251
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Molecular and spatial heterogeneity of microglia in Rasmussen encephalitis. Acta Neuropathol Commun 2022; 10:168. [PMID: 36411471 PMCID: PMC9677917 DOI: 10.1186/s40478-022-01472-y] [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: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 11/22/2022] Open
Abstract
Rasmussen encephalitis (RE) is a rare childhood neurological disease characterized by progressive unilateral loss of function, hemispheric atrophy and drug-resistant epilepsy. Affected brain tissue shows signs of infiltrating cytotoxic T-cells, microglial activation, and neuronal death, implicating an inflammatory disease process. Recent studies have identified molecular correlates of inflammation in RE, but cell-type-specific mechanisms remain unclear. We used single-nucleus RNA-sequencing (snRNA-seq) to assess gene expression across multiple cell types in brain tissue resected from two children with RE. We found transcriptionally distinct microglial populations enriched in RE compared to two age-matched individuals with unaffected brain tissue and two individuals with Type I focal cortical dysplasia (FCD). Specifically, microglia in RE tissues demonstrated increased expression of genes associated with cytokine signaling, interferon-mediated pathways, and T-cell activation. We extended these findings using spatial proteomic analysis of tissue from four surgical resections to examine expression profiles of microglia within their pathological context. Microglia that were spatially aggregated into nodules had increased expression of dynamic immune regulatory markers (PD-L1, CD14, CD11c), T-cell activation markers (CD40, CD80) and were physically located near distinct CD4+ and CD8+ lymphocyte populations. These findings help elucidate the complex immune microenvironment of RE.
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252
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Um S, Zhang B, Wattal S, Yoo Y. Software Components and Product Variety in a Platform Ecosystem: A Dynamic Network Analysis of WordPress. INFORMATION SYSTEMS RESEARCH 2022. [DOI: 10.1287/isre.2022.1172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Software components such as application programming interfaces (APIs) provided by external developers are vital to online digital platforms. Although APIs generally increase the variety of products according to anecdote, the precise relationship between the categories of APIs and product variety is not yet known. We find that APIs, regarding their use frequency, are categorized into three groups. The core is a group of frequently used APIs, whereas the periphery is a group of sparsely used APIs. In a large and mature platform ecosystem, an additional group of APIs, the regular core, mainly provided by third-party developers, emerges. APIs in the regular core are the main driver of product variety. However, we also find that the strength of this effect diminishes in a newly created product category when most of the new products are built by duplicating the usage of APIs from other products. A platform owner can stimulate developers’ creativity by acting as a bridge between digital product providers and third-party developers. It can collect functional needs from third-party developers and then share them with product providers. Therefore, the latter can build APIs that developers need.
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Affiliation(s)
- Sungyong Um
- Department of Information Systems and Analytics, School of Computing, National University of Singapore, Singapore 119391, Singapore
| | - Bin Zhang
- Department of Information and Operations Management, Mays Business School, Texas A&M University, College Station, Texas 77843
| | - Sunil Wattal
- Department of Management Information Systems, Fox School of Business, Temple University, Philadelphia, Pennsylvania 19122
| | - Youngjin Yoo
- Department of Design and Innovation, Weatherhead School of Management, Case Western Reserve University, Cleveland, Ohio 44106
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253
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Tissue dissociation for single-cell and single-nuclei RNA sequencing for low amounts of input material. Front Zool 2022; 19:27. [DOI: 10.1186/s12983-022-00472-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/27/2022] [Indexed: 11/15/2022] Open
Abstract
Abstract
Background
Recent technological advances opened the opportunity to simultaneously study gene expression for thousands of individual cells on a genome-wide scale. The experimental accessibility of such single-cell RNA sequencing (scRNAseq) approaches allowed gaining insights into the cell type composition of heterogeneous tissue samples of animal model systems and emerging models alike. A major prerequisite for a successful application of the method is the dissociation of complex tissues into individual cells, which often requires large amounts of input material and harsh mechanical, chemical and temperature conditions. However, the availability of tissue material may be limited for small animals, specific organs, certain developmental stages or if samples need to be acquired from collected specimens. Therefore, we evaluated different dissociation protocols to obtain single cells from small tissue samples of Drosophila melanogaster eye-antennal imaginal discs.
Results
We show that a combination of mechanical and chemical dissociation resulted in sufficient high-quality cells. As an alternative, we tested protocols for the isolation of single nuclei, which turned out to be highly efficient for fresh and frozen tissue samples. Eventually, we performed scRNAseq and single-nuclei RNA sequencing (snRNAseq) to show that the best protocols for both methods successfully identified relevant cell types. At the same time, snRNAseq resulted in less artificial gene expression that is caused by rather harsh dissociation conditions needed to obtain single cells for scRNAseq. A direct comparison of scRNAseq and snRNAseq data revealed that both datasets share biologically relevant genes among the most variable genes, and we showed differences in the relative contribution of the two approaches to identified cell types.
Conclusion
We present two dissociation protocols that allow isolating single cells and single nuclei, respectively, from low input material. Both protocols resulted in extraction of high-quality RNA for subsequent scRNAseq or snRNAseq applications. If tissue availability is limited, we recommend the snRNAseq procedure of fresh or frozen tissue samples as it is perfectly suited to obtain thorough insights into cellular diversity of complex tissue.
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254
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Wei JR, Hao ZZ, Xu C, Huang M, Tang L, Xu N, Liu R, Shen Y, Teichmann SA, Miao Z, Liu S. Identification of visual cortex cell types and species differences using single-cell RNA sequencing. Nat Commun 2022; 13:6902. [PMID: 36371428 PMCID: PMC9653448 DOI: 10.1038/s41467-022-34590-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
The primate neocortex exerts high cognitive ability and strong information processing capacity. Here, we establish a single-cell RNA sequencing dataset of 133,454 macaque visual cortical cells. It covers major cortical cell classes including 25 excitatory neuron types, 37 inhibitory neuron types and all glial cell types. We identified layer-specific markers including HPCAL1 and NXPH4, and also identified two cell types, an NPY-expressing excitatory neuron type that expresses the dopamine receptor D3 gene; and a primate specific activity-dependent OSTN + sensory neuron type. Comparisons of our dataset with humans and mice show that the gene expression profiles differ between species in relation to genes that are implicated in the synaptic plasticity and neuromodulation of excitatory neurons. The comparisons also revealed that glutamatergic neurons may be more diverse across species than GABAergic neurons and non-neuronal cells. These findings pave the way for understanding how the primary cortex fulfills the high-cognitive functions.
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Affiliation(s)
- Jia-Ru Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Zhao-Zhe Hao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Mengyao Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Lei Tang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Nana Xu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Ruifeng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yuhui Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
| | - Zhichao Miao
- GMU-GIBH Joint School of Life Sciences, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China.
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Cambridge, UK.
| | - Sheng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
- Guangdong Province Key Laboratory of Brain Function and Disease, Guangzhou, China.
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255
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Wang S, Ding P, Yuan J, Wang H, Zhang X, Chen D, Ma D, Zhang X, Wang F. Integrative cross-species analysis of GABAergic neuron cell types and their functions in Alzheimer's disease. Sci Rep 2022; 12:19358. [PMID: 36369318 PMCID: PMC9652313 DOI: 10.1038/s41598-022-21496-7] [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: 05/08/2022] [Accepted: 09/28/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding the phenotypic and functional diversity of cerebral cortical GABAergic neurons requires a comprehensive analysis of key transcriptional signatures and neuronal subtype identity. However, the diversity and conservation of GABAergic neurons across multiple mammals remain unclear. Here, we collected the single-nucleus RNA sequencing (snRNA-seq) datasets of cerebral cortex from human, macaque, mouse, and pig to identify the conserved neuronal cell types across species. After systematic analysis of the heterogeneity of GABAergic neurons, we defined four major conserved GABAergic neuron subclasses (Inc SST, Inc LAMP5, Inc PVALB, and Inc VIP) across species. We characterized the species-enriched subclasses of GABAergic neurons from four mammals, such as Inc Meis2 in mouse. Then, we depicted the genetic regulatory network (GRNs) of GABAergic neuron subclasses, which showed the conserved and species-specific GRNs for GABAergic neuron cell types. Finally, we investigated the GABAergic neuron subclass-specific expression modules of Alzheimer's disease (AD)-related genes in GABAergic neuron cell types. Overall, our study reveals the conserved and divergent GABAergic neuron subclasses and GRNs across multiple species and unravels the gene expression modules of AD-risk genes in GABAergic neuron subclasses, facilitating the GABAergic neurons research and clinical treatment.
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Affiliation(s)
- Shiyou Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Peiwen Ding
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Jingnan Yuan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Haoyu Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xiuqing Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Dongli Ma
- Department of Respiratory Diseases, Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, 518038, China
| | - Xingliang Zhang
- Department of Respiratory Diseases, Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, 518038, China.
- Department of Pediatrics, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China.
| | - Fei Wang
- BGI-Shenzhen, Shenzhen, 518083, China.
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
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256
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Wallace MN, Zobay O, Hardman E, Thompson Z, Dobbs P, Chakrabarti L, Palmer AR. The large numbers of minicolumns in the primary visual cortex of humans, chimpanzees and gorillas are related to high visual acuity. Front Neuroanat 2022; 16:1034264. [PMID: 36439196 PMCID: PMC9681811 DOI: 10.3389/fnana.2022.1034264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/21/2022] [Indexed: 11/10/2022] Open
Abstract
Minicolumns are thought to be a fundamental neural unit in the neocortex and their replication may have formed the basis of the rapid cortical expansion that occurred during primate evolution. We sought evidence of minicolumns in the primary visual cortex (V-1) of three great apes, three rodents and representatives from three other mammalian orders: Eulipotyphla (European hedgehog), Artiodactyla (domestic pig) and Carnivora (ferret). Minicolumns, identified by the presence of a long bundle of radial, myelinated fibers stretching from layer III to the white matter of silver-stained sections, were found in the human, chimpanzee, gorilla and guinea pig V-1. Shorter bundles confined to one or two layers were found in the other species but represent modules rather than minicolumns. The inter-bundle distance, and hence density of minicolumns, varied systematically both within a local area that might represent a hypercolumn but also across the whole visual field. The distance between all bundles had a similar range for human, chimpanzee, gorilla, ferret and guinea pig: most bundles were 20-45 μm apart. By contrast, the space between bundles was greater for the hedgehog and pig (20-140 μm). The mean density of minicolumns was greater in tangential sections of the gorilla and chimpanzee (1,243-1,287 bundles/mm2) than in human (314-422 bundles/mm2) or guinea pig (643 bundles/mm2). The minicolumnar bundles did not form a hexagonal lattice but were arranged in thin curving and branched bands separated by thicker bands of neuropil/somata. Estimates of the total number of modules/minicolumns within V-1 were strongly correlated with visual acuity.
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Affiliation(s)
- Mark N. Wallace
- Medical Research Council (MRC) Institute of Hearing Research, University Park, Nottingham, United Kingdom
- Hearing Sciences, Mental Health and Clinical Neurosciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Oliver Zobay
- Medical Research Council (MRC) Institute of Hearing Research, University Park, Nottingham, United Kingdom
- School of Medicine, University of Nottingham, Hearing Sciences—Scottish Section, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - Eden Hardman
- Medical Research Council (MRC) Institute of Hearing Research, University Park, Nottingham, United Kingdom
| | - Zoe Thompson
- Medical Research Council (MRC) Institute of Hearing Research, University Park, Nottingham, United Kingdom
| | - Phillipa Dobbs
- Veterinary Department, Twycross Zoo, East Midland Zoological Society, Atherstone, United Kingdom
| | - Lisa Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Nottingham, United Kingdom
| | - Alan R. Palmer
- Medical Research Council (MRC) Institute of Hearing Research, University Park, Nottingham, United Kingdom
- Hearing Sciences, Mental Health and Clinical Neurosciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom
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257
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Hogeveen J, Medalla M, Ainsworth M, Galeazzi JM, Hanlon CA, Mansouri FA, Costa VD. What Does the Frontopolar Cortex Contribute to Goal-Directed Cognition and Action? J Neurosci 2022; 42:8508-8513. [PMID: 36351824 PMCID: PMC9665930 DOI: 10.1523/jneurosci.1143-22.2022] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
Understanding the unique functions of different subregions of primate prefrontal cortex has been a longstanding goal in cognitive neuroscience. Yet, the anatomy and function of one of its largest subregions (the frontopolar cortex) remain enigmatic and underspecified. Our Society for Neuroscience minisymposium Primate Frontopolar Cortex: From Circuits to Complex Behaviors will comprise a range of new anatomic and functional approaches that have helped to clarify the basic circuit anatomy of the frontal pole, its functional involvement during performance of cognitively demanding behavioral paradigms in monkeys and humans, and its clinical potential as a target for noninvasive brain stimulation in patients with brain disorders. This review consolidates knowledge about the anatomy and connectivity of frontopolar cortex and provides an integrative summary of its function in primates. We aim to answer the question: what, if anything, does frontopolar cortex contribute to goal-directed cognition and action?
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Affiliation(s)
- Jeremy Hogeveen
- Department of Psychology & Psychology Clinical Neuroscience Center, University of New Mexico, Albuquerque, NM 87131
| | - Maria Medalla
- Department of Anatomy & Neurobiology, Boston University, Boston, MA 02118
| | - Matthew Ainsworth
- Department of Experimental Psychology, University of Oxford, Oxford, United Kingdom, OX2 6GG
| | - Juan M Galeazzi
- Department of Experimental Psychology, University of Oxford, Oxford, United Kingdom, OX2 6GG
| | - Colleen A Hanlon
- Department of Cancer Biology
- Department of Physiology and Pharmacology, Wake Forest School of Medicine, Winston-Salem, NC 27101
| | - Farshad Alizadeh Mansouri
- Department of Physiology, Monash Biomedicine Discovery Institute, Clayton Victoria, 3800, Australia
- ARC Centre for Integrative Brain Function, Monash University, Clayton Victoria, 3800, Australia
| | - Vincent D Costa
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR 97006
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258
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Spatially resolved gene regulatory and disease-related vulnerability map of the adult Macaque cortex. Nat Commun 2022; 13:6747. [PMID: 36347848 PMCID: PMC9643508 DOI: 10.1038/s41467-022-34413-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 10/24/2022] [Indexed: 11/09/2022] Open
Abstract
Single cell approaches have increased our knowledge about the cell type composition of the non-human primate (NHP), but a detailed characterization of area-specific regulatory features remains outstanding. We generated single-cell transcriptomic and chromatin accessibility (single-cell ATAC) data of 358,237 cells from prefrontal cortex (PFC), primary motor cortex (M1) and primary visual cortex (V1) of adult female cynomolgus monkey brain, and integrated this dataset with Stereo-seq (spatial enhanced resolution omics-sequencing) of the corresponding cortical areas to assign topographic information to molecular states. We identified area-specific chromatin accessible sites and their targeted genes, including the cell type-specific transcriptional regulatory network associated with excitatory neurons heterogeneity. We reveal calcium ion transport and axon guidance genes related to specialized functions of PFC and M1, identified the similarities and differences between adult macaque and human oligodendrocyte trajectories, and mapped the genetic variants and gene perturbations of human diseases to NHP cortical cells. This resource establishes a transcriptomic and chromatin accessibility combinatory regulatory landscape at a single-cell and spatially resolved resolution in NHP cortex.
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259
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Galakhova AA, Hunt S, Wilbers R, Heyer DB, de Kock CPJ, Mansvelder HD, Goriounova NA. Evolution of cortical neurons supporting human cognition. Trends Cogn Sci 2022; 26:909-922. [PMID: 36117080 PMCID: PMC9561064 DOI: 10.1016/j.tics.2022.08.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 01/12/2023]
Abstract
Human cognitive abilities are generally thought to arise from cortical expansion over the course of human brain evolution. In addition to increased neuron numbers, this cortical expansion might be driven by adaptations in the properties of single neurons and their local circuits. We review recent findings on the distinct structural, functional, and transcriptomic features of human cortical neurons and their organization in cortical microstructure. We focus on the supragranular cortical layers, which showed the most prominent expansion during human brain evolution, and the properties of their principal cells: pyramidal neurons. We argue that the evolutionary adaptations in neuronal features that accompany the expansion of the human cortex partially underlie interindividual variability in human cognitive abilities.
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Affiliation(s)
- A A Galakhova
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, The Netherlands
| | - S Hunt
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, The Netherlands
| | - R Wilbers
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, The Netherlands
| | - D B Heyer
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, The Netherlands
| | - C P J de Kock
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, The Netherlands
| | - H D Mansvelder
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, The Netherlands
| | - N A Goriounova
- Department of Integrative Neurophysiology, Amsterdam Neuroscience, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam 1081 HV, The Netherlands.
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260
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Roberts RJV, Pop S, Prieto-Godino LL. Evolution of central neural circuits: state of the art and perspectives. Nat Rev Neurosci 2022; 23:725-743. [DOI: 10.1038/s41583-022-00644-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2022] [Indexed: 11/09/2022]
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261
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Verkest C, Salinas M, Diochot S, Deval E, Lingueglia E, Baron A. Mechanisms of Action of the Peptide Toxins Targeting Human and Rodent Acid-Sensing Ion Channels and Relevance to Their In Vivo Analgesic Effects. Toxins (Basel) 2022; 14:toxins14100709. [PMID: 36287977 PMCID: PMC9612379 DOI: 10.3390/toxins14100709] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/30/2022] [Accepted: 10/02/2022] [Indexed: 11/16/2022] Open
Abstract
Acid-sensing ion channels (ASICs) are voltage-independent H+-gated cation channels largely expressed in the nervous system of rodents and humans. At least six isoforms (ASIC1a, 1b, 2a, 2b, 3 and 4) associate into homotrimers or heterotrimers to form functional channels with highly pH-dependent gating properties. This review provides an update on the pharmacological profiles of animal peptide toxins targeting ASICs, including PcTx1 from tarantula and related spider toxins, APETx2 and APETx-like peptides from sea anemone, and mambalgin from snake, as well as the dimeric protein snake toxin MitTx that have all been instrumental to understanding the structure and the pH-dependent gating of rodent and human cloned ASICs and to study the physiological and pathological roles of native ASICs in vitro and in vivo. ASICs are expressed all along the pain pathways and the pharmacological data clearly support a role for these channels in pain. ASIC-targeting peptide toxins interfere with ASIC gating by complex and pH-dependent mechanisms sometimes leading to opposite effects. However, these dual pH-dependent effects of ASIC-inhibiting toxins (PcTx1, mambalgin and APETx2) are fully compatible with, and even support, their analgesic effects in vivo, both in the central and the peripheral nervous system, as well as potential effects in humans.
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Affiliation(s)
- Clément Verkest
- CNRS (Centre National de la Recherche Scientifique), IPMC (Institut de Pharmacologie Moléculaire et Cellulaire), LabEx ICST (Laboratory of Excellence in Ion Channel Science and Therapeutics), FHU InovPain (Fédération Hospitalo-Universitaire “Innovative Solutions in Refractory Chronic Pain”), Université Côte d’Azur, 660 Route des Lucioles, Sophia-Antipolis, 06560 Nice, France
- Department of Anesthesiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Miguel Salinas
- CNRS (Centre National de la Recherche Scientifique), IPMC (Institut de Pharmacologie Moléculaire et Cellulaire), LabEx ICST (Laboratory of Excellence in Ion Channel Science and Therapeutics), FHU InovPain (Fédération Hospitalo-Universitaire “Innovative Solutions in Refractory Chronic Pain”), Université Côte d’Azur, 660 Route des Lucioles, Sophia-Antipolis, 06560 Nice, France
| | - Sylvie Diochot
- CNRS (Centre National de la Recherche Scientifique), IPMC (Institut de Pharmacologie Moléculaire et Cellulaire), LabEx ICST (Laboratory of Excellence in Ion Channel Science and Therapeutics), FHU InovPain (Fédération Hospitalo-Universitaire “Innovative Solutions in Refractory Chronic Pain”), Université Côte d’Azur, 660 Route des Lucioles, Sophia-Antipolis, 06560 Nice, France
| | - Emmanuel Deval
- CNRS (Centre National de la Recherche Scientifique), IPMC (Institut de Pharmacologie Moléculaire et Cellulaire), LabEx ICST (Laboratory of Excellence in Ion Channel Science and Therapeutics), FHU InovPain (Fédération Hospitalo-Universitaire “Innovative Solutions in Refractory Chronic Pain”), Université Côte d’Azur, 660 Route des Lucioles, Sophia-Antipolis, 06560 Nice, France
| | - Eric Lingueglia
- CNRS (Centre National de la Recherche Scientifique), IPMC (Institut de Pharmacologie Moléculaire et Cellulaire), LabEx ICST (Laboratory of Excellence in Ion Channel Science and Therapeutics), FHU InovPain (Fédération Hospitalo-Universitaire “Innovative Solutions in Refractory Chronic Pain”), Université Côte d’Azur, 660 Route des Lucioles, Sophia-Antipolis, 06560 Nice, France
| | - Anne Baron
- CNRS (Centre National de la Recherche Scientifique), IPMC (Institut de Pharmacologie Moléculaire et Cellulaire), LabEx ICST (Laboratory of Excellence in Ion Channel Science and Therapeutics), FHU InovPain (Fédération Hospitalo-Universitaire “Innovative Solutions in Refractory Chronic Pain”), Université Côte d’Azur, 660 Route des Lucioles, Sophia-Antipolis, 06560 Nice, France
- Correspondence:
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262
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Zheng Y, Shen S, Keleş S. Normalization and de-noising of single-cell Hi-C data with BandNorm and scVI-3D. Genome Biol 2022; 23:222. [PMID: 36253828 PMCID: PMC9575231 DOI: 10.1186/s13059-022-02774-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/19/2022] [Indexed: 11/10/2022] Open
Abstract
Single-cell high-throughput chromatin conformation capture methodologies (scHi-C) enable profiling of long-range genomic interactions. However, data from these technologies are prone to technical noise and biases that hinder downstream analysis. We develop a normalization approach, BandNorm, and a deep generative modeling framework, scVI-3D, to account for scHi-C specific biases. In benchmarking experiments, BandNorm yields leading performances in a time and memory efficient manner for cell-type separation, identification of interacting loci, and recovery of cell-type relationships, while scVI-3D exhibits advantages for rare cell types and under high sparsity scenarios. Application of BandNorm coupled with gene-associating domain analysis reveals scRNA-seq validated sub-cell type identification.
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Affiliation(s)
- Ye Zheng
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Siqi Shen
- Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison, Madison, USA
| | - Sündüz Keleş
- Department of Biostatistics and Medical Informatics, University of Wisconsin - Madison, Madison, USA
- Department of Statistics, University of Wisconsin - Madison, Madison, USA
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Batiuk MY, Tyler T, Dragicevic K, Mei S, Rydbirk R, Petukhov V, Deviatiiarov R, Sedmak D, Frank E, Feher V, Habek N, Hu Q, Igolkina A, Roszik L, Pfisterer U, Garcia-Gonzalez D, Petanjek Z, Adorjan I, Kharchenko PV, Khodosevich K. Upper cortical layer-driven network impairment in schizophrenia. SCIENCE ADVANCES 2022; 8:eabn8367. [PMID: 36223459 PMCID: PMC9555788 DOI: 10.1126/sciadv.abn8367] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 08/24/2022] [Indexed: 05/31/2023]
Abstract
Schizophrenia is one of the most widespread and complex mental disorders. To characterize the impact of schizophrenia, we performed single-nucleus RNA sequencing (snRNA-seq) of >220,000 neurons from the dorsolateral prefrontal cortex of patients with schizophrenia and matched controls. In addition, >115,000 neurons were analyzed topographically by immunohistochemistry. Compositional analysis of snRNA-seq data revealed a reduction in abundance of GABAergic neurons and a concomitant increase in principal neurons, most pronounced for upper cortical layer subtypes, which was substantiated by histological analysis. Many neuronal subtypes showed extensive transcriptomic changes, the most marked in upper-layer GABAergic neurons, including down-regulation in energy metabolism and up-regulation in neurotransmission. Transcription factor network analysis demonstrated a developmental origin of transcriptomic changes. Last, Visium spatial transcriptomics further corroborated upper-layer neuron vulnerability in schizophrenia. Overall, our results point toward general network impairment within upper cortical layers as a core substrate associated with schizophrenia symptomatology.
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Affiliation(s)
- Mykhailo Y. Batiuk
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Teadora Tyler
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest H-1085, Hungary
| | - Katarina Dragicevic
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Shenglin Mei
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Rasmus Rydbirk
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Viktor Petukhov
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ruslan Deviatiiarov
- The National Center for Personalized Medicine of Endocrine Diseases, Moscow 115478, Russia
- Kazan Federal University, Kazan 420043, Russia
| | - Dora Sedmak
- Croatian Institute for Brain Research and Center of Excellence for Basic, Clinical and Translational Neuroscience, School of Medicine, University of Zagreb, Zagreb 10000, Croatia
| | - Erzsebet Frank
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest H-1085, Hungary
| | - Virginia Feher
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest H-1085, Hungary
| | - Nikola Habek
- Croatian Institute for Brain Research and Center of Excellence for Basic, Clinical and Translational Neuroscience, School of Medicine, University of Zagreb, Zagreb 10000, Croatia
| | - Qiwen Hu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Igolkina
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
- St. Petersburg Polytechnical University, St. Petersburg 195251, Russia
| | - Lilla Roszik
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest H-1085, Hungary
| | - Ulrich Pfisterer
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Diego Garcia-Gonzalez
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Zdravko Petanjek
- Croatian Institute for Brain Research and Center of Excellence for Basic, Clinical and Translational Neuroscience, School of Medicine, University of Zagreb, Zagreb 10000, Croatia
| | - Istvan Adorjan
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest H-1085, Hungary
| | - Peter V. Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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264
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Valihrach L, Matusova Z, Zucha D, Klassen R, Benesova S, Abaffy P, Kubista M, Anderova M. Recent advances in deciphering oligodendrocyte heterogeneity with single-cell transcriptomics. Front Cell Neurosci 2022; 16:1025012. [PMID: 36313617 PMCID: PMC9606807 DOI: 10.3389/fncel.2022.1025012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/22/2022] [Indexed: 11/18/2022] Open
Abstract
Oligodendrocytes (OL) have been for decades considered a passive, homogenous population of cells that provide support to neurons, and show a limited response to pathological stimuli. This view has been dramatically changed by the introduction of powerful transcriptomic methods that have uncovered a broad spectrum of OL populations that co-exist within the healthy central nervous system (CNS) and also across a variety of diseases. Specifically, single-cell and single-nucleus RNA-sequencing (scRNA-seq, snRNA-seq) have been used to reveal OL variations in maturation, myelination and immune status. The newly discovered immunomodulatory role suggests that OL may serve as targets for future therapies. In this review, we summarize the current understanding of OL heterogeneity in mammalian CNS as revealed by scRNA-seq and snRNA-seq. We provide a list of key studies that identify consensus marker genes defining the currently known OL populations. This resource can be used to standardize analysis of OL related datasets and improve their interpretation, ultimately leading to a better understanding of OL functions in health and disease.
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Affiliation(s)
- Lukas Valihrach
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
| | - Zuzana Matusova
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
- Faculty of Science, Charles University, Prague, Czechia
| | - Daniel Zucha
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
- Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Ruslan Klassen
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
- Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Sarka Benesova
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
- Department of Informatics and Chemistry, Faculty of Chemical Technology, University of Chemistry and Technology, Prague, Czechia
| | - Pavel Abaffy
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Mikael Kubista
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
- TATAA Biocenter AB, Gothenburg, Sweden
| | - Miroslava Anderova
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, Prague, Czechia
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265
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Moore H, Lega BC, Konopka G. Riding brain "waves" to identify human memory genes. Curr Opin Cell Biol 2022; 78:102118. [PMID: 35947942 DOI: 10.1016/j.ceb.2022.102118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 01/31/2023]
Abstract
While there is extensive research on memory-related oscillations and brain gene expression, the relationship between oscillations and gene expression has rarely been studied. Recently, progress has been made to identify specific genes associated with oscillations that are correlated with episodic memory. Neocortical regions, in particular the temporal pole, have been examined in this line of research due to their accessibility during neurosurgical procedures. By harnessing this accessibility, a unique and powerful study design has allowed gene expression and intracranial oscillatory data to be sourced from the same human patients. These studies have identified a plethora of understudied gene targets that should be further characterized with respect to human brain function. Future work should extend to other brain regions to increase our understanding of the genetic signatures of oscillations and, ultimately, human cognition.
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Affiliation(s)
- Haley Moore
- Department of Neuroscience, UT Southwestern Medical Center, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, USA; Department of Neurosurgery, UT Southwestern Medical Center, USA
| | - Bradley C Lega
- Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, USA; Department of Neurosurgery, UT Southwestern Medical Center, USA.
| | - Genevieve Konopka
- Department of Neuroscience, UT Southwestern Medical Center, USA; Peter O'Donnell Jr. Brain Institute, UT Southwestern Medical Center, USA.
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266
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Revah O, Gore F, Kelley KW, Andersen J, Sakai N, Chen X, Li MY, Birey F, Yang X, Saw NL, Baker SW, Amin ND, Kulkarni S, Mudipalli R, Cui B, Nishino S, Grant GA, Knowles JK, Shamloo M, Huguenard JR, Deisseroth K, Pașca SP. Maturation and circuit integration of transplanted human cortical organoids. Nature 2022; 610:319-326. [PMID: 36224417 PMCID: PMC9556304 DOI: 10.1038/s41586-022-05277-w] [Citation(s) in RCA: 122] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 08/25/2022] [Indexed: 01/26/2023]
Abstract
Self-organizing neural organoids represent a promising in vitro platform with which to model human development and disease1-5. However, organoids lack the connectivity that exists in vivo, which limits maturation and makes integration with other circuits that control behaviour impossible. Here we show that human stem cell-derived cortical organoids transplanted into the somatosensory cortex of newborn athymic rats develop mature cell types that integrate into sensory and motivation-related circuits. MRI reveals post-transplantation organoid growth across multiple stem cell lines and animals, whereas single-nucleus profiling shows progression of corticogenesis and the emergence of activity-dependent transcriptional programs. Indeed, transplanted cortical neurons display more complex morphological, synaptic and intrinsic membrane properties than their in vitro counterparts, which enables the discovery of defects in neurons derived from individuals with Timothy syndrome. Anatomical and functional tracings show that transplanted organoids receive thalamocortical and corticocortical inputs, and in vivo recordings of neural activity demonstrate that these inputs can produce sensory responses in human cells. Finally, cortical organoids extend axons throughout the rat brain and their optogenetic activation can drive reward-seeking behaviour. Thus, transplanted human cortical neurons mature and engage host circuits that control behaviour. We anticipate that this approach will be useful for detecting circuit-level phenotypes in patient-derived cells that cannot otherwise be uncovered.
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Affiliation(s)
- Omer Revah
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute and Bio-X, Stanford University, Stanford, CA, USA
| | - Felicity Gore
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Kevin W Kelley
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute and Bio-X, Stanford University, Stanford, CA, USA
| | - Jimena Andersen
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute and Bio-X, Stanford University, Stanford, CA, USA
| | - Noriaki Sakai
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Xiaoyu Chen
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute and Bio-X, Stanford University, Stanford, CA, USA
| | - Min-Yin Li
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute and Bio-X, Stanford University, Stanford, CA, USA
| | - Fikri Birey
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute and Bio-X, Stanford University, Stanford, CA, USA
| | - Xiao Yang
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute and Bio-X, Stanford University, Stanford, CA, USA
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Nay L Saw
- Stanford Behavioral and Functional Neuroscience Laboratory, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Samuel W Baker
- Department of Comparative Medicine, Stanford University, Stanford, CA, USA
| | - Neal D Amin
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute and Bio-X, Stanford University, Stanford, CA, USA
| | - Shravanti Kulkarni
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute and Bio-X, Stanford University, Stanford, CA, USA
| | - Rachana Mudipalli
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Seiji Nishino
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Gerald A Grant
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Juliet K Knowles
- Department of Neurology and Neurological Sciences, Stanford, CA, USA
| | - Mehrdad Shamloo
- Stanford Behavioral and Functional Neuroscience Laboratory, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - John R Huguenard
- Department of Neurology and Neurological Sciences, Stanford, CA, USA
| | - Karl Deisseroth
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Sergiu P Pașca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
- Stanford Brain Organogenesis, Wu Tsai Neurosciences Institute and Bio-X, Stanford University, Stanford, CA, USA.
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267
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Ma S, Skarica M, Li Q, Xu C, Risgaard RD, Tebbenkamp AT, Mato-Blanco X, Kovner R, Krsnik Ž, de Martin X, Luria V, Martí-Pérez X, Liang D, Karger A, Schmidt DK, Gomez-Sanchez Z, Qi C, Gobeske KT, Pochareddy S, Debnath A, Hottman CJ, Spurrier J, Teo L, Boghdadi AG, Homman-Ludiye J, Ely JJ, Daadi EW, Mi D, Daadi M, Marín O, Hof PR, Rasin MR, Bourne J, Sherwood CC, Santpere G, Girgenti MJ, Strittmatter SM, Sousa AM, Sestan N. Molecular and cellular evolution of the primate dorsolateral prefrontal cortex. Science 2022; 377:eabo7257. [PMID: 36007006 PMCID: PMC9614553 DOI: 10.1126/science.abo7257] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The granular dorsolateral prefrontal cortex (dlPFC) is an evolutionary specialization of primates that is centrally involved in cognition. We assessed more than 600,000 single-nucleus transcriptomes from adult human, chimpanzee, macaque, and marmoset dlPFC. Although most cell subtypes defined transcriptomically are conserved, we detected several that exist only in a subset of species as well as substantial species-specific molecular differences across homologous neuronal, glial, and non-neural subtypes. The latter are exemplified by human-specific switching between expression of the neuropeptide somatostatin and tyrosine hydroxylase, the rate-limiting enzyme in dopamine production in certain interneurons. The above molecular differences are also illustrated by expression of the neuropsychiatric risk gene FOXP2, which is human-specific in microglia and primate-specific in layer 4 granular neurons. We generated a comprehensive survey of the dlPFC cellular repertoire and its shared and divergent features in anthropoid primates.
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Affiliation(s)
- Shaojie Ma
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Mario Skarica
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Qian Li
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Chuan Xu
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ryan D. Risgaard
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
- Medical Scientist Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Xoel Mato-Blanco
- Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), MELIS, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Rothem Kovner
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Željka Krsnik
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Xabier de Martin
- Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), MELIS, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Victor Luria
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Xavier Martí-Pérez
- Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), MELIS, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Dan Liang
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Amir Karger
- IT-Research Computing, Harvard Medical School, Boston, MA, USA
| | - Danielle K. Schmidt
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zachary Gomez-Sanchez
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Cai Qi
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Kevin T. Gobeske
- Division of Neurocritical Care and Emergency Neurology, Department of Neurology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sirisha Pochareddy
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ashwin Debnath
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Cade J. Hottman
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Joshua Spurrier
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Department of Neurology, Yale School of Medicine, New Haven, CT 06536, USA
| | - Leon Teo
- Australian Regenerative Medicine Institute, 15 Innovation Walk, Monash University, Clayton VIC, 3800, Australia
| | - Anthony G. Boghdadi
- Australian Regenerative Medicine Institute, 15 Innovation Walk, Monash University, Clayton VIC, 3800, Australia
| | - Jihane Homman-Ludiye
- Australian Regenerative Medicine Institute, 15 Innovation Walk, Monash University, Clayton VIC, 3800, Australia
| | - John J. Ely
- MAEBIOS, Alamogordo, NM 88310, USA
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, USA
| | - Etienne W. Daadi
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Da Mi
- Tsinghua-Peking Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Marcel Daadi
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, USA
- Department of Cell Systems & Anatomy, Radiology, Long School of Medicine, UT Health San Antonio
- NeoNeuron LLC, Palo Alto, CA 94306, USA
| | - Oscar Marín
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE1 1UL, UK
- MRC Centre for Neurodevelopmental Disorders, King’s College London, London SE1 1UL, UK
| | - Patrick R. Hof
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mladen-Roko Rasin
- Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - James Bourne
- Australian Regenerative Medicine Institute, 15 Innovation Walk, Monash University, Clayton VIC, 3800, Australia
| | - Chet C. Sherwood
- Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC, USA
| | - Gabriel Santpere
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), MELIS, Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
| | - Matthew J. Girgenti
- Department of Psychiatry, Yale School of Medicine, New Haven, CT 06510, USA
- National Center for PTSD, US Department of Veterans Affairs, White River Junction, VT, USA
| | - Stephen M. Strittmatter
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Department of Neurology, Yale School of Medicine, New Haven, CT 06536, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - André M.M. Sousa
- Waisman Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Psychiatry, Yale School of Medicine, New Haven, CT 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
- Departments of Genetics and Comparative Medicine, Program in Cellular Neuroscience, Neurodegeneration and Repair, and Yale Child Study Center, Yale School of Medicine, New Haven, CT 06510, USA
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268
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Habibey R, Rojo Arias JE, Striebel J, Busskamp V. Microfluidics for Neuronal Cell and Circuit Engineering. Chem Rev 2022; 122:14842-14880. [PMID: 36070858 PMCID: PMC9523714 DOI: 10.1021/acs.chemrev.2c00212] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Indexed: 02/07/2023]
Abstract
The widespread adoption of microfluidic devices among the neuroscience and neurobiology communities has enabled addressing a broad range of questions at the molecular, cellular, circuit, and system levels. Here, we review biomedical engineering approaches that harness the power of microfluidics for bottom-up generation of neuronal cell types and for the assembly and analysis of neural circuits. Microfluidics-based approaches are instrumental to generate the knowledge necessary for the derivation of diverse neuronal cell types from human pluripotent stem cells, as they enable the isolation and subsequent examination of individual neurons of interest. Moreover, microfluidic devices allow to engineer neural circuits with specific orientations and directionality by providing control over neuronal cell polarity and permitting the isolation of axons in individual microchannels. Similarly, the use of microfluidic chips enables the construction not only of 2D but also of 3D brain, retinal, and peripheral nervous system model circuits. Such brain-on-a-chip and organoid-on-a-chip technologies are promising platforms for studying these organs as they closely recapitulate some aspects of in vivo biological processes. Microfluidic 3D neuronal models, together with 2D in vitro systems, are widely used in many applications ranging from drug development and toxicology studies to neurological disease modeling and personalized medicine. Altogether, microfluidics provide researchers with powerful systems that complement and partially replace animal models.
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Affiliation(s)
- Rouhollah Habibey
- Department
of Ophthalmology, Universitäts-Augenklinik
Bonn, University of Bonn, Ernst-Abbe-Straße 2, D-53127 Bonn, Germany
| | - Jesús Eduardo Rojo Arias
- Wellcome—MRC
Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge
Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - Johannes Striebel
- Department
of Ophthalmology, Universitäts-Augenklinik
Bonn, University of Bonn, Ernst-Abbe-Straße 2, D-53127 Bonn, Germany
| | - Volker Busskamp
- Department
of Ophthalmology, Universitäts-Augenklinik
Bonn, University of Bonn, Ernst-Abbe-Straße 2, D-53127 Bonn, Germany
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269
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Arias A, Manubens-Gil L, Dierssen M. Fluorescent transgenic mouse models for whole-brain imaging in health and disease. Front Mol Neurosci 2022; 15:958222. [PMID: 36211979 PMCID: PMC9538927 DOI: 10.3389/fnmol.2022.958222] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
A paradigm shift is occurring in neuroscience and in general in life sciences converting biomedical research from a descriptive discipline into a quantitative, predictive, actionable science. Living systems are becoming amenable to quantitative description, with profound consequences for our ability to predict biological phenomena. New experimental tools such as tissue clearing, whole-brain imaging, and genetic engineering technologies have opened the opportunity to embrace this new paradigm, allowing to extract anatomical features such as cell number, their full morphology, and even their structural connectivity. These tools will also allow the exploration of new features such as their geometrical arrangement, within and across brain regions. This would be especially important to better characterize brain function and pathological alterations in neurological, neurodevelopmental, and neurodegenerative disorders. New animal models for mapping fluorescent protein-expressing neurons and axon pathways in adult mice are key to this aim. As a result of both developments, relevant cell populations with endogenous fluorescence signals can be comprehensively and quantitatively mapped to whole-brain images acquired at submicron resolution. However, they present intrinsic limitations: weak fluorescent signals, unequal signal strength across the same cell type, lack of specificity of fluorescent labels, overlapping signals in cell types with dense labeling, or undetectable signal at distal parts of the neurons, among others. In this review, we discuss the recent advances in the development of fluorescent transgenic mouse models that overcome to some extent the technical and conceptual limitations and tradeoffs between different strategies. We also discuss the potential use of these strains for understanding disease.
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Affiliation(s)
- Adrian Arias
- Department of System Biology, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Linus Manubens-Gil
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Mara Dierssen
- Department of System Biology, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
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270
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Lin JP, Kelly HM, Song Y, Kawaguchi R, Geschwind DH, Jacobson S, Reich DS. Transcriptomic architecture of nuclei in the marmoset CNS. Nat Commun 2022; 13:5531. [PMID: 36130924 PMCID: PMC9492672 DOI: 10.1038/s41467-022-33140-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/02/2022] [Indexed: 11/11/2022] Open
Abstract
To understand the cellular composition and region-specific specialization of white matter - a disease-relevant, glia-rich tissue highly expanded in primates relative to rodents - we profiled transcriptomes of ~500,000 nuclei from 19 tissue types of the central nervous system of healthy common marmoset and mapped 87 subclusters spatially onto a 3D MRI atlas. We performed cross-species comparison, explored regulatory pathways, modeled regional intercellular communication, and surveyed cellular determinants of neurological disorders. Here, we analyze this resource and find strong spatial segregation of microglia, oligodendrocyte progenitor cells, and astrocytes. White matter glia are diverse, enriched with genes involved in stimulus-response and biomolecule modification, and predicted to interact with other resident cells more extensively than their gray matter counterparts. Conversely, gray matter glia preserve the expression of neural tube patterning genes into adulthood and share six transcription factors that restrict transcriptome complexity. A companion Callithrix jacchus Primate Cell Atlas (CjPCA) is available through https://cjpca.ninds.nih.gov .
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Affiliation(s)
- Jing-Ping Lin
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Hannah M Kelly
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Yeajin Song
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Riki Kawaguchi
- Psychiatry, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Daniel H Geschwind
- Psychiatry, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Departments of Neurology and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Steven Jacobson
- Viral Immunology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
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271
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Pan L, Shan S, Tremmel R, Li W, Liao Z, Shi H, Chen Q, Zhang X, Li X. HTCA: a database with an in-depth characterization of the single-cell human transcriptome. Nucleic Acids Res 2022; 51:D1019-D1028. [PMID: 36130266 PMCID: PMC9825435 DOI: 10.1093/nar/gkac791] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/12/2022] [Accepted: 09/02/2022] [Indexed: 01/30/2023] Open
Abstract
Single-cell RNA-sequencing (scRNA-seq) is one of the most used single-cell omics in recent decades. The exponential growth of single-cell data has immense potential for large-scale integration and in-depth explorations that are more representative of the study population. Efforts have been made to consolidate published data, yet extensive characterization is still lacking. Many focused on raw-data database constructions while others concentrate mainly on gene expression queries. Hereby, we present HTCA (www.htcatlas.org), an interactive database constructed based on ∼2.3 million high-quality cells from ∼3000 scRNA-seq samples and comprised in-depth phenotype profiles of 19 healthy adult and matching fetal tissues. HTCA provides a one-stop interactive query to gene signatures, transcription factor (TF) activities, TF motifs, receptor-ligand interactions, enriched gene ontology (GO) terms, etc. across cell types in adult and fetal tissues. At the same time, HTCA encompasses single-cell splicing variant profiles of 16 adult and fetal tissues, spatial transcriptomics profiles of 11 adult and fetal tissues, and single-cell ATAC-sequencing (scATAC-seq) profiles of 27 adult and fetal tissues. Besides, HTCA provides online analysis tools to perform major steps in a typical scRNA-seq analysis. Altogether, HTCA allows real-time explorations of multi-omics adult and fetal phenotypic profiles and provides tools for a flexible scRNA-seq analysis.
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Affiliation(s)
| | | | - Roman Tremmel
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart 70376, Germany,University of Tuebingen, Tuebingen 72076, Germany
| | - Weiyuan Li
- School of Medicine, Yunnan University, Kunnan, Yunnan 650091, China
| | - Zehuan Liao
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Solna 17177, Sweden,School of Biological Sciences, Nanyang Technological University, 637 551, Singapore
| | - Hangyu Shi
- Department of Acupuncture, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100029, China
| | - Qishuang Chen
- Graduate School, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xiaolu Zhang
- Correspondence may also be addressed to Xiaolu Zhang.
| | - Xuexin Li
- To whom correspondence should be addressed. Tel: +46 0704998515;
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272
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Kartha VK, Duarte FM, Hu Y, Ma S, Chew JG, Lareau CA, Earl A, Burkett ZD, Kohlway AS, Lebofsky R, Buenrostro JD. Functional inference of gene regulation using single-cell multi-omics. CELL GENOMICS 2022; 2:100166. [PMID: 36204155 PMCID: PMC9534481 DOI: 10.1016/j.xgen.2022.100166] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 03/31/2022] [Accepted: 07/13/2022] [Indexed: 01/21/2023]
Abstract
Cells require coordinated control over gene expression when responding to environmental stimuli. Here we apply scATAC-seq and single-cell RNA sequencing (scRNA-seq) in resting and stimulated human blood cells. Collectively, we generate ~91,000 single-cell profiles, allowing us to probe the cis-regulatory landscape of the immunological response across cell types, stimuli, and time. Advancing tools to integrate multi-omics data, we develop functional inference of gene regulation (FigR), a framework to computationally pair scA-TAC-seq with scRNA-seq cells, connect distal cis-regulatory elements to genes, and infer gene-regulatory networks (GRNs) to identify candidate transcription factor (TF) regulators. Utilizing these paired multi-omics data, we define domains of regulatory chromatin (DORCs) of immune stimulation and find that cells alter chromatin accessibility and gene expression at timescales of minutes. Construction of the stimulation GRN elucidates TF activity at disease-associated DORCs. Overall, FigR enables elucidation of regulatory interactions across single-cell data, providing new opportunities to understand the function of cells within tissues.
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Affiliation(s)
- Vinay K. Kartha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Fabiana M. Duarte
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yan Hu
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sai Ma
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Caleb A. Lareau
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew Earl
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | | | - Jason D. Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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273
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Babiczky Á, Matyas F. Molecular characteristics and laminar distribution of prefrontal neurons projecting to the mesolimbic system. eLife 2022; 11:78813. [PMID: 36063145 PMCID: PMC9444245 DOI: 10.7554/elife.78813] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Prefrontal cortical influence over the mesolimbic system - including the nucleus accumbens (NAc) and the ventral tegmental area (VTA) - is implicated in various cognitive processes and behavioral malfunctions. The functional versatility of this system could be explained by an underlying anatomical complexity; however, the detailed characterization of the medial prefrontal cortical (mPFC) innervation of the NAc and VTA is still lacking. Therefore, combining classical retrograde and conditional viral tracing techniques with multiple fluorescent immunohistochemistry, we sought to deliver a precise, cell- and layer-specific anatomical description of the cortico-mesolimbic pathways in mice. We demonstrated that NAc- (mPFCNAc) and VTA-projecting mPFC (mPFCVTA) populations show different laminar distribution (layers 2/3-5a and 5b-6, respectively) and express different molecular markers. Specifically, calbindin and Ntsr1 are specific to mPFCNAc neurons, while mPFCVTA neurons express high levels of Ctip2 and FoxP2, indicating that these populations are mostly separated at the cellular level. We directly tested this with double retrograde tracing and Canine adenovirus type 2-mediated viral labeling and found that there is indeed minimal overlap between the two populations. Furthermore, whole-brain analysis revealed that the projection pattern of these populations is also different throughout the brain. Taken together, we demonstrated that the NAc and the VTA are innervated by two, mostly nonoverlapping mPFC populations with different laminar distribution and molecular profile. These results can contribute to the advancement in our understanding of mesocorticolimbic functions and its disorders in future studies.
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Affiliation(s)
- Ákos Babiczky
- Research Centre for Natural Sciences, Budapest, Hungary.,Institute of Experimental Medicine, Budapest, Hungary.,Doctoral School of Psychology/Cognitive Science, Budapest University of Technology and Economics, Budapest, Hungary
| | - Ferenc Matyas
- Research Centre for Natural Sciences, Budapest, Hungary.,Institute of Experimental Medicine, Budapest, Hungary.,Department of Anatomy and Histology, University of Veterinary Medicine, Budapest, Hungary
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274
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Woych J, Ortega Gurrola A, Deryckere A, Jaeger ECB, Gumnit E, Merello G, Gu J, Joven Araus A, Leigh ND, Yun M, Simon A, Tosches MA. Cell-type profiling in salamanders identifies innovations in vertebrate forebrain evolution. Science 2022; 377:eabp9186. [PMID: 36048957 PMCID: PMC10024926 DOI: 10.1126/science.abp9186] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The evolution of advanced cognition in vertebrates is associated with two independent innovations in the forebrain: the six-layered neocortex in mammals and the dorsal ventricular ridge (DVR) in sauropsids (reptiles and birds). How these innovations arose in vertebrate ancestors remains unclear. To reconstruct forebrain evolution in tetrapods, we built a cell-type atlas of the telencephalon of the salamander Pleurodeles waltl. Our molecular, developmental, and connectivity data indicate that parts of the sauropsid DVR trace back to tetrapod ancestors. By contrast, the salamander dorsal pallium is devoid of cellular and molecular characteristics of the mammalian neocortex yet shares similarities with the entorhinal cortex and subiculum. Our findings chart the series of innovations that resulted in the emergence of the mammalian six-layered neocortex and the sauropsid DVR.
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Affiliation(s)
- Jamie Woych
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Alonso Ortega Gurrola
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA.,Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Astrid Deryckere
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Eliza C B Jaeger
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Elias Gumnit
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Gianluca Merello
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Jiacheng Gu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Alberto Joven Araus
- Department of Cell and Molecular Biology, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Nicholas D Leigh
- Molecular Medicine and Gene Therapy, Wallenberg Centre for Molecular Medicine, Lund Stem Cell Center, Lund University, 221 84 Lund, Sweden
| | - Maximina Yun
- Technische Universität Dresden, CRTD/Center for Regenerative Therapies Dresden, 01307 Dresden, Germany.,Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - András Simon
- Department of Cell and Molecular Biology, Karolinska Institute, SE-171 77 Stockholm, Sweden
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275
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Hain D, Gallego-Flores T, Klinkmann M, Macias A, Ciirdaeva E, Arends A, Thum C, Tushev G, Kretschmer F, Tosches MA, Laurent G. Molecular diversity and evolution of neuron types in the amniote brain. Science 2022; 377:eabp8202. [PMID: 36048944 DOI: 10.1126/science.abp8202] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The existence of evolutionarily conserved regions in the vertebrate brain is well established. The rules and constraints underlying the evolution of neuron types, however, remain poorly understood. To compare neuron types across brain regions and species, we generated a cell type atlas of the brain of a bearded dragon and compared it with mouse datasets. Conserved classes of neurons could be identified from the expression of hundreds of genes, including homeodomain-type transcription factors and genes involved in connectivity. Within these classes, however, there are both conserved and divergent neuron types, precluding a simple categorization of the brain into ancestral and novel areas. In the thalamus, neuronal diversification correlates with the evolution of the cortex, suggesting that developmental origin and circuit allocation are drivers of neuronal identity and evolution.
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Affiliation(s)
- David Hain
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.,Faculty of Biological Sciences, Goethe University, Frankfurt am Main, Germany
| | - Tatiana Gallego-Flores
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.,Faculty of Biological Sciences, Goethe University, Frankfurt am Main, Germany
| | | | - Angeles Macias
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Elena Ciirdaeva
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Anja Arends
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Christina Thum
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Georgi Tushev
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | | | - Maria Antonietta Tosches
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany.,Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Gilles Laurent
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
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276
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Blum JA, Gitler AD. Singling out motor neurons in the age of single-cell transcriptomics. Trends Genet 2022; 38:904-919. [PMID: 35487823 PMCID: PMC9378604 DOI: 10.1016/j.tig.2022.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 01/07/2023]
Abstract
Motor neurons are a remarkably powerful cell type in the central nervous system. They innervate and control the contraction of virtually every muscle in the body and their dysfunction underlies numerous neuromuscular diseases. Some motor neurons seem resistant to degeneration whereas others are vulnerable. The intrinsic heterogeneity of motor neurons in adult organisms has remained elusive. The development of high-throughput single-cell transcriptomics has changed the paradigm, empowering rapid isolation and profiling of motor neuron nuclei, revealing remarkable transcriptional diversity within the skeletal and autonomic nervous systems. Here, we discuss emerging technologies for defining motor neuron heterogeneity in the adult motor system as well as implications for disease and spinal cord injury. We establish a roadmap for future applications of emerging techniques - such as epigenetic profiling, spatial RNA sequencing, and single-cell somatic mutational profiling to adult motor neurons, which will revolutionize our understanding of the healthy and degenerating adult motor system.
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Affiliation(s)
- Jacob A Blum
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Neurosciences Interdepartmental Program, Stanford University School of Medicine, Stanford, CA, USA.
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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277
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Ben-Simon Y, Kaefer K, Velicky P, Csicsvari J, Danzl JG, Jonas P. A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory. Nat Commun 2022; 13:4826. [PMID: 35974109 PMCID: PMC9381769 DOI: 10.1038/s41467-022-32559-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/03/2022] [Indexed: 11/08/2022] Open
Abstract
The mammalian hippocampal formation (HF) plays a key role in several higher brain functions, such as spatial coding, learning and memory. Its simple circuit architecture is often viewed as a trisynaptic loop, processing input originating from the superficial layers of the entorhinal cortex (EC) and sending it back to its deeper layers. Here, we show that excitatory neurons in layer 6b of the mouse EC project to all sub-regions comprising the HF and receive input from the CA1, thalamus and claustrum. Furthermore, their output is characterized by unique slow-decaying excitatory postsynaptic currents capable of driving plateau-like potentials in their postsynaptic targets. Optogenetic inhibition of the EC-6b pathway affects spatial coding in CA1 pyramidal neurons, while cell ablation impairs not only acquisition of new spatial memories, but also degradation of previously acquired ones. Our results provide evidence of a functional role for cortical layer 6b neurons in the adult brain.
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Affiliation(s)
- Yoav Ben-Simon
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
- Department of Neurophysiology and Pharmacology, Vienna Medical University, Vienna, Austria.
| | - Karola Kaefer
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
- Department of Neuroinformatics, Radboud University, Nijmegen, The Netherlands
| | - Philipp Velicky
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Jozsef Csicsvari
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Johann G Danzl
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Peter Jonas
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
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278
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Al-Amri AH, Armstrong P, Amici M, Ligneul C, Rouse J, El-Asrag ME, Pantiru A, Vancollie VE, Ng HW, Ogbeta JA, Goodchild K, Ellegood J, Lelliott CJ, Mullins JG, Bretman A, Al-Ali R, Beetz C, Al-Gazali L, Al Shamsi A, Lerch JP, Mellor JR, Al Sayegh A, Ali M, Inglehearn CF, Clapcote SJ. PDZD8 Disruption Causes Cognitive Impairment in Humans, Mice, and Fruit Flies. Biol Psychiatry 2022; 92:323-334. [PMID: 35227461 PMCID: PMC9302898 DOI: 10.1016/j.biopsych.2021.12.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND The discovery of coding variants in genes that confer risk of intellectual disability (ID) is an important step toward understanding the pathophysiology of this common developmental disability. METHODS Homozygosity mapping, whole-exome sequencing, and cosegregation analyses were used to identify gene variants responsible for syndromic ID with autistic features in two independent consanguineous families from the Arabian Peninsula. For in vivo functional studies of the implicated gene's function in cognition, Drosophila melanogaster and mice with targeted interference of the orthologous gene were used. Behavioral, electrophysiological, and structural magnetic resonance imaging analyses were conducted for phenotypic testing. RESULTS Homozygous premature termination codons in PDZD8, encoding an endoplasmic reticulum-anchored lipid transfer protein, showed cosegregation with syndromic ID in both families. Drosophila melanogaster with knockdown of the PDZD8 ortholog exhibited impaired long-term courtship-based memory. Mice homozygous for a premature termination codon in Pdzd8 exhibited brain structural, hippocampal spatial memory, and synaptic plasticity deficits. CONCLUSIONS These data demonstrate the involvement of homozygous loss-of-function mutations in PDZD8 in a neurodevelopmental cognitive disorder. Model organisms with manipulation of the orthologous gene replicate aspects of the human phenotype and suggest plausible pathophysiological mechanisms centered on disrupted brain development and synaptic function. These findings are thus consistent with accruing evidence that synaptic defects are a common denominator of ID and other neurodevelopmental conditions.
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Affiliation(s)
- Ahmed H. Al-Amri
- School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom,Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom,National Genetic Centre, Royal Hospital, Muscat, Oman
| | - Paul Armstrong
- School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | - Mascia Amici
- School of Physiology, Pharmacology & Neuroscience, University of Bristol, Bristol, United Kingdom
| | - Clemence Ligneul
- Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, United Kingdom
| | - James Rouse
- School of Biology, University of Leeds, Leeds, United Kingdom
| | - Mohammed E. El-Asrag
- Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom,Department of Zoology, Faculty of Science, Benha University, Benha, Egypt,Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham
| | - Andreea Pantiru
- School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | | | - Hannah W.Y. Ng
- School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | - Jennifer A. Ogbeta
- School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | - Kirstie Goodchild
- School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | - Jacob Ellegood
- Mouse Imaging Centre, Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | | - Amanda Bretman
- School of Biology, University of Leeds, Leeds, United Kingdom
| | | | | | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine & Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Aisha Al Shamsi
- Pediatrics Department, Tawam Hospital, Al Ain, United Arab Emirates
| | - Jason P. Lerch
- Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, United Kingdom
| | - Jack R. Mellor
- School of Physiology, Pharmacology & Neuroscience, University of Bristol, Bristol, United Kingdom
| | - Abeer Al Sayegh
- Genetics Department, Sultan Qaboos University Hospital, Muscat, Oman
| | - Manir Ali
- Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Chris F. Inglehearn
- Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Steven J. Clapcote
- School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom,Address correspondence to Steven J. Clapcote, Ph.D.
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279
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Pavón Arocas O, Branco T. Preparation of acute midbrain slices containing the superior colliculus and periaqueductal Gray for patch-clamp recordings. PLoS One 2022; 17:e0271832. [PMID: 35951507 PMCID: PMC9371254 DOI: 10.1371/journal.pone.0271832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/07/2022] [Indexed: 11/18/2022] Open
Abstract
This protocol is a practical guide for preparing acute coronal slices from the midbrain of young adult mice for electrophysiology experiments. It describes two different sets of solutions with their respective incubation strategies and two alternative procedures for brain extraction: decapitation under terminal isoflurane anaesthesia and intracardial perfusion with artificial cerebrospinal fluid under terminal isoflurane anaesthesia. Slices can be prepared from wild-type mice as well as from mice that have been genetically modified or transfected with viral constructs to label subsets of cells. The preparation can be used to investigate the electrophysiological properties of midbrain neurons in combination with pharmacology, opto- and chemogenetic manipulations, and calcium imaging; which can be followed by morphological reconstruction, immunohistochemistry, or single-cell transcriptomics. The protocol also provides a detailed list of materials and reagents including the design for a low-cost and easy to assemble 3D printed slice recovery chamber, general advice for troubleshooting common issues leading to suboptimal slice quality, and some suggestions to ensure good maintenance of a patch-clamp rig.
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Affiliation(s)
- Oriol Pavón Arocas
- Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London, United Kingdom
| | - Tiago Branco
- Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London, United Kingdom
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280
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York NS, Sanchez-Arias JC, McAdam ACH, Rivera JE, Arbour LT, Swayne LA. Mechanisms underlying the role of ankyrin-B in cardiac and neurological health and disease. Front Cardiovasc Med 2022; 9:964675. [PMID: 35990955 PMCID: PMC9386378 DOI: 10.3389/fcvm.2022.964675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
The ANK2 gene encodes for ankyrin-B (ANKB), one of 3 members of the ankyrin family of proteins, whose name is derived from the Greek word for anchor. ANKB was originally identified in the brain (B denotes “brain”) but has become most widely known for its role in cardiomyocytes as a scaffolding protein for ion channels and transporters, as well as an interacting protein for structural and signaling proteins. Certain loss-of-function ANK2 variants are associated with a primarily cardiac-presenting autosomal-dominant condition with incomplete penetrance and variable expressivity characterized by a predisposition to supraventricular and ventricular arrhythmias, arrhythmogenic cardiomyopathy, congenital and adult-onset structural heart disease, and sudden death. Another independent group of ANK2 variants are associated with increased risk for distinct neurological phenotypes, including epilepsy and autism spectrum disorders. The mechanisms underlying ANKB's roles in cells in health and disease are not fully understood; however, several clues from a range of molecular and cell biological studies have emerged. Notably, ANKB exhibits several isoforms that have different cell-type–, tissue–, and developmental stage– expression profiles. Given the conservation within ankyrins across evolution, model organism studies have enabled the discovery of several ankyrin roles that could shed important light on ANKB protein-protein interactions in heart and brain cells related to the regulation of cellular polarity, organization, calcium homeostasis, and glucose and fat metabolism. Along with this accumulation of evidence suggesting a diversity of important ANKB cellular functions, there is an on-going debate on the role of ANKB in disease. We currently have limited understanding of how these cellular functions link to disease risk. To this end, this review will examine evidence for the cellular roles of ANKB and the potential contribution of ANKB functional variants to disease risk and presentation. This contribution will highlight the impact of ANKB dysfunction on cardiac and neuronal cells and the significance of understanding the role of ANKB variants in disease.
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Affiliation(s)
- Nicole S. York
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | | | - Alexa C. H. McAdam
- Department of Medical Genetics, University of British Columbia, Victoria, BC, Canada
| | - Joel E. Rivera
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Laura T. Arbour
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Department of Medical Genetics, University of British Columbia, Victoria, BC, Canada
- *Correspondence: Laura T. Arbour
| | - Leigh Anne Swayne
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
- Department of Cellular and Physiological Sciences and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
- Leigh Anne Swayne
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281
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Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex. Nat Neurosci 2022; 25:1049-1058. [PMID: 35915179 PMCID: PMC9343253 DOI: 10.1038/s41593-022-01123-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/16/2022] [Indexed: 11/08/2022]
Abstract
Mammalian neocortical neurons span one of the most diverse cell type spectra of any tissue. Cortical neurons are born during embryonic development, and their maturation extends into postnatal life. The regulatory strategies underlying progressive neuronal development and maturation remain unclear. Here we present an integrated single-cell epigenomic and transcriptional analysis of individual mouse and marmoset cortical neuron classes, spanning both early postmitotic stages of identity acquisition and later stages of neuronal plasticity and circuit integration. We found that, in both species, the regulatory strategies controlling early and late stages of pan-neuronal development diverge. Early postmitotic neurons use more widely shared and evolutionarily conserved molecular regulatory programs. In contrast, programs active during later neuronal maturation are more brain- and neuron-specific and more evolutionarily divergent. Our work uncovers a temporal shift in regulatory choices during neuronal diversification and maturation in both mice and marmosets, which likely reflects unique evolutionary constraints on distinct events of neuronal development in the neocortex.
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282
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Langston RG, Beilina A, Reed X, Kaganovich A, Singleton AB, Blauwendraat C, Gibbs JR, Cookson MR. Association of a common genetic variant with Parkinson's disease is mediated by microglia. Sci Transl Med 2022; 14:eabp8869. [PMID: 35895835 PMCID: PMC9809150 DOI: 10.1126/scitranslmed.abp8869] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Studies of multiple neurodegenerative disorders have identified many genetic variants that are associated with risk of disease throughout a lifetime. For example, Parkinson's disease (PD) risk is attributed in part to both coding mutations in the leucine-rich repeat kinase 2 (LRRK2) gene and to a common noncoding variation in the 5' region of the LRRK2 locus, as identified by genome-wide association studies (GWAS). However, the mechanisms linking GWAS variants to pathogenicity are largely unknown. Here, we found that the influence of PD-associated noncoding variation on LRRK2 expression is specifically propagated through microglia and not by other cell types that express LRRK2 in the human brain. We find microglia-specific regulatory chromatin regions that modulate the LRRK2 expression in human frontal cortex and substantia nigra and confirm these results in a human-induced pluripotent stem cell-derived microglia model. We showed, using a large-scale clustered regularly interspaced short palindromic repeats interference (CRISPRi) screen, that a regulatory DNA element containing the single-nucleotide variant rs6581593 influences the LRRK2 expression in microglia. Our study demonstrates that cell type should be considered when evaluating the role of noncoding variation in disease pathogenesis and sheds light on the mechanism underlying the association of the 5' region of LRRK2 with PD risk.
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Affiliation(s)
- R. G. Langston
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
- University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - A. Beilina
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - X. Reed
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - A. Kaganovich
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - A. B. Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - C. Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - J. R. Gibbs
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - M. R. Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
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283
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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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284
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Shen S, Zheng Y, Keleş S. scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data. Bioinformatics 2022; 38:3642-3644. [PMID: 35652733 PMCID: PMC9272792 DOI: 10.1093/bioinformatics/btac372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/30/2022] [Accepted: 05/26/2022] [Indexed: 11/12/2022] Open
Abstract
SUMMARY Quantitative tools are needed to leverage the unprecedented resolution of single-cell high-throughput chromatin conformation (scHi-C) data and integrate it with other single-cell data modalities. We present single-cell gene associating domain (scGAD) scores as a dimension reduction and exploratory analysis tool for scHi-C data. scGAD enables summarization at the gene unit while accounting for inherent gene-level genomic biases. Low-dimensional projections with scGAD capture clustering of cells based on their 3D structures. Significant chromatin interactions within and between cell types can be identified with scGAD. We further show that scGAD facilitates the integration of scHi-C data with other single-cell data modalities by enabling its projection onto reference low-dimensional embeddings. This multi-modal data integration provides an automated and refined cell-type annotation for scHi-C data. AVAILABILITY AND IMPLEMENTATION scGAD is part of the BandNorm R package at https://sshen82.github.io/BandNorm/articles/scGAD-tutorial.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Siqi Shen
- Department of Biostatistics and Medical Informatics, University of Wisconsin—Madison, Madison, WI 53706, USA
| | - Ye Zheng
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Sündüz Keleş
- Department of Biostatistics and Medical Informatics, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Statistics, University of Wisconsin—Madison, Madison, WI 53706, USA
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285
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Nano PR, Bhaduri A. Evaluation of advances in cortical development using model systems. Dev Neurobiol 2022; 82:408-427. [PMID: 35644985 PMCID: PMC10924780 DOI: 10.1002/dneu.22879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 04/26/2022] [Accepted: 04/30/2022] [Indexed: 11/11/2022]
Abstract
Compared with that of even the closest primates, the human cortex displays a high degree of specialization and expansion that largely emerges developmentally. Although decades of research in the mouse and other model systems has revealed core tenets of cortical development that are well preserved across mammalian species, small deviations in transcription factor expression, novel cell types in primates and/or humans, and unique cortical architecture distinguish the human cortex. Importantly, many of the genes and signaling pathways thought to drive human-specific cortical expansion also leave the brain vulnerable to disease, as the misregulation of these factors is highly correlated with neurodevelopmental and neuropsychiatric disorders. However, creating a comprehensive understanding of human-specific cognition and disease remains challenging. Here, we review key stages of cortical development and highlight known or possible differences between model systems and the developing human brain. By identifying the developmental trajectories that may facilitate uniquely human traits, we highlight open questions in need of approaches to examine these processes in a human context and reveal translatable insights into human developmental disorders.
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Affiliation(s)
- Patricia R Nano
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
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286
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Fang R, Xia C, Close JL, Zhang M, He J, Huang Z, Halpern AR, Long B, Miller JA, Lein ES, Zhuang X. Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH. Science 2022; 377:56-62. [PMID: 35771910 PMCID: PMC9262715 DOI: 10.1126/science.abm1741] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The human cerebral cortex has tremendous cellular diversity. How different cell types are organized in the human cortex and how cellular organization varies across species remain unclear. In this study, we performed spatially resolved single-cell profiling of 4000 genes using multiplexed error-robust fluorescence in situ hybridization (MERFISH), identified more than 100 transcriptionally distinct cell populations, and generated a molecularly defined and spatially resolved cell atlas of the human middle and superior temporal gyrus. We further explored cell-cell interactions arising from soma contact or proximity in a cell type-specific manner. Comparison of the human and mouse cortices showed conservation in the laminar organization of cells and differences in somatic interactions across species. Our data revealed human-specific cell-cell proximity patterns and a markedly increased enrichment for interactions between neurons and non-neuronal cells in the human cortex.
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Affiliation(s)
- Rongxin Fang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Chenglong Xia
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | | | - Meng Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Jiang He
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Zhengkai Huang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Aaron R. Halpern
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Ed S. Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA
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287
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Detecting signatures of selection on gene expression. Nat Ecol Evol 2022; 6:1035-1045. [PMID: 35551249 DOI: 10.1038/s41559-022-01761-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/01/2022] [Indexed: 12/15/2022]
Abstract
A substantial amount of phenotypic diversity results from changes in gene expression levels and patterns. Understanding how the transcriptome evolves is therefore a key priority in identifying mechanisms of adaptive change. However, in contrast to powerful models of sequence evolution, we lack a consensus model of gene expression evolution. Furthermore, recent work has shown that many of the comparative approaches used to study gene expression are subject to biases that can lead to false signatures of selection. Here we first outline the main approaches for describing expression evolution and their inherent biases. Next, we bridge the gap between the fields of phylogenetic comparative methods and transcriptomics to reinforce the main pitfalls of inferring selection on expression patterns and use simulation studies to show that shifts in tissue composition can heavily bias inferences of selection. We close by highlighting the multi-dimensional nature of transcriptional variation and identifying major unanswered questions in disentangling how selection acts on the transcriptome.
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288
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Wu H, Fu R, Zhang YH, Liu Z, Chen ZH, Xu J, Tian Y, Jin W, Wong SZH, Wu QF. Single-Cell RNA Sequencing Unravels Upregulation of Immune Cell Crosstalk in Relapsed Pediatric Ependymoma. Front Immunol 2022; 13:903246. [PMID: 35844565 PMCID: PMC9281506 DOI: 10.3389/fimmu.2022.903246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Ependymoma (EPN) is a malignant glial tumor occurring throughout central nervous system, which commonly presents in children. Although recent studies have characterized EPN samples at both the bulk and single-cell level, intratumoral heterogeneity across subclones remains a confounding factor that impedes understanding of EPN biology. In this study, we generated a high-resolution single-cell dataset of pediatric ependymoma with a particular focus on the comparison of subclone differences within tumors and showed upregulation of cilium-associated genes in more highly differentiated subclone populations. As a proxy to traditional pseudotime analysis, we applied a novel trajectory scoring method to reveal cellular compositions associated with poor survival outcomes across primary and relapsed patients. Furthermore, we identified putative cell–cell communication features between relapsed and primary samples and showed upregulation of pathways associated with immune cell crosstalk. Our results revealed both inter- and intratumoral heterogeneity in EPN and provided a framework for studying transcriptomic signatures of individual subclones at single-cell resolution.
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Affiliation(s)
- Haoda Wu
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Haoda Wu, ; Samuel Zheng Hao Wong, ; Wenfei Jin, ; Yongji Tian,
| | - Ruiqing Fu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yu-Hong Zhang
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiming Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zhen-Hua Chen
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingkai Xu
- Department of Dermatology, China–Japan Friendship Hospital, Beijing, China
| | - Yongji Tian
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Haoda Wu, ; Samuel Zheng Hao Wong, ; Wenfei Jin, ; Yongji Tian,
| | - Wenfei Jin
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- *Correspondence: Haoda Wu, ; Samuel Zheng Hao Wong, ; Wenfei Jin, ; Yongji Tian,
| | - Samuel Zheng Hao Wong
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, United States
- *Correspondence: Haoda Wu, ; Samuel Zheng Hao Wong, ; Wenfei Jin, ; Yongji Tian,
| | - Qing-Feng Wu
- State Key Laboratory of Molecular Development Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- Beijing Children Hospital, Capital Medical University, Beijing, China
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289
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Loomba S, Straehle J, Gangadharan V, Heike N, Khalifa A, Motta A, Ju N, Sievers M, Gempt J, Meyer HS, Helmstaedter M. Connectomic comparison of mouse and human cortex. Science 2022; 377:eabo0924. [PMID: 35737810 DOI: 10.1126/science.abo0924] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The human cerebral cortex houses 1,000 times more neurons than the cerebral cortex of a mouse, but the possible differences in synaptic circuits between these species are still poorly understood. We used 3-dimensional electron microscopy of mouse, macaque and human cortical samples to study their cell type composition and synaptic circuit architecture. The 2.5-fold increase in interneurons in humans compared to mouse was compensated by a change in axonal connection probabilities and therefore did not yield a commensurate increase in inhibitory-vs-excitatory synaptic input balance on human pyramidal cells. Rather, increased inhibition created an expanded interneuron-to-interneuron network, driven by an expansion of interneuron-targeting interneuron types and an increase in their synaptic selectivity for interneuron innervation. These constitute key neuronal network alterations in human cortex.
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Affiliation(s)
- Sahil Loomba
- Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany.,Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Jakob Straehle
- Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Vijayan Gangadharan
- Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Natalie Heike
- Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Abdelrahman Khalifa
- Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Alessandro Motta
- Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Niansheng Ju
- Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany
| | - Meike Sievers
- Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany.,Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Jens Gempt
- Department of Neurosurgery, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Germany
| | - Hanno S Meyer
- Department of Neurosurgery, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Germany
| | - Moritz Helmstaedter
- Department of Connectomics, Max Planck Institute for Brain Research, Frankfurt, Germany
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290
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Lazar AA, Turkcan MK, Zhou Y. A Programmable Ontology Encompassing the Functional Logic of the Drosophila Brain. Front Neuroinform 2022; 16:853098. [PMID: 35795870 PMCID: PMC9252271 DOI: 10.3389/fninf.2022.853098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
The Drosophila brain has only a fraction of the number of neurons of higher organisms such as mice and humans. Yet the sheer complexity of its neural circuits recently revealed by large connectomics datasets suggests that computationally modeling the function of fruit fly brain circuits at this scale poses significant challenges. To address these challenges, we present here a programmable ontology that expands the scope of the current Drosophila brain anatomy ontologies to encompass the functional logic of the fly brain. The programmable ontology provides a language not only for modeling circuit motifs but also for programmatically exploring their functional logic. To achieve this goal, we tightly integrated the programmable ontology with the workflow of the interactive FlyBrainLab computing platform. As part of the programmable ontology, we developed NeuroNLP++, a web application that supports free-form English queries for constructing functional brain circuits fully anchored on the available connectome/synaptome datasets, and the published worldwide literature. In addition, we present a methodology for including a model of the space of odorants into the programmable ontology, and for modeling olfactory sensory circuits of the antenna of the fruit fly brain that detect odorant sources. Furthermore, we describe a methodology for modeling the functional logic of the antennal lobe circuit consisting of a massive number of local feedback loops, a characteristic feature observed across Drosophila brain regions. Finally, using a circuit library, we demonstrate the power of our methodology for interactively exploring the functional logic of the massive number of feedback loops in the antennal lobe.
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291
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Cell type matching in single-cell RNA-sequencing data using FR-Match. Sci Rep 2022; 12:9996. [PMID: 35705694 PMCID: PMC9200772 DOI: 10.1038/s41598-022-14192-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/02/2022] [Indexed: 11/26/2022] Open
Abstract
Reference cell atlases powered by single cell and spatial transcriptomics technologies are becoming available to study healthy and diseased tissue at single cell resolution. One important use of these data resources is to compare cell types from new dataset with cell types in the reference atlases to evaluate their phenotypic similarities and differences, for example, for identifying novel cell types under disease conditions. For this purpose, rigorously-validated computational algorithms are needed to perform these cell type matching tasks that can compare datasets from different experiment platforms and sample types. Here, we present significant enhancements to FR-Match (v2.0)—a multivariate nonparametric statistical testing approach for matching cell types in query datasets to reference atlases. FR-Match v2.0 includes a normalization procedure to facilitate cross-platform cluster-level comparisons (e.g., plate-based SMART-seq and droplet-based 10X Chromium single cell and single nucleus RNA-seq and spatial transcriptomics) and extends the pipeline to also allow cell-level matching. In the use cases evaluated, FR-Match showed robust and accurate performance for identifying common and novel cell types across tissue regions, for discovering sub-optimally clustered cell types, and for cross-platform and cross-sample cell type matching.
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292
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Osorno T, Rudolph S, Nguyen T, Kozareva V, Nadaf NM, Norton A, Macosko EZ, Lee WCA, Regehr WG. Candelabrum cells are ubiquitous cerebellar cortex interneurons with specialized circuit properties. Nat Neurosci 2022; 25:702-713. [PMID: 35578131 PMCID: PMC9548381 DOI: 10.1038/s41593-022-01057-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 03/21/2022] [Indexed: 01/22/2023]
Abstract
To understand how the cerebellar cortex transforms mossy fiber (MF) inputs into Purkinje cell (PC) outputs, it is vital to delineate the elements of this circuit. Candelabrum cells (CCs) are enigmatic interneurons of the cerebellar cortex that have been identified based on their morphology, but their electrophysiological properties, synaptic connections and function remain unknown. Here, we clarify these properties using electrophysiology, single-nucleus RNA sequencing, in situ hybridization and serial electron microscopy in mice. We find that CCs are the most abundant PC layer interneuron. They are GABAergic, molecularly distinct and present in all cerebellar lobules. Their high resistance renders CC firing highly sensitive to synaptic inputs. CCs are excited by MFs and granule cells and are strongly inhibited by PCs. CCs in turn primarily inhibit molecular layer interneurons, which leads to PC disinhibition. Thus, inputs, outputs and local signals converge onto CCs to allow them to assume a unique role in controlling cerebellar output.
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Affiliation(s)
- Tomas Osorno
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Stephanie Rudolph
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- Albert Einstein College of Medicine, New York, NY, USA
| | - Tri Nguyen
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Velina Kozareva
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Naeem M Nadaf
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Aliya Norton
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Evan Z Macosko
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Wei-Chung Allen Lee
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Wade G Regehr
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
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293
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Rahayel S, Tremblay C, Vo A, Zheng YQ, Lehéricy S, Arnulf I, Vidailhet M, Corvol JC, Gagnon JF, Postuma RB, Montplaisir J, Lewis S, Matar E, Ehgoetz Martens K, Borghammer P, Knudsen K, Hansen A, Monchi O, Misic B, Dagher A. Brain atrophy in prodromal synucleinopathy is shaped by structural connectivity and gene expression. Brain 2022; 145:3162-3178. [PMID: 35594873 DOI: 10.1093/brain/awac187] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/06/2022] [Accepted: 05/12/2022] [Indexed: 11/14/2022] Open
Abstract
Isolated REM sleep behaviour disorder (iRBD) is a synucleinopathy characterized by abnormal behaviours and vocalizations during REM sleep. Most iRBD patients develop dementia with Lewy bodies, Parkinson's disease, or multiple system atrophy over time. Patients with iRBD exhibit brain atrophy patterns that are reminiscent of those observed in overt synucleinopathies. However, the mechanisms linking brain atrophy to the underlying alpha-synuclein pathophysiology are poorly understood. Our objective was to investigate how the prion-like and regional vulnerability hypotheses of alpha-synuclein might explain brain atrophy in iRBD. Using a multicentric cohort of 182 polysomnography-confirmed iRBD patients who underwent T1-weighted MRI, we performed vertex-based cortical surface and deformation-based morphometry analyses to quantify brain atrophy in patients (67.8 years, 84% men) and 261 healthy controls (66.2 years, 75%) and investigated the morphological correlates of motor and cognitive functioning in iRBD. Next, we applied the agent-based Susceptible-Infected-Removed model (i.e., a computational model that simulates in silico the spread of pathologic alpha-synuclein based on structural connectivity and gene expression) and tested if it recreated atrophy in iRBD by statistically comparing simulated regional brain atrophy to the atrophy observed in patients. The impact of SNCA and GBA gene expression and brain connectivity was then evaluated by comparing the model fit to the one obtained in null models where either gene expression or connectivity was randomized. The results showed that iRBD patients present with cortical thinning and tissue deformation, which correlated with motor and cognitive functioning. Next, we found that the computational model recreated cortical thinning (r = 0.51, p = 0.0007) and tissue deformation (r = 0.52, p = 0.0005) in patients, and that the connectome's architecture along with SNCA and GBA gene expression contributed to shaping atrophy in iRBD. We further demonstrated that the full agent-based model performed better than network measures or gene expression alone in recreating the atrophy pattern in iRBD. In summary, atrophy in iRBD is extensive, correlates with motor and cognitive function, and can be recreated using the dynamics of agent-based modelling, structural connectivity, and gene expression. These findings support the concepts that both prion-like spread and regional susceptibility account for the atrophy observed in prodromal synucleinopathies. Therefore, the agent-based Susceptible-Infected-Removed model may be a useful tool for testing hypotheses underlying neurodegenerative diseases and new therapies aimed at slowing or stopping the spread of alpha-synuclein pathology.
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Affiliation(s)
- Shady Rahayel
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal H3A 2B4, Canada.,Centre for Advanced Research in Sleep Medicine, Hôpital du Sacré-Cœur de Montréal, Montreal H4J 1C5, Montreal, Canada
| | - Christina Tremblay
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal H3A 2B4, Canada
| | - Andrew Vo
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal H3A 2B4, Canada
| | - Ying-Qiu Zheng
- Wellcome Centre for Integrative Neuroimaging, Centre for Functional Magnetic Resonance Imaging of the Brain, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - Stéphane Lehéricy
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris 75013, France
| | - Isabelle Arnulf
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris 75013, France
| | - Marie Vidailhet
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris 75013, France
| | - Jean-Christophe Corvol
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris 75013, France
| | | | - Jean-François Gagnon
- Centre for Advanced Research in Sleep Medicine, Hôpital du Sacré-Cœur de Montréal, Montreal H4J 1C5, Montreal, Canada.,Department of Psychology, Université du Québec à Montréal, Montreal H2X 3P2, Canada.,Research Centre, Institut universitaire de gériatrie de Montréal, Montreal H3W 1W5, Canada
| | - Ronald B Postuma
- Centre for Advanced Research in Sleep Medicine, Hôpital du Sacré-Cœur de Montréal, Montreal H4J 1C5, Montreal, Canada.,Department of Neurology, Montreal General Hospital, Montreal H3G 1A4, Canada
| | - Jacques Montplaisir
- Centre for Advanced Research in Sleep Medicine, Hôpital du Sacré-Cœur de Montréal, Montreal H4J 1C5, Montreal, Canada.,Department of Psychiatry, Université de Montréal, Montreal H3 T 1J4, Canada
| | - Simon Lewis
- ForeFront Parkinson's Disease Research Clinic, Brain and Mind Centre, University of Sydney, Camperdown NSW 2050, Australia
| | - Elie Matar
- ForeFront Parkinson's Disease Research Clinic, Brain and Mind Centre, University of Sydney, Camperdown NSW 2050, Australia
| | - Kaylena Ehgoetz Martens
- ForeFront Parkinson's Disease Research Clinic, Brain and Mind Centre, University of Sydney, Camperdown NSW 2050, Australia.,Department of Kinesiology and Health Sciences, University of Waterloo, Waterloo N2L 3G1, Canada
| | - Per Borghammer
- Department of Nuclear Medicine and PET, Aarhus University Hospital, Aarhus DK-8200, Denmark
| | - Karoline Knudsen
- Department of Nuclear Medicine and PET, Aarhus University Hospital, Aarhus DK-8200, Denmark
| | - Allan Hansen
- Department of Nuclear Medicine and PET, Aarhus University Hospital, Aarhus DK-8200, Denmark
| | - Oury Monchi
- Research Centre, Institut universitaire de gériatrie de Montréal, Montreal H3W 1W5, Canada.,Departments of Clinical Neurosciences, Radiology, and Hotchkiss Brain Institute, University of Calgary, Calgary T2N 4N1, Canada
| | - Bratislav Misic
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal H3A 2B4, Canada
| | - Alain Dagher
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal H3A 2B4, Canada
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294
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Vinsland E, Linnarsson S. Single-cell RNA-sequencing of mammalian brain development: insights and future directions. Development 2022; 149:275457. [DOI: 10.1242/dev.200180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
ABSTRACT
Understanding human brain development is of fundamental interest but is also very challenging. Single-cell RNA-sequencing studies in mammals have revealed that brain development is a highly dynamic process with tremendous, previously concealed, cellular heterogeneity. This Spotlight discusses key insights from these studies and their implications for experimental models. We survey published single-cell RNA-sequencing studies of mouse and human brain development, organized by anatomical regions and developmental time points. We highlight remaining gaps in the field, predominantly concerning human brain development. We propose future directions to fill the remaining gaps, and necessary complementary techniques to create an atlas integrated in space and time of human brain development.
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Affiliation(s)
- Elin Vinsland
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 171 65 Stockholm, Sweden
| | - Sten Linnarsson
- Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solnavägen 9, 171 65 Stockholm, Sweden
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295
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Guo S, Xue J, Liu J, Ye X, Guo Y, Liu D, Zhao X, Xiong F, Han X, Peng H. Smart imaging to empower brain-wide neuroscience at single-cell levels. Brain Inform 2022; 9:10. [PMID: 35543774 PMCID: PMC9095808 DOI: 10.1186/s40708-022-00158-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/12/2022] [Indexed: 11/10/2022] Open
Abstract
A deep understanding of the neuronal connectivity and networks with detailed cell typing across brain regions is necessary to unravel the mechanisms behind the emotional and memorial functions as well as to find the treatment of brain impairment. Brain-wide imaging with single-cell resolution provides unique advantages to access morphological features of a neuron and to investigate the connectivity of neuron networks, which has led to exciting discoveries over the past years based on animal models, such as rodents. Nonetheless, high-throughput systems are in urgent demand to support studies of neural morphologies at larger scale and more detailed level, as well as to enable research on non-human primates (NHP) and human brains. The advances in artificial intelligence (AI) and computational resources bring great opportunity to 'smart' imaging systems, i.e., to automate, speed up, optimize and upgrade the imaging systems with AI and computational strategies. In this light, we review the important computational techniques that can support smart systems in brain-wide imaging at single-cell resolution.
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Affiliation(s)
- Shuxia Guo
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China.
| | - Jie Xue
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Jian Liu
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Xiangqiao Ye
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Yichen Guo
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Di Liu
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Xuan Zhao
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Feng Xiong
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Xiaofeng Han
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China.
| | - Hanchuan Peng
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China
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296
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Smith SJ, von Zastrow M. A Molecular Landscape of Mouse Hippocampal Neuromodulation. Front Neural Circuits 2022; 16:836930. [PMID: 35601530 PMCID: PMC9120848 DOI: 10.3389/fncir.2022.836930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/30/2022] [Indexed: 12/23/2022] Open
Abstract
Adaptive neuronal circuit function requires a continual adjustment of synaptic network parameters known as “neuromodulation.” This process is now understood to be based primarily on the binding of myriad secreted “modulatory” ligands such as dopamine, serotonin and the neuropeptides to G protein-coupled receptors (GPCRs) that, in turn, regulate the function of the ion channels that establish synaptic weights and membrane excitability. Many of the basic molecular mechanisms of neuromodulation are now known, but the organization of neuromodulation at a network level is still an enigma. New single-cell RNA sequencing data and transcriptomic neurotaxonomies now offer bright new lights to shine on this critical “dark matter” of neuroscience. Here we leverage these advances to explore the cell-type-specific expression of genes encoding GPCRs, modulatory ligands, ion channels and intervening signal transduction molecules in mouse hippocampus area CA1, with the goal of revealing broad outlines of this well-studied brain structure’s neuromodulatory network architecture.
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Affiliation(s)
- Stephen J Smith
- Allen Institute for Brain Science, Seattle, WA, United States
- *Correspondence: Stephen J Smith,
| | - Mark von Zastrow
- Departments of Psychiatry and Pharmacology, University of California, San Francisco, San Francisco, CA, United States
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297
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Networking brainstem and basal ganglia circuits for movement. Nat Rev Neurosci 2022; 23:342-360. [DOI: 10.1038/s41583-022-00581-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2022] [Indexed: 12/14/2022]
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298
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Tian D, Izumi SI. Transcranial Magnetic Stimulation and Neocortical Neurons: The Micro-Macro Connection. Front Neurosci 2022; 16:866245. [PMID: 35495053 PMCID: PMC9039343 DOI: 10.3389/fnins.2022.866245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/28/2022] [Indexed: 12/20/2022] Open
Abstract
Understanding the operation of cortical circuits is an important and necessary task in both neuroscience and neurorehabilitation. The functioning of the neocortex results from integrative neuronal activity, which can be probed non-invasively by transcranial magnetic stimulation (TMS). Despite a clear indication of the direct involvement of cortical neurons in TMS, no explicit connection model has been made between the microscopic neuronal landscape and the macroscopic TMS outcome. Here we have performed an integrative review of multidisciplinary evidence regarding motor cortex neurocytology and TMS-related neurophysiology with the aim of elucidating the micro–macro connections underlying TMS. Neurocytological evidence from animal and human studies has been reviewed to describe the landscape of the cortical neurons covering the taxonomy, morphology, circuit wiring, and excitatory–inhibitory balance. Evidence from TMS studies in healthy humans is discussed, with emphasis on the TMS pulse and paradigm selectivity that reflect the underlying neural circuitry constitution. As a result, we propose a preliminary neuronal model of the human motor cortex and then link the TMS mechanisms with the neuronal model by stimulus intensity, direction of induced current, and paired-pulse timing. As TMS bears great developmental potential for both a probe and modulator of neural network activity and neurotransmission, the connection model will act as a foundation for future combined studies of neurocytology and neurophysiology, as well as the technical advances and application of TMS.
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Affiliation(s)
- Dongting Tian
- Department of Physical Medicine and Rehabilitation, Tohoku University Graduates School of Medicine, Sendai, Japan
- *Correspondence: Dongting Tian,
| | - Shin-Ichi Izumi
- Department of Physical Medicine and Rehabilitation, Tohoku University Graduates School of Medicine, Sendai, Japan
- Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Shin-Ichi Izumi,
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299
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Antunes ASM, Martins-de-Souza D. Single-cell RNA-seq and its Applications in the Study of Psychiatric Disorders. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2022. [PMID: 37519459 PMCID: PMC10382703 DOI: 10.1016/j.bpsgos.2022.03.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Neuroscience is currently one of the most challenging research fields owing to the enormous complexity of the mammalian nervous system. We are yet to understand precise transcriptional programs that govern cell fate during neurodevelopment, resolve the connectome of the mammalian brain, and determine the etiology of various neurodegenerative and psychiatric disorders. Technological advances in the past decade, notably single-cell RNA sequencing, have enabled huge progress in our understanding of such features. Our current knowledge of the transcriptome is largely derived from bulk RNA sequencing, which reveals only the average gene expression of millions of cells, potentially missing out on minor transcriptome differences between cells detectable only at single-cell resolution. Since 2009, several single-cell RNA sequencing techniques have emerged that enable the accurate classification of neuronal and glial cell subtypes beyond classical molecular markers and electrophysiological features and allow the identification of previously unknown cell types. Furthermore, it enables the interrogation of molecular and disease-relevant mechanisms and offers further possibilities for the discovery of new drug targets and disease biomarkers. This review intends to familiarize the reader with the main single-cell RNA sequencing techniques developed throughout the past decade and discusses their application in the fields of brain cell taxonomy, neurodevelopment, and psychiatric disorders.
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300
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Amunts K, DeFelipe J, Pennartz C, Destexhe A, Migliore M, Ryvlin P, Furber S, Knoll A, Bitsch L, Bjaalie JG, Ioannidis Y, Lippert T, Sanchez-Vives MV, Goebel R, Jirsa V. Linking Brain Structure, Activity, and Cognitive Function through Computation. eNeuro 2022; 9:ENEURO.0316-21.2022. [PMID: 35217544 PMCID: PMC8925650 DOI: 10.1523/eneuro.0316-21.2022] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 01/19/2023] Open
Abstract
Understanding the human brain is a "Grand Challenge" for 21st century research. Computational approaches enable large and complex datasets to be addressed efficiently, supported by artificial neural networks, modeling and simulation. Dynamic generative multiscale models, which enable the investigation of causation across scales and are guided by principles and theories of brain function, are instrumental for linking brain structure and function. An example of a resource enabling such an integrated approach to neuroscientific discovery is the BigBrain, which spatially anchors tissue models and data across different scales and ensures that multiscale models are supported by the data, making the bridge to both basic neuroscience and medicine. Research at the intersection of neuroscience, computing and robotics has the potential to advance neuro-inspired technologies by taking advantage of a growing body of insights into perception, plasticity and learning. To render data, tools and methods, theories, basic principles and concepts interoperable, the Human Brain Project (HBP) has launched EBRAINS, a digital neuroscience research infrastructure, which brings together a transdisciplinary community of researchers united by the quest to understand the brain, with fascinating insights and perspectives for societal benefits.
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Affiliation(s)
- Katrin Amunts
- Institute of Neurosciences and Medicine (INM-1), Research Centre Jülich, Jülich 52425, Germany
- C. & O. Vogt Institute for Brain Research, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Javier DeFelipe
- Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Madrid 28223, Spain
- Instituto Cajal, Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28002, Spain
| | - Cyriel Pennartz
- Cognitive and Systems Neuroscience Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, 1098 XH, The Netherlands
| | - Alain Destexhe
- Centre National de la Recherche Scientifique, Institute of Neuroscience (NeuroPSI), Paris-Saclay University, Gif sur Yvette 91400, France
| | - Michele Migliore
- Institute of Biophysics, National Research Council, Palermo 90146, Italy
| | - Philippe Ryvlin
- Department of Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne CH-1011, Switzerland
| | - Steve Furber
- Department of Computer Science, The University of Manchester, Manchester M13 9PL, United Kingdom
| | - Alois Knoll
- Department of Informatics, Technical University of Munich, Garching 385748, Germany
| | - Lise Bitsch
- The Danish Board of Technology Foundation, Copenhagen, 2650 Hvidovre, Denmark
| | - Jan G Bjaalie
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Yannis Ioannidis
- ATHENA Research & Innovation Center, Athena 12125, Greece
- Department of Informatics & Telecom, Nat'l and Kapodistrian University of Athens, 157 84 Athens, Greece
| | - Thomas Lippert
- Institute for Advanced Simulation (IAS), Jülich Supercomputing Centre (JSC), Research Centre Jülich, Jülich 52425, Germany
| | - Maria V Sanchez-Vives
- ICREA and Systems Neuroscience, Institute of Biomedical Investigations August Pi i Sunyer, Barcelona 08036, Spain
| | - Rainer Goebel
- Department of Cognitive Neuroscience, Department of Cognitive Neuroscience, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht 6229 EV, The Netherlands
| | - Viktor Jirsa
- Aix Marseille Université, Institut National de la Santé et de la Recherche Médicale, Institut de Neurosciences des Systèmes (INS) UMR1106, Marseille 13005, France
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