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Coronel R, García-Moreno E, Siendones E, Barrero MJ, Martínez-Delgado B, Santos-Ocaña C, Liste I, Cascajo-Almenara MV. Brain organoid as a model to study the role of mitochondria in neurodevelopmental disorders: achievements and weaknesses. Front Cell Neurosci 2024; 18:1403734. [PMID: 38978706 PMCID: PMC11228165 DOI: 10.3389/fncel.2024.1403734] [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: 03/19/2024] [Accepted: 05/13/2024] [Indexed: 07/10/2024] Open
Abstract
Mitochondrial diseases are a group of severe pathologies that cause complex neurodegenerative disorders for which, in most cases, no therapy or treatment is available. These organelles are critical regulators of both neurogenesis and homeostasis of the neurological system. Consequently, mitochondrial damage or dysfunction can occur as a cause or consequence of neurodevelopmental or neurodegenerative diseases. As genetic knowledge of neurodevelopmental disorders advances, associations have been identified between genes that encode mitochondrial proteins and neurological symptoms, such as neuropathy, encephalomyopathy, ataxia, seizures, and developmental delays, among others. Understanding how mitochondrial dysfunction can alter these processes is essential in researching rare diseases. Three-dimensional (3D) cell cultures, which self-assemble to form specialized structures composed of different cell types, represent an accessible manner to model organogenesis and neurodevelopmental disorders. In particular, brain organoids are revolutionizing the study of mitochondrial-based neurological diseases since they are organ-specific and model-generated from a patient's cell, thereby overcoming some of the limitations of traditional animal and cell models. In this review, we have collected which neurological structures and functions recapitulate in the different types of reported brain organoids, focusing on those generated as models of mitochondrial diseases. In addition to advancements in the generation of brain organoids, techniques, and approaches for studying neuronal structures and physiology, drug screening and drug repositioning studies performed in brain organoids with mitochondrial damage and neurodevelopmental disorders have also been reviewed. This scope review will summarize the evidence on limitations in studying the function and dynamics of mitochondria in brain organoids.
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Affiliation(s)
- Raquel Coronel
- Neural Regeneration Unit, Functional Unit for Research on Chronic Diseases (UFIEC), National Institute of Health Carlos III (ISCIII), Madrid, Spain
- Department of Systems Biology, Faculty of Medicine and Health Sciences, University of Alcalá (UAH), Alcalá de Henares, Spain
| | - Enrique García-Moreno
- Andalusian Centre for Developmental Biology, CIBERER, National Institute of Health Carlos III (ISCIII), Pablo de Olavide University-CSIC-JA, Seville, Spain
| | - Emilio Siendones
- Andalusian Centre for Developmental Biology, CIBERER, National Institute of Health Carlos III (ISCIII), Pablo de Olavide University-CSIC-JA, Seville, Spain
| | - Maria J. Barrero
- Models and Mechanisms Unit, Institute of Rare Diseases Research (IIER), Spanish National Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Beatriz Martínez-Delgado
- Molecular Genetics Unit, Institute of Rare Diseases Research (IIER), CIBER of Rare Diseases (CIBERER), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Carlos Santos-Ocaña
- Andalusian Centre for Developmental Biology, CIBERER, National Institute of Health Carlos III (ISCIII), Pablo de Olavide University-CSIC-JA, Seville, Spain
| | - Isabel Liste
- Neural Regeneration Unit, Functional Unit for Research on Chronic Diseases (UFIEC), National Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - M. V. Cascajo-Almenara
- Andalusian Centre for Developmental Biology, CIBERER, National Institute of Health Carlos III (ISCIII), Pablo de Olavide University-CSIC-JA, Seville, Spain
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2
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Kural MH, Djakbarova U, Cakir B, Tanaka Y, Chan ET, Arteaga Muniz VI, Madraki Y, Qian H, Park J, Sewanan LR, Park IH, Niklason LE, Kural C. Mechano-inhibition of endocytosis sensitizes cancer cells to Fas-induced Apoptosis. Cell Death Dis 2024; 15:440. [PMID: 38909035 PMCID: PMC11193792 DOI: 10.1038/s41419-024-06822-3] [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: 12/08/2023] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024]
Abstract
The transmembrane death receptor Fas transduces apoptotic signals upon binding its ligand, FasL. Although Fas is highly expressed in cancer cells, insufficient cell surface Fas expression desensitizes cancer cells to Fas-induced apoptosis. Here, we show that the increase in Fas microaggregate formation on the plasma membrane in response to the inhibition of endocytosis sensitizes cancer cells to Fas-induced apoptosis. We used a clinically accessible Rho-kinase inhibitor, fasudil, that reduces endocytosis dynamics by increasing plasma membrane tension. In combination with exogenous soluble FasL (sFasL), fasudil promoted cancer cell apoptosis, but this collaborative effect was substantially weaker in nonmalignant cells. The combination of sFasL and fasudil prevented glioblastoma cell growth in embryonic stem cell-derived brain organoids and induced tumor regression in a xenograft mouse model. Our results demonstrate that sFasL has strong potential for apoptosis-directed cancer therapy when Fas microaggregate formation is augmented by mechano-inhibition of endocytosis.
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Affiliation(s)
- Mehmet H Kural
- Department of Anesthesiology, School of Medicine, Yale University, New Haven, CT, 06519, USA.
- Humacyte Inc., Durham, NC, 27213, USA.
| | | | - Bilal Cakir
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Yoshiaki Tanaka
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06519, USA
- Department of Medicine, Maisonneuve-Rosemont Hospital Research Center, University of Montreal, Montreal, QC, H1T 2M4, Canada
| | - Emily T Chan
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | | | - Yasaman Madraki
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Hong Qian
- Department of Anesthesiology, School of Medicine, Yale University, New Haven, CT, 06519, USA
- Humacyte Inc., Durham, NC, 27213, USA
| | - Jinkyu Park
- Yale Cardiovascular Research Center, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, 06519, USA
| | - Lorenzo R Sewanan
- Department of Internal Medicine, Columbia University, New York, NY, 10032, USA
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06519, USA
| | - Laura E Niklason
- Department of Anesthesiology, School of Medicine, Yale University, New Haven, CT, 06519, USA.
- Humacyte Inc., Durham, NC, 27213, USA.
| | - Comert Kural
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA.
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA.
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3
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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 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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4
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Kim HS, Xiao Y, Chen X, He S, Im J, Willner MJ, Finlayson MO, Xu C, Zhu H, Choi SJ, Mosharov EV, Kim H, Xu B, Leong KW. Chronic Opioid Treatment Arrests Neurodevelopment and Alters Synaptic Activity in Human Midbrain Organoids. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400847. [PMID: 38549185 PMCID: PMC11151039 DOI: 10.1002/advs.202400847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Indexed: 06/06/2024]
Abstract
Understanding the impact of long-term opioid exposure on the embryonic brain is critical due to the surging number of pregnant mothers with opioid dependency. However, this has been limited by human brain inaccessibility and cross-species differences in animal models. Here, a human midbrain model is established that uses hiPSC-derived midbrain organoids to assess cell-type-specific responses to acute and chronic fentanyl treatment and fentanyl withdrawal. Single-cell mRNA sequencing of 25,510 cells from organoids in different treatment groups reveals that chronic fentanyl treatment arrests neuronal subtype specification during early midbrain development and alters synaptic activity and neuron projection. In contrast, acute fentanyl treatment increases dopamine release but does not significantly alter gene expression related to cell lineage development. These results provide the first examination of the effects of opioid exposure on human midbrain development at the single-cell level.
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Affiliation(s)
- Hye Sung Kim
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
- Institute of Tissue Regeneration Engineering (ITREN)Dankook UniversityCheonan31116Republic of Korea
- Mechanobiology Dental Medicine Research CenterDankook UniversityCheonan31116Republic of Korea
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative MedicineDankook UniversityCheonan31116Republic of Korea
| | - Yang Xiao
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
| | - Xuejing Chen
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
- Department of PhysicsTsinghua UniversityBeijing100084China
| | - Siyu He
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
| | - Jongwon Im
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
| | - Moshe J. Willner
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
| | - Michael O. Finlayson
- Single Cell Analysis CoreJP Sulzberger Columbia Genome CenterColumbia University Irving Medical CenterNew YorkNY10032USA
| | - Cong Xu
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
| | - Huixiang Zhu
- Department of PsychiatryColumbia University Medical CenterNew YorkNY10032USA
| | - Se Joon Choi
- Department of PsychiatryColumbia University Medical CenterNew YorkNY10032USA
- Division of Molecular TherapeuticsNew York State Psychiatric InstituteNew YorkNY10032USA
| | - Eugene V. Mosharov
- Department of PsychiatryColumbia University Medical CenterNew YorkNY10032USA
- Division of Molecular TherapeuticsNew York State Psychiatric InstituteNew YorkNY10032USA
| | - Hae‐Won Kim
- Institute of Tissue Regeneration Engineering (ITREN)Dankook UniversityCheonan31116Republic of Korea
- Mechanobiology Dental Medicine Research CenterDankook UniversityCheonan31116Republic of Korea
- Department of Nanobiomedical Science and BK21 PLUS NBM Global Research Center for Regenerative MedicineDankook UniversityCheonan31116Republic of Korea
| | - Bin Xu
- Department of PsychiatryColumbia University Medical CenterNew YorkNY10032USA
| | - Kam W. Leong
- Department of Biomedical EngineeringColumbia UniversityNew YorkNY10027USA
- Department of Systems BiologyColumbia University Irving Medical CenterNew YorkNY10032USA
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5
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Tamada A, Muguruma K. Recapitulation and investigation of human brain development with neural organoids. IBRO Neurosci Rep 2024; 16:106-117. [PMID: 39007085 PMCID: PMC11240300 DOI: 10.1016/j.ibneur.2023.12.006] [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] [Indexed: 07/16/2024] Open
Abstract
Organoids are 3D cultured tissues derived from stem cells that resemble the structure of living organs. Based on the accumulated knowledge of neural development, neural organoids that recapitulate neural tissue have been created by inducing self-organized neural differentiation of stem cells. Neural organoid techniques have been applied to human pluripotent stem cells to differentiate 3D human neural tissues in culture. Various methods have been developed to generate neural tissues of different regions. Currently, neural organoid technology has several significant limitations, which are being overcome in an attempt to create neural organoids that more faithfully recapitulate the living brain. The rapidly advancing neural organoid technology enables the use of living human neural tissue as research material and contributes to our understanding of the development, structure and function of the human nervous system, and is expected to be used to overcome neurological diseases and for regenerative medicine.
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Affiliation(s)
- Atsushi Tamada
- Department of iPS Cell Applied Medicine, Faculty of Medicine, Kansai Medical University, Hirakata, Osaka 573-1010, Japan
| | - Keiko Muguruma
- Department of iPS Cell Applied Medicine, Faculty of Medicine, Kansai Medical University, Hirakata, Osaka 573-1010, Japan
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6
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Chen C, Lee S, Zyner KG, Fernando M, Nemeruck V, Wong E, Marshall LL, Wark JR, Aryamanesh N, Tam PPL, Graham ME, Gonzalez-Cordero A, Yang P. Trans-omic profiling uncovers molecular controls of early human cerebral organoid formation. Cell Rep 2024; 43:114219. [PMID: 38748874 DOI: 10.1016/j.celrep.2024.114219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/01/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024] Open
Abstract
Defining the molecular networks orchestrating human brain formation is crucial for understanding neurodevelopment and neurological disorders. Challenges in acquiring early brain tissue have incentivized the use of three-dimensional human pluripotent stem cell (hPSC)-derived neural organoids to recapitulate neurodevelopment. To elucidate the molecular programs that drive this highly dynamic process, here, we generate a comprehensive trans-omic map of the phosphoproteome, proteome, and transcriptome of the exit of pluripotency and neural differentiation toward human cerebral organoids (hCOs). These data reveal key phospho-signaling events and their convergence on transcriptional factors to regulate hCO formation. Comparative analysis with developing human and mouse embryos demonstrates the fidelity of our hCOs in modeling embryonic brain development. Finally, we demonstrate that biochemical modulation of AKT signaling can control hCO differentiation. Together, our data provide a comprehensive resource to study molecular controls in human embryonic brain development and provide a guide for the future development of hCO differentiation protocols.
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Affiliation(s)
- Carissa Chen
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; Embryology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Scott Lee
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Katherine G Zyner
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Milan Fernando
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Victoria Nemeruck
- Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Emilie Wong
- Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Lee L Marshall
- Bioinformatics Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Jesse R Wark
- Synapse Proteomics, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Nader Aryamanesh
- Bioinformatics Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Patrick P L Tam
- Embryology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Mark E Graham
- Synapse Proteomics, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.
| | - Anai Gonzalez-Cordero
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.
| | - Pengyi Yang
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia; Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia.
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7
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Cao J, Li C, Cui Z, Deng S, Lei T, Liu W, Yang H, Chen P. Spatial Transcriptomics: A Powerful Tool in Disease Understanding and Drug Discovery. Theranostics 2024; 14:2946-2968. [PMID: 38773973 PMCID: PMC11103497 DOI: 10.7150/thno.95908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/25/2024] [Indexed: 05/24/2024] Open
Abstract
Recent advancements in modern science have provided robust tools for drug discovery. The rapid development of transcriptome sequencing technologies has given rise to single-cell transcriptomics and single-nucleus transcriptomics, increasing the accuracy of sequencing and accelerating the drug discovery process. With the evolution of single-cell transcriptomics, spatial transcriptomics (ST) technology has emerged as a derivative approach. Spatial transcriptomics has emerged as a hot topic in the field of omics research in recent years; it not only provides information on gene expression levels but also offers spatial information on gene expression. This technology has shown tremendous potential in research on disease understanding and drug discovery. In this article, we introduce the analytical strategies of spatial transcriptomics and review its applications in novel target discovery and drug mechanism unravelling. Moreover, we discuss the current challenges and issues in this research field that need to be addressed. In conclusion, spatial transcriptomics offers a new perspective for drug discovery.
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Affiliation(s)
- Junxian Cao
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Analysis of Complex Effects of Proprietary Chinese Medicine, Hunan Provincial Key Laboratory, Yongzhou City, Hunan Province, China
| | - Caifeng Li
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Zhao Cui
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Shiwen Deng
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Analysis of Complex Effects of Proprietary Chinese Medicine, Hunan Provincial Key Laboratory, Yongzhou City, Hunan Province, China
| | - Tong Lei
- Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Wei Liu
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Hongjun Yang
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Analysis of Complex Effects of Proprietary Chinese Medicine, Hunan Provincial Key Laboratory, Yongzhou City, Hunan Province, China
| | - Peng Chen
- Beijing Key Laboratory of Traditional Chinese Medicine Basic Research on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing 100700, China
- Analysis of Complex Effects of Proprietary Chinese Medicine, Hunan Provincial Key Laboratory, Yongzhou City, Hunan Province, China
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8
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Fitzgerald MQ, Chu T, Puppo F, Blanch R, Chillón M, Subramaniam S, Muotri AR. Generation of 'semi-guided' cortical organoids with complex neural oscillations. Nat Protoc 2024:10.1038/s41596-024-00994-0. [PMID: 38702386 DOI: 10.1038/s41596-024-00994-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 02/22/2024] [Indexed: 05/06/2024]
Abstract
Temporal development of neural electrophysiology follows genetic programming, similar to cellular maturation and organization during development. The emergent properties of this electrophysiological development, namely neural oscillations, can be used to characterize brain development. Recently, we utilized the innate programming encoded in the human genome to generate functionally mature cortical organoids. In brief, stem cells are suspended in culture via continuous shaking and naturally aggregate into embryoid bodies before being exposed to media formulations for neural induction, differentiation and maturation. The specific culture format, media composition and duration of exposure to these media distinguish organoid protocols and determine whether a protocol is guided or unguided toward specific neural fate. The 'semi-guided' protocol presented here has shorter induction and differentiation steps with less-specific patterning molecules than most guided protocols but maintains the use of neurotrophic factors such as brain-derived growth factor and neurotrophin-3, unlike unguided approaches. This approach yields the cell type diversity of unguided approaches while maintaining reproducibility for disease modeling. Importantly, we characterized the electrophysiology of these organoids and found that they recapitulate the maturation of neural oscillations observed in the developing human brain, a feature not shown with other approaches. This protocol represents the potential first steps toward bridging molecular and cellular biology to human cognition, and it has already been used to discover underlying features of human brain development, evolution and neurological conditions. Experienced cell culture technicians can expect the protocol to take 1 month, with extended maturation, electrophysiology recording, and adeno-associated virus transduction procedure options.
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Affiliation(s)
- Michael Q Fitzgerald
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Tiffany Chu
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Francesca Puppo
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Rebeca Blanch
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Institut de Recerca Vall d'Hebron and Institut de Neurociències, Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Miguel Chillón
- Institut de Recerca Vall d'Hebron and Institut de Neurociències, Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Shankar Subramaniam
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Alysson R Muotri
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA.
- Center for Academic Research and Training in Anthropogeny and Archealization, University of California San Diego, La Jolla, CA, USA.
- Sanford Stem Cell Education and Integrated Space Stem Cell Orbital Research Center, Sanford Stem Cell Institute, University of California San Diego, La Jolla, CA, USA.
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9
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Giorgi C, Castelli V, d’Angelo M, Cimini A. Organoids Modeling Stroke in a Petri Dish. Biomedicines 2024; 12:877. [PMID: 38672231 PMCID: PMC11048104 DOI: 10.3390/biomedicines12040877] [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: 03/22/2024] [Revised: 04/10/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Stroke is a common neurological disorder, the second leading cause of death, and the third leading cause of disability. Unfortunately, the only approved drug for it is tissue plasminogen, but the therapeutic window is limited. In this context, preclinical studies are relevant to better dissect the underlying mechanisms of stroke and for the drug screening of potential therapies. Brain organoids could be relevant in this setting. They are derived from pluripotent stem cells or isolated organ progenitors that differentiate to form an organ-like tissue, exhibiting multiple cell types that self-organize to form a structure not unlike the organ in vivo. Brain organoids mimic many key features of early human brain development at molecular, cellular, structural, and functional levels and have emerged as novel model systems that can be used to investigate human brain diseases including stroke. Brain organoids are a promising and powerful tool for ischemic stroke studies; however, there are a few concerns that need to be addressed, including the lack of vascularization and the many cell types that are typically present in the human brain. The aim of this review is to discuss the potential of brain organoids as a novel model system for studying ischemic stroke, highlighting both the advantages and disadvantages in the use of this technology.
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Affiliation(s)
| | | | - Michele d’Angelo
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (C.G.); (V.C.)
| | - Annamaria Cimini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (C.G.); (V.C.)
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10
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Nicholson JG, Cirigliano S, Singhania R, Haywood C, Shahidi Dadras M, Yoshimura M, Vanderbilt D, Liechty B, Fine HA. Chronic hypoxia remodels the tumor microenvironment to support glioma stem cell growth. Acta Neuropathol Commun 2024; 12:46. [PMID: 38528608 DOI: 10.1186/s40478-024-01755-6] [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: 12/08/2023] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
Cerebral organoids co-cultured with patient derived glioma stem cells (GLICOs) are an experimentally tractable research tool useful for investigating the role of the human brain tumor microenvironment in glioblastoma. Here we describe long-term GLICOs, a novel model in which COs are grown from embryonic stem cell cultures containing low levels of GSCs and tumor development is monitored over extended durations (ltGLICOs). Single-cell profiling of ltGLICOs revealed an unexpectedly long latency period prior to GSC expansion, and that normal organoid development was unimpaired by the presence of low numbers of GSCs. However, as organoids age they experience chronic hypoxia and oxidative stress which remodels the tumor microenvironment to promote GSC expansion. Receptor-ligand modelling identified astrocytes, which secreted various pro-tumorigenic ligands including FGF1, as the primary cell type for GSC crosstalk and single-cell multi-omic analysis revealed these astrocytes were under the control of ischemic regulatory networks. Functional validation confirmed hypoxia as a driver of pro-tumorigenic astrocytic ligand secretion and that GSC expansion was accelerated by pharmacological induction of oxidative stress. When controlled for genotype, the close association between glioma aggressiveness and patient age has very few proposed biological explanations. Our findings indicate that age-associated increases in cerebral vascular insufficiency and associated regional chronic cerebral hypoxia may contribute to this phenomenon.
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Affiliation(s)
- J G Nicholson
- Department of Neurology, Weill Cornell Medicine, New York, NY, USA
| | - S Cirigliano
- Department of Neurology, Weill Cornell Medicine, New York, NY, USA
| | - R Singhania
- Department of Neurology, Weill Cornell Medicine, New York, NY, USA
| | - C Haywood
- Department of Neurology, Weill Cornell Medicine, New York, NY, USA
| | - M Shahidi Dadras
- Department of Neurology, Weill Cornell Medicine, New York, NY, USA
| | - M Yoshimura
- Department of Neurology, Weill Cornell Medicine, New York, NY, USA
| | - D Vanderbilt
- Department of Neurology, Weill Cornell Medicine, New York, NY, USA
| | - B Liechty
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine/New York-Presbyterian Hospital, New York, NY, USA
| | - H A Fine
- Department of Neurology, Weill Cornell Medicine, New York, NY, USA.
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11
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Giorgi C, Lombardozzi G, Ammannito F, Scenna MS, Maceroni E, Quintiliani M, d’Angelo M, Cimini A, Castelli V. Brain Organoids: A Game-Changer for Drug Testing. Pharmaceutics 2024; 16:443. [PMID: 38675104 PMCID: PMC11054008 DOI: 10.3390/pharmaceutics16040443] [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: 02/07/2024] [Revised: 03/12/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
Neurological disorders are the second cause of death and the leading cause of disability worldwide. Unfortunately, no cure exists for these disorders, but the actual therapies are only able to ameliorate people's quality of life. Thus, there is an urgent need to test potential therapeutic approaches. Brain organoids are a possible valuable tool in the study of the brain, due to their ability to reproduce different brain regions and maturation stages; they can be used also as a tool for disease modelling and target identification of neurological disorders. Recently, brain organoids have been used in drug-screening processes, even if there are several limitations to overcome. This review focuses on the description of brain organoid development and drug-screening processes, discussing the advantages, challenges, and limitations of the use of organoids in modeling neurological diseases. We also highlighted the potential of testing novel therapeutic approaches. Finally, we examine the challenges and future directions to improve the drug-screening process.
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Affiliation(s)
| | | | | | | | | | | | | | - Annamaria Cimini
- Department of Life, Health and Environmental Science, University of L’Aquila, 67100 L’Aquila, Italy; (C.G.); (G.L.); (F.A.); (M.S.S.); (E.M.); (M.Q.); (M.d.)
| | - Vanessa Castelli
- Department of Life, Health and Environmental Science, University of L’Aquila, 67100 L’Aquila, Italy; (C.G.); (G.L.); (F.A.); (M.S.S.); (E.M.); (M.Q.); (M.d.)
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12
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Zhao HH, Haddad G. Brain organoid protocols and limitations. Front Cell Neurosci 2024; 18:1351734. [PMID: 38572070 PMCID: PMC10987830 DOI: 10.3389/fncel.2024.1351734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/19/2024] [Indexed: 04/05/2024] Open
Abstract
Stem cell-derived organoid technology is a powerful tool that revolutionizes the field of biomedical research and extends the scope of our understanding of human biology and diseases. Brain organoids especially open an opportunity for human brain research and modeling many human neurological diseases, which have lagged due to the inaccessibility of human brain samples and lack of similarity with other animal models. Brain organoids can be generated through various protocols and mimic whole brain or region-specific. To provide an overview of brain organoid technology, we summarize currently available protocols and list several factors to consider before choosing protocols. We also outline the limitations of current protocols and challenges that need to be solved in future investigation of brain development and pathobiology.
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Affiliation(s)
- Helen H. Zhao
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
| | - Gabriel Haddad
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, United States
- The Rady Children's Hospital, San Diego, CA, United States
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13
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Adams L, Song MK, Yuen S, Tanaka Y, Kim YS. A single-nuclei paired multiomic analysis of the human midbrain reveals age- and Parkinson's disease-associated glial changes. NATURE AGING 2024; 4:364-378. [PMID: 38491288 DOI: 10.1038/s43587-024-00583-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/01/2024] [Indexed: 03/18/2024]
Abstract
Age is the primary risk factor for Parkinson's disease (PD), but how aging changes the expression and regulatory landscape of the brain remains unclear. Here we present a single-nuclei multiomic study profiling shared gene expression and chromatin accessibility of young, aged and PD postmortem midbrain samples. Combined multiomic analysis along a pseudopathogenesis trajectory reveals that all glial cell types are affected by age, but microglia and oligodendrocytes are further altered in PD. We present evidence for a disease-associated oligodendrocyte subtype and identify genes lost over the aging and disease process, including CARNS1, that may predispose healthy cells to develop a disease-associated phenotype. Surprisingly, we found that chromatin accessibility changed little over aging or PD within the same cell types. Peak-gene association patterns, however, are substantially altered during aging and PD, identifying cell-type-specific chromosomal loci that contain PD-associated single-nucleotide polymorphisms. Our study suggests a previously undescribed role for oligodendrocytes in aging and PD.
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Affiliation(s)
- Levi Adams
- RWJMS Institute for Neurological Therapeutics, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, USA
- Department of Biology, Bates College, Lewiston, ME, USA
| | - Min Kyung Song
- RWJMS Institute for Neurological Therapeutics, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, USA
- College of Nursing Science, Kyung Hee University, Seoul, Republic of Korea
| | - Samantha Yuen
- Department of Medicine, Maisonneuve-Rosemont Hospital Research Center (CRHMR), University of Montreal, Quebec, QC, Canada
| | - Yoshiaki Tanaka
- Department of Medicine, Maisonneuve-Rosemont Hospital Research Center (CRHMR), University of Montreal, Quebec, QC, Canada.
| | - Yoon-Seong Kim
- RWJMS Institute for Neurological Therapeutics, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, USA.
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14
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Pavon N, Diep K, Yang F, Sebastian R, Martinez-Martin B, Ranjan R, Sun Y, Pak C. Patterning ganglionic eminences in developing human brain organoids using a morphogen-gradient-inducing device. CELL REPORTS METHODS 2024; 4:100689. [PMID: 38228151 PMCID: PMC10831957 DOI: 10.1016/j.crmeth.2023.100689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/21/2023] [Accepted: 12/18/2023] [Indexed: 01/18/2024]
Abstract
In early neurodevelopment, the central nervous system is established through the coordination of various neural organizers directing tissue patterning and cell differentiation. Better recapitulation of morphogen gradient production and signaling will be crucial for establishing improved developmental models of the brain in vitro. Here, we developed a method by assembling polydimethylsiloxane devices capable of generating a sustained chemical gradient to produce patterned brain organoids, which we termed morphogen-gradient-induced brain organoids (MIBOs). At 3.5 weeks, MIBOs replicated dorsal-ventral patterning observed in the ganglionic eminences (GE). Analysis of mature MIBOs through single-cell RNA sequencing revealed distinct dorsal GE-derived CALB2+ interneurons, medium spiny neurons, and medial GE-derived cell types. Finally, we demonstrate long-term culturing capabilities with MIBOs maintaining stable neural activity in cultures grown up to 5.5 months. MIBOs demonstrate a versatile approach for generating spatially patterned brain organoids for embryonic development and disease modeling.
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Affiliation(s)
- Narciso Pavon
- Graduate Program in Neuroscience and Behavior, UMass Amherst, Amherst, MA 01003, USA; Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Karmen Diep
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Feiyu Yang
- Department of Mechanical and Industrial Engineering, UMass Amherst, Amherst, MA 01003, USA
| | - Rebecca Sebastian
- Graduate Program in Neuroscience and Behavior, UMass Amherst, Amherst, MA 01003, USA; Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Beatriz Martinez-Martin
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA; Graduate Program in Molecular and Cellular Biology, UMass Amherst, Amherst, MA 01003, USA
| | - Ravi Ranjan
- Genomics Core, Institute of Applied Life Sciences, UMass Amherst, Amherst, MA 01003, USA
| | - Yubing Sun
- Department of Mechanical and Industrial Engineering, UMass Amherst, Amherst, MA 01003, USA.
| | - ChangHui Pak
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA 01003, USA.
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15
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Sarieva K, Kagermeier T, Khakipoor S, Atay E, Yentür Z, Becker K, Mayer S. Human brain organoid model of maternal immune activation identifies radial glia cells as selectively vulnerable. Mol Psychiatry 2023; 28:5077-5089. [PMID: 36878967 PMCID: PMC9986664 DOI: 10.1038/s41380-023-01997-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 03/08/2023]
Abstract
Maternal immune activation (MIA) during critical windows of gestation is correlated with long-term neurodevelopmental deficits in the offspring, including increased risk for autism spectrum disorder (ASD) in humans. Interleukin 6 (IL-6) derived from the gestational parent is one of the major molecular mediators by which MIA alters the developing brain. In this study, we establish a human three-dimensional (3D) in vitro model of MIA by treating induced pluripotent stem cell-derived dorsal forebrain organoids with a constitutively active form of IL-6, Hyper-IL-6. We validate our model by showing that dorsal forebrain organoids express the molecular machinery necessary for responding to Hyper-IL-6 and activate STAT signaling upon Hyper-IL-6 treatment. RNA sequencing analysis reveals the upregulation of major histocompatibility complex class I (MHCI) genes in response to Hyper-IL-6 exposure, which have been implicated with ASD. We find a small increase in the proportion of radial glia cells after Hyper-IL-6 treatment through immunohistochemistry and single-cell RNA-sequencing. We further show that radial glia cells are the cell type with the highest number of differentially expressed genes, and Hyper-IL-6 treatment leads to the downregulation of genes related to protein translation in line with a mouse model of MIA. Additionally, we identify differentially expressed genes not found in mouse models of MIA, which might drive species-specific responses to MIA. Finally, we show abnormal cortical layering as a long-term consequence of Hyper-IL-6 treatment. In summary, we establish a human 3D model of MIA, which can be used to study the cellular and molecular mechanisms underlying the increased risk for developing disorders such as ASD.
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Affiliation(s)
- Kseniia Sarieva
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- International Max Planck Research School, Graduate Training Centre of Neuroscience, University of Tübingen, Tübingen, Germany
| | - Theresa Kagermeier
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- International Max Planck Research School, Graduate Training Centre of Neuroscience, University of Tübingen, Tübingen, Germany
| | - Shokoufeh Khakipoor
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Ezgi Atay
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Zeynep Yentür
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- International Max Planck Research School, Graduate Training Centre of Neuroscience, University of Tübingen, Tübingen, Germany
- Heidelberger Akademie der Wissenschaften, Heidelberg, Germany
| | - Katharina Becker
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Simone Mayer
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.
- International Max Planck Research School, Graduate Training Centre of Neuroscience, University of Tübingen, Tübingen, Germany.
- Heidelberger Akademie der Wissenschaften, Heidelberg, Germany.
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16
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Luo B, Liu K, Fan J. Bibliometric analysis of cerebral organoids and diseases in the last 10 years. IBRAIN 2023; 9:431-445. [PMID: 38680505 PMCID: PMC11045186 DOI: 10.1002/ibra.12139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/17/2023] [Accepted: 10/27/2023] [Indexed: 05/01/2024]
Abstract
Cerebral organoids have emerged as a powerful tool for mirroring the brain developmental processes and replicating its unique physiology. This bibliometric analysis aims to delineate the burgeoning trends in the application of cerebral organoids in disease research and offer insights for future investigations. We screened all relevant literature from the Web of Science on cerebral organoids in disease research during the period 2013-2022 and analyzed the research trends in the field using VOSviewer, CiteSpace, and Scimago Graphica software. According to the search strategy, 592 articles were screened out. The United States of America (USA) was the most productive, followed by China and Germany. The top nine institutions in terms of the number of publications include Canada and the United States, with the University of California, San Diego (USA), having the highest number of publications. The International Journal of Molecular Sciences was the most productive journal. Knoblich, Juergen A., and Lancaster, Madeline A. published the highest number of articles. Keyword cluster analysis showed that current research trends focused more on induced pluripotent stem cells to construct organoid models of cerebral diseases and the exploration of their mechanisms and therapeutic modalities. This study provides a comprehensive summary and analysis of global research trends in the field of cerebral organoids in diseases. In the past decade, the number of high-quality papers in this field has increased significantly, and cerebral organoids provide hope for simulating nervous system diseases (such as Alzheimer's disease).
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Affiliation(s)
- Bo‐Yan Luo
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic ChemistryChinese Academy of ScienceShanghaiChina
| | - Ke‐Qian Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic ChemistryChinese Academy of ScienceShanghaiChina
| | - Ji‐Sheng Fan
- ScienceComputer and Engineering of University of South AustraliaAdelaideSouth AustraliaAustralia
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17
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Harary PM, Jgamadze D, Kim J, Wolf JA, Song H, Ming GL, Cullen DK, Chen HI. Cell Replacement Therapy for Brain Repair: Recent Progress and Remaining Challenges for Treating Parkinson's Disease and Cortical Injury. Brain Sci 2023; 13:1654. [PMID: 38137103 PMCID: PMC10741697 DOI: 10.3390/brainsci13121654] [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: 10/19/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Neural transplantation represents a promising approach to repairing damaged brain circuitry. Cellular grafts have been shown to promote functional recovery through "bystander effects" and other indirect mechanisms. However, extensive brain lesions may require direct neuronal replacement to achieve meaningful restoration of function. While fetal cortical grafts have been shown to integrate with the host brain and appear to develop appropriate functional attributes, the significant ethical concerns and limited availability of this tissue severely hamper clinical translation. Induced pluripotent stem cell-derived cells and tissues represent a more readily scalable alternative. Significant progress has recently been made in developing protocols for generating a wide range of neural cell types in vitro. Here, we discuss recent progress in neural transplantation approaches for two conditions with distinct design needs: Parkinson's disease and cortical injury. We discuss the current status and future application of injections of dopaminergic cells for the treatment of Parkinson's disease as well as the use of structured grafts such as brain organoids for cortical repair.
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Affiliation(s)
- Paul M. Harary
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (P.M.H.)
| | - Dennis Jgamadze
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (P.M.H.)
| | - Jaeha Kim
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (P.M.H.)
| | - John A. Wolf
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (P.M.H.)
- Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA 19104, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guo-li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - D. Kacy Cullen
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (P.M.H.)
- Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - H. Isaac Chen
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (P.M.H.)
- Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, PA 19104, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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18
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Pagliaro A, Finger R, Zoutendijk I, Bunschuh S, Clevers H, Hendriks D, Artegiani B. Temporal morphogen gradient-driven neural induction shapes single expanded neuroepithelium brain organoids with enhanced cortical identity. Nat Commun 2023; 14:7361. [PMID: 38016960 PMCID: PMC10684874 DOI: 10.1038/s41467-023-43141-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 11/01/2023] [Indexed: 11/30/2023] Open
Abstract
Pluripotent stem cell (PSC)-derived human brain organoids enable the study of human brain development in vitro. Typically, the fate of PSCs is guided into subsequent specification steps through static medium switches. In vivo, morphogen gradients are critical for proper brain development and determine cell specification, and associated defects result in neurodevelopmental disorders. Here, we show that initiating neural induction in a temporal stepwise gradient guides the generation of brain organoids composed of a single, self-organized apical-out neuroepithelium, termed ENOs (expanded neuroepithelium organoids). This is at odds with standard brain organoid protocols in which multiple and independent neuroepithelium units (rosettes) are formed. We find that a prolonged, decreasing gradient of TGF-β signaling is a determining factor in ENO formation and allows for an extended phase of neuroepithelium expansion. In-depth characterization reveals that ENOs display improved cellular morphology and tissue architectural features that resemble in vivo human brain development, including expanded germinal zones. Consequently, cortical specification is enhanced in ENOs. ENOs constitute a platform to study the early events of human cortical development and allow interrogation of the complex relationship between tissue architecture and cellular states in shaping the developing human brain.
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Affiliation(s)
- Anna Pagliaro
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Roxy Finger
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Iris Zoutendijk
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Saskia Bunschuh
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Hans Clevers
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- Pharma, Research and Early Development (pRED) of F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Delilah Hendriks
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Benedetta Artegiani
- The Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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19
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Rudibaugh TT, Stuppy SR, Keung AJ. Reactive Oxygen Species Mediate Transcriptional Responses to Dopamine and Cocaine in Human Cerebral Organoids. Int J Mol Sci 2023; 24:16474. [PMID: 38003664 PMCID: PMC10671319 DOI: 10.3390/ijms242216474] [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: 10/24/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Dopamine signaling in the adult ventral forebrain regulates behavior, stress response, and memory formation and in neurodevelopment regulates neural differentiation and cell migration. Excessive dopamine levels, including those due to cocaine use in utero and in adults, could lead to long-term adverse consequences. The mechanisms underlying both homeostatic and pathological changes remain unclear, in part due to the diverse cellular responses elicited by dopamine and the reliance on animal models that exhibit species-specific differences in dopamine signaling. In this study, we use the human-derived ventral forebrain organoid model of Xiang-Tanaka and characterize their response to cocaine or dopamine. We explore dosing regimens of dopamine or cocaine to simulate acute or chronic exposure. We then use calcium imaging, cAMP imaging, and bulk RNA-sequencing to measure responses to cocaine or dopamine exposure. We observe an upregulation of inflammatory pathways in addition to indicators of oxidative stress following exposure. Using inhibitors of reactive oxygen species (ROS), we then show ROS to be necessary for multiple transcriptional responses of cocaine exposure. These results highlight novel response pathways and validate the potential of cerebral organoids as in vitro human models for studying complex biological processes in the brain.
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Affiliation(s)
| | | | - Albert J. Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27606, USA; (T.T.R.); (S.R.S.)
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20
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Kostic M, Raymond JJ, Freyre CAC, Henry B, Tumkaya T, Khlghatyan J, Dvornik J, Li J, Hsiao JS, Cheon SH, Chung J, Sun Y, Dolmetsch RE, Worringer KA, Ihry RJ. Patient Brain Organoids Identify a Link between the 16p11.2 Copy Number Variant and the RBFOX1 Gene. ACS Chem Neurosci 2023; 14:3993-4012. [PMID: 37903506 PMCID: PMC10655044 DOI: 10.1021/acschemneuro.3c00442] [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: 06/27/2023] [Accepted: 09/14/2023] [Indexed: 11/01/2023] Open
Abstract
Copy number variants (CNVs) that delete or duplicate 30 genes within the 16p11.2 genomic region give rise to a range of neurodevelopmental phenotypes with high penetrance in humans. Despite the identification of this small region, the mechanisms by which 16p11.2 CNVs lead to disease are unclear. Relevant models, such as human cortical organoids (hCOs), are needed to understand the human-specific mechanisms of neurodevelopmental disease. We generated hCOs from 17 patients and controls, profiling 167,958 cells with single-cell RNA-sequencing analysis, which revealed neuronal-specific differential expression of genes outside the 16p11.2 region that are related to cell-cell adhesion, neuronal projection growth, and neurodevelopmental disorders. Furthermore, 16p11.2 deletion syndrome organoids exhibited reduced mRNA and protein levels of RBFOX1, a gene that can also harbor CNVs linked to neurodevelopmental phenotypes. We found that the genes previously shown to be regulated by RBFOX1 are also perturbed in organoids from patients with the 16p11.2 deletion syndrome and thus identified a novel link between independent CNVs associated with neuronal development and autism. Overall, this work suggests convergent signaling, which indicates the possibility of a common therapeutic mechanism across multiple rare neuronal diseases.
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Affiliation(s)
- Milos Kostic
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Joseph J. Raymond
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Christophe A. C. Freyre
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Beata Henry
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Tayfun Tumkaya
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Cambridge 02139, Massachusetts, United States
| | - Jivan Khlghatyan
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Jill Dvornik
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Jingyao Li
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Jack S. Hsiao
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Seon Hye Cheon
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Jonathan Chung
- Chemical
Biology and Therapeutics, Novartis Institutes
for BioMedical Research, Cambridge 02139, Massachusetts, United States
| | - Yishan Sun
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Ricardo E. Dolmetsch
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Kathleen A. Worringer
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
| | - Robert J. Ihry
- Neuroscience, Novartis Institutes for BioMedical Research, Cambridge 02139, Massachusetts, United
States
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21
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Sato Y, Asahi T, Kataoka K. Integrative single-cell RNA-seq analysis of vascularized cerebral organoids. BMC Biol 2023; 21:245. [PMID: 37940920 PMCID: PMC10634128 DOI: 10.1186/s12915-023-01711-1] [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: 03/24/2023] [Accepted: 09/25/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Cerebral organoids are three-dimensional in vitro cultured brains that mimic the function and structure of the human brain. One of the major challenges for cerebral organoids is the lack of functional vasculature. Without perfusable vessels, oxygen and nutrient supplies may be insufficient for long-term culture, hindering the investigation of the neurovascular interactions. Recently, several strategies for the vascularization of human cerebral organoids have been reported. However, the generalizable trends and variability among different strategies are unclear due to the lack of a comprehensive characterization and comparison of these vascularization strategies. In this study, we aimed to explore the effect of different vascularization strategies on the nervous system and vasculature in human cerebral organoids. RESULTS We integrated single-cell RNA sequencing data of multiple vascularized and vascular organoids and fetal brains from publicly available datasets and assessed the protocol-dependent and culture-day-dependent effects on the cell composition and transcriptomic profiles in neuronal and vascular cells. We revealed the similarities and uniqueness of multiple vascularization strategies and demonstrated the transcriptomic effects of vascular induction on neuronal and mesodermal-like cell populations. Moreover, our data suggested that the interaction between neurons and mesodermal-like cell populations is important for the cerebrovascular-specific profile of endothelial-like cells. CONCLUSIONS This study highlights the current challenges to vascularization strategies in human cerebral organoids and offers a benchmark for the future fabrication of vascularized organoids.
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Affiliation(s)
- Yuya Sato
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Toru Asahi
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
- Comprehensive Research Organization, Waseda University, Tokyo, Japan.
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan.
| | - Kosuke Kataoka
- Comprehensive Research Organization, Waseda University, Tokyo, Japan.
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22
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Werner JM, Gillis J. Preservation of co-expression defines the primary tissue fidelity of human neural organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.31.535112. [PMID: 37034757 PMCID: PMC10081321 DOI: 10.1101/2023.03.31.535112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Human neural organoid models offer an exciting opportunity for studying often inaccessible human-specific brain development; however, it remains unclear how precisely organoids recapitulate fetal/primary tissue biology. Here, we characterize field-wide replicability and biological fidelity through a meta-analysis of single-cell RNA-sequencing data for first and second trimester human primary brain (2.95 million cells, 51 datasets) and neural organoids (1.63 million cells, 130 datasets). We quantify the degree to which primary tissue cell-type marker expression and co-expression are recapitulated in organoids across 12 different protocol types. By quantifying gene-level preservation of primary tissue co-expression, we show neural organoids lie on a spectrum ranging from virtually no signal to co-expression near indistinguishable from primary tissue data, demonstrating high fidelity is within the scope of current methods. Additionally, we show neural organoids preserve the cell-type specific co-expression of developing rather than adult cells, confirming organoids are an appropriate model for primary tissue development. Overall, quantifying the preservation of primary tissue co-expression is a powerful tool for uncovering unifying axes of variation across heterogeneous neural organoid experiments.
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Affiliation(s)
- Jonathan M Werner
- The Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jesse Gillis
- The Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
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23
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Chiaradia I, Imaz-Rosshandler I, Nilges BS, Boulanger J, Pellegrini L, Das R, Kashikar ND, Lancaster MA. Tissue morphology influences the temporal program of human brain organoid development. Cell Stem Cell 2023; 30:1351-1367.e10. [PMID: 37802039 PMCID: PMC10765088 DOI: 10.1016/j.stem.2023.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/22/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
Progression through fate decisions determines cellular composition and tissue architecture, but how that same architecture may impact cell fate is less clear. We took advantage of organoids as a tractable model to interrogate this interaction of form and fate. Screening methodological variations revealed that common protocol adjustments impacted various aspects of morphology, from macrostructure to tissue architecture. We examined the impact of morphological perturbations on cell fate through integrated single nuclear RNA sequencing (snRNA-seq) and spatial transcriptomics. Regardless of the specific protocol, organoids with more complex morphology better mimicked in vivo human fetal brain development. Organoids with perturbed tissue architecture displayed aberrant temporal progression, with cells being intermingled in both space and time. Finally, encapsulation to impart a simplified morphology led to disrupted tissue cytoarchitecture and a similar abnormal maturational timing. These data demonstrate that cells of the developing brain require proper spatial coordinates to undergo correct temporal progression.
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Affiliation(s)
- Ilaria Chiaradia
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Benedikt S Nilges
- Resolve Biosciences GmbH, Alfred-Nobel-Strasse 10, 40789 Monheim am Rhein, Germany
| | - Jerome Boulanger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Laura Pellegrini
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Richa Das
- Resolve Biosciences GmbH, Alfred-Nobel-Strasse 10, 40789 Monheim am Rhein, Germany
| | - Nachiket D Kashikar
- Resolve Biosciences GmbH, Alfred-Nobel-Strasse 10, 40789 Monheim am Rhein, Germany
| | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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24
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Simorgh S, Mousavi SA, To SK, Pasque V, Wierda K, Vervliet T, Yeganeh M, Pooyan P, Chai YC, Verfaillie C, Baharvand H. A facile method to generate cerebral organoids from human pluripotent stem cells. EXCLI JOURNAL 2023; 22:1055-1076. [PMID: 37927348 PMCID: PMC10620858 DOI: 10.17179/excli2023-6299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023]
Abstract
Human cerebral organoids (COs) are self-organizing three-dimensional (3D) neural structures that provide a human-specific platform to study the cellular and molecular processes that underlie different neurological events. The first step of CO generation from human pluripotent stem cells (hPSCs) is neural induction, which is an in vitro simulation of neural ectoderm development. Several signaling pathways cooperate during neural ectoderm development and in vitro differentiation of hPSCs toward neural cell lineages is also affected by them. In this study, we considered some of the known sources of these variable signaling cues arising from cell culture media components and sought to modulate their effects by applying a comprehensive combination of small molecules and growth factors for CO generation. Histological analysis demonstrated that these COs recapitulate the neural progenitor zone and early cortical layer organization, containing different types of neuronal and glial cells which was in accordance with single-nucleus transcriptome profiling results. Moreover, patch clamp and intracellular Ca2+ dynamic studies demonstrated that the COs behave as a functional neural network. Thus, this method serves as a facile protocol for generating hPSC-derived COs that faithfully mimic the features of their in vivo counterparts in the developing human brain. See also Figure 1(Fig. 1).
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Affiliation(s)
- Susan Simorgh
- Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Seyed Ahmad Mousavi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - San Kit To
- Department of Development and Regeneration, Lab for Epigenetic Reprogramming, Leuven Stem Cell Institute, Leuven Single-Cell Omics Institute and Leuven Cancer Institute, KU Leuven-University of Leuven, Leuven 3000, Belgium
| | - Vincent Pasque
- Department of Development and Regeneration, Lab for Epigenetic Reprogramming, Leuven Stem Cell Institute, Leuven Single-Cell Omics Institute and Leuven Cancer Institute, KU Leuven-University of Leuven, Leuven 3000, Belgium
| | - Keimpe Wierda
- VIB-KU Leuven Center for Brain & Disease Research, Leuven 3000, Belgium
- Electrophysiology Unit, Leuven 3000, Belgium
| | - Tim Vervliet
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Meghdad Yeganeh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Paria Pooyan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Yoke Chin Chai
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Catherine Verfaillie
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Hossein Baharvand
- Department of Developmental Biology, School of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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25
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Astorkia M, Liu Y, Pedrosa EM, Lachman HM, Zheng D. Molecular and network disruptions in neurodevelopment uncovered by single cell transcriptomics analysis of CHD8 heterozygous cerebral organoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559752. [PMID: 37808768 PMCID: PMC10557718 DOI: 10.1101/2023.09.27.559752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
About 100 genes have been associated with significantly increased risks of autism spectrum disorders (ASD) with an estimate of ~1000 genes that may be involved. The new challenge now is to investigate the molecular and cellular functions of these genes during neural and brain development, and then even more challenging, to link the altered molecular and cellular phenotypes to the ASD clinical manifestations. In this study, we use single cell RNA-seq analysis to study one of the top risk gene, CHD8, in cerebral organoids, which models early neural development. We identify 21 cell clusters in the organoid samples, representing non-neuronal cells, neural progenitors, and early differentiating neurons at the start of neural cell fate commitment. Comparisons of the cells with one copy of the CHD8 knockout and their isogenic controls uncover thousands of differentially expressed genes, which are enriched with function related to neural and brain development, with genes and pathways previously implicated in ASD, but surprisingly not for Schizophrenia and intellectual disability risk genes. The comparisons also find cell composition changes, indicating potential altered neural differential trajectories upon CHD8 reduction. Moreover, we find that cell-cell communications are affected in the CHD8 knockout organoids, including the interactions between neural and glial cells. Taken together, our results provide new data for understanding CHD8 functions in the early stages of neural lineage development and interaction.
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Affiliation(s)
- Maider Astorkia
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yang Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Erika M. Pedrosa
- Department of Psychiatry and Behavioral Science, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Herbert M. Lachman
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Psychiatry and Behavioral Science, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA
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26
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Guang S, O'Brien BM, Fine AS, Ying M, Fatemi A, Nemeth CL. Mutations in DARS2 result in global dysregulation of mRNA metabolism and splicing. Sci Rep 2023; 13:13042. [PMID: 37563224 PMCID: PMC10415389 DOI: 10.1038/s41598-023-40107-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 08/04/2023] [Indexed: 08/12/2023] Open
Abstract
Leukoencephalopathy with brainstem and spinal cord involvement and lactate elevation (LBSL) is a rare neurological disorder caused by the mutations in the DARS2 gene, which encodes the mitochondrial aspartyl-tRNA synthetase. The objective of this study was to understand the impact of DARS2 mutations on cell processes through evaluation of LBSL patient stem cell derived cerebral organoids and neurons. We generated human cerebral organoids (hCOs) from induced pluripotent stem cells (iPSCs) of seven LBSL patients and three healthy controls using an unguided protocol. Single cells from 70-day-old hCOs were subjected to SMART-seq2 sequencing and bioinformatic analysis to acquire high-resolution gene and transcript expression datasets. Global gene expression analysis demonstrated dysregulation of a number of genes involved in mRNA metabolism and splicing processes within LBSL hCOs. Importantly, there were distinct and divergent gene expression profiles based on the nature of the DARS2 mutation. At the transcript level, pervasive differential transcript usage and differential spliced exon events that are involved in protein translation and metabolism were identified in LBSL hCOs. Single-cell analysis of DARS2 (exon 3) showed that some LBSL cells exclusively express transcripts lacking exon 3, indicating that not all LBSL cells can benefit from the "leaky" nature common to splice site mutations. At the gene- and transcript-level, we uncovered that dysregulated RNA splicing, protein translation and metabolism may underlie at least some of the pathophysiological mechanisms in LBSL. To confirm hCO findings, iPSC-derived neurons (iNs) were generated by overexpressing Neurogenin 2 using lentiviral vector to study neuronal growth, splicing of DARS2 exon 3 and DARS2 protein expression. Live cell imaging revealed neuronal growth defects of LBSL iNs, which was consistent with the finding of downregulated expression of genes related to neuronal differentiation in LBSL hCOs. DARS2 protein was downregulated in iNs compared to iPSCs, caused by increased exclusion of exon 3. The scope and complexity of our data imply that DARS2 is potentially involved in transcription regulation beyond its canonical role of aminoacylation. Nevertheless, our work highlights transcript-level dysregulation as a critical, and relatively unexplored, mechanism linking genetic data with neurodegenerative disorders.
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Affiliation(s)
- S Guang
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute, 707 N Broadway, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - B M O'Brien
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute, 707 N Broadway, Baltimore, MD, 21205, USA
| | - A S Fine
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD, USA
| | - M Ying
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Kennedy Krieger Institute, Baltimore, MD, USA
| | - A Fatemi
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute, 707 N Broadway, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - C L Nemeth
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute, 707 N Broadway, Baltimore, MD, 21205, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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27
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Ghaffari S, Bouchonville KJ, Saleh E, Schmidt RE, Offer SM, Sinha S. BEDwARS: a robust Bayesian approach to bulk gene expression deconvolution with noisy reference signatures. Genome Biol 2023; 24:178. [PMID: 37537644 PMCID: PMC10399072 DOI: 10.1186/s13059-023-03007-7] [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: 10/25/2022] [Accepted: 07/05/2023] [Indexed: 08/05/2023] Open
Abstract
Differential gene expression in bulk transcriptomics data can reflect change of transcript abundance within a cell type and/or change in the proportions of cell types. Expression deconvolution methods can help differentiate these scenarios. BEDwARS is a Bayesian deconvolution method designed to address differences between reference signatures of cell types and corresponding true signatures underlying bulk transcriptomic profiles. BEDwARS is more robust to noisy reference signatures and outperforms leading in-class methods for estimating cell type proportions and signatures. Application of BEDwARS to dihydropyridine dehydrogenase deficiency identified the possible involvement of ciliopathy and impaired translational control in the etiology of the disorder.
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Affiliation(s)
- Saba Ghaffari
- Department of Computer Science, University of Illinois at Urbana-Champaign, Thomas M. Siebel Center, 201 N. Goodwin Ave., Urbana, IL, USA
| | - Kelly J Bouchonville
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Gonda 19-476, 200 First St. SW, Rochester, MN, 55905, USA
| | - Ehsan Saleh
- Department of Computer Science, University of Illinois at Urbana-Champaign, Thomas M. Siebel Center, 201 N. Goodwin Ave., Urbana, IL, USA
| | - Remington E Schmidt
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Gonda 19-476, 200 First St. SW, Rochester, MN, 55905, USA
| | - Steven M Offer
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Gonda 19-476, 200 First St. SW, Rochester, MN, 55905, USA.
| | - Saurabh Sinha
- Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University, Georgia Institute of Technology, 3108 U.A. Whitaker Bldg., 313 Ferst Drive, Atlanta, GA, 30332, USA.
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28
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Glass MR, Waxman EA, Yamashita S, Lafferty M, Beltran A, Farah T, Patel NK, Matoba N, Ahmed S, Srivastava M, Drake E, Davis LT, Yeturi M, Sun K, Love MI, Hashimoto-Torii K, French DL, Stein JL. Cross-site reproducibility of human cortical organoids reveals consistent cell type composition and architecture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.550873. [PMID: 37546772 PMCID: PMC10402155 DOI: 10.1101/2023.07.28.550873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Background Reproducibility of human cortical organoid (hCO) phenotypes remains a concern for modeling neurodevelopmental disorders. While guided hCO protocols reproducibly generate cortical cell types in multiple cell lines at one site, variability across sites using a harmonized protocol has not yet been evaluated. We present an hCO cross-site reproducibility study examining multiple phenotypes. Methods Three independent research groups generated hCOs from one induced pluripotent stem cell (iPSC) line using a harmonized miniaturized spinning bioreactor protocol. scRNA-seq, 3D fluorescent imaging, phase contrast imaging, qPCR, and flow cytometry were used to characterize the 3 month differentiations across sites. Results In all sites, hCOs were mostly cortical progenitor and neuronal cell types in reproducible proportions with moderate to high fidelity to the in vivo brain that were consistently organized in cortical wall-like buds. Cross-site differences were detected in hCO size and morphology. Differential gene expression showed differences in metabolism and cellular stress across sites. Although iPSC culture conditions were consistent and iPSCs remained undifferentiated, primed stem cell marker expression prior to differentiation correlated with cell type proportions in hCOs. Conclusions We identified hCO phenotypes that are reproducible across sites using a harmonized differentiation protocol. Previously described limitations of hCO models were also reproduced including off-target differentiations, necrotic cores, and cellular stress. Improving our understanding of how stem cell states influence early hCO cell types may increase reliability of hCO differentiations. Cross-site reproducibility of hCO cell type proportions and organization lays the foundation for future collaborative prospective meta-analytic studies modeling neurodevelopmental disorders in hCOs.
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Affiliation(s)
- Madison R Glass
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Elisa A Waxman
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Satoshi Yamashita
- Center for Neuroscience Research, Children's National Hospital, Washington, DC
| | - Michael Lafferty
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Alvaro Beltran
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Tala Farah
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Niyanta K Patel
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Nana Matoba
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sara Ahmed
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Mary Srivastava
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Emma Drake
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Liam T Davis
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Meghana Yeturi
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kexin Sun
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Departments of Pediatrics, and Pharmacology & Physiology, School of Medicine and Health Sciences, The George Washington University, Washington, DC
| | - Kazue Hashimoto-Torii
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Deborah L French
- Center for Cellular and Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | - Jason L Stein
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
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29
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Bertucci T, Bowles KR, Lotz S, Qi L, Stevens K, Goderie SK, Borden S, Oja LM, Lane K, Lotz R, Lotz H, Chowdhury R, Joy S, Arduini BL, Butler DC, Miller M, Baron H, Sandhof CA, Silva MC, Haggarty SJ, Karch CM, Geschwind DH, Goate AM, Temple S. Improved Protocol for Reproducible Human Cortical Organoids Reveals Early Alterations in Metabolism with MAPT Mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.11.548571. [PMID: 37503195 PMCID: PMC10369860 DOI: 10.1101/2023.07.11.548571] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Cerebral cortical-enriched organoids derived from human pluripotent stem cells (hPSCs) are valuable models for studying neurodevelopment, disease mechanisms, and therapeutic development. However, recognized limitations include the high variability of organoids across hPSC donor lines and experimental replicates. We report a 96-slitwell method for efficient, scalable, reproducible cortical organoid production. When hPSCs were cultured with controlled-release FGF2 and an SB431542 concentration appropriate for their TGFBR1 / ALK5 expression level, organoid cortical patterning and reproducibility were significantly improved. Well-patterned organoids included 16 neuronal and glial subtypes by single cell RNA sequencing (scRNA-seq), frequent neural progenitor rosettes and robust BCL11B+ and TBR1+ deep layer cortical neurons at 2 months by immunohistochemistry. In contrast, poorly-patterned organoids contain mesendoderm-related cells, identifiable by negative QC markers including COL1A2 . Using this improved protocol, we demonstrate increased sensitivity to study the impact of different MAPT mutations from patients with frontotemporal dementia (FTD), revealing early changes in key metabolic pathways.
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Adlakha YK. Human 3D brain organoids: steering the demolecularization of brain and neurological diseases. Cell Death Discov 2023; 9:221. [PMID: 37400464 DOI: 10.1038/s41420-023-01523-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/05/2023] Open
Abstract
Understanding of human brain development, dysfunction and neurological diseases has remained limited and challenging due to inability to recapitulate human brain-specific features in animal models. Though the anatomy and physiology of the human brain has been understood in a remarkable way using post-mortem, pathological samples of human and animal models, however, modeling of human brain development and neurological diseases remains a challenge owing to distinct complexity of human brain. In this perspective, three-dimensional (3D) brain organoids have shown a beam of light. Tremendous growth in stem cell technologies has permitted the differentiation of pluripotent stem cells under 3D culture conditions into brain organoids, which recapitulate the unique features of human brain in many ways and also offer the detailed investigation of brain development, dysfunction and neurological diseases. Their translational value has also emerged and will benefit the society once the protocols for the upscaling of brain organoids are in place. Here, we summarize new advancements in methods for generation of more complex brain organoids including vascularized and mixed lineage tissue from PSCs. How synthetic biomaterials and microfluidic technology is boosting brain organoid development, has also been highlighted. We discuss the applications of brain organoids in studying preterm birth associated brain dysfunction; viral infections mediated neuroinflammation, neurodevelopmental and neurodegenerative diseases. We also highlight the translational value of brain organoids and current challenges that the field is experiencing.
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Affiliation(s)
- Yogita K Adlakha
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, Uttar Pradesh, India.
- Maternal and Child Health Domain, Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana, India.
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31
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Barreras P, Pamies D, Hartung T, Pardo CA. Human brain microphysiological systems in the study of neuroinfectious disorders. Exp Neurol 2023; 365:114409. [PMID: 37061175 PMCID: PMC10205672 DOI: 10.1016/j.expneurol.2023.114409] [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: 02/06/2023] [Revised: 04/02/2023] [Accepted: 04/12/2023] [Indexed: 04/17/2023]
Abstract
Microphysiological systems (MPS) are 2D or 3D multicellular constructs able to mimic tissue microenvironments. The latest models encompass a range of techniques, including co-culturing of various cell types, utilization of scaffolds and extracellular matrix materials, perfusion systems, 3D culture methods, 3D bioprinting, organ-on-a-chip technology, and examination of tissue structures. Several human brain 3D cultures or brain MPS (BMPS) have emerged in the last decade. These organoids or spheroids are 3D culture systems derived from induced pluripotent cells or embryonic stem cells that contain neuronal and glial populations and recapitulate structural and physiological aspects of the human brain. BMPS have been introduced recently in the study and modeling of neuroinfectious diseases and have proven to be useful in establishing neurotropism of viral infections, cell-pathogen interactions needed for infection, assessing cytopathological effects, genomic and proteomic profiles, and screening therapeutic compounds. Here we review the different methodologies of organoids used in neuroinfectious diseases including spheroids, guided and unguided protocols as well as microglia and blood-brain barrier containing models, their specific applications, and limitations. The review provides an overview of the models existing for specific infections including Zika, Dengue, JC virus, Japanese encephalitis, measles, herpes, SARS-CoV2, and influenza viruses among others, and provide useful concepts in the modeling of disease and antiviral agent screening.
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Affiliation(s)
- Paula Barreras
- Division of Neuroimmunology and Neurological Infections, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - David Pamies
- Department of Biomedical Science, University of Lausanne, Lausanne, Switzerland; Swiss Centre for Applied Human Toxicology, Basel, Switzerland
| | - Thomas Hartung
- Center for Alternatives to Animal Testing (CAAT), Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, USA; CAAT-Europe, University of Konstanz, Germany
| | - Carlos A Pardo
- Division of Neuroimmunology and Neurological Infections, Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, USA.
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Sebastian R, Jin K, Pavon N, Bansal R, Potter A, Song Y, Babu J, Gabriel R, Sun Y, Aronow B, Pak C. Schizophrenia-associated NRXN1 deletions induce developmental-timing- and cell-type-specific vulnerabilities in human brain organoids. Nat Commun 2023; 14:3770. [PMID: 37355690 PMCID: PMC10290702 DOI: 10.1038/s41467-023-39420-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 06/13/2023] [Indexed: 06/26/2023] Open
Abstract
De novo mutations and copy number deletions in NRXN1 (2p16.3) pose a significant risk for schizophrenia (SCZ). It is unclear how NRXN1 deletions impact cortical development in a cell type-specific manner and disease background modulates these phenotypes. Here, we leveraged human pluripotent stem cell-derived forebrain organoid models carrying NRXN1 heterozygous deletions in isogenic and SCZ patient genetic backgrounds and conducted single-cell transcriptomic analysis over the course of brain organoid development from 3 weeks to 3.5 months. Intriguingly, while both deletions similarly impacted molecular pathways associated with ubiquitin-proteasome system, alternative splicing, and synaptic signaling in maturing glutamatergic and GABAergic neurons, SCZ-NRXN1 deletions specifically perturbed developmental trajectories of early neural progenitors and accumulated disease-specific transcriptomic signatures. Using calcium imaging, we found that both deletions led to long-lasting changes in spontaneous and synchronous neuronal networks, implicating synaptic dysfunction. Our study reveals developmental-timing- and cell-type-dependent actions of NRXN1 deletions in unique genetic contexts.
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Affiliation(s)
- Rebecca Sebastian
- Graduate Program in Neuroscience & Behavior, UMass Amherst, Amherst, MA, 01003, USA
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Kang Jin
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Narciso Pavon
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Ruby Bansal
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Andrew Potter
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Yoonjae Song
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Juliana Babu
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Rafael Gabriel
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA
| | - Yubing Sun
- Department of Mechanical and Industrial Engineering, UMass Amherst, Amherst, MA, 01003, USA
| | - Bruce Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Biomedical Informatics, University of Cincinnati, Cincinnati, OH, 45229, USA
- Department of Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, 45221, USA
- Department of Pediatrics, University of Cincinnati School of Medicine, Cincinnati, OH, 45256, USA
| | - ChangHui Pak
- Department of Biochemistry and Molecular Biology, UMass Amherst, Amherst, MA, 01003, USA.
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Hong H, Yoon SB, Park JE, Lee JI, Kim HY, Nam HJ, Cho H. MeCP2 dysfunction prevents proper BMP signaling and neural progenitor expansion in brain organoid. Ann Clin Transl Neurol 2023. [PMID: 37302988 DOI: 10.1002/acn3.51799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/26/2023] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
OBJECTIVES Sporadic mutations in MeCP2 are a hallmark of Rett syndrome (RTT). Many RTT brain organoid models have exhibited pathogenic phenotypes such as decreased spine density and small size of soma with altered electrophysiological signals. However, previous models are mainly focused on the phenotypes observed in the late phase and rarely provide clues for the defect of neural progenitors which generate different types of neurons and glial cells. METHODS We newly established the RTT brain organoid model derived from MeCP2-truncated iPS cells which were genetically engineered by CRISPR/Cas9 technology. By immunofluorescence imaging, we studied the development of NPC pool and its fate specification into glutamatergic neurons or astrocytes in RTT organoids. By total RNA sequencing, we investigated which signaling pathways were altered during the early brain development in RTT organoids. RESULTS Dysfunction of MeCP2 caused the defect of neural rosette formation in the early phase of cortical development. In total transcriptome analysis, BMP pathway-related genes are highly associated with MeCP2 depletion. Moreover, levels of pSMAD1/5 and BMP target genes are excessively increased, and treatment of BMP inhibitors partially rescues the cell cycle progression of neural progenitors. Subsequently, MeCP2 dysfunction reduced the glutamatergic neurogenesis and induced overproduction of astrocytes. Nevertheless, early inhibition of BMP pathway rescued VGLUT1 expression and suppressed astrocyte maturation. INTERPRETATION Our results demonstrate that MeCP2 is required for the expansion of neural progenitor cells by modulating BMP pathway at early stages of development, and this influence persists during neurogenesis and gliogenesis at later stages of brain organoid development.
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Affiliation(s)
- Hyowon Hong
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Sae-Bom Yoon
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jung Eun Park
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jung In Lee
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Hyun Young Kim
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Hye Jin Nam
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Heeyeong Cho
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
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Kiral FR, Cakir B, Tanaka Y, Kim J, Yang WS, Wehbe F, Kang YJ, Zhong M, Sancer G, Lee SH, Xiang Y, Park IH. Generation of ventralized human thalamic organoids with thalamic reticular nucleus. Cell Stem Cell 2023; 30:677-688.e5. [PMID: 37019105 PMCID: PMC10329908 DOI: 10.1016/j.stem.2023.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 02/06/2023] [Accepted: 03/09/2023] [Indexed: 04/07/2023]
Abstract
Human brain organoids provide unique platforms for modeling several aspects of human brain development and pathology. However, current brain organoid systems mostly lack the resolution to recapitulate the development of finer brain structures with subregional identity, including functionally distinct nuclei in the thalamus. Here, we report a method for converting human embryonic stem cells (hESCs) into ventral thalamic organoids (vThOs) with transcriptionally diverse nuclei identities. Notably, single-cell RNA sequencing revealed previously unachieved thalamic patterning with a thalamic reticular nucleus (TRN) signature, a GABAergic nucleus located in the ventral thalamus. Using vThOs, we explored the functions of TRN-specific, disease-associated genes patched domain containing 1 (PTCHD1) and receptor tyrosine-protein kinase (ERBB4) during human thalamic development. Perturbations in PTCHD1 or ERBB4 impaired neuronal functions in vThOs, albeit not affecting the overall thalamic lineage development. Together, vThOs present an experimental model for understanding nuclei-specific development and pathology in the thalamus of the human brain.
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Affiliation(s)
- Ferdi Ridvan Kiral
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Bilal Cakir
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yoshiaki Tanaka
- Department of Medicine, Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, QC H1T 2M4, Canada
| | - Jonghun Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Woo Sub Yang
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Fabien Wehbe
- Department of Medicine, Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, QC H1T 2M4, Canada
| | - Young-Jin Kang
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Mei Zhong
- Department of Cell Biology, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Gizem Sancer
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sang-Hun Lee
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Yangfei Xiang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA.
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35
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Walters RO, Haigh CL. Organoids for modeling prion diseases. Cell Tissue Res 2023; 392:97-111. [PMID: 35088182 PMCID: PMC9329493 DOI: 10.1007/s00441-022-03589-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/19/2022] [Indexed: 11/25/2022]
Abstract
Human cerebral organoids are an exciting and novel model system emerging in the field of neurobiology. Cerebral organoids are spheres of self-organizing, neuronal lineage tissue that can be differentiated from human pluripotent stem cells and that present the possibility of on-demand human neuronal cultures that can be used for non-invasively investigating diseases affecting the brain. Compared with existing humanized cell models, they provide a more comprehensive replication of the human cerebral environment. The potential of the human cerebral organoid model is only just beginning to be elucidated, but initial studies have indicated that they could prove to be a valuable model for neurodegenerative diseases such as prion disease. The application of the cerebral organoid model to prion disease, what has been learned so far and the future potential of this model are discussed in this review.
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Affiliation(s)
- Ryan O Walters
- Prion Cell Biology Unit, Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4th Street, Hamilton, MT, 59840, USA
| | - Cathryn L Haigh
- Prion Cell Biology Unit, Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 903 South 4th Street, Hamilton, MT, 59840, USA.
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36
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Wang L, Owusu-Hammond C, Sievert D, Gleeson JG. Stem Cell-Based Organoid Models of Neurodevelopmental Disorders. Biol Psychiatry 2023; 93:622-631. [PMID: 36759260 PMCID: PMC10022535 DOI: 10.1016/j.biopsych.2023.01.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/12/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
The past decade has seen an explosion in the identification of genetic causes of neurodevelopmental disorders, including Mendelian, de novo, and somatic factors. These discoveries provide opportunities to understand cellular and molecular mechanisms as well as potential gene-gene and gene-environment interactions to support novel therapies. Stem cell-based models, particularly human brain organoids, can capture disease-associated alleles in the context of the human genome, engineered to mirror disease-relevant aspects of cellular complexity and developmental timing. These models have brought key insights into neurodevelopmental disorders as diverse as microcephaly, autism, and focal epilepsy. However, intrinsic organoid-to-organoid variability, low levels of certain brain-resident cell types, and long culture times required to reach maturity can impede progress. Several recent advances incorporate specific morphogen gradients, mixtures of diverse brain cell types, and organoid engraftment into animal models. Together with nonhuman primate organoid comparisons, mechanisms of human neurodevelopmental disorders are emerging.
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Affiliation(s)
- Lu Wang
- From the Department of Neuroscience, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, California
| | - Charlotte Owusu-Hammond
- From the Department of Neuroscience, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, California
| | - David Sievert
- From the Department of Neuroscience, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, California
| | - Joseph G Gleeson
- From the Department of Neuroscience, Rady Children's Institute for Genomic Medicine, University of California, San Diego, San Diego, California.
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37
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Urenda JP, Del Dosso A, Birtele M, Quadrato G. Present and Future Modeling of Human Psychiatric Connectopathies With Brain Organoids. Biol Psychiatry 2023; 93:606-615. [PMID: 36759258 PMCID: PMC11229385 DOI: 10.1016/j.biopsych.2022.12.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 11/21/2022] [Accepted: 12/12/2022] [Indexed: 12/25/2022]
Abstract
Brain organoids derived from human pluripotent stem cells are emerging as a powerful tool to model cellular aspects of neuropsychiatric disorders, including alterations in cell proliferation, differentiation, migration, and lineage trajectory. To date, most contributions in the field have focused on modeling cellular impairment of the cerebral cortex, with few studies probing dysfunction in local network connectivity. However, it is increasingly more apparent that these psychiatric disorders are connectopathies involving multiple brain structures and the connections between them. Therefore, the lack of reproducible anatomical features in these 3-dimensional cultures represents a major bottleneck for effectively modeling brain connectivity at the micro(cellular) level and at the macroscale level between brain regions. In this perspective, we review the use of current organoid protocols to model neuropsychiatric disorders with a specific emphasis on the potential and limitations of the current strategies to model impairments in functional connectivity. Finally, we discuss the importance of adopting interdisciplinary strategies to establish next-generation, multiregional organoids that can model, with higher fidelity, the dysfunction in the development and functionality of long-range connections within the brain of patients affected by psychiatric disorders.
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Affiliation(s)
- Jean-Paul Urenda
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ashley Del Dosso
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Marcella Birtele
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Giorgia Quadrato
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California.
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38
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De Kleijn KMA, Zuure WA, Straasheijm KR, Martens MB, Avramut MC, Koning RI, Martens GJM. Human cortical spheroids with a high diversity of innately developing brain cell types. Stem Cell Res Ther 2023; 14:50. [PMID: 36959625 PMCID: PMC10035191 DOI: 10.1186/s13287-023-03261-3] [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: 06/03/2022] [Accepted: 02/28/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Three-dimensional (3D) human brain spheroids are instrumental to study central nervous system (CNS) development and (dys)function. Yet, in current brain spheroid models the limited variety of cell types hampers an integrated exploration of CNS (disease) mechanisms. METHODS Here we report a 5-month culture protocol that reproducibly generates H9 embryonic stem cell-derived human cortical spheroids (hCSs) with a large cell-type variety. RESULTS We established the presence of not only neuroectoderm-derived neural progenitor populations, mature excitatory and inhibitory neurons, astrocytes and oligodendrocyte (precursor) cells, but also mesoderm-derived microglia and endothelial cell populations in the hCSs via RNA-sequencing, qPCR, immunocytochemistry and transmission electron microscopy. Transcriptomic analysis revealed resemblance between the 5-months-old hCSs and dorsal frontal rather than inferior regions of human fetal brains of 19-26 weeks of gestational age. Pro-inflammatory stimulation of the generated hCSs induced a neuroinflammatory response, offering a proof-of-principle of the applicability of the spheroids. CONCLUSIONS Our protocol provides a 3D human brain cell model containing a wide variety of innately developing neuroectoderm- as well as mesoderm-derived cell types, furnishing a versatile platform for comprehensive examination of intercellular CNS communication and neurological disease mechanisms.
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Affiliation(s)
- Kim M A De Kleijn
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Centre for Neuroscience, Faculty of Science, Radboud University, 6525GA, Nijmegen, The Netherlands.
- NeuroDrug Research Ltd, 6525ED, Nijmegen, The Netherlands.
| | - Wieteke A Zuure
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Centre for Neuroscience, Faculty of Science, Radboud University, 6525GA, Nijmegen, The Netherlands
| | | | | | - M Cristina Avramut
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300RC, Leiden, The Netherlands
| | - Roman I Koning
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300RC, Leiden, The Netherlands
| | - Gerard J M Martens
- Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behavior, Centre for Neuroscience, Faculty of Science, Radboud University, 6525GA, Nijmegen, The Netherlands
- NeuroDrug Research Ltd, 6525ED, Nijmegen, The Netherlands
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39
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Wang SN, Wang Z, Wang XY, Zhang XP, Xu TY, Miao CY. Humanized cerebral organoids-based ischemic stroke model for discovering of potential anti-stroke agents. Acta Pharmacol Sin 2023; 44:513-523. [PMID: 36100766 PMCID: PMC9958103 DOI: 10.1038/s41401-022-00986-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/19/2022] [Indexed: 11/09/2022] Open
Abstract
Establishing a stoke experimental model, which is better in line with the physiology and function of human brain, is the bottleneck for the development of effective anti-stroke drugs. A three-dimensional cerebral organoids (COs) from human pluripotent stem cells can mimic cell composition, cortical structure, brain neural connectivity and epigenetic genomics of in-vivo human brain, which provides a promising application in establishing humanized ischemic stroke model. COs have been used for modeling low oxygen condition-induced hypoxic injury, but there is no report on the changes of COs in response to in vitro oxygen-glucose deprivation (OGD)-induced damage of ischemic stroke as well as its application in testing anti-stroke drugs. In this study we compared the cell composition of COs at different culture time and explored the cell types, cell ratios and volume size of COs at 85 days (85 d-CO). The 85 d-CO with diameter more than 2 mm was chosen for establishing humanized ischemic stroke model of OGD. By determining the time-injury relationship of the model, we observed aggravated ischemic injury of COs with OGD exposure time, obtaining first-hand evidence for the damage degree of COs under different OGD condition. The sensitivity of the model to ischemic injury and related treatment was validated by the proven pan-Caspase inhibitor Z-VAD-FMK (20 μM) and Bcl-2 inhibitor navitoclax (0.5 μM). Neuroprotective agents edaravone, butylphthalide, P7C3-A20 and ZL006 (10 μM for each) exerted similar beneficial effects in this model. Taken together, this study establishes a humanized ischemic stroke model based on COs, and provides evidence as a new research platform for anti-stroke drug development.
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Affiliation(s)
- Shu-Na Wang
- Department of Pharmacology, Second Military Medical University/Naval Medical University, Shanghai, 200433, China
| | - Zhi Wang
- Department of Pharmacology, Second Military Medical University/Naval Medical University, Shanghai, 200433, China
| | - Xi-Yuan Wang
- Department of Pharmacology, Second Military Medical University/Naval Medical University, Shanghai, 200433, China
| | - Xiu-Ping Zhang
- Department of Pharmacology, Second Military Medical University/Naval Medical University, Shanghai, 200433, China
| | - Tian-Ying Xu
- Department of Pharmacology, Second Military Medical University/Naval Medical University, Shanghai, 200433, China.
- Department of Anesthesia Pharmacology, Second Military Medical University/Naval Medical University, Shanghai, 200433, China.
| | - Chao-Yu Miao
- Department of Pharmacology, Second Military Medical University/Naval Medical University, Shanghai, 200433, China.
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40
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Kodera T, Takeuchi RF, Takahashi S, Suzuki K, Kassai H, Aiba A, Shiozawa S, Okano H, Osakada F. Modeling the marmoset brain using embryonic stem cell-derived cerebral assembloids. Biochem Biophys Res Commun 2023; 657:119-127. [PMID: 37002985 DOI: 10.1016/j.bbrc.2023.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/08/2023] [Indexed: 03/13/2023]
Abstract
Studying the non-human primate (NHP) brain is required for the translation of rodent research to humans, but remains a challenge for molecular, cellular, and circuit-level analyses in the NHP brain due to the lack of in vitro NHP brain system. Here, we report an in vitro NHP cerebral model using marmoset (Callithrix jacchus) embryonic stem cell-derived cerebral assembloids (CAs) that recapitulate inhibitory neuron migration and cortical network activity. Cortical organoids (COs) and ganglionic eminence organoids (GEOs) were induced from cjESCs and fused to generate CAs. GEO cells expressing the inhibitory neuron marker LHX6 migrated toward the cortical side of CAs. COs developed their spontaneous neural activity from a synchronized pattern to an unsynchronized pattern as COs matured. CAs containing excitatory and inhibitory neurons showed mature neural activity with an unsynchronized pattern. The CAs represent a powerful in vitro model for studying excitatory and inhibitory neuron interactions, cortical dynamics, and their dysfunction. The marmoset assembloid system will provide an in vitro platform for the NHP neurobiology and facilitate translation into humans in neuroscience research, regenerative medicine, and drug discovery.
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Guang S, O'Brien B, Fine AS, Ying M, Fatemi A, Nemeth C. Mutations in DARS2 result in global dysregulation of mRNA metabolism and splicing. RESEARCH SQUARE 2023:rs.3.rs-2603446. [PMID: 36909591 PMCID: PMC10002802 DOI: 10.21203/rs.3.rs-2603446/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation (LBSL) is a rare neurological disorder caused by the mutations in the DARS2 gene, which encodes the mitochondrial aspartyl-tRNA synthetase. The objective of this study was to understand the impact of DARS2 mutations on cell processes through evaluation of LBSL patient stem cell derived cerebral organoids and neurons. We generated human cerebral organoids (hCOs) from induced pluripotent stem cells (iPSCs) of seven LBSL patients and three healthy controls using an unguided protocol. Single cells from 70-day-old hCOs underwent SMART-seq2 sequencing and multiple bioinformatic analysis tools were applied to high-resolution gene and transcript expression analyses. To confirm hCO findings, iPSC-derived neurons (iNs) were generated by overexpressing Neurogenin 2 using lentiviral vector to study neuronal growth, splicing of DARS2 exon 3 and DARS2 protein expression. Global gene expression analysis demonstrated dysregulation of a number of genes involved in mRNA metabolism and splicing processes within LBSL hCOs. Importantly, there were distinct and divergent gene expression profiles based on the nature of the DARS2 mutation. At the transcript level, pervasive differential transcript usage and differential spliced exon events that are involved in protein translation and metabolism were identified in LBSL hCOs. Single-cell analysis of DARS2 (exon 3) showed that some LBSL cells exclusively express transcripts lacking exon 3, indicating that not all LBSL cells can benefit from the "leaky" nature common to splice site mutations. Live cell imaging revealed neuronal growth defects of LBSL iNs, which was consistent with the finding of downregulated expression of genes related to neuronal differentiation in LBSL hCOs. DARS2 protein was downregulated in iNs compared to iPSCs, caused by increased exclusion of exon 3. At the gene- and transcript-level, we uncovered that dysregulated RNA splicing, protein translation and metabolism may underlie at least some of the pathophysiological mechanisms in LBSL. The scope and complexity of our data imply that DARS2 is potentially involved in transcription regulation beyond its canonical role of aminoacylation. Nevertheless, our work highlights transcript-level dysregulation as a critical, and relatively unexplored, mechanism linking genetic data with neurodegenerative disorders.
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Affiliation(s)
- Shiqi Guang
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute
| | - Brett O'Brien
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute
| | - Amena Smith Fine
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute
| | | | - Ali Fatemi
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute
| | - Christina Nemeth
- Moser Center for Leukodystrophies at Kennedy Krieger, Kennedy Krieger Institute
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Transition from Animal-Based to Human Induced Pluripotent Stem Cells (iPSCs)-Based Models of Neurodevelopmental Disorders: Opportunities and Challenges. Cells 2023; 12:cells12040538. [PMID: 36831205 PMCID: PMC9954744 DOI: 10.3390/cells12040538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Neurodevelopmental disorders (NDDs) arise from the disruption of highly coordinated mechanisms underlying brain development, which results in impaired sensory, motor and/or cognitive functions. Although rodent models have offered very relevant insights to the field, the translation of findings to clinics, particularly regarding therapeutic approaches for these diseases, remains challenging. Part of the explanation for this failure may be the genetic differences-some targets not being conserved between species-and, most importantly, the differences in regulation of gene expression. This prompts the use of human-derived models to study NDDS. The generation of human induced pluripotent stem cells (hIPSCs) added a new suitable alternative to overcome species limitations, allowing for the study of human neuronal development while maintaining the genetic background of the donor patient. Several hIPSC models of NDDs already proved their worth by mimicking several pathological phenotypes found in humans. In this review, we highlight the utility of hIPSCs to pave new paths for NDD research and development of new therapeutic tools, summarize the challenges and advances of hIPSC-culture and neuronal differentiation protocols and discuss the best way to take advantage of these models, illustrating this with examples of success for some NDDs.
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Czerminski JT, King OD, Lawrence JB. Large-scale organoid study suggests effects of trisomy 21 on early fetal neurodevelopment are more subtle than variability between isogenic lines and experiments. Front Neurosci 2023; 16:972201. [PMID: 36817096 PMCID: PMC9935940 DOI: 10.3389/fnins.2022.972201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 12/08/2022] [Indexed: 02/05/2023] Open
Abstract
This study examines cortical organoids generated from a panel of isogenic trisomic and disomic iPSC lines (subclones) as a model of early fetal brain development in Down syndrome (DS). An initial experiment comparing organoids from one trisomic and one disomic line showed many genome-wide transcriptomic differences and modest differences in cell-type proportions, suggesting there may be a neurodevelopmental phenotype that is due to trisomy of chr21. To better control for multiple sources of variation, we undertook a highly robust study of ∼1,200 organoids using an expanded panel of six all-isogenic lines, three disomic, and three trisomic. The power of this experimental design was indicated by strong detection of the ∼1.5-fold difference in chr21 genes. However, the numerous expression differences in non-chr21 genes seen in the smaller experiment fell away, and the differences in cell-type representation between lines did not correlate with trisomy 21. Results suggest that the initial smaller experiment picked up differences between small organoid samples and individual isogenic lines, which "averaged out" in the larger panel of isogenic lines. Our results indicate that even when organoid and batch variability are better controlled for, variation between isogenic cell lines (even subclones) may obscure, or be conflated with, subtle neurodevelopmental phenotypes that may be present in ∼2nd trimester DS brain development. Interestingly, despite this variability between organoid batches and lines, and the "fetal stage" of these organoids, an increase in secreted Aβ40 peptide levels-an Alzheimer-related cellular phenotype-was more strongly associated with trisomy 21 status than were neurodevelopmental shifts in cell-type composition.
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Affiliation(s)
- Jan T. Czerminski
- Medical Scientist Training Program, Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Oliver D. King
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Jeanne B. Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, United States,Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, United States,*Correspondence: Jeanne B. Lawrence,
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Ressler AK, Sampaio GL, Dugger SA, Sapir T, Krizay D, Boland MJ, Reiner O, Goldstein DB. Evidence of shared transcriptomic dysregulation of HNRNPU-related disorder between human organoids and embryonic mice. iScience 2023; 26:105797. [PMID: 36594023 PMCID: PMC9804147 DOI: 10.1016/j.isci.2022.105797] [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: 03/24/2022] [Revised: 08/16/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Generating effective therapies for neurodevelopmental disorders has remained elusive. An emerging drug discovery approach for neurodevelopmental disorders is to characterize transcriptome-wide dysregulation in an appropriate model system and screen therapeutics based on their capacity to restore functionally relevant expression patterns. We characterized transcriptomic dysregulation in a human model of HNRNPU-related disorder to explore the potential of such a paradigm. We identified widespread dysregulation in functionally relevant pathways and then compared dysregulation in a human model to transcriptomic differences in embryonic and perinatal mice to determine whether dysregulation in an in vitro human model is partially replicated in an in vivo model of HNRNPU-related disorder. Strikingly, we find enrichment of co-dysregulation between 45-day-old human organoids and embryonic, but not perinatal, mice from distinct models of HNRNPU-related disorder. Thus, hnRNPU deficient human organoids may only be suitable to model transcriptional dysregulation in certain cell types within a specific developmental time window.
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Affiliation(s)
- Andrew K. Ressler
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Gabriela L.A. Sampaio
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Sarah A. Dugger
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tamar Sapir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Daniel Krizay
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Michael J. Boland
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY 10032, USA
| | - Orly Reiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- Incumbent of the Berstein-Mason Professorial Chair of Neurochemistry, Head of M. Judith Ruth Institute of Preclinical Brain Research, Weizmann Institute of Science, Rehovot, Israel
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA
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Castillo Bautista CM, Sterneckert J. Progress and challenges in directing the differentiation of human iPSCs into spinal motor neurons. Front Cell Dev Biol 2023; 10:1089970. [PMID: 36684437 PMCID: PMC9849822 DOI: 10.3389/fcell.2022.1089970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/21/2022] [Indexed: 01/07/2023] Open
Abstract
Motor neuron (MN) diseases, including amyotrophic lateral sclerosis, progressive bulbar palsy, primary lateral sclerosis and spinal muscular atrophy, cause progressive paralysis and, in many cases, death. A better understanding of the molecular mechanisms of pathogenesis is urgently needed to identify more effective therapies. However, studying MNs has been extremely difficult because they are inaccessible in the spinal cord. Induced pluripotent stem cells (iPSCs) can generate a theoretically limitless number of MNs from a specific patient, making them powerful tools for studying MN diseases. However, to reach their potential, iPSCs need to be directed to efficiently differentiate into functional MNs. Here, we review the reported differentiation protocols for spinal MNs, including induction with small molecules, expression of lineage-specific transcription factors, 2-dimensional and 3-dimensional cultures, as well as the implementation of microfluidics devices and co-cultures with other cell types, including skeletal muscle. We will summarize the advantages and disadvantages of each strategy. In addition, we will provide insights into how to address some of the remaining challenges, including reproducibly obtaining mature and aged MNs.
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Affiliation(s)
| | - Jared Sterneckert
- Center for Regenerative Therapies TU Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany,Medical Faculty Carl Gustav Carus of TU Dresden, Dresden, Germany,*Correspondence: Jared Sterneckert,
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Dixon TA, Muotri AR. Advancing preclinical models of psychiatric disorders with human brain organoid cultures. Mol Psychiatry 2023; 28:83-95. [PMID: 35948659 PMCID: PMC9812789 DOI: 10.1038/s41380-022-01708-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 01/11/2023]
Abstract
Psychiatric disorders are often distinguished from neurological disorders in that the former do not have characteristic lesions or findings from cerebrospinal fluid, electroencephalograms (EEGs), or brain imaging, and furthermore do not have commonly recognized convergent mechanisms. Psychiatric disorders commonly involve clinical diagnosis of phenotypic behavioral disturbances of mood and psychosis, often with a poorly understood contribution of environmental factors. As such, psychiatric disease has been challenging to model preclinically for mechanistic understanding and pharmaceutical development. This review compares commonly used animal paradigms of preclinical testing with evolving techniques of induced pluripotent cell culture with a focus on emerging three-dimensional models. Advances in complexity of 3D cultures, recapitulating electrical activity in utero, and disease modeling of psychosis, mood, and environmentally induced disorders are reviewed. Insights from these rapidly expanding technologies are discussed as they pertain to the utility of human organoid and other models in finding novel research directions, validating pharmaceutical action, and recapitulating human disease.
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Affiliation(s)
- Thomas Anthony Dixon
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA 92093 USA
| | - Alysson R. Muotri
- grid.266100.30000 0001 2107 4242Department of Pediatrics and Department of Cellular & Molecular Medicine, University of California San Diego, School of Medicine, Center for Academic Research and Training in Anthropogeny (CARTA), Kavli Institute for Brain and Mind, Archealization Center (ArchC), La Jolla, CA 92037 USA
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47
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Neurodevelopmental disorders-high-resolution rethinking of disease modeling. Mol Psychiatry 2023; 28:34-43. [PMID: 36434058 PMCID: PMC9812768 DOI: 10.1038/s41380-022-01876-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/06/2022] [Accepted: 11/07/2022] [Indexed: 11/27/2022]
Abstract
Neurodevelopmental disorders arise due to various risk factors that can perturb different stages of brain development, and a combinatorial impact of these risk factors programs the phenotype in adulthood. While modeling the complete phenotype of a neurodevelopmental disorder is challenging, individual developmental perturbations can be successfully modeled in vivo in animals and in vitro in human cellular models. Nevertheless, our limited knowledge of human brain development restricts modeling strategies and has raised questions of how well a model corresponds to human in vivo brain development. Recent progress in high-resolution analysis of human tissue with single-cell and spatial omics techniques has enhanced our understanding of the complex events that govern the development of the human brain in health and disease. This new knowledge can be utilized to improve modeling of neurodevelopmental disorders and pave the way to more accurately portraying the relevant developmental perturbations in disease models.
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48
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Microglia-containing human brain organoids for the study of brain development and pathology. Mol Psychiatry 2023; 28:96-107. [PMID: 36474001 PMCID: PMC9734443 DOI: 10.1038/s41380-022-01892-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 12/12/2022]
Abstract
Microglia are resident immune cells in the central nervous system, playing critical roles in brain development and homeostasis. Increasing evidence has implicated microglia dysfunction in the pathogenesis of various brain disorders ranging from psychiatric disorders to neurodegenerative diseases. Using a human cell-based model to illuminate the functional mechanisms of microglia will promote pathological studies and drug development. The recently developed microglia-containing human brain organoids (MC-HBOs), in-vitro three-dimensional cell cultures that recapitulate key features of the human brain, have provided a new avenue to model brain development and pathology. However, MC-HBOs generated from different methods differ in the origin, proportion, and fidelity of microglia within the organoids, and may have produced inconsistent results. To help researchers to develop a robust and reproducible model that recapitulates in-vivo signatures of human microglia to study brain development and pathology, this review summarized the current methods used to generate MC-HBOs and provided opinions on the use of MC-HBOs for disease modeling and functional studies.
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Kumar A, Cai S, Allam M, Henderson S, Ozbeyler M, Saiontz L, Coskun AF. Single-Cell and Spatial Analysis of Emergent Organoid Platforms. Methods Mol Biol 2023; 2660:311-344. [PMID: 37191807 DOI: 10.1007/978-1-0716-3163-8_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Organoids have emerged as a promising advancement of the two-dimensional (2D) culture systems to improve studies in organogenesis, drug discovery, precision medicine, and regenerative medicine applications. Organoids can self-organize as three-dimensional (3D) tissues derived from stem cells and patient tissues to resemble organs. This chapter presents growth strategies, molecular screening methods, and emerging issues of the organoid platforms. Single-cell and spatial analysis resolve organoid heterogeneity to obtain information about the structural and molecular cellular states. Culture media diversity and varying lab-to-lab practices have resulted in organoid-to-organoid variability in morphology and cell compositions. An essential resource is an organoid atlas that can catalog protocols and standardize data analysis for different organoid types. Molecular profiling of individual cells in organoids and data organization of the organoid landscape will impact biomedical applications from basic science to translational use.
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Affiliation(s)
- Aditi Kumar
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Shuangyi Cai
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Mayar Allam
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Samuel Henderson
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Melissa Ozbeyler
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Lilly Saiontz
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Ahmet F Coskun
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA, USA.
- Parker H. Petit Institute for Bioengineering and Bioscience, , Georgia Institute of Technology, Atlanta, GA, USA.
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50
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Karmirian K, Holubiec M, Goto-Silva L, Fernandez Bessone I, Vitória G, Mello B, Alloatti M, Vanderborght B, Falzone TL, Rehen S. Modeling Alzheimer's Disease Using Human Brain Organoids. Methods Mol Biol 2023; 2561:135-158. [PMID: 36399268 DOI: 10.1007/978-1-0716-2655-9_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Alzheimer's disease (AD) is the primary cause of dementia, to date. The urgent need to understand the biological and biochemical processes related to this condition, as well as the demand for reliable in vitro models for drug screening, has led to the development of novel techniques, among which stem cell methods are of utmost relevance for AD research, particularly the development of human brain organoids. Brain organoids are three-dimensional cellular aggregates derived from induced pluripotent stem cells (iPSCs) that recreate different neural cell interactions and tissue characteristics in culture. Here, we describe the protocol for the generation of brain organoids derived from AD patients and for the analysis of AD-derived pathology. AD organoids can recapitulate beta-amyloid and tau pathological features, making them a promising model for studying the molecular mechanisms underlying disease and for in vitro drug testing.
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Affiliation(s)
- Karina Karmirian
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
- Institute of Biomedical Sciences, Rio de Janeiro, Brazil
| | - Mariana Holubiec
- Instituto de Biología Celular y Neurociencia IBCN (UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Livia Goto-Silva
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
| | - Ivan Fernandez Bessone
- Instituto de Biología Celular y Neurociencia IBCN (UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gabriela Vitória
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
| | - Beatriz Mello
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
| | - Matias Alloatti
- Instituto de Biología Celular y Neurociencia IBCN (UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Bart Vanderborght
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
| | - Tomás L Falzone
- Instituto de Biología Celular y Neurociencia IBCN (UBA-CONICET), Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Investigación en Biomedicina de Buenos Aires IBioBA (CONICET), Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Stevens Rehen
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil.
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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