1
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Bosone C, Castaldi D, Burkard TR, Guzman SJ, Wyatt T, Cheroni C, Caporale N, Bajaj S, Bagley JA, Li C, Sorre B, Villa CE, Testa G, Krenn V, Knoblich JA. A polarized FGF8 source specifies frontotemporal signatures in spatially oriented cell populations of cortical assembloids. Nat Methods 2024:10.1038/s41592-024-02412-5. [PMID: 39294368 DOI: 10.1038/s41592-024-02412-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 08/12/2024] [Indexed: 09/20/2024]
Abstract
Organoids generating major cortical cell types in distinct compartments are used to study cortical development, evolution and disorders. However, the lack of morphogen gradients imparting cortical positional information and topography in current systems hinders the investigation of complex phenotypes. Here, we engineer human cortical assembloids by fusing an organizer-like structure expressing fibroblast growth factor 8 (FGF8) with an elongated organoid to enable the controlled modulation of FGF8 signaling along the longitudinal organoid axis. These polarized cortical assembloids mount a position-dependent transcriptional program that in part matches the in vivo rostrocaudal gene expression patterns and that is lost upon mutation in the FGFR3 gene associated with temporal lobe malformations and intellectual disability. By producing spatially oriented cell populations with signatures related to frontal and temporal area identity within individual assembloids, this model recapitulates in part the early transcriptional divergence embedded in the protomap and enables the study of cortical area-relevant alterations underlying human disorders.
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Affiliation(s)
- Camilla Bosone
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Davide Castaldi
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Thomas Rainer Burkard
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Segundo Jose Guzman
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Tom Wyatt
- Laboratoire "Matière et Systèmes Complexes" (MSC), UMR 7057 CNRS, University of Paris, Paris, France
| | | | - Nicolò Caporale
- Human Technopole, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Sunanjay Bajaj
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Department of Neurology, The University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Joshua Adam Bagley
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Chong Li
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Benoit Sorre
- Laboratoire "Matière et Systèmes Complexes" (MSC), UMR 7057 CNRS, University of Paris, Paris, France
- Physics of Cells and Cancer, Institut Curie, Université PSL, Sorbonne University, CNRS UMR168, Paris, France
| | | | - Giuseppe Testa
- Human Technopole, Milan, Italy.
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.
| | - Veronica Krenn
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
- Department of Biotechnology and Bioscience, University of Milan-Bicocca, Milan, Italy.
| | - Jürgen Arthur Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
- Department of Neurology, Medical University of Vienna, Vienna, Austria.
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2
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Glass MR, Waxman EA, Yamashita S, Lafferty M, Beltran AA, Farah T, Patel NK, Singla R, 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. Stem Cell Reports 2024; 19:1351-1367. [PMID: 39178845 PMCID: PMC11411306 DOI: 10.1016/j.stemcr.2024.07.008] [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: 02/21/2024] [Revised: 07/19/2024] [Accepted: 07/23/2024] [Indexed: 08/26/2024] Open
Abstract
While guided human cortical organoid (hCO) protocols reproducibly generate cortical cell types at one site, variability in hCO phenotypes across sites using a harmonized protocol has not yet been evaluated. To determine the cross-site reproducibility of hCO differentiation, three independent research groups assayed hCOs in multiple differentiation replicates from one induced pluripotent stem cell (iPSC) line using a harmonized miniaturized spinning bioreactor protocol across 3 months. hCOs were mostly cortical progenitor and neuronal cell types in reproducible proportions that were consistently organized in cortical wall-like buds. Cross-site differences were detected in hCO size and expression of metabolism and cellular stress genes. Variability in hCO phenotypes correlated with stem cell gene expression prior to differentiation and technical factors associated with seeding, suggesting iPSC quality and treatment are important for differentiation outcomes. Cross-site reproducibility of hCO cell type proportions and organization encourages future 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, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elisa A Waxman
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Satoshi Yamashita
- Center for Neuroscience Research, Children's National Hospital, Washington, DC, USA
| | - Michael Lafferty
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alvaro A Beltran
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tala Farah
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Niyanta K Patel
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rubal Singla
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nana Matoba
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sara Ahmed
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mary Srivastava
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Emma Drake
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Liam T Davis
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Meghana Yeturi
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kexin Sun
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kazue Hashimoto-Torii
- Center for Neuroscience Research, Children's National Hospital, Washington, DC, USA; Departments of Pediatrics, and Pharmacology & Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Deborah L French
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason L Stein
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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3
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Gonzalez-Ferrer J, Lehrer J, O'Farrell A, Paten B, Teodorescu M, Haussler D, Jonsson VD, Mostajo-Radji MA. SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis. CELL GENOMICS 2024; 4:100581. [PMID: 38823397 PMCID: PMC11228957 DOI: 10.1016/j.xgen.2024.100581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
Cell atlases serve as vital references for automating cell labeling in new samples, yet existing classification algorithms struggle with accuracy. Here we introduce SIMS (scalable, interpretable machine learning for single cell), a low-code data-efficient pipeline for single-cell RNA classification. We benchmark SIMS against datasets from different tissues and species. We demonstrate SIMS's efficacy in classifying cells in the brain, achieving high accuracy even with small training sets (<3,500 cells) and across different samples. SIMS accurately predicts neuronal subtypes in the developing brain, shedding light on genetic changes during neuronal differentiation and postmitotic fate refinement. Finally, we apply SIMS to single-cell RNA datasets of cortical organoids to predict cell identities and uncover genetic variations between cell lines. SIMS identifies cell-line differences and misannotated cell lineages in human cortical organoids derived from different pluripotent stem cell lines. Altogether, we show that SIMS is a versatile and robust tool for cell-type classification from single-cell datasets.
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Affiliation(s)
- Jesus Gonzalez-Ferrer
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Julian Lehrer
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Applied Mathematics, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Ash O'Farrell
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Benedict Paten
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Mircea Teodorescu
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - David Haussler
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Vanessa D Jonsson
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Applied Mathematics, University of California, Santa Cruz, Santa Cruz, CA 95060, USA.
| | - Mohammed A Mostajo-Radji
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA.
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4
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Sandoval SO, Cappuccio G, Kruth K, Osenberg S, Khalil SM, Méndez-Albelo NM, Padmanabhan K, Wang D, Niciu MJ, Bhattacharyya A, Stein JL, Sousa AMM, Waxman EA, Buttermore ED, Whye D, Sirois CL, Williams A, Maletic-Savatic M, Zhao X. Rigor and reproducibility in human brain organoid research: Where we are and where we need to go. Stem Cell Reports 2024; 19:796-816. [PMID: 38759644 PMCID: PMC11297560 DOI: 10.1016/j.stemcr.2024.04.008] [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: 01/02/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/19/2024] Open
Abstract
Human brain organoid models have emerged as a promising tool for studying human brain development and function. These models preserve human genetics and recapitulate some aspects of human brain development, while facilitating manipulation in an in vitro setting. Despite their potential to transform biology and medicine, concerns persist about their fidelity. To fully harness their potential, it is imperative to establish reliable analytic methods, ensuring rigor and reproducibility. Here, we review current analytical platforms used to characterize human forebrain cortical organoids, highlight challenges, and propose recommendations for future studies to achieve greater precision and uniformity across laboratories.
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Affiliation(s)
- Soraya O Sandoval
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Gerarda Cappuccio
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Karina Kruth
- Department of Psychiatry, University of Iowa Health Care, Iowa City, IA 52242, USA; Iowa Neuroscience Institute, University of Iowa Health Care, Iowa City, IA 52242, USA
| | - Sivan Osenberg
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Saleh M Khalil
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Natasha M Méndez-Albelo
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA; Molecular Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Krishnan Padmanabhan
- Department of Neuroscience, Center for Visual Science, Del Monte Institute for Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester NY 14642, USA
| | - Daifeng Wang
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Departments of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Mark J Niciu
- Department of Psychiatry, University of Iowa Health Care, Iowa City, IA 52242, USA; Iowa Neuroscience Institute, University of Iowa Health Care, Iowa City, IA 52242, USA
| | - Anita Bhattacharyya
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - André M M Sousa
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Elisa A Waxman
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Epilepsy and NeuroDevelopmental Disorders (ENDD), The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Elizabeth D Buttermore
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, USA; F.M. Kirby Neurobiology Department, Boston Children's Hospital, Boston, MA, USA
| | - Dosh Whye
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, USA; F.M. Kirby Neurobiology Department, Boston Children's Hospital, Boston, MA, USA
| | - Carissa L Sirois
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Aislinn Williams
- Department of Psychiatry, University of Iowa Health Care, Iowa City, IA 52242, USA; Iowa Neuroscience Institute, University of Iowa Health Care, Iowa City, IA 52242, USA.
| | - Mirjana Maletic-Savatic
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA; Center for Drug Discovery, Baylor College of Medicine, Houston, TX, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
| | - Xinyu Zhao
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.
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5
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Martins-Costa C, Wiegers A, Pham VA, Sidhaye J, Doleschall B, Novatchkova M, Lendl T, Piber M, Peer A, Möseneder P, Stuempflen M, Chow SYA, Seidl R, Prayer D, Höftberger R, Kasprian G, Ikeuchi Y, Corsini NS, Knoblich JA. ARID1B controls transcriptional programs of axon projection in an organoid model of the human corpus callosum. Cell Stem Cell 2024; 31:866-885.e14. [PMID: 38718796 DOI: 10.1016/j.stem.2024.04.014] [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: 05/17/2023] [Revised: 02/13/2024] [Accepted: 04/17/2024] [Indexed: 06/09/2024]
Abstract
Mutations in ARID1B, a member of the mSWI/SNF complex, cause severe neurodevelopmental phenotypes with elusive mechanisms in humans. The most common structural abnormality in the brain of ARID1B patients is agenesis of the corpus callosum (ACC), characterized by the absence of an interhemispheric white matter tract that connects distant cortical regions. Here, we find that neurons expressing SATB2, a determinant of callosal projection neuron (CPN) identity, show impaired maturation in ARID1B+/- neural organoids. Molecularly, a reduction in chromatin accessibility of genomic regions targeted by TCF-like, NFI-like, and ARID-like transcription factors drives the differential expression of genes required for corpus callosum (CC) development. Through an in vitro model of the CC tract, we demonstrate that this transcriptional dysregulation impairs the formation of long-range axonal projections, causing structural underconnectivity. Our study uncovers new functions of the mSWI/SNF during human corticogenesis, identifying cell-autonomous axonogenesis defects in SATB2+ neurons as a cause of ACC in ARID1B patients.
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Affiliation(s)
- Catarina Martins-Costa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Andrea Wiegers
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Vincent A Pham
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Jaydeep Sidhaye
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Balint Doleschall
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Thomas Lendl
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Marielle Piber
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Angela Peer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Paul Möseneder
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Marlene Stuempflen
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
| | - Siu Yu A Chow
- Institute of Industrial Science, The University of Tokyo, 153-8505 Tokyo, Japan; Institute for AI and Beyond, The University of Tokyo, 113-0032 Tokyo, Japan
| | - Rainer Seidl
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Daniela Prayer
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
| | - Romana Höftberger
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
| | - Gregor Kasprian
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, 153-8505 Tokyo, Japan; Institute for AI and Beyond, The University of Tokyo, 113-0032 Tokyo, Japan
| | - Nina S Corsini
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria.
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria; Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria.
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6
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Zhao HH, Haddad G. Brain organoid protocols and limitations. Front Cell Neurosci 2024; 18:1351734. [PMID: 38572070 PMCID: PMC10987830 DOI: 10.3389/fncel.2024.1351734] [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: 12/06/2023] [Accepted: 02/19/2024] [Indexed: 04/05/2024] Open
Abstract
Stem cell-derived organoid technology is a powerful tool that revolutionizes the field of biomedical research and extends the scope of our understanding of human biology and diseases. Brain organoids especially open an opportunity for human brain research and modeling many human neurological diseases, which have lagged due to the inaccessibility of human brain samples and lack of similarity with other animal models. Brain organoids can be generated through various protocols and mimic whole brain or region-specific. To provide an overview of brain organoid technology, we summarize currently available protocols and list several factors to consider before choosing protocols. We also outline the limitations of current protocols and challenges that need to be solved in future investigation of brain development and pathobiology.
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Affiliation(s)
- Helen H. Zhao
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
| | - Gabriel Haddad
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States
- The Rady Children's Hospital, San Diego, CA, United States
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7
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Andrews MG, Pearson CA. Toward an understanding of glucose metabolism in radial glial biology and brain development. Life Sci Alliance 2024; 7:e202302193. [PMID: 37798120 PMCID: PMC10556723 DOI: 10.26508/lsa.202302193] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 10/07/2023] Open
Abstract
Decades of research have sought to determine the intrinsic and extrinsic mechanisms underpinning the regulation of neural progenitor maintenance and differentiation. A series of precise temporal transitions within progenitor cell populations generates all the appropriate neural cell types while maintaining a pool of self-renewing progenitors throughout embryogenesis. Recent technological advances have enabled us to gain new insights at the single-cell level, revealing an interplay between metabolic state and developmental progression that impacts the timing of proliferation and neurogenesis. This can have long-term consequences for the developing brain's neuronal specification, maturation state, and organization. Furthermore, these studies have highlighted the need to reassess the instructive role of glucose metabolism in determining progenitor cell division, differentiation, and fate. This review focuses on glucose metabolism (glycolysis) in cortical progenitor cells and the emerging focus on glycolysis during neurogenic transitions. Furthermore, we discuss how the field can learn from other biological systems to improve our understanding of the spatial and temporal changes in glycolysis in progenitors and evaluate functional neurological outcomes.
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Affiliation(s)
- Madeline G Andrews
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Caroline A Pearson
- https://ror.org/02r109517 Center for Neurogenetics, Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
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8
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Reumann D, Krauditsch C, Novatchkova M, Sozzi E, Wong SN, Zabolocki M, Priouret M, Doleschall B, Ritzau-Reid KI, Piber M, Morassut I, Fieseler C, Fiorenzano A, Stevens MM, Zimmer M, Bardy C, Parmar M, Knoblich JA. In vitro modeling of the human dopaminergic system using spatially arranged ventral midbrain-striatum-cortex assembloids. Nat Methods 2023; 20:2034-2047. [PMID: 38052989 PMCID: PMC10703680 DOI: 10.1038/s41592-023-02080-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 10/10/2023] [Indexed: 12/07/2023]
Abstract
Ventral midbrain dopaminergic neurons project to the striatum as well as the cortex and are involved in movement control and reward-related cognition. In Parkinson's disease, nigrostriatal midbrain dopaminergic neurons degenerate and cause typical Parkinson's disease motor-related impairments, while the dysfunction of mesocorticolimbic midbrain dopaminergic neurons is implicated in addiction and neuropsychiatric disorders. Study of the development and selective neurodegeneration of the human dopaminergic system, however, has been limited due to the lack of an appropriate model and access to human material. Here, we have developed a human in vitro model that recapitulates key aspects of dopaminergic innervation of the striatum and cortex. These spatially arranged ventral midbrain-striatum-cortical organoids (MISCOs) can be used to study dopaminergic neuron maturation, innervation and function with implications for cell therapy and addiction research. We detail protocols for growing ventral midbrain, striatal and cortical organoids and describe how they fuse in a linear manner when placed in custom embedding molds. We report the formation of functional long-range dopaminergic connections to striatal and cortical tissues in MISCOs, and show that injected, ventral midbrain-patterned progenitors can mature and innervate the tissue. Using these assembloids, we examine dopaminergic circuit perturbations and show that chronic cocaine treatment causes long-lasting morphological, functional and transcriptional changes that persist upon drug withdrawal. Thus, our method opens new avenues to investigate human dopaminergic cell transplantation and circuitry reconstruction as well as the effect of drugs on the human dopaminergic system.
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Affiliation(s)
- Daniel Reumann
- Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Christian Krauditsch
- Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Edoardo Sozzi
- Department of Experimental Medical Science, Developmental and Regenerative Neurobiology, Wallenberg Neuroscience Center, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Sakurako Nagumo Wong
- Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Michael Zabolocki
- Laboratory for Human Neurophysiology and Genetics, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Marthe Priouret
- Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Balint Doleschall
- Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Kaja I Ritzau-Reid
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Marielle Piber
- Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
- Zebrafish Neurogenetics Unit, Institut Pasteur, Paris, France
| | - Ilaria Morassut
- Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
- Department of Basic Neurosciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Charles Fieseler
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Alessandro Fiorenzano
- Department of Experimental Medical Science, Developmental and Regenerative Neurobiology, Wallenberg Neuroscience Center, Lund Stem Cell Center, Lund University, Lund, Sweden
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics 'Adriano Buzzati Traverso' (IGB), CNR, Naples, Italy
| | - Molly M Stevens
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, London, UK
| | - Manuel Zimmer
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Cedric Bardy
- Laboratory for Human Neurophysiology and Genetics, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, South Australia, Australia
| | - Malin Parmar
- Department of Experimental Medical Science, Developmental and Regenerative Neurobiology, Wallenberg Neuroscience Center, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
- Department of Neurology, Medical University of Vienna, Vienna, Austria.
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9
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Martins‐Costa C, Pham VA, Sidhaye J, Novatchkova M, Wiegers A, Peer A, Möseneder P, Corsini NS, Knoblich JA. Morphogenesis and development of human telencephalic organoids in the absence and presence of exogenous extracellular matrix. EMBO J 2023; 42:e113213. [PMID: 37842725 PMCID: PMC10646563 DOI: 10.15252/embj.2022113213] [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: 12/06/2022] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
The establishment and maintenance of apical-basal polarity is a fundamental step in brain development, instructing the organization of neural progenitor cells (NPCs) and the developing cerebral cortex. Particularly, basally located extracellular matrix (ECM) is crucial for this process. In vitro, epithelial polarization can be achieved via endogenous ECM production, or exogenous ECM supplementation. While neuroepithelial development is recapitulated in neural organoids, the effects of different ECM sources in tissue morphogenesis remain underexplored. Here, we show that exposure to a solubilized basement membrane matrix substrate, Matrigel, at early neuroepithelial stages causes rapid tissue polarization and rearrangement of neuroepithelial architecture. In cultures exposed to pure ECM components or unexposed to any exogenous ECM, polarity acquisition is slower and driven by endogenous ECM production. After the onset of neurogenesis, tissue architecture and neuronal differentiation are largely independent of the initial ECM source, but Matrigel exposure has long-lasting effects on tissue patterning. These results advance the knowledge on mechanisms of exogenously and endogenously guided morphogenesis, demonstrating the self-sustainability of neuroepithelial cultures by endogenous processes.
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Affiliation(s)
- Catarina Martins‐Costa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenterViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Vincent A Pham
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenterViennaAustria
| | - Jaydeep Sidhaye
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenterViennaAustria
| | - Maria Novatchkova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenterViennaAustria
| | - Andrea Wiegers
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenterViennaAustria
| | - Angela Peer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenterViennaAustria
| | - Paul Möseneder
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenterViennaAustria
| | - Nina S Corsini
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenterViennaAustria
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenterViennaAustria
- Department of NeurologyMedical University of ViennaViennaAustria
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10
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Chiaradia I, Imaz-Rosshandler I, Nilges BS, Boulanger J, Pellegrini L, Das R, Kashikar ND, Lancaster MA. Tissue morphology influences the temporal program of human brain organoid development. Cell Stem Cell 2023; 30:1351-1367.e10. [PMID: 37802039 PMCID: PMC10765088 DOI: 10.1016/j.stem.2023.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/22/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
Progression through fate decisions determines cellular composition and tissue architecture, but how that same architecture may impact cell fate is less clear. We took advantage of organoids as a tractable model to interrogate this interaction of form and fate. Screening methodological variations revealed that common protocol adjustments impacted various aspects of morphology, from macrostructure to tissue architecture. We examined the impact of morphological perturbations on cell fate through integrated single nuclear RNA sequencing (snRNA-seq) and spatial transcriptomics. Regardless of the specific protocol, organoids with more complex morphology better mimicked in vivo human fetal brain development. Organoids with perturbed tissue architecture displayed aberrant temporal progression, with cells being intermingled in both space and time. Finally, encapsulation to impart a simplified morphology led to disrupted tissue cytoarchitecture and a similar abnormal maturational timing. These data demonstrate that cells of the developing brain require proper spatial coordinates to undergo correct temporal progression.
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Affiliation(s)
- Ilaria Chiaradia
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Benedikt S Nilges
- Resolve Biosciences GmbH, Alfred-Nobel-Strasse 10, 40789 Monheim am Rhein, Germany
| | - Jerome Boulanger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Laura Pellegrini
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Richa Das
- Resolve Biosciences GmbH, Alfred-Nobel-Strasse 10, 40789 Monheim am Rhein, Germany
| | - Nachiket D Kashikar
- Resolve Biosciences GmbH, Alfred-Nobel-Strasse 10, 40789 Monheim am Rhein, Germany
| | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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11
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Lo EKW, Velazquez JJ, Peng D, Kwon C, Ebrahimkhani MR, Cahan P. Platform-agnostic CellNet enables cross-study analysis of cell fate engineering protocols. Stem Cell Reports 2023; 18:1721-1742. [PMID: 37478860 PMCID: PMC10444577 DOI: 10.1016/j.stemcr.2023.06.008] [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: 09/07/2022] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/23/2023] Open
Abstract
Optimization of cell engineering protocols requires standard, comprehensive quality metrics. We previously developed CellNet, a computational tool to quantitatively assess the transcriptional fidelity of engineered cells compared with their natural counterparts, based on bulk-derived expression profiles. However, this platform and others were limited in their ability to compare data from different sources, and no current tool makes it easy to compare new protocols with existing state-of-the-art protocols in a standardized manner. Here, we utilized our prior application of the top-scoring pair transformation to build a computational platform, platform-agnostic CellNet (PACNet), to address both shortcomings. To demonstrate the utility of PACNet, we applied it to thousands of samples from over 100 studies that describe dozens of protocols designed to produce seven distinct cell types. We performed an in-depth examination of hepatocyte and cardiomyocyte protocols to identify the best-performing methods, characterize the extent of intra-protocol and inter-lab variation, and identify common off-target signatures, including a surprising neural/neuroendocrine signature in primary liver-derived organoids. We have made PACNet available as an easy-to-use web application, allowing users to assess their protocols relative to our database of reference engineered samples, and as open-source, extensible code.
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Affiliation(s)
- Emily K W Lo
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jeremy J Velazquez
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Da Peng
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Chulan Kwon
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mo R Ebrahimkhani
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA; McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Patrick Cahan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University, Baltimore, MD 21205, USA.
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12
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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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13
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Amin ND, Kelley KW, Hao J, Miura Y, Narazaki G, Li T, McQueen P, Kulkarni S, Pavlov S, Paşca SP. Generating human neural diversity with a multiplexed morphogen screen in organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.541819. [PMID: 37398073 PMCID: PMC10312596 DOI: 10.1101/2023.05.31.541819] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Morphogens choreograph the generation of remarkable cellular diversity in the developing nervous system. Differentiation of stem cells toward particular neural cell fates in vitro often relies upon combinatorial modulation of these signaling pathways. However, the lack of a systematic approach to understand morphogen-directed differentiation has precluded the generation of many neural cell populations, and knowledge of the general principles of regional specification remain in-complete. Here, we developed an arrayed screen of 14 morphogen modulators in human neural organoids cultured for over 70 days. Leveraging advances in multiplexed RNA sequencing technology and annotated single cell references of the human fetal brain we discovered that this screening approach generated considerable regional and cell type diversity across the neural axis. By deconvoluting morphogen-cell type relationships, we extracted design principles of brain region specification, including critical morphogen timing windows and combinatorics yielding an array of neurons with distinct neuro-transmitter identities. Tuning GABAergic neural subtype diversity unexpectedly led to the derivation of primate-specific interneurons. Taken together, this serves as a platform towards an in vitro morphogen atlas of human neural cell differentiation that will bring insights into human development, evolution, and disease.
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14
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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 PMCID: PMC10303776 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; (F.B.); (Z.D.); (T.G.)
| | - Zeynep Dokuzluoglu
- German Center for Neurodegenerative Diseases, 01307 Dresden, Germany; (F.B.); (Z.D.); (T.G.)
| | - Tobias Grass
- German Center for Neurodegenerative Diseases, 01307 Dresden, Germany; (F.B.); (Z.D.); (T.G.)
| | - Natalia Rodriguez-Muela
- German Center for Neurodegenerative Diseases, 01307 Dresden, Germany; (F.B.); (Z.D.); (T.G.)
- 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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15
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Wang M, Gage FH, Schafer ST. Transplantation Strategies to Enhance Maturity and Cellular Complexity in Brain Organoids. Biol Psychiatry 2023; 93:616-621. [PMID: 36739209 PMCID: PMC10662460 DOI: 10.1016/j.biopsych.2023.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/23/2022] [Accepted: 01/09/2023] [Indexed: 01/14/2023]
Abstract
Human brain organoids are 3-dimensional cell aggregates that are generated from pluripotent stem cells and recapitulate features of the early developing human brain. Brain organoids mainly consist of cells from the neural lineage, such as neural progenitor cells, neurons, and astrocytes. However, current brain organoid systems lack functional vasculature as well as other non-neuronal cells that are indispensable for oxygen and nutrient supply to the organoids, causing cell stress and formation of a necrotic center. Attempts to utilize intracerebral transplantation approaches have demonstrated successful vascularization of brain organoids and robust neurodifferentiation. In this review, we summarize recent progress and discuss ethical considerations in the field of brain organoid transplantation.
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Affiliation(s)
- Meiyan Wang
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California.
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California
| | - Simon T Schafer
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California; Department of Psychiatry and Psychotherapy, Medical School, Technical University of Munich, Munich, Germany; Center for Organoid Systems and Tissue Engineering, Technical University of Munich, Garching, Germany.
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16
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Eichmüller OL, Knoblich JA. Human cerebral organoids - a new tool for clinical neurology research. Nat Rev Neurol 2022; 18:661-680. [PMID: 36253568 PMCID: PMC9576133 DOI: 10.1038/s41582-022-00723-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2022] [Indexed: 11/21/2022]
Abstract
The current understanding of neurological diseases is derived mostly from direct analysis of patients and from animal models of disease. However, most patient studies do not capture the earliest stages of disease development and offer limited opportunities for experimental intervention, so rarely yield complete mechanistic insights. The use of animal models relies on evolutionary conservation of pathways involved in disease and is limited by an inability to recreate human-specific processes. In vitro models that are derived from human pluripotent stem cells cultured in 3D have emerged as a new model system that could bridge the gap between patient studies and animal models. In this Review, we summarize how such organoid models can complement classical approaches to accelerate neurological research. We describe our current understanding of neurodevelopment and how this process differs between humans and other animals, making human-derived models of disease essential. We discuss different methodologies for producing organoids and how organoids can be and have been used to model neurological disorders, including microcephaly, Zika virus infection, Alzheimer disease and other neurodegenerative disorders, and neurodevelopmental diseases, such as Timothy syndrome, Angelman syndrome and tuberous sclerosis. We also discuss the current limitations of organoid models and outline how organoids can be used to revolutionize research into the human brain and neurological diseases.
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Affiliation(s)
- Oliver L Eichmüller
- IMBA-Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
- University of Heidelberg, Heidelberg, Germany
| | - Juergen A Knoblich
- IMBA-Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
- Medical University of Vienna, Department of Neurology, Vienna, Austria.
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17
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Morales A, Andrews MG. Approaches to investigating metabolism in human neurodevelopment using organoids: insights from intestinal and cancer studies. Development 2022; 149:dev200506. [PMID: 36255366 PMCID: PMC9720749 DOI: 10.1242/dev.200506] [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] [Indexed: 06/16/2023]
Abstract
Interrogating the impact of metabolism during development is important for understanding cellular and tissue formation, organ and systemic homeostasis, and dysregulation in disease states. To evaluate the vital functions metabolism coordinates during human brain development and disease, pluripotent stem cell-derived models, such as organoids, provide tractable access to neurodevelopmental processes. Despite many strengths of neural organoid models, the extent of their replication of endogenous metabolic programs is currently unclear and requires direct investigation. Studies in intestinal and cancer organoids that functionally evaluate dynamic bioenergetic changes provide a framework that can be adapted for the study of neural metabolism. Validation of in vitro models remains a significant challenge; investigation using in vivo models and primary tissue samples is required to improve our in vitro model systems and, concomitantly, improve our understanding of human development.
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Affiliation(s)
- Alexandria Morales
- Schoolof Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
- Biomedical Engineering Graduate Program, Arizona State University, Tempe, AZ 85281, USA
| | - Madeline G. Andrews
- Schoolof Biological and Health Systems Engineering, Arizona State University, Tempe, AZ 85281, USA
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18
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Nowakowski TJ, Salama SR. Cerebral Organoids as an Experimental Platform for Human Neurogenomics. Cells 2022; 11:2803. [PMID: 36139380 PMCID: PMC9496777 DOI: 10.3390/cells11182803] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 01/25/2023] Open
Abstract
The cerebral cortex forms early in development according to a series of heritable neurodevelopmental instructions. Despite deep evolutionary conservation of the cerebral cortex and its foundational six-layered architecture, significant variations in cortical size and folding can be found across mammals, including a disproportionate expansion of the prefrontal cortex in humans. Yet our mechanistic understanding of neurodevelopmental processes is derived overwhelmingly from rodent models, which fail to capture many human-enriched features of cortical development. With the advent of pluripotent stem cells and technologies for differentiating three-dimensional cultures of neural tissue in vitro, cerebral organoids have emerged as an experimental platform that recapitulates several hallmarks of human brain development. In this review, we discuss the merits and limitations of cerebral organoids as experimental models of the developing human brain. We highlight innovations in technology development that seek to increase its fidelity to brain development in vivo and discuss recent efforts to use cerebral organoids to study regeneration and brain evolution as well as to develop neurological and neuropsychiatric disease models.
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Affiliation(s)
- Tomasz J. Nowakowski
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Psychiatry and Behavioral Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94158, USA
| | - Sofie R. Salama
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95060, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
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