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Huang R, Gao F, Yu L, Chen H, Zhu R. Generation of Neural Organoids and Their Application in Disease Modeling and Regenerative Medicine. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025:e01198. [PMID: 40411400 DOI: 10.1002/advs.202501198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2025] [Revised: 04/17/2025] [Indexed: 05/26/2025]
Abstract
The complexity and precision of the human nervous system have posed significant challenges for researchers seeking suitable models to elucidate refractory neural disorders. Traditional approaches, including monolayer cell cultures and animal models, often fail to replicate the intricacies of human neural tissue. The advent of organoid technology derived from stem cells has addressed many of these limitations, providing highly representative platforms for studying the structure and function of the human embryonic brain and spinal cord. Researchers have induced neural organoids with regional characteristics by mimicking morphogen gradients in neural development. Recent advancements have demonstrated the utility of neural organoids in disease modeling, offering insights into the pathophysiology of various neural disorders, as well as in the field of neural regeneration. Developmental defects in neural organoids due to the lack of microglia or vascular systems are addressed. In addition to induction methods, microfluidics is used to simulate the dynamic physiological environment; bio-manufacturing technologies are employed to regulate physical signaling and shape the structure of complex organs. These technologies further expand the construction strategies and application scope of neural organoids. With the emergence of new material paradigms and advances in AI, new possibilities in the realm of neural organoids are witnessed.
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Affiliation(s)
- Ruiqi Huang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital affiliated to Tongji University, School of Life Science and Technology, Tongji University, Shanghai, 200065, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200065, China
- Clinical Center for Brain and Spinal Cord Research, Tongji University, Shanghai, 200065, China
| | - Feng Gao
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital affiliated to Tongji University, School of Life Science and Technology, Tongji University, Shanghai, 200065, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200065, China
- Clinical Center for Brain and Spinal Cord Research, Tongji University, Shanghai, 200065, China
| | - Liqun Yu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital affiliated to Tongji University, School of Life Science and Technology, Tongji University, Shanghai, 200065, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200065, China
- Clinical Center for Brain and Spinal Cord Research, Tongji University, Shanghai, 200065, China
| | - Haokun Chen
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital affiliated to Tongji University, School of Life Science and Technology, Tongji University, Shanghai, 200065, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200065, China
- Clinical Center for Brain and Spinal Cord Research, Tongji University, Shanghai, 200065, China
| | - Rongrong Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital affiliated to Tongji University, School of Life Science and Technology, Tongji University, Shanghai, 200065, China
- Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, 200065, China
- Clinical Center for Brain and Spinal Cord Research, Tongji University, Shanghai, 200065, China
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2
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Sun Y, Ikeuchi Y, Guo F, Hyun I, Ming GL, Fu J. Bioengineering innovations for neural organoids with enhanced fidelity and function. Cell Stem Cell 2025; 32:689-709. [PMID: 40315834 PMCID: PMC12052258 DOI: 10.1016/j.stem.2025.03.014] [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: 08/05/2024] [Revised: 02/19/2025] [Accepted: 03/31/2025] [Indexed: 05/04/2025]
Abstract
Neural organoids have been utilized to recapitulate different aspects of the developing nervous system. While hailed as promising experimental tools for studying human neural development and neuropathology, current neural organoids do not fully recapitulate the anatomy or microcircuitry-level functionality of the developing brain, spinal cord, or peripheral nervous system. In this review, we discuss emerging bioengineering approaches that control morphogen signals and biophysical microenvironments, which have improved the efficiency, fidelity, and utility of neural organoids. Furthermore, advancements in bioengineered tools have facilitated more sophisticated analyses of neural organoid functions and applications, including improved neural-bioelectronic interfaces and organoid-based information processing. Emerging bioethical issues associated with advanced neural organoids are also discussed. Future opportunities of neural organoid research lie in enhancing their fidelity, maturity, and complexity and expanding their applications in a scalable manner.
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Affiliation(s)
- Yubing Sun
- Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, Amherst, MA 01003, USA.
| | - Yoshiho Ikeuchi
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan; Institute for AI and Beyond, The University of Tokyo, Tokyo 113-8654, Japan
| | - Feng Guo
- Department of Intelligent Systems Engineering, Indiana University Bloomington, Bloomington, IN 47408, USA
| | - Insoo Hyun
- Center for Life Sciences and Public Learning, Museum of Science, Boston, MA 02114, USA; Center for Bioethics, Harvard Medical School, Boston, MA 02115, USA
| | - Guo-Li Ming
- Department of Neuroscience, Perelman School of Medicine, Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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3
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Tao B, Li X, Hao M, Tian T, Li Y, Li X, Yang C, Li Q, Feng Q, Zhou H, Zhao Y, Wang D, Liu W. Organoid-Guided Precision Medicine: From Bench to Bedside. MedComm (Beijing) 2025; 6:e70195. [PMID: 40321594 PMCID: PMC12046123 DOI: 10.1002/mco2.70195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 03/16/2025] [Accepted: 03/18/2025] [Indexed: 05/08/2025] Open
Abstract
Organoid technology, as an emerging field within biotechnology, has demonstrated transformative potential in advancing precision medicine. This review systematically outlines the translational trajectory of organoids from bench to bedside, emphasizing their construction methodologies, key regulatory factors, and multifaceted applications in personalized healthcare. By recapitulating physiological architectures and disease phenotypes through three-dimensional culture systems, organoids leverage natural and synthetic scaffolds, stem cell sources, and spatiotemporal cytokine regulation to model tissue-specific microenvironments. Diverse organoid types-including skin, intestinal, lung, and tumor organoids-have facilitated breakthroughs in modeling tissue development, drug efficacy and toxicity screening, disease pathogenesis studies, and patient-tailored diagnostics. For instance, patient-derived tumor organoids preserve tumor heterogeneity and genomic profiles, serving as predictive platforms for individualized chemotherapy responses. In precision medicine, organoid-guided multiomics analyses identify actionable biomarkers and resistance mechanisms, while clustered regularly interspaced short palindromic repeats-based functional screens optimize therapeutic targeting. Despite preclinical successes, challenges persist in standardization, vascularization, and ethical considerations. Future integration of artificial intelligence, microfluidics, and spatial transcriptomics will enhance organoid scalability, reproducibility, and clinical relevance. By bridging molecular insights with patient-specific therapies, organoids are poised to revolutionize precision medicine, offering dynamic platforms for drug development, regenerative strategies, and individualized treatment paradigms.
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Affiliation(s)
- Boqiang Tao
- Department of Oral and Maxillofacial SurgeryHospital of StomatologyJilin UniversityChangchunChina
| | - Xiaolan Li
- Laboratory of Allergy and Precision MedicineChengdu Institute of Respiratory Healththe Third People's Hospital of ChengduAffiliated Hospital of Southwest Jiaotong UniversityChengduChina
| | - Ming Hao
- Department of Oral and Maxillofacial SurgeryHospital of StomatologyJilin UniversityChangchunChina
| | - Tian Tian
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
| | - Yuyang Li
- Department of Oral and Maxillofacial SurgeryHospital of StomatologyJilin UniversityChangchunChina
| | - Xiang Li
- Department of Oral and Maxillofacial SurgeryHospital of StomatologyJilin UniversityChangchunChina
| | - Chun Yang
- College of Basic MedicineBeihua UniversityJilinChina
| | - Qirong Li
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
| | - Qiang Feng
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
| | - Hengzong Zhou
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
| | - Yicheng Zhao
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
| | - Dongxu Wang
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
- Zhichuang Gene Editing Animal Model Research CenterWenzhou Institute of TechnologyWenzhouChina
| | - Weiwei Liu
- Department of Oral and Maxillofacial SurgeryHospital of StomatologyJilin UniversityChangchunChina
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Wu SR, Nowakowski TJ. Exploring human brain development and disease using assembloids. Neuron 2025; 113:1133-1150. [PMID: 40107269 PMCID: PMC12022838 DOI: 10.1016/j.neuron.2025.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 01/10/2025] [Accepted: 02/12/2025] [Indexed: 03/22/2025]
Abstract
How the human brain develops and what goes awry in neurological disorders represent two long-lasting questions in neuroscience. Owing to the limited access to primary human brain tissue, insights into these questions have been largely gained through animal models. However, there are fundamental differences between developing mouse and human brain, and neural organoids derived from human pluripotent stem cells (hPSCs) have recently emerged as a robust experimental system that mimics self-organizing and multicellular features of early human brain development. Controlled integration of multiple organoids into assembloids has begun to unravel principles of cell-cell interactions. Moreover, patient-derived or genetically engineered hPSCs provide opportunities to investigate phenotypic correlates of neurodevelopmental disorders and to develop therapeutic hypotheses. Here, we outline the advances in technologies that facilitate studies by using assembloids and summarize their applications in brain development and disease modeling. Lastly, we discuss the major roadblocks of the current system and potential solutions.
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Affiliation(s)
- Sih-Rong Wu
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Tomasz J Nowakowski
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
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5
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Choe MS, Lo C, Park IH. Modeling forebrain regional development and connectivity by human brain organoids. Curr Opin Genet Dev 2025; 91:102324. [PMID: 39983347 DOI: 10.1016/j.gde.2025.102324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Revised: 01/26/2025] [Accepted: 02/01/2025] [Indexed: 02/23/2025]
Abstract
The forebrain is one of the most important brain structures for modern human existence, which houses the uniquely sophisticated social and cognitive functions that distinguish our species. Therefore, modeling the forebrain development by using human cells is especially critical for our understanding of the intricacies of human development and devising treatments for related diseases. Recent advancements in brain organoid fields have offered unprecedented tools to investigate forebrain development from studies on specific regions to exploring tract formation and connectivity between different regions of the forebrain. In this review, we discuss the developmental biology of the forebrain and diverse methods for modeling its development by using organoids.
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Affiliation(s)
- Mu Seog Choe
- Interdepartmental Neuroscience Program, Department of Genetics, Yale Stem Cell Center, Yale Child Study Center, Wu Tsai Institute, Yale School of Medicine, New Haven, CT, United States
| | - Cynthia Lo
- Interdepartmental Neuroscience Program, Department of Genetics, Yale Stem Cell Center, Yale Child Study Center, Wu Tsai Institute, Yale School of Medicine, New Haven, CT, United States
| | - In-Hyun Park
- Interdepartmental Neuroscience Program, Department of Genetics, Yale Stem Cell Center, Yale Child Study Center, Wu Tsai Institute, Yale School of Medicine, New Haven, CT, United States.
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6
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Zhang H, Sun S, Izpisua Belmonte JC, Liu GH, Wang S, Zhang W, Qu J. Protocols for the application of human embryonic stem cell-derived neurons for aging modeling and gene manipulation. STAR Protoc 2025; 6:103633. [PMID: 39932849 PMCID: PMC11867521 DOI: 10.1016/j.xpro.2025.103633] [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: 08/28/2023] [Revised: 12/02/2024] [Accepted: 01/18/2025] [Indexed: 02/13/2025] Open
Abstract
In vitro models of neuronal aging and gene manipulation in human neurons (hNeurons) are valuable tools for investigating human brain aging and diseases. Here, we present a protocol for applying human embryonic stem cell (hESC)-derived neurons to model aging and the further application of small interfering RNA (siRNA)-mediated gene silencing for functional investigations. We describe steps for neuronal differentiation and culture, siRNA transfection, and technical considerations to ensure reproducibility. Our protocol enables investigations of the molecular mechanism underlying neuronal aging and facilitates drug evaluation. For complete details on the use and execution of this protocol, please refer to Zhang et al.1.
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Affiliation(s)
- Hui Zhang
- Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China
| | - Shuhui Sun
- Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China
| | | | - Guang-Hui Liu
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Aging Biomarker Consortium (ABC), Beijing 100101, China.
| | - Si Wang
- National Clinical Research Center for Geriatric Disorders, Aging Translational Medicine Center, Xuanwu Hospital Capital Medical University, Beijing 100053, China; Aging Biomarker Consortium (ABC), Beijing 100101, China.
| | - Weiqi Zhang
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; China National Center for Bioinformation, Beijing, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; Aging Biomarker Consortium (ABC), Beijing 100101, China.
| | - Jing Qu
- Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing Anzhen Hospital, Capital Medical University, Beijing 100029, China; Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Membrane Biology, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Aging Biomarker Consortium (ABC), Beijing 100101, China.
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7
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Artegiani B, Hendriks D. Organoids from pluripotent stem cells and human tissues: When two cultures meet each other. Dev Cell 2025; 60:493-511. [PMID: 39999776 DOI: 10.1016/j.devcel.2025.01.005] [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: 03/11/2024] [Revised: 06/13/2024] [Accepted: 01/10/2025] [Indexed: 02/27/2025]
Abstract
Human organoids are a widely used tool in cell biology to study homeostatic processes, disease, and development. The term organoids covers a plethora of model systems from different cellular origins that each have unique features and applications but bring their own challenges. This review discusses the basic principles underlying organoids generated from pluripotent stem cells (PSCs) as well as those derived from tissue stem cells (TSCs). We consider how well PSC- and TSC-organoids mimic the different intended organs in terms of cellular complexity, maturity, functionality, and the ongoing efforts to constitute predictive complex models of in vivo situations. We discuss the advantages and limitations associated with each system to answer different biological questions including in the field of cancer and developmental biology, and with respect to implementing emerging advanced technologies, such as (spatial) -omics analyses, CRISPR screens, and high-content imaging screens. We postulate how the two fields may move forward together, integrating advantages of one to the other.
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Affiliation(s)
| | - Delilah Hendriks
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
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8
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Velazquez Ojeda A, Awabdeh D, Brewster B, Rockne R, O'Meally D, Yin HH, Carlesso N, Brown CE, Gutova M, Barish ME. Modeling cerebral development in vitro with L- MYC -immortalized human neural stem cell-derived organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.12.637976. [PMID: 39990325 PMCID: PMC11844543 DOI: 10.1101/2025.02.12.637976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
A promising advance for ex vivo studies of human brain development and formulation of therapeutic strategies has been the adoption of brain organoids that, to a greater extent than monolayer or spheroid cultures, recapitulate to varying extents the patterns of tissue development and cell differentiation of human brain. Previously, such studies been hampered by limited access to relevant human tissue, inadequate human in vitro models, and the necessity of using rodent models that imperfectly reproduce human brain physiology. Here we present a novel organoid-based research platform utilizing L- MYC -immortalized human fetal neural stem cells (LMNSC01) grown in a physiological 4% oxygen environment. We visualized developmental processes in LMNSC01 brain organoids for over 120 days in vitro by immunofluorescence and NanoString gene expression profiling. Gene expression patterns revealed by NanoString profiling were quantitatively compared to those occurring during normal brain development (BrainSpan database) using the Singscore method. We observe similar developmental patterns in LMNSC01 organoids and developing cortex for genes characterizing neurons, astrocytes, and oligodendrocytes, and multiple pathways including those involved in apoptosis, neuronal cytoskeleton, neurotransmission, and metabolism. Notable properties of this LMNSC01 platform are its initiation with immortalized authentic human neural stem cells, growth in a physiological oxygen environment, the consistency of the organoids produced, and favorable comparison of their gene expression patterns with those reported for normal cortical development. SUMMARY E x vivo studies of human brain development has been advanced by adoption of organoids recapitulating to varying extents in utero patterns of tissue development and cell differentiation. We here present an organoid-based human cortical development platform employing immortalized fetal neural stem cells (LMNSC01) grown in a physiological (4% oxygen) environment. Characterizing LMNSC01 organoids for over 120 days in vitro by immunofluorescence and expression profiling (using NanoString), and then comparing these profiles to those of normal cortical development (BrainSpan database), revealed similar developmental patterns for neurons, astrocytes and oligodendrocytes. Notable properties of this platform are its initiation with immortalized authentic human NSCs, growth at physiological oxygen concentration, and subsequent favorable comparison of their gene expression patterns with those observed during cortical development.
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Glass MR, Matoba N, Beltran AA, Patel NK, Farah TM, Eswar K, Bhargava S, Huang K, Curtin I, Ahmed S, Srivastava M, Drake E, Davis LT, Yeturi M, Sun K, Love MI, Simon JM, St John T, Marrus N, Pandey J, Estes A, Dager S, Schultz RT, Botteron K, Evans A, Kim SH, Styner M, McKinstry RC, Collins DL, Volk H, Benke K, Zwaigenbaum L, Hazlett H, Beltran AS, Girault JB, Shen MD, Piven J, Stein JL. Early cell cycle genes in cortical organoid progenitors predict interindividual variability in infant brain growth trajectories. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.07.637106. [PMID: 39974968 PMCID: PMC11839139 DOI: 10.1101/2025.02.07.637106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
Abstract
Human induced pluripotent stem cell (iPSC) derived cortical organoids (hCOs) model neurogenesis on an individual's genetic background. The degree to which hCO phenotypes recapitulate the brain growth of the participants from which they were derived is not well established. We generated up to 3 iPSC clones from each of 18 participants in the Infant Brain Imaging Study, who have undergone longitudinal brain imaging during infancy. We identified consistent hCO morphology and cortical cell types across clones from the same participant. hCO cross-sectional area and production of cortical hem cells were associated with in vivo cortical growth rates. Cell cycle associated genes expression in early progenitors at the crux of fate decision trajectories were correlated with cortical growth rate from 6-12 months of age, and were enriched in microcephaly and neurodevelopmental disorder genes. Our data suggest the hCOs capture inter-individual variation in cortical cell types influencing infant cortical surface area expansion.
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Affiliation(s)
- Madison R Glass
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- These authors contributed equally
| | - Nana Matoba
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- These authors contributed equally
| | - Alvaro A Beltran
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Niyanta K Patel
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Tala M Farah
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Karthik Eswar
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Shivam Bhargava
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Karen Huang
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Ian Curtin
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Sara Ahmed
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Mary Srivastava
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Emma Drake
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Liam T Davis
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Meghana Yeturi
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Kexin Sun
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- UNC Neuroscience Center, 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
| | - Jeremy M Simon
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- Present address: Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Present address: Department of Biostatistics, Harvard T.H. Chan School of Public Health, MA, USA
| | - Tanya St John
- Department of Speech and Hearing Sciences, University of Washington; Seattle, WA, USA
- University of Washington Autism Center, University of Washington; Seattle, WA, USA
| | - Natasha Marrus
- Department of Psychiatry, Washington University School of Medicine; St. Louis, MO, USA
| | - Juhi Pandey
- Department of Psychiatry, University of Pennsylvania; Philadelphia, PA, USA
- Center for Autism Research, Children's Hospital of Philadelphia; Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania; Philadelphia, USA
| | - Annette Estes
- Department of Speech and Hearing Sciences, University of Washington; Seattle, WA, USA
- University of Washington Autism Center, University of Washington; Seattle, WA, USA
| | - Stephen Dager
- Department of Radiology, University of Washington; Seattle, WA, USA
- Department of Bioengineering, University of Washington; Seattle, WA, USA
| | - Robert T Schultz
- Department of Psychiatry, University of Pennsylvania; Philadelphia, PA, USA
- Center for Autism Research, Children's Hospital of Philadelphia; Philadelphia, PA, USA
- Department of Pediatrics, University of Pennsylvania; Philadelphia, USA
| | - Kelly Botteron
- Department of Psychiatry, Washington University School of Medicine; St. Louis, MO, USA
| | - Alan Evans
- Department of Neurology and Neurosurgery, McGill University; Montreal, QC, CA
- Department of Psychiatry, McGill University; Montreal, QC, CA
- Department of Biomedical Engineering, McGill University; Montreal, QC, CA
| | - Sun Hyung Kim
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Martin Styner
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- Department of Computer Sciences, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Robert C McKinstry
- Department of Psychiatry, Washington University School of Medicine; St. Louis, MO, USA
| | - D Louis Collins
- Department of Neurology and Neurosurgery, McGill University; Montreal, QC, CA
- Department of Biomedical Engineering, McGill University; Montreal, QC, CA
| | - Heather Volk
- School of Public Health, Johns Hopkins; Baltimore, MD, USA
| | - Kelly Benke
- School of Public Health, Johns Hopkins; Baltimore, MD, USA
| | - Lonnie Zwaigenbaum
- Department of Developmental Pediatrics, University of Alberta; Edmonton, AB, CA
| | - Heather Hazlett
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Adriana S Beltran
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
| | - Jessica B Girault
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- These authors jointly supervised
| | - Mark D Shen
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- These authors jointly supervised
| | - Joseph Piven
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- These authors jointly supervised
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill; Chapel Hill, NC, USA
- These authors jointly supervised
- Lead contact
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10
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Pagliaro A, Artegiani B, Hendriks D. Emerging approaches to enhance human brain organoid physiology. Trends Cell Biol 2025:S0962-8924(24)00254-X. [PMID: 39826996 DOI: 10.1016/j.tcb.2024.12.001] [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: 08/08/2024] [Revised: 11/27/2024] [Accepted: 12/09/2024] [Indexed: 01/22/2025]
Abstract
Brain organoids are important 3D models for studying human brain development, disease, and evolution. To overcome some of the existing limitations that affect organoid quality, reproducibility, characteristics, and in vivo resemblance, current efforts are directed to improve their physiological relevance by exploring different, yet interconnected, routes. In this review, these approaches and their latest developments are discussed, including stem cell optimization, refining morphogen administration strategies, altering the extracellular matrix (ECM) niche, and manipulating tissue architecture to mimic in vivo brain morphogenesis. Additionally, strategies to increase cell diversity and enhance organoid maturation, such as establishing co-cultures, assembloids, and organoid in vivo xenotransplantation, are reviewed. We explore how these various factors can be tuned and intermingled and speculate on future avenues towards even more physiologically-advanced brain organoids.
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Affiliation(s)
- Anna Pagliaro
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Delilah Hendriks
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
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11
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Kulasinghe A, Berrell N, Donovan ML, Nilges BS. Spatial-Omics Methods and Applications. Methods Mol Biol 2025; 2880:101-146. [PMID: 39900756 DOI: 10.1007/978-1-0716-4276-4_5] [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] [Indexed: 02/05/2025]
Abstract
Traditional tissue profiling approaches have evolved from bulk studies to single-cell analysis over the last decade; however, the spatial context in tissues and microenvironments has always been lost. Over the last 5 years, spatial technologies have emerged that enabled researchers to investigate tissues in situ for proteins and transcripts without losing anatomy and histology. The field of spatial-omics enables highly multiplexed analysis of biomolecules like RNAs and proteins in their native spatial context-and has matured from initial proof-of-concept studies to a thriving field with widespread applications from basic research to translational and clinical studies. While there has been wide adoption of spatial technologies, there remain challenges with the standardization of methodologies, sample compatibility, throughput, resolution, and ease of use. In this chapter, we discuss the current state of the field and highlight technological advances and limitations.
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Affiliation(s)
- Arutha Kulasinghe
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Queensland Spatial Biology Centre, Wesley Research Institute, The Wesley Hospital, Auchenflower, QLD, Australia
| | - Naomi Berrell
- Queensland Spatial Biology Centre, Wesley Research Institute, The Wesley Hospital, Auchenflower, QLD, Australia
| | - Meg L Donovan
- Queensland Spatial Biology Centre, Wesley Research Institute, The Wesley Hospital, Auchenflower, QLD, Australia
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12
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Lancaster MA. Pluripotent stem cell-derived organoids: A brief history of curiosity-led discoveries. Bioessays 2024; 46:e2400105. [PMID: 39101295 PMCID: PMC11589667 DOI: 10.1002/bies.202400105] [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: 04/29/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 08/06/2024]
Abstract
Organoids are quickly becoming an accepted model for understanding human biology and disease. Pluripotent stem cells (PSC) provide a starting point for many organs and enable modeling of the embryonic development and maturation of such organs. The foundation of PSC-derived organoids can be found in elegant developmental studies demonstrating the remarkable ability of immature cells to undergo histogenesis even when taken out of the embryo context. PSC-organoids are an evolution of earlier methods such as embryoid bodies, taken to a new level with finer control and in some cases going beyond tissue histogenesis to organ-like morphogenesis. But many of the discoveries that led to organoids were not necessarily planned, but rather the result of inquisitive minds with freedom to explore. Protecting such curiosity-led research through flexible funding will be important going forward if we are to see further ground-breaking discoveries.
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13
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Alani M, Altarturih H, Pars S, Al-mhanawi B, Wolvetang EJ, Shaker MR. A Roadmap for Selecting and Utilizing Optimal Features in scRNA Sequencing Data Analysis for Stem Cell Research: A Comprehensive Review. Int J Stem Cells 2024; 17:347-362. [PMID: 38531607 PMCID: PMC11612217 DOI: 10.15283/ijsc23170] [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: 10/23/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/28/2024] Open
Abstract
Stem cells and the cells they produce are unique because they vary from one cell to another. Traditional methods of studying cells often overlook these differences. However, the development of new technologies for studying individual cells has greatly changed biological research in recent years. Among these innovations, single-cell RNA sequencing (scRNA-seq) stands out. This technique allows scientists to examine the activity of genes in each cell, across thousands or even millions of cells. This makes it possible to understand the diversity of cells, identify new types of cells, and see how cells differ across different tissues, individuals, species, times, and conditions. This paper discusses the importance of scRNA-seq and the computational tools and software that are essential for analyzing the vast amounts of data generated by scRNA-seq studies. Our goal is to provide practical advice for bioinformaticians and biologists who are using scRNA-seq to study stem cells. We offer an overview of the scRNA-seq field, including the tools available, how they can be used, and how to present the results of these studies effectively. Our findings include a detailed overview and classification of tools used in scRNA-seq analysis, based on a review of 2,733 scientific publications. This review is complemented by information from the scRNA-tools database, which lists over 1,400 tools for analyzing scRNA-seq data. This database is an invaluable resource for researchers, offering a wide range of options for analyzing their scRNA-seq data.
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Affiliation(s)
- Maath Alani
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Hamza Altarturih
- Faculty of Computer Science and Information Technology, University of Malaya, Kuala Lumpur, Malaysia
| | - Selin Pars
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Bahaa Al-mhanawi
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Ernst J. Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Mohammed R. Shaker
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
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14
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Kjar A, Haschert MR, Zepeda JC, Simmons AJ, Yates A, Chavarria D, Fernandez M, Robertson G, Abdulrahman AM, Kim H, Marguerite NT, Moen RK, Drake LE, Curry CW, O'Grady BJ, Gama V, Lau KS, Grueter B, Brunger JM, Lippmann ES. Biofunctionalized gelatin hydrogels support development and maturation of iPSC-derived cortical organoids. Cell Rep 2024; 43:114874. [PMID: 39423129 PMCID: PMC11682736 DOI: 10.1016/j.celrep.2024.114874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 09/16/2024] [Accepted: 09/30/2024] [Indexed: 10/21/2024] Open
Abstract
Human neural organoid models have become an important tool for studying neurobiology. However, improving the representativeness of neural cell populations in such organoids remains a major effort. In this work, we compared Matrigel, a commercially available matrix, to a neural cadherin (N-cadherin) peptide-functionalized gelatin methacryloyl hydrogel (termed GelMA-Cad) for culturing cortical neural organoids. We determined that peptide presentation can tune cell fate and diversity in gelatin-based matrices during differentiation. Of particular note, cortical organoids cultured in GelMA-Cad hydrogels mapped more closely to human fetal populations and produced neurons with more spontaneous excitatory postsynaptic currents relative to Matrigel. These results provide compelling evidence that matrix-tethered signaling peptides can influence neural organoid differentiation, opening an avenue to control stem cell fate. Moreover, outcomes from this work showcase the technical utility of GelMA-Cad as a simple and defined hydrogel alternative to Matrigel for neural organoid culture.
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Affiliation(s)
- Andrew Kjar
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Mia R Haschert
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - José C Zepeda
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - A Joey Simmons
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alexis Yates
- Interdisciplinary Materials Science Program, Vanderbilt University, Nashville, TN, USA
| | - Daniel Chavarria
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Melanie Fernandez
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Gabriella Robertson
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Adam M Abdulrahman
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Hyosung Kim
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Nicole T Marguerite
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Rachel K Moen
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Lauren E Drake
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Corinne W Curry
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Brian J O'Grady
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Vivian Gama
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA; Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA
| | - Ken S Lau
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA; Chemical and Physical Biology Program, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brad Grueter
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA; Department of Anesthesiology, Vanderbilt University, Nashville, TN, USA; Vanderbilt Center for Addiction Research, Vanderbilt University, Nashville, TN, USA
| | - Jonathan M Brunger
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA; Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ethan S Lippmann
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA; Interdisciplinary Materials Science Program, Vanderbilt University, Nashville, TN, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA; Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, USA; Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Memory and Alzheimer's Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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15
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Gunapala KM, Gadban A, Noreen F, Schär P, Benvenisty N, Taylor V. Ascorbic Acid Ameliorates Molecular and Developmental Defects in Human-Induced Pluripotent Stem Cell and Cerebral Organoid Models of Fragile X Syndrome. Int J Mol Sci 2024; 25:12718. [PMID: 39684429 DOI: 10.3390/ijms252312718] [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: 10/03/2024] [Revised: 11/15/2024] [Accepted: 11/22/2024] [Indexed: 12/18/2024] Open
Abstract
Fragile X Syndrome (FX) is the most common form of inherited cognitive impairment and falls under the broader category of Autism Spectrum Disorders (ASD). FX is caused by a CGG trinucleotide repeat expansion in the non-coding region of the X-linked Fragile X Messenger Ribonucleoprotein 1 (FMR1) gene, leading to its hypermethylation and epigenetic silencing. Animal models of FX rely on the deletion of the Fmr1 gene, which fails to replicate the epigenetic silencing mechanism of the FMR1 gene observed in human patients. Human stem cells carrying FX repeat expansions have provided a better understanding of the basis of epigenetic silencing of FMR1. Previous studies have found that 5-Azacytidine (5Azac) can reverse this methylation; however, 5Azac can be toxic, which may limit its therapeutic potential. Here, we show that the dietary factor Ascorbic Acid (AsA) can reduce DNA methylation in the FMR1 locus and lead to an increase in FMR1 gene expression in FX iPSCs and cerebral organoids. In addition, AsA treatment rescued neuronal gene expression and morphological defects observed in FX iPSC-derived cerebral organoids. Hence, we demonstrate that the dietary co-factor AsA can partially revert the molecular and morphological defects seen in human FX models in vitro. Our findings have implications for the development of novel therapies for FX in the future.
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Affiliation(s)
- Keith M Gunapala
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Aseel Gadban
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Faiza Noreen
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 4031 Basel, Switzerland
| | - Primo Schär
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Verdon Taylor
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
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16
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Nishimura H, Li Y. Human pluripotent stem cell-derived models of the hippocampus. Int J Biochem Cell Biol 2024; 177:106695. [PMID: 39557338 DOI: 10.1016/j.biocel.2024.106695] [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: 08/31/2024] [Revised: 11/06/2024] [Accepted: 11/12/2024] [Indexed: 11/20/2024]
Abstract
The hippocampus is a crucial structure of the brain, recognised for its roles in the formation of memory, and our ability to navigate the world. Despite its importance, clear understanding of how the human hippocampus develops and its contribution to disease is limited due to the inaccessible nature of the human brain. In this regard, the advent of human pluripotent stem cell (hPSC) technologies has enabled the study of human biology in an unprecedented manner, through the ability to model development and disease as both 2D monolayers and 3D organoids. In this review, we explore the existing efforts to derive the hippocampal lineage from hPSCs and evaluate the various aspects of the in vivo hippocampus that are replicated in vitro. In addition, we highlight key diseases that have been modelled using hPSC-derived cultures and offer our perspective on future directions for this emerging field.
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Affiliation(s)
- Haruka Nishimura
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Yun Li
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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17
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Ikeda M, Doi D, Ebise H, Ozaki Y, Fujii M, Kikuchi T, Yoshida K, Takahashi J. Validation of non-destructive morphology-based selection of cerebral cortical organoids by paired morphological and single-cell RNA-seq analyses. Stem Cell Reports 2024; 19:1635-1646. [PMID: 39393360 PMCID: PMC11589179 DOI: 10.1016/j.stemcr.2024.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/14/2024] [Accepted: 09/16/2024] [Indexed: 10/13/2024] Open
Abstract
Organoids, self-organized cell aggregates, contribute significantly to developing disease models and cell-based therapies. Organoid-to-organoid variations, however, are inevitable despite the use of the latest differentiation protocols. Here, we focused on the morphology of organoids formed in a cerebral organoid differentiation culture and assessed their cellular compositions by single-cell RNA sequencing analysis. The data revealed that organoids primarily composed of non-neuronal cells, such as those from the neural crest and choroid plexus, showed unique morphological features. Moreover, we demonstrate that non-destructive morphological analysis can accurately distinguish organoids composed of cerebral cortical tissues from other cerebral tissues, thus enhancing experimental accuracy and reliability to ensure the safety of cell-based therapies.
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Affiliation(s)
- Megumi Ikeda
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan; Regenerative & Cellular Medicine Kobe Center, Sumitomo Pharma Co., Ltd., Chuo-ku, Kobe 650-0047, Japan
| | - Daisuke Doi
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Hayao Ebise
- Regenerative & Cellular Medicine Kobe Center, Sumitomo Pharma Co., Ltd., Chuo-ku, Kobe 650-0047, Japan
| | - Yuki Ozaki
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Misaki Fujii
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Tetsuhiro Kikuchi
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Kenji Yoshida
- Regenerative & Cellular Medicine Kobe Center, Sumitomo Pharma Co., Ltd., Chuo-ku, Kobe 650-0047, Japan
| | - Jun Takahashi
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan.
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18
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Ma S, Wang W, Zhou J, Liao S, Hai C, Hou Y, Zhou Z, Wang Z, Su Y, Zhu Y, Dai X, Zhao Y, Liao S, Cai Y, Xu X. Lamination-based organoid spatially resolved transcriptomics technique for primary lung and liver organoid characterization. Proc Natl Acad Sci U S A 2024; 121:e2408939121. [PMID: 39514315 PMCID: PMC11573637 DOI: 10.1073/pnas.2408939121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 09/28/2024] [Indexed: 11/16/2024] Open
Abstract
Spatial-transcriptomics technologies have demonstrated exceptional performance in characterizing brain and visceral organ tissues, as well as brain and retinal organoids. However, it has not yet been proven whether spatial transcriptomics can effectively characterize primary tissue-derived organoids, as the standardized tissue sectioning or slicing methods are not applicable for such organoids. Herein, we present a technique, lamination-based organoid spatially resolved transcriptomics (LOSRT), for organoid-spatially resolved transcriptomics based on organoid lamination. Primary mouse lung and liver-derived organoids were used in this study. The organoids were formulated using the droplet-engineering method and laminated using a homemade device with weight compression. This technique preserved most cells in individual organoids while maintaining delicate epithelium structures in laminated domains that can be recognized through visual segmentation. The mouse lung and liver organoids were resolved comprising various cell types, including alveolar cells, damage-associated transient progenitor cells, basal cells, macrophages, endothelial cells, fibroblasts, hepatocytes, and hepatic stellate cells. The distribution and count of cells were confirmed using immunohistology and identified with spatial transcriptomic features. This study reports an automated and integrated spatial transcriptomics method for primary organoids. It has the potential to standardize and rapidly characterize primary tissue-derived organoids.
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Affiliation(s)
- Shaohua Ma
- Tsinghua Shenzhen International Graduate School and Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen518055, China
| | - Wanlong Wang
- Tsinghua Shenzhen International Graduate School and Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen518055, China
| | - Jiaqi Zhou
- Tsinghua Shenzhen International Graduate School and Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen518055, China
| | - Shangfeng Liao
- The Beijing Genomics Institute Research, Shenzhen518083, China
- BGI Research, Sanya572025, China
| | - Cheng Hai
- Tsinghua Shenzhen International Graduate School and Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen518055, China
| | - Yibo Hou
- Tsinghua Shenzhen International Graduate School and Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen518055, China
| | - Zhichun Zhou
- The Beijing Genomics Institute Research, Shenzhen518083, China
| | - Zitian Wang
- Tsinghua Shenzhen International Graduate School and Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen518055, China
| | - Yingshi Su
- Synorg Biotechnology (Shenzhen) Co. Ltd., Shenzhen518107, China
| | - Yu Zhu
- Tsinghua Shenzhen International Graduate School and Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen518055, China
| | - Xiaoyong Dai
- Tsinghua Shenzhen International Graduate School and Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen518055, China
| | - Yuan Zhao
- The Beijing Genomics Institute Research, Shenzhen518083, China
| | - Sha Liao
- The Beijing Genomics Institute Research, Shenzhen518083, China
| | - Yongde Cai
- Synorg Biotechnology (Shenzhen) Co. Ltd., Shenzhen518107, China
| | - Xun Xu
- The Beijing Genomics Institute Research, Shenzhen518083, China
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19
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Masatti L, Marchetti M, Pirrotta S, Spagnol G, Corrà A, Ferrari J, Noventa M, Saccardi C, Calura E, Tozzi R. The unveiled mosaic of intra-tumor heterogeneity in ovarian cancer through spatial transcriptomic technologies: A systematic review. Transl Res 2024; 273:104-114. [PMID: 39111726 DOI: 10.1016/j.trsl.2024.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 07/16/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024]
Abstract
Epithelial ovarian cancer is a significant global health issue among women. Diagnosis and treatment pose challenges due to difficulties in predicting patient responses to therapy, primarily stemming from gaps in understanding tumor chemoresistance mechanisms. Recent advancements in transcriptomic technologies like single-cell RNA sequencing and spatial transcriptomics have greatly improved our understanding of ovarian cancer intratumor heterogeneity and tumor microenvironment composition. Spatial transcriptomics, in particular, comprises a plethora of technologies that enable the detection of hundreds of transcriptomes and their spatial distribution within a histological section, facilitating the study of cell types, states, and interactions within the tumor and its microenvironment. Studies investigating the spatial distribution of gene expression in ovarian cancer masses have identified specific features that impact prognosis and therapy outcomes. Emerging evidence suggests that specific spatial patterns of tumor cells and their immune and non-immune microenvironment significantly influence therapy response, as well as the behavior and progression of primary tumors and metastatic sites. The importance of spatially contextualizing ovarian cancer transcriptomes is underscored by these findings, which will advance our understanding and therapeutic approaches for this complex disease.
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Affiliation(s)
- Laura Masatti
- Department of Biology, University of Padova, Padova, Italy
| | - Matteo Marchetti
- Department of Gynecology and Obstetrics, Division of Women and Children, Padova University Hospital, Padova, Italy
| | | | - Giulia Spagnol
- Department of Gynecology and Obstetrics, Division of Women and Children, Padova University Hospital, Padova, Italy
| | - Anna Corrà
- Department of Biology, University of Padova, Padova, Italy; Fondazione Istituto di Ricerca Pediatrica Città della Speranza, Padova, Italy
| | - Jacopo Ferrari
- Department of Gynecology and Obstetrics, Division of Women and Children, Padova University Hospital, Padova, Italy
| | - Marco Noventa
- Department of Gynecology and Obstetrics, Division of Women and Children, Padova University Hospital, Padova, Italy
| | - Carlo Saccardi
- Department of Gynecology and Obstetrics, Division of Women and Children, Padova University Hospital, Padova, Italy
| | - Enrica Calura
- Department of Biology, University of Padova, Padova, Italy.
| | - Roberto Tozzi
- Department of Gynecology and Obstetrics, Division of Women and Children, Padova University Hospital, Padova, Italy
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20
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Cui X, Li X, Zheng H, Su Y, Zhang S, Li M, Hao X, Zhang S, Hu Z, Xia Z, Shi C, Xu Y, Mao C. Human midbrain organoids: a powerful tool for advanced Parkinson's disease modeling and therapy exploration. NPJ Parkinsons Dis 2024; 10:189. [PMID: 39428415 PMCID: PMC11491477 DOI: 10.1038/s41531-024-00799-8] [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: 01/06/2023] [Accepted: 10/02/2024] [Indexed: 10/22/2024] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder marked by the loss of dopaminergic neurons in the substantia nigra. Despite progress, the pathogenesis remains unclear. Human midbrain organoids (hMLOs) have emerged as a promising model for studying PD, drug screening, and potential treatments. This review discusses the development of hMLOs, their application in PD research, and current challenges in organoid construction, highlighting possible optimization strategies.
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Affiliation(s)
- Xin Cui
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Academy of Medical Sciences of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Xinwei Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Academy of Medical Sciences of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Huimin Zheng
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Yun Su
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Shuyu Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Neuro-Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mengjie Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Xiaoyan Hao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Shuo Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Academy of Medical Sciences of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Zhengwei Hu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Academy of Medical Sciences of Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
| | - Zongping Xia
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Clinical Systems Biology Laboratories, Zhengzhou University, Zhengzhou, China
| | - Changhe Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
| | - Yuming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China.
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China.
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China.
| | - Chengyuan Mao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China.
- Henan Key Laboratory of Cerebrovascular Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China.
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21
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Lancaster MA. Unraveling mechanisms of human brain evolution. Cell 2024; 187:5838-5857. [PMID: 39423803 PMCID: PMC7617105 DOI: 10.1016/j.cell.2024.08.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/19/2024] [Accepted: 08/28/2024] [Indexed: 10/21/2024]
Abstract
Evolutionary changes in human brain structure and function have enabled our specialized cognitive abilities. How these changes have come about genetically and functionally has remained an open question. However, new methods are providing a wealth of information about the genetic, epigenetic, and transcriptomic differences that set the human brain apart. Combined with in vitro models that allow access to developing brain tissue and the cells of our closest living relatives, the puzzle pieces are now coming together to yield a much more complete picture of what is actually unique about the human brain. The challenge now will be linking these observations and making the jump from correlation to causation. However, elegant genetic manipulations are now possible and, when combined with model systems such as organoids, will uncover a mechanistic understanding of how evolutionary changes at the genetic level have led to key differences in development and function that enable human cognition.
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Affiliation(s)
- Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Cambridge, UK; Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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22
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Whye D, Norabuena EM, Srinivasan GR, Wood D, Polanco TJ, Makhortova NR, Sahin M, Buttermore ED. A Hybrid 2D-to-3D in vitro Differentiation Platform Improves Outcomes of Cerebral Cortical Organoid Generation in hiPSCs. Curr Protoc 2024; 4:e70022. [PMID: 39400999 DOI: 10.1002/cpz1.70022] [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: 10/15/2024]
Abstract
Three-dimensional (3D) cerebral cortical organoids are popular in vitro cellular model systems widely used to study human brain development and disease, compared to traditional stem cell-derived methods that use two-dimensional (2D) monolayer cultures. Despite the advancements made in protocol development for cerebral cortical organoid derivation over the past decade, limitations due to biological, mechanistic, and technical variables remain in generating these complex 3D cellular systems. Building from our previously established differentiation system, we have made modifications to our existing 3D cerebral cortical organoid protocol that resolve several of these technical and biological challenges when working with diverse groups of human induced pluripotent stem cell (hiPSC) lines. This improved protocol blends a 2D monolayer culture format for the specification of neural stem cells and expansion of neuroepithelial progenitor cells with a 3D system for improved self-aggregation and subsequent organoid development. Furthermore, this "hybrid" approach is amenable to both an accelerated cerebral cortical organoid protocol as well as an alternative long-term differentiation protocol. In addition to establishing a hybrid technical format, this protocol also offers phenotypic and morphological characterization of stage-specific cellular profiles using antibodies and fluorescent-based dyes for live cell imaging. © 2024 Wiley Periodicals LLC. Basic Protocol 1: hiPSC-based 2D monolayer specification into neural stem cells (NSCs) Basic Protocol 2: Serial passaging and 2D monolayer expansion of neuroepithelial progenitor cells (NPCs) Support Protocol 1: Direct cryopreservation and rapid thawing of NSCs and NPCs Basic Protocol 3: Bulk aggregation of 3D neurospheres and accelerated cerebral cortical organoid differentiation Alternate Protocol 1: Bulk aggregation of 3D neurospheres and long-term cerebral cortical organoid differentiation Support Protocol 2: High-throughput 3D neurosphere formation and 2D neurosphere migration assay Support Protocol 3: LIVE/DEAD stain cell imaging assay of 3D neurospheres Support Protocol 4: NeuroFluor NeuO live cell dye for 3D cerebral cortical organoids.
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Affiliation(s)
- Dosh Whye
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, Massachusetts
- F.M. Kirby Neurobiology Department, Boston Children's Hospital, Boston, Massachusetts
| | - Erika M Norabuena
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, Massachusetts
- F.M. Kirby Neurobiology Department, Boston Children's Hospital, Boston, Massachusetts
| | - Gayathri Rajaram Srinivasan
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, Massachusetts
- F.M. Kirby Neurobiology Department, Boston Children's Hospital, Boston, Massachusetts
| | - Delaney Wood
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, Massachusetts
- F.M. Kirby Neurobiology Department, Boston Children's Hospital, Boston, Massachusetts
| | - Taryn J Polanco
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, Massachusetts
- F.M. Kirby Neurobiology Department, Boston Children's Hospital, Boston, Massachusetts
| | - Nina R Makhortova
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, Massachusetts
- F.M. Kirby Neurobiology Department, Boston Children's Hospital, Boston, Massachusetts
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
| | - Mustafa Sahin
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, Massachusetts
- F.M. Kirby Neurobiology Department, Boston Children's Hospital, Boston, Massachusetts
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
| | - Elizabeth D Buttermore
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, Massachusetts
- F.M. Kirby Neurobiology Department, Boston Children's Hospital, Boston, Massachusetts
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23
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Xu L, Ding H, Wu S, Xiong N, Hong Y, Zhu W, Chen X, Han X, Tao M, Wang Y, Wang D, Xu M, Huo D, Gu Z, Liu Y. Artificial Meshed Vessel-Induced Dimensional Breaking Growth of Human Brain Organoids and Multiregional Assembloids. ACS NANO 2024; 18. [PMID: 39270300 PMCID: PMC11440649 DOI: 10.1021/acsnano.4c07844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 09/06/2024] [Accepted: 09/10/2024] [Indexed: 09/15/2024]
Abstract
Brain organoids are widely used to model brain development and diseases. However, a major challenge in their application is the insufficient supply of oxygen and nutrients to the core region, restricting the size and maturation of the organoids. In order to vascularize brain organoids and enhance the nutritional supply to their core areas, two-photon polymerization (TPP) 3D printing is employed to fabricate high-resolution meshed vessels in this study. These vessels made of photoresist with densely distributed micropores with a diameter of 20 μm on the sidewall, are cocultured with brain organoids to facilitate the diffusion of culture medium into the organoids. The vascularized organoids exhibit dimensional breaking growth and enhanced proliferation, reduced hypoxia and apoptosis, suggesting that the 3D-printed meshed vessels partially mimic vascular function to promote the culture of organoids. Furthermore, cortical, striatal and medial ganglionic eminence (MGE) organoids are respectively differentiated to generate Cortico-Striatal-MGE assembloids by 3D-printed vessels. The enhanced migration, projection and excitatory signaling transduction are observed between different brain regional organoids in the assembloids. This study presents an approach using TPP 3D printing to construct vascularized brain organoids and assembloids for enhancing the development and assembly, offering a research model and platform for neurological diseases.
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Affiliation(s)
- Lei Xu
- State
Key Laboratory of Digital Medical Engineering, School of Biological
Science and Medical Engineering; Department of neurology, affiliated
Zhongda Hospital, Southeast University, Nanjing 210096, China
- State
Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
- Institute
of Stem Cell and Neural Regeneration, School of pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Haibo Ding
- State
Key Laboratory of Digital Medical Engineering, School of Biological
Science and Medical Engineering; Department of neurology, affiliated
Zhongda Hospital, Southeast University, Nanjing 210096, China
| | - Shanshan Wu
- State
Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
- Institute
of Stem Cell and Neural Regeneration, School of pharmacy, Nanjing Medical University, Nanjing 211166, China
- Key
Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative
Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Nankun Xiong
- State
Key Laboratory of Digital Medical Engineering, School of Biological
Science and Medical Engineering; Department of neurology, affiliated
Zhongda Hospital, Southeast University, Nanjing 210096, China
| | - Yuan Hong
- State
Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
- Institute
of Stem Cell and Neural Regeneration, School of pharmacy, Nanjing Medical University, Nanjing 211166, China
- Key
Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative
Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Wanying Zhu
- State
Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
- Institute
of Stem Cell and Neural Regeneration, School of pharmacy, Nanjing Medical University, Nanjing 211166, China
- Key
Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative
Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Xingyi Chen
- State
Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
- Institute
of Stem Cell and Neural Regeneration, School of pharmacy, Nanjing Medical University, Nanjing 211166, China
- Key
Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative
Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Xiao Han
- State
Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
- Institute
of Stem Cell and Neural Regeneration, School of pharmacy, Nanjing Medical University, Nanjing 211166, China
- Key
Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative
Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Mengdan Tao
- State
Key Laboratory of Digital Medical Engineering, School of Biological
Science and Medical Engineering; Department of neurology, affiliated
Zhongda Hospital, Southeast University, Nanjing 210096, China
| | - Yuanhao Wang
- State
Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
- Institute
of Stem Cell and Neural Regeneration, School of pharmacy, Nanjing Medical University, Nanjing 211166, China
- Key
Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative
Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Da Wang
- State
Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
- Institute
of Stem Cell and Neural Regeneration, School of pharmacy, Nanjing Medical University, Nanjing 211166, China
- Key
Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative
Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Min Xu
- State
Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
- Institute
of Stem Cell and Neural Regeneration, School of pharmacy, Nanjing Medical University, Nanjing 211166, China
- Key
Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative
Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Da Huo
- Key
Laboratory of Cardiovascular and Cerebrovascular Medicine, Department
of Pharmaceutics, School of Pharmacy, Nanjing
Medical University, Nanjing 211166, China
| | - Zhongze Gu
- State
Key Laboratory of Digital Medical Engineering, School of Biological
Science and Medical Engineering; Department of neurology, affiliated
Zhongda Hospital, Southeast University, Nanjing 210096, China
| | - Yan Liu
- State
Key Laboratory of Digital Medical Engineering, School of Biological
Science and Medical Engineering; Department of neurology, affiliated
Zhongda Hospital, Southeast University, Nanjing 210096, China
- State
Key Laboratory of Reproductive Medicine and Offspring Health, Nanjing Medical University, Nanjing 211166, China
- Institute
of Stem Cell and Neural Regeneration, School of pharmacy, Nanjing Medical University, Nanjing 211166, China
- Key
Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative
Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
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24
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Bhaduri A. Chimeric brain organoids capture human genetic diversity. Nature 2024; 631:32-33. [PMID: 38926554 DOI: 10.1038/d41586-024-01648-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
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25
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Islam R, Noman H, Azimi A, Siu R, Chinchalongporn V, Schuurmans C, Morshead CM. Primitive and Definitive Neural Precursor Cells Are Present in Human Cerebral Organoids. Int J Mol Sci 2024; 25:6549. [PMID: 38928255 PMCID: PMC11203442 DOI: 10.3390/ijms25126549] [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: 05/01/2024] [Revised: 06/04/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
Activation of neural stem cells (NSCs) correlates with improved functional outcomes in mouse models of injury. In the murine brain, NSCs have been extensively characterized and comprise (1) primitive NSCs (pNSCs) and (2) definitive NSCs (dNSCs). pNSCs are the earliest cells in the NSC lineage giving rise to dNSCs in the embryonic and adult mouse brain. pNSCs are quiescent under baseline conditions and can be activated upon injury. Herein, we asked whether human pNSCs and dNSCs can be isolated during the maturation of human cerebral organoids (COs) and activated by drugs known to regulate mouse NSC behavior. We demonstrate that self-renewing, multipotent pNSC and dNSC populations are present in human COs and express genes previously characterized in mouse NSCs. The drug NWL283, an inhibitor of apoptosis, reduced cell death in COs but did not improve NSC survival. Metformin, a drug used to treat type II diabetes that is known to promote NSC activation in mice, was found to expand human NSC pools. Together, these findings are the first to identify and characterize human pNSCs, advancing our understanding of the human NSC lineage and highlighting drugs that enhance their activity.
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Affiliation(s)
- Rehnuma Islam
- Institute of Medical Science, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 3E1, Canada
| | - Humna Noman
- Institute of Medical Science, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 3E1, Canada
| | - Ashkan Azimi
- Department of Surgery, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
| | - Ricky Siu
- Department of Surgery, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
| | | | - Carol Schuurmans
- Sunnybrook Research Institute, 2075 Bayview Avenue, Toronto, ON M4N 3M5, Canada
- Department of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 3E1, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 3E1, Canada
| | - Cindi M. Morshead
- Institute of Medical Science, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 3E1, Canada
- Department of Surgery, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Institute of Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON M5S 3G9, Canada
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26
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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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27
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Leal H, Carvalhas-Almeida C, Álvaro AR, Cavadas C. Modeling hypothalamic pathophysiology in vitro for metabolic, circadian, and sleep disorders. Trends Endocrinol Metab 2024; 35:505-517. [PMID: 38307813 DOI: 10.1016/j.tem.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/04/2024]
Abstract
The hypothalamus, a small and intricate brain structure, orchestrates numerous neuroendocrine functions through specialized neurons and nuclei. Disruption of this complex circuitry can result in various diseases, including metabolic, circadian, and sleep disorders. Advances in in vitro models and their integration with new technologies have significantly benefited research on hypothalamic function and pathophysiology. We explore existing in vitro hypothalamic models and address their challenges and limitations as well as translational findings. We also highlight how collaborative efforts among multidisciplinary teams are essential to develop relevant and translational experimental models capable of replicating intricate neural circuits and neuroendocrine pathways, thereby advancing our understanding of therapeutic targets and drug discovery in hypothalamus-related disorders.
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Affiliation(s)
- Helena Leal
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Center for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Catarina Carvalhas-Almeida
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Center for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Ana Rita Álvaro
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Center for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Cláudia Cavadas
- Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Center for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.
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28
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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] [Grants] [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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29
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Boyd JL. Moral considerability of brain organoids from the perspective of computational architecture. OXFORD OPEN NEUROSCIENCE 2024; 3:kvae004. [PMID: 38595940 PMCID: PMC10995847 DOI: 10.1093/oons/kvae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/06/2024] [Accepted: 02/27/2024] [Indexed: 04/11/2024]
Abstract
Human brain organoids equipped with complex cytoarchitecture and closed-loop feedback from virtual environments could provide insights into neural mechanisms underlying cognition. Yet organoids with certain cognitive capacities might also merit moral consideration. A precautionary approach has been proposed to address these ethical concerns by focusing on the epistemological question of whether organoids possess neural structures for morally-relevant capacities that bear resemblance to those found in human brains. Critics challenge this similarity approach on philosophical, scientific, and practical grounds but do so without a suitable alternative. Here, I introduce an architectural approach that infers the potential for cognitive-like processing in brain organoids based on the pattern of information flow through the system. The kind of computational architecture acquired by an organoid then informs the kind of cognitive capacities that could, theoretically, be supported and empirically investigated. The implications of this approach for the moral considerability of brain organoids are discussed.
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Affiliation(s)
- J Lomax Boyd
- Berman Institute of Bioethics, Johns Hopkins University, 1809 Ashland Ave, Baltimore, MD 21205, USA
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Massimo M, Long KR. In preprints: shaping the developing human brain. Development 2023; 150:dev202567. [PMID: 38078654 DOI: 10.1242/dev.202567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Affiliation(s)
- Marco Massimo
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, UK
| | - Katherine R Long
- Centre for Developmental Neurobiology and MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, UK
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