1
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Rueda-Alaña E, Grillo M, Vázquez E, Salas SM, Senovilla-Ganzo R, Escobar L, Quintas A, Benguría A, Aransay AM, Bengoa-Vergniory N, Dopazo A, Encinas JM, Nilsson M, García-Moreno F. BirthSeq, a new method to isolate and analyze dated cells in different vertebrates. Development 2024; 151:dev202429. [PMID: 38856078 DOI: 10.1242/dev.202429] [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: 10/19/2023] [Accepted: 05/27/2024] [Indexed: 06/11/2024]
Abstract
Embryonic development is a complex and dynamic process that unfolds over time and involves the production and diversification of increasing numbers of cells. The impact of developmental time on the formation of the central nervous system is well documented, with evidence showing that time plays a crucial role in establishing the identity of neuronal subtypes. However, the study of how time translates into genetic instructions driving cell fate is limited by the scarcity of suitable experimental tools. We introduce BirthSeq, a new method for isolating and analyzing cells based on their birth date. This innovative technique allows for in vivo labeling of cells, isolation via fluorescence-activated cell sorting, and analysis using high-throughput techniques. We calibrated the BirthSeq method for developmental organs across three vertebrate species (mouse, chick and gecko), and utilized it for single-cell RNA sequencing and novel spatially resolved transcriptomic approaches in mouse and chick, respectively. Overall, BirthSeq provides a versatile tool for studying virtually any tissue in different vertebrate organisms, aiding developmental biology research by targeting cells and their temporal cues.
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Affiliation(s)
- Eneritz Rueda-Alaña
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
- Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
| | - Marco Grillo
- Science for Life Laboratory, Department of Biophysics and Biochemistry, Stockholm University, 17165, Solna, Sweden
| | - Enrique Vázquez
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Sergio Marco Salas
- Science for Life Laboratory, Department of Biophysics and Biochemistry, Stockholm University, 17165, Solna, Sweden
| | - Rodrigo Senovilla-Ganzo
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
- Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
| | - Laura Escobar
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
| | - Ana Quintas
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Alberto Benguría
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Ana María Aransay
- Genome Analysis Platform, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 48160 Derio, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Nora Bengoa-Vergniory
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
- Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
- IKERBASQUE Foundation, María Díaz de Haro 3, 6th Floor, 48013 BilbaoSpain
| | - Ana Dopazo
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Juan Manuel Encinas
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
- Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
- IKERBASQUE Foundation, María Díaz de Haro 3, 6th Floor, 48013 BilbaoSpain
| | - Mats Nilsson
- Science for Life Laboratory, Department of Biophysics and Biochemistry, Stockholm University, 17165, Solna, Sweden
| | - Fernando García-Moreno
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
- Department of Neuroscience, Faculty of Medicine and Odontology, UPV/EHU, Barrio Sarriena s/n, 48940 Leioa, Bizkaia, Spain
- IKERBASQUE Foundation, María Díaz de Haro 3, 6th Floor, 48013 BilbaoSpain
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2
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Prince GS, Reynolds M, Martina V, Sun H. Gene-environmental regulation of the postnatal post-mitotic neuronal maturation. Trends Genet 2024; 40:480-494. [PMID: 38658255 PMCID: PMC11153025 DOI: 10.1016/j.tig.2024.03.006] [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: 01/30/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
Embryonic neurodevelopment, particularly neural progenitor differentiation into post-mitotic neurons, has been extensively studied. While the number and composition of post-mitotic neurons remain relatively constant from birth to adulthood, the brain undergoes significant postnatal maturation marked by major property changes frequently disrupted in neural diseases. This review first summarizes recent characterizations of the functional and molecular maturation of the postnatal nervous system. We then review regulatory mechanisms controlling the precise gene expression changes crucial for the intricate sequence of maturation events, highlighting experience-dependent versus cell-intrinsic genetic timer mechanisms. Despite significant advances in understanding of the gene-environmental regulation of postnatal neuronal maturation, many aspects remain unknown. The review concludes with our perspective on exciting future research directions in the next decade.
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Affiliation(s)
- Gabrielle S Prince
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Molly Reynolds
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Verdion Martina
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - HaoSheng Sun
- Department of Cell, Developmental, and Integrative Biology, The University of Alabama at Birmingham, Birmingham, AL, USA; Freeman Hrabowski Scholar, Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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3
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Yang L, Liu F, Hahm H, Okuda T, Li X, Zhang Y, Kalyanaraman V, Heitmeier MR, Samineni VK. Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590975. [PMID: 38712231 PMCID: PMC11071495 DOI: 10.1101/2024.04.24.590975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Single-cell multiomic techniques have sparked immense interest in developing a comprehensive multi-modal map of diverse neuronal cell types and their brain wide projections. However, investigating the spatial organization, transcriptional and epigenetic landscapes of brain wide projection neurons is hampered by the lack of efficient and easily adoptable tools. Here we introduce Projection-TAGs, a retrograde AAV platform that allows multiplex tagging of projection neurons using RNA barcodes. By using Projection-TAGs, we performed multiplex projection tracing of the mouse cortex and high-throughput single-cell profiling of the transcriptional and epigenetic landscapes of the cortical projection neurons. Projection-TAGs can be leveraged to obtain a snapshot of activity-dependent recruitment of distinct projection neurons and their molecular features in the context of a specific stimulus. Given its flexibility, usability, and compatibility, we envision that Projection-TAGs can be readily applied to build a comprehensive multi-modal map of brain neuronal cell types and their projections.
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Affiliation(s)
- Lite Yang
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
- Neuroscience Graduate Program, Division of Biology & Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, United States
| | - Fang Liu
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Hannah Hahm
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Takao Okuda
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Xiaoyue Li
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Yufen Zhang
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Vani Kalyanaraman
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Monique R. Heitmeier
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Vijay K. Samineni
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
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4
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Liu Y, Chen X, Ma Y, Song C, Ma J, Chen C, Su J, Ma L, Saiyin H. Endogenous mutant Huntingtin alters the corticogenesis via lowering Golgi recruiting ARF1 in cortical organoid. Mol Psychiatry 2024:10.1038/s41380-024-02562-0. [PMID: 38654124 DOI: 10.1038/s41380-024-02562-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/10/2024] [Accepted: 04/12/2024] [Indexed: 04/25/2024]
Abstract
Pathogenic mutant huntingtin (mHTT) infiltrates the adult Huntington's disease (HD) brain and impairs fetal corticogenesis. However, most HD animal models rarely recapitulate neuroanatomical alterations in adult HD and developing brains. Thus, the human cortical organoid (hCO) is an alternative approach to decode mHTT pathogenesis precisely during human corticogenesis. Here, we replicated the altered corticogenesis in the HD fetal brain using HD patient-derived hCOs. Our HD-hCOs had pathological phenotypes, including deficient junctional complexes in the neural tubes, delayed postmitotic neuronal maturation, dysregulated fate specification of cortical neuron subtypes, and abnormalities in early HD subcortical projections during corticogenesis, revealing a causal link between impaired progenitor cells and chaotic cortical neuronal layering in the HD brain. We identified novel long, oriented, and enriched polyQ assemblies of HTTs that hold large flat Golgi stacks and scaffold clathrin+ vesicles in the neural tubes of hCOs. Flat Golgi stacks conjugated polyQ assemblies by ADP-ribosylation factor 1 (ARF1). Inhibiting ARF1 activation with Brefeldin A (BFA) disassociated polyQ assemblies from Golgi. PolyQ assembles with mHTT scaffolded fewer ARF1 and formed shorter polyQ assembles with fewer and shorter Golgi and clathrin vesicles in neural tubes of HD-hCOs compared with those in hCOs. Inhibiting the activation of ARF1 by BFA in healthy hCOs replicated impaired junctional complexes in the neural tubes. Together, endogenous polyQ assemblies with mHTT reduced the Golgi recruiting ARF1 in the neuroepithelium, impaired the Golgi structure and activities, and altered the corticogenesis in HD-hCO.
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Affiliation(s)
- Yang Liu
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xinyu Chen
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yunlong Ma
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Chenyun Song
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jixin Ma
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Cheng Chen
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Jianzhong Su
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Lixiang Ma
- Department of Anatomy and Histology & Embryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| | - Hexige Saiyin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China.
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5
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Ciceri G, Studer L. Epigenetic control and manipulation of neuronal maturation timing. Curr Opin Genet Dev 2024; 85:102164. [PMID: 38412562 PMCID: PMC11175593 DOI: 10.1016/j.gde.2024.102164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/29/2024]
Abstract
During brain development, the sequence of developmental steps and the underlying transcriptional regulatory logic are largely conserved across species. However, the temporal unfolding of developmental programs varies dramatically across species and within a given species varies across brain regions and cell identities. The maturation of neurons in the human cerebral cortex is particularly slow and lasts for many years compared with only a few weeks for the corresponding mouse neurons. The mechanisms setting the 'schedule' of neuronal maturation remain unclear but appear to be linked to a cell-intrinsic 'clock'. Here, we discuss recent findings that highlight a role for epigenetic factors in the timing of neuronal maturation. Manipulations of those factors in stem cell-based models can override the intrinsic pace of neuronal maturation, including its protracted nature in human cortical neurons. We then contextualize the epigenetic regulation of maturation programs with findings from other model systems and propose potential interactions between epigenetic pathways and other drivers of developmental rates.
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Affiliation(s)
- Gabriele Ciceri
- The Center for Stem Cell Biology and Developmental Biology program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Lorenz Studer
- The Center for Stem Cell Biology and Developmental Biology program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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6
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Xu P, Peng J, Yuan T, Chen Z, He H, Wu Z, Li T, Li X, Wang L, Gao L, Yan J, Wei W, Li CT, Luo ZG, Chen Y. High-throughput mapping of single-neuron projection and molecular features by retrograde barcoded labeling. eLife 2024; 13:e85419. [PMID: 38390967 PMCID: PMC10914349 DOI: 10.7554/elife.85419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/22/2024] [Indexed: 02/24/2024] Open
Abstract
Deciphering patterns of connectivity between neurons in the brain is a critical step toward understanding brain function. Imaging-based neuroanatomical tracing identifies area-to-area or sparse neuron-to-neuron connectivity patterns, but with limited throughput. Barcode-based connectomics maps large numbers of single-neuron projections, but remains a challenge for jointly analyzing single-cell transcriptomics. Here, we established a rAAV2-retro barcode-based multiplexed tracing method that simultaneously characterizes the projectome and transcriptome at the single neuron level. We uncovered dedicated and collateral projection patterns of ventromedial prefrontal cortex (vmPFC) neurons to five downstream targets and found that projection-defined vmPFC neurons are molecularly heterogeneous. We identified transcriptional signatures of projection-specific vmPFC neurons, and verified Pou3f1 as a marker gene enriched in neurons projecting to the lateral hypothalamus, denoting a distinct subset with collateral projections to both dorsomedial striatum and lateral hypothalamus. In summary, we have developed a new multiplexed technique whose paired connectome and gene expression data can help reveal organizational principles that form neural circuits and process information.
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Affiliation(s)
- Peibo Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jian Peng
- School of Life Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech UniversityShanghaiChina
| | - Tingli Yuan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
| | - Zhaoqin Chen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
| | - Hui He
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ziyan Wu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
| | - Ting Li
- School of Life Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech UniversityShanghaiChina
| | - Xiaodong Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Luyue Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of ScienceShanghaiChina
| | - Le Gao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
| | - Jun Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
- Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
- School of Future Technology, University of Chinese Academy of SciencesBeijingChina
| | - Wu Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of ScienceShanghaiChina
- Lingang LaboratoryShanghaiChina
| | - Chengyu T Li
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
- Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
- School of Future Technology, University of Chinese Academy of SciencesBeijingChina
- Lingang LaboratoryShanghaiChina
| | - Zhen-Ge Luo
- School of Life Science and Technology & State Key Laboratory of Advanced Medical Materials and Devices, ShanghaiTech UniversityShanghaiChina
| | - Yuejun Chen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai Center for Brain Science and Brain-Inspired TechnologyShanghaiChina
- Shanghai Center for Brain Science and Brain-Inspired Intelligence TechnologyShanghaiChina
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7
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Zhang A, Jin L, Yao S, Matsuyama M, van Velthoven CTJ, Sullivan HA, Sun N, Kellis M, Tasic B, Wickersham I, Chen X. Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing. eLife 2024; 12:RP87866. [PMID: 38319699 PMCID: PMC10942611 DOI: 10.7554/elife.87866] [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] [Indexed: 02/07/2024] Open
Abstract
Mapping the connectivity of diverse neuronal types provides the foundation for understanding the structure and function of neural circuits. High-throughput and low-cost neuroanatomical techniques based on RNA barcode sequencing have the potential to map circuits at cellular resolution and a brain-wide scale, but existing Sindbis virus-based techniques can only map long-range projections using anterograde tracing approaches. Rabies virus can complement anterograde tracing approaches by enabling either retrograde labeling of projection neurons or monosynaptic tracing of direct inputs to genetically targeted postsynaptic neurons. However, barcoded rabies virus has so far been only used to map non-neuronal cellular interactions in vivo and synaptic connectivity of cultured neurons. Here we combine barcoded rabies virus with single-cell and in situ sequencing to perform retrograde labeling and transsynaptic labeling in the mouse brain. We sequenced 96 retrogradely labeled cells and 295 transsynaptically labeled cells using single-cell RNA-seq, and 4130 retrogradely labeled cells and 2914 transsynaptically labeled cells in situ. We found that the transcriptomic identities of rabies virus-infected cells can be robustly identified using both single-cell RNA-seq and in situ sequencing. By associating gene expression with connectivity inferred from barcode sequencing, we distinguished long-range projecting cortical cell types from multiple cortical areas and identified cell types with converging or diverging synaptic connectivity. Combining in situ sequencing with barcoded rabies virus complements existing sequencing-based neuroanatomical techniques and provides a potential path for mapping synaptic connectivity of neuronal types at scale.
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Affiliation(s)
- Aixin Zhang
- Allen Institute for Brain ScienceSeattleUnited States
| | - Lei Jin
- McGovern Institute for Brain Research, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Shenqin Yao
- Allen Institute for Brain ScienceSeattleUnited States
| | - Makoto Matsuyama
- McGovern Institute for Brain Research, Massachusetts Institute of TechnologyCambridgeUnited States
| | | | - Heather Anne Sullivan
- McGovern Institute for Brain Research, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Na Sun
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Broad Institute of MIT and HarvardCambridgeUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
| | - Manolis Kellis
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Broad Institute of MIT and HarvardCambridgeUnited States
- Broad Institute of MIT and HarvardCambridgeUnited States
| | | | - Ian Wickersham
- McGovern Institute for Brain Research, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Xiaoyin Chen
- Allen Institute for Brain ScienceSeattleUnited States
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8
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Ciceri G, Baggiolini A, Cho HS, Kshirsagar M, Benito-Kwiecinski S, Walsh RM, Aromolaran KA, Gonzalez-Hernandez AJ, Munguba H, Koo SY, Xu N, Sevilla KJ, Goldstein PA, Levitz J, Leslie CS, Koche RP, Studer L. An epigenetic barrier sets the timing of human neuronal maturation. Nature 2024; 626:881-890. [PMID: 38297124 PMCID: PMC10881400 DOI: 10.1038/s41586-023-06984-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 12/15/2023] [Indexed: 02/02/2024]
Abstract
The pace of human brain development is highly protracted compared with most other species1-7. The maturation of cortical neurons is particularly slow, taking months to years to develop adult functions3-5. Remarkably, such protracted timing is retained in cortical neurons derived from human pluripotent stem cells (hPSCs) during in vitro differentiation or upon transplantation into the mouse brain4,8,9. Those findings suggest the presence of a cell-intrinsic clock setting the pace of neuronal maturation, although the molecular nature of this clock remains unknown. Here we identify an epigenetic developmental programme that sets the timing of human neuronal maturation. First, we developed a hPSC-based approach to synchronize the birth of cortical neurons in vitro which enabled us to define an atlas of morphological, functional and molecular maturation. We observed a slow unfolding of maturation programmes, limited by the retention of specific epigenetic factors. Loss of function of several of those factors in cortical neurons enables precocious maturation. Transient inhibition of EZH2, EHMT1 and EHMT2 or DOT1L, at progenitor stage primes newly born neurons to rapidly acquire mature properties upon differentiation. Thus our findings reveal that the rate at which human neurons mature is set well before neurogenesis through the establishment of an epigenetic barrier in progenitor cells. Mechanistically, this barrier holds transcriptional maturation programmes in a poised state that is gradually released to ensure the prolonged timeline of human cortical neuron maturation.
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Affiliation(s)
- Gabriele Ciceri
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Arianna Baggiolini
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Institute of Oncology Research (IOR), Bellinzona Institutes of Science (BIOS+), Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Hyein S Cho
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meghana Kshirsagar
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Microsoft AI for Good Research, Redmond, WA, USA
| | - Silvia Benito-Kwiecinski
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryan M Walsh
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Hermany Munguba
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - So Yeon Koo
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Neuroscience PhD Program, New York, NY, USA
| | - Nan Xu
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaylin J Sevilla
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter A Goldstein
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorenz Studer
- The Center for Stem Cell Biology and Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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9
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Wallace JL, Pollen AA. Human neuronal maturation comes of age: cellular mechanisms and species differences. Nat Rev Neurosci 2024; 25:7-29. [PMID: 37996703 DOI: 10.1038/s41583-023-00760-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2023] [Indexed: 11/25/2023]
Abstract
The delayed and prolonged postmitotic maturation of human neurons, compared with neurons from other species, may contribute to human-specific cognitive abilities and neurological disorders. Here we review the mechanisms of neuronal maturation, applying lessons from model systems to understand the specific features of protracted human cortical maturation and species differences. We cover cell-intrinsic features of neuronal maturation, including transcriptional, epigenetic and metabolic mechanisms, as well as cell-extrinsic features, including the roles of activity and synapses, the actions of glial cells and the contribution of the extracellular matrix. We discuss evidence for species differences in biochemical reaction rates, the proposed existence of an epigenetic maturation clock and the contributions of both general and modular mechanisms to species-specific maturation timing. Finally, we suggest approaches to measure, improve and accelerate the maturation of human neurons in culture, examine crosstalk and interactions among these different aspects of maturation and propose conceptual models to guide future studies.
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Affiliation(s)
- Jenelle L Wallace
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
| | - Alex A Pollen
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
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10
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Zhang A, Jin L, Yao S, Matsuyama M, van Velthoven C, Sullivan H, Sun N, Kellis M, Tasic B, Wickersham IR, Chen X. Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.532873. [PMID: 36993334 PMCID: PMC10055146 DOI: 10.1101/2023.03.16.532873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Mapping the connectivity of diverse neuronal types provides the foundation for understanding the structure and function of neural circuits. High-throughput and low-cost neuroanatomical techniques based on RNA barcode sequencing have the potential to map circuits at cellular resolution and a brain-wide scale, but existing Sindbis virus-based techniques can only map long-range projections using anterograde tracing approaches. Rabies virus can complement anterograde tracing approaches by enabling either retrograde labeling of projection neurons or monosynaptic tracing of direct inputs to genetically targeted postsynaptic neurons. However, barcoded rabies virus has so far been only used to map non-neuronal cellular interactions in vivo and synaptic connectivity of cultured neurons. Here we combine barcoded rabies virus with single-cell and in situ sequencing to perform retrograde labeling and transsynaptic labeling in the mouse brain. We sequenced 96 retrogradely labeled cells and 295 transsynaptically labeled cells using single-cell RNA-seq, and 4,130 retrogradely labeled cells and 2,914 transsynaptically labeled cells in situ. We found that the transcriptomic identities of rabies virus-infected cells can be robustly identified using both single-cell RNA-seq and in situ sequencing. By associating gene expression with connectivity inferred from barcode sequencing, we distinguished long-range projecting cortical cell types from multiple cortical areas and identified cell types with converging or diverging synaptic connectivity. Combining in situ sequencing with barcoded rabies virus complements existing sequencing-based neuroanatomical techniques and provides a potential path for mapping synaptic connectivity of neuronal types at scale.
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Affiliation(s)
- Aixin Zhang
- Allen Institute for Brain Science, Seattle, WA
| | - Lei Jin
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA
- Current address: Lingang Laboratory, Shanghai, China
| | - Shenqin Yao
- Allen Institute for Brain Science, Seattle, WA
| | - Makoto Matsuyama
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA
- Current address: Metcela Inc., Kawasaki, Kanagawa, Japan
| | | | - Heather Sullivan
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Na Sun
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manolis Kellis
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Ian R. Wickersham
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA
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11
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Paolino A, Haines EH, Bailey EJ, Black DA, Moey C, García-Moreno F, Richards LJ, Suárez R, Fenlon LR. Non-uniform temporal scaling of developmental processes in the mammalian cortex. Nat Commun 2023; 14:5950. [PMID: 37741828 PMCID: PMC10517946 DOI: 10.1038/s41467-023-41652-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023] Open
Abstract
The time that it takes the brain to develop is highly variable across animals. Although staging systems equate major developmental milestones between mammalian species, it remains unclear how distinct processes of cortical development scale within these timeframes. Here, we compare the timing of cortical development in two mammals of similar size but different developmental pace: eutherian mice and marsupial fat-tailed dunnarts. Our results reveal that the temporal relationship between cell birth and laminar specification aligns to equivalent stages between these species, but that migration and axon extension do not scale uniformly according to the developmental stages, and are relatively more advanced in dunnarts. We identify a lack of basal intermediate progenitor cells in dunnarts that likely contributes in part to this timing difference. These findings demonstrate temporal limitations and differential plasticity of cortical developmental processes between similarly sized Therians and provide insight into subtle temporal changes that may have contributed to the early diversification of the mammalian brain.
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Affiliation(s)
- Annalisa Paolino
- The University of Queensland, School of Biomedical Sciences, Brisbane, QLD 4072, Australia
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
| | - Elizabeth H Haines
- The University of Queensland, School of Biomedical Sciences, Brisbane, QLD 4072, Australia
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
| | - Evan J Bailey
- The University of Queensland, School of Biomedical Sciences, Brisbane, QLD 4072, Australia
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
| | - Dylan A Black
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
| | - Ching Moey
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
| | - Fernando García-Moreno
- Achucarro Basque Center for Neuroscience, Scientific Park of the University of the Basque Country (UPV/EHU), 48940, Leioa, Spain
- IKERBASQUE Foundation, María Díaz de Haro 3, 48013, Bilbao, Spain
| | - Linda J Richards
- The University of Queensland, School of Biomedical Sciences, Brisbane, QLD 4072, Australia
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia
- Washington University in St Louis School of Medicine, Department of Neuroscience, St Louis, MO, 63108, USA
| | - Rodrigo Suárez
- The University of Queensland, School of Biomedical Sciences, Brisbane, QLD 4072, Australia.
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia.
| | - Laura R Fenlon
- The University of Queensland, School of Biomedical Sciences, Brisbane, QLD 4072, Australia.
- The University of Queensland, Queensland Brain Institute, Brisbane, QLD 4072, Australia.
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12
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Huilgol D, Russ JB, Srivas S, Huang ZJ. The progenitor basis of cortical projection neuron diversity. Curr Opin Neurobiol 2023; 81:102726. [PMID: 37148649 PMCID: PMC10557529 DOI: 10.1016/j.conb.2023.102726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 04/04/2023] [Accepted: 04/09/2023] [Indexed: 05/08/2023]
Abstract
Diverse glutamatergic projection neurons (PNs) mediate myriad processing streams and output channels of the cerebral cortex. Yet, how different types of neural progenitors, such as radial glia (RGs) and intermediate progenitors (IPs), produce PN diversity, and hierarchical organization remains unclear. A fundamental issue is whether RGs constitute a homogeneous, multipotent lineage capable of generating all major PN types through a temporally regulated developmental program, or whether RGs comprise multiple transcriptionally heterogenous pools, each fated to generate a subset of PNs. Beyond RGs, the role of IPs in PN diversification remains underexplored. Addressing these questions requires tracking PN developmental trajectories with cell-type resolution - from transcription factor-defined RGs and IPs to their PN progeny, which are defined not only by laminar location but also by projection patterns and gene expression. Advances in cell-type resolution genetic fate mapping, axon tracing, and spatial transcriptomics may provide the technical capability for answering these fundamental questions.
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Affiliation(s)
- Dhananjay Huilgol
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Jeffrey B Russ
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Pediatrics, Division of Neurology, Duke University Medical Center, Durham, NC 27710, USA
| | - Sweta Srivas
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Z Josh Huang
- Department of Neurobiology, Duke University Medical Center, Durham, NC 27710, USA; Department of Biomedical Engineering, Duke University Pratt School of Engineering, Durham, NC 27708, USA.
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13
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Mohylyak I, Bengochea M, Pascual-Caro C, Asfogo N, Fonseca-Topp S, Danda N, Atak ZK, De Waegeneer M, Plaçais PY, Preat T, Aerts S, Corti O, de Juan-Sanz J, Hassan BA. Developmental transcriptional control of mitochondrial homeostasis is required for activity-dependent synaptic connectivity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.11.544500. [PMID: 37333418 PMCID: PMC10274921 DOI: 10.1101/2023.06.11.544500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
During neuronal circuit formation, local control of axonal organelles ensures proper synaptic connectivity. Whether this process is genetically encoded is unclear and if so, its developmental regulatory mechanisms remain to be identified. We hypothesized that developmental transcription factors regulate critical parameters of organelle homeostasis that contribute to circuit wiring. We combined cell type-specific transcriptomics with a genetic screen to discover such factors. We identified Telomeric Zinc finger-Associated Protein (TZAP) as a temporal developmental regulator of neuronal mitochondrial homeostasis genes, including Pink1 . In Drosophila , loss of dTzap function during visual circuit development leads to loss of activity-dependent synaptic connectivity, that can be rescued by Pink1 expression. At the cellular level, loss of dTzap/TZAP leads to defects in mitochondrial morphology, attenuated calcium uptake and reduced synaptic vesicle release in fly and mammalian neurons. Our findings highlight developmental transcriptional regulation of mitochondrial homeostasis as a key factor in activity-dependent synaptic connectivity.
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14
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Sun H, Hobert O. Temporal transitions in the postembryonic nervous system of the nematode Caenorhabditis elegans: Recent insights and open questions. Semin Cell Dev Biol 2023; 142:67-80. [PMID: 35688774 DOI: 10.1016/j.semcdb.2022.05.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 10/18/2022]
Abstract
After the generation, differentiation and integration into functional circuitry, post-mitotic neurons continue to change certain phenotypic properties throughout postnatal juvenile stages until an animal has reached a fully mature state in adulthood. We will discuss such changes in the context of the nervous system of the nematode C. elegans, focusing on recent descriptions of anatomical and molecular changes that accompany postembryonic maturation of neurons. We summarize the characterization of genetic timer mechanisms that control these temporal transitions or maturational changes, and discuss that many but not all of these transitions relate to sexual maturation of the animal. We describe how temporal, spatial and sex-determination pathways are intertwined to sculpt the emergence of cell-type specific maturation events. Finally, we lay out several unresolved questions that should be addressed to move the field forward, both in C. elegans and in vertebrates.
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Affiliation(s)
- Haosheng Sun
- Department of Cell, Developmental, and Integrative Biology. University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, New York, USA
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15
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Klingler E. Temporal controls over cortical projection neuron fate diversity. Curr Opin Neurobiol 2023; 79:102677. [PMID: 36736108 DOI: 10.1016/j.conb.2023.102677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/19/2022] [Accepted: 01/04/2023] [Indexed: 02/04/2023]
Abstract
During neocortex development, cortical projection neurons (PN) are sequentially produced and assemble into circuits underlying our interactions with the environment. Cortical PN are heterogeneous in terms of birthdate, layer position, molecular identity, connectivity, and function. This diversity increases in evolutionarily most recent species, but when and how it emerges during corticogenesis is still debated. While time-locked expression of determinant genes and early stochasticity allow the production of different types of PN, temporal differences in unfolding similar transcriptional programs, rather than fundamental differences in these programs, further account for anatomical variability between PN subtypes and across species. Altogether, these mechanisms, which will be discussed here, participate in increasing cortical PN diversity.
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Affiliation(s)
- Esther Klingler
- Department of Basic Neurosciences, University of Geneva, 1 Rue Michel Servet, 1211, Geneva, Switzerland.
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16
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Yao Z, van Velthoven CTJ, Kunst M, Zhang M, McMillen D, Lee C, Jung W, Goldy J, Abdelhak A, Baker P, Barkan E, Bertagnolli D, Campos J, Carey D, Casper T, Chakka AB, Chakrabarty R, Chavan S, Chen M, Clark M, Close J, Crichton K, Daniel S, Dolbeare T, Ellingwood L, Gee J, Glandon A, Gloe J, Gould J, Gray J, Guilford N, Guzman J, Hirschstein D, Ho W, Jin K, Kroll M, Lathia K, Leon A, Long B, Maltzer Z, Martin N, McCue R, Meyerdierks E, Nguyen TN, Pham T, Rimorin C, Ruiz A, Shapovalova N, Slaughterbeck C, Sulc J, Tieu M, Torkelson A, Tung H, Cuevas NV, Wadhwani K, Ward K, Levi B, Farrell C, Thompson CL, Mufti S, Pagan CM, Kruse L, Dee N, Sunkin SM, Esposito L, Hawrylycz MJ, Waters J, Ng L, Smith KA, Tasic B, Zhuang X, Zeng H. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531121. [PMID: 37034735 PMCID: PMC10081189 DOI: 10.1101/2023.03.06.531121] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The mammalian brain is composed of millions to billions of cells that are organized into numerous cell types with specific spatial distribution patterns and structural and functional properties. An essential step towards understanding brain function is to obtain a parts list, i.e., a catalog of cell types, of the brain. Here, we report a comprehensive and high-resolution transcriptomic and spatial cell type atlas for the whole adult mouse brain. The cell type atlas was created based on the combination of two single-cell-level, whole-brain-scale datasets: a single-cell RNA-sequencing (scRNA-seq) dataset of ~7 million cells profiled, and a spatially resolved transcriptomic dataset of ~4.3 million cells using MERFISH. The atlas is hierarchically organized into five nested levels of classification: 7 divisions, 32 classes, 306 subclasses, 1,045 supertypes and 5,200 clusters. We systematically analyzed the neuronal, non-neuronal, and immature neuronal cell types across the brain and identified a high degree of correspondence between transcriptomic identity and spatial specificity for each cell type. The results reveal unique features of cell type organization in different brain regions, in particular, a dichotomy between the dorsal and ventral parts of the brain: the dorsal part contains relatively fewer yet highly divergent neuronal types, whereas the ventral part contains more numerous neuronal types that are more closely related to each other. We also systematically characterized cell-type specific expression of neurotransmitters, neuropeptides, and transcription factors. The study uncovered extraordinary diversity and heterogeneity in neurotransmitter and neuropeptide expression and co-expression patterns in different cell types across the brain, suggesting they mediate a myriad of modes of intercellular communications. Finally, we found that transcription factors are major determinants of cell type classification in the adult mouse brain and identified a combinatorial transcription factor code that defines cell types across all parts of the brain. The whole-mouse-brain transcriptomic and spatial cell type atlas establishes a benchmark reference atlas and a foundational resource for deep and integrative investigations of cell type and circuit function, development, and evolution of the mammalian brain.
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Affiliation(s)
- Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Meng Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | | | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Won Jung
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Pamela Baker
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Daniel Carey
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Min Chen
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jennie Close
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Scott Daniel
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - James Gee
- University of Pennsylvania, Philadelphia, PA, USA
| | | | - Jessica Gloe
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - James Gray
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Windy Ho
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Kelly Jin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Arielle Leon
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zoe Maltzer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Naomi Martin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Rachel McCue
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | | | - Josef Sulc
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Herman Tung
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Katelyn Ward
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Boaz Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Shoaib Mufti
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
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17
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Yuan L, Chen X, Zhan H, Gilbert HL, Zador AM. Massive Multiplexing of Spatially Resolved Single Neuron Projections with Axonal BARseq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.18.528865. [PMID: 36824753 PMCID: PMC9949159 DOI: 10.1101/2023.02.18.528865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Neurons in the cortex are heterogenous, sending diverse axonal projections to multiple brain regions. Unraveling the logic of these projections requires single-neuron resolution. Although a growing number of techniques have enabled high-throughput reconstruction, these techniques are typically limited to dozens or at most hundreds of neurons per brain, requiring that statistical analyses combine data from different specimens. Here we present axonal BARseq, a high-throughput approach based on reading out nucleic acid barcodes using in situ RNA sequencing, which enables analysis of even densely labeled neurons. As a proof of principle, we have mapped the long-range projections of >8000 mouse primary auditory cortex neurons from a single brain. We identified major cell types based on projection targets and axonal trajectory. The large sample size enabled us to systematically quantify the projections of intratelencephalic (IT) neurons, and revealed that individual IT neurons project to different layers in an area-dependent fashion. Axonal BARseq is a powerful technique for studying the heterogeneity of single neuronal projections at high throughput within individual brains.
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Affiliation(s)
- Li Yuan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xiaoyin Chen
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Huiqing Zhan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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18
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Vanderhaeghen P, Polleux F. Developmental mechanisms underlying the evolution of human cortical circuits. Nat Rev Neurosci 2023; 24:213-232. [PMID: 36792753 PMCID: PMC10064077 DOI: 10.1038/s41583-023-00675-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2023] [Indexed: 02/17/2023]
Abstract
The brain of modern humans has evolved remarkable computational abilities that enable higher cognitive functions. These capacities are tightly linked to an increase in the size and connectivity of the cerebral cortex, which is thought to have resulted from evolutionary changes in the mechanisms of cortical development. Convergent progress in evolutionary genomics, developmental biology and neuroscience has recently enabled the identification of genomic changes that act as human-specific modifiers of cortical development. These modifiers influence most aspects of corticogenesis, from the timing and complexity of cortical neurogenesis to synaptogenesis and the assembly of cortical circuits. Mutations of human-specific genetic modifiers of corticogenesis have started to be linked to neurodevelopmental disorders, providing evidence for their physiological relevance and suggesting potential relationships between the evolution of the human brain and its sensitivity to specific diseases.
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Affiliation(s)
- Pierre Vanderhaeghen
- VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium.
| | - Franck Polleux
- Department of Neuroscience, Columbia University Medical Center, New York, NY, USA.
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
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19
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Abstract
The generation of an internal body model and its continuous update is essential in sensorimotor control. Although known to rely on proprioceptive sensory feedback, the underlying mechanism that transforms this sensory feedback into a dynamic body percept remains poorly understood. However, advances in the development of genetic tools for proprioceptive circuit elements, including the sensory receptors, are beginning to offer new and unprecedented leverage to dissect the central pathways responsible for proprioceptive encoding. Simultaneously, new data derived through emerging bionic neural machine-interface technologies reveal clues regarding the relative importance of kinesthetic sensory feedback and insights into the functional proprioceptive substrates that underlie natural motor behaviors.
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Affiliation(s)
- Paul D Marasco
- Laboratory for Bionic Integration, Department of Biomedical Engineering, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA;
- Charles Shor Epilepsy Center, Cleveland Clinic, Cleveland, Ohio, USA
- Advanced Platform Technology Center, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Joriene C de Nooij
- Department of Neurology and the Columbia University Motor Neuron Center, Columbia University Medical Center, New York, NY, USA;
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20
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Gandal MJ, Haney JR, Wamsley B, Yap CX, Parhami S, Emani PS, Chang N, Chen GT, Hoftman GD, de Alba D, Ramaswami G, Hartl CL, Bhattacharya A, Luo C, Jin T, Wang D, Kawaguchi R, Quintero D, Ou J, Wu YE, Parikshak NN, Swarup V, Belgard TG, Gerstein M, Pasaniuc B, Geschwind DH. Broad transcriptomic dysregulation occurs across the cerebral cortex in ASD. Nature 2022; 611:532-539. [PMID: 36323788 PMCID: PMC9668748 DOI: 10.1038/s41586-022-05377-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 09/21/2022] [Indexed: 11/17/2022]
Abstract
Neuropsychiatric disorders classically lack defining brain pathologies, but recent work has demonstrated dysregulation at the molecular level, characterized by transcriptomic and epigenetic alterations1-3. In autism spectrum disorder (ASD), this molecular pathology involves the upregulation of microglial, astrocyte and neural-immune genes, the downregulation of synaptic genes, and attenuation of gene-expression gradients in cortex1,2,4-6. However, whether these changes are limited to cortical association regions or are more widespread remains unknown. To address this issue, we performed RNA-sequencing analysis of 725 brain samples spanning 11 cortical areas from 112 post-mortem samples from individuals with ASD and neurotypical controls. We find widespread transcriptomic changes across the cortex in ASD, exhibiting an anterior-to-posterior gradient, with the greatest differences in primary visual cortex, coincident with an attenuation of the typical transcriptomic differences between cortical regions. Single-nucleus RNA-sequencing and methylation profiling demonstrate that this robust molecular signature reflects changes in cell-type-specific gene expression, particularly affecting excitatory neurons and glia. Both rare and common ASD-associated genetic variation converge within a downregulated co-expression module involving synaptic signalling, and common variation alone is enriched within a module of upregulated protein chaperone genes. These results highlight widespread molecular changes across the cerebral cortex in ASD, extending beyond association cortex to broadly involve primary sensory regions.
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Affiliation(s)
- Michael J Gandal
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Center for Autism Research and Treatment, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA.
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Lifespan Brain Institute at Penn Medicine and The Children's Hospital of Philadelphia, Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jillian R Haney
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Brie Wamsley
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Chloe X Yap
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Sepideh Parhami
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Prashant S Emani
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Nathan Chang
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT, USA
| | - George T Chen
- Center for Autism Research and Treatment, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Gil D Hoftman
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Diego de Alba
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Gokul Ramaswami
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Christopher L Hartl
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Arjun Bhattacharya
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Chongyuan Luo
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Ting Jin
- Waisman Center and Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Daifeng Wang
- Waisman Center and Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Riki Kawaguchi
- Center for Autism Research and Treatment, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Diana Quintero
- Center for Autism Research and Treatment, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Jing Ou
- Center for Autism Research and Treatment, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Ye Emily Wu
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Neelroop N Parikshak
- Center for Autism Research and Treatment, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Vivek Swarup
- Center for Autism Research and Treatment, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | | | - Mark Gerstein
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Center for Autism Research and Treatment, Semel Institute of Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA.
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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21
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Park SHE, Ortiz AK, Konopka G. Corticogenesis across species at single-cell resolution. Dev Neurobiol 2022; 82:517-532. [PMID: 35932776 PMCID: PMC9481703 DOI: 10.1002/dneu.22896] [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: 01/22/2022] [Revised: 07/11/2022] [Accepted: 07/22/2022] [Indexed: 11/07/2022]
Abstract
The neocortex (or pallium) consists of diverse cell types that are organized in a highly species-specific manner under strict spatiotemporal control during development. Many of the cell types are present transiently throughout development but contribute to permanent species-specific cortical features that are acquired through evolution. Therefore, capturing cell type-specific biological information has always been an important quest in the field of neurodevelopment. The progress in achieving fine cellular resolution has been slow due to technical challenges. However, with recent advancements in single-cell and multi-omics technologies, many laboratories have begun to successfully interrogate cellular and molecular mechanisms driving corticogenesis at single-cell resolution. In this review, we provide summarized results from many primary publications and several in-depth review articles that utilize or address single-cell genomics techniques to understand important topics, such as cellular and molecular mechanisms governing cortical progenitor proliferation, cell lineage progression, neuronal specification, and arealization, across multiple gyrencephalic (i.e., human and non-human primates) and lissencephalic species (i.e., mouse, reptiles, and songbirds). We also examine findings from recent studies involving epigenomic and posttranscriptional regulation of corticogenesis. In the discussion section, we provide our insights on the challenges the field currently faces as well as promising future applications of single cell technologies.
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Affiliation(s)
- Seon Hye E Park
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Ana K Ortiz
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, Texas, USA
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22
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Zeng H. What is a cell type and how to define it? Cell 2022; 185:2739-2755. [PMID: 35868277 DOI: 10.1016/j.cell.2022.06.031] [Citation(s) in RCA: 138] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 12/20/2022]
Abstract
Cell types are the basic functional units of an organism. Cell types exhibit diverse phenotypic properties at multiple levels, making them challenging to define, categorize, and understand. This review provides an overview of the basic principles of cell types rooted in evolution and development and discusses approaches to characterize and classify cell types and investigate how they contribute to the organism's function, using the mammalian brain as a primary example. I propose a roadmap toward a conceptual framework and knowledge base of cell types that will enable a deeper understanding of the dynamic changes of cellular function under healthy and diseased conditions.
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Affiliation(s)
- Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
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23
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Cai L, Yang JW, Wang CF, Chou SJ, Luhmann HJ, Karayannis T. Identification of a Developmental Switch in Information Transfer between Whisker S1 and S2 Cortex in Mice. J Neurosci 2022; 42:4435-4448. [PMID: 35501157 PMCID: PMC9172289 DOI: 10.1523/jneurosci.2246-21.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/03/2022] Open
Abstract
The whiskers of rodents are a key sensory organ that provides critical tactile information for animal navigation and object exploration throughout life. Previous work has explored the developmental sensory-driven activation of the primary sensory cortex processing whisker information (wS1), also called barrel cortex. This body of work has shown that the barrel cortex is already activated by sensory stimuli during the first postnatal week. However, it is currently unknown when over the course of development these stimuli begin being processed by higher-order cortical areas, such as secondary whisker somatosensory area (wS2). Here we investigate the developmental engagement of wS2 by whisker stimuli and the emergence of corticocortical communication from wS1 to wS2. Using in vivo wide-field imaging and multielectrode recordings in control and conditional KO mice of either sex with thalamocortical innervation defects, we find that wS1 and wS2 are able to process bottom-up information coming from the thalamus from birth. We also identify that it is only at the end of the first postnatal week that wS1 begins to provide functional excitation into wS2, switching to more inhibitory actions after the second postnatal week. Therefore, we have uncovered a developmental window when information transfer between wS1 and wS2 reaches mature function.SIGNIFICANCE STATEMENT At the end of the first postnatal week, the primary whisker somatosensory area starts providing excitatory input to the secondary whisker somatosensory area 2. This excitatory drive weakens during the second postnatal week and switches to inhibition in the adult.
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Affiliation(s)
- Linbi Cai
- Laboratory of Neural Circuit Assembly, Brain Research Institute, University of Zürich, CH-8057, Zürich, Switzerland
| | - Jenq-Wei Yang
- Laboratory of Neural Circuit Assembly, Brain Research Institute, University of Zürich, CH-8057, Zürich, Switzerland
- Institute of Physiology, University Medical Center, Johannes Gutenberg University Mainz, 55128, Mainz, Germany
| | - Chia-Fang Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Shen-Ju Chou
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Heiko J Luhmann
- Institute of Physiology, University Medical Center, Johannes Gutenberg University Mainz, 55128, Mainz, Germany
| | - Theofanis Karayannis
- Laboratory of Neural Circuit Assembly, Brain Research Institute, University of Zürich, CH-8057, Zürich, Switzerland
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24
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Panagiotakos G, Pasca SP. A matter of space and time: Emerging roles of disease-associated proteins in neural development. Neuron 2022; 110:195-208. [PMID: 34847355 PMCID: PMC8776599 DOI: 10.1016/j.neuron.2021.10.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/11/2021] [Accepted: 10/25/2021] [Indexed: 01/21/2023]
Abstract
Recent genetic studies of neurodevelopmental disorders point to synaptic proteins and ion channels as key contributors to disease pathogenesis. Although many of these proteins, such as the L-type calcium channel Cav1.2 or the postsynaptic scaffolding protein SHANK3, have well-studied functions in mature neurons, new evidence indicates that they may subserve novel, distinct roles in immature cells as the nervous system is assembled in prenatal development. Emerging tools and technologies, including single-cell sequencing and human cellular models of disease, are illuminating differential isoform utilization, spatiotemporal expression, and subcellular localization of ion channels and synaptic proteins in the developing brain compared with the adult, providing new insights into the regulation of developmental processes. We propose that it is essential to consider the temporally distinct and cell-specific roles of these proteins during development and maturity in our framework for understanding neuropsychiatric disorders.
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Affiliation(s)
- Georgia Panagiotakos
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA; Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA.
| | - Sergiu P Pasca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA; Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
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25
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A critical period of translational control during brain development at codon resolution. Nat Struct Mol Biol 2022; 29:1277-1290. [PMID: 36482253 PMCID: PMC9758057 DOI: 10.1038/s41594-022-00882-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 10/19/2022] [Indexed: 12/13/2022]
Abstract
Translation modulates the timing and amplification of gene expression after transcription. Brain development requires uniquely complex gene expression patterns, but large-scale measurements of translation directly in the prenatal brain are lacking. We measure the reactants, synthesis and products of mRNA translation spanning mouse neocortex neurogenesis, and discover a transient window of dynamic regulation at mid-gestation. Timed translation upregulation of chromatin-binding proteins like Satb2, which is essential for neuronal subtype differentiation, restricts protein expression in neuronal lineages despite broad transcriptional priming in progenitors. In contrast, translation downregulation of ribosomal proteins sharply decreases ribosome biogenesis, coinciding with a major shift in protein synthesis dynamics at mid-gestation. Changing activity of eIF4EBP1, a direct inhibitor of ribosome biogenesis, is concurrent with ribosome downregulation and affects neurogenesis of the Satb2 lineage. Thus, the molecular logic of brain development includes the refinement of transcriptional programs by translation. Modeling of the developmental neocortex translatome is provided as an open-source searchable resource at https://shiny.mdc-berlin.de/cortexomics .
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