1
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Cao T, Pang JC, Segal A, Chen Y, Aquino KM, Breakspear M, Fornito A. Mode-based morphometry: A multiscale approach to mapping human neuroanatomy. Hum Brain Mapp 2024; 45:e26640. [PMID: 38445545 PMCID: PMC10915742 DOI: 10.1002/hbm.26640] [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: 05/30/2023] [Revised: 02/06/2024] [Accepted: 02/18/2024] [Indexed: 03/07/2024] Open
Abstract
Voxel-based morphometry (VBM) and surface-based morphometry (SBM) are two widely used neuroimaging techniques for investigating brain anatomy. These techniques rely on statistical inferences at individual points (voxels or vertices), clusters of points, or a priori regions-of-interest. They are powerful tools for describing brain anatomy, but offer little insights into the generative processes that shape a particular set of findings. Moreover, they are restricted to a single spatial resolution scale, precluding the opportunity to distinguish anatomical variations that are expressed across multiple scales. Drawing on concepts from classical physics, here we develop an approach, called mode-based morphometry (MBM), that can describe any empirical map of anatomical variations in terms of the fundamental, resonant modes-eigenmodes-of brain anatomy, each tied to a specific spatial scale. Hence, MBM naturally yields a multiscale characterization of the empirical map, affording new opportunities for investigating the spatial frequency content of neuroanatomical variability. Using simulated and empirical data, we show that the validity and reliability of MBM are either comparable or superior to classical vertex-based SBM for capturing differences in cortical thickness maps between two experimental groups. Our approach thus offers a robust, accurate, and informative method for characterizing empirical maps of neuroanatomical variability that can be directly linked to a generative physical process.
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Affiliation(s)
- Trang Cao
- The Turner Institute for Brain and Mental HealthSchool of Psychological Sciences, and Monash Biomedical Imaging, Monash UniversityClaytonVictoriaAustralia
| | - James C. Pang
- The Turner Institute for Brain and Mental HealthSchool of Psychological Sciences, and Monash Biomedical Imaging, Monash UniversityClaytonVictoriaAustralia
| | - Ashlea Segal
- The Turner Institute for Brain and Mental HealthSchool of Psychological Sciences, and Monash Biomedical Imaging, Monash UniversityClaytonVictoriaAustralia
| | - Yu‐Chi Chen
- The Turner Institute for Brain and Mental HealthSchool of Psychological Sciences, and Monash Biomedical Imaging, Monash UniversityClaytonVictoriaAustralia
| | - Kevin M. Aquino
- School of PhysicsUniversity of SydneyCamperdownNew South WalesAustralia
| | - Michael Breakspear
- School of Psychological SciencesUniversity of NewcastleCallaghanNew South WalesAustralia
| | - Alex Fornito
- The Turner Institute for Brain and Mental HealthSchool of Psychological Sciences, and Monash Biomedical Imaging, Monash UniversityClaytonVictoriaAustralia
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2
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Arnatkeviciute A, Markello RD, Fulcher BD, Misic B, Fornito A. Toward Best Practices for Imaging Transcriptomics of the Human Brain. Biol Psychiatry 2023; 93:391-404. [PMID: 36725139 DOI: 10.1016/j.biopsych.2022.10.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/03/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
Abstract
Modern brainwide transcriptional atlases provide unprecedented opportunities for investigating the molecular correlates of brain organization, as quantified using noninvasive neuroimaging. However, integrating neuroimaging data with transcriptomic measures is not straightforward, and careful consideration is required to make valid inferences. In this article, we review recent work exploring how various methodological choices affect 3 main phases of imaging transcriptomic analyses, including 1) processing of transcriptional atlas data; 2) relating transcriptional measures to independently derived neuroimaging phenotypes; and 3) evaluating the functional implications of identified associations through gene enrichment analyses. Our aim is to facilitate the development of standardized and reproducible approaches for this rapidly growing field. We identify sources of methodological variability, key choices that can affect findings, and considerations for mitigating false positive and/or spurious results. Finally, we provide an overview of freely available open-source toolboxes implementing current best-practice procedures across all 3 analysis phases.
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Affiliation(s)
- Aurina Arnatkeviciute
- Turner Institute for Brain and Mental Health, School of Psychological Science, Monash University, Melbourne, Victoria, Australia.
| | - Ross D Markello
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Ben D Fulcher
- School of Physics, The University of Sydney, Sydney, New South Wales, Australia
| | - Bratislav Misic
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Alex Fornito
- Turner Institute for Brain and Mental Health, School of Psychological Science, Monash University, Melbourne, Victoria, Australia
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3
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Cao T, Pang JC, Segal A, Chen YC, Aquino KM, Breakspear M, Fornito A. Mode-based morphometry: A multiscale approach to mapping human neuroanatomy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.26.529328. [PMID: 36909539 PMCID: PMC10002616 DOI: 10.1101/2023.02.26.529328] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Voxel-based morphometry (VBM) and surface-based morphometry (SBM) are two widely used neuroimaging techniques for investigating brain anatomy. These techniques rely on statistical inferences at individual points (voxels or vertices), clusters of points, or a priori regions-of-interest. They are powerful tools for describing brain anatomy, but offer little insights into the generative processes that shape a particular set of findings. Moreover, they are restricted to a single spatial resolution scale, precluding the opportunity to distinguish anatomical variations that are expressed across multiple scales. Drawing on concepts from classical physics, here we develop an approach, called mode-based morphometry (MBM), that can describe any empirical map of anatomical variations in terms of the fundamental, resonant modes--eigenmodes--of brain anatomy, each tied to a specific spatial scale. Hence, MBM naturally yields a multiscale characterization of the empirical map, affording new opportunities for investigating the spatial frequency content of neuroanatomical variability. Using simulated and empirical data, we show that the validity and reliability of MBM are either comparable or superior to classical vertex-based SBM for capturing differences in cortical thickness maps between two experimental groups. Our approach thus offers a robust, accurate, and informative method for characterizing empirical maps of neuroanatomical variability that can be directly linked to a generative physical process.
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Affiliation(s)
- Trang Cao
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, 762-772 Blackburn Rd, Clayton VIC 3168, Australia
| | - James C Pang
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, 762-772 Blackburn Rd, Clayton VIC 3168, Australia
| | - Ashlea Segal
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, 762-772 Blackburn Rd, Clayton VIC 3168, Australia
| | - Yu-Chi Chen
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, 762-772 Blackburn Rd, Clayton VIC 3168, Australia
| | - Kevin M Aquino
- School of Physics, University of Sydney, Physics Rd, Camperdown NSW 2006, Australia
| | - Michael Breakspear
- School of Psychological Sciences, University of Newcastle, University Dr, Callaghan NSW 2308, Australia
| | - Alex Fornito
- The Turner Institute for Brain and Mental Health, School of Psychological Sciences, and Monash Biomedical Imaging, Monash University, 762-772 Blackburn Rd, Clayton VIC 3168, Australia
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4
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Nano PR, Bhaduri A. Evaluation of advances in cortical development using model systems. Dev Neurobiol 2022; 82:408-427. [PMID: 35644985 PMCID: PMC10924780 DOI: 10.1002/dneu.22879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/26/2022] [Accepted: 04/30/2022] [Indexed: 11/11/2022]
Abstract
Compared with that of even the closest primates, the human cortex displays a high degree of specialization and expansion that largely emerges developmentally. Although decades of research in the mouse and other model systems has revealed core tenets of cortical development that are well preserved across mammalian species, small deviations in transcription factor expression, novel cell types in primates and/or humans, and unique cortical architecture distinguish the human cortex. Importantly, many of the genes and signaling pathways thought to drive human-specific cortical expansion also leave the brain vulnerable to disease, as the misregulation of these factors is highly correlated with neurodevelopmental and neuropsychiatric disorders. However, creating a comprehensive understanding of human-specific cognition and disease remains challenging. Here, we review key stages of cortical development and highlight known or possible differences between model systems and the developing human brain. By identifying the developmental trajectories that may facilitate uniquely human traits, we highlight open questions in need of approaches to examine these processes in a human context and reveal translatable insights into human developmental disorders.
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Affiliation(s)
- Patricia R Nano
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
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5
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Qin J, Wang M, Zhao T, Xiao X, Li X, Yang J, Yi L, Goffinet AM, Qu Y, Zhou L. Early Forebrain Neurons and Scaffold Fibers in Human Embryos. Cereb Cortex 2021; 30:913-928. [PMID: 31298263 DOI: 10.1093/cercor/bhz136] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/21/2019] [Accepted: 05/31/2019] [Indexed: 12/24/2022] Open
Abstract
Neural progenitor proliferation, neuronal migration, areal organization, and pioneer axon wiring are critical events during early forebrain development, yet remain incompletely understood, especially in human. Here, we studied forebrain development in human embryos aged 5 to 8 postconceptional weeks (WPC5-8), stages that correspond to the neuroepithelium/early marginal zone (WPC5), telencephalic preplate (WPC6 & 7), and incipient cortical plate (WPC8). We show that early telencephalic neurons are formed at the neuroepithelial stage; the most precocious ones originate from local telencephalic neuroepithelium and possibly from the olfactory placode. At the preplate stage, forebrain organization is quite similar in human and mouse in terms of areal organization and of differentiation of Cajal-Retzius cells, pioneer neurons, and axons. Like in mice, axons from pioneer neurons in prethalamus, ventral telencephalon, and cortical preplate cross the diencephalon-telencephalon junction and the pallial-subpallial boundary, forming scaffolds that could guide thalamic and cortical axons at later stages. In accord with this model, at the early cortical plate stage, corticofugal axons run in ventral telencephalon in close contact with scaffold neurons, which express CELSR3 and FZD3, two molecules that regulates formation of similar scaffolds in mice.
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Affiliation(s)
- Jingwen Qin
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Ministry of Education CNS Regeneration Collaborative Joint Laboratory Jinan University Guangzhou, P R China
| | - Meizhi Wang
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Ministry of Education CNS Regeneration Collaborative Joint Laboratory Jinan University Guangzhou, P R China
| | - Tianyun Zhao
- Department of Anesthesiology, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou, P R China
| | - Xue Xiao
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Ministry of Education CNS Regeneration Collaborative Joint Laboratory Jinan University Guangzhou, P R China
| | - Xuejun Li
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Ministry of Education CNS Regeneration Collaborative Joint Laboratory Jinan University Guangzhou, P R China
| | - Jieping Yang
- Department of Obstetrics and Gynecology, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou, P R China
| | - Lisha Yi
- Department of Obstetrics and Gynecology, Guangzhou Women and Children's Medical Center Guangzhou Medical University Guangzhou, P R China
| | - Andre M Goffinet
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Ministry of Education CNS Regeneration Collaborative Joint Laboratory Jinan University Guangzhou, P R China
| | - Yibo Qu
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Ministry of Education CNS Regeneration Collaborative Joint Laboratory Jinan University Guangzhou, P R China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory Guangzhou, P R China
| | - Libing Zhou
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Ministry of Education CNS Regeneration Collaborative Joint Laboratory Jinan University Guangzhou, P R China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory Guangzhou, P R China.,Key Laboratory of Neuroscience, School of Basic Medical Sciences; Institute of Neuroscience, The Second Affiliated Hospital Guangzhou Medical University Guangzhou, P R China
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6
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Park BY, Bethlehem RAI, Paquola C, Larivière S, Rodríguez-Cruces R, Vos de Wael R, Bullmore ET, Bernhardt BC. An expanding manifold in transmodal regions characterizes adolescent reconfiguration of structural connectome organization. eLife 2021; 10:e64694. [PMID: 33787489 PMCID: PMC8087442 DOI: 10.7554/elife.64694] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 03/30/2021] [Indexed: 12/13/2022] Open
Abstract
Adolescence is a critical time for the continued maturation of brain networks. Here, we assessed structural connectome development in a large longitudinal sample ranging from childhood to young adulthood. By projecting high-dimensional connectomes into compact manifold spaces, we identified a marked expansion of structural connectomes, with strongest effects in transmodal regions during adolescence. Findings reflected increased within-module connectivity together with increased segregation, indicating increasing differentiation of higher-order association networks from the rest of the brain. Projection of subcortico-cortical connectivity patterns into these manifolds showed parallel alterations in pathways centered on the caudate and thalamus. Connectome findings were contextualized via spatial transcriptome association analysis, highlighting genes enriched in cortex, thalamus, and striatum. Statistical learning of cortical and subcortical manifold features at baseline and their maturational change predicted measures of intelligence at follow-up. Our findings demonstrate that connectome manifold learning can bridge the conceptual and empirical gaps between macroscale network reconfigurations, microscale processes, and cognitive outcomes in adolescent development.
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Affiliation(s)
- Bo-yong Park
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
- Department of Data Science, Inha UniversityIncheonRepublic of Korea
| | - Richard AI Bethlehem
- Autism Research Centre, Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
- Brain Mapping Unit, Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
| | - Casey Paquola
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
- Institute of Neuroscience and Medicine (INM-1), Forschungszentrum JülichJülichGermany
| | - Sara Larivière
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
| | - Raul Rodríguez-Cruces
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
| | - Reinder Vos de Wael
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
| | - Edward T Bullmore
- Brain Mapping Unit, Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
| | - Boris C Bernhardt
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
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7
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Nehme R, Zuccaro E, Ghosh SD, Li C, Sherwood JL, Pietilainen O, Barrett LE, Limone F, Worringer KA, Kommineni S, Zang Y, Cacchiarelli D, Meissner A, Adolfsson R, Haggarty S, Madison J, Muller M, Arlotta P, Fu Z, Feng G, Eggan K. Combining NGN2 Programming with Developmental Patterning Generates Human Excitatory Neurons with NMDAR-Mediated Synaptic Transmission. Cell Rep 2019; 23:2509-2523. [PMID: 29791859 PMCID: PMC6003669 DOI: 10.1016/j.celrep.2018.04.066] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/07/2018] [Accepted: 04/14/2018] [Indexed: 11/05/2022] Open
Abstract
Transcription factor programming of pluripotent stem cells (PSCs) has emerged as an approach to generate human neurons for disease modeling. However, programming schemes produce a variety of cell types, and those neurons that are made often retain an immature phenotype, which limits their utility in modeling neuronal processes, including synaptic transmission. We report that combining NGN2 programming with SMAD and WNT inhibition generates human patterned induced neurons (hpiNs). Single-cell analyses showed that hpiN cultures contained cells along a developmental continuum, ranging from poorly differentiated neuronal progenitors to well-differentiated, excitatory glutamatergic neurons. The most differentiated neurons could be identified using a CAMK2A::GFP reporter gene and exhibited greater functionality, including NMDAR-mediated synaptic transmission. We conclude that utilizing single-cell and reporter gene approaches for selecting successfully programmed cells for study will greatly enhance the utility of hpiNs and other programmed neuronal populations in the modeling of nervous system disorders.
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Affiliation(s)
- Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Emanuela Zuccaro
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sulagna Dia Ghosh
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chenchen Li
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - John L Sherwood
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Olli Pietilainen
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Lindy E Barrett
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Francesco Limone
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Sravya Kommineni
- Novartis Institutes for Biomedical Research, Novartis, Cambridge, MA 02139, USA
| | - Ying Zang
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Davide Cacchiarelli
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alex Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rolf Adolfsson
- Umea University, Faculty of Medicine, Department of Clinical Sciences, Psychiatry, 901 85 Umea, Sweden
| | - Stephen Haggarty
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jon Madison
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Matthias Muller
- Novartis Institutes for Biomedical Research, Novartis, 4056 Basel, Switzerland
| | - Paola Arlotta
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Zhanyan Fu
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Guoping Feng
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; McGovern Institute for Brain Research in the Department of Brain and Cognitive Sciences at MIT, Cambridge, MA 02139, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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8
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Li J, Wang GZ. Application of Computational Biology to Decode Brain Transcriptomes. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 17:367-380. [PMID: 31655213 PMCID: PMC6943780 DOI: 10.1016/j.gpb.2019.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 02/21/2019] [Accepted: 03/15/2019] [Indexed: 01/03/2023]
Abstract
The rapid development of high-throughput sequencing technologies has generated massive valuable brain transcriptome atlases, providing great opportunities for systematically investigating gene expression characteristics across various brain regions throughout a series of developmental stages. Recent studies have revealed that the transcriptional architecture is the key to interpreting the molecular mechanisms of brain complexity. However, our knowledge of brain transcriptional characteristics remains very limited. With the immense efforts to generate high-quality brain transcriptome atlases, new computational approaches to analyze these high-dimensional multivariate data are greatly needed. In this review, we summarize some public resources for brain transcriptome atlases and discuss the general computational pipelines that are commonly used in this field, which would aid in making new discoveries in brain development and disorders.
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Affiliation(s)
- Jie Li
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang-Zhong Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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9
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Ha TJ, Zhang PGY, Robert R, Yeung J, Swanson DJ, Mathelier A, Wasserman WW, Im S, Itoh M, Kawaji H, Lassmann T, Daub CO, Arner E, Carninci P, Hayashizaki Y, Forrest ARR, Goldowitz D. Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis. BMC Genomics 2019; 20:718. [PMID: 31533632 PMCID: PMC6751898 DOI: 10.1186/s12864-019-6063-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 08/26/2019] [Indexed: 12/11/2022] Open
Abstract
Background The work of the FANTOM5 Consortium has brought forth a new level of understanding of the regulation of gene transcription and the cellular processes involved in creating diversity of cell types. In this study, we extended the analysis of the FANTOM5 Cap Analysis of Gene Expression (CAGE) transcriptome data to focus on understanding the genetic regulators involved in mouse cerebellar development. Results We used the HeliScopeCAGE library sequencing on cerebellar samples over 8 embryonic and 4 early postnatal times. This study showcases temporal expression pattern changes during cerebellar development. Through a bioinformatics analysis that focused on transcription factors, their promoters and binding sites, we identified genes that appear as strong candidates for involvement in cerebellar development. We selected several candidate transcriptional regulators for validation experiments including qRT-PCR and shRNA transcript knockdown. We observed marked and reproducible developmental defects in Atf4, Rfx3, and Scrt2 knockdown embryos, which support the role of these genes in cerebellar development. Conclusions The successful identification of these novel gene regulators in cerebellar development demonstrates that the FANTOM5 cerebellum time series is a high-quality transcriptome database for functional investigation of gene regulatory networks in cerebellar development. Electronic supplementary material The online version of this article (10.1186/s12864-019-6063-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas J Ha
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Division of Neurology, Department of Pediatrics, University of British Columbia and BC Children's Hospital, Vancouver, BC, Canada
| | - Peter G Y Zhang
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Remi Robert
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Joanna Yeung
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Douglas J Swanson
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Anthony Mathelier
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318, Oslo, Norway.,Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, 0372, Oslo, Norway
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Sujin Im
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Masayoshi Itoh
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Hideya Kawaji
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Timo Lassmann
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan.,Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, Subiaco, Western Australia, 6008, Australia
| | - Carsten O Daub
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Erik Arner
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | | | - Piero Carninci
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Alistair R R Forrest
- RIKEN Omics Science Center (OSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.,RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Daniel Goldowitz
- Centre for Molecular Medicine and Therapeutics at the BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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10
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Alzu'bi A, Clowry GJ. Expression of ventral telencephalon transcription factors ASCL1 and DLX2 in the early fetal human cerebral cortex. J Anat 2019; 235:555-568. [PMID: 30861584 PMCID: PMC6704271 DOI: 10.1111/joa.12971] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2019] [Indexed: 01/21/2023] Open
Abstract
In rodent ventral telencephalon, diffusible morphogens induce expression of the proneural transcription factor ASCL1, which in turn induces expression of the transcription factor DLX2 that controls differentiation of cortical interneuron precursors and their tangential migration to the cerebral cortex. RNAseq analysis of human fetal samples of dorsal telencephalon revealed consistently high cortical expression of ASCL1 and increasing expression of DLX2 between 7.5 and 17 post-conceptional weeks (PCW). We explored whether cortical expression of these genes represented a population of intracortically derived interneuron precursors. Immunohistochemistry revealed an ASCL1+ /DLX2+ population of progenitor cells in the human ganglionic eminences between 6.5 and 12 PCW, but in the cortex there also existed a population of ASCL1+ /DLX2- progenitors in the subventricular zone (SVZ) that largely co-expressed cortical markers PAX6 or TBR2, although a few ASCL1+ /PAX6- progenitors were observed in the ventricular zone (VZ) and ASCL1+ cells expressing the interneuron marker GAD67 were present in the SVZ. Although rare in the VZ, DLX2+ cells progressively increased in number between 8 and 12 PCW across the cortical wall and the majority co-expressed LHX6 and originated either in the MGE, migrating to the lateral cortex, or from the septum, populating the medial wall. A minority co-expressed COUP-TFII, which identifies cells from the caudal ganglionic eminence (CGE). By 19 PCW, a significant increase in expression of DLX2 and ASCL1 was observed in the cortical VZ with a small proportion expressing both proteins. The DLX2+ cells did not co-express a cell division marker, so were not progenitors. The majority of DLX2+ cells throughout the cortical plate expressed COUP-TFII rather than LHX6+ . As the VZ declined as a proliferative zone it appeared to be re-defined as a migration pathway for COUP-TFII+ /DLX2+ interneurons from CGE to cortex. Therefore, in developing human cortex, ASCL1 expression predominantly marks a population of intermediate progenitors giving rise to glutamatergic neurons. DLX2 expression predominantly defines post-mitotic interneuron precursors.
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Affiliation(s)
- Ayman Alzu'bi
- The institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- The Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUK
- The Department of Basic Medical SciencesYarmouk UniversityIrbidJordan
| | - Gavin J. Clowry
- The institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
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11
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Molnár Z, Clowry GJ, Šestan N, Alzu'bi A, Bakken T, Hevner RF, Hüppi PS, Kostović I, Rakic P, Anton ES, Edwards D, Garcez P, Hoerder‐Suabedissen A, Kriegstein A. New insights into the development of the human cerebral cortex. J Anat 2019; 235:432-451. [PMID: 31373394 PMCID: PMC6704245 DOI: 10.1111/joa.13055] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2019] [Indexed: 12/12/2022] Open
Abstract
The cerebral cortex constitutes more than half the volume of the human brain and is presumed to be responsible for the neuronal computations underlying complex phenomena, such as perception, thought, language, attention, episodic memory and voluntary movement. Rodent models are extremely valuable for the investigation of brain development, but cannot provide insight into aspects that are unique or highly derived in humans. Many human psychiatric and neurological conditions have developmental origins but cannot be studied adequately in animal models. The human cerebral cortex has some unique genetic, molecular, cellular and anatomical features, which need to be further explored. The Anatomical Society devoted its summer meeting to the topic of Human Brain Development in June 2018 to tackle these important issues. The meeting was organized by Gavin Clowry (Newcastle University) and Zoltán Molnár (University of Oxford), and held at St John's College, Oxford. The participants provided a broad overview of the structure of the human brain in the context of scaling relationships across the brains of mammals, conserved principles and recent changes in the human lineage. Speakers considered how neuronal progenitors diversified in human to generate an increasing variety of cortical neurons. The formation of the earliest cortical circuits of the earliest generated neurons in the subplate was discussed together with their involvement in neurodevelopmental pathologies. Gene expression networks and susceptibility genes associated to neurodevelopmental diseases were discussed and compared with the networks that can be identified in organoids developed from induced pluripotent stem cells that recapitulate some aspects of in vivo development. New views were discussed on the specification of glutamatergic pyramidal and γ-aminobutyric acid (GABA)ergic interneurons. With the advancement of various in vivo imaging methods, the histopathological observations can be now linked to in vivo normal conditions and to various diseases. Our review gives a general evaluation of the exciting new developments in these areas. The human cortex has a much enlarged association cortex with greater interconnectivity of cortical areas with each other and with an expanded thalamus. The human cortex has relative enlargement of the upper layers, enhanced diversity and function of inhibitory interneurons and a highly expanded transient subplate layer during development. Here we highlight recent studies that address how these differences emerge during development focusing on diverse facets of our evolution.
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Affiliation(s)
- Zoltán Molnár
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Gavin J. Clowry
- Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Nenad Šestan
- Department of Neuroscience, Yale University School of MedicineNew HavenCTUSA
| | - Ayman Alzu'bi
- Department of Basic Medical SciencesFaculty of MedicineYarmouk UniversityIrbidJordan
| | | | | | - Petra S. Hüppi
- Dept. de l'enfant et de l'adolescentHôpitaux Universitaires de GenèveGenèveSwitzerland
| | - Ivica Kostović
- Croatian Institute for Brain ResearchSchool of MedicineUniversity of ZagrebZagrebCroatia
| | - Pasko Rakic
- Department of Neuroscience, Yale University School of MedicineNew HavenCTUSA
| | - E. S. Anton
- UNC Neuroscience CenterDepartment of Cell and Molecular PhysiologyThe University of North Carolina School of MedicineChapel HillNCUSA
| | - David Edwards
- Centre for the Developing BrainBiomedical Engineering and Imaging Sciences,King's College LondonLondonUK
| | - Patricia Garcez
- Federal University of Rio de Janeiro, UFRJInstitute of Biomedical SciencesRio de JaneiroBrazil
| | | | - Arnold Kriegstein
- Department of NeurologyUniversity of California, San Francisco (UCSF)San FranciscoCAUSA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell ResearchUCSFSan FranciscoCAUSA
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12
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Rostrocaudal Areal Patterning of Human PSC-Derived Cortical Neurons by FGF8 Signaling. eNeuro 2018; 5:eN-NWR-0368-17. [PMID: 29707616 PMCID: PMC5917473 DOI: 10.1523/eneuro.0368-17.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 04/08/2018] [Accepted: 04/09/2018] [Indexed: 12/11/2022] Open
Abstract
The cerebral cortex is subdivided into distinct areas that have particular functions. The rostrocaudal (R-C) gradient of fibroblast growth factor 8 (FGF8) signaling defines this areal identity during neural development. In this study, we recapitulated cortical R-C patterning in human pluripotent stem cell (PSC) cultures. Modulation of FGF8 signaling appropriately regulated the R-C markers, and the patterns of global gene expression resembled those of the corresponding areas of human fetal brains. Furthermore, we demonstrated the utility of this culture system in modeling the area-specific forebrain phenotypes [presumptive upper motor neuron (UMN) phenotypes] of amyotrophic lateral sclerosis (ALS). We anticipate that our culture system will contribute to studies of human neurodevelopment and neurological disease modeling.
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13
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The logistics of afferent cortical specification in mice and men. Semin Cell Dev Biol 2018; 76:112-119. [DOI: 10.1016/j.semcdb.2017.08.047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 11/17/2022]
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14
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Fuertes M, Tkatch J, Rosmino J, Nieto L, Guitelman MA, Arzt E. New Insights in Cushing Disease Treatment With Focus on a Derivative of Vitamin A. Front Endocrinol (Lausanne) 2018; 9:262. [PMID: 29881371 PMCID: PMC5976796 DOI: 10.3389/fendo.2018.00262] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/07/2018] [Indexed: 12/19/2022] Open
Abstract
Cushing's disease (CD) is an endocrine disorder originated by a corticotroph tumor. It is linked with high mortality and morbidity due to chronic hypercortisolism. Treatment goals are to control cortisol excess and achieve long-term remission, therefore, reducing both complications and patient's mortality. First-line of treatment for CD is pituitary's surgery. However, 30% of patients who undergo surgery experience recurrence in long-term follow-up. Persistent or recurrent CD demands second-line treatments, such as pituitary radiotherapy, adrenal surgery, and/or pharmacological therapy. The latter plays a key role in cortisol excess control. Its targets are inhibition of adrenocorticotropic hormone (ACTH) production, inhibition of adrenal steroidogenesis, or antagonism of cortisol action at its peripheral receptor. Retinoic acid (RA) is a metabolic product of vitamin A (retinol) and has been studied for its antiproliferative effects on corticotroph tumor cells. It has been shown that this drug regulates the expression of pro-opiomelanocortin (POMC), ACTH secretion, and tumor growth in corticotroph tumor mouse cell lines and in the nude mice experimental model, via inhibition of POMC transcription. It has been shown to result in tumor reduction, normalization of cortisol levels and clinical improvement in dogs treated with RA for 6 months. The orphan nuclear receptor COUP-TFI is expressed in normal corticotroph cells, but not in corticotroph tumoral cells, and inhibits RA pathways. A first clinical human study demonstrated clinical and biochemical effectiveness in 5/7 patients treated with RA for a period of up to 12 months. In a recent second clinical trial, 25% of 16 patients achieved eucortisolemia, and all achieved a cortisol reduction after 6- to 12-month treatment. The goal of this review is to discuss in the context of the available and future pharmacological treatments of CD, RA mechanisms of action on corticotroph tumor cells, and future perspectives, focusing on potential clinical implementation.
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Affiliation(s)
- Mariana Fuertes
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) – CONICET – Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Julieta Tkatch
- División Endocrinología, Hospital General de Agudos “Carlos G. Durand”, Buenos Aires, Argentina
| | - Josefina Rosmino
- División Endocrinología, Hospital General de Agudos “Carlos G. Durand”, Buenos Aires, Argentina
| | - Leandro Nieto
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) – CONICET – Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | | | - Eduardo Arzt
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) – CONICET – Partner Institute of the Max Planck Society, Buenos Aires, Argentina
- Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- *Correspondence: Eduardo Arzt,
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15
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Floruta CM, Du R, Kang H, Stein JL, Weick JP. Default Patterning Produces Pan-cortical Glutamatergic and CGE/LGE-like GABAergic Neurons from Human Pluripotent Stem Cells. Stem Cell Reports 2017; 9:1463-1476. [PMID: 29107596 PMCID: PMC5831028 DOI: 10.1016/j.stemcr.2017.09.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 10/25/2022] Open
Abstract
Default differentiation of human pluripotent stem cells has been promoted as a model of cortical development. In this study, a developmental transcriptome analysis of default-differentiated hPSNs revealed a gene expression program resembling in vivo CGE/LGE subpallial domains and GABAergic signaling. A combination of bioinformatic, functional, and immunocytochemical analysis further revealed that hPSNs consist of both cortical glutamatergic and CGE-like GABAergic neurons. This study provides a comprehensive characterization of the heterogeneous group of neurons produced by default differentiation and insight into future directed differentiation strategies.
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Affiliation(s)
- Crina M. Floruta
- Department of Neurosciences, University of New Mexico-Health Science Center, Albuquerque, NM 87131, USA
| | - Ruofei Du
- UNM Comprehensive Cancer Center, University of New Mexico-Health Science Center, Albuquerque, NM 87131, USA
| | - Huining Kang
- UNM Comprehensive Cancer Center, University of New Mexico-Health Science Center, Albuquerque, NM 87131, USA,Department of Internal Medicine, University of New Mexico-Health Science Center, Albuquerque, NM 87131, USA
| | - Jason L. Stein
- Department of Genetics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA,UNC Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jason P. Weick
- Department of Neurosciences, University of New Mexico-Health Science Center, Albuquerque, NM 87131, USA,Corresponding author
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16
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Alzu'bi A, Lindsay SJ, Harkin LF, McIntyre J, Lisgo SN, Clowry GJ. The Transcription Factors COUP-TFI and COUP-TFII have Distinct Roles in Arealisation and GABAergic Interneuron Specification in the Early Human Fetal Telencephalon. Cereb Cortex 2017; 27:4971-4987. [PMID: 28922831 PMCID: PMC5903418 DOI: 10.1093/cercor/bhx185] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 06/12/2017] [Accepted: 07/03/2017] [Indexed: 12/13/2022] Open
Abstract
In human telencephalon at 8-12 postconceptional weeks, ribonucleic acid quantitative sequencing and immunohistochemistry revealed cortical chicken ovalbumin upstream promotor-transcription factor 1 (COUP-TFI) expression in a high ventro-posterior to low anterior gradient except for raised immunoreactivity in the anterior ventral pallium. Unlike in mouse, COUP-TFI and SP8 were extensively co-expressed in dorsal sensory neocortex and dorsal hippocampus whereas COUPTFI/COUPTFII co-expression defined ventral temporal cortex and ventral hippocampus. In the ganglionic eminences (GEs) COUP-TFI immunoreactivity demarcated the proliferative zones of caudal GE (CGE), dorsal medial GE (MGE), MGE/lateral GE (LGE) boundary, and ventral LGE whereas COUP-TFII was limited to ventral CGE and the MGE/LGE boundary. Co-labeling with gamma amino butyric acidergic interneuron markers revealed that COUP-TFI was expressed in subpopulations of either MGE-derived (SOX6+) or CGE-derived (calretinin+/SP8+) interneurons. COUP-TFII was mainly confined to CGE-derived interneurons. Twice as many GAD67+ cortical cells co-labeled for COUP-TFI than for COUP-TFII. A fifth of COUP-TFI cells also co-expressed COUP-TFII, and cells expressing either transcription factor followed posterior or anterio-lateral pathways into the cortex, therefore, a segregation of migration pathways according to COUP-TF expression as proposed in mouse was not observed. In cultures differentiated from isolated human cortical progenitors, many cells expressed either COUP-TF and 30% also co-expressed GABA, however no cells expressed NKX2.1. This suggests interneurons could be generated intracortically from progenitors expressing either COUP-TF.
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Affiliation(s)
- Ayman Alzu'bi
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Susan J Lindsay
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Lauren F Harkin
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
- Present address: School of Healthcare Science, Manchester Metropolitan University, UK
| | - Jack McIntyre
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Steven N Lisgo
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Gavin J Clowry
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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17
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Charting the protomap of the human telencephalon. Semin Cell Dev Biol 2017; 76:3-14. [PMID: 28834762 DOI: 10.1016/j.semcdb.2017.08.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/15/2017] [Indexed: 12/16/2022]
Abstract
The cerebral cortex is divided stereotypically into a number of functionally distinct areas. According to the protomap hypothesis formulated by Rakic neural progenitors in the ventricular zone form a mosaic of proliferative units that provide a primordial species-specific cortical map. Positional information of newborn neurons is maintained during their migration to the overlying cortical plate. Much evidence has been found to support this hypothesis from studies of primary cortical areas in mouse models in particular. Differential expansion of cortical areas and the introduction of new functional modules during evolution might be the result of changes in the progenitor cells. The human cerebral cortex shows a wide divergence from the mouse containing a much higher proportion of association cortex and a more complicated regionalised repertoire of neuron sub-types. To what extent does the protomap hypothesis hold true for the primate brain? This review summarises a growing number of studies exploring arealised gene expression in the early developing human telencephalon. The evidence so far is that the human and mouse brain do share fundamental mechanisms of areal specification, however there are subtle differences which could lead us to a better understanding of cortical evolution and the origins of neurodevelopmental diseases.
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18
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Harkin LF, Lindsay SJ, Xu Y, Alzu'bi A, Ferrara A, Gullon EA, James OG, Clowry GJ. Neurexins 1-3 Each Have a Distinct Pattern of Expression in the Early Developing Human Cerebral Cortex. Cereb Cortex 2017; 27:216-232. [PMID: 28013231 PMCID: PMC5654756 DOI: 10.1093/cercor/bhw394] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/16/2016] [Accepted: 12/02/2016] [Indexed: 12/17/2022] Open
Abstract
Neurexins (NRXNs) are presynaptic terminal proteins and candidate neurodevelopmental disorder susceptibility genes; mutations presumably upset synaptic stabilization and function. However, analysis of human cortical tissue samples by RNAseq and quantitative real-time PCR at 8-12 postconceptional weeks, prior to extensive synapse formation, showed expression of all three NRXNs as well as several potential binding partners. However, the levels of expression were not identical; NRXN1 increased with age and NRXN2 levels were consistently higher than for NRXN3. Immunohistochemistry for each NRXN also revealed different expression patterns at this stage of development. NRXN1 and NRXN3 immunoreactivity was generally strongest in the cortical plate and increased in the ventricular zone with age, but was weak in the synaptogenic presubplate (pSP) and marginal zone. On the other hand, NRXN2 colocalized with synaptophysin in neurites of the pSP, but especially with GAP43 and CASK in growing axons of the intermediate zone. Alternative splicing modifies the role of NRXNs and we found evidence by RNAseq for exon skipping at splice site 4 and concomitant expression of KHDBRS proteins which control this splicing. NRXN2 may play a part in early cortical synaptogenesis, but NRXNs could have diverse roles in development including axon guidance, and intercellular communication between proliferating cells and/or migrating neurons.
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Affiliation(s)
- Lauren F Harkin
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
- Present address: School of Healthcare Science, Manchester Metropolitan University, Manchester, M1 5GD, UK
| | - Susan J Lindsay
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
| | - Yaobo Xu
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
- Present address: Wellcome Trust, Sanger Institute, Cambridge, CB10 1SA, UK
| | - Ayman Alzu'bi
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
| | - Alexandra Ferrara
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
| | - Emily A Gullon
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
| | - Owen G James
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne NE1 3BZ, UK
- Present address: MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Gavin J Clowry
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
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19
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Alzu'bi A, Lindsay S, Kerwin J, Looi SJ, Khalil F, Clowry GJ. Distinct cortical and sub-cortical neurogenic domains for GABAergic interneuron precursor transcription factors NKX2.1, OLIG2 and COUP-TFII in early fetal human telencephalon. Brain Struct Funct 2016; 222:2309-2328. [PMID: 27905023 PMCID: PMC5504260 DOI: 10.1007/s00429-016-1343-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/18/2016] [Indexed: 01/03/2023]
Abstract
The extent of similarities and differences between cortical GABAergic interneuron generation in rodent and primate telencephalon remains contentious. We examined expression of three interneuron precursor transcription factors, alongside other markers, using immunohistochemistry on 8–12 post-conceptional weeks (PCW) human telencephalon sections. NKX2.1, OLIG2, and COUP-TFII expression occupied distinct (although overlapping) neurogenic domains which extended into the cortex and revealed three CGE compartments: lateral, medial, and ventral. NKX2.1 expression was very largely confined to the MGE, medial CGE, and ventral septum confirming that, at this developmental stage, interneuron generation from NKX2.1+ precursors closely resembles the process observed in rodents. OLIG2 immunoreactivity was observed in GABAergic cells of the proliferative zones of the MGE and septum, but not necessarily co-expressed with NKX2.1, and OLIG2 expression was also extensively seen in the LGE, CGE, and cortex. At 8 PCW, OLIG2+ cells were only present in the medial and anterior cortical wall suggesting a migratory pathway for interneuron precursors via the septum into the medial cortex. By 12 PCW, OLIG2+ cells were present throughout the cortex and many were actively dividing but without co-expressing cortical progenitor markers. Dividing COUP-TFII+ progenitor cells were localized to ventral CGE as previously described but were also numerous in adjacent ventral cortex; in both the cases, COUP-TFII was co-expressed with PAX6 in proliferative zones and TBR1 or calretinin in post-mitotic cortical neurons. Thus COUP-TFII+ progenitors gave rise to pyramidal cells, but also interneurons which not only migrated posteriorly into the cortex from ventral CGE but also anteriorly via the LGE.
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Affiliation(s)
- Ayman Alzu'bi
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK.,Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne, NE1 3BZ, UK
| | - Susan Lindsay
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne, NE1 3BZ, UK.
| | - Janet Kerwin
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne, NE1 3BZ, UK
| | - Shi Jie Looi
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK.,Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne, NE1 3BZ, UK
| | - Fareha Khalil
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK.,Institute of Genetic Medicine, Newcastle University, International Centre for Life, Parkway Drive, Newcastle upon Tyne, NE1 3BZ, UK
| | - Gavin J Clowry
- Institute of Neuroscience, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK.
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20
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Lindsay SJ, Xu Y, Lisgo SN, Harkin LF, Copp AJ, Gerrelli D, Clowry GJ, Talbot A, Keogh MJ, Coxhead J, Santibanez-Koref M, Chinnery PF. HDBR Expression: A Unique Resource for Global and Individual Gene Expression Studies during Early Human Brain Development. Front Neuroanat 2016; 10:86. [PMID: 27833533 PMCID: PMC5080337 DOI: 10.3389/fnana.2016.00086] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/12/2016] [Indexed: 12/21/2022] Open
Affiliation(s)
- Susan J Lindsay
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | - Yaobo Xu
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | - Steven N Lisgo
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | - Lauren F Harkin
- Institute of Genetic Medicine, Newcastle UniversityNewcastle upon Tyne, UK; Institute of Neuroscience, Newcastle UniversityNewcastle upon Tyne, UK
| | - Andrew J Copp
- Institute of Child Health, University College London London, UK
| | - Dianne Gerrelli
- Institute of Child Health, University College London London, UK
| | - Gavin J Clowry
- Institute of Neuroscience, Newcastle University Newcastle upon Tyne, UK
| | - Aysha Talbot
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | - Michael J Keogh
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | - Jonathan Coxhead
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
| | | | - Patrick F Chinnery
- Institute of Genetic Medicine, Newcastle University Newcastle upon Tyne, UK
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21
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The marmoset: An emerging model to unravel the evolution and development of the primate neocortex. Dev Neurobiol 2016; 77:263-272. [DOI: 10.1002/dneu.22425] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 07/25/2016] [Accepted: 07/29/2016] [Indexed: 12/13/2022]
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22
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Silbereis JC, Pochareddy S, Zhu Y, Li M, Sestan N. The Cellular and Molecular Landscapes of the Developing Human Central Nervous System. Neuron 2016; 89:248-68. [PMID: 26796689 DOI: 10.1016/j.neuron.2015.12.008] [Citation(s) in RCA: 440] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The human CNS follows a pattern of development typical of all mammals, but certain neurodevelopmental features are highly derived. Building the human CNS requires the precise orchestration and coordination of myriad molecular and cellular processes across a staggering array of cell types and over a long period of time. Dysregulation of these processes affects the structure and function of the CNS and can lead to neurological or psychiatric disorders. Recent technological advances and increased focus on human neurodevelopment have enabled a more comprehensive characterization of the human CNS and its development in both health and disease. The aim of this review is to highlight recent advancements in our understanding of the molecular and cellular landscapes of the developing human CNS, with focus on the cerebral neocortex, and the insights these findings provide into human neural evolution, function, and dysfunction.
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Affiliation(s)
- John C Silbereis
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sirisha Pochareddy
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ying Zhu
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Mingfeng Li
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Department of Genetics and Department of Psychiatry, Yale School of Medicine, New Haven, CT 06510, USA; Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT 06510, USA; Section of Comparative Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Yale Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
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23
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Motono M, Ioroi Y, Ogura T, Takahashi J. WNT-C59, a Small-Molecule WNT Inhibitor, Efficiently Induces Anterior Cortex That Includes Cortical Motor Neurons From Human Pluripotent Stem Cells. Stem Cells Transl Med 2016; 5:552-60. [PMID: 26941358 DOI: 10.5966/sctm.2015-0261] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/16/2015] [Indexed: 01/07/2023] Open
Abstract
UNLABELLED The recapitulation of human neural development in a controlled, defined manner from pluripotent stem cells (PSCs) has considerable potential for studies of human neural development, circuit formation and function, and the construction of in vitro models of neurological diseases. The inhibition of Wnt signaling, often by the recombinant protein DKK1, is important for the induction of cortical neurons. Here, we report a novel differentiation method using a small-molecule WNT inhibitor, WNT-C59 (C59), to efficiently induce human anterior cortex. We compared two types of small molecules, C59 and XAV939 (XAV), as substitutes for DKK1 to induce cortical neurons from PSCs in serum-free embryoid body-like aggregate culture. DKK1 and XAV inhibited only the canonical pathway of Wnt signaling, whereas C59 inhibited both the canonical and noncanonical pathways. C59 efficiently induced CTIP2+/COUP-TF1- cells, which are characteristic of the cells found in the anterior cortex. In addition, when grafted into the cortex of adult mice, the C59-induced cells showed abundant axonal fiber extension toward the spinal cord. These results raise the possibility of C59 contributing to cell replacement therapy for motor neuron diseases or insults. SIGNIFICANCE For a cell therapy against damaged corticospinal tract caused by neurodegenerative diseases or insults, cortical motor neurons are needed. Currently, their induction from pluripotent stem cells is considered very promising; however, an efficient protocol to induce motor neurons is not available. For efficient induction of anterior cortex, where motor neurons are located, various WNT inhibitors were investigated. It was found that one of them could induce anterior cortical cells efficiently. In addition, when grafted into the cortex of adult mice, the induced cells showed more abundant axonal fiber extension toward spinal cord. These results raise the possibility that this inhibitor contributes to a cell-replacement therapy for motor neuron diseases or insults.
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Affiliation(s)
- Makoto Motono
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yoshihiko Ioroi
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan Department of Neurosurgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takenori Ogura
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan Department of Neurosurgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Jun Takahashi
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan Department of Neurosurgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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24
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Harkin LF, Gerrelli D, Gold Diaz DC, Santos C, Alzu'bi A, Austin CA, Clowry GJ. Distinct expression patterns for type II topoisomerases IIA and IIB in the early foetal human telencephalon. J Anat 2015; 228:452-63. [PMID: 26612825 PMCID: PMC4832326 DOI: 10.1111/joa.12416] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2015] [Indexed: 01/16/2023] Open
Abstract
TOP2A and TOP2B are type II topoisomerase enzymes that have important but distinct roles in DNA replication and RNA transcription. Recently, TOP2B has been implicated in the transcription of long genes in particular that play crucial roles in neural development and are susceptible to mutations contributing to neurodevelopmental conditions such as autism and schizophrenia. This study maps their expression in the early foetal human telencephalon between 9 and 12 post‐conceptional weeks. TOP2A immunoreactivity was restricted to cell nuclei of the proliferative layers of the cortex and ganglionic eminences (GE), including the ventricular zone and subventricular zone (SVZ) closely matching expression of the proliferation marker KI67. Comparison with sections immunolabelled for NKX2.1, a medial GE (MGE) marker, and PAX6, a cortical progenitor cell and lateral GE (LGE) marker, revealed that TOP2A‐expressing cells were more abundant in MGE than the LGE. In the cortex, TOP2B is expressed in cell nuclei in both proliferative (SVZ) and post‐mitotic compartments (intermediate zone and cortical plate) as revealed by comparison with immunostaining for PAX6 and the post‐mitotic neuron marker TBR1. However, co‐expression with KI67 was rare. In the GE, TOP2B was also expressed by proliferative and post‐mitotic compartments. In situ hybridisation studies confirmed these patterns of expression, except that TOP2A mRNA is restricted to cells in the G2/M phase of division. Thus, during early development, TOP2A is likely to have a role in cell proliferation, whereas TOP2B is expressed in post‐mitotic cells and may be important in controlling expression of long genes even at this early stage.
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Affiliation(s)
- Lauren F Harkin
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Chloe Santos
- HDBR Resource, UCL Institute of Child Health, London, UK
| | - Ayman Alzu'bi
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Caroline A Austin
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Gavin J Clowry
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
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25
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Mahfouz A, Ziats MN, Rennert OM, Lelieveldt BPF, Reinders MJT. Shared Pathways Among Autism Candidate Genes Determined by Co-expression Network Analysis of the Developing Human Brain Transcriptome. J Mol Neurosci 2015; 57:580-94. [PMID: 26399424 PMCID: PMC4644211 DOI: 10.1007/s12031-015-0641-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 08/14/2015] [Indexed: 11/24/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental syndrome known to have a significant but complex genetic etiology. Hundreds of diverse genes have been implicated in ASD; yet understanding how many genes, each with disparate function, can all be linked to a single clinical phenotype remains unclear. We hypothesized that understanding functional relationships between autism candidate genes during normal human brain development may provide convergent mechanistic insight into the genetic heterogeneity of ASD. We analyzed the co-expression relationships of 455 genes previously implicated in autism using the BrainSpan human transcriptome database, across 16 anatomical brain regions spanning prenatal life through adulthood. We discovered modules of ASD candidate genes with biologically relevant temporal co-expression dynamics, which were enriched for functional ontologies related to synaptogenesis, apoptosis, and GABA-ergic neurons. Furthermore, we also constructed co-expression networks from the entire transcriptome and found that ASD candidate genes were enriched in modules related to mitochondrial function, protein translation, and ubiquitination. Hub genes central to these ASD-enriched modules were further identified, and their functions supported these ontological findings. Overall, our multi-dimensional co-expression analysis of ASD candidate genes in the normal developing human brain suggests the heterogeneous set of ASD candidates share transcriptional networks related to synapse formation and elimination, protein turnover, and mitochondrial function.
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Affiliation(s)
- Ahmed Mahfouz
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands. .,Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands.
| | - Mark N Ziats
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.,University of Cambridge, Cambridge, UK.,Baylor College of Medicine, Houston, TX, USA
| | - Owen M Rennert
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Boudewijn P F Lelieveldt
- Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Intelligent Systems, Delft University of Technology, Delft, The Netherlands
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
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26
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Al-Jaberi N, Lindsay S, Sarma S, Bayatti N, Clowry GJ. The early fetal development of human neocortical GABAergic interneurons. Cereb Cortex 2015; 25:631-45. [PMID: 24047602 PMCID: PMC4318531 DOI: 10.1093/cercor/bht254] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
GABAergic interneurons are crucial to controlling the excitability and responsiveness of cortical circuitry. Their developmental origin may differ between rodents and human. We have demonstrated the expression of 12 GABAergic interneuron-associated genes in samples from human neocortex by quantitative rtPCR from 8 to 12 postconceptional weeks (PCW) and shown a significant anterior to posterior expression gradient, confirmed by in situ hybridization or immunohistochemistry for GAD1 and 2, DLX1, 2, and 5, ASCL1, OLIG2, and CALB2. Following cortical plate (CP) formation from 8 to 9 PCW, a proportion of cells were strongly stained for all these markers in the CP and presubplate. ASCL1 and DLX2 maintained high expression in the proliferative zones and showed extensive immunofluorescent double-labeling with the cell division marker Ki-67. CALB2-positive cells increased steadily in the SVZ/VZ from 10 PCW but were not double-labeled with Ki-67. Expression of GABAergic genes was generally higher in the dorsal pallium than in the ganglionic eminences, with lower expression in the intervening ventral pallium. It is widely accepted that the cortical proliferative zones may generate CALB2-positive interneurons from mid-gestation; we now show that the anterior neocortical proliferative layers especially may be a rich source of interneurons in the early neocortex.
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Affiliation(s)
- Nahidh Al-Jaberi
- Institute of Neuroscience Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Susan Lindsay
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Subrot Sarma
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Nadhim Bayatti
- Institute of Neuroscience Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK Current address: Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
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27
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Onorati M, Castiglioni V, Biasci D, Cesana E, Menon R, Vuono R, Talpo F, Laguna Goya R, Lyons PA, Bulfamante GP, Muzio L, Martino G, Toselli M, Farina C, Barker RA, Biella G, Cattaneo E. Molecular and functional definition of the developing human striatum. Nat Neurosci 2014; 17:1804-15. [PMID: 25383901 DOI: 10.1038/nn.3860] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 10/09/2014] [Indexed: 02/07/2023]
Abstract
The complexity of the human brain derives from the intricate interplay of molecular instructions during development. Here we systematically investigated gene expression changes in the prenatal human striatum and cerebral cortex during development from post-conception weeks 2 to 20. We identified tissue-specific gene coexpression networks, differentially expressed genes and a minimal set of bimodal genes, including those encoding transcription factors, that distinguished striatal from neocortical identities. Unexpected differences from mouse striatal development were discovered. We monitored 36 determinants at the protein level, revealing regional domains of expression and their refinement, during striatal development. We electrophysiologically profiled human striatal neurons differentiated in vitro and determined their refined molecular and functional properties. These results provide a resource and opportunity to gain global understanding of how transcriptional and functional processes converge to specify human striatal and neocortical neurons during development.
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Affiliation(s)
- Marco Onorati
- Department of Biosciences and Center for Stem Cell Research, Università degli Studi di Milano, Italy
| | - Valentina Castiglioni
- Department of Biosciences and Center for Stem Cell Research, Università degli Studi di Milano, Italy
| | - Daniele Biasci
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Elisabetta Cesana
- Department of Biology and Biotechnologies, University of Pavia, Pavia, Italy
| | - Ramesh Menon
- Institute of Experimental Neurology, San Raffaele Scientific Institute, Milan, Italy
| | - Romina Vuono
- John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, UK
| | - Francesca Talpo
- Department of Biology and Biotechnologies, University of Pavia, Pavia, Italy
| | - Rocio Laguna Goya
- John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, UK
| | - Paul A Lyons
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Gaetano P Bulfamante
- Department of Health Sciences, Università degli Studi di Milano-San Paolo Hospital, Milan, Italy
| | - Luca Muzio
- Institute of Experimental Neurology, San Raffaele Scientific Institute, Milan, Italy
| | - Gianvito Martino
- Institute of Experimental Neurology, San Raffaele Scientific Institute, Milan, Italy
| | - Mauro Toselli
- Department of Biology and Biotechnologies, University of Pavia, Pavia, Italy
| | - Cinthia Farina
- Institute of Experimental Neurology, San Raffaele Scientific Institute, Milan, Italy
| | - Roger A Barker
- John van Geest Centre for Brain Repair, University of Cambridge, Cambridge, UK
| | - Gerardo Biella
- Department of Biology and Biotechnologies, University of Pavia, Pavia, Italy
| | - Elena Cattaneo
- Department of Biosciences and Center for Stem Cell Research, Università degli Studi di Milano, Italy
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28
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The developmental transcriptome of the human brain: implications for neurodevelopmental disorders. Curr Opin Neurol 2014; 27:149-56. [PMID: 24565942 DOI: 10.1097/wco.0000000000000069] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE OF REVIEW Recent characterizations of the transcriptome of the developing human brain by several groups have generated comprehensive datasets on coding and noncoding RNAs that will be instrumental for illuminating the underlying biology of complex neurodevelopmental disorders. This review summarizes recent studies successfully utilizing these data to increase our understanding of the molecular mechanisms of pathogenesis. RECENT FINDINGS Several approaches have successfully integrated developmental transcriptome data with gene discovery to generate testable hypotheses about when and where in the developing human brain disease-associated genes converge. Specifically, these include the projection neurons in the prefrontal and primary motor--somatosensory cortex during mid-fetal development in autism spectrum disorder and the frontal cortex during fetal development in schizophrenia. SUMMARY Developmental transcriptome data is a key to interpreting disease-associated mutations and transcriptional changes. Novel approaches integrating the spatial and temporal dimensions of these data have increased our understanding of when and where disease occurs. Refinement of spatial and temporal properties and expanding these findings to other neurodevelopmental disorders will provide critical insights for understanding disease biology.
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29
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Godar SC, Mosher LJ, Di Giovanni G, Bortolato M. Animal models of tic disorders: a translational perspective. J Neurosci Methods 2014; 238:54-69. [PMID: 25244952 DOI: 10.1016/j.jneumeth.2014.09.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/09/2014] [Accepted: 09/11/2014] [Indexed: 12/30/2022]
Abstract
Tics are repetitive, sudden movements and/or vocalizations, typically enacted as maladaptive responses to intrusive premonitory urges. The most severe tic disorder, Tourette syndrome (TS), is a childhood-onset condition featuring multiple motor and at least one phonic tic for a duration longer than 1 year. The pharmacological treatment of TS is mainly based on antipsychotic agents; while these drugs are often effective in reducing tic severity and frequency, their therapeutic compliance is limited by serious motor and cognitive side effects. The identification of novel therapeutic targets and development of better treatments for tic disorders is conditional on the development of animal models with high translational validity. In addition, these experimental tools can prove extremely useful to test hypotheses on the etiology and neurobiological bases of TS and related conditions. In recent years, the translational value of these animal models has been enhanced, thanks to a significant re-organization of our conceptual framework of neuropsychiatric disorders, with a greater focus on endophenotypes and quantitative indices, rather than qualitative descriptors. Given the complex and multifactorial nature of TS and other tic disorders, the selection of animal models that can appropriately capture specific symptomatic aspects of these conditions can pose significant theoretical and methodological challenges. In this article, we will review the state of the art on the available animal models of tic disorders, based on genetic mutations, environmental interventions as well as pharmacological manipulations. Furthermore, we will outline emerging lines of translational research showing how some of these experimental preparations have led to significant progress in the identification of novel therapeutic targets for tic disorders.
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Affiliation(s)
- Sean C Godar
- Department of Pharmacology and Toxicology, School of Pharmacy; University of Kansas, Lawrence, KS, USA
| | - Laura J Mosher
- Department of Pharmacology and Toxicology, School of Pharmacy; University of Kansas, Lawrence, KS, USA
| | - Giuseppe Di Giovanni
- Department of Physiology and Biochemistry, University of Malta, Msida, Malta; School of Biosciences, Cardiff University, Cardiff, UK
| | - Marco Bortolato
- Department of Pharmacology and Toxicology, School of Pharmacy; University of Kansas, Lawrence, KS, USA; Consortium for Translational Research on Aggression and Drug Abuse (ConTRADA), University of Kansas, Lawrence, KS, USA.
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30
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Hladnik A, Džaja D, Darmopil S, Jovanov-Milošević N, Petanjek Z. Spatio-temporal extension in site of origin for cortical calretinin neurons in primates. Front Neuroanat 2014; 8:50. [PMID: 25018702 PMCID: PMC4072090 DOI: 10.3389/fnana.2014.00050] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/03/2014] [Indexed: 11/13/2022] Open
Abstract
The vast majority of cortical GABAergic neurons can be defined by parvalbumin, somatostatin or calretinin expression. In most mammalians, parvalbumin and somatostatin interneurons have constant proportions, each representing 5-7% of the total neuron number. In contrast, there is a threefold increase in the proportion of calretinin interneurons, which do not exceed 4% in rodents and reach 12% in higher order areas of primate cerebral cortex. In rodents, almost all parvalbumin and somatostatin interneurons originate from the medial part of the subpallial proliferative structure, the ganglionic eminence (GE), while almost all calretinin interneurons originate from its caudal part. The spatial pattern of cortical GABAergic neurons origin from the GE is preserved in the monkey and human brain. However, it could be expected that the evolution is changing developmental rules to enable considerable expansion of calretinin interneuron population. During the early fetal period in primates, cortical GABAergic neurons are almost entirely generated in the subpallium, as in rodents. Already at that time, the primate caudal ganglionic eminence (CGE) shows a relative increase in size and production of calretinin interneurons. During the second trimester of gestation, that is the main neurogenetic stage in primates without clear correlates found in rodents, the pallial production of cortical GABAergic neurons together with the extended persistence of the GE is observed. We propose that the CGE could be the main source of calretinin interneurons for the posterior and lateral cortical regions, but not for the frontal cortex. The associative granular frontal cortex represents around one third of the cortical surface and contains almost half of cortical calretinin interneurons. The majority of calretinin interneurons destined for the frontal cortex could be generated in the pallium, especially in the newly evolved outer subventricular zone that becomes the main pool of cortical progenitors.
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Affiliation(s)
- Ana Hladnik
- Department of Anatomy and Clinical Anatomy, School of Medicine, University of Zagreb Zagreb, Croatia
| | - Domagoj Džaja
- Department of Neuroscience, Croatian Institute for Brain Research, School of Medicine, University of Zagreb Zagreb, Croatia
| | - Sanja Darmopil
- Department of Anatomy and Clinical Anatomy, School of Medicine, University of Zagreb Zagreb, Croatia ; Department of Neuroscience, Croatian Institute for Brain Research, School of Medicine, University of Zagreb Zagreb, Croatia
| | - Nataša Jovanov-Milošević
- Department of Neuroscience, Croatian Institute for Brain Research, School of Medicine, University of Zagreb Zagreb, Croatia
| | - Zdravko Petanjek
- Department of Anatomy and Clinical Anatomy, School of Medicine, University of Zagreb Zagreb, Croatia ; Department of Neuroscience, Croatian Institute for Brain Research, School of Medicine, University of Zagreb Zagreb, Croatia
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31
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Clowry GJ. An enhanced role and expanded developmental origins for gamma-aminobutyric acidergic interneurons in the human cerebral cortex. J Anat 2014; 227:384-93. [PMID: 24839870 DOI: 10.1111/joa.12198] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2014] [Indexed: 12/16/2022] Open
Abstract
Human beings have considerably expanded cognitive abilities compared with all other species and they also have a relatively larger cerebral cortex compared with their body size. But is a bigger brain the only reason for higher cognition or have other features evolved in parallel? Humans have more and different types of GABAergic interneurons, found in different places, than our model species. Studies are beginning to show differences in function. Is this expanded repertoire of functional types matched by an evolution of their developmental origins? Recent studies support the idea that generation of interneurons in the ventral telencephalon may be more complicated in primates, which have evolved a large and complex outer subventricular zone in the ganglionic eminences. In addition, proportionally more interneurons appear to be produced in the caudal ganglionic eminence, the majority of which populate the superficial layers of the cortex. Whether or not the cortical proliferative zones are a source of interneurogenesis, and to what extent and of what significance, is a contentious issue. As there is growing evidence that conditions such as autism, schizophrenia and congenital epilepsy may have developmental origins in the failure of interneuron production and migration, it is important we understand fully the similarities and differences between human development and our animal models.
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Affiliation(s)
- Gavin J Clowry
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
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32
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Pletikos M, Sousa AMM, Sedmak G, Meyer KA, Zhu Y, Cheng F, Li M, Kawasawa YI, Sestan N. Temporal specification and bilaterality of human neocortical topographic gene expression. Neuron 2013; 81:321-32. [PMID: 24373884 DOI: 10.1016/j.neuron.2013.11.018] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2013] [Indexed: 01/09/2023]
Abstract
Transcriptional events involved in the development of human cerebral neocortex are poorly understood. Here, we analyzed the temporal dynamics and laterality of gene expression in human and macaque monkey neocortex. We found that interareal differences exhibit a temporal hourglass pattern, dividing the human neocortical development into three major phases. The first phase, corresponding to prenatal development, is characterized by the highest number of differential expressed genes among areas and gradient-like expression patterns, including those that are different between human and macaque. The second, preadolescent phase, is characterized by lesser interareal expression differences and by an increased synchronization of areal transcriptomes. During the third phase, from adolescence onward, differential expression among areas increases again driven predominantly by a subset of areas, without obvious gradient-like patterns. Analyses of left-right gene expression revealed population-level global symmetry throughout the fetal and postnatal time span. Thus, human neocortical topographic gene expression is temporally specified and globally symmetric.
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Affiliation(s)
- Mihovil Pletikos
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Graduate Program in Neuroscience, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - André M M Sousa
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Graduate Program in Areas of Basic and Applied Biology, Abel Salazar Biomedical Sciences Institute, University of Porto, 4099-003 Porto, Portugal
| | - Goran Sedmak
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Graduate Program in Neuroscience, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Kyle A Meyer
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ying Zhu
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Feng Cheng
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL 33612, USA
| | - Mingfeng Li
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Yuka Imamura Kawasawa
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Nenad Sestan
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
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33
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Buckner RL, Krienen FM. The evolution of distributed association networks in the human brain. Trends Cogn Sci 2013; 17:648-65. [DOI: 10.1016/j.tics.2013.09.017] [Citation(s) in RCA: 475] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/28/2013] [Accepted: 09/30/2013] [Indexed: 01/25/2023]
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34
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von Hohenberg CC, Wigand MC, Kubicki M, Leicht G, Giegling I, Karch S, Hartmann AM, Konte B, Friedl M, Ballinger T, Eckbo R, Bouix S, Jäger L, Shenton ME, Rujescu D, Mulert C. CNTNAP2 polymorphisms and structural brain connectivity: a diffusion-tensor imaging study. J Psychiatr Res 2013; 47:1349-56. [PMID: 23871450 PMCID: PMC3780783 DOI: 10.1016/j.jpsychires.2013.07.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/27/2013] [Accepted: 07/02/2013] [Indexed: 11/16/2022]
Abstract
CNTNAP2 is a gene on chromosome 7 that has shown associations with autism and schizophrenia, and there is evidence that it plays an important role for neuronal synchronization and brain connectivity. In this study, we assessed the relationship between Diffusion Tensor Imaging (DTI), a putative marker of anatomical brain connectivity, and multiple single nucleotide polymorphisms (SNPs) spread out over this large gene. 81 healthy controls and 44 patients with schizophrenia (all Caucasian) underwent DTI and genotyping of 31 SNPs within CNTNAP2. We employed Tract-based Spatial Statistics (TBSS) for inter-subject brain registration and computed average diffusivity values for six major white matter tracts. Analyses of Covariance (ANCOVAs) were computed to test for possible associations with genotypes. The strongest association, which survived rigorous Bonferroni correction, was between rs2710126 genotype and Fractional Anisotropy (FA) in the uncinate fasciculus (p = .00003). This anatomical location is particularly interesting given the enriched fronto-temporal expression of CNTNAP2 in the developing brain. For this SNP, no phenotype association has been reported before. There were several further genotype-DTI associations that were nominally significant but did not survive Bonferroni correction, including an association between axial diffusivity in the dorsal cingulum bundle and a region in intron 13 (represented by rs2710102, rs759178, rs2538991), which has previously been reported to be associated with anterior-posterior functional connectivity. We present new evidence about the effects of CNTNAP2 on brain connectivity, whose disruption has been hypothesized to be central to schizophrenia pathophysiology.
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Affiliation(s)
- Christian Clemm von Hohenberg
- Psychiatry Neuroimaging Laboratory, Brigham and Women's
Hospital and Harvard Medical School, Boston, MA,Department of Psychiatry, Faculty of Medicine,
Ludwig-Maximilians-Universität, Munich, Germany,Psychiatry Neuroimaging Branch, Imaging Center NeuroImage Nord and
Department of Psychiatry and Psychotherapy, University Medical Center
Hamburg-Eppendorf, Germany
| | - Marlene C. Wigand
- Psychiatry Neuroimaging Laboratory, Brigham and Women's
Hospital and Harvard Medical School, Boston, MA,Department of Psychiatry, Faculty of Medicine,
Ludwig-Maximilians-Universität, Munich, Germany,Psychiatry Neuroimaging Branch, Imaging Center NeuroImage Nord and
Department of Psychiatry and Psychotherapy, University Medical Center
Hamburg-Eppendorf, Germany
| | - Marek Kubicki
- Psychiatry Neuroimaging Laboratory, Brigham and Women's
Hospital and Harvard Medical School, Boston, MA,Departments of Psychiatry and Radiology, Harvard Medical School,
Boston, MA
| | - Gregor Leicht
- Psychiatry Neuroimaging Branch, Imaging Center NeuroImage Nord and
Department of Psychiatry and Psychotherapy, University Medical Center
Hamburg-Eppendorf, Germany
| | - Ina Giegling
- Department of Psychiatry, Faculty of Medicine,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Susanne Karch
- Department of Psychiatry, Faculty of Medicine,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Annette M. Hartmann
- Department of Psychiatry, Faculty of Medicine,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Bettina Konte
- Department of Psychiatry, Faculty of Medicine,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Marion Friedl
- Department of Psychiatry, Faculty of Medicine,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Thomas Ballinger
- Psychiatry Neuroimaging Laboratory, Brigham and Women's
Hospital and Harvard Medical School, Boston, MA
| | - Ryan Eckbo
- Psychiatry Neuroimaging Laboratory, Brigham and Women's
Hospital and Harvard Medical School, Boston, MA
| | - Sylvain Bouix
- Psychiatry Neuroimaging Laboratory, Brigham and Women's
Hospital and Harvard Medical School, Boston, MA,Departments of Psychiatry and Radiology, Harvard Medical School,
Boston, MA
| | - Lorenz Jäger
- Department of Radiology, Faculty of Medicine,
Ludwig-Maximilians-Universität, Munich, Germany
| | - Martha E. Shenton
- Psychiatry Neuroimaging Laboratory, Brigham and Women's
Hospital and Harvard Medical School, Boston, MA,Departments of Psychiatry and Radiology, Harvard Medical School,
Boston, MA,Clinical Neuroscience Division, Laboratory of Neuroscience, Veterans
Affairs Boston Healthcare System, Brockton Division, Brockton, MA
| | - Dan Rujescu
- Department of Psychiatry, Faculty of Medicine,
Ludwig-Maximilians-Universität, Munich, Germany,Department of Psychiatry, University Hospital and Faculty of
Medicine, Martin-Luther-Universität Halle-Wittenberg, Germany
| | - Christoph Mulert
- Psychiatry Neuroimaging Branch, Imaging Center NeuroImage Nord and
Department of Psychiatry and Psychotherapy, University Medical Center
Hamburg-Eppendorf, Germany
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35
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Poluch S, Juliano SL. Fine-tuning of neurogenesis is essential for the evolutionary expansion of the cerebral cortex. ACTA ACUST UNITED AC 2013; 25:346-64. [PMID: 23968831 DOI: 10.1093/cercor/bht232] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We used several animal models to study global and regional cortical surface expansion: The lissencephalic mouse, gyrencephalic normal ferrets, in which the parietal cortex expands more than the temporal cortex, and moderately lissencephalic ferrets, showing a similar degree of temporal and parietal expansion. We found that overall cortical surface expansion is achieved when specific events occur prior to surpragranular layer formation. (1) The subventricular zone (SVZ) shows substantial growth, (2) the inner SVZ contains an increased number of outer radial glia and intermediate progenitor cells expressing Pax6, and (3) the outer SVZ contains a progenitor cell composition similar to the combined VZ and inner SVZ. A greater parietal expansion is also achieved by eliminating the latero-dorsal neurogenic gradient, so that neurogenesis displays a similar developmental degree between parietal and temporal regions. In contrast, mice or lissencephalic ferrets show more advanced neurogenesis in the temporal region. In conclusion, we propose that global and regional cortical surface expansion rely on similar strategies consisting in altering the timing of neurogenic events prior to the surpragranular layer formation, so that more progenitor cells, and ultimately more neurons, are produced. This hypothesis is supported by findings from a ferret model of lissencephaly obtained by transiently blocking neurogenesis during the formation of layer IV.
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Affiliation(s)
- Sylvie Poluch
- Department of Anatomy, Physiology, and Genetics Department of Neuroscience, Uniformed Services University, Bethesda, MD, USA
| | - Sharon L Juliano
- Department of Anatomy, Physiology, and Genetics Department of Neuroscience, Uniformed Services University, Bethesda, MD, USA
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36
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D'Angelo A, De Angelis A, Avallone B, Piscopo I, Tammaro R, Studer M, Franco B. Ofd1 controls dorso-ventral patterning and axoneme elongation during embryonic brain development. PLoS One 2012; 7:e52937. [PMID: 23300826 PMCID: PMC3531334 DOI: 10.1371/journal.pone.0052937] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 11/26/2012] [Indexed: 01/04/2023] Open
Abstract
Oral-facial-digital type I syndrome (OFDI) is a human X-linked dominant-male-lethal developmental disorder caused by mutations in the OFD1 gene. Similar to other inherited disorders associated to ciliary dysfunction OFD type I patients display neurological abnormalities. We characterized the neuronal phenotype that results from Ofd1 inactivation in early phases of mouse embryonic development and at post-natal stages. We determined that Ofd1 plays a crucial role in forebrain development, and in particular, in the control of dorso-ventral patterning and early corticogenesis. We observed abnormal activation of Sonic hedgehog (Shh), a major pathway modulating brain development. Ultrastructural studies demonstrated that early Ofd1 inactivation results in the absence of ciliary axonemes despite the presence of mature basal bodies that are correctly orientated and docked. Ofd1 inducible-mediated inactivation at birth does not affect ciliogenesis in the cortex, suggesting a developmental stage-dependent role for a basal body protein in ciliogenesis. Moreover, we showed defects in cytoskeletal organization and apical-basal polarity in Ofd1 mutant embryos, most likely due to lack of ciliary axonemes. Thus, the present study identifies Ofd1 as a developmental disease gene that is critical for forebrain development and ciliogenesis in embryonic life, and indicates that Ofd1 functions after docking and before elaboration of the axoneme in vivo.
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Affiliation(s)
- Anna D'Angelo
- Telethon Institute of Genetics and Medicine (TIGEM), Via Pietro Castellino 111, Naples, Italy
| | - Amalia De Angelis
- Telethon Institute of Genetics and Medicine (TIGEM), Via Pietro Castellino 111, Naples, Italy
| | - Bice Avallone
- Department of Biological Science, University of Naples “Federico II”, Naples, Italy
| | - Immacolata Piscopo
- Telethon Institute of Genetics and Medicine (TIGEM), Via Pietro Castellino 111, Naples, Italy
| | - Roberta Tammaro
- Telethon Institute of Genetics and Medicine (TIGEM), Via Pietro Castellino 111, Naples, Italy
| | - Michèle Studer
- Telethon Institute of Genetics and Medicine (TIGEM), Via Pietro Castellino 111, Naples, Italy
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine (TIGEM), Via Pietro Castellino 111, Naples, Italy
- Medical Genetics, Department of Pediatrics, Federico II University, Naples, Italy
- * E-mail:
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37
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Abstract
Rodents and primates both show considerable variation in the overall size, the radial and tangential dimensions, folding and subdivisions into distinct areas of their cerebral cortex. Our current understanding of brain development is based on a handful of model systems. A detailed comparative analysis of the cellular and molecular mechanisms that regulate neural progenitor production, cell migration, and circuit assembly can provide much needed insights into the working of neocortical evolution. From the limited comparative data currently available, it is apparent that the emergence and variation of the neuronal progenitor cells have led to the production of increased neuronal populations and the evolution of the cortex. Further diversification and compartmentalization of the germinal zone together with changing proportions of radial glia in the ventricular zone and various intermediate progenitors in the subventricular zone may have been the driving force behind increased cell numbers in larger brains both in rodents and primates. Radial and tangential migratory patterns are both present in rodents and primates, but in different proportions. There are apparent differences between mouse and human in the generation and elaboration of the interneuronal subtypes and also in gene expression patterns associated with the appearance of distinct cortical areas. The increased cortical dimensions and the formation of a more elaborate cortical architecture in primates require a larger and more compartmentalized transient subplate zone during development. More comparative analysis in rodent and primate species with large, small, and smooth and folded brains is needed to reveal the biological significance of the alterations in these cortical developmental programs.
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38
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Kang HJ, Kawasawa YI, Cheng F, Zhu Y, Xu X, Li M, Sousa AMM, Pletikos M, Meyer KA, Sedmak G, Guennel T, Shin Y, Johnson MB, Krsnik Z, Mayer S, Fertuzinhos S, Umlauf S, Lisgo SN, Vortmeyer A, Weinberger DR, Mane S, Hyde TM, Huttner A, Reimers M, Kleinman JE, Sestan N. Spatio-temporal transcriptome of the human brain. Nature 2011; 478:483-9. [PMID: 22031440 PMCID: PMC3566780 DOI: 10.1038/nature10523] [Citation(s) in RCA: 1420] [Impact Index Per Article: 109.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2010] [Accepted: 08/30/2011] [Indexed: 12/14/2022]
Abstract
Brain development and function depend on the precise regulation of gene expression. However, our understanding of the complexity and dynamics of the transcriptome of the human brain is incomplete. Here we report the generation and analysis of exon-level transcriptome and associated genotyping data, representing males and females of different ethnicities, from multiple brain regions and neocortical areas of developing and adult post-mortem human brains. We found that 86 per cent of the genes analysed were expressed, and that 90 per cent of these were differentially regulated at the whole-transcript or exon level across brain regions and/or time. The majority of these spatio-temporal differences were detected before birth, with subsequent increases in the similarity among regional transcriptomes. The transcriptome is organized into distinct co-expression networks, and shows sex-biased gene expression and exon usage. We also profiled trajectories of genes associated with neurobiological categories and diseases, and identified associations between single nucleotide polymorphisms and gene expression. This study provides a comprehensive data set on the human brain transcriptome and insights into the transcriptional foundations of human neurodevelopment.
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Affiliation(s)
- Hyo Jung Kang
- Department of Neurobiology and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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39
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Jun G, Nicolaou M, Morrison MA, Buros J, Morgan DJ, Radeke MJ, Yonekawa Y, Tsironi EE, Kotoula MG, Zacharaki F, Mollema N, Yuan Y, Miller JW, Haider NB, Hageman GS, Kim IK, Schaumberg DA, Farrer LA, DeAngelis MM. Influence of ROBO1 and RORA on risk of age-related macular degeneration reveals genetically distinct phenotypes in disease pathophysiology. PLoS One 2011; 6:e25775. [PMID: 21998696 PMCID: PMC3188561 DOI: 10.1371/journal.pone.0025775] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Accepted: 09/09/2011] [Indexed: 01/10/2023] Open
Abstract
ROBO1 is a strong candidate gene for age-related macular degeneration (AMD) based upon its location under a linkage peak on chromosome 3p12, its expression pattern, and its purported function in a pathway that includes RORA, a gene previously associated with risk for neovascular AMD. Previously, we observed that expression of ROBO1 and RORA is down-regulated among wet AMD cases, as compared to their unaffected siblings. Thus, we hypothesized that contribution of association signals in ROBO1, and interaction between these two genes may be important for both wet and dry AMD. We evaluated association of 19 single nucleotide polymorphisms (SNPs) in ROBO1 with wet and dry stages of AMD in a sibling cohort and a Greek case-control cohort containing 491 wet AMD cases, 174 dry AMD cases and 411 controls. Association signals and interaction results were replicated in an independent prospective cohort (1070 controls, 164 wet AMD cases, 293 dry AMD cases). The most significantly associated ROBO1 SNPs were rs1387665 under an additive model (meta P = 0.028) for wet AMD and rs9309833 under a recessive model (meta P = 6 × 10(-4)) for dry AMD. Further analyses revealed interaction between ROBO1 rs9309833 and RORA rs8034864 for both wet and dry AMD (interaction P<0.05). These studies were further supported by whole transcriptome expression profile studies from 66 human donor eyes and chromatin immunoprecipitation assays from mouse retinas. These findings suggest that distinct ROBO1 variants may influence the risk of wet and dry AMD, and the effects of ROBO1 on AMD risk may be modulated by RORA variants.
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Affiliation(s)
- Gyungah Jun
- Medicine (Biomedical Genetics), Boston University Schools of Medicine and Public Health, Boston, Massachusetts, United States of America
- Ophthalmology, Boston University Schools of Medicine and Public Health, Boston, Massachusetts, United States of America
- Biostatistics, Boston University Schools of Medicine and Public Health, Boston, Massachusetts United States of America
| | - Michael Nicolaou
- Medicine (Biomedical Genetics), Boston University Schools of Medicine and Public Health, Boston, Massachusetts, United States of America
| | - Margaux A. Morrison
- Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States of America
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, Center for Translational Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Jacqueline Buros
- Medicine (Biomedical Genetics), Boston University Schools of Medicine and Public Health, Boston, Massachusetts, United States of America
| | - Denise J. Morgan
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, Center for Translational Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Monte J. Radeke
- Center for the Study of Macular Degeneration, Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Yoshihiro Yonekawa
- Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States of America
- Ophthalmology, Weill Cornell Medical College, New York, New York, United States of America
| | | | | | | | - Nissa Mollema
- Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Yang Yuan
- Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Joan W. Miller
- Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States of America
| | - Neena B. Haider
- Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Gregory S. Hageman
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, Center for Translational Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Ivana K. Kim
- Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States of America
| | - Debra A. Schaumberg
- Division of Preventive Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Lindsay A. Farrer
- Medicine (Biomedical Genetics), Boston University Schools of Medicine and Public Health, Boston, Massachusetts, United States of America
- Ophthalmology, Boston University Schools of Medicine and Public Health, Boston, Massachusetts, United States of America
- Biostatistics, Boston University Schools of Medicine and Public Health, Boston, Massachusetts United States of America
- Neurology Boston University Schools of Medicine and Public Health, Boston, Massachusetts, United States of America
- Epidemiology, Boston University Schools of Medicine and Public Health, Boston, Massachusetts, United States of America
| | - Margaret M. DeAngelis
- Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States of America
- Ophthalmology and Visual Sciences, John A. Moran Eye Center, Center for Translational Medicine, University of Utah, Salt Lake City, Utah, United States of America
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40
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Ip BK, Bayatti N, Howard NJ, Lindsay S, Clowry GJ. The corticofugal neuron-associated genes ROBO1, SRGAP1, and CTIP2 exhibit an anterior to posterior gradient of expression in early fetal human neocortex development. Cereb Cortex 2011; 21:1395-407. [PMID: 21060114 PMCID: PMC3097990 DOI: 10.1093/cercor/bhq219] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Developing neocortical progenitors express transcription factors in gradients that induce programs of region-specific gene expression. Our previous work identified anteriorly upregulated expression gradients of a number of corticofugal neuron-associated gene probe sets along the anterior-posterior axis of the human neocortex (8-12 postconceptional weeks [PCW]). Here, we demonstrate by real-time polymerase chain reaction, in situ hybridization and immunohistochemistry that 3 such genes, ROBO1, SRGAP1, and CTIP2 are highly expressed anteriorly between 8-12 PCW, in comparison with other genes (FEZF2, SOX5) expressed by Layer V, VI, and subplate neurons. All 3 were prominently expressed by early postmitotic neurons in the subventricular zone, intermediate zone, and cortical plate (CP) from 8 to 10 PCW. Between 12 and 15 PCW expression patterns for ER81 and SATB2 (Layer V), TBR1 (Layer V/VI) and NURR1 (Layer VI) revealed Layer V forming. By 15 PCW, ROBO1 and SRGAP1 expression was confined to Layer V, whereas CTIP2 was expressed throughout the CP anteriorly. We observed ROBO1 and SRGAP1 immunoreactivity in medullary corticospinal axons from 11 PCW onward. Thus, we propose that the coexpression of these 3 markers in the anterior neocortex may mark the early location of the human motor cortex, including its corticospinal projection neurons, allowing further study of their early differentiation.
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Affiliation(s)
- Bui Kar Ip
- Institute of Human Genetics and Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
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41
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Abstract
AbstractThe young human brain is highly plastic and thus early brain lesions can lead to aberrant development of connectivity and mapping of functions. This is why initially in cerebral palsy only subtle changes in spontaneous movements are seen after the time of lesion, followed by a progressive evolution of a movement disorder over many months and years. Thus we propose that interventions to treat cerebral palsy should be initiated as soon as possible in order to restore the nervous system to the correct developmental trajectory. One such treatment might be autologous stem cell transplantation either intracerebrally or intravenously. All babies come with an accessible supply of stem cells, the umbilical cord, which can supply cells that could theoretically replace missing neural cell types, or act indirectly by supplying trophic support or modulating inflammatory responses to hypoxia/ischaemia. However, for such radical treatment to be proposed, it is necessary to be able to detect and accurately predict the outcomes of brain injury from a very early age. This article reviews our current understanding of perinatal injuries that lead to cerebral palsy, how well modern imaging might predict outcomes, what stem cells are yielded from umbilical cord blood and experimental models of brain repair using stem cells.
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42
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ZUKO AMILA, BOUYAIN SAMUEL, VAN DER ZWAAG BERT, BURBACH JPETERH. Contactins: structural aspects in relation to developmental functions in brain disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2011; 84:143-80. [PMID: 21846565 PMCID: PMC9921585 DOI: 10.1016/b978-0-12-386483-3.00001-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The contactins are members of a protein subfamily of neural immunoglobulin (Ig) domain-containing cell adhesion molecules. Their architecture is based on six N-terminal Ig domains, four fibronectin type III domains, and a C-terminal glycophosphatidylinositol (GPI)-anchor to the extracellular part of the cell membrane. Genetics of neuropsychiatric disorders, particularly autism spectrum disorders, have pinpointed contactin-4, -5, and -6 (CNTN4, -5, and -6) as potential disease genes in neurodevelopmental disorders and suggested that they participate in pathways important for appropriate brain development. These contactins have distinct but overlapping patterns of brain expression, and null-mutation causes subtle morphological and functional defects in the brain. The molecular basis of their neurodevelopmental functions is likely conferred by heterophilic protein interactions. Cntn4, -5, and -6 interact with protein tyrosine phosphatase receptor gamma (Ptptg) using a shared binding site that spans their second and third Ig repeats. Interactions with amyloid precursor protein (APP), Notch, and other IgCAMs have also been indicated. The present data indicate that Cntn4, -5, and -6 proteins may be part of heteromeric receptor complexes as well as serve as ligands themselves.
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Affiliation(s)
- AMILA ZUKO
- Department of Neuroscience and Pharmacology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - SAMUEL BOUYAIN
- Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - BERT VAN DER ZWAAG
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - J. PETER H. BURBACH
- Department of Neuroscience and Pharmacology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
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43
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Abstract
Many specifically human psychiatric and neurological conditions have developmental origins. Rodent models are extremely valuable for the investigation of brain development, but cannot provide insight into aspects that are specifically human. The human brain, and particularly the cerebral cortex, has some unique genetic, molecular, cellular and anatomical features, and these need to be further explored. Cortical expansion in human is not just quantitative; there are some novel types of neurons and cytoarchitectonic areas identified by their gene expression, connectivity and functions that do not exist in rodents. Recent research into human brain development has revealed more elaborated neurogenetic compartments, radial and tangential migration, transient cell layers in the subplate, and a greater diversity of early-generated neurons, including predecessor neurons. Recently there has been a renaissance of the study of human brain development because of these unique differences, made possible by the availability of new techniques. This review gives a flavour of the recent studies stemming from this renewed focus on the developing human brain.
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Affiliation(s)
- Gavin Clowry
- Institute of Neuroscience, Newcastle UniversityNewcastle upon Tyne, UK
| | - Zoltán Molnár
- Department of Physiology, Anatomy and Genetics, University of OxfordOxford, UK
| | - Pasko Rakic
- Department of Neurobiology, Kavli Institute of Neuroscience, Yale University School of MedicineNew Haven, CT, USA
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44
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Bourne JA. Unravelling the development of the visual cortex: implications for plasticity and repair. J Anat 2010; 217:449-68. [PMID: 20722872 DOI: 10.1111/j.1469-7580.2010.01275.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The visual cortex comprises over 50 areas in the human, each with a specified role and distinct physiology, connectivity and cellular morphology. How these individual areas emerge during development still remains something of a mystery and, although much attention has been paid to the initial stages of the development of the visual cortex, especially its lamination, very little is known about the mechanisms responsible for the arealization and functional organization of this region of the brain. In recent years we have started to discover that it is the interplay of intrinsic (molecular) and extrinsic (afferent connections) cues that are responsible for the maturation of individual areas, and that there is a spatiotemporal sequence in the maturation of the primary visual cortex (striate cortex, V1) and the multiple extrastriate/association areas. Studies in both humans and non-human primates have started to highlight the specific neural underpinnings responsible for the maturation of the visual cortex, and how experience-dependent plasticity and perturbations to the visual system can impact upon its normal development. Furthermore, damage to specific nuclei of the visual cortex, such as the primary visual cortex (V1), is a common occurrence as a result of a stroke, neurotrauma, disease or hypoxia in both neonates and adults alike. However, the consequences of a focal injury differ between the immature and adult brain, with the immature brain demonstrating a higher level of functional resilience. With better techniques for examining specific molecular and connectional changes, we are now starting to uncover the mechanisms responsible for the increased neural plasticity that leads to significant recovery following injury during this early phase of life. Further advances in our understanding of postnatal development/maturation and plasticity observed during early life could offer new strategies to improve outcomes by recapitulating aspects of the developmental program in the adult brain.
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Affiliation(s)
- James A Bourne
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria 3800, Australia.
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