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Li M, Yuan Y, Hou Z, Hao S, Jin L, Wang B. Human brain organoid: trends, evolution, and remaining challenges. Neural Regen Res 2024; 19:2387-2399. [PMID: 38526275 PMCID: PMC11090441 DOI: 10.4103/1673-5374.390972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/26/2023] [Accepted: 10/28/2023] [Indexed: 03/26/2024] Open
Abstract
Advanced brain organoids provide promising platforms for deciphering the cellular and molecular processes of human neural development and diseases. Although various studies and reviews have described developments and advancements in brain organoids, few studies have comprehensively summarized and analyzed the global trends in this area of neuroscience. To identify and further facilitate the development of cerebral organoids, we utilized bibliometrics and visualization methods to analyze the global trends and evolution of brain organoids in the last 10 years. First, annual publications, countries/regions, organizations, journals, authors, co-citations, and keywords relating to brain organoids were identified. The hotspots in this field were also systematically identified. Subsequently, current applications for brain organoids in neuroscience, including human neural development, neural disorders, infectious diseases, regenerative medicine, drug discovery, and toxicity assessment studies, are comprehensively discussed. Towards that end, several considerations regarding the current challenges in brain organoid research and future strategies to advance neuroscience will be presented to further promote their application in neurological research.
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Affiliation(s)
- Minghui Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yuhan Yuan
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Zongkun Hou
- School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Shilei Hao
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Liang Jin
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Bochu Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
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2
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Kim SK, Seo S, Stein-O'Brien G, Jaishankar A, Ogawa K, Micali N, Luria V, Karger A, Wang Y, Kim H, Hyde TM, Kleinman JE, Voss T, Fertig EJ, Shin JH, Bürli R, Cross AJ, Brandon NJ, Weinberger DR, Chenoweth JG, Hoeppner DJ, Sestan N, Colantuoni C, McKay RD. Individual variation in the emergence of anterior-to-posterior neural fates from human pluripotent stem cells. Stem Cell Reports 2024; 19:1336-1350. [PMID: 39151428 DOI: 10.1016/j.stemcr.2024.07.004] [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: 09/18/2023] [Revised: 07/16/2024] [Accepted: 07/16/2024] [Indexed: 08/19/2024] Open
Abstract
Variability between human pluripotent stem cell (hPSC) lines remains a challenge and opportunity in biomedicine. In this study, hPSC lines from multiple donors were differentiated toward neuroectoderm and mesendoderm lineages. We revealed dynamic transcriptomic patterns that delineate the emergence of these lineages, which were conserved across lines, along with individual line-specific transcriptional signatures that were invariant throughout differentiation. These transcriptomic signatures predicted an antagonism between SOX21-driven forebrain fates and retinoic acid-induced hindbrain fates. Replicate lines and paired adult tissue demonstrated the stability of these line-specific transcriptomic traits. We show that this transcriptomic variation in lineage bias had both genetic and epigenetic origins, aligned with the anterior-to-posterior structure of early mammalian development, and was present across a large collection of hPSC lines. These findings contribute to developing systematic analyses of PSCs to define the origin and consequences of variation in the early events orchestrating individual human development.
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Affiliation(s)
- Suel-Kee Kim
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Seungmae Seo
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | | | - Amritha Jaishankar
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Kazuya Ogawa
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Nicola Micali
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Victor Luria
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Amir Karger
- IT-Research Computing, Harvard Medical School, Boston, MA 02115, USA
| | - Yanhong Wang
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Hyojin Kim
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Departments of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Departments of Psychiatry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Departments of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Ty Voss
- Division of Preclinical Innovation, Nation Center for Advancing Translational Science, NIH, Bethesda, MD 20892, USA
| | - Elana J Fertig
- Departments of Oncology, Biomedical Engineering, and Applied Mathematics and Statistics, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Joo-Heon Shin
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Roland Bürli
- Astra-Zeneca Neuroscience iMED., 141 Portland Street, Cambridge, MA 01239, USA
| | - Alan J Cross
- Astra-Zeneca Neuroscience iMED., 141 Portland Street, Cambridge, MA 01239, USA
| | - Nicholas J Brandon
- Astra-Zeneca Neuroscience iMED., 141 Portland Street, Cambridge, MA 01239, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Departments of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Departments of Psychiatry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Departments of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Joshua G Chenoweth
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Daniel J Hoeppner
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Departments of Genetics, Psychiatry, and Comparative Medicine, Kavli Institute for Neuroscience, Program in Cellular Neuroscience, Neurodegeneration and Repair, Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Carlo Colantuoni
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Departments of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Departments of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
| | - Ronald D McKay
- Lieber Institute for Brain Development, 855 North Wolfe Street, Baltimore, MD 21205, USA; Departments of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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3
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Zhao Y, Kohl C, Rosebrock D, Hu Q, Hu Y, Vingron M. CAbiNet: joint clustering and visualization of cells and genes for single-cell transcriptomics. Nucleic Acids Res 2024; 52:e57. [PMID: 38850160 PMCID: PMC11260446 DOI: 10.1093/nar/gkae480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 04/10/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024] Open
Abstract
A fundamental analysis task for single-cell transcriptomics data is clustering with subsequent visualization of cell clusters. The genes responsible for the clustering are only inferred in a subsequent step. Clustering cells and genes together would be the remit of biclustering algorithms, which are often bogged down by the size of single-cell data. Here we present 'Correspondence Analysis based Biclustering on Networks' (CAbiNet) for joint clustering and visualization of single-cell RNA-sequencing data. CAbiNet performs efficient co-clustering of cells and their respective marker genes and jointly visualizes the biclusters in a non-linear embedding for easy and interactive visual exploration of the data.
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Affiliation(s)
- Yan Zhao
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, Guangdong, P.R. China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
| | - Clemens Kohl
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Daniel Rosebrock
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Qinan Hu
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, Guangdong, P.R. China
- Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology,1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
| | - Yuhui Hu
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, Guangdong, P.R. China
- Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology,1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
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Rahav N, Marrero D, Soffer A, Glickman E, Beldjilali‐Labro M, Yaffe Y, Tadmor K, Leichtmann‐Bardoogo Y, Ashery U, Maoz BM. Multi-Sensor Origami Platform: A Customizable System for Obtaining Spatiotemporally Precise Functional Readouts in 3D Models. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305555. [PMID: 38634605 PMCID: PMC11200086 DOI: 10.1002/advs.202305555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 03/14/2024] [Indexed: 04/19/2024]
Abstract
Bioprinting technology offers unprecedented opportunities to construct in vitro tissue models that recapitulate the 3D morphology and functionality of native tissue. Yet, it remains difficult to obtain adequate functional readouts from such models. In particular, it is challenging to position sensors in desired locations within pre-fabricated 3D bioprinted structures. At the same time, bioprinting tissue directly onto a sensing device is not feasible due to interference with the printer head. As such, a multi-sensing platform inspired by origami that overcomes these challenges by "folding" around a separately fabricated 3D tissue structure is proposed, allowing for the insertion of electrodes into precise locations, which are custom-defined using computer-aided-design software. The multi-sensing origami platform (MSOP) can be connected to a commercial multi-electrode array (MEA) system for data-acquisition and processing. To demonstrate the platform, how integrated 3D MEA electrodes can record neuronal electrical activity in a 3D model of a neurovascular unit is shown. The MSOP also enables a microvascular endothelial network to be cultured separately and integrated with the 3D tissue structure. Accordingly, how impedance-based sensors in the platform can measure endothelial barrier function is shown. It is further demonstrated the device's versatility by using it to measure neuronal activity in brain organoids.
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Affiliation(s)
- Noam Rahav
- School of Neurobiology, Biochemistry and BiophysicsThe George S. Wise Faculty of Life SciencesTel Aviv UniversityTel Aviv69978Israel
| | - Denise Marrero
- Instituto de Microelectrónica de Barcelona (IMB‐CNM, CSIC)Campus UABBellaterraBarcelona08193Spain
- Centro de Investigación Biomédica en Red en Bioingeniería Biomateriales y NanomedicinaMadrid50018Spain
- Department of Biomedical EngineeringTel Aviv UniversityTel Aviv69978Israel
| | - Adi Soffer
- Department of Biomedical EngineeringTel Aviv UniversityTel Aviv69978Israel
| | - Emma Glickman
- Department of Biomedical EngineeringTel Aviv UniversityTel Aviv69978Israel
| | | | - Yakey Yaffe
- Sagol Center for Regenerative MedicineTel Aviv UniversityTel Aviv69978Israel
| | - Keshet Tadmor
- Sagol School of NeuroscienceTel Aviv UniversityTel Aviv69978Israel
| | | | - Uri Ashery
- School of Neurobiology, Biochemistry and BiophysicsThe George S. Wise Faculty of Life SciencesTel Aviv UniversityTel Aviv69978Israel
- Sagol Center for Regenerative MedicineTel Aviv UniversityTel Aviv69978Israel
- Sagol School of NeuroscienceTel Aviv UniversityTel Aviv69978Israel
| | - Ben M. Maoz
- Department of Biomedical EngineeringTel Aviv UniversityTel Aviv69978Israel
- Sagol Center for Regenerative MedicineTel Aviv UniversityTel Aviv69978Israel
- Sagol School of NeuroscienceTel Aviv UniversityTel Aviv69978Israel
- The Center for Nanoscience and NanotechnologyTel Aviv UniversityTel Aviv69978Israel
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5
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Zyuz'kov GN, Miroshnichenko LA, Polyakova TY, Simanina EV, Chaikovsky AV, Agafonov VI, Stavrova LA, Udut EV, Churin AA, Zhdanov VV. The Role of Smad3 in the Realization of the Growth Potential of Different Types of Neural Progenitor Cells and the Secretory Function of Neuroglia. Bull Exp Biol Med 2024; 177:35-38. [PMID: 38954301 DOI: 10.1007/s10517-024-06126-8] [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: 10/13/2023] [Indexed: 07/04/2024]
Abstract
The features of the participation of Smad3 in the functioning of neural stem cells (NSC), neuronal committed precursors (NCP), and neuroglial elements were studied in vitro. It was found that this intracellular signaling molecule enhances the clonogenic and proliferative activities of NCP and inhibits specialization of neuronal precursors. At the same time, Smad3 does not participate in the realization of the growth potential of NSC. With regard to the secretory function (production of neurotrophic growth factors) of neuroglial cells, the stimulating role of Smad3-mediated signaling was shown. These results indicate the promise of studying the possibility of using Smad3 as a fundamentally new target for neuroregenerative agents.
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Affiliation(s)
- G N Zyuz'kov
- E. D. Goldberg Research Institute of Pharmacology and Regenerative Medicine, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia.
| | - L A Miroshnichenko
- E. D. Goldberg Research Institute of Pharmacology and Regenerative Medicine, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - T Yu Polyakova
- E. D. Goldberg Research Institute of Pharmacology and Regenerative Medicine, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
- Siberian State Medical University, Ministry of Health of the Russian Federation, Tomsk, Russia
| | - E V Simanina
- E. D. Goldberg Research Institute of Pharmacology and Regenerative Medicine, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - A V Chaikovsky
- E. D. Goldberg Research Institute of Pharmacology and Regenerative Medicine, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - V I Agafonov
- E. D. Goldberg Research Institute of Pharmacology and Regenerative Medicine, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
- Siberian State Medical University, Ministry of Health of the Russian Federation, Tomsk, Russia
| | - L A Stavrova
- E. D. Goldberg Research Institute of Pharmacology and Regenerative Medicine, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - E V Udut
- E. D. Goldberg Research Institute of Pharmacology and Regenerative Medicine, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
- Siberian State Medical University, Ministry of Health of the Russian Federation, Tomsk, Russia
| | - A A Churin
- E. D. Goldberg Research Institute of Pharmacology and Regenerative Medicine, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - V V Zhdanov
- E. D. Goldberg Research Institute of Pharmacology and Regenerative Medicine, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
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6
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Elkabetz Y. It takes two to expand the cortex. Nat Cell Biol 2024; 26:667-669. [PMID: 38714851 DOI: 10.1038/s41556-024-01416-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Affiliation(s)
- Yechiel Elkabetz
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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7
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Walsh RM, Luongo R, Giacomelli E, Ciceri G, Rittenhouse C, Verrillo A, Galimberti M, Bocchi VD, Wu Y, Xu N, Mosole S, Muller J, Vezzoli E, Jungverdorben J, Zhou T, Barker RA, Cattaneo E, Studer L, Baggiolini A. Generation of human cerebral organoids with a structured outer subventricular zone. Cell Rep 2024; 43:114031. [PMID: 38583153 PMCID: PMC11322983 DOI: 10.1016/j.celrep.2024.114031] [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: 01/30/2023] [Revised: 12/12/2023] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
Outer radial glia (oRG) emerge as cortical progenitor cells that support the development of an enlarged outer subventricular zone (oSVZ) and the expansion of the neocortex. The in vitro generation of oRG is essential to investigate the underlying mechanisms of human neocortical development and expansion. By activating the STAT3 signaling pathway using leukemia inhibitory factor (LIF), which is not expressed in guided cortical organoids, we define a cortical organoid differentiation method from human pluripotent stem cells (hPSCs) that recapitulates the expansion of a progenitor pool into the oSVZ. The oSVZ comprises progenitor cells expressing specific oRG markers such as GFAP, LIFR, and HOPX, closely matching human fetal oRG. Finally, incorporating neural crest-derived LIF-producing cortical pericytes into cortical organoids recapitulates the effects of LIF treatment. These data indicate that increasing the cellular complexity of the organoid microenvironment promotes the emergence of oRG and supports a platform to study oRG in hPSC-derived brain organoids routinely.
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Affiliation(s)
- Ryan M Walsh
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Raffaele Luongo
- Institute of Oncology Research (IOR), Bellinzona Institutes of Science (BIOS+), 6500 Bellinzona, Switzerland; Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Elisa Giacomelli
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Gabriele Ciceri
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chelsea Rittenhouse
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Medicine Graduate School of Medical Sciences, Department of Neuroscience, New York, NY 1300, USA
| | - Antonietta Verrillo
- Institute of Oncology Research (IOR), Bellinzona Institutes of Science (BIOS+), 6500 Bellinzona, Switzerland; Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland
| | - Maura Galimberti
- Laboratory of Stem Cell Biology and Pharmacology of Neurodegenerative Diseases, Department of Biosciences, University of Milan, 20122 Milan, Italy; INGM, Istituto Nazionale Genetica Molecolare, 20122 Milan, Italy
| | - Vittoria Dickinson Bocchi
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Youjun Wu
- The SKI Stem Cell Research Facility, The Center for Stem Cell Biology and Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Nan Xu
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY 10065, USA
| | - Simone Mosole
- Institute of Oncology Research (IOR), Bellinzona Institutes of Science (BIOS+), 6500 Bellinzona, Switzerland; Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland
| | - James Muller
- Developmental Biology and Immunology Programs, Sloan Kettering Institute, New York, NY 10065, USA
| | - Elena Vezzoli
- Laboratory of Stem Cell Biology and Pharmacology of Neurodegenerative Diseases, Department of Biosciences, University of Milan, 20122 Milan, Italy; INGM, Istituto Nazionale Genetica Molecolare, 20122 Milan, Italy
| | - Johannes Jungverdorben
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ting Zhou
- The SKI Stem Cell Research Facility, The Center for Stem Cell Biology and Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, NY 10065, USA
| | - Roger A Barker
- Cambridge Stem Cell Institute and John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, Forvie Site, University of Cambridge, Cambridge, UK
| | - Elena Cattaneo
- Laboratory of Stem Cell Biology and Pharmacology of Neurodegenerative Diseases, Department of Biosciences, University of Milan, 20122 Milan, Italy; INGM, Istituto Nazionale Genetica Molecolare, 20122 Milan, Italy
| | - Lorenz Studer
- Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Medicine Graduate School of Medical Sciences, Department of Neuroscience, New York, NY 1300, USA.
| | - Arianna Baggiolini
- Institute of Oncology Research (IOR), Bellinzona Institutes of Science (BIOS+), 6500 Bellinzona, Switzerland; Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland.
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8
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Xu Z, Qin Q, Wang Y, Zhang H, Liu S, Li X, Chen Y, Wang Y, Ruan H, He W, Zhang T, Yan X, Wang C, Xu D, Jiang X. Deubiquitinase Mysm1 regulates neural stem cell proliferation and differentiation by controlling Id4 expression. Cell Death Dis 2024; 15:129. [PMID: 38342917 PMCID: PMC10859383 DOI: 10.1038/s41419-024-06530-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: 09/26/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/13/2024]
Abstract
Neural stem cells (NSCs) are critical for brain development and maintenance of neurogenesis. However, the molecular mechanisms that regulate NSC proliferation and differentiation remain unclear. Mysm1 is a deubiquitinase and is essential for the self-renewal and differentiation of several stem cells. It is unknown whether Mysm1 plays an important role in NSCs. Here, we found that Mysm1 was expressed in NSCs and its expression was increased with age in mice. Mice with Mysm1 knockdown by crossing Mysm1 floxed mice with Nestin-Cre mice exhibited abnormal brain development with microcephaly. Mysm1 deletion promoted NSC proliferation and apoptosis, resulting in depletion of the stem cell pool. In addition, Mysm1-deficient NSCs skewed toward neurogenesis instead of astrogliogenesis. Mechanistic investigations with RNA sequencing and genome-wide CUT&Tag analysis revealed that Mysm1 epigenetically regulated Id4 transcription by regulating histone modification at the promoter region. After rescuing the expression of Id4, the hyperproliferation and imbalance differentiation of Mysm1-deficient NSCs was reversed. Additionally, knockdown Mysm1 in aged mice could promote NSC proliferation. Collectively, the present study identified a new factor Mysm1 which is essential for NSC homeostasis and Mysm1-Id4 axis may be an ideal target for proper NSC proliferation and differentiation.
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Affiliation(s)
- Zhenhua Xu
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Qiaozhen Qin
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, 100124, China
| | - Yan Wang
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
- Anhui Medical University, Hefei, 230032, Anhui, China
| | - Heyang Zhang
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Shuirong Liu
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Xiaotong Li
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Yue Chen
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Yuqing Wang
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Huaqiang Ruan
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Wenyan He
- China National Clinical Research Center for Neurological Diseases, Jing-Jin Center for Neuroinflammation, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100050, China
| | - Tao Zhang
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China
| | - Xinlong Yan
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, 100124, China
| | - Changyong Wang
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China.
| | - Donggang Xu
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China.
| | - Xiaoxia Jiang
- Beijing Institute of Basic Medical Sciences, 27 Taiping Road, Haidian District, Beijing, 100850, China.
- Anhui Medical University, Hefei, 230032, Anhui, China.
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9
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Acharya P, Choi NY, Shrestha S, Jeong S, Lee MY. Brain organoids: A revolutionary tool for modeling neurological disorders and development of therapeutics. Biotechnol Bioeng 2024; 121:489-506. [PMID: 38013504 PMCID: PMC10842775 DOI: 10.1002/bit.28606] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 10/03/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023]
Abstract
Brain organoids are self-organized, three-dimensional (3D) aggregates derived from pluripotent stem cells that have cell types and cellular architectures resembling those of the developing human brain. The current understanding of human brain developmental processes and neurological disorders has advanced significantly with the introduction of this in vitro model. Brain organoids serve as a translational link between two-dimensional (2D) cultures and in vivo models which imitate the neural tube formation at the early and late stages and the differentiation of neuroepithelium with whole-brain regionalization. In addition, the generation of region-specific brain organoids made it possible to investigate the pathogenic and etiological aspects of acquired and inherited brain disease along with drug discovery and drug toxicity testing. In this review article, we first summarize an overview of the existing methods and platforms used for generating brain organoids and their limitations and then discuss the recent advancement in brain organoid technology. In addition, we discuss how brain organoids have been used to model aspects of neurodevelopmental and neurodegenerative diseases, including autism spectrum disorder (ASD), Rett syndrome, Zika virus-related microcephaly, Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD).
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Affiliation(s)
- Prabha Acharya
- Department of Biomedical Engineering, University of North Texas, Denton, Texas, USA
| | - Na Young Choi
- Department of Biomedical Engineering, University of North Texas, Denton, Texas, USA
- Department of Healthcare Information Technology, Inje University, Gimhae, Republic of Korea
| | - Sunil Shrestha
- Department of Biomedical Engineering, University of North Texas, Denton, Texas, USA
| | - Sehoon Jeong
- Department of Healthcare Information Technology, Inje University, Gimhae, Republic of Korea
| | - Moo-Yeal Lee
- Department of Biomedical Engineering, University of North Texas, Denton, Texas, USA
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10
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Pavon N, Diep K, Yang F, Sebastian R, Martinez-Martin B, Ranjan R, Sun Y, Pak C. Patterning ganglionic eminences in developing human brain organoids using a morphogen-gradient-inducing device. CELL REPORTS METHODS 2024; 4:100689. [PMID: 38228151 PMCID: PMC10831957 DOI: 10.1016/j.crmeth.2023.100689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/21/2023] [Accepted: 12/18/2023] [Indexed: 01/18/2024]
Abstract
In early neurodevelopment, the central nervous system is established through the coordination of various neural organizers directing tissue patterning and cell differentiation. Better recapitulation of morphogen gradient production and signaling will be crucial for establishing improved developmental models of the brain in vitro. Here, we developed a method by assembling polydimethylsiloxane devices capable of generating a sustained chemical gradient to produce patterned brain organoids, which we termed morphogen-gradient-induced brain organoids (MIBOs). At 3.5 weeks, MIBOs replicated dorsal-ventral patterning observed in the ganglionic eminences (GE). Analysis of mature MIBOs through single-cell RNA sequencing revealed distinct dorsal GE-derived CALB2+ interneurons, medium spiny neurons, and medial GE-derived cell types. Finally, we demonstrate long-term culturing capabilities with MIBOs maintaining stable neural activity in cultures grown up to 5.5 months. MIBOs demonstrate a versatile approach for generating spatially patterned brain organoids for embryonic development and disease modeling.
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Affiliation(s)
- Narciso Pavon
- Graduate Program in Neuroscience and Behavior, UMass Amherst, Amherst, MA 01003, USA; Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Karmen Diep
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Feiyu Yang
- Department of Mechanical and Industrial Engineering, UMass Amherst, Amherst, MA 01003, USA
| | - Rebecca Sebastian
- Graduate Program in Neuroscience and Behavior, UMass Amherst, Amherst, MA 01003, USA; Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Beatriz Martinez-Martin
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA; Graduate Program in Molecular and Cellular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Ravi Ranjan
- Genomics Core, Institute of Applied Life Sciences, UMass Amherst, Amherst, MA 01003, USA
| | - Yubing Sun
- Department of Mechanical and Industrial Engineering, UMass Amherst, Amherst, MA 01003, USA.
| | - ChangHui Pak
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA.
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11
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Chau CW, Sugimura R. Organoids in COVID-19: can we break the glass ceiling? J Leukoc Biol 2024; 115:85-99. [PMID: 37616269 DOI: 10.1093/jleuko/qiad098] [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: 01/30/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
COVID-19 emerged in September 2020 as a disease caused by the virus SARS-CoV-2. The disease presented as pneumonia at first but later was shown to cause multisystem infections and long-term complications. Many efforts have been put into discovering the exact pathogenesis of the disease. In this review, we aim to discuss an emerging tool in disease modeling, organoids, in the investigation of COVID-19. This review will introduce some methods and breakthroughs achieved by organoids and the limitations of this system.
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Affiliation(s)
- Chiu Wang Chau
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 21 Sassoon Rd, Pokfulam 99077, Hong Kong
| | - Ryohichi Sugimura
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, 21 Sassoon Rd, Pokfulam 99077, Hong Kong
- Centre for Translational Stem Cell Biology, 17 Science Park W Ave, Science Park 999077, Hong Kong
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12
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Pagliaro A, Finger R, Zoutendijk I, Bunschuh S, Clevers H, Hendriks D, Artegiani B. Temporal morphogen gradient-driven neural induction shapes single expanded neuroepithelium brain organoids with enhanced cortical identity. Nat Commun 2023; 14:7361. [PMID: 38016960 PMCID: PMC10684874 DOI: 10.1038/s41467-023-43141-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 11/01/2023] [Indexed: 11/30/2023] Open
Abstract
Pluripotent stem cell (PSC)-derived human brain organoids enable the study of human brain development in vitro. Typically, the fate of PSCs is guided into subsequent specification steps through static medium switches. In vivo, morphogen gradients are critical for proper brain development and determine cell specification, and associated defects result in neurodevelopmental disorders. Here, we show that initiating neural induction in a temporal stepwise gradient guides the generation of brain organoids composed of a single, self-organized apical-out neuroepithelium, termed ENOs (expanded neuroepithelium organoids). This is at odds with standard brain organoid protocols in which multiple and independent neuroepithelium units (rosettes) are formed. We find that a prolonged, decreasing gradient of TGF-β signaling is a determining factor in ENO formation and allows for an extended phase of neuroepithelium expansion. In-depth characterization reveals that ENOs display improved cellular morphology and tissue architectural features that resemble in vivo human brain development, including expanded germinal zones. Consequently, cortical specification is enhanced in ENOs. ENOs constitute a platform to study the early events of human cortical development and allow interrogation of the complex relationship between tissue architecture and cellular states in shaping the developing human brain.
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Affiliation(s)
- Anna Pagliaro
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Roxy Finger
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Iris Zoutendijk
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Saskia Bunschuh
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Hans Clevers
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- Pharma, Research and Early Development (pRED) of F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Delilah Hendriks
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Benedetta Artegiani
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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Lavekar SS, Patel MD, Montalvo-Parra MD, Krencik R. Asteroid impact: the potential of astrocytes to modulate human neural networks within organoids. Front Neurosci 2023; 17:1305921. [PMID: 38075269 PMCID: PMC10702564 DOI: 10.3389/fnins.2023.1305921] [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: 10/02/2023] [Accepted: 11/08/2023] [Indexed: 02/12/2024] Open
Abstract
Astrocytes are a vital cellular component of the central nervous system that impact neuronal function in both healthy and pathological states. This includes intercellular signals to neurons and non-neuronal cells during development, maturation, and aging that can modulate neural network formation, plasticity, and maintenance. Recently, human pluripotent stem cell-derived neural aggregate cultures, known as neurospheres or organoids, have emerged as improved experimental platforms for basic and pre-clinical neuroscience compared to traditional approaches. Here, we summarize the potential capability of using organoids to further understand the mechanistic role of astrocytes upon neural networks, including the production of extracellular matrix components and reactive signaling cues. Additionally, we discuss the application of organoid models to investigate the astrocyte-dependent aspects of neuropathological diseases and to test astrocyte-inspired technologies. We examine the shortcomings of organoid-based experimental platforms and plausible improvements made possible by cutting-edge neuroengineering technologies. These advancements are expected to enable the development of improved diagnostic strategies and high-throughput translational applications regarding neuroregeneration.
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Affiliation(s)
| | | | | | - R. Krencik
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX, United States
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14
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Zhou JQ, Zeng LH, Li CT, He DH, Zhao HD, Xu YN, Jin ZT, Gao C. Brain organoids are new tool for drug screening of neurological diseases. Neural Regen Res 2023; 18:1884-1889. [PMID: 36926704 PMCID: PMC10233755 DOI: 10.4103/1673-5374.367983] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/08/2022] [Accepted: 12/12/2022] [Indexed: 01/19/2023] Open
Abstract
At the level of in vitro drug screening, the development of a phenotypic analysis system with high-content screening at the core provides a strong platform to support high-throughput drug screening. There are few systematic reports on brain organoids, as a new three-dimensional in vitro model, in terms of model stability, key phenotypic fingerprint, and drug screening schemes, and particularly regarding the development of screening strategies for massive numbers of traditional Chinese medicine monomers. This paper reviews the development of brain organoids and the advantages of brain organoids over induced neurons or cells in simulated diseases. The paper also highlights the prospects from model stability, induction criteria of brain organoids, and the screening schemes of brain organoids based on the characteristics of brain organoids and the application and development of a high-content screening system.
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Affiliation(s)
- Jin-Qi Zhou
- School of Medicine, Institute of Brain and Cognitive Science, Hangzhou City University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang Province, China
| | - Ling-Hui Zeng
- School of Medicine, Institute of Brain and Cognitive Science, Hangzhou City University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang Province, China
| | - Chen-Tao Li
- School of Medicine, Institute of Brain and Cognitive Science, Hangzhou City University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang Province, China
| | - Da-Hong He
- School of Medicine, Institute of Brain and Cognitive Science, Hangzhou City University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang Province, China
| | - Hao-Duo Zhao
- School of Medicine, Institute of Brain and Cognitive Science, Hangzhou City University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang Province, China
| | - Yan-Nan Xu
- School of Medicine, Institute of Brain and Cognitive Science, Hangzhou City University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang Province, China
| | - Zi-Tian Jin
- School of Medicine, Institute of Brain and Cognitive Science, Hangzhou City University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang Province, China
| | - Chong Gao
- School of Medicine, Institute of Brain and Cognitive Science, Hangzhou City University, Hangzhou, Zhejiang Province, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang Province, China
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15
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Park SHE, Kulkarni A, Konopka G. FOXP1 orchestrates neurogenesis in human cortical basal radial glial cells. PLoS Biol 2023; 21:e3001852. [PMID: 37540706 PMCID: PMC10431666 DOI: 10.1371/journal.pbio.3001852] [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: 09/19/2022] [Revised: 08/16/2023] [Accepted: 06/21/2023] [Indexed: 08/06/2023] Open
Abstract
During cortical development, human basal radial glial cells (bRGCs) are highly capable of sustained self-renewal and neurogenesis. Selective pressures on this cell type may have contributed to the evolution of the human neocortex, leading to an increase in cortical size. bRGCs have enriched expression for Forkhead Box P1 (FOXP1), a transcription factor implicated in neurodevelopmental disorders (NDDs) such as autism spectrum disorder. However, the cell type-specific roles of FOXP1 in bRGCs during cortical development remain unexplored. Here, we examine the requirement for FOXP1 gene expression regulation underlying the production of bRGCs using human brain organoids. We examine a developmental time point when FOXP1 expression is highest in the cortical progenitors, and the bRGCs, in particular, begin to actively produce neurons. With the loss of FOXP1, we show a reduction in the number of bRGCs, as well as reduced proliferation and differentiation of the remaining bRGCs, all of which lead to reduced numbers of excitatory cortical neurons over time. Using single-nuclei RNA sequencing and cell trajectory analysis, we uncover a role for FOXP1 in directing cortical progenitor proliferation and differentiation by regulating key signaling pathways related to neurogenesis and NDDs. Together, these results demonstrate that FOXP1 regulates human-specific features in early cortical development.
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Affiliation(s)
- Seon Hye E. Park
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, United States of America
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Ashwinikumar Kulkarni
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, United States of America
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, Texas, United States of America
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, United States of America
- Peter O’Donnell Jr. Brain Institute, UT Southwestern Medical Center, Dallas, Texas, United States of America
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16
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Cerneckis J, Bu G, Shi Y. Pushing the boundaries of brain organoids to study Alzheimer's disease. Trends Mol Med 2023; 29:659-672. [PMID: 37353408 PMCID: PMC10374393 DOI: 10.1016/j.molmed.2023.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 06/25/2023]
Abstract
Progression of Alzheimer's disease (AD) entails deterioration or aberrant function of multiple brain cell types, eventually leading to neurodegeneration and cognitive decline. Defining how complex cell-cell interactions become dysregulated in AD requires novel human cell-based in vitro platforms that could recapitulate the intricate cytoarchitecture and cell diversity of the human brain. Brain organoids (BOs) are 3D self-organizing tissues that partially resemble the human brain architecture and can recapitulate AD-relevant pathology. In this review, we highlight the versatile applications of different types of BOs to model AD pathogenesis, including amyloid-β and tau aggregation, neuroinflammation, myelin breakdown, vascular dysfunction, and other phenotypes, as well as to accelerate therapeutic development for AD.
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Affiliation(s)
- Jonas Cerneckis
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Guojun Bu
- SciNeuro Pharmaceuticals, Rockville, MD 20850, USA
| | - Yanhong Shi
- Department of Neurodegenerative Diseases, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA.
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17
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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: 2] [Impact Index Per Article: 2.0] [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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18
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Bertucci T, Bowles KR, Lotz S, Qi L, Stevens K, Goderie SK, Borden S, Oja LM, Lane K, Lotz R, Lotz H, Chowdhury R, Joy S, Arduini BL, Butler DC, Miller M, Baron H, Sandhof CA, Silva MC, Haggarty SJ, Karch CM, Geschwind DH, Goate AM, Temple S. Improved Protocol for Reproducible Human Cortical Organoids Reveals Early Alterations in Metabolism with MAPT Mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.11.548571. [PMID: 37503195 PMCID: PMC10369860 DOI: 10.1101/2023.07.11.548571] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Cerebral cortical-enriched organoids derived from human pluripotent stem cells (hPSCs) are valuable models for studying neurodevelopment, disease mechanisms, and therapeutic development. However, recognized limitations include the high variability of organoids across hPSC donor lines and experimental replicates. We report a 96-slitwell method for efficient, scalable, reproducible cortical organoid production. When hPSCs were cultured with controlled-release FGF2 and an SB431542 concentration appropriate for their TGFBR1 / ALK5 expression level, organoid cortical patterning and reproducibility were significantly improved. Well-patterned organoids included 16 neuronal and glial subtypes by single cell RNA sequencing (scRNA-seq), frequent neural progenitor rosettes and robust BCL11B+ and TBR1+ deep layer cortical neurons at 2 months by immunohistochemistry. In contrast, poorly-patterned organoids contain mesendoderm-related cells, identifiable by negative QC markers including COL1A2 . Using this improved protocol, we demonstrate increased sensitivity to study the impact of different MAPT mutations from patients with frontotemporal dementia (FTD), revealing early changes in key metabolic pathways.
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19
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Ni P, Zhou C, Liang S, Jiang Y, Liu D, Shao Z, Noh H, Zhao L, Tian Y, Zhang C, Wei J, Li X, Yu H, Ni R, Yu X, Qi X, Zhang Y, Ma X, Deng W, Guo W, Wang Q, Sham PC, Chung S, Li T. YBX1-Mediated DNA Methylation-Dependent SHANK3 Expression in PBMCs and Developing Cortical Interneurons in Schizophrenia. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300455. [PMID: 37211699 PMCID: PMC10369273 DOI: 10.1002/advs.202300455] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/05/2023] [Indexed: 05/23/2023]
Abstract
Schizophrenia (SCZ) is a severe psychiatric and neurodevelopmental disorder. The pathological process of SCZ starts early during development, way before the first onset of psychotic symptoms. DNA methylation plays an important role in regulating gene expression and dysregulated DNA methylation is involved in the pathogenesis of various diseases. The methylated DNA immunoprecipitation-chip (MeDIP-chip) is performed to investigate genome-wide DNA methylation dysregulation in peripheral blood mononuclear cells (PBMCs) of patients with first-episode SCZ (FES). Results show that the SHANK3 promoter is hypermethylated, and this hypermethylation (HyperM) is negatively correlated with the cortical surface area in the left inferior temporal cortex and positively correlated with the negative symptom subscores in FES. The transcription factor YBX1 is further found to bind to the HyperM region of SHANK3 promoter in induced pluripotent stem cells (iPSCs)-derived cortical interneurons (cINs) but not glutamatergic neurons. Furthermore, a direct and positive regulatory effect of YBX1 on the expression of SHANK3 is confirmed in cINs using shRNAs. In summary, the dysregulated SHANK3 expression in cINs suggests the potential role of DNA methylation in the neuropathological mechanism underlying SCZ. The results also suggest that HyperM of SHANK3 in PBMCs can serve as a potential peripheral biomarker of SCZ.
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Affiliation(s)
- Peiyan Ni
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
- Department of PsychiatryMcLean Hospital/Harvard Medical SchoolBelmontMA02478USA
- Department of Cell Biology and AnatomyNew York Medical CollegeValhallaNY10595USA
| | - Chuqing Zhou
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Sugai Liang
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Youhui Jiang
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Dongxin Liu
- Department of Cell Biology and AnatomyNew York Medical CollegeValhallaNY10595USA
| | - Zhicheng Shao
- Department of PsychiatryMcLean Hospital/Harvard Medical SchoolBelmontMA02478USA
| | - Haneul Noh
- Department of PsychiatryMcLean Hospital/Harvard Medical SchoolBelmontMA02478USA
- Department of Cell Biology and AnatomyNew York Medical CollegeValhallaNY10595USA
| | - Liansheng Zhao
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Yang Tian
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Chengcheng Zhang
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Jinxue Wei
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Xiaojing Li
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Hua Yu
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Rongjun Ni
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Xueli Yu
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- NHC and CAMS Key Laboratory of Medical NeurobiologyMOE Frontier Science Center for Brain Science and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouZhejiang310058China
| | - Xueyu Qi
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- NHC and CAMS Key Laboratory of Medical NeurobiologyMOE Frontier Science Center for Brain Science and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouZhejiang310058China
| | - Yamin Zhang
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Xiaohong Ma
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Wei Deng
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- NHC and CAMS Key Laboratory of Medical NeurobiologyMOE Frontier Science Center for Brain Science and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouZhejiang310058China
| | - Wanjun Guo
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- NHC and CAMS Key Laboratory of Medical NeurobiologyMOE Frontier Science Center for Brain Science and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouZhejiang310058China
| | - Qiang Wang
- The Mental Health Center and Psychiatric LaboratoryState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu610041P. R. China
| | - Pak C. Sham
- Department of PsychiatryLi Ka Shing Faculty of MedicineThe University of Hong KongHong Kong, SAR999077China
- Centre for PanorOmic SciencesThe University of Hong KongHong Kong, SAR999077China
| | - Sangmi Chung
- Department of PsychiatryMcLean Hospital/Harvard Medical SchoolBelmontMA02478USA
- Department of Cell Biology and AnatomyNew York Medical CollegeValhallaNY10595USA
| | - Tao Li
- Department of NeurobiologyAffiliated Mental Health Center & Hangzhou Seventh People's HospitalZhejiang University School of MedicineHangzhouZhejiang310058China
- NHC and CAMS Key Laboratory of Medical NeurobiologyMOE Frontier Science Center for Brain Science and Brain‐Machine IntegrationSchool of Brain Science and Brain MedicineZhejiang UniversityHangzhouZhejiang310058China
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20
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Shabani K, Pigeon J, Benaissa Touil Zariouh M, Liu T, Saffarian A, Komatsu J, Liu E, Danda N, Becmeur-Lefebvre M, Limame R, Bohl D, Parras C, Hassan BA. The temporal balance between self-renewal and differentiation of human neural stem cells requires the amyloid precursor protein. SCIENCE ADVANCES 2023; 9:eadd5002. [PMID: 37327344 PMCID: PMC10275593 DOI: 10.1126/sciadv.add5002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/11/2023] [Indexed: 06/18/2023]
Abstract
Neurogenesis in the developing human cerebral cortex occurs at a particularly slow rate owing in part to cortical neural progenitors preserving their progenitor state for a relatively long time, while generating neurons. How this balance between the progenitor and neurogenic state is regulated, and whether it contributes to species-specific brain temporal patterning, is poorly understood. Here, we show that the characteristic potential of human neural progenitor cells (NPCs) to remain in a progenitor state as they generate neurons for a prolonged amount of time requires the amyloid precursor protein (APP). In contrast, APP is dispensable in mouse NPCs, which undergo neurogenesis at a much faster rate. Mechanistically, APP cell-autonomously contributes to protracted neurogenesis through suppression of the proneurogenic activator protein-1 transcription factor and facilitation of canonical WNT signaling. We propose that the fine balance between self-renewal and differentiation is homeostatically regulated by APP, which may contribute to human-specific temporal patterns of neurogenesis.
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Affiliation(s)
- Khadijeh Shabani
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Julien Pigeon
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Marwan Benaissa Touil Zariouh
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Tengyuan Liu
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Azadeh Saffarian
- Scipio bioscience, iPEPS-ICM, Hôpital Pitié-Salpêtrière, Paris, France
| | - Jun Komatsu
- Scipio bioscience, iPEPS-ICM, Hôpital Pitié-Salpêtrière, Paris, France
| | - Elise Liu
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Natasha Danda
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Mathilde Becmeur-Lefebvre
- Genetics and Foetopathology, Centre Hospitalier Regional d’Orleans–Hôpital de la Source, Orleans, France
| | - Ridha Limame
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Delphine Bohl
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Carlos Parras
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Bassem A. Hassan
- Institut du Cerveau–Paris Brain Institute–ICM, Sorbonne Université, INSERM, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
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21
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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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22
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Smirnov A, Melino G, Candi E. Gene expression in organoids: an expanding horizon. Biol Direct 2023; 18:11. [PMID: 36964575 PMCID: PMC10038780 DOI: 10.1186/s13062-023-00360-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/20/2023] [Indexed: 03/26/2023] Open
Abstract
Recent development of human three-dimensional organoid cultures has opened new doors and opportunities ranging from modelling human development in vitro to personalised cancer therapies. These new in vitro systems are opening new horizons to the classic understanding of human development and disease. However, the complexity and heterogeneity of these models requires cutting-edge techniques to capture and trace global changes in gene expression to enable identification of key players and uncover the underlying molecular mechanisms. Rapid development of sequencing approaches made possible global transcriptome analyses and epigenetic profiling. Despite challenges in organoid culture and handling, these techniques are now being adapted to embrace organoids derived from a wide range of human tissues. Here, we review current state-of-the-art multi-omics technologies, such as single-cell transcriptomics and chromatin accessibility assays, employed to study organoids as a model for development and a platform for precision medicine.
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Affiliation(s)
- Artem Smirnov
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Gerry Melino
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy
| | - Eleonora Candi
- Department of Experimental Medicine, Torvergata Oncoscience Research, University of Rome "Tor Vergata", Via Montpellier 1, 00133, Rome, Italy.
- Biochemistry Laboratory, Istituto Dermopatico Immacolata (IDI-IRCCS), 00166, Rome, Italy.
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23
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Walsh R, Giacomelli E, Ciceri G, Rittenhouse C, Galimberti M, Wu Y, Muller J, Vezzoli E, Jungverdorben J, Zhou T, Barker RA, Cattaneo E, Studer L, Baggiolini A. Generation of human cerebral organoids with a structured outer subventricular zone. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.17.528906. [PMID: 36824730 PMCID: PMC9949131 DOI: 10.1101/2023.02.17.528906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Mammalian outer radial glia (oRG) emerge as cortical progenitor cells that directly support the development of an enlarged outer subventricular zone (oSVZ) and, in turn, the expansion of the neocortex. The in vitro generation of oRG is essential to model and investigate the underlying mechanisms of human neocortical development and expansion. By activating the STAT3 pathway using LIF, which is not produced in guided cortical organoids, we developed a cerebral organoid differentiation method from human pluripotent stem cells (hPSCs) that recapitulates the expansion of a progenitor pool into the oSVZ. The structured oSVZ is composed of progenitor cells expressing specific oRG markers such as GFAP, LIFR, HOPX , which closely matches human oRG in vivo . In this microenvironment, cortical neurons showed faster maturation with enhanced metabolic and functional activity. Incorporation of hPSC-derived brain vascular LIF- producing pericytes in cerebral organoids mimicked the effects of LIF treatment. These data indicate that the cellular complexity of the cortical microenvironment, including cell-types of the brain vasculature, favors the appearance of oRG and provides a platform to routinely study oRG in hPSC-derived brain organoids.
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24
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Daoutsali E, Pepers BA, Stamatakis S, van der Graaf LM, Terwindt GM, Parfitt DA, Buijsen RAM, van Roon-Mom WMC. Amyloid beta accumulations and enhanced neuronal differentiation in cerebral organoids of Dutch-type cerebral amyloid angiopathy patients. Front Aging Neurosci 2023; 14:1048584. [PMID: 36733499 PMCID: PMC9887998 DOI: 10.3389/fnagi.2022.1048584] [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: 09/19/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023] Open
Abstract
Introduction ADutch-type cerebral amyloid angiopathy (D-CAA) is a hereditary brain disorder caused by a point mutation in the amyloid precursor protein (APP) gene. The mutation is located within the amyloid beta (Aβ) domain of APP and leads to Aβ peptide accumulation in and around the cerebral vasculature. There lack of disease models to study the cellular and molecular pathological mechanisms of D-CAA together with the absence of a disease phenotype in vitro in overexpression cell models, as well as the limited availability of D-CAA animal models indicates the need for a D-CAA patient-derived model. Methods We generated cerebral organoids from four D-CAA patients and four controls, cultured them up to 110 days and performed immunofluorescent and targeted gene expression analyses at two time points (D52 and D110). Results D-CAA cerebral organoids exhibited Aβ accumulations, showed enhanced neuronal and astrocytic gene expression and TGFβ pathway de-regulation. Conclusions These results illustrate the potential of cerebral organoids as in vitro disease model of D-CAA that can be used to understand disease mechanisms of D-CAA and can serve as therapeutic intervention platform for various Aβ-related disorders.
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Affiliation(s)
- Elena Daoutsali
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands,*Correspondence: Willeke M. C. van Roon-Mom, ; Elena Daoutsali,
| | - Barry A. Pepers
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Stavros Stamatakis
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Gisela M. Terwindt
- Department of Neurology, Leiden University Medical Center, Leiden, Netherlands
| | - David A. Parfitt
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Ronald A. M. Buijsen
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Willeke M. C. van Roon-Mom
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands,*Correspondence: Willeke M. C. van Roon-Mom, ; Elena Daoutsali,
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25
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Zang Z, Yin H, Du Z, Xie R, Yang L, Cai Y, Wang L, Zhang D, Li X, Liu T, Gong H, Gao J, Yang H, Warner M, Gustafsson JA, Xu H, Fan X. Valproic acid exposure decreases neurogenic potential of outer radial glia in human brain organoids. Front Mol Neurosci 2022; 15:1023765. [PMID: 36523605 PMCID: PMC9744776 DOI: 10.3389/fnmol.2022.1023765] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 11/08/2022] [Indexed: 07/29/2023] Open
Abstract
Valproic acid (VPA) exposure during pregnancy leads to a higher risk of autism spectrum disorder (ASD) susceptibility in offspring. Human dorsal forebrain organoids were used to recapitulate course of cortical neurogenesis in the developing human brain. Combining morphological characterization with massive parallel RNA sequencing (RNA-seq) on organoids to analyze the pathogenic effects caused by VPA exposure and critical signaling pathway. We found that VPA exposure in organoids caused a reduction in the size and impairment in the proliferation and expansion of neural progenitor cells (NPCs) in a dose-dependent manner. VPA exposure typically decreased the production of outer radial glia-like cells (oRGs), a subtype of NPCs contributing to mammalian neocortical expansion and delayed their fate toward upper-layer neurons. Transcriptomics analysis revealed that VPA exposure influenced ASD risk gene expression in organoids, which markedly overlapped with irregulated genes in brains or organoids originating from ASD patients. We also identified that VPA-mediated Wnt/β-catenin signaling pathway activation is essential for sustaining cortical neurogenesis and oRGs output. Taken together, our study establishes the use of dorsal forebrain organoids as an effective platform for modeling VPA-induced teratogenic pathways involved in the cortical neurogenesis and oRGs output, which might contribute to ASD pathogenesis in the developing brain.
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Affiliation(s)
- Zhenle Zang
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University (Army Medical University), Chongqing, China
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Huachun Yin
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Zhulin Du
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University (Army Medical University), Chongqing, China
| | - Ruxin Xie
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University (Army Medical University), Chongqing, China
| | - Ling Yang
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yun Cai
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University (Army Medical University), Chongqing, China
| | - Liuyongwei Wang
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University (Army Medical University), Chongqing, China
| | - Dandan Zhang
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xin Li
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University (Army Medical University), Chongqing, China
| | - Tianyao Liu
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University (Army Medical University), Chongqing, China
| | - Hong Gong
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University (Army Medical University), Chongqing, China
| | - Junwei Gao
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University (Army Medical University), Chongqing, China
| | - Hui Yang
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Margaret Warner
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX, United States
| | - Jan-Ake Gustafsson
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX, United States
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Haiwei Xu
- Southwest Hospital and Southwest Eye Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xiaotang Fan
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University (Army Medical University), Chongqing, China
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26
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Atamian A, Birtele M, Quadrato G. Not all cortical organoids are created equal. Nat Cell Biol 2022; 24:805-806. [PMID: 35697780 PMCID: PMC11216691 DOI: 10.1038/s41556-022-00890-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In the last decade, we have witnessed the establishment of multiple methods for deriving human cortical organoids. This study systematically compares patterning strategies and shows that combined WNT/Dual SMAD inhibition is superior to Dual SMAD inhibition in inducing robust cortical identity in 3D human pluripotent stem cells aggregates.
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Affiliation(s)
- Alexander Atamian
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at the University of Southern California, Los Angeles, CA, USA
| | - Marcella Birtele
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at the University of Southern California, Los Angeles, CA, USA
| | - Giorgia Quadrato
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at the University of Southern California, Los Angeles, CA, USA.
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