1
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Bhattacharjee R, Jolly LA, Corbett MA, Wee IC, Rao SR, Gardner AE, Ritchie T, van Hugte EJH, Ciptasari U, Piltz S, Noll JE, Nazri N, van Eyk CL, White M, Fornarino D, Poulton C, Baynam G, Collins-Praino LE, Snel MF, Nadif Kasri N, Hemsley KM, Thomas PQ, Kumar R, Gecz J. Compromised transcription-mRNA export factor THOC2 causes R-loop accumulation, DNA damage and adverse neurodevelopment. Nat Commun 2024; 15:1210. [PMID: 38331934 PMCID: PMC10853216 DOI: 10.1038/s41467-024-45121-5] [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: 06/16/2023] [Accepted: 01/15/2024] [Indexed: 02/10/2024] Open
Abstract
We implicated the X-chromosome THOC2 gene, which encodes the largest subunit of the highly-conserved TREX (Transcription-Export) complex, in a clinically complex neurodevelopmental disorder with intellectual disability as the core phenotype. To study the molecular pathology of this essential eukaryotic gene, we generated a mouse model based on a hypomorphic Thoc2 exon 37-38 deletion variant of a patient with ID, speech delay, hypotonia, and microcephaly. The Thoc2 exon 37-38 deletion male (Thoc2Δ/Y) mice recapitulate the core phenotypes of THOC2 syndrome including smaller size and weight, and significant deficits in spatial learning, working memory and sensorimotor functions. The Thoc2Δ/Y mouse brain development is significantly impacted by compromised THOC2/TREX function resulting in R-loop accumulation, DNA damage and consequent cell death. Overall, we suggest that perturbed R-loop homeostasis, in stem cells and/or differentiated cells in mice and the patient, and DNA damage-associated functional alterations are at the root of THOC2 syndrome.
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Affiliation(s)
- Rudrarup Bhattacharjee
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Lachlan A Jolly
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Mark A Corbett
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Ing Chee Wee
- Discipline of Anatomy and Pathology, School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Sushma R Rao
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Proteomics, Metabolomics and MS-imaging Core Facility, South Australian Health and Medical Research Institute, and Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Alison E Gardner
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Tarin Ritchie
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Eline J H van Hugte
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, 6500, HB, the Netherlands
| | - Ummi Ciptasari
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, 6500, HB, the Netherlands
| | - Sandra Piltz
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Jacqueline E Noll
- School of Biomedicine, Faculty of Health and Medical Sciences, University of Adelaide and Precision Cancer Medicine Theme, Solid Tumour Program, South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Nazzmer Nazri
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health & Medical Research Institute, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Clare L van Eyk
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Melissa White
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Dani Fornarino
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Cathryn Poulton
- Undiagnosed Diseases Program, Genetic Services of WA, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia
| | - Gareth Baynam
- Undiagnosed Diseases Program, Genetic Services of WA, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Subiaco, WA, 6008, Australia
- Rare Care Centre, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Lyndsey E Collins-Praino
- Discipline of Anatomy and Pathology, School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Marten F Snel
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Proteomics, Metabolomics and MS-imaging Core Facility, South Australian Health and Medical Research Institute, and Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, 6500, HB, the Netherlands
| | - Kim M Hemsley
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Childhood Dementia Research Group, College of Medicine and Public Health, Flinders Health & Medical Research Institute, Flinders University, Bedford Park, Adelaide, SA, 5042, Australia
| | - Paul Q Thomas
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
- School of Biomedicine, The University of Adelaide, Adelaide, SA, 5005, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Raman Kumar
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jozef Gecz
- Adelaide Medical School, The University of Adelaide, Adelaide, SA, 5005, Australia.
- Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5005, Australia.
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2
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Ciceri G, Baggiolini A, Cho HS, Kshirsagar M, Benito-Kwiecinski S, Walsh RM, Aromolaran KA, Gonzalez-Hernandez AJ, Munguba H, Koo SY, Xu N, Sevilla KJ, Goldstein PA, Levitz J, Leslie CS, Koche RP, Studer L. An epigenetic barrier sets the timing of human neuronal maturation. Nature 2024; 626:881-890. [PMID: 38297124 PMCID: PMC10881400 DOI: 10.1038/s41586-023-06984-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 12/15/2023] [Indexed: 02/02/2024]
Abstract
The pace of human brain development is highly protracted compared with most other species1-7. The maturation of cortical neurons is particularly slow, taking months to years to develop adult functions3-5. Remarkably, such protracted timing is retained in cortical neurons derived from human pluripotent stem cells (hPSCs) during in vitro differentiation or upon transplantation into the mouse brain4,8,9. Those findings suggest the presence of a cell-intrinsic clock setting the pace of neuronal maturation, although the molecular nature of this clock remains unknown. Here we identify an epigenetic developmental programme that sets the timing of human neuronal maturation. First, we developed a hPSC-based approach to synchronize the birth of cortical neurons in vitro which enabled us to define an atlas of morphological, functional and molecular maturation. We observed a slow unfolding of maturation programmes, limited by the retention of specific epigenetic factors. Loss of function of several of those factors in cortical neurons enables precocious maturation. Transient inhibition of EZH2, EHMT1 and EHMT2 or DOT1L, at progenitor stage primes newly born neurons to rapidly acquire mature properties upon differentiation. Thus our findings reveal that the rate at which human neurons mature is set well before neurogenesis through the establishment of an epigenetic barrier in progenitor cells. Mechanistically, this barrier holds transcriptional maturation programmes in a poised state that is gradually released to ensure the prolonged timeline of human cortical neuron maturation.
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Affiliation(s)
- Gabriele Ciceri
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Arianna Baggiolini
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Institute of Oncology Research (IOR), Bellinzona Institutes of Science (BIOS+), Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Hyein S Cho
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meghana Kshirsagar
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Microsoft AI for Good Research, Redmond, WA, USA
| | - Silvia Benito-Kwiecinski
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryan M Walsh
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Hermany Munguba
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - So Yeon Koo
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Neuroscience PhD Program, New York, NY, USA
| | - Nan Xu
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaylin J Sevilla
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter A Goldstein
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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3
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Konishi M, Kishi K, Morita R, Yamada A, Onuma TA, Nishida H. Formation of the brain by stem cell divisions of large neuroblasts in Oikopleura dioica, a simple chordate. Dev Genes Evol 2023:10.1007/s00427-023-00704-y. [PMID: 37231211 DOI: 10.1007/s00427-023-00704-y] [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: 01/13/2023] [Accepted: 05/04/2023] [Indexed: 05/27/2023]
Abstract
Stem cell division contributes to the generation of various cell types during animal development, especially a diverse pool of neural cells in the nervous system. One example is reiterated unequal stem cell divisions, in which a large stem cell undergoes a series of oriented unequal divisions to produce a chain of small daughter cells that differentiate. We show that reiterated unequal stem cell divisions are involved in the formation of the brain in simple chordate appendicularians (larvaceans). Two large neuroblasts in the anterior and middle of the brain-forming region of hatched larvae were observed. They produced at least 30 neural cells out of 96 total brain cells before completion of brain formation at 10 hours after fertilization by reiterated unequal stem cell divisions. The daughter cells of the anterior neuroblast were postmitotic, and the number was at least 19. The neuroblast produced small daughter neural cells posteriorly every 20 min. The neural cells first moved toward the dorsal side, turned in the anterior direction, aligned in a single line according to their birth order, and showed collective movement to accumulate in the anterior part of the brain. The anterior neuroblast originated from the right-anterior blastomeres of the eight-cell embryos and the right a222 blastomere of the 64-cell embryo. The posterior neuroblast also showed reiterated unequal stem cell divisions, and generated at least 11 neural cells. Sequential unequal stem cell divisions without stem cell growth have been observed in protostomes, such as insects and annelids. The results provide the first examples of this kind of stem cell division during brain formation in non-vertebrate deuterostomes.
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Affiliation(s)
- Misako Konishi
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan
| | - Kanae Kishi
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan
| | - Ryo Morita
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan
| | - Atsuko Yamada
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan
| | - Takeshi A Onuma
- Faculty of Science, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka, 560-0043, Japan.
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4
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Lange J, Zhou H, McTague A. Cerebral Organoids and Antisense Oligonucleotide Therapeutics: Challenges and Opportunities. Front Mol Neurosci 2022; 15:941528. [PMID: 35836547 PMCID: PMC9274522 DOI: 10.3389/fnmol.2022.941528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/09/2022] [Indexed: 11/18/2022] Open
Abstract
The advent of stem cell-derived cerebral organoids has already advanced our understanding of disease mechanisms in neurological diseases. Despite this, many remain without effective treatments, resulting in significant personal and societal health burden. Antisense oligonucleotides (ASOs) are one of the most widely used approaches for targeting RNA and modifying gene expression, with significant advancements in clinical trials for epilepsy, neuromuscular disorders and other neurological conditions. ASOs have further potential to address the unmet need in other neurological diseases for novel therapies which directly target the causative genes, allowing precision treatment. Induced pluripotent stem cell (iPSC) derived cerebral organoids represent an ideal platform in which to evaluate novel ASO therapies. In patient-derived organoids, disease-causing mutations can be studied in the native genetic milieu, opening the door to test personalized ASO therapies and n-of-1 approaches. In addition, CRISPR-Cas9 can be used to generate isogenic iPSCs to assess the effects of ASOs, by either creating disease-specific mutations or correcting available disease iPSC lines. Currently, ASO therapies face a number of challenges to wider translation, including insufficient uptake by distinct and preferential cell types in central nervous system and inability to cross the blood brain barrier necessitating intrathecal administration. Cerebral organoids provide a practical model to address and improve these limitations. In this review we will address the current use of organoids to test ASO therapies, opportunities for future applications and challenges including those inherent to cerebral organoids, issues with organoid transfection and choice of appropriate read-outs.
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Affiliation(s)
- Jenny Lange
- Department for Developmental Neurosciences, Zayed Centre for Research Into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Haiyan Zhou
- Genetics and Genomic Medicine Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, United Kingdom
| | - Amy McTague
- Department for Developmental Neurosciences, Zayed Centre for Research Into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, United Kingdom
- *Correspondence: Amy McTague,
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5
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Pérez-Dones D, Ledesma-Terrón M, Míguez DG. Quantitative Approaches to Study Retinal Neurogenesis. Biomedicines 2021; 9:1222. [PMID: 34572408 PMCID: PMC8471905 DOI: 10.3390/biomedicines9091222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/07/2021] [Accepted: 09/11/2021] [Indexed: 11/16/2022] Open
Abstract
The study of the development of the vertebrate retina can be addressed from several perspectives: from a purely qualitative to a more quantitative approach that takes into account its spatio-temporal features, its three-dimensional structure and also the regulation and properties at the systems level. Here, we review the ongoing transition toward a full four-dimensional characterization of the developing vertebrate retina, focusing on the challenges at the experimental, image acquisition, image processing and quantification. Using the developing zebrafish retina, we illustrate how quantitative data extracted from these type of highly dense, three-dimensional tissues depend strongly on the image quality, image processing and algorithms used to segment and quantify. Therefore, we propose that the scientific community that focuses on developmental systems could strongly benefit from a more detailed disclosure of the tools and pipelines used to process and analyze images from biological samples.
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Affiliation(s)
- Diego Pérez-Dones
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Física de la Materia Condensada (IFIMAC), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Mario Ledesma-Terrón
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Física de la Materia Condensada (IFIMAC), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - David G Míguez
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Física de la Materia Condensada (IFIMAC), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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6
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Umemura M, Kaneko Y, Tanabe R, Takahashi Y. ATF5 deficiency causes abnormal cortical development. Sci Rep 2021; 11:7295. [PMID: 33790322 PMCID: PMC8012588 DOI: 10.1038/s41598-021-86442-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/15/2021] [Indexed: 11/29/2022] Open
Abstract
Activating transcription factor 5 (ATF5) is a member of the cAMP response element binding protein (CREB)/ATF family of basic leucine zipper transcription factors. We previously reported that ATF5-deficient (ATF5−/−) mice exhibited behavioural abnormalities, including abnormal social interactions, reduced behavioural flexibility, increased anxiety-like behaviours, and hyperactivity in novel environments. ATF5−/− mice may therefore be a useful animal model for psychiatric disorders. ATF5 is highly expressed in the ventricular zone and subventricular zone during cortical development, but its physiological role in higher-order brain structures remains unknown. To investigate the cause of abnormal behaviours exhibited by ATF5−/− mice, we analysed the embryonic cerebral cortex of ATF5−/− mice. The ATF5−/− embryonic cerebral cortex was slightly thinner and had reduced numbers of radial glial cells and neural progenitor cells, compared to a wild-type cerebral cortex. ATF5 deficiency also affected the basal processes of radial glial cells, which serve as a scaffold for radial migration during cortical development. Further, the radial migration of cortical upper layer neurons was impaired in ATF5−/− mice. These results suggest that ATF5 deficiency affects cortical development and radial migration, which may partly contribute to the observed abnormal behaviours.
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Affiliation(s)
- Mariko Umemura
- Laboratory of Environmental Molecular Physiology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan.
| | - Yasuyuki Kaneko
- Laboratory of Environmental Molecular Physiology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Ryoko Tanabe
- Laboratory of Environmental Molecular Physiology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
| | - Yuji Takahashi
- Laboratory of Environmental Molecular Physiology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, 192-0392, Japan
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7
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Sidhaye J, Knoblich JA. Brain organoids: an ensemble of bioassays to investigate human neurodevelopment and disease. Cell Death Differ 2021; 28:52-67. [PMID: 32483384 PMCID: PMC7853143 DOI: 10.1038/s41418-020-0566-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/07/2020] [Accepted: 05/15/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding etiology of human neurological and psychiatric diseases is challenging. Genomic changes, protracted development, and histological features unique to human brain development limit the disease aspects that can be investigated using model organisms. Hence, in order to study phenotypes associated with human brain development, function, and disease, it is necessary to use alternative experimental systems that are accessible, ethically justified, and replicate human context. Human pluripotent stem cell (hPSC)-derived brain organoids offer such a system, which recapitulates features of early human neurodevelopment in vitro, including the generation, proliferation, and differentiation of neural progenitors into neurons and glial cells and the complex interactions among the diverse, emergent cell types of the developing brain in three-dimensions (3-D). In recent years, numerous brain organoid protocols and related techniques have been developed to recapitulate aspects of embryonic and fetal brain development in a reproducible and predictable manner. Altogether, these different organoid technologies provide distinct bioassays to unravel novel, disease-associated phenotypes and mechanisms. In this review, we summarize how the diverse brain organoid methods can be utilized to enhance our understanding of brain disorders. FACTS: Brain organoids offer an in vitro approach to study aspects of human brain development and disease. Diverse brain organoid techniques offer bioassays to investigate new phenotypes associated with human brain disorders that are difficult to study in monolayer cultures. Brain organoids have been particularly useful to study phenomena and diseases associated with neural progenitor morphology, survival, proliferation, and differentiation. OPEN QUESTION: Future brain organoid research needs to aim at later stages of neurodevelopment, linked with neuronal activity and connections, to unravel further disease-associated phenotypes. Continued improvement of existing organoid protocols is required to generate standardized methods that recapitulate in vivo-like spatial diversity and complexity.
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Affiliation(s)
- Jaydeep Sidhaye
- Institute of Molecular Biotechnology of Austrian academy of sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Jürgen A Knoblich
- Institute of Molecular Biotechnology of Austrian academy of sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria.
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8
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Baldassari S, Musante I, Iacomino M, Zara F, Salpietro V, Scudieri P. Brain Organoids as Model Systems for Genetic Neurodevelopmental Disorders. Front Cell Dev Biol 2020; 8:590119. [PMID: 33154971 PMCID: PMC7586734 DOI: 10.3389/fcell.2020.590119] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/18/2020] [Indexed: 12/18/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are a group of disorders in which the development of the central nervous system (CNS) is disturbed, resulting in different neurological and neuropsychiatric features, such as impaired motor function, learning, language or non-verbal communication. Frequent comorbidities include epilepsy and movement disorders. Advances in DNA sequencing technologies revealed identifiable genetic causes in an increasingly large proportion of NDDs, highlighting the need of experimental approaches to investigate the defective genes and the molecular pathways implicated in abnormal brain development. However, targeted approaches to investigate specific molecular defects and their implications in human brain dysfunction are prevented by limited access to patient-derived brain tissues. In this context, advances of both stem cell technologies and genome editing strategies during the last decade led to the generation of three-dimensional (3D) in vitro-models of cerebral organoids, holding the potential to recapitulate precise stages of human brain development with the aim of personalized diagnostic and therapeutic approaches. Recent progresses allowed to generate 3D-structures of both neuronal and non-neuronal cell types and develop either whole-brain or region-specific cerebral organoids in order to investigate in vitro key brain developmental processes, such as neuronal cell morphogenesis, migration and connectivity. In this review, we summarized emerging methodological approaches in the field of brain organoid technologies and their application to dissect disease mechanisms underlying an array of pediatric brain developmental disorders, with a particular focus on autism spectrum disorders (ASDs) and epileptic encephalopathies.
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Affiliation(s)
- Simona Baldassari
- Medical Genetics Unit, IRCSS Giannina Gaslini Institute, Genoa, Italy
| | - Ilaria Musante
- Medical Genetics Unit, IRCSS Giannina Gaslini Institute, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy
| | - Michele Iacomino
- Medical Genetics Unit, IRCSS Giannina Gaslini Institute, Genoa, Italy
| | - Federico Zara
- Medical Genetics Unit, IRCSS Giannina Gaslini Institute, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy
| | - Vincenzo Salpietro
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy.,Pediatric Neurology and Muscular Diseases Unit, IRCSS Giannina Gaslini Institute, Genoa, Italy.,Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Paolo Scudieri
- Medical Genetics Unit, IRCSS Giannina Gaslini Institute, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy
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9
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Rayon T, Stamataki D, Perez-Carrasco R, Garcia-Perez L, Barrington C, Melchionda M, Exelby K, Lazaro J, Tybulewicz VLJ, Fisher EMC, Briscoe J. Species-specific pace of development is associated with differences in protein stability. Science 2020; 369:eaba7667. [PMID: 32943498 PMCID: PMC7116327 DOI: 10.1126/science.aba7667] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022]
Abstract
Although many molecular mechanisms controlling developmental processes are evolutionarily conserved, the speed at which the embryo develops can vary substantially between species. For example, the same genetic program, comprising sequential changes in transcriptional states, governs the differentiation of motor neurons in mouse and human, but the tempo at which it operates differs between species. Using in vitro directed differentiation of embryonic stem cells to motor neurons, we show that the program runs more than twice as fast in mouse as in human. This is not due to differences in signaling, nor the genomic sequence of genes or their regulatory elements. Instead, there is an approximately two-fold increase in protein stability and cell cycle duration in human cells compared with mouse cells. This can account for the slower pace of human development and suggests that differences in protein turnover play a role in interspecies differences in developmental tempo.
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Affiliation(s)
- Teresa Rayon
- The Francis Crick Institute, London NW1 1AT, UK.
| | | | - Ruben Perez-Carrasco
- The Francis Crick Institute, London NW1 1AT, UK
- Department of Mathematics, University College London, London WC1E 6BT, UK
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | | | | | | | | | | | - Victor L J Tybulewicz
- The Francis Crick Institute, London NW1 1AT, UK
- Department of Immunology and Inflammation, Imperial College, London W12 0NN, UK
| | - Elizabeth M C Fisher
- UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
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10
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Hashimoto Y, Greco TM, Cristea IM. Contribution of Mass Spectrometry-Based Proteomics to Discoveries in Developmental Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:143-154. [PMID: 31347046 DOI: 10.1007/978-3-030-15950-4_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Understanding multicellular organism development from a molecular perspective is no small feat, yet this level of comprehension affords clinician-scientists the ability to identify root causes and mechanisms of congenital diseases. Inarguably, the maturation of molecular biology tools has significantly contributed to the identification of genetic loci that underlie normal and aberrant developmental programs. In combination with cell biology approaches, these tools have begun to elucidate the spatiotemporal expression and function of developmentally-regulated proteins. The emergence of quantitative mass spectrometry (MS) for biological applications has accelerated the pace at which these proteins can be functionally characterized, driving the construction of an increasingly detailed systems biology picture of developmental processes. Here, we review the quantitative MS-based proteomic technologies that have contributed significantly to understanding the role of proteome regulation in developmental processes. We provide a brief overview of these methodologies, focusing on their ability to provide precise and accurate proteome measurements. We then highlight the use of discovery-based and targeted mass spectrometry approaches in model systems to study cellular differentiation states, tissue phenotypes, and spatiotemporal subcellular organization. We also discuss the current application and future perspectives of MS proteomics to study PTM coordination and the role of protein complexes during development.
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Affiliation(s)
- Yutaka Hashimoto
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Todd M Greco
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA.
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11
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Pathological priming causes developmental gene network heterochronicity in autistic subject-derived neurons. Nat Neurosci 2019; 22:243-255. [PMID: 30617258 PMCID: PMC6402576 DOI: 10.1038/s41593-018-0295-x] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 11/13/2018] [Indexed: 12/16/2022]
Abstract
Autism spectrum disorder (ASD) is thought to emerge during early cortical development. However, the exact developmental stages and associated molecular networks that prime disease propensity are elusive. To profile early neurodevelopmental alterations in ASD with macrocephaly, we monitored patient-derived induced pluripotent stem cells (iPSCs) throughout the recapitulation of cortical development. Our analysis revealed ASD-associated changes in the maturational sequence of early neuron development, involving temporal dysregulation of specific gene networks and morphological growth acceleration. The observed changes tracked back to a pathologically primed stage in neural stem cells (NSCs), reflected by altered chromatin accessibility. Concerted overrepresentation of network factors in control NSCs was sufficient to trigger ASD-like features, and circumventing the NSC stage by direct conversion of ASD iPSCs into induced neurons (iPSC-iNs) abolished ASD-associated phenotypes. Our findings identify heterochronic dynamics of a gene network that, while established earlier in development, contributes to subsequent neurodevelopmental aberrations in ASD.
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Vitali I, Fièvre S, Telley L, Oberst P, Bariselli S, Frangeul L, Baumann N, McMahon JJ, Klingler E, Bocchi R, Kiss JZ, Bellone C, Silver DL, Jabaudon D. Progenitor Hyperpolarization Regulates the Sequential Generation of Neuronal Subtypes in the Developing Neocortex. Cell 2018; 174:1264-1276.e15. [PMID: 30057116 DOI: 10.1016/j.cell.2018.06.036] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/20/2018] [Accepted: 06/18/2018] [Indexed: 12/29/2022]
Abstract
During corticogenesis, ventricular zone progenitors sequentially generate distinct subtypes of neurons, accounting for the diversity of neocortical cells and the circuits they form. While activity-dependent processes are critical for the differentiation and circuit assembly of postmitotic neurons, how bioelectrical processes affect nonexcitable cells, such as progenitors, remains largely unknown. Here, we reveal that, in the developing mouse neocortex, ventricular zone progenitors become more hyperpolarized as they generate successive subtypes of neurons. Experimental in vivo hyperpolarization shifted the transcriptional programs and division modes of these progenitors to a later developmental status, with precocious generation of intermediate progenitors and a forward shift in the laminar, molecular, morphological, and circuit features of their neuronal progeny. These effects occurred through inhibition of the Wnt-beta-catenin signaling pathway by hyperpolarization. Thus, during corticogenesis, bioelectric membrane properties are permissive for specific molecular pathways to coordinate the temporal progression of progenitor developmental programs and thus neocortical neuron diversity.
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Affiliation(s)
- Ilaria Vitali
- Department of Basic Neurosciences, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland
| | - Sabine Fièvre
- Department of Basic Neurosciences, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland
| | - Ludovic Telley
- Department of Basic Neurosciences, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland
| | - Polina Oberst
- Department of Basic Neurosciences, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland
| | - Sebastiano Bariselli
- Department of Basic Neurosciences, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland
| | - Laura Frangeul
- Department of Basic Neurosciences, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland
| | - Natalia Baumann
- Department of Basic Neurosciences, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland
| | - John J McMahon
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 224 Carl Building, Durham, NC 27710, USA
| | - Esther Klingler
- Department of Basic Neurosciences, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland
| | - Riccardo Bocchi
- Department of Basic Neurosciences, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland
| | - Jozsef Z Kiss
- Department of Basic Neurosciences, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland
| | - Camilla Bellone
- Department of Basic Neurosciences, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland
| | - Debra L Silver
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 224 Carl Building, Durham, NC 27710, USA
| | - Denis Jabaudon
- Department of Basic Neurosciences, University of Geneva, 1 Rue Michel Servet, 1211 Geneva, Switzerland; Department of Neurology, Geneva University Hospital, 4 Rue Gabrielle-Perret-Gentil, 1205 Geneva, Switzerland.
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13
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Abstract
Biology is dynamic. Timescales range from frenetic sub-second ion fluxes and enzymatic reactions to the glacial millions of years of evolutionary change. Falling somewhere in the middle of this range are the processes we usually study in development: cell division and differentiation, gene expression, cell-cell signalling, and morphogenesis. But what sets the tempo and manages the order of developmental events? Are the order and tempo different between species? How is the sequence of multiple events coordinated? Here, we discuss the importance of time for developing embryos, highlighting the necessity for global as well as cell-autonomous control. New reagents and tools in imaging and genomic engineering, combined with in vitro culture, are beginning to offer fresh perspectives and molecular insight into the origin and mechanisms of developmental time.
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Affiliation(s)
- Miki Ebisuya
- RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - James Briscoe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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14
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Nomura T, Yamashita W, Gotoh H, Ono K. Species-Specific Mechanisms of Neuron Subtype Specification Reveal Evolutionary Plasticity of Amniote Brain Development. Cell Rep 2018; 22:3142-3151. [DOI: 10.1016/j.celrep.2018.02.086] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 11/19/2017] [Accepted: 02/22/2018] [Indexed: 10/17/2022] Open
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15
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Kumamoto T, Hanashima C. Evolutionary conservation and conversion of Foxg1 function in brain development. Dev Growth Differ 2017; 59:258-269. [PMID: 28581027 DOI: 10.1111/dgd.12367] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 05/01/2017] [Accepted: 05/01/2017] [Indexed: 12/31/2022]
Abstract
Among the forkhead box protein family, Foxg1 is a unique transcription factor that plays pleiotropic and non-redundant roles in vertebrate brain development. The emergence of the telencephalon at the rostral end of the neural tube and its subsequent expansion that is mediated by Foxg1 was a key reason for the vertebrate brain to acquire higher order information processing, where Foxg1 is repetitively used in the sequential events of telencephalic development to control multi-steps of brain circuit formation ranging from cell cycle control to neuronal differentiation in a clade- and species-specific manner. The objective of this review is to discuss how the evolutionary changes in cis- and trans-regulatory network that is mediated by a single transcription factor has contributed to determining the fundamental vertebrate brain structure and its divergent roles in instructing species-specific neuronal circuitry and functional specialization.
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Affiliation(s)
- Takuma Kumamoto
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U968, CNRS UMR 7210, Institut de la Vision, 75012, Paris, France
| | - Carina Hanashima
- Faculty of Education and Integrated Arts and Sciences, Waseda University, Shinjuku-ku, Tokyo, 162-8480, Japan.,Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku-ku, Tokyo, 162-8480, Japan.,Laboratory for Neocortical Development, RIKEN Center for Developmental Biology, Kobe, 650-0047, Japan
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16
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Affiliation(s)
- Ayano Kawaguchi
- a Department of Anatomy and Cell Biology , Nagoya University Graduate School of Medicine , Nagoya , Aichi , Japan
| | - Fumio Matsuzaki
- b Laboratory for Cell Asymmetry, Center for Developmental Biology, RIKEN Kobe Institute , Kobe , Hyogo , Japan
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17
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Hanashima C, Nishimura T, Nakamura H, Stern CD. Time in Development. Preface. Dev Growth Differ 2016; 58:3-5. [PMID: 26818823 DOI: 10.1111/dgd.12265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Carina Hanashima
- Laboratory for Neocortical Development, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.,Department of Biology, Graduate School of Science, Kobe University, Rokkodai-cho, Nada-ku, 657-8501, Kobe, Japan
| | - Takashi Nishimura
- Laboratory for Growth Control Signaling, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.,Graduate School of Biological Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0101, Nara, Japan
| | - Harukazu Nakamura
- Frontier Research Institute for Interdisciplinary Sciences (FRIS), Tohoku University, Aoba-ku, 980-8578, Sendai, Japan
| | - Claudio D Stern
- Department of Cell and Developmental Biology, University College London, Gower Street (Anatomy building), London, WC1E 6BT, UK
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