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Qian X, Coleman K, Jiang S, Kriz AJ, Marciano JH, Luo C, Cai C, Manam MD, Caglayan E, Otani A, Ghosh U, Shao DD, Andersen RE, Neil JE, Johnson R, LeFevre A, Hecht JL, Miller MB, Sun L, Stringer C, Li M, Walsh CA. Spatial Single-cell Analysis Decodes Cortical Layer and Area Specification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.05.597673. [PMID: 38915567 PMCID: PMC11195106 DOI: 10.1101/2024.06.05.597673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The human cerebral cortex, pivotal for advanced cognitive functions, is composed of six distinct layers and dozens of functionally specialized areas1,2. The layers and areas are distinguished both molecularly, by diverse neuronal and glial cell subtypes, and structurally, through intricate spatial organization3,4. While single-cell transcriptomics studies have advanced molecular characterization of human cortical development, a critical gap exists due to the loss of spatial context during cell dissociation5,6,7,8. Here, we utilized multiplexed error-robust fluorescence in situ hybridization (MERFISH)9, augmented with deep-learning-based cell segmentation, to examine the molecular, cellular, and cytoarchitectural development of human fetal cortex with spatially resolved single-cell resolution. Our extensive spatial atlas, encompassing 16 million single cells, spans eight cortical areas across four time points in the second and third trimesters. We uncovered an early establishment of the six-layer structure, identifiable in the laminar distribution of excitatory neuronal subtypes by mid-gestation, long before the emergence of cytoarchitectural layers. Notably, while anterior-posterior gradients of neuronal subtypes were generally observed in most cortical areas, a striking exception was the sharp molecular border between primary (V1) and secondary visual cortices (V2) at gestational week 20. Here we discovered an abrupt binary shift in neuronal subtype specification at the earliest stages, challenging the notion that continuous morphogen gradients dictate mid-gestation cortical arealization6,10. Moreover, integrating single-nuclei RNA-sequencing and in situ whole transcriptomics revealed an early upregulation of synaptogenesis in V1-specific Layer 4 neurons, suggesting a role of synaptogenesis in this discrete border formation. Collectively, our findings underscore the crucial role of spatial relationships in determining the molecular specification of cortical layers and areas. This work not only provides a valuable resource for the field, but also establishes a spatially resolved single-cell analysis paradigm that paves the way for a comprehensive developmental atlas of the human brain.
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Affiliation(s)
- Xuyu Qian
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- These authors contributed equally: Xuyu Qian, Kyle Coleman, Shunzhou Jiang
| | - Kyle Coleman
- Statistical Center for Single-Cell and Spatial Genomics, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- These authors contributed equally: Xuyu Qian, Kyle Coleman, Shunzhou Jiang
| | - Shunzhou Jiang
- Statistical Center for Single-Cell and Spatial Genomics, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- These authors contributed equally: Xuyu Qian, Kyle Coleman, Shunzhou Jiang
| | - Andrea J. Kriz
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jack H. Marciano
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Chunyu Luo
- Statistical Center for Single-Cell and Spatial Genomics, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Chunhui Cai
- Research Computing, Department of Information Technology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Monica Devi Manam
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Emre Caglayan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Aoi Otani
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Urmi Ghosh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Diane D. Shao
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rebecca E. Andersen
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jennifer E. Neil
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Robert Johnson
- University of Maryland Brain and Tissue Bank, Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Alexandra LeFevre
- University of Maryland Brain and Tissue Bank, Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jonathan L. Hecht
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Michael B. Miller
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Division of Neuropathology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Liang Sun
- Research Computing, Department of Information Technology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Carsen Stringer
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Mingyao Li
- Statistical Center for Single-Cell and Spatial Genomics, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christopher A. Walsh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Departments of Pediatrics and Neurology, Harvard Medical School, Boston, Massachusetts, USA
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2
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Liu Z, Li A, Gong H, Yang X, Luo Q, Feng Z, Li X. The cytoarchitectonic landscape revealed by deep learning method facilitated precise positioning in mouse neocortex. Cereb Cortex 2024; 34:bhae229. [PMID: 38836835 DOI: 10.1093/cercor/bhae229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/13/2024] [Accepted: 05/23/2024] [Indexed: 06/06/2024] Open
Abstract
Neocortex is a complex structure with different cortical sublayers and regions. However, the precise positioning of cortical regions can be challenging due to the absence of distinct landmarks without special preparation. To address this challenge, we developed a cytoarchitectonic landmark identification pipeline. The fluorescence micro-optical sectioning tomography method was employed to image the whole mouse brain stained by general fluorescent nucleotide dye. A fast 3D convolution network was subsequently utilized to segment neuronal somas in entire neocortex. By approach, the cortical cytoarchitectonic profile and the neuronal morphology were analyzed in 3D, eliminating the influence of section angle. And the distribution maps were generated that visualized the number of neurons across diverse morphological types, revealing the cytoarchitectonic landscape which characterizes the landmarks of cortical regions, especially the typical signal pattern of barrel cortex. Furthermore, the cortical regions of various ages were aligned using the generated cytoarchitectonic landmarks suggesting the structural changes of barrel cortex during the aging process. Moreover, we observed the spatiotemporally gradient distributions of spindly neurons, concentrated in the deep layer of primary visual area, with their proportion decreased over time. These findings could improve structural understanding of neocortex, paving the way for further exploration with this method.
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Affiliation(s)
- Zhixiang Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430070, China
| | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430070, China
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, No. 58 Renmin Road, Haikou 570228, China
- HUST-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, No. 388 Ruoshui Road, Suzhou 215000, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430070, China
- HUST-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, No. 388 Ruoshui Road, Suzhou 215000, China
| | - Xiaoquan Yang
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, No. 58 Renmin Road, Haikou 570228, China
- HUST-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, No. 388 Ruoshui Road, Suzhou 215000, China
| | - Qingming Luo
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, No. 58 Renmin Road, Haikou 570228, China
| | - Zhao Feng
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, No. 58 Renmin Road, Haikou 570228, China
- HUST-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, No. 388 Ruoshui Road, Suzhou 215000, China
| | - Xiangning Li
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, No. 58 Renmin Road, Haikou 570228, China
- HUST-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, No. 388 Ruoshui Road, Suzhou 215000, China
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3
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Liu Z, Deng C, Zhou Z, Xiao Y, Jiang S, Zhu B, Naler LB, Jia X, Yao DD, Lu C. Epigenomic tomography for probing spatially defined chromatin state in the brain. CELL REPORTS METHODS 2024; 4:100738. [PMID: 38508188 PMCID: PMC10985265 DOI: 10.1016/j.crmeth.2024.100738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 12/24/2023] [Accepted: 02/27/2024] [Indexed: 03/22/2024]
Abstract
Spatially resolved epigenomic profiling is critical for understanding biology in the mammalian brain. Single-cell spatial epigenomic assays were developed recently for this purpose, but they remain costly and labor intensive for examining brain tissues across substantial dimensions and surveying a collection of brain samples. Here, we demonstrate an approach, epigenomic tomography, that maps spatial epigenomes of mouse brain at the scale of centimeters. We individually profiled neuronal and glial fractions of mouse neocortex slices with 0.5 mm thickness. Tri-methylation of histone 3 at lysine 27 (H3K27me3) or acetylation of histone 3 at lysine 27 (H3K27ac) features across these slices were grouped into clusters based on their spatial variation patterns to form epigenomic brain maps. As a proof of principle, our approach reveals striking dynamics in the frontal cortex due to kainic-acid-induced seizure, linked with transmembrane ion transporters, exocytosis of synaptic vesicles, and secretion of neurotransmitters. Epigenomic tomography provides a powerful and cost-effective tool for characterizing brain disorders based on the spatial epigenome.
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Affiliation(s)
- Zhengzhi Liu
- Department of Biomedical Engineering and Mechanics, Virginia Tech, Blacksburg, VA, USA
| | - Chengyu Deng
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Zirui Zhou
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Ya Xiao
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Shan Jiang
- Bradley Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Bohan Zhu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Xiaoting Jia
- Bradley Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, VA, USA
| | | | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA.
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4
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Geller E, Noble MA, Morales M, Gockley J, Emera D, Uebbing S, Cotney JL, Noonan JP. Massively parallel disruption of enhancers active in human neural stem cells. Cell Rep 2024; 43:113693. [PMID: 38271204 PMCID: PMC11078116 DOI: 10.1016/j.celrep.2024.113693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 11/02/2023] [Accepted: 01/05/2024] [Indexed: 01/27/2024] Open
Abstract
Changes in gene regulation have been linked to the expansion of the human cerebral cortex and to neurodevelopmental disorders, potentially by altering neural progenitor proliferation. However, the effects of genetic variation within regulatory elements on neural progenitors remain obscure. We use sgRNA-Cas9 screens in human neural stem cells (hNSCs) to disrupt 10,674 genes and 26,385 conserved regions in 2,227 enhancers active in the developing human cortex and determine effects on proliferation. Genes with proliferation phenotypes are associated with neurodevelopmental disorders and show biased expression in specific fetal human brain neural progenitor populations. Although enhancer disruptions overall have weaker effects than gene disruptions, we identify enhancer disruptions that severely alter hNSC self-renewal. Disruptions in human accelerated regions, implicated in human brain evolution, also alter proliferation. Integrating proliferation phenotypes with chromatin interactions reveals regulatory relationships between enhancers and their target genes contributing to neurogenesis and potentially to human cortical evolution.
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Affiliation(s)
- Evan Geller
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Mark A Noble
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Matheo Morales
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Jake Gockley
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Deena Emera
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Justin L Cotney
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Wu Tsai Institute, Yale University, New Haven, CT 06510, USA.
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5
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Napoli AJ, Laderwager S, Zoodsma JD, Biju B, Mucollari O, Schubel SK, Aprea C, Sayed A, Morgan K, Napoli A, Flanagan S, Wollmuth LP, Sirotkin HI. Developmental loss of NMDA receptors results in supernumerary forebrain neurons through delayed maturation of transit-amplifying neuroblasts. Sci Rep 2024; 14:3395. [PMID: 38336823 PMCID: PMC10858180 DOI: 10.1038/s41598-024-53910-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/06/2024] [Indexed: 02/12/2024] Open
Abstract
Developmental neurogenesis is a tightly regulated spatiotemporal process with its dysregulation implicated in neurodevelopmental disorders. NMDA receptors are glutamate-gated ion channels that are widely expressed in the early nervous system, yet their contribution to neurogenesis is poorly understood. Notably, a variety of mutations in genes encoding NMDA receptor subunits are associated with neurodevelopmental disorders. To rigorously define the role of NMDA receptors in developmental neurogenesis, we used a mutant zebrafish line (grin1-/-) that lacks all NMDA receptors yet survives to 10 days post-fertilization, offering the opportunity to study post-embryonic neurodevelopment in the absence of NMDA receptors. Focusing on the forebrain, we find that these fish have a progressive supernumerary neuron phenotype confined to the telencephalon at the end of embryonic neurogenesis, but which extends to all forebrain regions during postembryonic neurogenesis. This enhanced neuron population does not arise directly from increased numbers or mitotic activity of radial glia cells, the principal neural stem cells. Rather, it stems from a lack of timely maturation of transit-amplifying neuroblasts into post-mitotic neurons, as indicated by a decrease in expression of the ontogenetically-expressed chloride transporter, KCC2. Pharmacological blockade with MK-801 recapitulates the grin1-/- supernumerary neuron phenotype, indicating a requirement for ionotropic signaling. Thus, NMDA receptors are required for suppression of indirect, transit amplifying cell-driven neurogenesis by promoting maturational termination of mitosis. Loss of suppression results in neuronal overpopulation that can fundamentally change brain circuitry and may be a key factor in pathogenesis of neurodevelopmental disorders caused by NMDA receptor dysfunction.
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Affiliation(s)
- Amalia J Napoli
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA
| | - Stephanie Laderwager
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA
- Graduate Program in Neuroscience, Stony Brook University, Stony Brook, NY, 11794-5230, USA
| | - Josiah D Zoodsma
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA
| | - Bismi Biju
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA
| | - Olgerta Mucollari
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA
| | - Sarah K Schubel
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA
| | - Christieann Aprea
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA
| | - Aaliya Sayed
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA
| | - Kiele Morgan
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA
| | - Annelysia Napoli
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA
| | - Stephanie Flanagan
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA
| | - Lonnie P Wollmuth
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, 11794-5215, USA
- Center for Nervous System Disorders, Stony Brook University, Stony Brook, NY, 11794-5230, USA
| | - Howard I Sirotkin
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY, 11794-5230, USA.
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6
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Wagstyl K, Adler S, Seidlitz J, Vandekar S, Mallard TT, Dear R, DeCasien AR, Satterthwaite TD, Liu S, Vértes PE, Shinohara RT, Alexander-Bloch A, Geschwind DH, Raznahan A. Transcriptional cartography integrates multiscale biology of the human cortex. eLife 2024; 12:RP86933. [PMID: 38324465 PMCID: PMC10945526 DOI: 10.7554/elife.86933] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024] Open
Abstract
The cerebral cortex underlies many of our unique strengths and vulnerabilities, but efforts to understand human cortical organization are challenged by reliance on incompatible measurement methods at different spatial scales. Macroscale features such as cortical folding and functional activation are accessed through spatially dense neuroimaging maps, whereas microscale cellular and molecular features are typically measured with sparse postmortem sampling. Here, we integrate these distinct windows on brain organization by building upon existing postmortem data to impute, validate, and analyze a library of spatially dense neuroimaging-like maps of human cortical gene expression. These maps allow spatially unbiased discovery of cortical zones with extreme transcriptional profiles or unusually rapid transcriptional change which index distinct microstructure and predict neuroimaging measures of cortical folding and functional activation. Modules of spatially coexpressed genes define a family of canonical expression maps that integrate diverse spatial scales and temporal epochs of human brain organization - ranging from protein-protein interactions to large-scale systems for cognitive processing. These module maps also parse neuropsychiatric risk genes into subsets which tag distinct cyto-laminar features and differentially predict the location of altered cortical anatomy and gene expression in patients. Taken together, the methods, resources, and findings described here advance our understanding of human cortical organization and offer flexible bridges to connect scientific fields operating at different spatial scales of human brain research.
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Affiliation(s)
- Konrad Wagstyl
- Wellcome Centre for Human Neuroimaging, University College LondonLondonUnited Kingdom
| | - Sophie Adler
- UCL Great Ormond Street Institute for Child HealthHolbornUnited Kingdom
| | - Jakob Seidlitz
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Simon Vandekar
- Department of Biostatistics, Vanderbilt UniversityNashvilleUnited States
| | - Travis T Mallard
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Psychiatry, Harvard Medical SchoolBostonUnited States
| | - Richard Dear
- Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
| | - Alex R DeCasien
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
| | - Theodore D Satterthwaite
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Lifespan Informatics and Neuroimaging Center, University of Pennsylvania School of MedicinePhiladelphiaUnited States
| | - Siyuan Liu
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
| | - Petra E Vértes
- Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
| | - Russell T Shinohara
- Penn Statistics in Imaging and Visualization Center, Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Aaron Alexander-Bloch
- Department of Psychiatry, University of PennsylvaniaPhiladelphiaUnited States
- Department of Child and Adolescent Psychiatry and Behavioral Science, The Children's Hospital of PhiladelphiaPhiladelphiaUnited States
| | - Daniel H Geschwind
- Center for Autism Research and Treatment, Semel Institute, Program in Neurogenetics, Department of Neurology and Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Armin Raznahan
- Section on Developmental Neurogenomics, Human Genetics Branch, National Institute of Mental HealthBethesdaUnited States
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7
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Luu P, Tucker DM. Continuity and change in neural plasticity through embryonic morphogenesis, fetal activity-dependent synaptogenesis, and infant memory consolidation. Dev Psychobiol 2023; 65:e22439. [PMID: 38010309 DOI: 10.1002/dev.22439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/09/2023] [Accepted: 10/18/2023] [Indexed: 11/29/2023]
Abstract
There is an apparent continuity in human neural development that can be traced to venerable themes of vertebrate morphogenesis that have shaped the evolution of the reptilian telencephalon (including both primitive three-layered cortex and basal ganglia) and then the subsequent evolution of the mammalian six-layered neocortex. In this theoretical analysis, we propose that an evolutionary-developmental analysis of these general morphogenetic themes can help to explain the embryonic development of the dual divisions of the limbic system that control the dorsal and ventral networks of the human neocortex. These include the archicortical (dorsal limbic) Papez circuits regulated by the hippocampus that organize spatial, contextual memory, as well as the paleocortical (ventral limbic) circuits that organize object memory. We review evidence that these dorsal and ventral limbic divisions are controlled by the differential actions of brainstem lemnothalamic and midbrain collothalamic arousal control systems, respectively, thereby traversing the vertebrate subcortical neuraxis. These dual control systems are first seen shaping the phyletic morphogenesis of the archicortical and paleocortical foundations of the forebrain in embryogenesis. They then provide dual modes of activity-dependent synaptic organization in the active (lemnothalamic) and quiet (collothalamic) stages of fetal sleep. Finally, these regulatory systems mature to form the major systems of memory consolidation of postnatal development, including the rapid eye movement (lemnothalamic) consolidation of implicit memory and social attachment in the first year, and then-in a subsequent stage-the non-REM (collothalamic) consolidation of explicit memory that is integral to the autonomy and individuation of the second year of life.
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Affiliation(s)
- Phan Luu
- Brain Electrophysiology Laboratory Company, Eugene, Oregon, USA
- Department of Psychology, University of Oregon, Eugene, Oregon, USA
| | - Don M Tucker
- Brain Electrophysiology Laboratory Company, Eugene, Oregon, USA
- Department of Psychology, University of Oregon, Eugene, Oregon, USA
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8
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Krockenberger MS, Saleh-Mattesich TO, Evrard HC. Cytoarchitectonic and connection stripes in the dysgranular insular cortex in the macaque monkey. J Comp Neurol 2023; 531:2019-2043. [PMID: 38105579 DOI: 10.1002/cne.25571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 11/09/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023]
Abstract
The insula has been classically divided into broad granular, dysgranular, and agranular architectonic sectors. We previously proposed a novel partition, dividing each sector into four to seven sharply delimited architectonic areas, with the dysgranular areas being possibly further subdivided into subtle horizontal partitions or "stripes." In architectonics, discrete subparcellations are prone to subjective variability and need being supported with additional neuroanatomical methods. Here, using a secondary analysis of indirect connectional data in the rhesus macaque monkey, we examined the spatial relationship between the dysgranular architectonic stripes and tract-tracing labeling patterns produced in the insula with injections of neuronal tracers in other cortical regions. The injections consistently produced sharply delimited patches of anterograde and/or retrograde labeling, which formed stripes across consecutive coronal sections of the insula. While the overall pattern of labeling on individual coronal sections varied with the injection site, the boundaries of the patches consistently coincided with architectonic boundaries on an adjacent cyto- (Nissl) and/or myelo- (Gallyas) architectonic section. This overlap supports the existence of a fine dysgranular stripe-like partition of the primate insula, with possibly major implications for interoceptive processing in primates including humans. The modular organization of the insula could underlie a serial stream of integration from a dorsal primary interoceptive cortex toward progressively more ventral egocentric "self-agency" and allocentric "social" dysgranular processing units.
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Affiliation(s)
- Matthias S Krockenberger
- Werner Reichardt Center for Integrative Neuroscience, Karl Eberhard University of Tübingen, Tübingen, Germany
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Tatianna O Saleh-Mattesich
- Werner Reichardt Center for Integrative Neuroscience, Karl Eberhard University of Tübingen, Tübingen, Germany
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
| | - Henry C Evrard
- Werner Reichardt Center for Integrative Neuroscience, Karl Eberhard University of Tübingen, Tübingen, Germany
- Max Planck Institute for Biological Cybernetics, Tübingen, Germany
- International Center for Primate Brain Research (ICPBR), Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
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9
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Korologou-Linden R, Schuurmans IK, Cecil CAM, White T, Banaschewski T, Bokde ALW, Desrivières S, Grigis A, Garavan H, Gowland P, Heinz A, Brühl R, Martinot JL, Martinot MLP, Artiges E, Nees F, Orfanos DP, Paus T, Poustka L, Holz N, Fröhner JH, Smolka M, Walter H, Winterer J, Whelan R, Schumann G, Howe LD, Ben-Shlomo Y, Davies NM, Anderson EL. The bidirectional effects between cognitive ability and brain morphology: A life course Mendelian randomization analysis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.17.23297145. [PMID: 38014064 PMCID: PMC10680890 DOI: 10.1101/2023.11.17.23297145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Introduction Little is understood about the dynamic interplay between brain morphology and cognitive ability across the life course. Additionally, most existing research has focused on global morphology measures such as estimated total intracranial volume, mean thickness, and total surface area. Methods Mendelian randomization was used to estimate the bidirectional effects between cognitive ability, global and regional measures of cortical thickness and surface area, estimated total intracranial volume, total white matter, and the volume of subcortical structures (N=37,864). Analyses were stratified for developmental periods (childhood, early adulthood, mid-to-late adulthood; age range: 8-81 years). Results The earliest effects were observed in childhood and early adulthood in the frontoparietal lobes. A bidirectional relationship was identified between higher cognitive ability, larger estimated total intracranial volume (childhood, mid-to-late adulthood) and total surface area (all life stages). A thicker posterior cingulate cortex and a larger surface area in the caudal middle frontal cortex and temporal pole were associated with greater cognitive ability. Contrary, a thicker temporal pole was associated with lower cognitive ability. Discussion Stable effects of cognitive ability on brain morphology across the life course suggests that childhood is potentially an important window for intervention.
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10
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Zhou Z, Li Y, Zhang Y, Liu J, Ai H, Liu M, Qiu J, Luo YJ, Xu P. Differential effects of generalized anxiety and separation anxiety on brain structural development during adolescence. J Affect Disord 2023; 339:478-485. [PMID: 37442456 DOI: 10.1016/j.jad.2023.07.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 06/17/2023] [Accepted: 07/08/2023] [Indexed: 07/15/2023]
Abstract
Excessive anxiety is highly prevalent during childhood and adolescence, with detrimental effects on somatic and mental health, and quality of life. Although structural abnormalities in the brain have been found in people with anxiety disorders, whether anxiety affects the brain development of children and adolescents remains unknown. Here, we applied a multivariate approach to two single-site MRI datasets consisting of 733 and 775 participants aged 5-18 years. Using linear support vector regression and cross-validation, brain age is estimated by predicting the chronological age from the features that combine cortical thickness and surface area of 68 brain regions. We found that gray matter can predict the chronological age of children and adolescents with a low mean absolute error. Compared to specific brain network, the whole structural brain measures predicted brain age better. Importantly, adolescents with higher generalized anxiety and those with lower separation anxiety showed lower brain age, indicating a slow development of brain structures. The relationship between anxiety and brain age of youths could also be found in parent-reported separation anxiety. The findings highlight differential effects of different anxiety types on brain structural development and suggest that different types of anxiety during childhood and adolescence should be treated differently.
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Affiliation(s)
- Zheyi Zhou
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China
| | - Yiman Li
- School of Psychology, Shenzhen University, Shenzhen, China
| | - Yuqi Zhang
- School of Psychology, Shenzhen University, Shenzhen, China
| | - Jing Liu
- The China Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing, China; Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, China
| | - Hui Ai
- Institute of Applied Psychology, Tianjin University, Tianjin, China; Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Mingfang Liu
- Community Health Service Center, Beijing Normal University, Beijing, China
| | - Jianyin Qiu
- Shanghai Mental Health Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yue-Jia Luo
- State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University, Beijing, China; Institute for Neuropsychological Rehabilitation, University of Health and Rehabilitation Sciences, Qingdao, China; School of Psychology, Chengdu Medical College, Chengdu, China.
| | - Pengfei Xu
- Beijing Key Laboratory of Applied Experimental Psychology, National Demonstration Center for Experimental Psychology Education (BNU), Faculty of Psychology, Beijing Normal University, Beijing, China; Center for Neuroimaging, Shenzhen Institute of Neuroscience, Shenzhen, China.
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11
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Kirschner M, Paquola C, Khundrakpam BS, Vainik U, Bhutani N, Hodzic-Santor B, Georgiadis F, Al-Sharif NB, Misic B, Bernhardt BC, Evans AC, Dagher A. Schizophrenia Polygenic Risk During Typical Development Reflects Multiscale Cortical Organization. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2023; 3:1083-1093. [PMID: 37881579 PMCID: PMC10593879 DOI: 10.1016/j.bpsgos.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/23/2022] [Accepted: 08/04/2022] [Indexed: 10/15/2022] Open
Abstract
Background Schizophrenia is widely recognized as a neurodevelopmental disorder. Abnormal cortical development in otherwise typically developing children and adolescents may be revealed using polygenic risk scores for schizophrenia (PRS-SCZ). Methods We assessed PRS-SCZ and cortical morphometry in typically developing children and adolescents (3-21 years, 46.8% female) using whole-genome genotyping and T1-weighted magnetic resonance imaging (n = 390) from the PING (Pediatric Imaging, Neurocognition, and Genetics) cohort. We contextualized the findings using 1) age-matched transcriptomics, 2) histologically defined cytoarchitectural types and functionally defined networks, and 3) case-control differences of schizophrenia and other major psychiatric disorders derived from meta-analytic data of 6 ENIGMA (Enhancing Neuro Imaging Genetics through Meta Analysis) working groups, including a total of 12,876 patients and 15,670 control participants. Results Higher PRS-SCZ was associated with greater cortical thickness, which was most prominent in areas with heightened gene expression of dendrites and synapses. PRS-SCZ-related increases in vertexwise cortical thickness were mainly distributed in association cortical areas, particularly the ventral attention network, while relatively sparing koniocortical type cortex (i.e., primary sensory areas). The large-scale pattern of cortical thickness increases related to PRS-SCZ mirrored the pattern of cortical thinning in schizophrenia and mood-related psychiatric disorders derived from the ENIGMA consortium. Age group models illustrate a possible trajectory from PRS-SCZ-associated cortical thickness increases in early childhood toward thinning in late adolescence, with the latter resembling the adult brain phenotype of schizophrenia. Conclusions Collectively, combining imaging genetics with multiscale mapping, our work provides novel insight into how genetic risk for schizophrenia affects the cortex early in life.
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Affiliation(s)
- Matthias Kirschner
- Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
- Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric Hospital, University of Zürich, Zürich, Switzerland
- Division of Adult Psychiatry, Department of Psychiatry, University Hospitals of Geneva, Geneva, Switzerland
| | - Casey Paquola
- Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
- Institute of Neuroscience and Medicine, Forschungszentrum Jülich, Jülich, Germany
| | | | - Uku Vainik
- Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
- Institute of Psychology, Faculty of Social Sciences, Tartu, Estonia
| | - Neha Bhutani
- Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | | | - Foivos Georgiadis
- Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric Hospital, University of Zürich, Zürich, Switzerland
| | - Noor B. Al-Sharif
- Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | - Bratislav Misic
- Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | - Boris C. Bernhardt
- Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | - Alan C. Evans
- Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
| | - Alain Dagher
- Montreal Neurological Institute, McGill University, Montreal, Québec, Canada
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Napoli AJ, Laderwager S, Zoodsma JD, Biju B, Mucollari O, Schubel SK, Aprea C, Sayed A, Morgan K, Napoli A, Flanagan S, Wollmuth LP, Sirotkin HI. Loss of NMDA receptor function during development results in decreased KCC2 expression and increased neurons in the zebrafish forebrain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554812. [PMID: 37786708 PMCID: PMC10541604 DOI: 10.1101/2023.08.25.554812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Developmental neurogenesis is a tightly regulated spatiotemporal process with its dysregulation implicated in neurodevelopmental disorders. NMDA receptors are glutamate-gated ion channels that are widely expressed in the early nervous system, yet their contribution to neurogenesis is poorly understood. Notably, a variety of mutations in genes encoding NMDA receptor subunits are associated with neurodevelopmental disorders. To rigorously define the role of NMDA receptors in developmental neurogenesis, we used a mutant zebrafish line ( grin1 -/- ) that lacks all NMDA receptors yet survives to 10 days post-fertilization, offering the opportunity to study post-embryonic neurodevelopment in the absence of NMDA receptors. Focusing on the forebrain, we find that these fish have a progressive supernumerary neuron phenotype confined to the telencephalon at the end of embryonic neurogenesis, but which extends to all forebrain regions during postembryonic neurogenesis. This enhanced neuron population does not arise directly from increased numbers or mitotic activity of radial glia cells, the principal neural stem cells. Rather, it stems from a lack of timely maturation of transit-amplifying neuroblasts into post-mitotic neurons, as indicated by a decrease in expression of the ontogenetically-expressed chloride transporter, KCC2. Pharmacological blockade with MK-801 recapitulates the grin1 -/- supernumerary neuron phenotype, indicating a requirement for ionotropic signaling. Thus, NMDA receptors are required for suppression of indirect, transit amplifying cell-driven neurogenesis by promoting maturational termination of mitosis. Loss of suppression results in neuronal overpopulation that can fundamentally change brain circuitry and may be a key factor in pathogenesis of neurodevelopmental disorders caused by NMDA receptor dysfunction.
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Zhou Y, Tao L, Zhu Y. TempShift Reveals the Sequential Development of Human Neocortex and Skewed Developmental Timing of Down Syndrome Brains. Brain Sci 2023; 13:1070. [PMID: 37509002 PMCID: PMC10377154 DOI: 10.3390/brainsci13071070] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/01/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Development is a complex process involving precise regulation. Developmental regulation may vary in tissues and individuals, and is often altered in disorders. Currently, the regulation of developmental timing across neocortical areas and developmental changes in Down syndrome (DS) brains remain unclear. The changes in regulation are often accompanied by changes in the gene expression trajectories, which can be divided into two scenarios: (1) changes of gene expression trajectory shape that reflect changes in cell type composition or altered molecular machinery; (2) temporal shift of gene expression trajectories that indicate different regulation of developmental timing. Therefore, we developed an R package TempShift to separates these two scenarios and demonstrated that TempShift can distinguish temporal shift from different shape (DiffShape) of expression trajectories, and can accurately estimate the time difference between multiple trajectories. We applied TempShift to identify sequential gene expression across 11 neocortical areas, which suggested sequential occurrence of synapse formation and axon guidance, as well as reconstructed interneuron migration pathways within neocortex. Comparison between healthy and DS brains revealed increased microglia, shortened neuronal migration process, and delayed synaptogenesis and myelination in DS. These applications also demonstrate the potential of TempShift in understanding gene expression temporal dynamics during different biological processes.
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Affiliation(s)
- Yuqiu Zhou
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200032, China
| | - Li Tao
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200032, China
| | - Ying Zhu
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai 200032, China
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14
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Xu H, Xu C, Yang Z, Bai G, Yin B. Two sides of the same coin: distinct neuroanatomical patterns predict crystallized and fluid intelligence in adults. Front Neurosci 2023; 17:1199106. [PMID: 37304014 PMCID: PMC10249781 DOI: 10.3389/fnins.2023.1199106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/08/2023] [Indexed: 06/13/2023] Open
Abstract
Background Crystallized intelligence (Gc) and fluid intelligence (Gf) are regarded as distinct intelligence components that statistically correlate with each other. However, the distinct neuroanatomical signatures of Gc and Gf in adults remain contentious. Methods Machine learning cross-validated elastic net regression models were performed on the Human Connectome Project Young Adult dataset (N = 1089) to characterize the neuroanatomical patterns of structural magnetic resonance imaging variables that are associated with Gc and Gf. The observed relationships were further examined by linear mixed-effects models. Finally, intraclass correlations were computed to examine the similarity of the neuroanatomical correlates between Gc and Gf. Results The results revealed distinct multi-region neuroanatomical patterns predicted Gc and Gf, respectively, which were robust in a held-out test set (R2 = 2.40, 1.97%, respectively). The relationship of these regions with Gc and Gf was further supported by the univariate linear mixed effects models. Besides that, Gc and Gf displayed poor neuroanatomical similarity. Conclusion These findings provided evidence that distinct machine learning-derived neuroanatomical patterns could predict Gc and Gf in healthy adults, highlighting differential neuroanatomical signatures of different aspects of intelligence.
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Affiliation(s)
- Hui Xu
- Department of Neurosurgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Peter Boris Centre for Addictions Research, St. Joseph’s Healthcare Hamilton, McMaster University, Hamilton, ON, Canada
| | - Cheng Xu
- School of Psychology and Cognitive Science, East China Normal University, Shanghai, China
| | - Zhenliang Yang
- Faculty of Psychology, Tianjin Normal University, Tianjin, China
| | - Guanghui Bai
- Department of Radiology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Bo Yin
- Department of Neurosurgery, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
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15
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Ji L, Wang A, Sonthalia S, Naiman DQ, Younes L, Colantuoni C, Geman D. CellCover Defines Conserved Cell Types and Temporal Progression in scRNA-seq Data across Mammalian Neocortical Development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.06.535943. [PMID: 37383947 PMCID: PMC10299349 DOI: 10.1101/2023.04.06.535943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Accurate identification of cell classes across the tissues of living organisms is central in the analysis of growing atlases of single-cell RNA sequencing (scRNA-seq) data across biomedicine. Such analyses are often based on the existence of highly discriminating "marker genes" for specific cell classes which enables a deeper functional understanding of these classes as well as their identification in new, related datasets. Currently, marker genes are defined by methods that serially assess the level of differential expression (DE) of individual genes across landscapes of diverse cells. This serial approach has been extremely useful, but is limited because it ignores possible redundancy or complementarity across genes, that can only be captured by analyzing several genes at the same time. We wish to identify discriminating panels of genes. To efficiently explore the vast space of possible marker panels, leverage the large number of cells often sequenced, and overcome zero-inflation in scRNA-seq data, we propose viewing panel selection as a variation of the "minimal set-covering problem" in combinatorial optimization which can be solved with integer programming. In this formulation, the covering elements are genes, and the objects to be covered are cells of a particular class, where a cell is covered by a gene if that gene is expressed in that cell. Our method, CellCover, identifies a panel of marker genes in scRNA-seq data that covers one class of cells within a population. We apply this method to generate covering marker gene panels which characterize cells of the developing mouse neocortex as postmitotic neurons are generated from neural progenitor cells (NPCs). We show that CellCover captures cell class-specific signals distinct from those defined by DE methods and that CellCover's compact gene panels can be expanded to explore cell type specific function.Transfer learning experiments exploring these covering panels across in vivo mouse, primate, and human scRNA-seq datasets demonstrate that CellCover identifies markers of conserved cell classes in neurogenesis, as well as markers of temporal progression in the molecular identity of these cell types across development of the mammalian neocortex. The gene covering panels we identify across cell types and developmental time can be freely explored in visualizations across all the public data we use in this report at with NeMo Analytics [1] through https://nemoanalytics.org/p?l=CellCover . The code for CellCover is written in R and the Gurobi R interface and is available at [2].
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16
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Romero DM, Zaidi D, Cifuentes-Diaz C, Maillard C, Grannec G, Selloum M, Birling MC, Bahi-Buisson N, Francis F. A human dynein heavy chain mutation impacts cortical progenitor cells causing developmental defects, reduced brain size and altered brain architecture. Neurobiol Dis 2023; 180:106085. [PMID: 36933672 DOI: 10.1016/j.nbd.2023.106085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 02/27/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
Dynein heavy chain (DYNC1H1) mutations can either lead to severe cerebral cortical malformations, or alternatively may be associated with the development of spinal muscular atrophy with lower extremity predominance (SMA-LED). To assess the origin of such differences, we studied a new Dync1h1 knock-in mouse carrying the cortical malformation p.Lys3334Asn mutation. Comparing with an existing neurodegenerative Dync1h1 mutant (Legs at odd angles, Loa, +/p.Phe580Tyr), we assessed Dync1h1's roles in cortical progenitor and especially radial glia functions during embryogenesis, and assessed neuronal differentiation. p.Lys3334Asn /+ mice exhibit reduced brain and body size. Embryonic brains show increased and disorganized radial glia: interkinetic nuclear migration occurs in mutants, however there are increased basally positioned cells and abventricular mitoses. The ventricular boundary is disorganized potentially contributing to progenitor mislocalization and death. Morphologies of mitochondria and Golgi apparatus are perturbed in vitro, with different effects also in Loa mice. Perturbations of neuronal migration and layering are also observed in p.Lys3334Asn /+ mutants. Overall, we identify specific developmental effects due to a severe cortical malformation mutation in Dync1h1, highlighting the differences with a mutation known instead to primarily affect motor function.
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Affiliation(s)
- Delfina M Romero
- INSERM UMR-S 1270, F-75005 Paris, France; Sorbonne University, F-75005 Paris, France; Institut du Fer à Moulin, F-75005 Paris, France
| | - Donia Zaidi
- INSERM UMR-S 1270, F-75005 Paris, France; Sorbonne University, F-75005 Paris, France; Institut du Fer à Moulin, F-75005 Paris, France
| | - Carmen Cifuentes-Diaz
- INSERM UMR-S 1270, F-75005 Paris, France; Sorbonne University, F-75005 Paris, France; Institut du Fer à Moulin, F-75005 Paris, France
| | - Camille Maillard
- Laboratory of Genetics and Development of the Cerebral Cortex, INSERM UMR-S 1163, Imagine Institute, Paris, France; Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Gael Grannec
- INSERM UMR-S 1270, F-75005 Paris, France; Sorbonne University, F-75005 Paris, France; Institut du Fer à Moulin, F-75005 Paris, France
| | - Mohammed Selloum
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964 Illkirch, France; Université de Strasbourg, Illkirch, France; CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), Illkirch-Graffenstaden, France
| | - Marie-Christine Birling
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964 Illkirch, France; Université de Strasbourg, Illkirch, France; CELPHEDIA, PHENOMIN, Institut Clinique de la Souris (ICS), Illkirch-Graffenstaden, France
| | - Nadia Bahi-Buisson
- Laboratory of Genetics and Development of the Cerebral Cortex, INSERM UMR-S 1163, Imagine Institute, Paris, France; Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France; Pediatric Neurology APHP- Necker Enfants Malades University Hospital, Paris, France.; Centre de Référence, Déficiences Intellectuelles de Causes Rares, APHP- Necker Enfants Malades University Hospital, Paris, France
| | - Fiona Francis
- INSERM UMR-S 1270, F-75005 Paris, France; Sorbonne University, F-75005 Paris, France; Institut du Fer à Moulin, F-75005 Paris, France.
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Makowski C, Wang H, Srinivasan A, Qi A, Qiu Y, van der Meer D, Frei O, Zou J, Visscher P, Yang J, Chen CH. Larger cerebral cortex is genetically correlated with greater frontal area and dorsal thickness. Proc Natl Acad Sci U S A 2023; 120:e2214834120. [PMID: 36893272 PMCID: PMC10089183 DOI: 10.1073/pnas.2214834120] [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: 08/30/2022] [Accepted: 01/18/2023] [Indexed: 03/11/2023] Open
Abstract
Human cortical expansion has occurred non-uniformly across the brain. We assessed the genetic architecture of cortical global expansion and regionalization by comparing two sets of genome-wide association studies of 24 cortical regions with and without adjustment for global measures (i.e., total surface area, mean cortical thickness) using a genetically informed parcellation in 32,488 adults. We found 393 and 756 significant loci with and without adjusting for globals, respectively, where 8% and 45% loci were associated with more than one region. Results from analyses without adjustment for globals recovered loci associated with global measures. Genetic factors that contribute to total surface area of the cortex particularly expand anterior/frontal regions, whereas those contributing to thicker cortex predominantly increase dorsal/frontal-parietal thickness. Interactome-based analyses revealed significant genetic overlap of global and dorsolateral prefrontal modules, enriched for neurodevelopmental and immune system pathways. Consideration of global measures is important in understanding the genetic variants underlying cortical morphology.
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Affiliation(s)
- Carolina Makowski
- Department of Radiology, University of California San Diego, La Jolla, CA92093
| | - Hao Wang
- Department of Radiology, University of California San Diego, La Jolla, CA92093
| | - Anjali Srinivasan
- Department of Radiology, University of California San Diego, La Jolla, CA92093
| | - Anna Qi
- Department of Radiology, University of California San Diego, La Jolla, CA92093
| | - Yuqi Qiu
- School of Statistics, East China Normal University, Shanghai20050, China
| | - Dennis van der Meer
- Norwegian Centre for Mental Disorders Research Centre, Division of Mental Health and Addiction, University of Oslo, Oslo0450, Norway
| | - Oleksandr Frei
- Norwegian Centre for Mental Disorders Research Centre, Division of Mental Health and Addiction, University of Oslo, Oslo0450, Norway
| | - Jingjing Zou
- Division of Biostatistics and Bioinformatics, University of California San Diego, La Jolla, CA92093
| | - Peter M. Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD4072, Australia
| | - Jian Yang
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang310024, China
| | - Chi-Hua Chen
- Department of Radiology, University of California San Diego, La Jolla, CA92093
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Wu X, Sarpong GA, Zhang J, Sugihara I. Divergent topographic projection of cerebral cortical areas to overlapping cerebellar lobules through distinct regions of the pontine nuclei. Heliyon 2023; 9:e14352. [PMID: 37025843 PMCID: PMC10070096 DOI: 10.1016/j.heliyon.2023.e14352] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/09/2023] [Accepted: 03/01/2023] [Indexed: 03/11/2023] Open
Abstract
The massive axonal projection from the cerebrum to the cerebellum through the pontine nuclei supports the cerebrocerebellar coordination of motor and nonmotor functions. However, the cerebrum and cerebellum have distinct patterns of functional localization in their cortices. We addressed this issue by bidirectional neuronal tracing from 22 various locations of the pontine nuclei in the mouse in a comprehensive manner. Cluster analyses of the distribution patterns of labeled cortical pyramidal cells and cerebellar mossy fiber terminals classified all cases into six groups located in six different subareas of the pontine nuclei. The lateral (insular), mediorostral (cingulate and prefrontal), and caudal (visual and auditory) cortical areas of the cerebrum projected to the medial, rostral, and lateral subareas of the pontine nuclei, respectively. These pontine subareas then projected mainly to the crus I, central vermis, and paraflocculus divergently. The central (motor and somatosensory) cortical areas projected to the centrorostral, centrocaudal and caudal subareas of the pontine nuclei, which then projected mainly to the rostral and caudal lobules with a somatotopic arrangement. The results indicate a new pontine nuclei-centric view of the corticopontocerebellar projection: the generally parallel corticopontine projection to pontine nuclei subareas is relayed to the highly divergent pontocerebellar projection terminating in overlapping specific lobules of the cerebellum. Consequently, the mode of the pontine nuclei relay underlies the cerebellar functional organization.
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Greig LC, Woodworth MB, Poulopoulos A, Lim S, Macklis JD. BEAM: a combinatorial recombinase toolbox for binary gene expression and mosaic analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528875. [PMID: 36824714 PMCID: PMC9949094 DOI: 10.1101/2023.02.16.528875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Genetic mosaic analysis, in which mutant cells reside intermingled with wild-type cells, is a powerful experimental approach, but has not been widely used in mice because existing genome-based strategies require complicated and protracted breeding schemes. We have developed an alternative approach termed BEAM (for Binary Expression Aleatory Mosaic) that relies on sparse recombinase activation to generate two genetically distinct, non-overlapping populations of cells for comparative analysis. Following delivery of DNA constructs by transfection or viral transduction, combinatorial recombinase activity generates two distinct populations of cells labeled with either green or red fluorescent protein. Any gene of interest can be mis-expressed or deleted in one population for comparison with intermingled control cells. We have extensively optimized and characterized this system both in vitro and in vivo , and demonstrate its power for investigating cell autonomy, identifying temporally or spatially aberrant phenotypes, revealing changes in cell proliferation or death, and controlling for procedural variability.
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Li S, Hannenhalli S, Ovcharenko I. De novo human brain enhancers created by single-nucleotide mutations. SCIENCE ADVANCES 2023; 9:eadd2911. [PMID: 36791193 PMCID: PMC9931207 DOI: 10.1126/sciadv.add2911] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 01/12/2023] [Indexed: 05/30/2023]
Abstract
Advanced human cognition is attributed to increased neocortex size and complexity, but the underlying evolutionary and regulatory mechanisms are largely unknown. Using human and macaque embryonic neocortical H3K27ac data coupled with a deep learning model of enhancers, we identified ~4000 enhancer gains in humans, which, per our model, can often be attributed to single-nucleotide essential mutations. Our analyses suggest that functional gains in embryonic brain development are associated with de novo enhancers whose putative target genes exhibit increased expression in progenitor cells and interneurons and partake in critical neural developmental processes. Essential mutations alter enhancer activity through altered binding of key transcription factors (TFs) of embryonic neocortex, including ISL1, POU3F2, PITX1/2, and several SOX TFs, and are associated with central nervous system disorders. Overall, our results suggest that essential mutations lead to gain of embryonic neocortex enhancers, which orchestrate expression of genes involved in critical developmental processes associated with human cognition.
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Affiliation(s)
- Shan Li
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
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21
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Kopić J, Junaković A, Salamon I, Rasin MR, Kostović I, Krsnik Ž. Early Regional Patterning in the Human Prefrontal Cortex Revealed by Laminar Dynamics of Deep Projection Neuron Markers. Cells 2023; 12:231. [PMID: 36672166 PMCID: PMC9856843 DOI: 10.3390/cells12020231] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
Early regional patterning and laminar position of cortical projection neurons is determined by activation and deactivation of transcriptional factors (TFs) and RNA binding proteins (RBPs) that regulate spatiotemporal framework of neurogenetic processes (proliferation, migration, aggregation, postmigratory differentiation, molecular identity acquisition, axonal growth, dendritic development, and synaptogenesis) within transient cellular compartments. Deep-layer projection neurons (DPN), subplate (SPN), and Cajal-Retzius neurons (CRN) are early-born cells involved in the establishment of basic laminar and regional cortical architecture; nonetheless, laminar dynamics of their molecular transcriptional markers remain underexplored. Here we aimed to analyze laminar dynamics of DPN markers, i.e., transcription factors TBR1, CTIP2, TLE4, SOX5, and RBP CELF1 on histological serial sections of the human frontal cortex between 7.5-15 postconceptional weeks (PCW) in reference to transient proliferative, migratory, and postmigratory compartments. The subtle signs of regional patterning were seen during the late preplate phase in the pattern of sublaminar organization of TBR1+/Reelin+ CRN and TBR1+ pioneering SPN. During the cortical plate (CP)-formation phase, TBR1+ neurons became radially aligned, forming continuity from a well-developed subventricular zone to CP showing clear lateral to medial regional gradients. The most prominent regional patterning was seen during the subplate formation phase (around 13 PCW) when a unique feature of the orbitobasal frontal cortex displays a "double plate" pattern. In other portions of the frontal cortex (lateral, dorsal, medial) deep portion of CP becomes loose and composed of TBR1+, CTIP2+, TLE4+, and CELF1+ neurons of layer six and later-born SPN, which later become constituents of the expanded SP (around 15 PCW). Overall, TFs and RBPs mark characteristic regional laminar dynamics of DPN, SPN, and CRN subpopulations during remarkably early fetal phases of the highly ordered association cortex development.
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Affiliation(s)
- Janja Kopić
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Salata 12, 10000 Zagreb, Croatia
| | - Alisa Junaković
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Salata 12, 10000 Zagreb, Croatia
| | - Iva Salamon
- Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, 675 Hoes Lane West, Piscataway, NJ 08854, USA
- School of Graduate Studies, Rutgers University, New Brunswick, NJ 08854, USA
| | - Mladen-Roko Rasin
- Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, 675 Hoes Lane West, Piscataway, NJ 08854, USA
| | - Ivica Kostović
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Salata 12, 10000 Zagreb, Croatia
| | - Željka Krsnik
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Salata 12, 10000 Zagreb, Croatia
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22
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De Gregorio R, Subah G, Chan JC, Speranza L, Zhang X, Ramakrishnan A, Shen L, Maze I, Stanton PK, Sze JY. Sex-biased effects on hippocampal circuit development by perinatal SERT expression in CA3 pyramidal neurons. Development 2022; 149:dev200549. [PMID: 36178075 PMCID: PMC10655925 DOI: 10.1242/dev.200549] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022]
Abstract
Neurodevelopmental disorders ranging from autism to intellectual disability display sex-biased prevalence and phenotypical presentations. Despite increasing knowledge about temporospatial cortical map development and genetic variants linked to neurodevelopmental disorders, when and how sex-biased neural circuit derailment may arise in diseased brain remain unknown. Here, we identify in mice that serotonin uptake transporter (SERT) in non-serotonergic neurons - hippocampal and prefrontal pyramidal neurons - confers sex-biased effects specifically during neural circuit development. A set of gradient-patterned CA3 pyramidal neurons transiently express SERT to clear extracellular serotonin, coinciding with hippocampal synaptic circuit establishment. Ablating pyramidal neuron SERT (SERTPyramidΔ) alters dendritic spine developmental trajectory in the hippocampus, and precipitates sex-biased impairments in long-term activity-dependent hippocampal synaptic plasticity and cognitive behaviors. Transcriptomic analyses identify sex-biased alterations in gene sets associated with autism, dendritic spine structure, synaptic function and male-specific enrichment of dysregulated genes in glial cells in early postnatal SERTPyramidΔ hippocampus. Our data suggest that SERT function in these pyramidal neurons underscores a temporal- and brain region-specific regulation of normal sex-dimorphic circuit development and a source for sex-biased vulnerability to cognitive and behavioral impairments. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Roberto De Gregorio
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Galadu Subah
- Department of Cell Biology & Anatomy, New York Medical College, Valhalla, NY 10595, USA
| | - Jennifer C. Chan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NY 10029, USA
| | - Luisa Speranza
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Xiaolei Zhang
- Department of Cell Biology & Anatomy, New York Medical College, Valhalla, NY 10595, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NY 10029, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NY 10029, USA
| | - Ian Maze
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NY 10029, USA
| | - Patric K. Stanton
- Department of Cell Biology & Anatomy, New York Medical College, Valhalla, NY 10595, USA
| | - Ji Y. Sze
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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23
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Sun BB, Loomis SJ, Pizzagalli F, Shatokhina N, Painter JN, Foley CN, Jensen ME, McLaren DG, Chintapalli SS, Zhu AH, Dixon D, Islam T, Ba Gari I, Runz H, Medland SE, Thompson PM, Jahanshad N, Whelan CD. Genetic map of regional sulcal morphology in the human brain from UK biobank data. Nat Commun 2022; 13:6071. [PMID: 36241887 PMCID: PMC9568560 DOI: 10.1038/s41467-022-33829-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 10/05/2022] [Indexed: 12/24/2022] Open
Abstract
Genetic associations with macroscopic brain structure can provide insights into brain function and disease. However, specific associations with measures of local brain folding are largely under-explored. Here, we conducted large-scale genome- and exome-wide associations of regional cortical sulcal measures derived from magnetic resonance imaging scans of 40,169 individuals in UK Biobank. We discovered 388 regional brain folding associations across 77 genetic loci, with genes in associated loci enriched for expression in the cerebral cortex, neuronal development processes, and differential regulation during early brain development. We integrated brain eQTLs to refine genes for various loci, implicated several genes involved in neurodevelopmental disorders, and highlighted global genetic correlations with neuropsychiatric phenotypes. We provide an interactive 3D visualisation of our summary associations, emphasising added resolution of regional analyses. Our results offer new insights into the genetic architecture of brain folding and provide a resource for future studies of sulcal morphology in health and disease.
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Affiliation(s)
- Benjamin B Sun
- Translational Biology, Research & Development, Biogen Inc., Cambridge, MA, US.
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
| | - Stephanie J Loomis
- Translational Biology, Research & Development, Biogen Inc., Cambridge, MA, US
| | - Fabrizio Pizzagalli
- Department of Neuroscience "Rita Levi Montalcini", University of Turin, Turin, Italy
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, US
| | - Natalia Shatokhina
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, US
| | - Jodie N Painter
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Christopher N Foley
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Optima Partners, Edinburgh, UK
| | - Megan E Jensen
- Clinical Sciences, Research & Development, Biogen Inc., Cambridge, MA, US
| | - Donald G McLaren
- Clinical Sciences, Research & Development, Biogen Inc., Cambridge, MA, US
| | | | - Alyssa H Zhu
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, US
| | - Daniel Dixon
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, US
| | - Tasfiya Islam
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, US
| | - Iyad Ba Gari
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, US
| | - Heiko Runz
- Translational Biology, Research & Development, Biogen Inc., Cambridge, MA, US
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, US.
| | - Neda Jahanshad
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, US.
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24
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Fasano G, Compagnucci C, Dallapiccola B, Tartaglia M, Lauri A. Teleost Fish and Organoids: Alternative Windows Into the Development of Healthy and Diseased Brains. Front Mol Neurosci 2022; 15:855786. [PMID: 36034498 PMCID: PMC9403253 DOI: 10.3389/fnmol.2022.855786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
The variety in the display of animals’ cognition, emotions, and behaviors, typical of humans, has its roots within the anterior-most part of the brain: the forebrain, giving rise to the neocortex in mammals. Our understanding of cellular and molecular events instructing the development of this domain and its multiple adaptations within the vertebrate lineage has progressed in the last decade. Expanding and detailing the available knowledge on regionalization, progenitors’ behavior and functional sophistication of the forebrain derivatives is also key to generating informative models to improve our characterization of heterogeneous and mechanistically unexplored cortical malformations. Classical and emerging mammalian models are irreplaceable to accurately elucidate mechanisms of stem cells expansion and impairments of cortex development. Nevertheless, alternative systems, allowing a considerable reduction of the burden associated with animal experimentation, are gaining popularity to dissect basic strategies of neural stem cells biology and morphogenesis in health and disease and to speed up preclinical drug testing. Teleost vertebrates such as zebrafish, showing conserved core programs of forebrain development, together with patients-derived in vitro 2D and 3D models, recapitulating more accurately human neurogenesis, are now accepted within translational workflows spanning from genetic analysis to functional investigation. Here, we review the current knowledge of common and divergent mechanisms shaping the forebrain in vertebrates, and causing cortical malformations in humans. We next address the utility, benefits and limitations of whole-brain/organism-based fish models or neuronal ensembles in vitro for translational research to unravel key genes and pathological mechanisms involved in neurodevelopmental diseases.
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25
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Sato H, Hatakeyama J, Iwasato T, Araki K, Yamamoto N, Shimamura K. Thalamocortical axons control the cytoarchitecture of neocortical layers by area-specific supply of VGF. eLife 2022; 11:67549. [PMID: 35289744 PMCID: PMC8959604 DOI: 10.7554/elife.67549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/12/2022] [Indexed: 11/13/2022] Open
Abstract
Neuronal abundance and thickness of each cortical layer are specific to each area, but how this fundamental feature arises during development remains poorly understood. While some of area-specific features are controlled by intrinsic cues such as morphogens and transcription factors, the exact influence and mechanisms of action by cues extrinsic to the cortex, in particular the thalamic axons, have not been fully established. Here, we identify a thalamus-derived factor, VGF, which is indispensable for thalamocortical axons to maintain the proper amount of layer 4 neurons in the mouse sensory cortices. This process is prerequisite for further maturation of the primary somatosensory area, such as barrel field formation instructed by a neuronal activity-dependent mechanism. Our results provide an actual case in which highly site-specific axon projection confers further regional complexity upon the target field through locally secreting signaling molecules from axon terminals.
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Affiliation(s)
- Haruka Sato
- Department of Brain Morphogenesis, Kumamoto University, Kumamoto, Japan
| | - Jun Hatakeyama
- Department of Brain Morphogenesis, Kumamoto University, Kumamoto, Japan
| | - Takuji Iwasato
- Laboratory of Mammalian Neural Circuits, National Institute of Genetics, Mishima, Japan
| | - Kimi Araki
- Department of Brain Morphogenesis, Kumamoto University, Kumamoto, Japan
| | - Nobuhiko Yamamoto
- Laboratory of Cellular and Molecular Neurobiology, Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Kenji Shimamura
- Department of Brain Morphogenesis, Kumamoto University, Kumamoto, Japan
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26
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Zhao Q, Voon V, Zhang L, Shen C, Zhang J, Feng J. The ABCD Study: Brain Heterogeneity in Intelligence During a Neurodevelopmental Transition Stage. Cereb Cortex 2022; 32:3098-3109. [PMID: 35037940 PMCID: PMC9290553 DOI: 10.1093/cercor/bhab403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 08/31/2021] [Accepted: 09/28/2021] [Indexed: 11/29/2022] Open
Abstract
A complex curvilinear relationship exists between intelligence and age during the neurodevelopment of cortical thickness. To parse out a more fine-grained relationship between intelligence and cortical thickness and surface area, we used a large-scale data set focusing on a critical transition juncture in neurodevelopment in preadolescence. Cortical thickness was derived from T1-weighted structural magnetic resonance images of a large sample of 9- and 11-year-old children from the Adolescent Brain Cognitive Development study. The NIH Toolbox Cognition Battery composite scores, which included fluid, crystallized, and total scores, were used to assess intelligence. Using a double generalized linear model, we assessed the independent association between the mean and dispersion of cortical thickness/surface area and intelligence. Higher intelligence in preadolescents was associated with higher mean cortical thickness in orbitofrontal and primary sensory cortices but with lower thickness in the dorsolateral and medial prefrontal cortex and particularly in the rostral anterior cingulate. The rostral anterior cingulate findings were particularly evident across all subscales of intelligence. Higher intelligence was also associated with greater interindividual similarity in the rostral cingulate. Intelligence during this key transition juncture in preadolescence appears to reflect a dissociation between the cortical development of basic cognitive processes and higher-order executive and motivational processes.
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Affiliation(s)
| | | | - Lingli Zhang
- Developmental and Behavioral Pediatric & Child Primary Care Department, Ministry of Education-Shanghai Key Laboratory of Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, PR China
| | - Chun Shen
- Institute of Science and Technology for Brain Inspired Intelligence, Fudan University, Shanghai 200433, PR China
| | - Jie Zhang
- Address correspondence to Professor Jianfeng Feng, Institute of Science and Technology for Brain Inspired Intelligence, Fudan University, Shanghai 200433, PR China. ; Professor Jie Zhang, Institute of Science and Technology for Brain Inspired Intelligence, Fudan University, Shanghai 200433, PR China.
| | - Jianfeng Feng
- Address correspondence to Professor Jianfeng Feng, Institute of Science and Technology for Brain Inspired Intelligence, Fudan University, Shanghai 200433, PR China. ; Professor Jie Zhang, Institute of Science and Technology for Brain Inspired Intelligence, Fudan University, Shanghai 200433, PR China.
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27
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Xia K, Schmitt JE, Jha SC, Girault JB, Cornea E, Li G, Shen D, Styner M, Gilmore JH. Genetic Influences on Longitudinal Trajectories of Cortical Thickness and Surface Area during the First 2 Years of Life. Cereb Cortex 2022; 32:367-379. [PMID: 34231837 PMCID: PMC8897991 DOI: 10.1093/cercor/bhab213] [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: 01/15/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 11/14/2022] Open
Abstract
Genetic influences on cortical thickness (CT) and surface area (SA) are known to vary across the life span. Little is known about the extent to which genetic factors influence CT and SA in infancy and toddlerhood. We performed the first longitudinal assessment of genetic influences on variation in CT and SA in 501 twins who were aged 0-2 years. We observed substantial additive genetic influences on both average CT (0.48 in neonates, 0.37 in 1-year-olds, and 0.44 in 2-year-olds) and total SA (0.59 in neonates, 0.74 in 1-year-olds, and 0.73 in 2-year-olds). In addition, we found strong heritability of the change in average CT (0.49) from neonates to 1-year-olds, but not from 1- to 2-year-olds. Moreover, we found strong genetic correlations for average CT (rG = 0.92) between 1- and 2-year-olds and strong genetic correlations for total SA across all timepoints (rG = 0.96 between neonates and 1-year-olds, rG = 1 between 1- and 2-year-olds). In addition, we found CT and SA are strongly genetic correlated at birth, but weaken over time. Overall, results suggest a dynamic genetic relationship between CT and SA during first 2 years of life and provide novel insights into how genetic influences shape the cortical structure during early brain development.
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Affiliation(s)
- Kai Xia
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC 27599-7160, USA
| | - J Eric Schmitt
- Brain Behavior Laboratory, Department of Psychiatry, Neuropsychiatry Section, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shaili C Jha
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Jessica B Girault
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC 27599-7160, USA
| | - Emil Cornea
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC 27599-7160, USA
| | - Gang Li
- Department of Radiology, University of North Carolina, Chapel Hill, NC 27599-7320, USA
| | - Dinggang Shen
- Department of Radiology, University of North Carolina, Chapel Hill, NC 27599-7320, USA
| | - Martin Styner
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC 27599-7160, USA
| | - John H Gilmore
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC 27599-7160, USA
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28
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Tocco C, Bertacchi M, Studer M. Structural and Functional Aspects of the Neurodevelopmental Gene NR2F1: From Animal Models to Human Pathology. Front Mol Neurosci 2022; 14:767965. [PMID: 34975398 PMCID: PMC8715095 DOI: 10.3389/fnmol.2021.767965] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/25/2021] [Indexed: 01/28/2023] Open
Abstract
The assembly and maturation of the mammalian brain result from an intricate cascade of highly coordinated developmental events, such as cell proliferation, migration, and differentiation. Any impairment of this delicate multi-factorial process can lead to complex neurodevelopmental diseases, sharing common pathogenic mechanisms and molecular pathways resulting in multiple clinical signs. A recently described monogenic neurodevelopmental syndrome named Bosch-Boonstra-Schaaf Optic Atrophy Syndrome (BBSOAS) is caused by NR2F1 haploinsufficiency. The NR2F1 gene, coding for a transcriptional regulator belonging to the steroid/thyroid hormone receptor superfamily, is known to play key roles in several brain developmental processes, from proliferation and differentiation of neural progenitors to migration and identity acquisition of neocortical neurons. In a clinical context, the disruption of these cellular processes could underlie the pathogenesis of several symptoms affecting BBSOAS patients, such as intellectual disability, visual impairment, epilepsy, and autistic traits. In this review, we will introduce NR2F1 protein structure, molecular functioning, and expression profile in the developing mouse brain. Then, we will focus on Nr2f1 several functions during cortical development, from neocortical area and cell-type specification to maturation of network activity, hippocampal development governing learning behaviors, assembly of the visual system, and finally establishment of cortico-spinal descending tracts regulating motor execution. Whenever possible, we will link experimental findings in animal or cellular models to corresponding features of the human pathology. Finally, we will highlight some of the unresolved questions on the diverse functions played by Nr2f1 during brain development, in order to propose future research directions. All in all, we believe that understanding BBSOAS mechanisms will contribute to further unveiling pathophysiological mechanisms shared by several neurodevelopmental disorders and eventually lead to effective treatments.
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Affiliation(s)
- Chiara Tocco
- Université Côte d'Azur, CNRS, Inserm, iBV, Nice, France
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29
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Wilsch-Bräuninger M, Huttner WB. Primary Cilia and Centrosomes in Neocortex Development. Front Neurosci 2021; 15:755867. [PMID: 34744618 PMCID: PMC8566538 DOI: 10.3389/fnins.2021.755867] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/20/2021] [Indexed: 12/26/2022] Open
Abstract
During mammalian brain development, neural stem and progenitor cells generate the neurons for the six-layered neocortex. The proliferative capacity of the different types of progenitor cells within the germinal zones of the developing neocortex is a major determinant for the number of neurons generated. Furthermore, the various modes of progenitor cell divisions, for which the orientation of the mitotic spindle of progenitor cells has a pivotal role, are a key parameter to ensure the appropriate size and proper cytoarchitecture of the neocortex. Here, we review the roles of primary cilia and centrosomes of progenitor cells in these processes during neocortical development. We specifically focus on the apical progenitor cells in the ventricular zone. In particular, we address the alternating, dual role of the mother centriole (i) as a component of one of the spindle poles during mitosis, and (ii) as the basal body of the primary cilium in interphase, which is pivotal for the fate of apical progenitor cells and their proliferative capacity. We also discuss the interactions of these organelles with the microtubule and actin cytoskeleton, and with junctional complexes. Centriolar appendages have a specific role in this interaction with the cell cortex and the plasma membrane. Another topic of this review is the specific molecular composition of the ciliary membrane and the membrane vesicle traffic to the primary cilium of apical progenitors, which underlie the ciliary signaling during neocortical development; this signaling itself, however, is not covered in depth here. We also discuss the recently emerging evidence regarding the composition and roles of primary cilia and centrosomes in basal progenitors, a class of progenitors thought to be of particular importance for neocortex expansion in development and evolution. While the tight interplay between primary cilia and centrosomes makes it difficult to allocate independent roles to either organelle, mutations in genes encoding ciliary and/or centrosome proteins indicate that both are necessary for the formation of a properly sized and functioning neocortex during development. Human neocortical malformations, like microcephaly, underpin the importance of primary cilia/centrosome-related processes in neocortical development and provide fundamental insight into the underlying mechanisms involved.
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Affiliation(s)
| | - Wieland B Huttner
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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30
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Enhanced phosphorylation of S6 protein in mouse cortical layer V and subplate neurons. Neuroreport 2021; 31:762-769. [PMID: 32453020 DOI: 10.1097/wnr.0000000000001479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The mammalian neocortex is composed of six major layers of neurons. Each group of neurons in the cortical layers has distinct characteristics based on the expression of specific genes and connectivity patterns of neural circuits. Neuronal subtype transition and regional identity acquisition are established by temporal cues and interaction between several transcription factors during neurogenesis. The impairment of cortical lamination or neural circuits results in a wide range of neurodevelopmental disorders such as autism, schizophrenia, and certain forms of childhood epilepsy. Despite continuous efforts to classify neurons with the aid of genetic and epigenetic analyses, the neuron-specific properties associated with post-transcriptional modification remain unclear. In the present study, the distribution of phosphorylated S6-positive layers across the neocortex was examined using several layer markers. The development of pS6 S235/236 layers in layer V and the subplate was spatiotemporally regulated in the mouse brain. In addition, enhanced phosphorylation of ribosomal protein S6 in Ctip2-positive layer V neurons in vivo was sustained under in-vitro conditions using a culture of primary cortical neurons.
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31
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Palmer CE, Zhao W, Loughnan R, Zou J, Fan CC, Thompson WK, Dale AM, Jernigan TL. Distinct Regionalization Patterns of Cortical Morphology are Associated with Cognitive Performance Across Different Domains. Cereb Cortex 2021; 31:3856-3871. [PMID: 33825852 PMCID: PMC8258441 DOI: 10.1093/cercor/bhab054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/26/2021] [Accepted: 02/16/2021] [Indexed: 02/02/2023] Open
Abstract
Cognitive performance in children is predictive of academic and social outcomes; therefore, understanding neurobiological mechanisms underlying individual differences in cognition during development may be important for improving quality of life. The belief that a single, psychological construct underlies many cognitive processes is pervasive throughout society. However, it is unclear if there is a consistent neural substrate underlying many cognitive processes. Here, we show that a distributed configuration of cortical surface area and apparent thickness, when controlling for global imaging measures, is differentially associated with cognitive performance on different types of tasks in a large sample (N = 10 145) of 9-11-year-old children from the Adolescent Brain and Cognitive DevelopmentSM (ABCD) study. The minimal overlap in these regionalization patterns of association has implications for competing theories about developing intellectual functions. Surprisingly, not controlling for sociodemographic factors increased the similarity between these regionalization patterns. This highlights the importance of understanding the shared variance between sociodemographic factors, cognition and brain structure, particularly with a population-based sample such as ABCD.
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Affiliation(s)
- C E Palmer
- Center for Human Development, University of California, San Diego, La Jolla, CA 92161, USA
| | - W Zhao
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92093, USA
| | - R Loughnan
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92093, USA
| | - J Zou
- Division of Biostatistics, Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA 92161, USA
| | - C C Fan
- Center for Human Development, University of California, San Diego, La Jolla, CA 92161, USA
- Center for Multimodal Imaging and Genetics, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
| | - W K Thompson
- Division of Biostatistics, Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA 92161, USA
| | - A M Dale
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Radiology, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
- Department of Neuroscience, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
- Department of Psychiatry, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
| | - T L Jernigan
- Center for Human Development, University of California, San Diego, La Jolla, CA 92161, USA
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Radiology, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
- Department of Psychiatry, University of California, San Diego School of Medicine, La Jolla, CA 92037, USA
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32
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De Gregorio R, Chen X, Petit EI, Dobrenis K, Sze JY. Disruption of Transient SERT Expression in Thalamic Glutamatergic Neurons Alters Trajectory of Postnatal Interneuron Development in the Mouse Cortex. Cereb Cortex 2021; 30:1623-1636. [PMID: 31504267 DOI: 10.1093/cercor/bhz191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 06/29/2019] [Accepted: 07/16/2019] [Indexed: 12/13/2022] Open
Abstract
In mice, terminal differentiation of subpopulations of interneurons occurs in late postnatal stages, paralleling the emergence of the adult cortical architecture. Here, we investigated the effects of altered initial cortical architecture on later interneuron development. We identified that a class of somatostatin (SOM)-expressing GABAergic interneurons undergoes terminal differentiation between 2nd and 3rd postnatal week in the mouse somatosensory barrel cortex and upregulates Reelin expression during neurite outgrowth. Our previous work demonstrated that transient expression (E15-P10) of serotonin uptake transporter (SERT) in thalamocortical projection neurons regulates barrel elaboration during cortical map establishment. We show here that in thalamic neuron SERT knockout mice, these SOM-expressing interneurons develop at the right time, reach correct positions and express correct neurochemical markers, but only 70% of the neurons remain in the adult barrel cortex. Moreover, those neurons that remain display altered dendritic patterning. Our data indicate that a precise architecture at the cortical destination is not essential for specifying late-developing interneuron identities, their cortical deposition, and spatial organization, but dictates their number and dendritic structure ultimately integrated into the cortex. Our study illuminates how disruption of temporal-specific SERT function and related key regulators during cortical map establishment can alter interneuron development trajectory that persists to adult central nervous system.
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Affiliation(s)
- Roberto De Gregorio
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, The Bronx, NY 10461, USA
| | - Xiaoning Chen
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, The Bronx, NY 10461, USA
| | - Emilie I Petit
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, The Bronx, NY 10461, USA
| | - Kostantin Dobrenis
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, The Bronx, NY 10461, USA
| | - Ji Ying Sze
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, The Bronx, NY 10461, USA
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Romero S, Hight AE, Clayton KK, Resnik J, Williamson RS, Hancock KE, Polley DB. Cellular and Widefield Imaging of Sound Frequency Organization in Primary and Higher Order Fields of the Mouse Auditory Cortex. Cereb Cortex 2021; 30:1603-1622. [PMID: 31667491 DOI: 10.1093/cercor/bhz190] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The mouse auditory cortex (ACtx) contains two core fields-primary auditory cortex (A1) and anterior auditory field (AAF)-arranged in a mirror reversal tonotopic gradient. The best frequency (BF) organization and naming scheme for additional higher order fields remain a matter of debate, as does the correspondence between smoothly varying global tonotopy and heterogeneity in local cellular tuning. Here, we performed chronic widefield and two-photon calcium imaging from the ACtx of awake Thy1-GCaMP6s reporter mice. Data-driven parcellation of widefield maps identified five fields, including a previously unidentified area at the ventral posterior extreme of the ACtx (VPAF) and a tonotopically organized suprarhinal auditory field (SRAF) that extended laterally as far as ectorhinal cortex. Widefield maps were stable over time, where single pixel BFs fluctuated by less than 0.5 octaves throughout a 1-month imaging period. After accounting for neuropil signal and frequency tuning strength, BF organization in neighboring layer 2/3 neurons was intermediate to the heterogeneous salt and pepper organization and the highly precise local organization that have each been described in prior studies. Multiscale imaging data suggest there is no ultrasonic field or secondary auditory cortex in the mouse. Instead, VPAF and a dorsal posterior (DP) field emerged as the strongest candidates for higher order auditory areas.
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Affiliation(s)
- Sandra Romero
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | - Ariel E Hight
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | - Kameron K Clayton
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | - Jennifer Resnik
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA.,Department of Otolaryngology, Harvard Medical School, Boston, MA 02114, USA
| | - Ross S Williamson
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA.,Department of Otolaryngology, Harvard Medical School, Boston, MA 02114, USA
| | - Kenneth E Hancock
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA.,Department of Otolaryngology, Harvard Medical School, Boston, MA 02114, USA
| | - Daniel B Polley
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA.,Department of Otolaryngology, Harvard Medical School, Boston, MA 02114, USA
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34
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Alvarez I, Finlayson NJ, Ei S, de Haas B, Greenwood JA, Schwarzkopf DS. Heritable functional architecture in human visual cortex. Neuroimage 2021; 239:118286. [PMID: 34153449 PMCID: PMC7611349 DOI: 10.1016/j.neuroimage.2021.118286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/08/2021] [Accepted: 06/17/2021] [Indexed: 11/23/2022] Open
Abstract
We analyzed retinotopic maps from monozygotic and dizygotic twin pairs. Visual field maps in V1-V3 are more similar in monozygotic twins. Heritability is greater in V1 and V3 for polar angle and population receptive field sizes. Eccentricity maps show lesser degree of heritability. Further evidence for link between cortical morphology and topology of retinotopic maps.
How much of the functional organization of our visual system is inherited? Here we tested the heritability of retinotopic maps in human visual cortex using functional magnetic resonance imaging. We demonstrate that retinotopic organization shows a closer correspondence in monozygotic (MZ) compared to dizygotic (DZ) twin pairs, suggesting a partial genetic determination. Using population receptive field (pRF) analysis to examine the preferred spatial location and selectivity of these neuronal populations, we estimate a heritability around 10–20% for polar angle preferences and spatial selectivity, as quantified by pRF size, in extrastriate areas V2 and V3. Our findings are consistent with heritability in both the macroscopic arrangement of visual regions and stimulus tuning properties of visual cortex. This could constitute a neural substrate for variations in a range of perceptual effects, which themselves have been found to be at least partially genetically determined. These findings also add convergent evidence for the hypothesis that functional map topology is linked with cortical morphology.
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Affiliation(s)
- Ivan Alvarez
- Helen Wills Neuroscience Institute, University of California, Berkeley, United States; Wellcome Centre for Integrative Neuroimaging, University of Oxford, United Kingdom
| | - Nonie J Finlayson
- Experimental Psychology, University College London, United Kingdom; Ipsos, Brisbane, Queensland, Australia
| | - Shwe Ei
- Experimental Psychology, University College London, United Kingdom; GKT School of Medical Education, Kings College London, United Kingdom
| | - Benjamin de Haas
- Experimental Psychology, University College London, United Kingdom; Department of Psychology, Justus-Liebig University, Giessen, Germany
| | - John A Greenwood
- Experimental Psychology, University College London, United Kingdom
| | - D Samuel Schwarzkopf
- Experimental Psychology, University College London, United Kingdom; School of Optometry & Vision Science, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
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35
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Bauer R, Clowry GJ, Kaiser M. Creative Destruction: A Basic Computational Model of Cortical Layer Formation. Cereb Cortex 2021; 31:3237-3253. [PMID: 33625496 PMCID: PMC8196252 DOI: 10.1093/cercor/bhab003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022] Open
Abstract
One of the most characteristic properties of many vertebrate neural systems is the layered organization of different cell types. This cytoarchitecture exists in the cortex, the retina, the hippocampus, and many other parts of the central nervous system. The developmental mechanisms of neural layer formation have been subject to substantial experimental efforts. Here, we provide a general computational model for cortical layer formation in 3D physical space. We show that this multiscale, agent-based model, comprising two distinct stages of apoptosis, can account for the wide range of neuronal numbers encountered in different cortical areas and species. Our results demonstrate the phenotypic richness of a basic state diagram structure. Importantly, apoptosis allows for changing the thickness of one layer without automatically affecting other layers. Therefore, apoptosis increases the flexibility for evolutionary change in layer architecture. Notably, slightly changed gene regulatory dynamics recapitulate the characteristic properties observed in neurodevelopmental diseases. Overall, we propose a novel computational model using gene-type rules, exhibiting many characteristics of normal and pathological cortical development.
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Affiliation(s)
- Roman Bauer
- Department of Computer Science, University of Surrey, Guildford, GU2 7XH, UK
| | - Gavin J Clowry
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Marcus Kaiser
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, UK
- Precision Imaging Beacon, School of Medicine, University of Nottingham, Nottingham NG7 2UH, UK
- Rui Jin Hospital, Shanghai Jiao Tong University, Shanghai 200025, China
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36
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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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37
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Schmidt AR, Gariboldi MC, Cortasa SA, Proietto S, Corso MC, Inserra PIF, Jaime VS, Halperin J, Vitullo AD, Dorfman VB. Neocortical Anatomy in the South American Plains Vizcacha, Lagostomus maximus, Reveals Different Strategies in Encephalic Development among Hystricomorpha and Myomorpha Rodents. BRAIN, BEHAVIOR AND EVOLUTION 2021; 95:318-329. [PMID: 33910193 DOI: 10.1159/000515638] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/02/2021] [Indexed: 11/19/2022]
Abstract
Depending on the presence or absence of sulci and convolutions, the brains of mammals are classified as gyrencephalic or lissencephalic. We analyzed the encephalic anatomy of the hystricomorph rodent Lagostomus maximus in comparison with other evolutionarily related species. The encephalization quotient (EQ), gyrencephaly index (GI), and minimum cortical thickness (MCT) were calculated for the plains vizcacha as well as for other myomorph and hystricomorph rodents. The vizcacha showed a gyrencephalic brain with a sagittal longitudinal fissure that divides both hemispheres, and 3 pairs of sulci with bilateral symmetry; that is, lateral-rostral, intraparietal, and transverse sulci. The EQ had one of the lowest values among Hystricomorpha, while GI was one of the highest. Besides, the MCT was close to the mean value for the suborder. The comparison of EQ, GI, and MCT values between hystricomorph and myomorph species allowed the detection of significant variations. Both EQ and GI showed a significant increase in Hystricomorpha compared to Myomorpha, whereas a Pearson's analysis between EQ and GI depicted an inverse correlation pattern for Hystricomorpha. Furthermore, the ratio between MCT and GI also showed a negative correlation for Hystricomorpha and Myomorpha. Our phylogenetic analyses showed that Hystricomorpha and Myomorpha do not differ in their allometric patterning between the brain and body mass, GI and brain mass, and MCT and GI. In conclusion, gyrencephalic neuroanatomy in the vizcacha could have developed from the balance between the brain size, the presence of invaginations, and the cortical thickness, which resulted in a mixed encephalization strategy for the species. Gyrencephaly in the vizcacha, as well as in other Hystricomorpha, advocates in favor of the proposal that in the more recently evolved Myomorpha lissencephaly would have arisen from a phenotype reversal process.
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Affiliation(s)
- Alejandro Raúl Schmidt
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Constanza Gariboldi
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina
| | - Santiago Andrés Cortasa
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Sofía Proietto
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Clara Corso
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Pablo Ignacio Felipe Inserra
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Vanina Soledad Jaime
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina
| | - Julia Halperin
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Alfredo Daniel Vitullo
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Verónica Berta Dorfman
- Centro de Estudios Biomédicos Básicos, Aplicados y Desarrollo (CEBBAD), Universidad Maimónides, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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38
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Gryglewski G, Murgaš M, Klöbl M, Reed MB, Unterholzner J, Michenthaler P, Lanzenberger R. Enrichment of Disease-Associated Genes in Cortical Areas Defined by Transcriptome-Based Parcellation. BIOLOGICAL PSYCHIATRY: COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2021; 7:10-23. [PMID: 33711548 DOI: 10.1016/j.bpsc.2021.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/05/2021] [Accepted: 02/23/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Parcellation of the cerebral cortex serves the investigation of the emergence of uniquely human brain functions and disorders. Transcriptome data enable the characterization of the molecular properties of cortical areas in unprecedented detail. Previously, we predicted the expression of 18,686 genes in the entire human brain based on microarray data. Here, we employed these data to parcellate the cortex and study the regional enrichment of disease-associated genes. METHODS We performed agglomerative hierarchical clustering based on normalized transcriptome data to delineate areas with distinct gene expression profiles. Subsequently, we tested these profiles for the enrichment of gene sets associated with brain disorders by genome-wide association studies and expert-curated databases using gene set enrichment analysis. RESULTS Transcriptome-based parcellation identified borders in line with major anatomical landmarks and the functional differentiation of primary motor, somatosensory, visual, and auditory areas. Gene set enrichment analysis based on curated databases suggested new roles of specific areas in psychiatric and neurological disorders while reproducing well-established links for movement and neurodegenerative disorders, for example, amyotrophic lateral sclerosis (motor cortex) and Alzheimer's disease (entorhinal cortex). Meanwhile, gene sets derived from genome-wide association studies on psychiatric disorders exhibited similar enrichment patterns driven by pleiotropic genes expressed in the posterior fusiform gyrus and inferior parietal lobule. CONCLUSIONS The identified enrichment patterns suggest the vulnerability of specific cortical areas to various influences that might alter the risk of developing one or several brain disorders. For several diseases, specific genes were highlighted, which could lead to the discovery of novel disease mechanisms and urgently needed treatments.
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Affiliation(s)
- Gregor Gryglewski
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Matej Murgaš
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Manfred Klöbl
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Murray Bruce Reed
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Jakob Unterholzner
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Paul Michenthaler
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Rupert Lanzenberger
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria.
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39
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Morozov YM, Mackie K, Rakic P. Cannabinoid Type 1 Receptor is Undetectable in Rodent and Primate Cerebral Neural Stem Cells but Participates in Radial Neuronal Migration. Int J Mol Sci 2020; 21:ijms21228657. [PMID: 33212822 PMCID: PMC7696736 DOI: 10.3390/ijms21228657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/13/2020] [Accepted: 11/15/2020] [Indexed: 12/14/2022] Open
Abstract
Cannabinoid type 1 receptor (CB1R) is expressed and participates in several aspects of cerebral cortex embryonic development as demonstrated with whole-transcriptome mRNA sequencing and other contemporary methods. However, the cellular location of CB1R, which helps to specify molecular mechanisms, remains to be documented. Using three-dimensional (3D) electron microscopic reconstruction, we examined CB1R immunolabeling in proliferating neural stem cells (NSCs) and migrating neurons in the embryonic mouse (Mus musculus) and rhesus macaque (Macaca mulatta) cerebral cortex. We found that the mitotic and postmitotic ventricular and subventricular zone (VZ and SVZ) cells are immunonegative in both species while radially migrating neurons in the intermediate zone (IZ) and cortical plate (CP) contain CB1R-positive intracellular vesicles. CB1R immunolabeling was more numerous and more extensive in monkeys compared to mice. In CB1R-knock out mice, projection neurons in the IZ show migration abnormalities such as an increased number of lateral processes. Thus, in radially migrating neurons CB1R provides a molecular substrate for the regulation of cell movement. Undetectable level of CB1R in VZ/SVZ cells indicates that previously suggested direct CB1R-transmitted regulation of cellular proliferation and fate determination demands rigorous re-examination. More abundant CB1R expression in monkey compared to mouse suggests that therapeutic or recreational cannabis use may be more distressing for immature primate neurons than inferred from experiments with rodents.
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Affiliation(s)
- Yury M. Morozov
- Department of Neuroscience, Kavli Institute for Neuroscience, Yale School of Medicine, Yale University, New Haven, CT 6510, USA
- Correspondence: (Y.M.M.); (P.R.)
| | - Ken Mackie
- Gill Center for Biomolecular Science, Indiana University, Bloomington, IN 47405-2204, USA;
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405-2204, USA
| | - Pasko Rakic
- Department of Neuroscience, Kavli Institute for Neuroscience, Yale School of Medicine, Yale University, New Haven, CT 6510, USA
- Correspondence: (Y.M.M.); (P.R.)
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40
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Fjell AM, Chen CH, Sederevicius D, Sneve MH, Grydeland H, Krogsrud SK, Amlien I, Ferschmann L, Ness H, Folvik L, Beck D, Mowinckel AM, Tamnes CK, Westerhausen R, Håberg AK, Dale AM, Walhovd KB. Continuity and Discontinuity in Human Cortical Development and Change From Embryonic Stages to Old Age. Cereb Cortex 2020; 29:3879-3890. [PMID: 30357317 DOI: 10.1093/cercor/bhy266] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/28/2018] [Indexed: 11/12/2022] Open
Abstract
The human cerebral cortex is highly regionalized, and this feature emerges from morphometric gradients in the cerebral vesicles during embryonic development. We tested if this principle of regionalization could be traced from the embryonic development to the human life span. Data-driven fuzzy clustering was used to identify regions of coordinated longitudinal development of cortical surface area (SA) and thickness (CT) (n = 301, 4-12 years). The principal divide for the developmental SA clusters extended from the inferior-posterior to the superior-anterior cortex, corresponding to the major embryonic morphometric anterior-posterior (AP) gradient. Embryonic factors showing a clear AP gradient were identified, and we found significant differences in gene expression of these factors between the anterior and posterior clusters. Further, each identified developmental SA and CT clusters showed distinguishable life span trajectories in a larger longitudinal dataset (4-88 years, 1633 observations), and the SA and CT clusters showed differential relationships to cognitive functions. This means that regions that developed together in childhood also changed together throughout life, demonstrating continuity in regionalization of cortical changes. The AP divide in SA development also characterized genetic patterning obtained in an adult twin sample. In conclusion, the development of cortical regionalization is a continuous process from the embryonic stage throughout life.
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Affiliation(s)
- Anders M Fjell
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway.,Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
| | - Chi-Hua Chen
- Department of Radiology, University of California, San Diego, La Jolla, CA, USA
| | - Donatas Sederevicius
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway
| | - Markus H Sneve
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway
| | - Håkon Grydeland
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway
| | - Stine K Krogsrud
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway
| | - Inge Amlien
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway
| | - Lia Ferschmann
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway
| | - Hedda Ness
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway
| | - Line Folvik
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway
| | - Dani Beck
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway
| | - Athanasia M Mowinckel
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway
| | - Christian K Tamnes
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway
| | - René Westerhausen
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway
| | - Asta K Håberg
- Department of Medical Imaging, St. Olav's Hospital, Trondheim, Norway.,Department of Neuroscience, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Anders M Dale
- Department of Radiology, University of California, San Diego, La Jolla, CA, USA.,Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Kristine B Walhovd
- Department of Psychology, Center for Lifespan Changes in Brain and Cognition, University of Oslo, Oslo, Norway.,Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
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41
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Save L, Baude A, Cossart R. Temporal Embryonic Origin Critically Determines Cellular Physiology in the Dentate Gyrus. Cereb Cortex 2020; 29:2639-2652. [PMID: 29878074 DOI: 10.1093/cercor/bhy132] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/12/2018] [Indexed: 01/19/2023] Open
Abstract
The dentate gyrus, the entry gate to the hippocampus, comprises 3 types of glutamatergic cells, the granule, the mossy and the semilunar granule cells. Whereas accumulating evidence indicates that specification of subclasses of neocortical neurons starts at the time of their final mitotic divisions, when cellular diversity is specified in the Dentate Gyrus remains largely unknown. Here we show that semilunar cells, like mossy cells, originate from the earliest stages of developmental neurogenesis and that early born neurons form age-matched circuits with each other. Besides morphology, adult semilunar cells display characteristic electrophysiological features that differ from most neurons but are shared among early born granule cells. Therefore, an early birthdate specifies adult granule cell physiology and connectivity whereas additional factors may combine to produce morphological identity.
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Affiliation(s)
- Laurène Save
- Inserm, Marseille, France.,Aix-Marseille University, UMR, Marseille, France.,INMED, Marseille, France
| | - Agnès Baude
- Inserm, Marseille, France.,Aix-Marseille University, UMR, Marseille, France.,INMED, Marseille, France
| | - Rosa Cossart
- Inserm, Marseille, France.,Aix-Marseille University, UMR, Marseille, France.,INMED, Marseille, France
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42
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Kim H, Berens NC, Ochandarena NE, Philpot BD. Region and Cell Type Distribution of TCF4 in the Postnatal Mouse Brain. Front Neuroanat 2020; 14:42. [PMID: 32765228 PMCID: PMC7379912 DOI: 10.3389/fnana.2020.00042] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 06/22/2020] [Indexed: 12/14/2022] Open
Abstract
Transcription factor 4 is a class I basic helix-loop-helix transcription factor regulating gene expression. Altered TCF4 gene expression has been linked to non-syndromic intellectual disability, schizophrenia, and a severe neurodevelopmental disorder known as Pitt-Hopkins syndrome. An understanding of the cell types expressing TCF4 protein in the mouse brain is needed to help identify potential pathophysiological mechanisms and targets for therapeutic delivery in TCF4-linked disorders. Here we developed a novel green fluorescent protein reporter mouse to visualize TCF4-expressing cells throughout the brain. Using this TCF4 reporter mouse, we observed prominent expression of TCF4 in the pallial region and cerebellum of the postnatal brain. At the cellular level, both glutamatergic and GABAergic neurons express TCF4 in the cortex and hippocampus, while only a subset of GABAergic interneurons express TCF4 in the striatum. Among glial cell groups, TCF4 is present in astrocytes and immature and mature oligodendrocytes. In the cerebellum, cells in the granule and molecular layer express TCF4. Our findings greatly extend our knowledge of the spatiotemporal and cell type-specific expression patterns of TCF4 in the brain, and hence, lay the groundwork to better understand TCF4-linked neurological disorders. Any effort to restore TCF4 functions through small molecule or genetic therapies should target these brain regions and cell groups to best recapitulate TCF4 expression patterns.
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Affiliation(s)
- Hyojin Kim
- Department of Cell Biology & Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Noah C. Berens
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Nicole E. Ochandarena
- MD-Ph.D. Program, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Benjamin D. Philpot
- Department of Cell Biology & Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Carolina Institute for Developmental Disabilities, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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43
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Markovic A, Kaess M, Tarokh L. Environmental Factors Shape Sleep EEG Connectivity During Early Adolescence. Cereb Cortex 2020; 30:5780-5791. [DOI: 10.1093/cercor/bhaa151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 04/12/2020] [Accepted: 05/06/2020] [Indexed: 02/01/2023] Open
Abstract
Abstract
Quantifying the degree to which genetic and environmental factors shape brain network connectivity is critical to furthering our understanding of the developing human brain. Sleep, a state of sensory disengagement, provides a unique opportunity to study brain network activity noninvasively by means of sleep electroencephalography (EEG) coherence. We conducted a high-density sleep EEG study in monozygotic (MZ; n = 38; mean age = 12.46; 20 females) and dizygotic (DZ; n = 24; mean age = 12.50; 12 females) twins to assess the heritability of sleep EEG coherence in early adolescence—a period of significant brain rewiring. Structural equation modeling was used to estimate three latent factors: genes, environmental factors shared between twins and environmental factors unique to each twin. We found a strong contribution of unique environmental factors (66% of the variance) and moderate genetic influence (19% of the variance) on sleep EEG coherence across frequencies and sleep states. An exception to this was sleep spindle activity, an index of the thalamocortical network, which showed on average a genetic contribution of 48% across connections. Furthermore, we observed high intraindividual stability of coherence across two consecutive nights suggesting that despite only a modest genetic contribution, sleep EEG coherence is like a trait. Our findings in adolescent humans are in line with earlier findings in animals that show the primordial cerebral map and its connections are plastic and it is through interaction with the environment that the pattern of brain network connectivity is shaped. Therefore, even in twins living together, small differences in the environment may cascade into meaningful differences in brain connectivity.
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Affiliation(s)
- Andjela Markovic
- University Hospital of Child and Adolescent Psychiatry and Psychotherapy, University of Bern, Bern 3000, Switzerland
- Graduate School for Health Sciences, University of Bern, Bern 3000, Switzerland
| | - Michael Kaess
- University Hospital of Child and Adolescent Psychiatry and Psychotherapy, University of Bern, Bern 3000, Switzerland
- Section for Translational Psychobiology in Child and Adolescent Psychiatry, Department of Child and Adolescent Psychiatry, Center for Psychosocial Medicine, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Leila Tarokh
- University Hospital of Child and Adolescent Psychiatry and Psychotherapy, University of Bern, Bern 3000, Switzerland
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44
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Shafik AM, Allen EG, Jin P. Dynamic N6-methyladenosine RNA methylation in brain and diseases. Epigenomics 2020; 12:371-380. [PMID: 32081027 DOI: 10.2217/epi-2019-0260] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
N6-methyladenosine (m6A) is a dynamic RNA modification that regulates various aspects of RNA metabolism and has been implicated in many biological processes and transitions. m6A is highly abundant in the brain; however, only recently has the role of m6A in brain development been a focus. The machinery that controls m6A is critically important for proper neurodevelopment, and the precise mechanisms by which m6A regulates these processes are starting to emerge. However, the role of m6A in neurodegenerative and neuropsychiatric diseases still requires much elucidation. This review discusses and summarizes the current body of knowledge surrounding the function of the m6A modification in regulating normal brain development, neurodegenerative diseases and outlines possible future directions.
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Affiliation(s)
- Andrew M Shafik
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Emily G Allen
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
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45
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Subramanian L, Calcagnotto ME, Paredes MF. Cortical Malformations: Lessons in Human Brain Development. Front Cell Neurosci 2020; 13:576. [PMID: 32038172 PMCID: PMC6993122 DOI: 10.3389/fncel.2019.00576] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 12/16/2019] [Indexed: 12/11/2022] Open
Abstract
Creating a functional cerebral cortex requires a series of complex and well-coordinated developmental steps. These steps have evolved across species with the emergence of cortical gyrification and coincided with more complex behaviors. The presence of diverse progenitor cells, a protracted timeline for neuronal migration and maturation, and diverse neuronal types are developmental features that have emerged in the gyrated cortex. These factors could explain how the human brain has expanded in size and complexity. However, their complex nature also renders new avenues of vulnerability by providing additional cell types that could contribute to disease and longer time windows that could impact the composition and organization of the cortical circuit. We aim to discuss the unique developmental steps observed in human corticogenesis and propose how disruption of these species-unique processes could lead to malformations of cortical development.
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Affiliation(s)
- Lakshmi Subramanian
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, United States
| | - Maria Elisa Calcagnotto
- Neurophysiology and Neurochemistry of Neuronal Excitability and Synaptic Plasticity Laboratory, Department of Biochemistry, ICBS, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Graduate Program in Biological Sciences: Biochemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Graduate Program in Neuroscience, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Mercedes F Paredes
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, United States.,Department of Neurology, University of California, San Francisco, San Francisco, CA, United States.,Neuroscience Graduate Division, University of California, San Francisco, San Francisco, CA, United States
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46
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Tadayon E, Pascual-Leone A, Santarnecchi E. Differential Contribution of Cortical Thickness, Surface Area, and Gyrification to Fluid and Crystallized Intelligence. Cereb Cortex 2020; 30:215-225. [PMID: 31329833 PMCID: PMC7029693 DOI: 10.1093/cercor/bhz082] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 03/12/2019] [Accepted: 03/28/2019] [Indexed: 01/30/2023] Open
Abstract
Human intelligence can be broadly subdivided into fluid (gf) and crystallized (gc) intelligence, each tapping into distinct cognitive abilities. Although neuroanatomical correlates of intelligence have been previously studied, differential contribution of cortical morphologies to gf and gc has not been fully delineated. Here, we tried to disentangle the contribution of cortical thickness, cortical surface area, and cortical gyrification to gf and gc in a large sample of healthy young subjects (n = 740, Human Connectome Project) with high-resolution MRIs, followed by replication in a separate data set with distinct cognitive measures indexing gf and gc. We found that while gyrification in distributed cortical regions had positive association with both gf and gc, surface area and thickness showed more regional associations. Specifically, higher performance in gf was associated with cortical expansion in regions related to working memory, attention, and visuo-spatial processing, while gc was associated with thinner cortex as well as higher cortical surface area in language-related networks. We discuss the results in a framework where "horizontal" cortical expansion enables higher resource allocation, computational capacity, and functional specificity relevant to gf and gc, while lower cortical thickness possibly reflects cortical pruning facilitating "vertical" intracolumnar efficiency in knowledge-based tasks relevant mostly to gc.
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Affiliation(s)
- Ehsan Tadayon
- Berenson-Allen Center for Noninvasive Brain Stimulation, Division of Cognitive Neurology, Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Alvaro Pascual-Leone
- Berenson-Allen Center for Noninvasive Brain Stimulation, Division of Cognitive Neurology, Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Emiliano Santarnecchi
- Berenson-Allen Center for Noninvasive Brain Stimulation, Division of Cognitive Neurology, Department of Neurology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
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47
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Shin J, French L, Xu T, Leonard G, Perron M, Pike GB, Richer L, Veillette S, Pausova Z, Paus T. Cell-Specific Gene-Expression Profiles and Cortical Thickness in the Human Brain. Cereb Cortex 2019; 28:3267-3277. [PMID: 28968835 DOI: 10.1093/cercor/bhx197] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/13/2017] [Indexed: 01/25/2023] Open
Abstract
Neurobiological underpinnings of cortical thickness in the human brain are largely unknown. Here we use cell-type-specific gene markers to evaluate the contribution of 9 neural cell-types in explaining inter-regional variations in cortical thickness and age-related cortical thinning in the adolescent brain. Gene-expression data were derived from the Allen Human Brain Atlas (and validated using the BrainSpan Atlas). Values of cortical thickness/thinning were obtained with magnetic resonance imaging in a sample of 987 adolescents. We show that inter-regional profiles in cortical thickness relate to those in the expression of genes marking CA1 pyramidal cells, astrocytes, and microglia; taken together, the 3 cell types explain 70% of regional variation in cortical thickness. We also show that inter-regional profiles in cortical thinning relate to those in the expression of genes marking CA1 and S1 pyramidal cells, astrocytes and microglia. Using Gene Ontology analysis, we demonstrate that the difference in the contribution of CA1 and S1 pyramidal cells may relate to biological processes such as neuronal plasticity and potassium channel activity, respectively. This "virtual histology" approach (scripts provided) can be used to examine neurobiological underpinnings of cortical profiles associated with development, aging, and various disorders.
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Affiliation(s)
- Jean Shin
- The Hospital for Sick Children, University of Toronto, Toronto, Canada.,Rotman Research Institute, University of Toronto, Toronto, Canada
| | - Leon French
- Centre for Addition and Mental Health, Toronto, Canada.,Department of Psychiatry, University of Toronto, Toronto, Canada.,Institute of Medical Sciences, University of Toronto, Toronto, Canada
| | - Ting Xu
- Center for Developing Brain, Child Mind Institute, New York, NY, USA
| | - Gabriel Leonard
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | | | - G Bruce Pike
- Departments of Radiology & Clinical Neuroscience, University of Calgary, Calgary, Canada
| | - Louis Richer
- Department of Psychology, University of Quebec in Chicoutimi, Chicoutimi, Canada
| | | | - Zdenka Pausova
- The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Tomáš Paus
- Rotman Research Institute, University of Toronto, Toronto, Canada.,Department of Psychiatry, University of Toronto, Toronto, Canada.,Center for Developing Brain, Child Mind Institute, New York, NY, USA.,Department of Psychology, University of Toronto, Toronto,Canada
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48
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White TJH. Brain Development and Stochastic Processes During Prenatal and Early Life: You Can't Lose It if You've Never Had It; But It's Better to Have It and Lose It, Than Never to Have Had It at All. J Am Acad Child Adolesc Psychiatry 2019; 58:1042-1050. [PMID: 31327672 DOI: 10.1016/j.jaac.2019.02.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/04/2019] [Accepted: 02/22/2019] [Indexed: 11/29/2022]
Abstract
Brain development, although largely driven by genetic processes, also is influenced by environmental factors. However, there has been little discussion in the psychiatric literature on the role of stochastic, or chance, events that take place during neurodevelopment. Studies suggest that the brain capitalizes on and regulates the extent of stochastic processes during development. Furthermore, because neurodevelopment is influenced by environmental factors, there is emerging evidence that fostering those positive environmental factors during prenatal and early life could optimize neurodevelopment and provide greater resilience, including those potentially resulting from stochastic processes. Evidence for the role of environmental factors in optimizing early brain development is supported by work in large population-based studies of child development, randomized control trials in high-risk populations, and early-life adoption studies. The public health message is that creating an environment that fosters optimal brain development during prenatal and early life could prevent psychopathology and provide the developing brain the best chance against negative stochastic processes and potential stressors that are inevitable later in life.
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Affiliation(s)
- Tonya J H White
- Erasmus University Medical Centre, Rotterdam, The Netherlands.
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49
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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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50
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Franz H, Villarreal A, Heidrich S, Videm P, Kilpert F, Mestres I, Calegari F, Backofen R, Manke T, Vogel T. DOT1L promotes progenitor proliferation and primes neuronal layer identity in the developing cerebral cortex. Nucleic Acids Res 2019; 47:168-183. [PMID: 30329130 PMCID: PMC6326801 DOI: 10.1093/nar/gky953] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/04/2018] [Indexed: 01/01/2023] Open
Abstract
Cortical development is controlled by transcriptional programs, which are orchestrated by transcription factors. Yet, stable inheritance of spatio-temporal activity of factors influencing cell fate and localization in different layers is only partly understood. Here we find that deletion of Dot1l in the murine telencephalon leads to cortical layering defects, indicating DOT1L activity and chromatin methylation at H3K79 impact on the cell cycle, and influence transcriptional programs conferring upper layer identity in early progenitors. Specifically, DOT1L prevents premature differentiation by increasing expression of genes that regulate asymmetric cell division (Vangl2, Cenpj). Loss of DOT1L results in reduced numbers of progenitors expressing genes including SoxB1 gene family members. Loss of DOT1L also leads to altered cortical distribution of deep layer neurons that express either TBR1, CTIP2 or SOX5, and less activation of transcriptional programs that are characteristic for upper layer neurons (Satb2, Pou3f3, Cux2, SoxC family members). Data from three different mouse models suggest that DOT1L balances transcriptional programs necessary for proper neuronal composition and distribution in the six cortical layers. Furthermore, because loss of DOT1L in the pre-neurogenic phase of development impairs specifically generation of SATB2-expressing upper layer neurons, our data suggest that DOT1L primes upper layer identity in cortical progenitors.
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Affiliation(s)
- Henriette Franz
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Alejandro Villarreal
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Stefanie Heidrich
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Pavankumar Videm
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, 79110 Freiburg, Germany
| | - Fabian Kilpert
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Ivan Mestres
- DFG-Research Center and Cluster of Excellence for Regenerative Therapies (CRTD), School of Medicine, Technical University Dresden, 01307 Dresden, Germany
| | - Federico Calegari
- DFG-Research Center and Cluster of Excellence for Regenerative Therapies (CRTD), School of Medicine, Technical University Dresden, 01307 Dresden, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, 79110 Freiburg, Germany.,Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany.,Center for non-coding RNA in Technology and Health, University of Copenhagen, DK-1870 Frederiksberg C, Denmark
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Tanja Vogel
- Institute of Anatomy and Cell Biology, Department of Molecular Embryology, Medical Faculty, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
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