord blood units (CBUs) homozygous for the most common HLA-A, HLA-B and HLA-DRB1 haplotypes. Seven donors were selected with haplotypes covering 21.37% of the haplotypes of the Spanish population. CD34-positive hematopoietic progenitors were isolated from the mononuclear cell fraction of frozen cord blood units from each donor by density gradient centrifugation and further by immune magnetic labeling and separation using purification columns. Purified CD34 + cells were reprogrammed to iPSCs by transduction with the CTS CytoTune-iPS 2.1 Sendai Reprogramming Kit. RESULTS The iPSCs generated from the 7 donors were expanded, characterized, banked and registered. Master cell banks (MCBs) and working cell banks (WCBs) from the iPSCs of each donor were produced under GMP conditions in qualified clean rooms. CONCLUSIONS Here, we present the first clinical-grade, iPSC haplobank in Spain made from CD34 + cells from seven cord blood units homozygous for the most common HLA-A, HLA-B and HLA-DRB1 haplotypes within the Spanish population. We describe their generation by transduction with Sendai viral vectors and their GMP-compliant expansion and banking. These haplolines will constitute starting materials for advanced therapy medicinal product development (ATMP).
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Affiliation(s)
- B Kuebler
- Pluripotent Stem Cell Group, Regenerative Medicine Program, Institut d'Investigació Biomédica de Bellvitge (IDIBELL), Hospital Duran I Reynals, Gran Via de L'Hospitalet, 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Program for Translation of Regenerative Medicine in Catalonia (P-[CMRC]), Hospital Duran I Reynals, Gran Via de L'Hospitalet, 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - B Alvarez-Palomo
- Advanced and Cell Therapy Service, Banc de Sang I Teixits, Edifici Dr. Frederic Duran I Jordà, Passeig de Taulat, 106-116, 08005, Barcelona, Spain
| | - B Aran
- Pluripotent Stem Cell Group, Regenerative Medicine Program, Institut d'Investigació Biomédica de Bellvitge (IDIBELL), Hospital Duran I Reynals, Gran Via de L'Hospitalet, 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Program for Translation of Regenerative Medicine in Catalonia (P-[CMRC]), Hospital Duran I Reynals, Gran Via de L'Hospitalet, 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - J Castaño
- Advanced and Cell Therapy Service, Banc de Sang I Teixits, Edifici Dr. Frederic Duran I Jordà, Passeig de Taulat, 106-116, 08005, Barcelona, Spain
- Advanced Therapy Platform, Hospital Sant Joan de Déu de Barcelona, Pg. de Sant Joan de Déu, 2, Espluges de Llobregat, 08950, Barcelona, Spain
| | - L Rodriguez
- Advanced and Cell Therapy Service, Banc de Sang I Teixits, Edifici Dr. Frederic Duran I Jordà, Passeig de Taulat, 106-116, 08005, Barcelona, Spain
| | - A Raya
- Program for Translation of Regenerative Medicine in Catalonia (P-[CMRC]), Hospital Duran I Reynals, Gran Via de L'Hospitalet, 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain.
- Stem Cell Potency Group, Regenerative Medicine Program, Institut d´Investigació Biomédica de Bellvitge (IDIBELL), Hospital Duran I Reynals, Gran Via de L'Hospitalet, 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain.
- Centre for Networked Biomedical Research On Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain.
- Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain.
| | - S Querol Giner
- Advanced and Cell Therapy Service, Banc de Sang I Teixits, Edifici Dr. Frederic Duran I Jordà, Passeig de Taulat, 106-116, 08005, Barcelona, Spain.
- Transfusional Medicine Group, Vall d'Hebron Research Institute, Autonomous University of Barcelona (UAB), Barcelona, Spain.
| | - A Veiga
- Pluripotent Stem Cell Group, Regenerative Medicine Program, Institut d'Investigació Biomédica de Bellvitge (IDIBELL), Hospital Duran I Reynals, Gran Via de L'Hospitalet, 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain.
- Program for Translation of Regenerative Medicine in Catalonia (P-[CMRC]), Hospital Duran I Reynals, Gran Via de L'Hospitalet, 199-203, L'Hospitalet de Llobregat, 08908, Barcelona, Spain.
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14
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Nath SC, Menendez L, Friedrich Ben-Nun I. Overcoming the Variability of iPSCs in the Manufacturing of Cell-Based Therapies. Int J Mol Sci 2023; 24:16929. [PMID: 38069252 PMCID: PMC10706975 DOI: 10.3390/ijms242316929] [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: 11/09/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Various factors are known to contribute to the diversity of human induced pluripotent stem cells (hiPSCs). Among these are the donor's genetic background and family history, the somatic cell source, the iPSC reprogramming method, and the culture system of choice. Moreover, variability is seen even in iPSC clones, generated in a single reprogramming event, where the donor, somatic cell type, and reprogramming platform are the same. The diversity seen in iPSC lines often translates to epigenetic differences, as well as to differences in the expansion rate, iPSC line culture robustness, and their ability to differentiate into specific cell types. As such, the diversity of iPSCs presents a hurdle to standardizing iPSC-based cell therapy manufacturing. In this review, we will expand on the various factors that impact iPSC diversity and the strategies and tools that could be taken by the industry to overcome the differences amongst various iPSC lines, therefore enabling robust and reproducible iPSC-based cell therapy manufacturing processes.
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Affiliation(s)
- Suman C. Nath
- Cell Therapy Process Department, Lonza Inc., Houston, TX 77047, USA; (S.C.N.); (L.M.)
| | - Laura Menendez
- Cell Therapy Process Department, Lonza Inc., Houston, TX 77047, USA; (S.C.N.); (L.M.)
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15
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Margolis EA, Friend NE, Rolle MW, Alsberg E, Putnam AJ. Manufacturing the multiscale vascular hierarchy: progress toward solving the grand challenge of tissue engineering. Trends Biotechnol 2023; 41:1400-1416. [PMID: 37169690 PMCID: PMC10593098 DOI: 10.1016/j.tibtech.2023.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/05/2023] [Accepted: 04/14/2023] [Indexed: 05/13/2023]
Abstract
In human vascular anatomy, blood flows from the heart to organs and tissues through a hierarchical vascular tree, comprising large arteries that branch into arterioles and further into capillaries, where gas and nutrient exchange occur. Engineering a complete, integrated vascular hierarchy with vessels large enough to suture, strong enough to withstand hemodynamic forces, and a branching structure to permit immediate perfusion of a fluidic circuit across scales would be transformative for regenerative medicine (RM), enabling the translation of engineered tissues of clinically relevant size, and perhaps whole organs. How close are we to solving this biological plumbing problem? In this review, we highlight advances in engineered vasculature at individual scales and focus on recent strategies to integrate across scales.
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Affiliation(s)
- Emily A Margolis
- University of Michigan, Department of Biomedical Engineering, Ann Arbor, MI, USA
| | - Nicole E Friend
- University of Michigan, Department of Biomedical Engineering, Ann Arbor, MI, USA
| | - Marsha W Rolle
- Worcester Polytechnic Institute, Department of Biomedical Engineering, Worcester, MA, USA
| | - Eben Alsberg
- University of Illinois at Chicago, Department of Biomedical Engineering, Chicago, IL, USA
| | - Andrew J Putnam
- University of Michigan, Department of Biomedical Engineering, Ann Arbor, MI, USA.
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16
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Smela MP, Pepe V, Church GM. SeqVerify: An accessible analysis tool for cell line genomic integrity, contamination, and gene editing outcomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559766. [PMID: 37829615 PMCID: PMC10565884 DOI: 10.1101/2023.09.27.559766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
1Over the last decade, advances in genome editing and pluripotent stem cell (PSC) culture have let researchers generate edited PSC lines to study a wide variety of biological questions. However, abnormalities in cell lines such as aneuploidy, on-target and off-target editing errors, and microbial contamination can arise during PSC culture or due to undesired editing outcomes. Any of these abnormalities can invalidate experiments, so detecting them is crucial. The ongoing decline of next-generation sequencing prices has made whole genome sequencing (WGS) an effective quality control option, since WGS can detect any abnormality involving changes to DNA sequences or presence of unwanted sequences. However, this approach has suffered from a lack of easily usable data analysis software. Here, we present SeqVerify, a computational pipeline designed to take raw WGS data and a list of intended edits, and verify that the edits are present and that there are no abnormalities. We anticipate that SeqVerify will be a useful tool for researchers generating edited PSCs, and more broadly, for cell line quality control in general.
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Affiliation(s)
- Merrick Pierson Smela
- Wyss Institute at Harvard University, Cambridge, Massachusetts, United States of America
- Equal contributions
| | - Valerio Pepe
- Wyss Institute at Harvard University, Cambridge, Massachusetts, United States of America
- Equal contributions
| | - George M. Church
- Wyss Institute at Harvard University, Cambridge, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Harvard University, Cambridge, Massachusetts, United States of America
- Lead contact
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Wen W, Chen X, Shen XY, Li HY, Zhang F, Fang FQ, Zhang XB. Enhancing cord blood stem cell-derived NK cell growth and differentiation through hyperosmosis. Stem Cell Res Ther 2023; 14:295. [PMID: 37840146 PMCID: PMC10578005 DOI: 10.1186/s13287-023-03461-x] [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: 07/25/2023] [Accepted: 08/21/2023] [Indexed: 10/17/2023] Open
Abstract
BACKGROUND Natural killer (NK) cells hold great promise in treating diverse hematopoietic and solid tumors. Despite their availability from peripheral blood and cord blood, stem cell-derived NK cells offer an 'off-the-shelf' solution. Hematopoietic stem and progenitor cells (HSPCs) derived from cord blood pose no risk to the newborn or mother and are virtually ideal sources for NK cell differentiation. METHODS We developed a modified protocol to differentiate HSPCs to NK cells under serum-free conditions using defined factors. The HSPC-derived NK (HSC-NK) cells could be expanded in a K562 feeder cell-dependent manner. Furthermore, using lentivirus transduction, chimeric antigen receptor (CAR)-modified HSPCs could be differentiated into NK cells, leading to the establishment of CAR-NK cells. RESULTS The efficiency of NK cell differentiation from HSPCs was increased through the simple modulation of osmotic pressure by the addition of sodium chloride or glucose. Furthermore, the hyperosmosis-primed HSC-NK cells exhibited enhanced proliferation capacity and maintained normal functional characteristics, including transcriptome and antitumor efficacy. The optimized protocol yielded approximately 1.8 million NK cells from a single CD34-positive cell within a 28-day cycle, which signifies more than a ten-fold increase in efficiency relative to the conventional methods. This optimized protocol was also suitable for generating CAR-NK cells with high yields compared to standard conditions. CONCLUSIONS The results of this study establish high osmotic pressure as a simple yet powerful adjustment that significantly enhances the efficiency and functionality of HSC-NK cells, including CAR-NK cells. This optimized protocol could lead to cost-effective, high-yield NK cell therapies, potentially revolutionizing cancer immunotherapy strategies.
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Affiliation(s)
- Wei Wen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Xiang Chen
- Department of Oncology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xin-Yi Shen
- College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, China
| | - Hua-Yu Li
- College of Computer Science and Technology, China University of Petroleum (East China), Qingdao, China
| | - Feng Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Feng-Qi Fang
- Department of Oncology, The First Affiliated Hospital of Dalian Medical University, Dalian, China.
| | - Xiao-Bing Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.
- Tianjin Institutes of Health Science, Tianjin, China.
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18
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Zhang H, Jin ZB. A rational consideration of the genomic instability of human-induced pluripotent stem cells for clinical applications. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2198-2200. [PMID: 37296348 DOI: 10.1007/s11427-023-2354-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/24/2023] [Indexed: 06/12/2023]
Affiliation(s)
- Hang Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China.
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19
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Abe Y, Sato Y, Tanaka M, Ochiai D. Development of a new treatment for preterm birth complications using amniotic fluid stem cell therapy. Histol Histopathol 2023; 38:965-974. [PMID: 36971371 DOI: 10.14670/hh-18-607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
This paper describes the current status of studies and clinical trials on the use of mesenchymal stem cells (MSCs) and amniotic fluid stem cells (AFSCs) for complications of preterm birth (PTB), an urgent issue in the perinatal field. PTB is a serious challenge in clinical medicine that is increasing globally, and effective control of its complications is necessary for newborns' subsequent long life. Classical treatments are inadequate, and many patients have PTB complications. A growing body of evidence provided by translational medicine and others indicates that MSCs, and among them, the readily available AFSCs, may be useful in treating PTB complications. AFSCs are the only MSCs available prenatally and are known to be highly anti-inflammatory and tissue-protective and do not form tumors when transplanted. Furthermore, because they are derived from the amniotic fluid, a medical waste product, no ethical issues are involved. AFSCs are an ideal cell resource for MSC therapy in neonates. This paper targets the brain, lungs, and intestines, which are the vital organs most likely to be damaged by PTB complications. The evidence to date and future prospects with MSCs and AFSCs for these organs are described.
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Affiliation(s)
- Yushi Abe
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Yu Sato
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Mamoru Tanaka
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Daigo Ochiai
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
- Department of Obstetrics and Gynecology, Kitasato University School of Medicine, Kanagawa, Japan.
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Yurchenko AA, Fresneau B, Borghese B, Rajabi F, Tata Z, Genestie C, Sarasin A, Nikolaev SI. Early-onset gynecological tumors in DNA repair-deficient xeroderma pigmentosum group C patients: a case series. COMMUNICATIONS MEDICINE 2023; 3:109. [PMID: 37567969 PMCID: PMC10421935 DOI: 10.1038/s43856-023-00341-6] [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: 03/01/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND Xeroderma pigmentosum (XP) is a group of rare hereditary disorders with highly increased risk of skin tumors due to defective DNA repair. Recently we reported 34-fold increased risk of internal tumors in XP patients in comparison with general population. The molecular data and clinical practice on the internal tumors treatment in XP patients is limited and scarcely represented in the medical literature. In this work, we describe young patients with constitutive biallelic deactivation of the XPC gene developing gynecological tumors with somatic DICER1 mutations. METHODS Whole genome sequencing was used to analyze in detail somatic mutational landscape and driver events of these rare tumors. RESULTS We describe five early-onset gynecological tumors in four xeroderma pigmentosum group C (XP-C) young patients (11 to 19 years old) including vaginal embryonal rhabdomyosarcomas in monozygotic twin sisters, juvenile granulosa-cell tumor of the ovary and poorly differentiated stage IA Sertoli-Leydig cell tumor in 19-years old patient, and FIGO stage IC1 tumor of ovary in 13-years old patient. XP-C ovarian tumors harbor 4.4 times more single base substitutions than sporadic tissue-matched cancers and demonstrate XP-C specific mutation signature with strong transcriptional bias indicating inability of the cells to repair bulky DNA lesions of unknown etiology. A special mode of treatment was applied to avoid usage of chemotherapy which is toxic for XP patients. CONCLUSIONS XP-C status should be accounted for prevention and specific treatment of gynecological tumors in young DNA repair-deficient XP patients.
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Affiliation(s)
- Andrey A Yurchenko
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Brice Fresneau
- Department of Children and Adolescents Oncology, Gustave Roussy, Villejuif, France
- Université Paris-Saclay, UVSQ, Inserm, CESP, Villejuif, France
| | - Bruno Borghese
- Centre de Recherche des Cordeliers, « Equipe labélisée Ligue Contre le Cancer », CNRS SNC 5096, Sorbonne Université, Université de Paris Cité, INSERM, Paris, France
- Université de Paris Cité, Paris, France
- Institut du Cancer Paris CARPEM, AP-HP, APHP Centre, Department of Gynecological Surgery, Hôpital Cochin, Paris, France
| | - Fatemeh Rajabi
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
| | - Zora Tata
- Liberal Endocrinologist, Algiers, Algeria
| | | | - Alain Sarasin
- CNRS UMR9019 Genome Integrity and Cancers, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Sergey I Nikolaev
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France.
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21
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Barker RA, Carpenter M, Jamieson CHM, Murry CE, Pellegrini G, Rao RC, Song J. Lessons learnt, and still to learn, in first in human stem cell trials. Stem Cell Reports 2023; 18:1599-1609. [PMID: 36563687 PMCID: PMC10444539 DOI: 10.1016/j.stemcr.2022.11.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Developing cellular therapies is not straightforward. This Perspective summarizes the experience of a group of academic stem cell investigators working in different clinical areas and aims to share insight into what we wished we knew before starting. These include (1) choosing the stem cell line and assessing the genome of both the starting and final product, (2) familiarity with GMP manufacturing, reagent validation, and supply chain management, (3) product delivery issues and the additional regulatory challenges, (4) the relationship between clinical trial design and preclinical studies, and (5) the market approval requirements, pathways, and partnerships needed.
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Affiliation(s)
- Roger A Barker
- Department of Clinical Neuroscience and Wellcome-MRC Cambridge Stem Institute, John van Geest Centre for Brain Repair, Forvie Site, Robinson Way, Cambridge CB2 0QQ, UK.
| | | | - Catriona H M Jamieson
- Division of Regenerative Medicine, Department of Medicine, Sanford Stem Cell Clinical Center, University of California San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive #0695, La Jolla, CA 92037-0695, USA
| | - Charles E Murry
- Institute for Stem Cell and Regenerative Medicine, Center for Cardiovascular Biology; Departments of Laboratory Medicine & Pathology, Bioengineering, and Medicine/Cardiology, University of Washington, Seattle, WA 98109, USA; Sana Biotechnology, Seattle, WA 98102, USA
| | - Graziella Pellegrini
- Centre for Regenerative Medicine, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Rajesh C Rao
- Departments of Ophthalmology & Visual Sciences, Pathology, and Human Genetics, University of Michigan, Surgery Service, VA Ann Arbor Health System, Ann Arbor, MI 48105, USA
| | - Jihwan Song
- Jihwan Song, Department of Biomedical Science, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13488, Republic of Korea; iPS Bio, Inc., 16 Daewangpangyo-ro 712 Beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do 13488, Republic of Korea
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22
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Benarroch L, Madsen-Østerbye J, Abdelhalim M, Mamchaoui K, Ohana J, Bigot A, Mouly V, Bonne G, Bertrand AT, Collas P. Cellular and Genomic Features of Muscle Differentiation from Isogenic Fibroblasts and Myoblasts. Cells 2023; 12:1995. [PMID: 37566074 PMCID: PMC10417614 DOI: 10.3390/cells12151995] [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: 06/30/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
The ability to recapitulate muscle differentiation in vitro enables the exploration of mechanisms underlying myogenesis and muscle diseases. However, obtaining myoblasts from patients with neuromuscular diseases or from healthy subjects poses ethical and procedural challenges that limit such investigations. An alternative consists in converting skin fibroblasts into myogenic cells by forcing the expression of the myogenic regulator MYOD. Here, we directly compared cellular phenotype, transcriptome, and nuclear lamina-associated domains (LADs) in myo-converted human fibroblasts and myotubes differentiated from myoblasts. We used isogenic cells from a 16-year-old donor, ruling out, for the first time to our knowledge, genetic factors as a source of variations between the two myogenic models. We show that myo-conversion of fibroblasts upregulates genes controlling myogenic pathways leading to multinucleated cells expressing muscle cell markers. However, myotubes are more advanced in myogenesis than myo-converted fibroblasts at the phenotypic and transcriptomic levels. While most LADs are shared between the two cell types, each also displays unique domains of lamin A/C interactions. Furthermore, myotube-specific LADs are more gene-rich and less heterochromatic than shared LADs or LADs unique to myo-converted fibroblasts, and they uniquely sequester developmental genes. Thus, myo-converted fibroblasts and myotubes retain cell type-specific features of radial and functional genome organization. Our results favor a view of myo-converted fibroblasts as a practical model to investigate the phenotypic and genomic properties of muscle cell differentiation in normal and pathological contexts, but also highlight current limitations in using fibroblasts as a source of myogenic cells.
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Affiliation(s)
- Louise Benarroch
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Julia Madsen-Østerbye
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (J.M.-Ø.); (M.A.)
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0372 Oslo, Norway
| | - Mohamed Abdelhalim
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (J.M.-Ø.); (M.A.)
| | - Kamel Mamchaoui
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Jessica Ohana
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Anne Bigot
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Vincent Mouly
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Gisèle Bonne
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Anne T. Bertrand
- Sorbonne Université, Inserm, Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France; (L.B.); (K.M.); (J.O.); (A.B.); (V.M.); (G.B.)
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway; (J.M.-Ø.); (M.A.)
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0372 Oslo, Norway
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23
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Jiang F, Wang L, Dong Y, Nie W, Zhou H, Gao J, Zheng P. DPPA5A suppresses the mutagenic TLS and MMEJ pathways by modulating the cryptic splicing of Rev1 and Polq in mouse embryonic stem cells. Proc Natl Acad Sci U S A 2023; 120:e2305187120. [PMID: 37459543 PMCID: PMC10372678 DOI: 10.1073/pnas.2305187120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/13/2023] [Indexed: 07/20/2023] Open
Abstract
Genetic alterations are often acquired during prolonged propagation of pluripotent stem cells (PSCs). This ruins the stem cell quality and hampers their full applications. Understanding how PSCs maintain genomic integrity would provide the clues to overcome the hurdle. It has been known that embryonic stem cells (ESCs) utilize high-fidelity pathways to ensure genomic stability, but the underlying mechanisms remain largely elusive. Here, we show that many DNA damage response and repair genes display differential alternative splicing in mouse ESCs compared to differentiated cells. Particularly, Rev1 and Polq, two key genes for mutagenic translesion DNA synthesis (TLS) and microhomology-mediated end joining (MMEJ) repair pathways, respectively, display a significantly higher rate of cryptic exon (CE) inclusion in ESCs. The frequent CE inclusion disrupts the normal protein expressions of REV1 and POLθ, thereby suppressing the mutagenic TLS and MMEJ. Further, we identify an ESC-specific RNA binding protein DPPA5A which stimulates the CE inclusion in Rev1 and Polq. Depletion of DPPA5A in mouse ESCs decreased the CE inclusion of Rev1 and Polq, induced the protein expression, and stimulated the TLS and MMEJ activity. Enforced expression of DPPA5A in NIH3T3 cells displayed reverse effects. Mechanistically, we found that DPPA5A directly regulated CE splicing of Rev1. DPPA5A associates with U2 small nuclear ribonucleoprotein of the spliceosome and binds to the GA-rich motif in the CE of Rev1 to promote CE inclusion. Thus, our study uncovers a mechanism to suppress mutagenic TLS and MMEJ pathways in ESCs.
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Affiliation(s)
- Fangjie Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- University of Chinese Academy of Sciences, Beijing101408, China
- Department of Reproductive Medicine, The Second Affiliated Hospital of Kunming Medical University,Kunming650101, China
| | - Lin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Yuping Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- University of Chinese Academy of Sciences, Beijing101408, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Wenhui Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Hu Zhou
- Department of Analytical Chemistry and Key Laboratory of Receptor Research of Chinese Academy of Sciences, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
| | - Jing Gao
- Department of Analytical Chemistry and Key Laboratory of Receptor Research of Chinese Academy of Sciences, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- The Chinese University of Hong Kong and Kunming Institute of Zoology Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
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24
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Gracia-Diaz C, Perdomo JE, Khan ME, Disanza B, Cajka GG, Lei S, Gagne A, Maguire JA, Roule T, Shalem O, Bhoj EJ, Ahrens-Nicklas RC, French D, Goldberg EM, Wang K, Glessner J, Akizu N. High density SNP array and reanalysis of genome sequencing uncovers CNVs associated with neurodevelopmental disorders in KOLF2.1J iPSCs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546614. [PMID: 37425875 PMCID: PMC10327134 DOI: 10.1101/2023.06.26.546614] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The KOLF2.1J iPSC line was recently proposed as a reference iPSC to promote the standardization of research studies in the stem cell field. Due to overall good performance differentiating to neural cell lineages, high gene editing efficiency, and absence of genetic variants associated to neurological disorders KOLF2.1J iPSC line was particularly recommended for neurodegenerative disease modeling. However, our work uncovers that KOLF2.1J hPSCs carry heterozygous small copy number variants (CNVs) that cause DTNBP1, JARID2 and ASTN2 haploinsufficiencies, all of which are associated with neurological disorders. We further determine that these CNVs arose in vitro over the course of KOLF2.1J iPSC generation from a healthy donor-derived KOLF2 iPSC line and affect the expression of DNTBP1, JARID2 and ASTN2 proteins in KOLF2.1J iPSCs and neural progenitors. Therefore, our study suggests that KOLF2.1J iPSCs carry genetic variants that may be deleterious for neural cell lineages. This data is essential for a careful interpretation of neural cell studies derived from KOLF2.1J iPSCs and highlights the need for a catalogue of iPSC lines that includes a comprehensive genome characterization analysis.
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Affiliation(s)
- Carolina Gracia-Diaz
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan E. Perdomo
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- School of Biomedical Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Munir E. Khan
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Brianna Disanza
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
| | - Gregory G. Cajka
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Sunyimeng Lei
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alyssa Gagne
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jean Ann Maguire
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas Roule
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ophir Shalem
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth J. Bhoj
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca C. Ahrens-Nicklas
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA, USA
| | - Deborah French
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ethan M. Goldberg
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Departmen of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph Glessner
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Naiara Akizu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Lead contact
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25
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Caballero M, Koren A. The landscape of somatic mutations in lymphoblastoid cell lines. CELL GENOMICS 2023; 3:100305. [PMID: 37388907 PMCID: PMC10300552 DOI: 10.1016/j.xgen.2023.100305] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/03/2023] [Accepted: 03/28/2023] [Indexed: 07/01/2023]
Abstract
Somatic mutations have important biological ramifications while exerting substantial rate, type, and genomic location heterogeneity. Yet, their sporadic occurrence makes them difficult to study at scale and across individuals. Lymphoblastoid cell lines (LCLs), a model system for human population and functional genomics, harbor large numbers of somatic mutations and have been extensively genotyped. By comparing 1,662 LCLs, we report that the mutational landscape of the genome varies across individuals in terms of the number of mutations, their genomic locations, and their spectra; this variation may itself be modulated by somatic trans-acting mutations. Mutations attributed to the translesion DNA polymerase η follow two different modes of formation, with one mode accounting for the hypermutability of the inactive X chromosome. Nonetheless, the distribution of mutations along the inactive X chromosome appears to follow an epigenetic memory of the active form.
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Affiliation(s)
- Madison Caballero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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26
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Hogrebe NJ, Ishahak M, Millman JR. Developments in stem cell-derived islet replacement therapy for treating type 1 diabetes. Cell Stem Cell 2023; 30:530-548. [PMID: 37146579 PMCID: PMC10167558 DOI: 10.1016/j.stem.2023.04.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/20/2023] [Accepted: 04/05/2023] [Indexed: 05/07/2023]
Abstract
The generation of islet-like endocrine clusters from human pluripotent stem cells (hPSCs) has the potential to provide an unlimited source of insulin-producing β cells for the treatment of diabetes. In order for this cell therapy to become widely adopted, highly functional and well-characterized stem cell-derived islets (SC-islets) need to be manufactured at scale. Furthermore, successful SC-islet replacement strategies should prevent significant cell loss immediately following transplantation and avoid long-term immune rejection. This review highlights the most recent advances in the generation and characterization of highly functional SC-islets as well as strategies to ensure graft viability and safety after transplantation.
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Affiliation(s)
- Nathaniel J Hogrebe
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO 63130, USA.
| | - Matthew Ishahak
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO 63130, USA
| | - Jeffrey R Millman
- Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, MSC 8127-057-08, 660 South Euclid Avenue, St. Louis, MO 63130, USA; Department of Biomedical Engineering, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA.
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27
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Yang C, Du XY, Luo W. Clinical application prospects and transformation value of dental follicle stem cells in oral and neurological diseases. World J Stem Cells 2023; 15:136-149. [PMID: 37181000 PMCID: PMC10173814 DOI: 10.4252/wjsc.v15.i4.136] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/18/2023] [Accepted: 03/21/2023] [Indexed: 04/26/2023] Open
Abstract
Since dental pulp stem cells (DPSCs) were first reported, six types of dental SCs (DSCs) have been isolated and identified. DSCs originating from the craniofacial neural crest exhibit dental-like tissue differentiation potential and neuro-ectodermal features. As a member of DSCs, dental follicle SCs (DFSCs) are the only cell type obtained at the early developing stage of the tooth prior to eruption. Dental follicle tissue has the distinct advantage of large tissue volume compared with other dental tissues, which is a prerequisite for obtaining a sufficient number of cells to meet the needs of clinical applications. Furthermore, DFSCs exhibit a significantly higher cell proliferation rate, higher colony-formation capacity, and more primitive and better anti-inflammatory effects than other DSCs. In this respect, DFSCs have the potential to be of great clinical significance and translational value in oral and neurological diseases, with natural advantages based on their origin. Lastly, cryopreservation preserves the biological properties of DFSCs and enables them to be used as off-shelf products for clinical applications. This review summarizes and comments on the properties, application potential, and clinical transformation value of DFSCs, thereby inspiring novel perspectives in the future treatment of oral and neurological diseases.
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Affiliation(s)
- Chao Yang
- Research and Development Department, Shenzhen Uni-medica Technology Co., Ltd, Shenzhen 518051, Guangdong Province, China
- Department of Stomatology, The People’s Hospital of Longhua, Shenzhen 518109, Guangdong Province, China
| | - Xin-Ya Du
- Department of Stomatology, The People’s Hospital of Longhua, Shenzhen 518109, Guangdong Province, China
| | - Wen Luo
- Department of Stomatology, The First Affiliated Hospital of Hainan Medical University, Haikou 570102, Hainan Province, China
- School of Stomatology, Hainan Medical University, Haikou 571199, Hainan Province, China
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28
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Puigdevall P, Jerber J, Danecek P, Castellano S, Kilpinen H. Somatic mutations alter the differentiation outcomes of iPSC-derived neurons. CELL GENOMICS 2023; 3:100280. [PMID: 37082143 PMCID: PMC10112289 DOI: 10.1016/j.xgen.2023.100280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 11/11/2022] [Accepted: 02/23/2023] [Indexed: 04/22/2023]
Abstract
The use of induced pluripotent stem cells (iPSC) as models for development and human disease has enabled the study of otherwise inaccessible tissues. A remaining challenge in developing reliable models is our limited understanding of the factors driving irregular differentiation of iPSCs, particularly the impact of acquired somatic mutations. We leveraged data from a pooled dopaminergic neuron differentiation experiment of 238 iPSC lines profiled with single-cell RNA and whole-exome sequencing to study how somatic mutations affect differentiation outcomes. We found that deleterious somatic mutations in key developmental genes, notably the BCOR gene, are strongly associated with failure in dopaminergic neuron differentiation and a larger proliferation rate in culture. We further identified broad differences in cell type composition between incorrectly and successfully differentiating lines, as well as significant changes in gene expression contributing to the inhibition of neurogenesis. Our work calls for caution in interpreting differentiation-related phenotypes in disease-modeling experiments.
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Affiliation(s)
- Pau Puigdevall
- UCL Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Haartmaninkatu 8, PO Box 63, Helsinki 00014, Finland
| | - Julie Jerber
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Sergi Castellano
- UCL Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
| | - Helena Kilpinen
- UCL Great Ormond Street Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Haartmaninkatu 8, PO Box 63, Helsinki 00014, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1, PO Box 65, Helsinki 00014, Finland
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29
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Chen J, Huang L, Yang Y, Xu W, Qin Q, Qin R, Liang X, Lai X, Huang X, Xie M, Chen L. Somatic Cell Reprogramming for Nervous System Diseases: Techniques, Mechanisms, Potential Applications, and Challenges. Brain Sci 2023; 13:brainsci13030524. [PMID: 36979334 PMCID: PMC10046178 DOI: 10.3390/brainsci13030524] [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: 02/04/2023] [Revised: 03/14/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Nervous system diseases present significant challenges to the neuroscience community due to ethical and practical constraints that limit access to appropriate research materials. Somatic cell reprogramming has been proposed as a novel way to obtain neurons. Various emerging techniques have been used to reprogram mature and differentiated cells into neurons. This review provides an overview of somatic cell reprogramming for neurological research and therapy, focusing on neural reprogramming and generating different neural cell types. We examine the mechanisms involved in reprogramming and the challenges that arise. We herein summarize cell reprogramming strategies to generate neurons, including transcription factors, small molecules, and microRNAs, with a focus on different types of cells.. While reprogramming somatic cells into neurons holds the potential for understanding neurological diseases and developing therapeutic applications, its limitations and risks must be carefully considered. Here, we highlight the potential benefits of somatic cell reprogramming for neurological disease research and therapy. This review contributes to the field by providing a comprehensive overview of the various techniques used to generate neurons by cellular reprogramming and discussing their potential applications.
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Affiliation(s)
- Jiafeng Chen
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Lijuan Huang
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Yue Yang
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Wei Xu
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Qingchun Qin
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Rongxing Qin
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Xiaojun Liang
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Xinyu Lai
- Key Laboratory of Longevity and Aging-Related Diseases of Chinese Ministry of Education, Nanning 530021, China
| | - Xiaoying Huang
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Minshan Xie
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Li Chen
- Department of Neurology, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
- Key Laboratory of Longevity and Aging-Related Diseases of Chinese Ministry of Education, Nanning 530021, China
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30
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Silva-Pedrosa R, Salgado AJ, Ferreira PE. Revolutionizing Disease Modeling: The Emergence of Organoids in Cellular Systems. Cells 2023; 12:930. [PMID: 36980271 PMCID: PMC10047824 DOI: 10.3390/cells12060930] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/03/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Cellular models have created opportunities to explore the characteristics of human diseases through well-established protocols, while avoiding the ethical restrictions associated with post-mortem studies and the costs associated with researching animal models. The capability of cell reprogramming, such as induced pluripotent stem cells (iPSCs) technology, solved the complications associated with human embryonic stem cells (hESC) usage. Moreover, iPSCs made significant contributions for human medicine, such as in diagnosis, therapeutic and regenerative medicine. The two-dimensional (2D) models allowed for monolayer cellular culture in vitro; however, they were surpassed by the three-dimensional (3D) cell culture system. The 3D cell culture provides higher cell-cell contact and a multi-layered cell culture, which more closely respects cellular morphology and polarity. It is more tightly able to resemble conditions in vivo and a closer approach to the architecture of human tissues, such as human organoids. Organoids are 3D cellular structures that mimic the architecture and function of native tissues. They are generated in vitro from stem cells or differentiated cells, such as epithelial or neural cells, and are used to study organ development, disease modeling, and drug discovery. Organoids have become a powerful tool for understanding the cellular and molecular mechanisms underlying human physiology, providing new insights into the pathogenesis of cancer, metabolic diseases, and brain disorders. Although organoid technology is up-and-coming, it also has some limitations that require improvements.
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Affiliation(s)
- Rita Silva-Pedrosa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.J.S.); (P.E.F.)
- ICVS/3B’s—PT Government Associate Laboratory, 4710-057 Braga, Portugal
- Centre of Biological Engineering (CEB), Department of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - António José Salgado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.J.S.); (P.E.F.)
- ICVS/3B’s—PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Pedro Eduardo Ferreira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal; (A.J.S.); (P.E.F.)
- ICVS/3B’s—PT Government Associate Laboratory, 4710-057 Braga, Portugal
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31
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Balusu S, Praschberger R, Lauwers E, De Strooper B, Verstreken P. Neurodegeneration cell per cell. Neuron 2023; 111:767-786. [PMID: 36787752 DOI: 10.1016/j.neuron.2023.01.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/12/2022] [Accepted: 01/18/2023] [Indexed: 02/16/2023]
Abstract
The clinical definition of neurodegenerative diseases is based on symptoms that reflect terminal damage of specific brain regions. This is misleading as it tells little about the initial disease processes. Circuitry failures that underlie the clinical symptomatology are themselves preceded by clinically mostly silent, slowly progressing multicellular processes that trigger or are triggered by the accumulation of abnormally folded proteins such as Aβ, Tau, TDP-43, and α-synuclein, among others. Methodological advances in single-cell omics, combined with complex genetics and novel ways to model complex cellular interactions using induced pluripotent stem (iPS) cells, make it possible to analyze the early cellular phase of neurodegenerative disorders. This will revolutionize the way we study those diseases and will translate into novel diagnostics and cell-specific therapeutic targets, stopping these disorders in their early track before they cause difficult-to-reverse damage to the brain.
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Affiliation(s)
- Sriram Balusu
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Roman Praschberger
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Elsa Lauwers
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium
| | - Bart De Strooper
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium; UK Dementia Research Institute, London, UK.
| | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium; KU Leuven Department of Neurosciences, Leuven Brain Institute, Leuven, Belgium.
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32
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Yoshida S, Kato TM, Sato Y, Umekage M, Ichisaka T, Tsukahara M, Takasu N, Yamanaka S. A clinical-grade HLA haplobank of human induced pluripotent stem cells matching approximately 40% of the Japanese population. MED 2023; 4:51-66.e10. [PMID: 36395757 DOI: 10.1016/j.medj.2022.10.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/02/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND Human induced pluripotent stem cells (iPSCs) are expected to be useful for regenerative medicine for many diseases. Many researchers have focused on and enabled the generation of differentiated cells or tissue-like structures, including organoids, which help to ameliorate target diseases. To promote such cell therapies, we established a clinically applicable iPSC haplobank matching as many people as possible in Japan. METHODS Through cooperation with several organizations, we recruited donors whose human leukocyte antigens (HLAs) involved in immunorejection were homozygous. The peripheral or umbilical cord blood collected from the donors was used for iPSC production by electroporation of episomal vectors. These iPSC lines were then subjected to testing, including genome analyses and sterility, to maximize safety. FINDINGS We constructed a clinical-grade haplobank of 27 iPSC lines from 7 donors according to good manufacturing practice regulations. However, reasons to avoid using iPSC lines include the presence of residual episomal vectors or genetic mutations in cancer-related genes. CONCLUSIONS This haplobank provides HLA-matched iPSC lines for approximately 40% of the Japanese population. Since the haplobank's release in 2015, these iPSC lines have been used in more than 10 clinical trials. The establishment of this haplobank is an important step toward the clinical application of iPSCs in cell therapies. FUNDING This study was supported by a research center network for the realization of regenerative medicine of the Japan Agency for Medical Research and Development (AMED) under grant number JP20bm0104001h0108.
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Affiliation(s)
- Shinsuke Yoshida
- CiRA Foundation, 53 Shogoin kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Tomoaki M Kato
- CiRA Foundation, 53 Shogoin kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Yoshiko Sato
- Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Masafumi Umekage
- CiRA Foundation, 53 Shogoin kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Tomoko Ichisaka
- CiRA Foundation, 53 Shogoin kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | | | - Naoko Takasu
- CiRA Foundation, 53 Shogoin kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan
| | - Shinya Yamanaka
- CiRA Foundation, 53 Shogoin kawahara-cho, Sakyo-ku, Kyoto 606-8397, Japan; Center for iPS Cell Research and Application, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan; Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA.
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33
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Al-Ahmad AJ. Human-Induced Pluripotent Stem Cell-Based Model of the Blood-Brain at 10 Years: A Retrospective on Past and Current Disease Models. Handb Exp Pharmacol 2023; 281:141-156. [PMID: 36943490 DOI: 10.1007/164_2023_645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The initial discovery and derivation of induced pluripotent stem cells (iPSCs) by Yamanaka and colleagues in 2006 revolutionized the field of personalized medicine, as it opened the possibility to model diseases using patient-derived stem cells. A decade of adoption of iPSCs within the community of the blood-brain barrier (BBB) significantly opened the door for modeling diseases at the BBB, a task until then considered challenging, if not impossible.In this book chapter, we provided an extensive review of the literature on the use of iPSC-based models of the human BBB to model neurological diseases including infectious diseases (COVID-19, Streptococcus, Neisseria) neurodevelopmental diseases (adrenoleukodystrophy, Allan-Herndon-Dudley Syndrome, Batten's disease, GLUT1 deficiency syndrome), and neurodegenerative diseases (Alzheimer's disease, the current findings and observations, but also the challenges and limitations inherent to the use of iPSC-based models in reproducing the human BBB during health and diseases in a Petri dish.
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Affiliation(s)
- Abraham J Al-Ahmad
- Department of Pharmaceutical Sciences, Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, USA.
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34
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Wnt signaling and the regulation of pluripotency. Curr Top Dev Biol 2023; 153:95-119. [PMID: 36967203 DOI: 10.1016/bs.ctdb.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The role of Wnt signaling in stem cells has been mired in seemingly contradictory findings. On one hand, Wnt has been heralded as a self-renewal factor. On the other hand, Wnt's association with differentiation and lineage commitment is indisputable. This apparent contradiction is particularly evident in pluripotent stem cells, where Wnt promotes self-renewal as well as differentiation. To resolve this discrepancy one must delve into fundamental principles of pluripotency and gain an appreciation for the concept of pluripotency states, which exist in a continuum with intermediate metastable states, some of which have been stabilized in vitro. Wnt signaling is a critical regulator of transitions between pluripotent states. Here, we will discuss Wnt's roles in maintaining pluripotency, promoting differentiation, as well as stimulating reprogramming of somatic cells to an induced pluripotent state.
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35
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Abstract
Human induced pluripotent stem cells (iPSCs), since their discovery in 2007, have rapidly become a starting cell type of choice for the differentiation of many mature cell types. Their flexibility, amenability to gene editing and functional equivalence to embryonic stem cells ensured their subsequent adoption by many manufacturing processes for cellular products. In this chapter, we will discuss the process whereby iPSCs are generated, key quality control steps which should be considered during manufacturing, the application of good manufacturing practice to production processes and iPSC-derived cellular products which are already undergoing clinical trials. iPSCs provide a new avenue for the next generation of cellular therapeutics and by combining new differentiation protocols, quality control and reproducible manufacturing, iPSC-derived cellular products could provide treatments for many currently untreatable diseases, allowing the large-scale manufacture of high-quality cell therapies.
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Affiliation(s)
- Moyra Lawrence
- Centre for iPS Cell Research and Application (CiRA) and Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.
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36
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Andrews PW, Barbaric I, Benvenisty N, Draper JS, Ludwig T, Merkle FT, Sato Y, Spits C, Stacey GN, Wang H, Pera MF. The consequences of recurrent genetic and epigenetic variants in human pluripotent stem cells. Cell Stem Cell 2022; 29:1624-1636. [PMID: 36459966 DOI: 10.1016/j.stem.2022.11.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/08/2022] [Accepted: 11/08/2022] [Indexed: 12/05/2022]
Abstract
It is well established that human pluripotent stem cells (hPSCs) can acquire genetic and epigenetic changes during culture in vitro. Given the increasing use of hPSCs in research and therapy and the vast expansion in the number of hPSC lines available for researchers, the International Society for Stem Cell Research has recognized the need to reassess quality control standards for ensuring the genetic integrity of hPSCs. Here, we summarize current knowledge of the nature of recurrent genetic and epigenetic variants in hPSC culture, the methods for their detection, and what is known concerning their effects on cell behavior in vitro or in vivo. We argue that the potential consequences of low-level contamination of cell therapy products with cells bearing oncogenic variants are essentially unknown at present. We highlight the key challenges facing the field with particular reference to safety assessment of hPSC-derived cellular therapeutics.
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Affiliation(s)
- Peter W Andrews
- Centre for Stem Cell Biology, School of Biological Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK; Steering Committee, International Stem Cell Initiative
| | - Ivana Barbaric
- Centre for Stem Cell Biology, School of Biological Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK; Steering Committee, International Stem Cell Initiative
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel; Steering Committee, International Stem Cell Initiative
| | - Jonathan S Draper
- Stem Cell Network, 501 Smyth Road, Ottawa, ON, K1H 8L6, Canada; Steering Committee, International Stem Cell Initiative
| | - Tenneille Ludwig
- WiCell Research Institute, Madison, WI, USA; University of Wisconsin-Madison, Madison, WI 53719, USA; Steering Committee, International Stem Cell Initiative
| | - Florian T Merkle
- Wellcome Trust-Medical Research Council Institute of Metabolic Science, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0QQ, UK; Steering Committee, International Stem Cell Initiative
| | - Yoji Sato
- Division of Cell-Based Therapeutic Products, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki Ward, Kawasaki City, Kanagawa 210-9501, Japan; Steering Committee, International Stem Cell Initiative
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; Steering Committee, International Stem Cell Initiative
| | - Glyn N Stacey
- International Stem Cell Banking Initiative, 2 High Street, Barley, UK; National Stem Cell Resource Centre, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100190, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China; Steering Committee, International Stem Cell Initiative
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China; Beijing Institute for Stem Cell and Regenerative Medicine, 100101, Beijing, China; Steering Committee, International Stem Cell Initiative
| | - Martin F Pera
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA; Steering Committee, International Stem Cell Initiative.
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37
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Pantazis CB, Yang A, Lara E, McDonough JA, Blauwendraat C, Peng L, Oguro H, Kanaujiya J, Zou J, Sebesta D, Pratt G, Cross E, Blockwick J, Buxton P, Kinner-Bibeau L, Medura C, Tompkins C, Hughes S, Santiana M, Faghri F, Nalls MA, Vitale D, Ballard S, Qi YA, Ramos DM, Anderson KM, Stadler J, Narayan P, Papademetriou J, Reilly L, Nelson MP, Aggarwal S, Rosen LU, Kirwan P, Pisupati V, Coon SL, Scholz SW, Priebe T, Öttl M, Dong J, Meijer M, Janssen LJM, Lourenco VS, van der Kant R, Crusius D, Paquet D, Raulin AC, Bu G, Held A, Wainger BJ, Gabriele RMC, Casey JM, Wray S, Abu-Bonsrah D, Parish CL, Beccari MS, Cleveland DW, Li E, Rose IVL, Kampmann M, Calatayud Aristoy C, Verstreken P, Heinrich L, Chen MY, Schüle B, Dou D, Holzbaur ELF, Zanellati MC, Basundra R, Deshmukh M, Cohen S, Khanna R, Raman M, Nevin ZS, Matia M, Van Lent J, Timmerman V, Conklin BR, Johnson Chase K, Zhang K, Funes S, Bosco DA, Erlebach L, Welzer M, Kronenberg-Versteeg D, Lyu G, Arenas E, Coccia E, Sarrafha L, Ahfeldt T, Marioni JC, Skarnes WC, Cookson MR, Ward ME, Merkle FT. A reference human induced pluripotent stem cell line for large-scale collaborative studies. Cell Stem Cell 2022; 29:1685-1702.e22. [PMID: 36459969 PMCID: PMC9782786 DOI: 10.1016/j.stem.2022.11.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 10/07/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022]
Abstract
Human induced pluripotent stem cell (iPSC) lines are a powerful tool for studying development and disease, but the considerable phenotypic variation between lines makes it challenging to replicate key findings and integrate data across research groups. To address this issue, we sub-cloned candidate human iPSC lines and deeply characterized their genetic properties using whole genome sequencing, their genomic stability upon CRISPR-Cas9-based gene editing, and their phenotypic properties including differentiation to commonly used cell types. These studies identified KOLF2.1J as an all-around well-performing iPSC line. We then shared KOLF2.1J with groups around the world who tested its performance in head-to-head comparisons with their own preferred iPSC lines across a diverse range of differentiation protocols and functional assays. On the strength of these findings, we have made KOLF2.1J and its gene-edited derivative clones readily accessible to promote the standardization required for large-scale collaborative science in the stem cell field.
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Affiliation(s)
- Caroline B Pantazis
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Andrian Yang
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK; Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Erika Lara
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | | | - Cornelis Blauwendraat
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Lirong Peng
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA; Integrated Research Facility, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Hideyuki Oguro
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Jitendra Kanaujiya
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Jizhong Zou
- iPS Cell Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | | | | | | | | | - Marianita Santiana
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Faraz Faghri
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA
| | - Daniel Vitale
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA
| | - Shannon Ballard
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA; Data Tecnica International LLC, Washington, DC, USA
| | - Yue A Qi
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel M Ramos
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Kailyn M Anderson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Julia Stadler
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Priyanka Narayan
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Genetics and Biochemistry Branch, NIDDK, NINDS, National Institutes of Health, Bethesda, MD 20814, USA
| | - Jason Papademetriou
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Luke Reilly
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Matthew P Nelson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sanya Aggarwal
- Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Leah U Rosen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Peter Kirwan
- Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Venkat Pisupati
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK; John van Geest Centre for Brain Repair, University of Cambridge, Cambridge CB2 0PY, UK
| | - Steven L Coon
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA; Department of Neurology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Theresa Priebe
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Miriam Öttl
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Jian Dong
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Marieke Meijer
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Lara J M Janssen
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Vanessa S Lourenco
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands
| | - Rik van der Kant
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam de Boelelaan 1087, 1081 HV Amsterdam, the Netherlands; Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, the Netherlands
| | - Dennis Crusius
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, 81377 Munich, Germany
| | - Dominik Paquet
- Institute for Stroke and Dementia Research, University Hospital, LMU Munich, 81377 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 81377 Munich, Germany
| | | | - Guojun Bu
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Aaron Held
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian J Wainger
- Department of Neurology, Sean M. Healey & AMG Center for ALS, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Department of Anesthesiology, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA; Harvard Stem Cell Institute, Cambridge, MA, USA; Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Rebecca M C Gabriele
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Jackie M Casey
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Selina Wray
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Dad Abu-Bonsrah
- The Florey Institute of Neuroscience & Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia; Department of Pediatrics, University of Melbourne, Parkville, VIC 3052, Australia
| | - Clare L Parish
- The Florey Institute of Neuroscience & Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Melinda S Beccari
- Department of Cellular and Molecular Medicine and Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Don W Cleveland
- Department of Cellular and Molecular Medicine and Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Emmy Li
- Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Indigo V L Rose
- Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Carles Calatayud Aristoy
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven, Belgium
| | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, Mission Lucidity, Leuven, Belgium
| | - Laurin Heinrich
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Max Y Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Birgitt Schüle
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dan Dou
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erika L F Holzbaur
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maria Clara Zanellati
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richa Basundra
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mohanish Deshmukh
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah Cohen
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Richa Khanna
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | - Malavika Raman
- Department of Developmental Molecular and Chemical Biology, Tufts University School of Medicine, Boston, MA, USA
| | | | | | - Jonas Van Lent
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp 2610, Belgium
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp 2610, Belgium
| | | | | | - Ke Zhang
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - Salome Funes
- Department of Neurology, UMass Chan Medical School, Worcester, MA, USA
| | - Daryl A Bosco
- Department of Neurology, UMass Chan Medical School, Worcester, MA, USA
| | - Lena Erlebach
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Marc Welzer
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Deborah Kronenberg-Versteeg
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany; German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Guochang Lyu
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ernest Arenas
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Elena Coccia
- Nash Family Department of Neuroscience; Departments of Neurology and Cell, Developmental and Regenerative Biology; Ronald M. Loeb Center for Alzheimer's Disease; Friedman Brain Institute; Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Lily Sarrafha
- Nash Family Department of Neuroscience; Departments of Neurology and Cell, Developmental and Regenerative Biology; Ronald M. Loeb Center for Alzheimer's Disease; Friedman Brain Institute; Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience; Departments of Neurology and Cell, Developmental and Regenerative Biology; Ronald M. Loeb Center for Alzheimer's Disease; Friedman Brain Institute; Black Family Stem Cell Institute at Mount Sinai, New York, NY, USA
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Mark R Cookson
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
| | - Michael E Ward
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| | - Florian T Merkle
- Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK.
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Sharma V, Nehra S, Do LH, Ghosh A, Deshpande AJ, Singhal N. Biphasic cell cycle defect causes impaired neurogenesis in down syndrome. Front Genet 2022; 13:1007519. [PMID: 36313423 PMCID: PMC9596798 DOI: 10.3389/fgene.2022.1007519] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/30/2022] [Indexed: 11/29/2022] Open
Abstract
Impaired neurogenesis in Down syndrome (DS) is characterized by reduced neurons, increased glial cells, and delayed cortical lamination. However, the underlying cause for impaired neurogenesis in DS is not clear. Using both human and mouse iPSCs, we demonstrate that DS impaired neurogenesis is due to biphasic cell cycle dysregulation during the generation of neural progenitors from iPSCs named the “neurogenic stage” of neurogenesis. Upon neural induction, DS cells showed reduced proliferation during the early phase followed by increased proliferation in the late phase of the neurogenic stage compared to control cells. While reduced proliferation in the early phase causes reduced neural progenitor pool, increased proliferation in the late phase leads to delayed post mitotic neuron generation in DS. RNAseq analysis of late-phase DS progenitor cells revealed upregulation of S phase-promoting regulators, Notch, Wnt, Interferon pathways, and REST, and downregulation of several genes of the BAF chromatin remodeling complex. NFIB and POU3F4, neurogenic genes activated by the interaction of PAX6 and the BAF complex, were downregulated in DS cells. ChIPseq analysis of late-phase neural progenitors revealed aberrant PAX6 binding with reduced promoter occupancy in DS cells. Together, these data indicate that impaired neurogenesis in DS is due to biphasic cell cycle dysregulation during the neurogenic stage of neurogenesis.
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Affiliation(s)
| | | | - Long H. Do
- Department of Neuroscience, University of California, San Diego, San Diego, CA, United States
| | - Anwesha Ghosh
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | | | - Nishant Singhal
- National Centre for Cell Science, Pune, India
- *Correspondence: Nishant Singhal,
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