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Cuomo ASE, Nathan A, Raychaudhuri S, MacArthur DG, Powell JE. Single-cell genomics meets human genetics. Nat Rev Genet 2023; 24:535-549. [PMID: 37085594 PMCID: PMC10784789 DOI: 10.1038/s41576-023-00599-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2023] [Indexed: 04/23/2023]
Abstract
Single-cell genomic technologies are revealing the cellular composition, identities and states in tissues at unprecedented resolution. They have now scaled to the point that it is possible to query samples at the population level, across thousands of individuals. Combining single-cell information with genotype data at this scale provides opportunities to link genetic variation to the cellular processes underpinning key aspects of human biology and disease. This strategy has potential implications for disease diagnosis, risk prediction and development of therapeutic solutions. But, effectively integrating large-scale single-cell genomic data, genetic variation and additional phenotypic data will require advances in data generation and analysis methods. As single-cell genetics begins to emerge as a field in its own right, we review its current state and the challenges and opportunities ahead.
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Affiliation(s)
- Anna S E Cuomo
- Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia.
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Divisions of Rheumatology and Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Divisions of Rheumatology and Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Joseph E Powell
- Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales, Australia.
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, New South Wales, Australia.
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52
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Marion W, Koppe T, Chen CC, Wang D, Frenis K, Fierstein S, Sensharma P, Aumais O, Peters M, Ruiz-Torres S, Chihanga T, Boettcher S, Shimamura A, Bauer DE, Schlaeger T, Wells SI, Ebert BL, Starczynowski D, da Rocha EL, Rowe RG. RUNX1 mutations mitigate quiescence to promote transformation of hematopoietic progenitors in Fanconi anemia. Leukemia 2023; 37:1698-1708. [PMID: 37391485 PMCID: PMC11009868 DOI: 10.1038/s41375-023-01945-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/25/2023] [Accepted: 06/13/2023] [Indexed: 07/02/2023]
Abstract
Many inherited bone marrow failure syndromes (IBMFSs) present a high risk of transformation to myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). During transformation of IBMFSs, hematopoietic stem and progenitor cells (HSPCs) with poor fitness gain ectopic, dysregulated self-renewal secondary to somatic mutations via undefined mechanisms. Here, in the context of the prototypical IBMFS Fanconi anemia (FA), we performed multiplexed gene editing of mutational hotspots in MDS-associated genes in human induced pluripotent stem cells (iPSCs) followed by hematopoietic differentiation. We observed aberrant self-renewal and impaired differentiation of HSPCs with enrichment of RUNX1 insertions and deletions (indels), generating a model of IBMFS-associated MDS. We observed that compared to the failure state, FA MDS cells show mutant RUNX1-mediated blunting of the G1/S cell cycle checkpoint that is normally activated in FA in response to DNA damage. RUNX1 indels also lead to activation of innate immune signaling, which stabilizes the homologous recombination (HR) effector BRCA1, and this pathway can be targeted to abrogate viability and restore sensitivity to genotoxins in FA MDS. Together, these studies develop a paradigm for modeling clonal evolution in IBMFSs, provide basic understanding of the pathogenesis of MDS, and uncover a therapeutic target in FA-associated MDS.
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Affiliation(s)
- William Marion
- Department of Hematology-Oncology, Boston Children's Hospital, Boston, MA, USA
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
| | - Tiago Koppe
- Department of Hematology-Oncology, Boston Children's Hospital, Boston, MA, USA
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
| | - Chun-Chin Chen
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dahai Wang
- Department of Hematology-Oncology, Boston Children's Hospital, Boston, MA, USA
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
| | - Katie Frenis
- Department of Hematology-Oncology, Boston Children's Hospital, Boston, MA, USA
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
| | - Sara Fierstein
- Department of Hematology-Oncology, Boston Children's Hospital, Boston, MA, USA
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
| | - Prerana Sensharma
- Department of Hematology-Oncology, Boston Children's Hospital, Boston, MA, USA
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA
| | - Olivia Aumais
- Department of Hematology-Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Michael Peters
- Department of Hematology-Oncology, Boston Children's Hospital, Boston, MA, USA
| | | | | | - Steffen Boettcher
- Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology and Hematology, University of Zurich and University Hospital of Zurich, Zurich, Switzerland
| | - Akiko Shimamura
- Department of Hematology-Oncology, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Daniel E Bauer
- Department of Hematology-Oncology, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | - Susanne I Wells
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Benjamin L Ebert
- Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Daniel Starczynowski
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- University of Cincinnati Cancer Center, Cincinnati, OH, USA
| | | | - R Grant Rowe
- Department of Hematology-Oncology, Boston Children's Hospital, Boston, MA, USA.
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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53
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Glass MR, Waxman EA, Yamashita S, Lafferty M, Beltran A, Farah T, Patel NK, Matoba N, Ahmed S, Srivastava M, Drake E, Davis LT, Yeturi M, Sun K, Love MI, Hashimoto-Torii K, French DL, Stein JL. Cross-site reproducibility of human cortical organoids reveals consistent cell type composition and architecture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.550873. [PMID: 37546772 PMCID: PMC10402155 DOI: 10.1101/2023.07.28.550873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Background Reproducibility of human cortical organoid (hCO) phenotypes remains a concern for modeling neurodevelopmental disorders. While guided hCO protocols reproducibly generate cortical cell types in multiple cell lines at one site, variability across sites using a harmonized protocol has not yet been evaluated. We present an hCO cross-site reproducibility study examining multiple phenotypes. Methods Three independent research groups generated hCOs from one induced pluripotent stem cell (iPSC) line using a harmonized miniaturized spinning bioreactor protocol. scRNA-seq, 3D fluorescent imaging, phase contrast imaging, qPCR, and flow cytometry were used to characterize the 3 month differentiations across sites. Results In all sites, hCOs were mostly cortical progenitor and neuronal cell types in reproducible proportions with moderate to high fidelity to the in vivo brain that were consistently organized in cortical wall-like buds. Cross-site differences were detected in hCO size and morphology. Differential gene expression showed differences in metabolism and cellular stress across sites. Although iPSC culture conditions were consistent and iPSCs remained undifferentiated, primed stem cell marker expression prior to differentiation correlated with cell type proportions in hCOs. Conclusions We identified hCO phenotypes that are reproducible across sites using a harmonized differentiation protocol. Previously described limitations of hCO models were also reproduced including off-target differentiations, necrotic cores, and cellular stress. Improving our understanding of how stem cell states influence early hCO cell types may increase reliability of hCO differentiations. Cross-site reproducibility of hCO cell type proportions and organization lays the foundation for future collaborative prospective meta-analytic studies modeling neurodevelopmental disorders in hCOs.
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Affiliation(s)
- Madison R Glass
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Elisa A Waxman
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Satoshi Yamashita
- Center for Neuroscience Research, Children's National Hospital, Washington, DC
| | - Michael Lafferty
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Alvaro Beltran
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Tala Farah
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Niyanta K Patel
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Nana Matoba
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sara Ahmed
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Mary Srivastava
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Emma Drake
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Liam T Davis
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Meghana Yeturi
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kexin Sun
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Departments of Pediatrics, and Pharmacology & Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC
| | - Kazue Hashimoto-Torii
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Deborah L French
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jason L Stein
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
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Shevade K, Peddada S, Mader K, Przybyla L. Functional genomics in stem cell models: considerations and applications. Front Cell Dev Biol 2023; 11:1236553. [PMID: 37554308 PMCID: PMC10404852 DOI: 10.3389/fcell.2023.1236553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023] Open
Abstract
Protocols to differentiate human pluripotent stem cells have advanced in terms of cell type specificity and tissue-level complexity over the past 2 decades, which has facilitated human disease modeling in the most relevant cell types. The ability to generate induced PSCs (iPSCs) from patients further enables the study of disease mutations in an appropriate cellular context to reveal the mechanisms that underlie disease etiology and progression. As iPSC-derived disease models have improved in robustness and scale, they have also been adopted more widely for use in drug screens to discover new therapies and therapeutic targets. Advancement in genome editing technologies, in particular the discovery of CRISPR-Cas9, has further allowed for rapid development of iPSCs containing disease-causing mutations. CRISPR-Cas9 technologies have now evolved beyond creating single gene edits, aided by the fusion of inhibitory (CRISPRi) or activation (CRISPRa) domains to a catalytically dead Cas9 protein, enabling inhibition or activation of endogenous gene loci. These tools have been used in CRISPR knockout, CRISPRi, or CRISPRa screens to identify genetic modifiers that synergize or antagonize with disease mutations in a systematic and unbiased manner, resulting in identification of disease mechanisms and discovery of new therapeutic targets to accelerate drug discovery research. However, many technical challenges remain when applying large-scale functional genomics approaches to differentiated PSC populations. Here we review current technologies in the field of iPSC disease modeling and CRISPR-based functional genomics screens and practical considerations for implementation across a range of modalities, applications, and disease areas, as well as explore CRISPR screens that have been performed in iPSC models to-date and the insights and therapies these screens have produced.
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Affiliation(s)
- Kaivalya Shevade
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Sailaja Peddada
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Karl Mader
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Laralynne Przybyla
- Laboratory for Genomics Research, San Francisco, CA, United States
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
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Trionfini P, Romano E, Varinelli M, Longaretti L, Rizzo P, Giampietro R, Caroli A, Aiello S, Todeschini M, Casiraghi F, Remuzzi G, Benigni A, Tomasoni S. Hypoimmunogenic Human Pluripotent Stem Cells as a Powerful Tool for Liver Regenerative Medicine. Int J Mol Sci 2023; 24:11810. [PMID: 37511568 PMCID: PMC10380710 DOI: 10.3390/ijms241411810] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Induced pluripotent stem cells (iPSC) have huge potential as cell therapy for various diseases, given their potential for unlimited self-renewal and capability to differentiate into a wide range of cell types. Although autologous iPSCs represents the ideal source for patient-tailored regenerative medicine, the high costs of the extensive and time-consuming production process and the impracticability for treating acute conditions hinder their use for broad applications. An allogeneic iPSC-based strategy may overcome these issues, but it carries the risk of triggering an immune response. So far, several approaches based on genome-editing techniques to silence human leukocyte antigen class I (HLA-I) or II (HLA-II) expression have been explored to overcome the immune rejection of allogeneic iPSCs. In this study, we employed the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9) system to delete the β2-Microglobulin (B2M) and the Class II Major Histocompatibility Complex Transactivator (CIITA) genes, essential for the correct surface expression of HLA-I and HLA-II proteins. The resulting hypoimmunogenic iPSC line has a normal karyotype, expresses the pluripotency stem cell markers, and is capable of differentiating into the three embryonic germ layers. Furthermore, we showed that it specifically retains the ability to differentiate towards different liver cells, such as endothelial-like cells, hepatocyte-like cells, and hepatic stellate-like cells. Our results indicate that hypoimmunogenic iPSCs could give a new cost-effective and off-the-shelf opportunity for cell therapy in liver diseases.
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Affiliation(s)
- Piera Trionfini
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Elena Romano
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Marco Varinelli
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Lorena Longaretti
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Paola Rizzo
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Roberta Giampietro
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Annalina Caroli
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Sistiana Aiello
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Marta Todeschini
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Federica Casiraghi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Giuseppe Remuzzi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Ariela Benigni
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
| | - Susanna Tomasoni
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24126 Bergamo, Italy
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56
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Laber S, Strobel S, Mercader JM, Dashti H, dos Santos FR, Kubitz P, Jackson M, Ainbinder A, Honecker J, Agrawal S, Garborcauskas G, Stirling DR, Leong A, Figueroa K, Sinnott-Armstrong N, Kost-Alimova M, Deodato G, Harney A, Way GP, Saadat A, Harken S, Reibe-Pal S, Ebert H, Zhang Y, Calabuig-Navarro V, McGonagle E, Stefek A, Dupuis J, Cimini BA, Hauner H, Udler MS, Carpenter AE, Florez JC, Lindgren C, Jacobs SB, Claussnitzer M. Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler. CELL GENOMICS 2023; 3:100346. [PMID: 37492099 PMCID: PMC10363917 DOI: 10.1016/j.xgen.2023.100346] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 08/22/2022] [Accepted: 05/26/2023] [Indexed: 07/27/2023]
Abstract
A primary obstacle in translating genetic associations with disease into therapeutic strategies is elucidating the cellular programs affected by genetic risk variants and effector genes. Here, we introduce LipocyteProfiler, a cardiometabolic-disease-oriented high-content image-based profiling tool that enables evaluation of thousands of morphological and cellular profiles that can be systematically linked to genes and genetic variants relevant to cardiometabolic disease. We show that LipocyteProfiler allows surveillance of diverse cellular programs by generating rich context- and process-specific cellular profiles across hepatocyte and adipocyte cell-state transitions. We use LipocyteProfiler to identify known and novel cellular mechanisms altered by polygenic risk of metabolic disease, including insulin resistance, fat distribution, and the polygenic contribution to lipodystrophy. LipocyteProfiler paves the way for large-scale forward and reverse deep phenotypic profiling in lipocytes and provides a framework for the unbiased identification of causal relationships between genetic variants and cellular programs relevant to human disease.
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Affiliation(s)
- Samantha Laber
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Sophie Strobel
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Josep M. Mercader
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Hesam Dashti
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Felipe R.C. dos Santos
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Phil Kubitz
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Else Kröner-Fresenius-Centre for Nutritional Medicine, School of Life Sciences, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Maya Jackson
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alina Ainbinder
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Julius Honecker
- Else Kröner-Fresenius-Centre for Nutritional Medicine, School of Life Sciences, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
| | - Saaket Agrawal
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Garrett Garborcauskas
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David R. Stirling
- Imaging Platform, Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aaron Leong
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Katherine Figueroa
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nasa Sinnott-Armstrong
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Stanford University, San Francisco, CA, USA
| | - Maria Kost-Alimova
- Imaging Platform, Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Giacomo Deodato
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alycen Harney
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Gregory P. Way
- Imaging Platform, Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alham Saadat
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sierra Harken
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Saskia Reibe-Pal
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7FZ, UK
| | - Hannah Ebert
- Institute of Nutritional Science, University Hohenheim, 70599 Stuttgart, Germany
| | - Yixin Zhang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Virtu Calabuig-Navarro
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute of Nutritional Science, University Hohenheim, 70599 Stuttgart, Germany
| | - Elizabeth McGonagle
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Adam Stefek
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC H3A 1G1, Canada
| | - Beth A. Cimini
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hans Hauner
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
- Else Kröner-Fresenius-Centre for Nutritional Medicine, School of Life Sciences, Technical University of Munich, 85354 Freising-Weihenstephan, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Miriam S. Udler
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Anne E. Carpenter
- Imaging Platform, Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jose C. Florez
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Cecilia Lindgren
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Suzanne B.R. Jacobs
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Melina Claussnitzer
- Programs in Metabolism and Medical and Population Genetics, Type 2 Diabetes Systems Genomics Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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57
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She R, Fair T, Schaefer NK, Saunders RA, Pavlovic BJ, Weissman JS, Pollen AA. Comparative landscape of genetic dependencies in human and chimpanzee stem cells. Cell 2023; 186:2977-2994.e23. [PMID: 37343560 PMCID: PMC10461406 DOI: 10.1016/j.cell.2023.05.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/14/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023]
Abstract
Comparative studies of great apes provide a window into our evolutionary past, but the extent and identity of cellular differences that emerged during hominin evolution remain largely unexplored. We established a comparative loss-of-function approach to evaluate whether human cells exhibit distinct genetic dependencies. By performing genome-wide CRISPR interference screens in human and chimpanzee pluripotent stem cells, we identified 75 genes with species-specific effects on cellular proliferation. These genes comprised coherent processes, including cell-cycle progression and lysosomal signaling, which we determined to be human-derived by comparison with orangutan cells. Human-specific robustness to CDK2 and CCNE1 depletion persisted in neural progenitor cells and cerebral organoids, supporting the G1-phase length hypothesis as a potential evolutionary mechanism in human brain expansion. Our findings demonstrate that evolutionary changes in human cells reshaped the landscape of essential genes and establish a platform for systematically uncovering latent cellular and molecular differences between species.
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Affiliation(s)
- Richard She
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Tyler Fair
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Nathan K Schaefer
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Reuben A Saunders
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA
| | - Bryan J Pavlovic
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute Technology, Cambridge, MA 02142, USA.
| | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
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58
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Hills R, Mossman JA, Bratt-Leal AM, Tran H, Williams RM, Stouffer DG, Sokolova IV, Sanna PP, Loring JF, Lelos MJ. Neurite Outgrowth and Gene Expression Profile Correlate with Efficacy of Human Induced Pluripotent Stem Cell-Derived Dopamine Neuron Grafts. Stem Cells Dev 2023; 32:387-397. [PMID: 37166357 PMCID: PMC10398740 DOI: 10.1089/scd.2023.0043] [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: 02/27/2023] [Accepted: 05/08/2023] [Indexed: 05/12/2023] Open
Abstract
Transplantation of human induced pluripotent stem cell-derived dopaminergic (iPSC-DA) neurons is a promising therapeutic strategy for Parkinson's disease (PD). To assess optimal cell characteristics and reproducibility, we evaluated the efficacy of iPSC-DA neuron precursors from two individuals with sporadic PD by transplantation into a hemiparkinsonian rat model after differentiation for either 18 (d18) or 25 days (d25). We found similar graft size and dopamine (DA) neuron content in both groups, but only the d18 cells resulted in recovery of motor impairments. In contrast, we report that d25 grafts survived equally as well and produced grafts rich in tyrosine hydroxylase-positive neurons, but were incapable of alleviating any motor deficits. We identified the mechanism of action as the extent of neurite outgrowth into the host brain, with d18 grafts supporting significantly more neurite outgrowth than nonfunctional d25 grafts. RNAseq analysis of the cell preparation suggests that graft efficacy may be enhanced by repression of differentiation-associated genes by REST, defining the optimal predifferentiation state for transplantation. This study demonstrates for the first time that DA neuron grafts can survive well in vivo while completely lacking the capacity to induce recovery from motor dysfunction. In contrast to other recent studies, we demonstrate that neurite outgrowth is the key factor determining graft efficacy and our gene expression profiling revealed characteristics of the cells that may predict their efficacy. These data have implication for the generation of DA neuron grafts for clinical application.
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Affiliation(s)
- Rachel Hills
- Brain Repair Group, School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Jim A. Mossman
- Independent Bioinformatics Consultant, Del Mar, California, USA
| | - Andres M. Bratt-Leal
- Department of Molecular Medicine, Center for Regenerative Medicine, Scripps Research, La Jolla, California, USA
- Summit for Stem Cell Foundation, San Diego, California, USA
| | - Ha Tran
- Department of Molecular Medicine, Center for Regenerative Medicine, Scripps Research, La Jolla, California, USA
- Summit for Stem Cell Foundation, San Diego, California, USA
| | - Roy M. Williams
- Department of Molecular Medicine, Center for Regenerative Medicine, Scripps Research, La Jolla, California, USA
| | - David G. Stouffer
- Department of Molecular Medicine, Center for Regenerative Medicine, Scripps Research, La Jolla, California, USA
| | - Irina V. Sokolova
- Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA
| | - Pietro P. Sanna
- Department of Immunology and Microbiology, Scripps Research, La Jolla, California, USA
| | - Jeanne F. Loring
- Department of Molecular Medicine, Center for Regenerative Medicine, Scripps Research, La Jolla, California, USA
| | - Mariah J. Lelos
- Brain Repair Group, School of Biosciences, Cardiff University, Cardiff, United Kingdom
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59
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Tenreiro MF, Branco MA, Cotovio JP, Cabral JMS, Fernandes TG, Diogo MM. Advancing organoid design through co-emergence, assembly, and bioengineering. Trends Biotechnol 2023; 41:923-938. [PMID: 36653200 DOI: 10.1016/j.tibtech.2022.12.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/19/2022] [Accepted: 12/30/2022] [Indexed: 01/18/2023]
Abstract
Human adult stem cells and patient-derived induced pluripotent stem cells represent promising tools to understand human biology, development, and disease. Under a permissive environment, stem cell derivatives can self-organize and reconstruct their native milieu, resulting in the creation of organ-like entities known as organoids. Although organoids represent a breakthrough in the stem cell field, there are still considerable shortcomings preventing their widespread use, namely their variability, limited function, and reductionist size. In the past few years, sophisticated methodologies have been proposed to allow the design of organoids with improved biological fidelity and physiological relevance. Here, we summarize these emerging technologies and provide insights into how they can be utilized to fulfill the potential of stem cells.
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Affiliation(s)
- Miguel F Tenreiro
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Mariana A Branco
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - João P Cotovio
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Joaquim M S Cabral
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Tiago G Fernandes
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Maria Margarida Diogo
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal; Associate Laboratory i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal.
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60
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Jensen KB, Little MH. Organoids are not organs: Sources of variation and misinformation in organoid biology. Stem Cell Reports 2023; 18:1255-1270. [PMID: 37315519 DOI: 10.1016/j.stemcr.2023.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 06/16/2023] Open
Abstract
In the past decade, the term organoid has moved from obscurity to common use to describe a 3D in vitro cellular model of a tissue that recapitulates structural and functional elements of the in vivo organ it models. The term organoid is now applied to structures formed as a result of two distinct processes: the capacity for adult epithelial stem cells to re-create a tissue niche in vitro and the ability to direct the differentiation of pluripotent stem cells to a 3D self-organizing multicellular model of organogenesis. While these two organoid fields rely upon different stem cell types and recapitulate different processes, both share common challenges around robustness, accuracy, and reproducibility. Critically, organoids are not organs. This commentary serves to discuss these challenges, how they impact genuine utility, and shine a light on the need to improve the standards applied to all organoid approaches.
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Affiliation(s)
- Kim Bak Jensen
- Novo Nordisk Foundation Centre for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Melissa Helen Little
- Novo Nordisk Foundation Centre for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Centre for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, Melbourne, VIC 3052, Australia.
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61
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Edwards MM, Wang N, Massey DJ, Egli D, Koren A. Incomplete Reprogramming of DNA Replication Timing in Induced Pluripotent Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544654. [PMID: 37398435 PMCID: PMC10312660 DOI: 10.1101/2023.06.12.544654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Induced pluripotent stem cells (iPSC) are a widely used cell system and a foundation for cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which have the potential to affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing - a process linked to both genome regulation and genome stability - is efficiently reprogrammed to the embryonic state. To answer this, we profiled and compared genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicated their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibit delayed replication at heterochromatic regions containing genes downregulated in iPSC with incompletely reprogrammed DNA methylation. DNA replication delays were not the result of gene expression and DNA methylation aberrations and persisted after differentiating cells to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and lead to undesirable phenotypes in iPSCs, establishing it as an important genomic feature to consider when evaluating iPSC lines.
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Affiliation(s)
- Matthew M. Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Dashiell J. Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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62
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Neavin DR, Steinmann AM, Farbehi N, Chiu HS, Daniszewski MS, Arora H, Bermudez Y, Moutinho C, Chan CL, Bax M, Tyebally M, Gnanasambandapillai V, Lam CE, Nguyen U, Hernández D, Lidgerwood GE, Graham RM, Hewitt AW, Pébay A, Palpant NJ, Powell JE. A village in a dish model system for population-scale hiPSC studies. Nat Commun 2023; 14:3240. [PMID: 37296104 PMCID: PMC10256711 DOI: 10.1038/s41467-023-38704-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 04/26/2023] [Indexed: 06/12/2023] Open
Abstract
The mechanisms by which DNA alleles contribute to disease risk, drug response, and other human phenotypes are highly context-specific, varying across cell types and different conditions. Human induced pluripotent stem cells are uniquely suited to study these context-dependent effects but cell lines from hundreds or thousands of individuals are required. Village cultures, where multiple induced pluripotent stem lines are cultured and differentiated in a single dish, provide an elegant solution for scaling induced pluripotent stem experiments to the necessary sample sizes required for population-scale studies. Here, we show the utility of village models, demonstrating how cells can be assigned to an induced pluripotent stem line using single-cell sequencing and illustrating that the genetic, epigenetic or induced pluripotent stem line-specific effects explain a large percentage of gene expression variation for many genes. We demonstrate that village methods can effectively detect induced pluripotent stem line-specific effects, including sensitive dynamics of cell states.
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Affiliation(s)
- Drew R Neavin
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | - Angela M Steinmann
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | - Nona Farbehi
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
- Graduate School of Biomedical Engineering, University of New South Wales, Kensington, 2033, Sydney, Australia
| | - Han Sheng Chiu
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Maciej S Daniszewski
- Department of Anatomy and Physiology, the University of Melbourne, Melbourne, Australia
| | - Himanshi Arora
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | - Yasmin Bermudez
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | - Cátia Moutinho
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | - Chia-Ling Chan
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | - Monique Bax
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
| | - Mubarika Tyebally
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | | | - Chuan E Lam
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | - Uyen Nguyen
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia
| | - Damián Hernández
- Department of Anatomy and Physiology, the University of Melbourne, Melbourne, Australia
| | - Grace E Lidgerwood
- Department of Anatomy and Physiology, the University of Melbourne, Melbourne, Australia
| | - Robert M Graham
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
- UNSW Medicine & Health, UNSW Sydney, Kensington, NSW, Australia
- St Vincent's Hospital, Darlinghurst, 2010, NSW, Australia
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, Melbourne, Australia
- School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, the University of Melbourne, Melbourne, Australia
- Department of Surgery, Royal Melbourne Hospital, Anatomy and Neuroscience, the University of Melbourne, Melbourne, Australia
| | - Nathan J Palpant
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, 2010, Sydney, Australia.
- UNSW Cellular Genomics Futures Institute, School of Medical Sciences, University of New South Wales, 2052, Sydney, Australia.
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63
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Williams J, Hurling C, Munir S, Harley P, Machado CB, Cujba AM, Alvarez-Fallas M, Danovi D, Lieberam I, Sancho R, Beales P, Watt FM. Modelling renal defects in Bardet-Biedl syndrome patients using human iPS cells. Front Cell Dev Biol 2023; 11:1163825. [PMID: 37333983 PMCID: PMC10272764 DOI: 10.3389/fcell.2023.1163825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/19/2023] [Indexed: 06/20/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is a ciliopathy with pleiotropic effects on multiple tissues, including the kidney. Here we have compared renal differentiation of iPS cells from healthy and BBS donors. High content image analysis of WT1-expressing kidney progenitors showed that cell proliferation, differentiation and cell shape were similar in healthy, BBS1, BBS2, and BBS10 mutant lines. We then examined three patient lines with BBS10 mutations in a 3D kidney organoid system. The line with the most deleterious mutation, with low BBS10 expression, expressed kidney marker genes but failed to generate 3D organoids. The other two patient lines expressed near normal levels of BBS10 mRNA and generated multiple kidney lineages within organoids when examined at day 20 of organoid differentiation. However, on prolonged culture (day 27) the proximal tubule compartment degenerated. Introducing wild type BBS10 into the most severely affected patient line restored organoid formation, whereas CRISPR-mediated generation of a truncating BBS10 mutation in a healthy line resulted in failure to generate organoids. Our findings provide a basis for further mechanistic studies of the role of BBS10 in the kidney.
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Affiliation(s)
- James Williams
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Chloe Hurling
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Sabrina Munir
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Peter Harley
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Carolina Barcellos Machado
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Ana-Maria Cujba
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Mario Alvarez-Fallas
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Davide Danovi
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, London, United Kingdom
- Bit.bio, Babraham Research Campus, Cambridge, United Kingdom
| | - Ivo Lieberam
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, London, United Kingdom
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, King’s College London, London, United Kingdom
| | - Rocio Sancho
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Philip Beales
- Institute of Child Health, Genetic and Genomic Medicine, University College London, London, United Kingdom
| | - Fiona M. Watt
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, Guy’s Hospital, London, United Kingdom
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64
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Kumasaka N, Rostom R, Huang N, Polanski K, Meyer KB, Patel S, Boyd R, Gomez C, Barnett SN, Panousis NI, Schwartzentruber J, Ghoussaini M, Lyons PA, Calero-Nieto FJ, Göttgens B, Barnes JL, Worlock KB, Yoshida M, Nikolić MZ, Stephenson E, Reynolds G, Haniffa M, Marioni JC, Stegle O, Hagai T, Teichmann SA. Mapping interindividual dynamics of innate immune response at single-cell resolution. Nat Genet 2023; 55:1066-1075. [PMID: 37308670 PMCID: PMC10260404 DOI: 10.1038/s41588-023-01421-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 04/27/2023] [Indexed: 06/14/2023]
Abstract
Common genetic variants across individuals modulate the cellular response to pathogens and are implicated in diverse immune pathologies, yet how they dynamically alter the response upon infection is not well understood. Here, we triggered antiviral responses in human fibroblasts from 68 healthy donors, and profiled tens of thousands of cells using single-cell RNA-sequencing. We developed GASPACHO (GAuSsian Processes for Association mapping leveraging Cell HeterOgeneity), a statistical approach designed to identify nonlinear dynamic genetic effects across transcriptional trajectories of cells. This approach identified 1,275 expression quantitative trait loci (local false discovery rate 10%) that manifested during the responses, many of which were colocalized with susceptibility loci identified by genome-wide association studies of infectious and autoimmune diseases, including the OAS1 splicing quantitative trait locus in a COVID-19 susceptibility locus. In summary, our analytical approach provides a unique framework for delineation of the genetic variants that shape a wide spectrum of transcriptional responses at single-cell resolution.
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Affiliation(s)
- Natsuhiko Kumasaka
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Medical Support Center of Japan Environment and Children's Study (JECS), National Center for Child Health and Development, Tokyo, Japan
| | - Raghd Rostom
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sharad Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Rachel Boyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Celine Gomez
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sam N Barnett
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Jeremy Schwartzentruber
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, UK
| | - Maya Ghoussaini
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, UK
| | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Josephine L Barnes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Emily Stephenson
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Gary Reynolds
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Department of Dermatology, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - John C Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Oliver Stegle
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center, Heidelberg, Germany
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Tzachi Hagai
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK.
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65
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Buchner F, Dokuzluoglu Z, Grass T, Rodriguez-Muela N. Spinal Cord Organoids to Study Motor Neuron Development and Disease. Life (Basel) 2023; 13:1254. [PMID: 37374039 DOI: 10.3390/life13061254] [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: 05/02/2023] [Accepted: 05/18/2023] [Indexed: 06/29/2023] Open
Abstract
Motor neuron diseases (MNDs) are a heterogeneous group of disorders that affect the cranial and/or spinal motor neurons (spMNs), spinal sensory neurons and the muscular system. Although they have been investigated for decades, we still lack a comprehensive understanding of the underlying molecular mechanisms; and therefore, efficacious therapies are scarce. Model organisms and relatively simple two-dimensional cell culture systems have been instrumental in our current knowledge of neuromuscular disease pathology; however, in the recent years, human 3D in vitro models have transformed the disease-modeling landscape. While cerebral organoids have been pursued the most, interest in spinal cord organoids (SCOs) is now also increasing. Pluripotent stem cell (PSC)-based protocols to generate SpC-like structures, sometimes including the adjacent mesoderm and derived skeletal muscle, are constantly being refined and applied to study early human neuromuscular development and disease. In this review, we outline the evolution of human PSC-derived models for generating spMN and recapitulating SpC development. We also discuss how these models have been applied to exploring the basis of human neurodevelopmental and neurodegenerative diseases. Finally, we provide an overview of the main challenges to overcome in order to generate more physiologically relevant human SpC models and propose some exciting new perspectives.
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Affiliation(s)
- Felix Buchner
- German Center for Neurodegenerative Diseases, 01307 Dresden, Germany
| | | | - Tobias Grass
- German Center for Neurodegenerative Diseases, 01307 Dresden, Germany
| | - Natalia Rodriguez-Muela
- German Center for Neurodegenerative Diseases, 01307 Dresden, Germany
- Center for Regenerative Therapies Dresden, Technische Universität Dresden, 01307 Dresden, Germany
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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66
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Luo J, Wu X, Cheng Y, Chen G, Wang J, Song X. Expression quantitative trait locus studies in the era of single-cell omics. Front Genet 2023; 14:1182579. [PMID: 37284065 PMCID: PMC10239882 DOI: 10.3389/fgene.2023.1182579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/26/2023] [Indexed: 06/08/2023] Open
Abstract
Genome-wide association studies have revealed that the regulation of gene expression bridges genetic variants and complex phenotypes. Profiling of the bulk transcriptome coupled with linkage analysis (expression quantitative trait locus (eQTL) mapping) has advanced our understanding of the relationship between genetic variants and gene regulation in the context of complex phenotypes. However, bulk transcriptomics has inherited limitations as the regulation of gene expression tends to be cell-type-specific. The advent of single-cell RNA-seq technology now enables the identification of the cell-type-specific regulation of gene expression through a single-cell eQTL (sc-eQTL). In this review, we first provide an overview of sc-eQTL studies, including data processing and the mapping procedure of the sc-eQTL. We then discuss the benefits and limitations of sc-eQTL analyses. Finally, we present an overview of the current and future applications of sc-eQTL discoveries.
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Affiliation(s)
- Jie Luo
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro‐products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yuan Cheng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guang Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro‐products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jian Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro‐products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xijiao Song
- State Key Laboratory for Managing Biotic and Chemical Threats to The Quality and Safety of Agro‐products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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67
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Morris JA, Caragine C, Daniloski Z, Domingo J, Barry T, Lu L, Davis K, Ziosi M, Glinos DA, Hao S, Mimitou EP, Smibert P, Roeder K, Katsevich E, Lappalainen T, Sanjana NE. Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens. Science 2023; 380:eadh7699. [PMID: 37141313 PMCID: PMC10518238 DOI: 10.1126/science.adh7699] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023]
Abstract
Most variants associated with complex traits and diseases identified by genome-wide association studies (GWAS) map to noncoding regions of the genome with unknown effects. Using ancestrally diverse, biobank-scale GWAS data, massively parallel CRISPR screens, and single-cell transcriptomic and proteomic sequencing, we discovered 124 cis-target genes of 91 noncoding blood trait GWAS loci. Using precise variant insertion through base editing, we connected specific variants with gene expression changes. We also identified trans-effect networks of noncoding loci when cis target genes encoded transcription factors or microRNAs. Networks were themselves enriched for GWAS variants and demonstrated polygenic contributions to complex traits. This platform enables massively parallel characterization of the target genes and mechanisms of human noncoding variants in both cis and trans.
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Affiliation(s)
- John A. Morris
- New York Genome Center, New York, NY, 10013, USA
- Department of Biology, New York University, New York, NY, 10003, USA
| | | | - Zharko Daniloski
- New York Genome Center, New York, NY, 10013, USA
- Department of Biology, New York University, New York, NY, 10003, USA
| | | | - Timothy Barry
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Lu Lu
- New York Genome Center, New York, NY, 10013, USA
| | - Kyrie Davis
- New York Genome Center, New York, NY, 10013, USA
| | | | | | - Stephanie Hao
- Technology Innovation Lab, New York Genome Center, New York, NY, 10013, USA
| | - Eleni P. Mimitou
- Technology Innovation Lab, New York Genome Center, New York, NY, 10013, USA
| | - Peter Smibert
- Technology Innovation Lab, New York Genome Center, New York, NY, 10013, USA
| | - Kathryn Roeder
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Eugene Katsevich
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, 10013, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, 171 65 Solna, Stockholm, Sweden
| | - Neville E. Sanjana
- New York Genome Center, New York, NY, 10013, USA
- Department of Biology, New York University, New York, NY, 10003, USA
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68
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Han JL, Heinson YW, Chua CJ, Liu W, Entcheva E. CRISPRi Gene Modulation and All-Optical Electrophysiology in Post-Differentiated Human iPSC-Cardiomyocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.07.539756. [PMID: 37214814 PMCID: PMC10197536 DOI: 10.1101/2023.05.07.539756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Uncovering gene-phenotype relationships can be enabled by precise gene modulation in human induced pluripotent stem-cell-derived cardiomyocytes (iPSC-CMs) and follow up phenotyping using scalable all-optical electrophysiology platforms. Such efforts towards human functional genomics can be aided by recent CRISPR-derived technologies for reversible gene inhibition or activation (CRISPRi/a). We set out to characterize the performance of CRISPRi in post-differentiated iPSC-CMs, targeting key cardiac ion channel genes, KCNH2, KCNJ2, and GJA1, and providing a multiparametric quantification of the effects on cardiac repolarization, stability of the resting membrane potential and conduction properties using all-optical tools. More potent CRISPRi effectors, e.g. Zim3, and optimized viral delivery led to improved performance on par with the use of CRISPRi iPSC lines. Confirmed mild yet specific phenotype changes when CRISPRi is deployed in non-dividing differentiated heart cells is an important step towards more holistic pre-clinical cardiotoxicity testing and for future therapeutic use in vivo.
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Affiliation(s)
- Julie L. Han
- Department of Biomedical Engineering, The George Washington University, Washington DC 20052, USA
| | - Yuli W. Heinson
- Department of Biomedical Engineering, The George Washington University, Washington DC 20052, USA
| | - Christianne J. Chua
- Department of Biomedical Engineering, The George Washington University, Washington DC 20052, USA
| | - Wei Liu
- Department of Biomedical Engineering, The George Washington University, Washington DC 20052, USA
| | - Emilia Entcheva
- Department of Biomedical Engineering, The George Washington University, Washington DC 20052, USA
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69
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Eade KT, Ansell BRE, Giles S, Fallon R, Harkins-Perry S, Nagasaki T, Tzaridis S, Wallace M, Mills EA, Farashi S, Johnson A, Sauer L, Hart B, Diaz-Rubio ME, Bahlo M, Metallo C, Allikmets R, Gantner ML, Bernstein PS, Friedlander M. iPSC-derived retinal pigmented epithelial cells from patients with macular telangiectasia show decreased mitochondrial function. J Clin Invest 2023; 133:e163771. [PMID: 37115691 PMCID: PMC10145939 DOI: 10.1172/jci163771] [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: 07/21/2022] [Accepted: 03/14/2023] [Indexed: 04/29/2023] Open
Abstract
Patient-derived induced pluripotent stem cells (iPSCs) provide a powerful tool for identifying cellular and molecular mechanisms of disease. Macular telangiectasia type 2 (MacTel) is a rare, late-onset degenerative retinal disease with an extremely heterogeneous genetic architecture, lending itself to the use of iPSCs. Whole-exome sequencing screens and pedigree analyses have identified rare causative mutations that account for less than 5% of cases. Metabolomic surveys of patient populations and GWAS have linked MacTel to decreased circulating levels of serine and elevated levels of neurotoxic 1-deoxysphingolipids (1-dSLs). However, retina-specific, disease-contributing factors have yet to be identified. Here, we used iPSC-differentiated retinal pigmented epithelial (iRPE) cells derived from donors with or without MacTel to screen for novel cell-intrinsic pathological mechanisms. We show that MacTel iRPE cells mimicked the low serine levels observed in serum from patients with MacTel. Through RNA-Seq and gene set enrichment pathway analysis, we determined that MacTel iRPE cells are enriched in cellular stress pathways and dysregulation of central carbon metabolism. Using respirometry and mitochondrial stress testing, we functionally validated that MacTel iRPE cells had a reduction in mitochondrial function that was independent of defects in serine biosynthesis and 1-dSL accumulation. Thus, we identified phenotypes that may constitute alternative disease mechanisms beyond the known serine/sphingolipid pathway.
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Affiliation(s)
- Kevin T. Eade
- The Lowy Medical Research Institute, La Jolla, California, USA
- Department of Molecular Medicine, The Scripps Research Institute (TSRI), La Jolla, California, USA
| | - Brendan Robert E. Ansell
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Sarah Giles
- The Lowy Medical Research Institute, La Jolla, California, USA
- Department of Molecular Medicine, The Scripps Research Institute (TSRI), La Jolla, California, USA
| | - Regis Fallon
- The Lowy Medical Research Institute, La Jolla, California, USA
- Department of Molecular Medicine, The Scripps Research Institute (TSRI), La Jolla, California, USA
| | - Sarah Harkins-Perry
- The Lowy Medical Research Institute, La Jolla, California, USA
- Department of Molecular Medicine, The Scripps Research Institute (TSRI), La Jolla, California, USA
| | - Takayuki Nagasaki
- Department of Ophthalmology and
- Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | - Simone Tzaridis
- The Lowy Medical Research Institute, La Jolla, California, USA
- Department of Molecular Medicine, The Scripps Research Institute (TSRI), La Jolla, California, USA
| | - Martina Wallace
- Institute of Food and Health, School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Elizabeth A. Mills
- The Lowy Medical Research Institute, La Jolla, California, USA
- Department of Molecular Medicine, The Scripps Research Institute (TSRI), La Jolla, California, USA
| | - Samaneh Farashi
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Alec Johnson
- The Lowy Medical Research Institute, La Jolla, California, USA
| | - Lydia Sauer
- Moran Eye Center, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Barbara Hart
- Moran Eye Center, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - M. Elena Diaz-Rubio
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Melanie Bahlo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Christian Metallo
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Rando Allikmets
- Department of Ophthalmology and
- Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | - Marin L. Gantner
- The Lowy Medical Research Institute, La Jolla, California, USA
- Department of Molecular Medicine, The Scripps Research Institute (TSRI), La Jolla, California, USA
| | - Paul S. Bernstein
- Moran Eye Center, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Martin Friedlander
- The Lowy Medical Research Institute, La Jolla, California, USA
- Department of Molecular Medicine, The Scripps Research Institute (TSRI), La Jolla, California, USA
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70
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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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71
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Aydin S, Pham DT, Zhang T, Keele GR, Skelly DA, Paulo JA, Pankratz M, Choi T, Gygi SP, Reinholdt LG, Baker CL, Churchill GA, Munger SC. Genetic dissection of the pluripotent proteome through multi-omics data integration. CELL GENOMICS 2023; 3:100283. [PMID: 37082146 PMCID: PMC10112288 DOI: 10.1016/j.xgen.2023.100283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/12/2022] [Accepted: 02/27/2023] [Indexed: 04/22/2023]
Abstract
Genetic background drives phenotypic variability in pluripotent stem cells (PSCs). Most studies to date have used transcript abundance as the primary molecular readout of cell state in PSCs. We performed a comprehensive proteogenomics analysis of 190 genetically diverse mouse embryonic stem cell (mESC) lines. The quantitative proteome is highly variable across lines, and we identified pluripotency-associated pathways that were differentially activated in the proteomics data that were not evident in transcriptome data from the same lines. Integration of protein abundance to transcript levels and chromatin accessibility revealed broad co-variation across molecular layers as well as shared and unique drivers of quantitative variation in pluripotency-associated pathways. Quantitative trait locus (QTL) mapping localized the drivers of these multi-omic signatures to genomic hotspots. This study reveals post-transcriptional mechanisms and genetic interactions that underlie quantitative variability in the pluripotent proteome and provides a regulatory map for mESCs that can provide a basis for future mechanistic studies.
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Affiliation(s)
- Selcan Aydin
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Duy T. Pham
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Tian Zhang
- Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | - Ted Choi
- Predictive Biology, Inc., Carlsbad, CA 92010, USA
| | | | - Laura G. Reinholdt
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Christopher L. Baker
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Gary A. Churchill
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
| | - Steven C. Munger
- The Jackson Laboratory, Bar Harbor, ME 04609, USA
- Graduate School of Biomedical Sciences, Tufts University, Boston, MA 02111, USA
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72
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Kerimov N, Tambets R, Hayhurst JD, Rahu I, Kolberg P, Raudvere U, Kuzmin I, Chowdhary A, Vija A, Teras HJ, Kanai M, Ulirsch J, Ryten M, Hardy J, Guelfi S, Trabzuni D, Kim-Hellmuth S, Rayner W, Finucane H, Peterson H, Mosaku A, Parkinson H, Alasoo K. Systematic visualisation of molecular QTLs reveals variant mechanisms at GWAS loci. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535816. [PMID: 37066341 PMCID: PMC10104061 DOI: 10.1101/2023.04.06.535816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Splicing quantitative trait loci (QTLs) have been implicated as a common mechanism underlying complex trait associations. However, utilising splicing QTLs in target discovery and prioritisation has been challenging due to extensive data normalisation which often renders the direction of the genetic effect as well as its magnitude difficult to interpret. This is further complicated by the fact that strong expression QTLs often manifest as weak splicing QTLs and vice versa, making it difficult to uniquely identify the underlying molecular mechanism at each locus. We find that these ambiguities can be mitigated by visualising the association between the genotype and average RNA sequencing read coverage in the region. Here, we generate these QTL coverage plots for 1.7 million molecular QTL associations in the eQTL Catalogue identified with five quantification methods. We illustrate the utility of these QTL coverage plots by performing colocalisation between vitamin D levels in the UK Biobank and all molecular QTLs in the eQTL Catalogue. We find that while visually confirmed splicing QTLs explain just 6/53 of the colocalising signals, they are significantly less pleiotropic than eQTLs and identify a prioritised causal gene in 4/6 cases. All our association summary statistics and QTL coverage plots are freely available at https://www.ebi.ac.uk/eqtl/.
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Affiliation(s)
- Nurlan Kerimov
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ralf Tambets
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - James D Hayhurst
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ida Rahu
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Peep Kolberg
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Uku Raudvere
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Ivan Kuzmin
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Anshika Chowdhary
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Andreas Vija
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Hans J Teras
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Masahiro Kanai
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob Ulirsch
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - John Hardy
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Sebastian Guelfi
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Daniah Trabzuni
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London
| | - Sarah Kim-Hellmuth
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital LMU Munich, Munich, Germany
| | - Will Rayner
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Hilary Finucane
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hedi Peterson
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
| | - Abayomi Mosaku
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Helen Parkinson
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kaur Alasoo
- Institute of Computer Science, University of Tartu, Tartu, 51009, Estonia
- Open Targets, South Building, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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73
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She R, Fair T, Schaefer NK, Saunders RA, Pavlovic BJ, Weissman JS, Pollen AA. Comparative landscape of genetic dependencies in human and chimpanzee stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.19.533346. [PMID: 36993685 PMCID: PMC10055274 DOI: 10.1101/2023.03.19.533346] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Comparative studies of great apes provide a window into our evolutionary past, but the extent and identity of cellular differences that emerged during hominin evolution remain largely unexplored. We established a comparative loss-of-function approach to evaluate whether changes in human cells alter requirements for essential genes. By performing genome-wide CRISPR interference screens in human and chimpanzee pluripotent stem cells, we identified 75 genes with species-specific effects on cellular proliferation. These genes comprised coherent processes, including cell cycle progression and lysosomal signaling, which we determined to be human-derived by comparison with orangutan cells. Human-specific robustness to CDK2 and CCNE1 depletion persisted in neural progenitor cells, providing support for the G1-phase length hypothesis as a potential evolutionary mechanism in human brain expansion. Our findings demonstrate that evolutionary changes in human cells can reshape the landscape of essential genes and establish a platform for systematically uncovering latent cellular and molecular differences between species.
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Affiliation(s)
- Richard She
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- These authors contributed equally: Richard She, Tyler Fair
| | - Tyler Fair
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- These authors contributed equally: Richard She, Tyler Fair
| | - Nathan K. Schaefer
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Reuben A. Saunders
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA, USA
| | - Bryan J. Pavlovic
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan S. Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute Technology, Cambridge 02142, MA
| | - Alex A. Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Lead contact
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74
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Pandemic city: Village-in-a-dish unlocks dynamic genetic effects in the brain. Cell Stem Cell 2023; 30:239-241. [PMID: 36868190 DOI: 10.1016/j.stem.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
In this issue, Wells et al. combine genetic multiplexing ("village-in-a-dish") and Stem-cell-derived NGN2-accelerated Progenitors (SNaPs) to evaluate genotype-phenotype relationships across 100 donors in the context of Zika virus infection in the developing brain. This resource will be broadly applicable in uncovering how genetic variation underlies risk for neurodevelopmental disorders.
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75
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Păun O, Tan YX, Patel H, Strohbuecker S, Ghanate A, Cobolli-Gigli C, Llorian Sopena M, Gerontogianni L, Goldstone R, Ang SL, Guillemot F, Dias C. Pioneer factor ASCL1 cooperates with the mSWI/SNF complex at distal regulatory elements to regulate human neural differentiation. Genes Dev 2023; 37:218-242. [PMID: 36931659 PMCID: PMC10111863 DOI: 10.1101/gad.350269.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023]
Abstract
Pioneer transcription factors are thought to play pivotal roles in developmental processes by binding nucleosomal DNA to activate gene expression, though mechanisms through which pioneer transcription factors remodel chromatin remain unclear. Here, using single-cell transcriptomics, we show that endogenous expression of neurogenic transcription factor ASCL1, considered a classical pioneer factor, defines a transient population of progenitors in human neural differentiation. Testing ASCL1's pioneer function using a knockout model to define the unbound state, we found that endogenous expression of ASCL1 drives progenitor differentiation by cis-regulation both as a classical pioneer factor and as a nonpioneer remodeler, where ASCL1 binds permissive chromatin to induce chromatin conformation changes. ASCL1 interacts with BAF SWI/SNF chromatin remodeling complexes, primarily at targets where it acts as a nonpioneer factor, and we provide evidence for codependent DNA binding and remodeling at a subset of ASCL1 and SWI/SNF cotargets. Our findings provide new insights into ASCL1 function regulating activation of long-range regulatory elements in human neurogenesis and uncover a novel mechanism of its chromatin remodeling function codependent on partner ATPase activity.
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Affiliation(s)
- Oana Păun
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Yu Xuan Tan
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Harshil Patel
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Stephanie Strohbuecker
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Avinash Ghanate
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Clementina Cobolli-Gigli
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Miriam Llorian Sopena
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Lina Gerontogianni
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Robert Goldstone
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Siew-Lan Ang
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - François Guillemot
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom;
| | - Cristina Dias
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom;
- Medical and Molecular Genetics, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London SE1 9RT, United Kingdom
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76
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Dang X, Liu J, Zhang Z, Luo XJ. Mendelian Randomization Study Using Dopaminergic Neuron-Specific eQTL Identifies Novel Risk Genes for Schizophrenia. Mol Neurobiol 2023; 60:1537-1546. [PMID: 36517655 DOI: 10.1007/s12035-022-03160-3] [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: 06/06/2022] [Accepted: 12/04/2022] [Indexed: 12/23/2022]
Abstract
Multiple integrative studies have been performed to identify the potential target genes of the non-coding schizophrenia (SCZ) risk variants. However, all the integrative studies used expression quantitative trait loci (eQTL) data from bulk tissues. Considering the cell type-specific regulatory effect of many genetic variants, it is important to conduct integrative studies using cell type-specific eQTL data. Here, we conduct a Mendelian randomization (MR) study by integrating genome-wide associations of SCZ (74,776 cases and 101,023 controls) and eQTL data (N = 215) from dopaminergic neurons, which were differentiated from human-induced pluripotent stem cell (iPSC) lines. For eQTL from young post-mitotic dopaminergic neurons (differentiation of iPSC for 30 days, D30), we identified 34 genes whose genetically regulated expression in dopaminergic neurons may have a causal role in SCZ. Among which, ARL3 showed the most significant associations with SCZ. For eQTL from more mature dopaminergic neurons (D52), we identified 37 potential SCZ causal genes, and ARL3 and GNL3 showed the most significant associations. Only 12 genes showed significant associations with SCZ in both D30 and D52 eQTL datasets, indicating the time point-specific genetic regulatory effects in young post-mitotic dopaminergic neurons and more mature dopaminergic neurons. Comparing the results from dopaminergic neurons with bulk brain tissues prioritized 2 high-confidence risk genes, including DDHD2 and GALNT10. Our study identifies multiple risk genes whose genetically regulated expression in dopaminergic neurons may have a causal role in SCZ. Further mechanistic investigation will provide pivotal insights into SCZ pathophysiology.
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Affiliation(s)
- Xinglun Dang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Jiewei Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Zhijun Zhang
- Zhongda Hospital, Advanced Institute for Life and Health, Southeast University, Nanjing, 210096, China
- Department of Neurology, School of Medicine, Affiliated Zhongda Hospital, Research Institution of Neuropsychiatry, Southeast University, Nanjing, 210009, Jiangsu Province, China
| | - Xiong-Jian Luo
- Zhongda Hospital, Advanced Institute for Life and Health, Southeast University, Nanjing, 210096, China.
- Department of Neurology, School of Medicine, Affiliated Zhongda Hospital, Research Institution of Neuropsychiatry, Southeast University, Nanjing, 210009, Jiangsu Province, China.
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77
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Lu C, Zaucha J, Gam R, Fang H, Ben Smithers, Oates ME, Bernabe-Rubio M, Williams J, Zelenka N, Pandurangan AP, Tandon H, Shihab H, Kalaivani R, Sung M, Sardar AJ, Tzovoras BG, Danovi D, Gough J. Hypothesis-free phenotype prediction within a genetics-first framework. Nat Commun 2023; 14:919. [PMID: 36808136 PMCID: PMC9938118 DOI: 10.1038/s41467-023-36634-6] [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: 02/16/2022] [Accepted: 02/10/2023] [Indexed: 02/19/2023] Open
Abstract
Cohort-wide sequencing studies have revealed that the largest category of variants is those deemed 'rare', even for the subset located in coding regions (99% of known coding variants are seen in less than 1% of the population. Associative methods give some understanding how rare genetic variants influence disease and organism-level phenotypes. But here we show that additional discoveries can be made through a knowledge-based approach using protein domains and ontologies (function and phenotype) that considers all coding variants regardless of allele frequency. We describe an ab initio, genetics-first method making molecular knowledge-based interpretations for exome-wide non-synonymous variants for phenotypes at the organism and cellular level. By using this reverse approach, we identify plausible genetic causes for developmental disorders that have eluded other established methods and present molecular hypotheses for the causal genetics of 40 phenotypes generated from a direct-to-consumer genotype cohort. This system offers a chance to extract further discovery from genetic data after standard tools have been applied.
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Affiliation(s)
- Chang Lu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jan Zaucha
- Department of Computer Science, University of Bristol, Bristol, BS8 1UB, UK
| | - Rihab Gam
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Hai Fang
- Department of Computer Science, University of Bristol, Bristol, BS8 1UB, UK
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ben Smithers
- Department of Computer Science, University of Bristol, Bristol, BS8 1UB, UK
| | - Matt E Oates
- Department of Computer Science, University of Bristol, Bristol, BS8 1UB, UK
| | - Miguel Bernabe-Rubio
- Centre for Gene Therapy and Regenerative Medicine, King's College London, Guy's Hospital, Floor 28, Tower Wing, Great Maze Pond, London, SE1 9RT, UK
| | - James Williams
- Centre for Gene Therapy and Regenerative Medicine, King's College London, Guy's Hospital, Floor 28, Tower Wing, Great Maze Pond, London, SE1 9RT, UK
| | - Natalie Zelenka
- Department of Computer Science, University of Bristol, Bristol, BS8 1UB, UK
| | - Arun Prasad Pandurangan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Himani Tandon
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Hashem Shihab
- Department of Computer Science, University of Bristol, Bristol, BS8 1UB, UK
| | - Raju Kalaivani
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Minkyung Sung
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Adam J Sardar
- Department of Computer Science, University of Bristol, Bristol, BS8 1UB, UK
| | | | - Davide Danovi
- Centre for Gene Therapy and Regenerative Medicine, King's College London, Guy's Hospital, Floor 28, Tower Wing, Great Maze Pond, London, SE1 9RT, UK
| | - Julian Gough
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
- Department of Computer Science, University of Bristol, Bristol, BS8 1UB, UK.
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78
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Wang Y, Liu C, Qiao X, Han X, Liu ZP. PKI: A bioinformatics method of quantifying the importance of nodes in gene regulatory network via a pseudo knockout index. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194911. [PMID: 36804477 DOI: 10.1016/j.bbagrm.2023.194911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/09/2023] [Accepted: 01/30/2023] [Indexed: 02/18/2023]
Abstract
BACKGROUND Gene regulatory network (GRN) is a model that characterizes the complex relationships between genes and thereby provides an informatics environment to measure the importance of nodes. The evaluation of important nodes in a GRN can effectively refer to their functional implications severing as key players in particular biological processes, such as master regulator and driver gene. Currently, it is mainly based on network topological parameters and focuses only on evaluating a single node individually. However, genes and products play their functions by interacting with each other. It is worth noting that the effects of gene combinations in GRN are not simply additive. Key combinations discovery is of significance in revealing gene sets with important functions. Recently, with the development of single-cell RNA-sequencing (scRNA-seq) technology, we can quantify gene expression profiles of individual cells that provide the potential to identify crucial nodes in gene regulations regarding specific condition, e.g., stem cell differentiation. RESULTS In this paper, we propose a bioinformatics method, called Pseudo Knockout Importance (PKI), to quantify the importance of node and node sets in a specific GRN structure using time-course scRNA-seq data. First, we construct ordinary differential equations to approach the gene regulations during cell differentiation. Then we design gene pseudo knockout experiments and define PKI score evaluation criteria based on the coefficient of determination. The importance of nodes can be described as the influence on the ODE system of removing variables. For key gene combinations, PKI is derived as a combinatorial optimization problem of quantifying the in silico gene knockout effects. CONCLUSIONS Here, we focus our analyses on the specific GRN of embryonic stem cells with time series gene expression profile. To verify the effectiveness and advantage of PKI method, we compare its node importance rankings with other twelve kinds of centrality-based methods, such as degree and Latora closeness. For key node combinations, we compare the results with the method based on minimum dominant set. Moreover, the famous combinations of transcription factors in induced pluripotent stem cell are also employed to verify the vital gene combinations identified by PKI. These results demonstrate the reliability and superiority of the proposed method.
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Affiliation(s)
- Yijuan Wang
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China
| | - Chao Liu
- Department of Orthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Xu Qiao
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China
| | - Xianhua Han
- Faculty of Science, Yamaguchi University, Yamaguchi 753-8511, Japan
| | - Zhi-Ping Liu
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China.
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79
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Minaya MA, Mahali S, Iyer AK, Eteleeb AM, Martinez R, Huang G, Budde J, Temple S, Nana AL, Seeley WW, Spina S, Grinberg LT, Harari O, Karch CM. Conserved gene signatures shared among MAPT mutations reveal defects in calcium signaling. Front Mol Biosci 2023; 10:1051494. [PMID: 36845551 PMCID: PMC9948093 DOI: 10.3389/fmolb.2023.1051494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/13/2023] [Indexed: 02/11/2023] Open
Abstract
Introduction: More than 50 mutations in the MAPT gene result in heterogeneous forms of frontotemporal lobar dementia with tau inclusions (FTLD-Tau). However, early pathogenic events that lead to disease and the degree to which they are common across MAPT mutations remain poorly understood. The goal of this study is to determine whether there is a common molecular signature of FTLD-Tau. Methods: We analyzed genes differentially expressed in induced pluripotent stem cell-derived neurons (iPSC-neurons) that represent the three major categories of MAPT mutations: splicing (IVS10 + 16), exon 10 (p.P301L), and C-terminal (p.R406W) compared with isogenic controls. The genes that were commonly differentially expressed in MAPT IVS10 + 16, p.P301L, and p.R406W neurons were enriched in trans-synaptic signaling, neuronal processes, and lysosomal function. Many of these pathways are sensitive to disruptions in calcium homeostasis. One gene, CALB1, was significantly reduced across the three MAPT mutant iPSC-neurons and in a mouse model of tau accumulation. We observed a significant reduction in calcium levels in MAPT mutant neurons compared with isogenic controls, pointing to a functional consequence of this disrupted gene expression. Finally, a subset of genes commonly differentially expressed across MAPT mutations were also dysregulated in brains from MAPT mutation carriers and to a lesser extent in brains from sporadic Alzheimer disease and progressive supranuclear palsy, suggesting that molecular signatures relevant to genetic and sporadic forms of tauopathy are captured in a dish. The results from this study demonstrate that iPSC-neurons capture molecular processes that occur in human brains and can be used to pinpoint common molecular pathways involving synaptic and lysosomal function and neuronal development, which may be regulated by disruptions in calcium homeostasis.
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Affiliation(s)
- Miguel A. Minaya
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Sidhartha Mahali
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Abhirami K. Iyer
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Abdallah M. Eteleeb
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Rita Martinez
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Guangming Huang
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - John Budde
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
| | - Sally Temple
- Neural Stem Cell Institute, Rensselaer, NY, United States
| | - Alissa L. Nana
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - William W. Seeley
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Salvatore Spina
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
| | - Lea T. Grinberg
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Department of Pathology, University of Sao Paulo, Sao Paulo, Brazil
| | - Oscar Harari
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
- Hope Center for Neurological Disorders, Washington University in St Louis, St Louis, MO, United States
- NeuroGenomics and Informatics Center, Washington University in St Louis, St Louis, MO, United States
| | - Celeste M. Karch
- Department of Psychiatry, Washington University in St Louis, St Louis, MO, United States
- Hope Center for Neurological Disorders, Washington University in St Louis, St Louis, MO, United States
- NeuroGenomics and Informatics Center, Washington University in St Louis, St Louis, MO, United States
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80
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Transition from Animal-Based to Human Induced Pluripotent Stem Cells (iPSCs)-Based Models of Neurodevelopmental Disorders: Opportunities and Challenges. Cells 2023; 12:cells12040538. [PMID: 36831205 PMCID: PMC9954744 DOI: 10.3390/cells12040538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Neurodevelopmental disorders (NDDs) arise from the disruption of highly coordinated mechanisms underlying brain development, which results in impaired sensory, motor and/or cognitive functions. Although rodent models have offered very relevant insights to the field, the translation of findings to clinics, particularly regarding therapeutic approaches for these diseases, remains challenging. Part of the explanation for this failure may be the genetic differences-some targets not being conserved between species-and, most importantly, the differences in regulation of gene expression. This prompts the use of human-derived models to study NDDS. The generation of human induced pluripotent stem cells (hIPSCs) added a new suitable alternative to overcome species limitations, allowing for the study of human neuronal development while maintaining the genetic background of the donor patient. Several hIPSC models of NDDs already proved their worth by mimicking several pathological phenotypes found in humans. In this review, we highlight the utility of hIPSCs to pave new paths for NDD research and development of new therapeutic tools, summarize the challenges and advances of hIPSC-culture and neuronal differentiation protocols and discuss the best way to take advantage of these models, illustrating this with examples of success for some NDDs.
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81
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Castillo Bautista CM, Sterneckert J. Progress and challenges in directing the differentiation of human iPSCs into spinal motor neurons. Front Cell Dev Biol 2023; 10:1089970. [PMID: 36684437 PMCID: PMC9849822 DOI: 10.3389/fcell.2022.1089970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/21/2022] [Indexed: 01/07/2023] Open
Abstract
Motor neuron (MN) diseases, including amyotrophic lateral sclerosis, progressive bulbar palsy, primary lateral sclerosis and spinal muscular atrophy, cause progressive paralysis and, in many cases, death. A better understanding of the molecular mechanisms of pathogenesis is urgently needed to identify more effective therapies. However, studying MNs has been extremely difficult because they are inaccessible in the spinal cord. Induced pluripotent stem cells (iPSCs) can generate a theoretically limitless number of MNs from a specific patient, making them powerful tools for studying MN diseases. However, to reach their potential, iPSCs need to be directed to efficiently differentiate into functional MNs. Here, we review the reported differentiation protocols for spinal MNs, including induction with small molecules, expression of lineage-specific transcription factors, 2-dimensional and 3-dimensional cultures, as well as the implementation of microfluidics devices and co-cultures with other cell types, including skeletal muscle. We will summarize the advantages and disadvantages of each strategy. In addition, we will provide insights into how to address some of the remaining challenges, including reproducibly obtaining mature and aged MNs.
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Affiliation(s)
| | - Jared Sterneckert
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany,Medical Faculty Carl Gustav Carus of TU Dresden, Dresden, Germany,*Correspondence: Jared Sterneckert,
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82
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Ismaili D, Schulz C, Horváth A, Koivumäki JT, Mika D, Hansen A, Eschenhagen T, Christ T. Human induced pluripotent stem cell-derived cardiomyocytes as an electrophysiological model: Opportunities and challenges-The Hamburg perspective. Front Physiol 2023; 14:1132165. [PMID: 36875015 PMCID: PMC9978010 DOI: 10.3389/fphys.2023.1132165] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
Models based on human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) are proposed in almost any field of physiology and pharmacology. The development of human induced pluripotent stem cell-derived cardiomyocytes is expected to become a step forward to increase the translational power of cardiovascular research. Importantly they should allow to study genetic effects on an electrophysiological background close to the human situation. However, biological and methodological issues revealed when human induced pluripotent stem cell-derived cardiomyocytes were used in experimental electrophysiology. We will discuss some of the challenges that should be considered when human induced pluripotent stem cell-derived cardiomyocytes will be used as a physiological model.
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Affiliation(s)
- Djemail Ismaili
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Cardiology, University Heart and Vascular Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Carl Schulz
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - András Horváth
- Translational Cardiology, Department of Cardiology, Inselspital, University Hospital Bern, University of Bern, Bern, Switzerland
| | - Jussi T Koivumäki
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Delphine Mika
- Inserm, UMR-S 1180, Université Paris-Saclay, Orsay, France
| | - Arne Hansen
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Thomas Eschenhagen
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
| | - Torsten Christ
- Institute of Experimental Pharmacology and Toxicology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Hamburg, Germany
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83
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Hart A, Nguyen LK. Meta-Dynamic Network Modelling for Biochemical Networks. Methods Mol Biol 2023; 2634:167-189. [PMID: 37074579 DOI: 10.1007/978-1-0716-3008-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
ODE modelling requires accurate knowledge of parameter and state variable values to deliver accurate and robust predictions. Parameters and state variables, however, are rarely static and immutable entities, especially in a biological context. This observation undermines the predictions made by ODE models that rely on specific parameter and state variable values and limits the contexts in which their predictions remain accurate and useful. Meta-dynamic network (MDN) modelling is a technique that can be synergistically integrated into an ODE modelling pipeline to assist in overcoming these limitations. The core mechanic of MDN modelling is the generation of a large number of model instances, each with a unique set of parameters and/or state variable values, followed by the simulation of each to determine how parameter and state variable variation affects protein dynamics. This process reveals the range of possible protein dynamics for a given network topology. Since MDN modelling is integrated with traditional ODE modelling, it can also be used to investigate the underlying causal mechanics. This technique is particularly suited to the investigation of network behaviors in systems that are highly heterogenous or systems wherein the network properties can change over time. MDN is a collection of principles rather than a strict protocol, so in this chapter, we have introduced the core principles using an example, the Hippo-ERK crosstalk signalling network.
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Affiliation(s)
- Anthony Hart
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, Australia
| | - Lan K Nguyen
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, VIC, Australia.
- Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
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84
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Identification of marker genes to monitor residual iPSCs in iPSC-derived products. Cytotherapy 2023; 25:59-67. [PMID: 36319564 DOI: 10.1016/j.jcyt.2022.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/08/2022] [Accepted: 09/27/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND Engineered tissues and cell therapies based on human induced pluripotent stem cells (iPSCs) represent a promising approach for novel medicines. However, iPSC-derived cells and tissues may contain residual undifferentiated iPSCs that could lead to teratoma formation after implantation into patients. As a consequence, highly sensitive and specific methods for detecting residual undifferentiated iPSCs are indispensable for safety evaluations of iPSC-based therapies. The present study provides an approach for identifying potential marker genes for iPSC impurities in iPSC-derived cells using RNA sequencing data from iPSCs and various differentiated cell types. METHODS Identifying iPSC marker genes for each cell type individually provided a larger and more specific set of potential marker genes than considering all cell types in the analysis. Thus, the authors focused on identifying markers for iPSC impurities in iPSC-derived cardiomyocytes (iCMs) and validated the selected genes by reverse transcription quantitative polymerase chain reaction. The sensitivity of the candidate genes was determined by spiking different amounts of iPSCs into iCMs and their performance was compared with the previously suggested marker lin-28 homolog A (LIN28A). RESULTS Embryonic stem cell-related gene (ESRG), long intergenic non-protein coding RNA 678 (LINC00678), CaM kinase-like vesicle-associated (CAMKV), indoleamine 2,3-dioxygenase 1 (IDO1), chondromodulin (CNMD), LINE1-type transposase domain containing 1 (L1DT1), LIN28A, lymphocyte-specific protein tyrosine kinase (LCK), vertebrae development-associated (VRTN) and zinc finger and SCAN domain containing 10 (ZSCAN10) detected contaminant iPSCs among iCMs with a limit of detection that ranged from 0.001% to 0.1% depending on the gene and iCM batch used. CONCLUSIONS Using the example of iCMs, the authors provide a strategy for identifying a set of highly specific and sensitive markers that can be used for quality assessment of iPSC-derived products.
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85
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Weber CM, Moiz B, Zic SM, Alpízar Vargas V, Li A, Clyne AM. Induced pluripotent stem cell-derived cells model brain microvascular endothelial cell glucose metabolism. Fluids Barriers CNS 2022; 19:98. [PMID: 36494870 PMCID: PMC9733016 DOI: 10.1186/s12987-022-00395-z] [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: 09/15/2022] [Accepted: 11/27/2022] [Indexed: 12/13/2022] Open
Abstract
Glucose transport from the blood into the brain is tightly regulated by brain microvascular endothelial cells (BMEC), which also use glucose as their primary energy source. To study how BMEC glucose transport contributes to cerebral glucose hypometabolism in diseases such as Alzheimer's disease, it is essential to understand how these cells metabolize glucose. Human primary BMEC (hpBMEC) can be used for BMEC metabolism studies; however, they have poor barrier function and may not recapitulate in vivo BMEC function. iPSC-derived BMEC-like cells (hiBMEC) are readily available and have good barrier function but may have an underlying epithelial signature. In this study, we examined differences between hpBMEC and hiBMEC glucose metabolism using a combination of dynamic metabolic measurements, metabolic mass spectrometry, RNA sequencing, and Western blots. hiBMEC had decreased glycolytic flux relative to hpBMEC, and the overall metabolomes and metabolic enzyme levels were different between the two cell types. However, hpBMEC and hiBMEC had similar glucose metabolism, including nearly identical glucose labeled fractions of glycolytic and TCA cycle metabolites. Treatment with astrocyte conditioned media and high glucose increased glycolysis in both hpBMEC and hiBMEC, though hpBMEC decreased glycolysis in response to fluvastatin while hiBMEC did not. Together, these results suggest that hiBMEC can be used to model cerebral vascular glucose metabolism, which expands their use beyond barrier models.
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Affiliation(s)
| | - Bilal Moiz
- University of Maryland, College Park, MD, 20742, USA
| | - Sophia M Zic
- University of Maryland, College Park, MD, 20742, USA
| | | | - Andrew Li
- University of Maryland, College Park, MD, 20742, USA
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86
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Kaneski CR, Hanover JA, Schueler Hoffman UH. Generation of GLA-knockout human embryonic stem cell lines to model peripheral neuropathy in Fabry disease. Mol Genet Metab Rep 2022; 33:100914. [PMID: 36092250 PMCID: PMC9449667 DOI: 10.1016/j.ymgmr.2022.100914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Christine R. Kaneski
- Corresponding author at: National Institutes of Health, Bldg. 8, Room B122, Bethesda, MD 20892, USA.
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87
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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: 58] [Impact Index Per Article: 29.0] [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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88
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Chear S, Perry S, Wilson R, Bindoff A, Talbot J, Ware TL, Grubman A, Vickers JC, Pébay A, Ruddle JB, King AE, Hewitt AW, Cook AL. Lysosomal alterations and decreased electrophysiological activity in CLN3 disease patient-derived cortical neurons. Dis Model Mech 2022; 15:dmm049651. [PMID: 36453132 PMCID: PMC10655821 DOI: 10.1242/dmm.049651] [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: 05/10/2022] [Accepted: 11/17/2022] [Indexed: 12/02/2022] Open
Abstract
CLN3 disease is a lysosomal storage disorder associated with fatal neurodegeneration that is caused by mutations in CLN3, with most affected individuals carrying at least one allele with a 966 bp deletion. Using CRISPR/Cas9, we corrected the 966 bp deletion mutation in human induced pluripotent stem cells (iPSCs) of a compound heterozygous patient (CLN3 Δ 966 bp and E295K). We differentiated these isogenic iPSCs, and iPSCs from an unrelated healthy control donor, to neurons and identified disease-related changes relating to protein synthesis, trafficking and degradation, and in neuronal activity, which were not apparent in CLN3-corrected or healthy control neurons. CLN3 neurons showed numerous membrane-bound vacuoles containing diverse storage material and hyperglycosylation of the lysosomal LAMP1 protein. Proteomic analysis showed increase in lysosomal-related proteins and many ribosomal subunit proteins in CLN3 neurons, accompanied by downregulation of proteins related to axon guidance and endocytosis. CLN3 neurons also had lower electrophysical activity as recorded using microelectrode arrays. These data implicate inter-related pathways in protein homeostasis and neurite arborization as contributing to CLN3 disease, and which could be potential targets for therapy.
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Affiliation(s)
- Sueanne Chear
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Sharn Perry
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, TAS 7001, Australia
| | - Aidan Bindoff
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Jana Talbot
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Tyson L. Ware
- Department of Paediatrics, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - Alexandra Grubman
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - James C. Vickers
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC 3010, Australia
- Department of Surgery, Royal Melbourne Hospital, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jonathan B. Ruddle
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Anna E. King
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Alex W. Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7001, Australia
| | - Anthony L. Cook
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
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89
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Tabet D, Parikh V, Mali P, Roth FP, Claussnitzer M. Scalable Functional Assays for the Interpretation of Human Genetic Variation. Annu Rev Genet 2022; 56:441-465. [PMID: 36055970 DOI: 10.1146/annurev-genet-072920-032107] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Scalable sequence-function studies have enabled the systematic analysis and cataloging of hundreds of thousands of coding and noncoding genetic variants in the human genome. This has improved clinical variant interpretation and provided insights into the molecular, biophysical, and cellular effects of genetic variants at an astonishing scale and resolution across the spectrum of allele frequencies. In this review, we explore current applications and prospects for the field and outline the principles underlying scalable functional assay design, with a focus on the study of single-nucleotide coding and noncoding variants.
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Affiliation(s)
- Daniel Tabet
- Donnelly Centre, Department of Molecular Genetics, and Department of Computer Science, University of Toronto, Toronto, Ontario, Canada;
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Victoria Parikh
- Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Prashant Mali
- Department of Bioengineering, University of California, San Diego, California, USA
| | - Frederick P Roth
- Donnelly Centre, Department of Molecular Genetics, and Department of Computer Science, University of Toronto, Toronto, Ontario, Canada;
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, Ontario, Canada
| | - Melina Claussnitzer
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Genomic Medicine and Endocrine Division, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Harvard University, Boston, Massachusetts, USA;
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90
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Greater genetic diversity is needed in human pluripotent stem cell models. Nat Commun 2022; 13:7301. [PMID: 36435871 PMCID: PMC9701202 DOI: 10.1038/s41467-022-34940-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 11/11/2022] [Indexed: 11/28/2022] Open
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91
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Kunitomi A, Hirohata R, Arreola V, Osawa M, Kato TM, Nomura M, Kawaguchi J, Hara H, Kusano K, Takashima Y, Takahashi K, Fukuda K, Takasu N, Yamanaka S. Improved Sendai viral system for reprogramming to naive pluripotency. CELL REPORTS METHODS 2022; 2:100317. [PMID: 36447645 PMCID: PMC9701587 DOI: 10.1016/j.crmeth.2022.100317] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/07/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Naive human induced pluripotent stem cells (iPSCs) can be generated by reprogramming somatic cells with Sendai virus (SeV) vectors. However, only dermal fibroblasts have been successfully reprogrammed this way, and the process requires culture on feeder cells. Moreover, SeV vectors are highly persistent and inhibit subsequent differentiation of iPSCs. Here, we report a modified SeV vector system to generate transgene-free naive human iPSCs with superior differentiation potential. The modified method can be applied not only to fibroblasts but also to other somatic cell types. SeV vectors disappear quickly at early passages, and this approach enables the generation of naive iPSCs in a feeder-free culture. The naive iPSCs generated by this method show better differentiation to trilineage and extra-embryonic trophectoderm than those derived by conventional methods. This method can expand the application of iPSCs to research on early human development and regenerative medicine.
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Affiliation(s)
- Akira Kunitomi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Ryoko Hirohata
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
- CiRA Foundation, Kyoto 606-8397, Japan
| | - Vanessa Arreola
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Mitsujiro Osawa
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Tomoaki M. Kato
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
- CiRA Foundation, Kyoto 606-8397, Japan
| | - Masaki Nomura
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
- CiRA Foundation, Kyoto 606-8397, Japan
| | | | - Hiroto Hara
- ID Pharma Co., Ltd., Ibaraki 300-2611, Japan
| | | | - Yasuhiro Takashima
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Kazutoshi Takahashi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
| | - Keiichi Fukuda
- Department of Cardiology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Naoko Takasu
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
- CiRA Foundation, Kyoto 606-8397, Japan
| | - Shinya Yamanaka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
- CiRA Foundation, Kyoto 606-8397, Japan
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
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92
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Zhao Q, Liu K, Zhang L, Li Z, Wang L, Cao J, Xu Y, Zheng A, Chen Q, Zhao T. BNIP3-dependent mitophagy safeguards ESC genomic integrity via preventing oxidative stress-induced DNA damage and protecting homologous recombination. Cell Death Dis 2022; 13:976. [PMID: 36402748 PMCID: PMC9675825 DOI: 10.1038/s41419-022-05413-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 11/03/2022] [Accepted: 11/07/2022] [Indexed: 11/21/2022]
Abstract
Embryonic stem cells (ESCs) have a significantly lower mutation load compared to somatic cells, but the mechanisms that guard genomic integrity in ESCs remain largely unknown. Here we show that BNIP3-dependent mitophagy protects genomic integrity in mouse ESCs. Deletion of Bnip3 increases cellular reactive oxygen species (ROS) and decreases ATP generation. Increased ROS in Bnip3-/- ESCs compromised self-renewal and were partially rescued by either NAC treatment or p53 depletion. The decreased cellular ATP in Bnip3-/- ESCs induced AMPK activation and deteriorated homologous recombination, leading to elevated mutation load during long-term propagation. Whereas activation of AMPK in X-ray-treated Bnip3+/+ ESCs dramatically ascended mutation rates, inactivation of AMPK in Bnip3-/- ESCs under X-ray stress remarkably decreased the mutation load. In addition, enhancement of BNIP3-dependent mitophagy during reprogramming markedly decreased mutation accumulation in established iPSCs. In conclusion, we demonstrated a novel pathway in which BNIP3-dependent mitophagy safeguards ESC genomic stability, and that could potentially be targeted to improve pluripotent stem cell genomic integrity for regenerative medicine.
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Affiliation(s)
- Qian Zhao
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences Beijing, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
| | - Kun Liu
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences Beijing, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
| | - Lin Zhang
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences Beijing, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zheng Li
- grid.24696.3f0000 0004 0369 153XDepartment of Gastroenterology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070 China
| | - Liang Wang
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences Beijing, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jiani Cao
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences Beijing, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
| | - Youqing Xu
- grid.24696.3f0000 0004 0369 153XDepartment of Gastroenterology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070 China
| | - Aihua Zheng
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences Beijing, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Quan Chen
- grid.216938.70000 0000 9878 7032College of Life Sciences, Nankai University, Tianjin, 300073 China
| | - Tongbiao Zhao
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences Beijing, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
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93
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Brunner JW, Lammertse HCA, van Berkel AA, Koopmans F, Li KW, Smit AB, Toonen RF, Verhage M, van der Sluis S. Power and optimal study design in iPSC-based brain disease modelling. Mol Psychiatry 2022; 28:1545-1556. [PMID: 36385170 DOI: 10.1038/s41380-022-01866-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 10/17/2022] [Accepted: 10/28/2022] [Indexed: 11/17/2022]
Abstract
Studies using induced pluripotent stem cells (iPSCs) are gaining momentum in brain disorder modelling, but optimal study designs are poorly defined. Here, we compare commonly used designs and statistical analysis for different research aims. Furthermore, we generated immunocytochemical, electrophysiological, and proteomic data from iPSC-derived neurons of five healthy subjects, analysed data variation and conducted power simulations. These analyses show that published case-control iPSC studies are generally underpowered. Designs using isogenic iPSC lines typically have higher power than case-control designs, but generalization of conclusions is limited. We show that, for the realistic settings used in this study, a multiple isogenic pair design increases absolute power up to 60% or requires up to 5-fold fewer lines. A free web tool is presented to explore the power of different study designs, using any (pilot) data.
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Affiliation(s)
- Jessie W Brunner
- Dept. Functional Genomics, CNCR, VU University Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Hanna C A Lammertse
- Dept. Functional Genomics, CNCR, VU University Amsterdam, 1081 HV, Amsterdam, The Netherlands.,Functional Genomics, Department of Human Genetics, CNCR, Amsterdam, UMC, 1081 HV, Amsterdam, The Netherlands
| | - Annemiek A van Berkel
- Dept. Functional Genomics, CNCR, VU University Amsterdam, 1081 HV, Amsterdam, The Netherlands.,Functional Genomics, Department of Human Genetics, CNCR, Amsterdam, UMC, 1081 HV, Amsterdam, The Netherlands
| | - Frank Koopmans
- Dept. Functional Genomics, CNCR, VU University Amsterdam, 1081 HV, Amsterdam, The Netherlands.,Dept. Molecular & Cellular Neurobiology, CNCR, VU University Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Ka Wan Li
- Dept. Molecular & Cellular Neurobiology, CNCR, VU University Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - August B Smit
- Dept. Molecular & Cellular Neurobiology, CNCR, VU University Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Ruud F Toonen
- Dept. Functional Genomics, CNCR, VU University Amsterdam, 1081 HV, Amsterdam, The Netherlands
| | - Matthijs Verhage
- Dept. Functional Genomics, CNCR, VU University Amsterdam, 1081 HV, Amsterdam, The Netherlands. .,Functional Genomics, Department of Human Genetics, CNCR, Amsterdam, UMC, 1081 HV, Amsterdam, The Netherlands.
| | - Sophie van der Sluis
- Dept. Complex Trait Genetics, CNCR, VU University Amsterdam, 1081 HV, Amsterdam, The Netherlands. .,Dept. of Child and Adolescence Psychiatry, section Complex Trait Genetics, Amsterdam UMC, Amsterdam, The Netherlands.
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94
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Wang G, Xu Y, Wang Q, Chai Y, Sun X, Yang F, Zhang J, Wu M, Liao X, Yu X, Sheng X, Liu Z, Zhang J. Rare and undiagnosed diseases: From disease-causing gene identification to mechanism elucidation. FUNDAMENTAL RESEARCH 2022; 2:918-928. [PMID: 38933382 PMCID: PMC11197726 DOI: 10.1016/j.fmre.2022.09.002] [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: 07/16/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 11/27/2022] Open
Abstract
Rare and undiagnosed diseases substantially decrease patient quality of life and have increasingly become a heavy burden on healthcare systems. Because of the challenges in disease-causing gene identification and mechanism elucidation, patients are often confronted with difficulty obtaining a precise diagnosis and treatment. Due to advances in sequencing and multiomics analysis approaches combined with patient-derived iPSC models and gene-editing platforms, substantial progress has been made in the diagnosis and treatment of rare and undiagnosed diseases. The aforementioned techniques also provide an operational basis for future precision medicine studies. In this review, we summarize recent progress in identifying disease-causing genes based on GWAS/WES/WGS-guided multiomics analysis approaches. In addition, we discuss recent advances in the elucidation of pathogenic mechanisms and treatment of diseases with state-of-the-art iPSC and organoid models, which are improved by cell maturation level and gene editing technology. The comprehensive strategies described above will generate a new paradigm of disease classification that will significantly promote the precision and efficiency of diagnosis and treatment for rare and undiagnosed diseases.
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Affiliation(s)
- Gang Wang
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China
| | - Yuyan Xu
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qintao Wang
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yi Chai
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiangwei Sun
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Fan Yang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China
| | - Jian Zhang
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Mengchen Wu
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xufeng Liao
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiaomin Yu
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xin Sheng
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhihong Liu
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Zhejiang University School of Medicine, Hangzhou 310058, China
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China
| | - Jin Zhang
- Zhejiang Laboratory for Systems & Precision Medicine, Zhejiang University Medical Center, Hangzhou 311121, China
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, The First Affiliated Hospital, Zhejiang University School of Medicine; Center of Gene/Cell Engineering and Genome Medicine of Zhejiang Province, Hangzhou 310058, China
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95
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Kimura M, Iguchi T, Iwasawa K, Dunn A, Thompson WL, Yoneyama Y, Chaturvedi P, Zorn AM, Wintzinger M, Quattrocelli M, Watanabe-Chailland M, Zhu G, Fujimoto M, Kumbaji M, Kodaka A, Gindin Y, Chung C, Myers RP, Subramanian GM, Hwa V, Takebe T. En masse organoid phenotyping informs metabolic-associated genetic susceptibility to NASH. Cell 2022; 185:4216-4232.e16. [PMID: 36240780 PMCID: PMC9617783 DOI: 10.1016/j.cell.2022.09.031] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 08/01/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022]
Abstract
Genotype-phenotype associations for common diseases are often compounded by pleiotropy and metabolic state. Here, we devised a pooled human organoid-panel of steatohepatitis to investigate the impact of metabolic status on genotype-phenotype association. En masse population-based phenotypic analysis under insulin insensitive conditions predicted key non-alcoholic steatohepatitis (NASH)-genetic factors including the glucokinase regulatory protein (GCKR)-rs1260326:C>T. Analysis of NASH clinical cohorts revealed that GCKR-rs1260326-T allele elevates disease severity only under diabetic state but protects from fibrosis under non-diabetic states. Transcriptomic, metabolomic, and pharmacological analyses indicate significant mitochondrial dysfunction incurred by GCKR-rs1260326, which was not reversed with metformin. Uncoupling oxidative mechanisms mitigated mitochondrial dysfunction and permitted adaptation to increased fatty acid supply while protecting against oxidant stress, forming a basis for future therapeutic approaches for diabetic NASH. Thus, "in-a-dish" genotype-phenotype association strategies disentangle the opposing roles of metabolic-associated gene variant functions and offer a rich mechanistic, diagnostic, and therapeutic inference toolbox toward precision hepatology. VIDEO ABSTRACT.
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Affiliation(s)
- Masaki Kimura
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Takuma Iguchi
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kentaro Iwasawa
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Andrew Dunn
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Wendy L Thompson
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Yosuke Yoneyama
- Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Praneet Chaturvedi
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Aaron M Zorn
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Michelle Wintzinger
- Division of Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Mattia Quattrocelli
- Division of Molecular Cardiovascular Biology, Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Miki Watanabe-Chailland
- NMR-Based Metabolomics Core Facility, Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Gaohui Zhu
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Masanobu Fujimoto
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Meenasri Kumbaji
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Asuka Kodaka
- Communication Design Center, Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan
| | | | | | - Robert P Myers
- Gilead Sciences, Foster City, CA 94404, USA; The Liver Company, Inc., Palo Alto, CA 94303, USA
| | - G Mani Subramanian
- Gilead Sciences, Foster City, CA 94404, USA; The Liver Company, Inc., Palo Alto, CA 94303, USA
| | - Vivian Hwa
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Takanori Takebe
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Communication Design Center, Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan.
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96
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Cuevas-Diaz Duran R, González-Orozco JC, Velasco I, Wu JQ. Single-cell and single-nuclei RNA sequencing as powerful tools to decipher cellular heterogeneity and dysregulation in neurodegenerative diseases. Front Cell Dev Biol 2022; 10:884748. [PMID: 36353512 PMCID: PMC9637968 DOI: 10.3389/fcell.2022.884748] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 10/06/2022] [Indexed: 08/10/2023] Open
Abstract
Neurodegenerative diseases affect millions of people worldwide and there are currently no cures. Two types of common neurodegenerative diseases are Alzheimer's (AD) and Parkinson's disease (PD). Single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq) have become powerful tools to elucidate the inherent complexity and dynamics of the central nervous system at cellular resolution. This technology has allowed the identification of cell types and states, providing new insights into cellular susceptibilities and molecular mechanisms underlying neurodegenerative conditions. Exciting research using high throughput scRNA-seq and snRNA-seq technologies to study AD and PD is emerging. Herein we review the recent progress in understanding these neurodegenerative diseases using these state-of-the-art technologies. We discuss the fundamental principles and implications of single-cell sequencing of the human brain. Moreover, we review some examples of the computational and analytical tools required to interpret the extensive amount of data generated from these assays. We conclude by highlighting challenges and limitations in the application of these technologies in the study of AD and PD.
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Affiliation(s)
| | | | - Iván Velasco
- Instituto de Fisiología Celular—Neurociencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Laboratorio de Reprogramación Celular, Instituto Nacional de Neurología y Neurocirugía “Manuel Velasco Suárez”, Mexico City, Mexico
| | - Jia Qian Wu
- The Vivian L. Smith Department of Neurosurgery, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
- Center for Stem Cell and Regenerative Medicine, UT Brown Foundation Institute of Molecular Medicine, Houston, TX, United States
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
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97
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Large-scale genomic analysis of human iPSCs identifies recurrent somatic driver mutations. Nat Genet 2022; 54:1271-1272. [PMID: 36064797 DOI: 10.1038/s41588-022-01169-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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98
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Rouhani FJ, Zou X, Danecek P, Badja C, Amarante TD, Koh G, Wu Q, Memari Y, Durbin R, Martincorena I, Bassett AR, Gaffney D, Nik-Zainal S. Substantial somatic genomic variation and selection for BCOR mutations in human induced pluripotent stem cells. Nat Genet 2022; 54:1406-1416. [PMID: 35953586 PMCID: PMC9470532 DOI: 10.1038/s41588-022-01147-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/24/2022] [Indexed: 12/27/2022]
Abstract
We explored human induced pluripotent stem cells (hiPSCs) derived from different tissues to gain insights into genomic integrity at single-nucleotide resolution. We used genome sequencing data from two large hiPSC repositories involving 696 hiPSCs and daughter subclones. We find ultraviolet light (UV)-related damage in ~72% of skin fibroblast-derived hiPSCs (F-hiPSCs), occasionally resulting in substantial mutagenesis (up to 15 mutations per megabase). We demonstrate remarkable genomic heterogeneity between independent F-hiPSC clones derived during the same round of reprogramming due to oligoclonal fibroblast populations. In contrast, blood-derived hiPSCs (B-hiPSCs) had fewer mutations and no UV damage but a high prevalence of acquired BCOR mutations (26.9% of lines). We reveal strong selection pressure for BCOR mutations in F-hiPSCs and B-hiPSCs and provide evidence that they arise in vitro. Directed differentiation of hiPSCs and RNA sequencing showed that BCOR mutations have functional consequences. Our work strongly suggests that detailed nucleotide-resolution characterization is essential before using hiPSCs.
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Affiliation(s)
- Foad J Rouhani
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Xueqing Zou
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
- Academic Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Cherif Badja
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
- Academic Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Tauanne Dias Amarante
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Gene Koh
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
- Academic Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Qianxin Wu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yasin Memari
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Inigo Martincorena
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Andrew R Bassett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Daniel Gaffney
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Genomics plc, King Charles House, Oxford, UK
| | - Serena Nik-Zainal
- Early Cancer Institute, Hutchison/MRC Research Centre, Cambridge Biomedical Research Campus, Cambridge, UK.
- Academic Department of Medical Genetics, Addenbrooke's Treatment Centre, Cambridge Biomedical Research Campus, Cambridge, UK.
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99
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Challenges and opportunities for the next generation of cardiovascular tissue engineering. Nat Methods 2022; 19:1064-1071. [PMID: 36064773 DOI: 10.1038/s41592-022-01591-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 07/07/2022] [Indexed: 12/21/2022]
Abstract
Engineered cardiac tissues derived from human induced pluripotent stem cells offer unique opportunities for patient-specific disease modeling, drug discovery and cardiac repair. Since the first engineered hearts were introduced over two decades ago, human induced pluripotent stem cell-based three-dimensional cardiac organoids and heart-on-a-chip systems have now become mainstays in basic cardiovascular research as valuable platforms for investigating fundamental human pathophysiology and development. However, major obstacles remain to be addressed before the field can truly advance toward commercial and clinical translation. Here we provide a snapshot of the state-of-the-art methods in cardiac tissue engineering, with a focus on in vitro models of the human heart. Looking ahead, we discuss major challenges and opportunities in the field and suggest strategies for enabling broad acceptance of engineered cardiac tissues as models of cardiac pathophysiology and testbeds for the development of therapies.
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100
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Jowett GM, Read E, Roberts LB, Coman D, Vilà González M, Zabinski T, Niazi U, Reis R, Trieu TJ, Danovi D, Gentleman E, Vallier L, Curtis MA, Lord GM, Neves JF. Organoids capture tissue-specific innate lymphoid cell development in mice and humans. Cell Rep 2022; 40:111281. [PMID: 36044863 PMCID: PMC9638027 DOI: 10.1016/j.celrep.2022.111281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 01/06/2022] [Accepted: 08/05/2022] [Indexed: 12/21/2022] Open
Abstract
Organoid-based models of murine and human innate lymphoid cell precursor (ILCP) maturation are presented. First, murine intestinal and pulmonary organoids are harnessed to demonstrate that the epithelial niche is sufficient to drive tissue-specific maturation of all innate lymphoid cell (ILC) groups in parallel, without requiring subset-specific cytokine supplementation. Then, more complex human induced pluripotent stem cell (hiPSC)-based gut and lung organoid models are used to demonstrate that human epithelial cells recapitulate maturation of ILC from a stringent systemic human ILCP population, but only when the organoid-associated stromal cells are depleted. These systems offer versatile and reductionist models to dissect the impact of environmental and mucosal niche cues on ILC maturation. In the future, these could provide insight into how ILC activity and development might become dysregulated in chronic inflammatory diseases.
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Affiliation(s)
- Geraldine M Jowett
- School for Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK; Centre for Host Microbiome Interactions, King's College London, London SE1 9RT, UK; Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK; Centre for Gene Therapy & Regenerative Medicine, King's College London, London SE1 9RT, UK; Wellcome Trust Cell Therapies and Regenerative Medicine Ph.D. Programme, London SE1 9RT, UK
| | - Emily Read
- School for Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK; Centre for Host Microbiome Interactions, King's College London, London SE1 9RT, UK; Centre for Gene Therapy & Regenerative Medicine, King's College London, London SE1 9RT, UK
| | - Luke B Roberts
- School for Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | - Diana Coman
- Centre for Host Microbiome Interactions, King's College London, London SE1 9RT, UK
| | - Marta Vilà González
- Wellcome and MRC Cambridge Stem Cell Institute, Puddicombe Way, Cambridge CB2 0AW, UK; Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Hills Road, Cambridge CB2 0QQ, UK
| | - Tomasz Zabinski
- School for Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | - Umar Niazi
- Guy's and St. Thomas' National Health Service Foundation Trust and King's College London National Institute for Health and Care Research Biomedical Research Centre Translational Bioinformatics Platform, Guy's Hospital, London SE1 9RT, UK
| | - Rita Reis
- School for Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | - Tung-Jui Trieu
- Centre for Host Microbiome Interactions, King's College London, London SE1 9RT, UK; Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Davide Danovi
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK; bit.bio, Babraham Research Campus, The Dorothy Hodgkin Building, Cambridge CB22 3FH, UK
| | - Eileen Gentleman
- Centre for Craniofacial and Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Ludovic Vallier
- Wellcome and MRC Cambridge Stem Cell Institute, Puddicombe Way, Cambridge CB2 0AW, UK; Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Hills Road, Cambridge CB2 0QQ, UK
| | - Michael A Curtis
- Centre for Host Microbiome Interactions, King's College London, London SE1 9RT, UK
| | - Graham M Lord
- School for Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK; Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Joana F Neves
- School for Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK; Centre for Host Microbiome Interactions, King's College London, London SE1 9RT, UK.
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