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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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Barandela M, Núñez-González C, Suzuki DG, Jiménez-López C, Pombal MA, Pérez-Fernández J. Unravelling the functional development of vertebrate pathways controlling gaze. Front Cell Dev Biol 2023; 11:1298486. [PMID: 37965576 PMCID: PMC10640995 DOI: 10.3389/fcell.2023.1298486] [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: 09/21/2023] [Accepted: 10/13/2023] [Indexed: 11/16/2023] Open
Abstract
Animals constantly redirect their gaze away or towards relevant targets and, besides these goal-oriented responses, stabilizing movements clamp the visual scene avoiding image blurring. The vestibulo-ocular (VOR) and the optokinetic reflexes are the main contributors to gaze stabilization, whereas the optic tectum integrates multisensory information and generates orienting/evasive gaze movements in all vertebrates. Lampreys show a unique stepwise development of the visual system whose understanding provides important insights into the evolution and development of vertebrate vision. Although the developmental emergence of the visual components, and the retinofugal pathways have been described, the functional development of the visual system and the development of the downstream pathways controlling gaze are still unknown. Here, we show that VOR followed by light-evoked eye movements are the first to appear already in larvae, despite their burrowed lifestyle. However, the circuits controlling goal-oriented responses emerge later, in larvae in non-parasitic lampreys but during late metamorphosis in parasitic lampreys. The appearance of stabilizing responses earlier than goal-oriented in the lamprey development shows a stepwise transition from simpler to more complex visual systems, offering a unique opportunity to isolate the functioning of their underlying circuits.
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Affiliation(s)
- Marta Barandela
- CINBIO, Universidade de Vigo, Neurocircuits Group, Campus universitario Lagoas, Marcosende, Vigo, Spain
| | - Carmen Núñez-González
- CINBIO, Universidade de Vigo, Neurocircuits Group, Campus universitario Lagoas, Marcosende, Vigo, Spain
| | - Daichi G. Suzuki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Cecilia Jiménez-López
- CINBIO, Universidade de Vigo, Neurocircuits Group, Campus universitario Lagoas, Marcosende, Vigo, Spain
| | - Manuel A. Pombal
- Department of Functional Biology and Health Sciences, Facultade de Bioloxía-IBIV, Universidade de Vigo, Campus universitario Lagoas, Marcosende, Vigo, Spain
| | - Juan Pérez-Fernández
- CINBIO, Universidade de Vigo, Neurocircuits Group, Campus universitario Lagoas, Marcosende, Vigo, Spain
- Department of Functional Biology and Health Sciences, Facultade de Bioloxía-IBIV, Universidade de Vigo, Campus universitario Lagoas, Marcosende, Vigo, Spain
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Einspieler C, Prayer D, Marschik PB. Fetal movements: the origin of human behaviour. Dev Med Child Neurol 2021; 63:1142-1148. [PMID: 33973235 DOI: 10.1111/dmcn.14918] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/15/2021] [Indexed: 02/01/2023]
Abstract
The study of the onset and ontogeny of human behaviour has made it clear that a multitude of fetal movement patterns are spontaneously generated, and that there is a close association between activity and the development of peripheral and central structures. The embryo starts moving by 7.5 week's gestation; 2 to 3 weeks later, a number of movement patterns including general movements, isolated limb and head movements, hiccup, and breathing movements, appear. Some movements (e.g. yawning, smiling, 'pointing'; we show these in eight videos in this review) precede life-long patterns; others have intrauterine functions, such as sucking/swallowing for amniotic fluid regulation, breathing movements for lung development, or eye movements for retinal cell diversity. In cases of developmental brain dysfunction, fetal general movements alter their sequence and gestalt, which suggests a dysfunction of the developing nervous system. The scarcity of longitudinal studies calls for further comprehensive research on the predictive value of prenatal functional deviations. What this paper adds Motor output can occur in the absence of sensory input. Structural development is activity-dependent. Fetal general movements are among the first movement patterns to occur. Pregnancy-related and maternal factors impact quantity and modulation of fetal general movements. Prenatal general movement assessment has not yet brought the expected breakthrough.
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Affiliation(s)
- Christa Einspieler
- Research Unit iDN, Interdisciplinary Developmental Neuroscience, Division of Phoniatrics, Medical University of Graz, Graz, Austria
| | - Daniela Prayer
- Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Peter B Marschik
- Research Unit iDN, Interdisciplinary Developmental Neuroscience, Division of Phoniatrics, Medical University of Graz, Graz, Austria.,Child and Adolescent Psychiatry and Psychotherapy, University Medical Center Göttingen and LeibnizScience Campus Primate Cognition, Göttingen, Germany.,Department of Women's and Children's Health, Center of Neurodevelopmental Disorders (KIND), Karolinska Institutet, Stockholm, Sweden
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