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Wiener DM, Huynh E, Jeyakumar I, Bax S, Sama S, Cabrera JP, Todorova V, Vangipuram M, Vaid S, Otsuka F, Sakai Y, Leonetti MD, Gómez-Sjöberg R. An open-source FACS automation system for high-throughput cell biology. PLoS One 2024; 19:e0299402. [PMID: 38512845 PMCID: PMC10956866 DOI: 10.1371/journal.pone.0299402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 02/08/2024] [Indexed: 03/23/2024] Open
Abstract
Recent advances in gene editing are enabling the engineering of cells with an unprecedented level of scale. To capitalize on this opportunity, new methods are needed to accelerate the different steps required to manufacture and handle engineered cells. Here, we describe the development of an integrated software and hardware platform to automate Fluorescence-Activated Cell Sorting (FACS), a central step for the selection of cells displaying desired molecular attributes. Sorting large numbers of samples is laborious, and, to date, no automated system exists to sequentially manage FACS samples, likely owing to the need to tailor sorting conditions ("gating") to each individual sample. Our platform is built around a commercial instrument and integrates the handling and transfer of samples to and from the instrument, autonomous control of the instrument's software, and the algorithmic generation of sorting gates, resulting in walkaway functionality. Automation eliminates operator errors, standardizes gating conditions by eliminating operator-to-operator variations, and reduces hands-on labor by 93%. Moreover, our strategy for automating the operation of a commercial instrument control software in the absence of an Application Program Interface (API) exemplifies a universal solution for other instruments that lack an API. Our software and hardware designs are fully open-source and include step-by-step build documentation to contribute to a growing open ecosystem of tools for high-throughput cell biology.
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Affiliation(s)
- Diane M. Wiener
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Emily Huynh
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Ilakkiyan Jeyakumar
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Sophie Bax
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Samia Sama
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Joana P. Cabrera
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Verina Todorova
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Madhuri Vangipuram
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Shivanshi Vaid
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Fumitaka Otsuka
- Medical Business Group, Sony Corporation, San Jose, California, United States of America
| | - Yoshitsugu Sakai
- Medical Business Group, Sony Corporation, San Jose, California, United States of America
| | - Manuel D. Leonetti
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
| | - Rafael Gómez-Sjöberg
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
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Neumayer G, Torkelson JL, Li S, McCarthy K, Zhen HH, Vangipuram M, Jackow J, Rami A, Hansen C, Guo Z, Gaddam S, Pappalardo A, Li L, Cramer A, Roy KR, Nguyen TM, Tanabe K, McGrath PS, Bruckner A, Bilousova G, Roop D, Bailey I, Tang JY, Christiano A, Steinmetz LM, Wernig M, Oro AE. A scalable, GMP-compatible, autologous organotypic cell therapy for Dystrophic Epidermolysis Bullosa. bioRxiv 2023:2023.02.28.529447. [PMID: 36909618 PMCID: PMC10002612 DOI: 10.1101/2023.02.28.529447] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Background Gene editing in induced pluripotent stem (iPS) cells has been hailed to enable new cell therapies for various monogenetic diseases including dystrophic epidermolysis bullosa (DEB). However, manufacturing, efficacy and safety roadblocks have limited the development of genetically corrected, autologous iPS cell-based therapies. Methods We developed Dystrophic Epidermolysis Bullosa Cell Therapy (DEBCT), a new generation GMP-compatible (cGMP), reproducible, and scalable platform to produce autologous clinical-grade iPS cell-derived organotypic induced skin composite (iSC) grafts to treat incurable wounds of patients lacking type VII collagen (C7). DEBCT uses a combined high-efficiency reprogramming and CRISPR-based genetic correction single step to generate genome scar-free, COL7A1 corrected clonal iPS cells from primary patient fibroblasts. Validated iPS cells are converted into epidermal, dermal and melanocyte progenitors with a novel 2D organoid differentiation protocol, followed by CD49f enrichment and expansion to minimize maturation heterogeneity. iSC product characterization by single cell transcriptomics was followed by mouse xenografting for disease correcting activity at 1 month and toxicology analysis at 1-6 months. Culture-acquired mutations, potential CRISPR-off targets, and cancer-driver variants were evaluated by targeted and whole genome sequencing. Findings iPS cell-derived iSC grafts were reproducibly generated from four recessive DEB patients with different pathogenic mutations. Organotypic iSC grafts onto immune-compromised mice developed into stable stratified skin with functional C7 restoration. Single cell transcriptomic characterization of iSCs revealed prominent holoclone stem cell signatures in keratinocytes and the recently described Gibbin-dependent signature in dermal fibroblasts. The latter correlated with enhanced graftability. Multiple orthogonal sequencing and subsequent computational approaches identified random and non-oncogenic mutations introduced by the manufacturing process. Toxicology revealed no detectable tumors after 3-6 months in DEBCT-treated mice. Interpretation DEBCT successfully overcomes previous roadblocks and represents a robust, scalable, and safe cGMP manufacturing platform for production of a CRISPR-corrected autologous organotypic skin graft to heal DEB patient wounds.
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Affiliation(s)
- Gernot Neumayer
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology, and Department of Chemical and Systems Biology
| | - Jessica L. Torkelson
- Program in Epithelial Biology and Department of Dermatology
- Center for Definitive and Curative Medicine
| | - Shengdi Li
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Kelly McCarthy
- Program in Epithelial Biology and Department of Dermatology
- Center for Definitive and Curative Medicine
| | - Hanson H. Zhen
- Program in Epithelial Biology and Department of Dermatology
- Center for Definitive and Curative Medicine
| | - Madhuri Vangipuram
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology, and Department of Chemical and Systems Biology
| | - Joanna Jackow
- Department of Dermatology, Columbia University, New York, NY 10032
- St John’s Institute of Dermatology, King’s College London, London, UK
| | - Avina Rami
- Department of Dermatology, Columbia University, New York, NY 10032
| | - Corey Hansen
- Department of Dermatology, Columbia University, New York, NY 10032
| | - Zongyou Guo
- Department of Dermatology, Columbia University, New York, NY 10032
| | - Sadhana Gaddam
- Program in Epithelial Biology and Department of Dermatology
| | | | - Lingjie Li
- Program in Epithelial Biology and Department of Dermatology
| | - Amber Cramer
- Program in Epithelial Biology and Department of Dermatology
| | - Kevin R. Roy
- Department of Genetics and Stanford Genome Technology Center, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thuylinh Michelle Nguyen
- Department of Genetics and Stanford Genome Technology Center, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Patrick S. McGrath
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Anna Bruckner
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ganna Bilousova
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Dennis Roop
- Department of Dermatology, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Irene Bailey
- Program in Epithelial Biology and Department of Dermatology
- Center for Definitive and Curative Medicine
| | - Jean Y. Tang
- Program in Epithelial Biology and Department of Dermatology
- Center for Definitive and Curative Medicine
| | | | - Lars M. Steinmetz
- Department of Genetics and Stanford Genome Technology Center, Stanford University School of Medicine, Stanford, CA 94305, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology, and Department of Chemical and Systems Biology
| | - Anthony E. Oro
- Program in Epithelial Biology and Department of Dermatology
- Center for Definitive and Curative Medicine
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Wöhr M, Fong WM, Janas JA, Mall M, Thome C, Vangipuram M, Meng L, Südhof TC, Wernig M. Myt1l haploinsufficiency leads to obesity and multifaceted behavioral alterations in mice. Mol Autism 2022; 13:19. [PMID: 35538503 PMCID: PMC9087967 DOI: 10.1186/s13229-022-00497-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 08/09/2021] [Accepted: 04/15/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The zinc finger domain containing transcription factor Myt1l is tightly associated with neuronal identity and is the only transcription factor known that is both neuron-specific and expressed in all neuronal subtypes. We identified Myt1l as a powerful reprogramming factor that, in combination with the proneural bHLH factor Ascl1, could induce neuronal fate in fibroblasts. Molecularly, we found it to repress many non-neuronal gene programs, explaining its supportive role to induce and safeguard neuronal identity in combination with proneural bHLH transcriptional activators. Moreover, human genetics studies found MYT1L mutations to cause intellectual disability and autism spectrum disorder often coupled with obesity. METHODS Here, we generated and characterized Myt1l-deficient mice. A comprehensive, longitudinal behavioral phenotyping approach was applied. RESULTS Myt1l was necessary for survival beyond 24 h but not for overall histological brain organization. Myt1l heterozygous mice became increasingly overweight and exhibited multifaceted behavioral alterations. In mouse pups, Myt1l haploinsufficiency caused mild alterations in early socio-affective communication through ultrasonic vocalizations. In adulthood, Myt1l heterozygous mice displayed hyperactivity due to impaired habituation learning. Motor performance was reduced in Myt1l heterozygous mice despite intact motor learning, possibly due to muscular hypotonia. While anxiety-related behavior was reduced, acoustic startle reactivity was enhanced, in line with higher sensitivity to loud sound. Finally, Myt1l haploinsufficiency had a negative impact on contextual fear memory retrieval, while cued fear memory retrieval appeared to be intact. LIMITATIONS In future studies, additional phenotypes might be identified and a detailed characterization of direct reciprocal social interaction behavior might help to reveal effects of Myt1l haploinsufficiency on social behavior in juvenile and adult mice. CONCLUSIONS Behavioral alterations in Myt1l haploinsufficient mice recapitulate several clinical phenotypes observed in humans carrying heterozygous MYT1L mutations and thus serve as an informative model of the human MYT1L syndrome.
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Affiliation(s)
- Markus Wöhr
- grid.168010.e0000000419368956Department of Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305 USA ,grid.5596.f0000 0001 0668 7884Research Unit Brain and Cognition, Laboratory of Biological Psychology, Social and Affective Neuroscience Research Group, Faculty of Psychology and Educational Sciences, KU Leuven, 3000 Leuven, Belgium ,grid.5596.f0000 0001 0668 7884Leuven Brain Institute, KU Leuven, 3000 Leuven, Belgium ,grid.10253.350000 0004 1936 9756Faculty of Psychology, Experimental and Biological Psychology, Behavioral Neuroscience, Philipps-University of Marburg, 35032 Marburg, Germany ,grid.10253.350000 0004 1936 9756Center for Mind, Brain and Behavior, Philipps-University of Marburg, 35032 Marburg, Germany
| | - Wendy M. Fong
- grid.168010.e0000000419368956Departments of Pathology and Chemical and Systems Biology, School of Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305 USA
| | - Justyna A. Janas
- grid.168010.e0000000419368956Departments of Pathology and Chemical and Systems Biology, School of Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305 USA
| | - Moritz Mall
- grid.168010.e0000000419368956Departments of Pathology and Chemical and Systems Biology, School of Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305 USA ,grid.7497.d0000 0004 0492 0584Present Address: Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany ,Present Address: HITBR Hector Institute for Translational Brain Research gGmbH, 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Present Address: Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159 Mannheim, Germany
| | - Christian Thome
- grid.168010.e0000000419368956Departments of Pathology and Chemical and Systems Biology, School of Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305 USA
| | - Madhuri Vangipuram
- grid.168010.e0000000419368956Departments of Pathology and Chemical and Systems Biology, School of Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305 USA
| | - Lingjun Meng
- grid.168010.e0000000419368956Departments of Pathology and Chemical and Systems Biology, School of Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305 USA
| | - Thomas C. Südhof
- grid.168010.e0000000419368956Department of Molecular and Cellular Physiology, School of Medicine, Stanford University, Stanford, CA 94305 USA ,grid.168010.e0000000419368956School of Medicine, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305 USA
| | - Marius Wernig
- grid.168010.e0000000419368956Departments of Pathology and Chemical and Systems Biology, School of Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305 USA
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