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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Gatla H, Uth N, Levinson Y, Navaei A, Sargent A, Ramaswamy S, Friedrich Ben-Nun I. Enabling Allogeneic T Cell-Based Therapies: Scalable Stirred-Tank Bioreactor Mediated Manufacturing. Front Med Technol 2022; 4:850565. [PMID: 35707712 PMCID: PMC9189297 DOI: 10.3389/fmedt.2022.850565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/20/2022] [Indexed: 01/09/2023] Open
Abstract
Allogeneic T cells are key immune therapeutic cells to fight cancer and other clinical indications. High T cell dose per patient and increasing patient numbers result in clinical demand for a large number of allogeneic T cells. This necessitates a manufacturing platform that can be scaled up while retaining cell quality. Here we present a closed and scalable platform for T cell manufacturing to meet clinical demand. Upstream manufacturing steps of T cell activation and expansion are done in-vessel, in a stirred-tank bioreactor. T cell selection, which is necessary for CAR-T-based therapy, is done in the bioreactor itself, thus maintaining optimal culture conditions through the selection step. Platform's attributes of automation and performing the steps of T cell activation, expansion, and selection in-vessel, greatly contribute to enhancing process control, cell quality, and to the reduction of manual labor and contamination risk. In addition, the viability of integrating a closed, automated, downstream process of cell concentration, is demonstrated. The presented T cell manufacturing platform has scale-up capabilities while preserving key factors of cell quality and process control.
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Saragusty J, Diecke S, Drukker M, Durrant B, Friedrich Ben-Nun I, Galli C, Göritz F, Hayashi K, Hermes R, Holtze S, Johnson S, Lazzari G, Loi P, Loring JF, Okita K, Renfree MB, Seet S, Voracek T, Stejskal J, Ryder OA, Hildebrandt TB. Rewinding the process of mammalian extinction. Zoo Biol 2016; 35:280-92. [PMID: 27142508 DOI: 10.1002/zoo.21284] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/11/2016] [Indexed: 12/15/2022]
Abstract
With only three living individuals left on this planet, the northern white rhinoceros (Ceratotherium simum cottoni) could be considered doomed for extinction. It might still be possible, however, to rescue the (sub)species by combining novel stem cell and assisted reproductive technologies. To discuss the various practical options available to us, we convened a multidisciplinary meeting under the name "Conservation by Cellular Technologies." The outcome of this meeting and the proposed road map that, if successfully implemented, would ultimately lead to a self-sustaining population of an extremely endangered species are outlined here. The ideas discussed here, while centered on the northern white rhinoceros, are equally applicable, after proper adjustments, to other mammals on the brink of extinction. Through implementation of these ideas we hope to establish the foundation for reversal of some of the effects of what has been termed the sixth mass extinction event in the history of Earth, and the first anthropogenic one. Zoo Biol. 35:280-292, 2016. © 2016 The Authors. Zoo Biology published by Wiley Periodicals, Inc.
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Affiliation(s)
- Joseph Saragusty
- The Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | | | - Micha Drukker
- Institute of Stem Cell Research, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
| | - Barbara Durrant
- San Diego Zoo Institute for Conservation Research, Escondido, California
| | - Inbar Friedrich Ben-Nun
- Department of Chemical Physiology, Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, California
| | - Cesare Galli
- Avantea srl, Laboratorio di Tecnologie della Riproduzione, Cremona, Italy.,Dipartimento Scienze Mediche Veterinarie, Università di Bologna, Ozzano dell'Emilia, Italy.,Fondazione Avantea, Cremona, Italy
| | - Frank Göritz
- The Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Katsuhiko Hayashi
- Faculty of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Robert Hermes
- The Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Susanne Holtze
- The Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | | | - Giovanna Lazzari
- Avantea srl, Laboratorio di Tecnologie della Riproduzione, Cremona, Italy.,Fondazione Avantea, Cremona, Italy
| | - Pasqualino Loi
- Faculty of Veterinary Medicine, Univeristy of Teramo, Campus Coste San Agostino, Teramo, Italy
| | - Jeanne F Loring
- Department of Chemical Physiology, Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, California
| | - Keisuke Okita
- Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Steven Seet
- The Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | | | - Jan Stejskal
- ZOO Dvůr Králové, Dvůr Králové nad Labem, Czech Republic
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, California
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Gallego Romero I, Pavlovic BJ, Hernando-Herraez I, Zhou X, Ward MC, Banovich NE, Kagan CL, Burnett JE, Huang CH, Mitrano A, Chavarria CI, Friedrich Ben-Nun I, Li Y, Sabatini K, Leonardo TR, Parast M, Marques-Bonet T, Laurent LC, Loring JF, Gilad Y. A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics. eLife 2015; 4:e07103. [PMID: 26102527 PMCID: PMC4502404 DOI: 10.7554/elife.07103] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 06/22/2015] [Indexed: 12/20/2022] Open
Abstract
Comparative genomics studies in primates are restricted due to our limited access to samples. In order to gain better insight into the genetic processes that underlie variation in complex phenotypes in primates, we must have access to faithful model systems for a wide range of cell types. To facilitate this, we generated a panel of 7 fully characterized chimpanzee induced pluripotent stem cell (iPSC) lines derived from healthy donors. To demonstrate the utility of comparative iPSC panels, we collected RNA-sequencing and DNA methylation data from the chimpanzee iPSCs and the corresponding fibroblast lines, as well as from 7 human iPSCs and their source lines, which encompass multiple populations and cell types. We observe much less within-species variation in iPSCs than in somatic cells, indicating the reprogramming process erases many inter-individual differences. The low within-species regulatory variation in iPSCs allowed us to identify many novel inter-species regulatory differences of small magnitude. DOI:http://dx.doi.org/10.7554/eLife.07103.001 Comparing the genomes of different species can reveal how they are related to one another. Such comparative studies can also reveal how genomes are modified in species-specific ways to regulate gene activity. The genomes of humans and chimpanzees are very similar in sequence. It is therefore likely that differing patterns of gene regulation underlie many of the differences observed between the two species. However, only a few kinds of chimpanzee cell that can be grown in the laboratory are available for research; this lack of samples has limited the ability of researchers to perform such comparative studies. One way around this problem is to use induced pluripotent stem cells (or iPSCs). IPSCs are created by exposing mature cells—for example, skin cells—to conditions and molecules that convert them into an embryonic-like state. This state—called ‘induced pluripotency’—allows the cells to be coaxed into becoming many different cell types that can be grown in the laboratory. But it is more difficult to establish high quality iPSCs from chimpanzees than it is from humans or mice. Gallego Romero, Pavlovic et al. have now addressed this problem by creating iPSCs from skin cells taken from seven healthy chimpanzees. These cell lines were then analysed and compared to each other and to seven iPSC lines created from human cells. The chimpanzee iPSC lines were found to be much more similar to each other than the mature cells that were used to make them. Similar results were also observed for the human iSPCs, which likely reflects the conserved changes that take place when the genomes of mature cells are reprogrammed to pluripotency. This high level of similarity between iPSCs from different individuals of the same species allowed Gallego Romero, Pavlovic et al. to discover many subtle differences in gene regulation between chimpanzees and humans. For example, over 4500 genes were found to be expressed differently in human and chimpanzee iPSCs, and over 3500 genomic regions had different patterns of certain DNA modifications that can help to regulate gene expression. These newly created chimpanzee iPSC lines represent a valuable resource for comparative studies of gene regulation. In the future, this resource could help researchers to identify further differences in gene regulation between closely related primate species. DOI:http://dx.doi.org/10.7554/eLife.07103.002
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Affiliation(s)
| | - Bryan J Pavlovic
- Department of Human Genetics, University of Chicago, Chicago, United States
| | | | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, United States
| | - Michelle C Ward
- Department of Human Genetics, University of Chicago, Chicago, United States
| | | | - Courtney L Kagan
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Jonathan E Burnett
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Constance H Huang
- Department of Human Genetics, University of Chicago, Chicago, United States
| | - Amy Mitrano
- Department of Human Genetics, University of Chicago, Chicago, United States
| | | | - Inbar Friedrich Ben-Nun
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| | - Yingchun Li
- Department of Pathology, University of California San Diego, San Diego, United States
| | - Karen Sabatini
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| | - Trevor R Leonardo
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| | - Mana Parast
- Department of Pathology, University of California San Diego, San Diego, United States
| | | | - Louise C Laurent
- Sanford Consortium for Regenerative Medicine, La Jolla, United States
| | - Jeanne F Loring
- Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, United States
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Abstract
For some highly endangered species there are too few reproductively capable animals to maintain adequate genetic diversity, and extraordinary measures are necessary to prevent their extinction. Cellular reprogramming is a means to capture the genomes of individual animals as induced pluripotent stem cells (iPSCs), which may eventually facilitate reintroduction of genetic material into breeding populations. Here, we describe a method for generating iPSCs from fibroblasts of mammalian endangered species.
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Affiliation(s)
- Inbar Friedrich Ben-Nun
- Department of Chemical Physiology, Center for Regenerative Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
| | - Susanne C Montague
- Department of Chemical Physiology, Center for Regenerative Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Marlys L Houck
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | - Oliver Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | - Jeanne F Loring
- Department of Chemical Physiology, Center for Regenerative Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
- Department of Reproductive Medicine, University of California, San Diego, La Jolla, CA, USA
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Abstract
Human embryonic stem cells (HESCs) are pluripotent cell lines derived from the inner cell mass (ICM) of embryos at the blastocyst stage. These cells possess self renewal capacity and differentiation potential to all three embryonic germ layers. These unique characters made HESCs an attractive research tool for studying early human developmental processes as well as a potential therapeutic tool for various human diseases. Here, we focus on HESCs as a cellular model for human disorders. The advantages of such models as well as the various methodologies to achieve HESCs carrying a genetic defect will be discussed.
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Affiliation(s)
- Inbar Friedrich Ben-Nun
- Department of Genetics, Life Science Institute, The Hebrew University, Jerusalem 91904, Israel
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