1
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Abbondanza A, Urushadze A, Alves-Barboza AR, Janickova H. Expression and function of nicotinic acetylcholine receptors in specific neuronal populations: Focus on striatal and prefrontal circuits. Pharmacol Res 2024; 204:107190. [PMID: 38704107 DOI: 10.1016/j.phrs.2024.107190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/06/2024]
Abstract
Nicotinic acetylcholine receptors (nAChRs) are widely expressed in the central nervous system and play an important role in the control of neural functions including neuronal activity, transmitter release and synaptic plasticity. Although the common subtypes of nAChRs are abundantly expressed throughout the brain, their expression in different brain regions and by individual neuronal types is not homogeneous or incidental. In recent years, several studies have emerged showing that particular subtypes of nAChRs are expressed by specific neuronal populations in which they have major influence on the activity of local circuits and behavior. It has been demonstrated that even nAChRs expressed by relatively rare neuronal types can induce significant changes in behavior and contribute to pathological processes. Depending on the identity and connectivity of the particular nAChRs-expressing neuronal populations, the activation of nAChRs can have distinct or even opposing effects on local neuronal signaling. In this review, we will summarize the available literature describing the expression of individual nicotinic subunits by different neuronal types in two crucial brain regions, the striatum and the prefrontal cortex. The review will also briefly discuss nicotinic expression in non-neuronal, glial cells, as they cannot be ignored as potential targets of nAChRs-modulating drugs. The final section will discuss options that could allow us to target nAChRs in a neuronal-type-specific manner, not only in the experimental field, but also eventually in clinical practice.
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Affiliation(s)
- Alice Abbondanza
- Laboratory of Neurochemistry, Institute of Physiology of the Czech Academy of Sciences, Prague 14200, Czech Republic
| | - Anna Urushadze
- Laboratory of Neurochemistry, Institute of Physiology of the Czech Academy of Sciences, Prague 14200, Czech Republic
| | - Amanda Rosanna Alves-Barboza
- Laboratory of Neurochemistry, Institute of Physiology of the Czech Academy of Sciences, Prague 14200, Czech Republic
| | - Helena Janickova
- Laboratory of Neurochemistry, Institute of Physiology of the Czech Academy of Sciences, Prague 14200, Czech Republic.
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2
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Bhagavan H, Wei AD, Oliveira LM, Aldinger KA, Ramirez JM. Chronic intermittent hypoxia elicits distinct transcriptomic responses among neurons and oligodendrocytes within the brainstem of mice. Am J Physiol Lung Cell Mol Physiol 2024; 326:L698-L712. [PMID: 38591125 DOI: 10.1152/ajplung.00320.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/22/2024] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Chronic intermittent hypoxia (CIH) is a prevalent condition characterized by recurrent episodes of oxygen deprivation, linked to respiratory and neurological disorders. Prolonged CIH is known to have adverse effects, including endothelial dysfunction, chronic inflammation, oxidative stress, and impaired neuronal function. These factors can contribute to serious comorbidities, including metabolic disorders and cardiovascular diseases. To investigate the molecular impact of CIH, we examined male C57BL/6J mice exposed to CIH for 21 days, comparing with normoxic controls. We used single-nucleus RNA sequencing to comprehensively examine the transcriptomic impact of CIH on key cell classes within the brainstem, specifically excitatory neurons, inhibitory neurons, and oligodendrocytes. These cell classes regulate essential physiological functions, including autonomic tone, cardiovascular control, and respiration. Through analysis of 10,995 nuclei isolated from pontine-medullary tissue, we identified seven major cell classes, further subdivided into 24 clusters. Our findings among these cell classes, revealed significant differential gene expression, underscoring their distinct responses to CIH. Notably, neurons exhibited transcriptional dysregulation of genes associated with synaptic transmission, and structural remodeling. In addition, we found dysregulated genes encoding ion channels and inflammatory response. Concurrently, oligodendrocytes exhibited dysregulated genes associated with oxidative phosphorylation and oxidative stress. Utilizing CellChat network analysis, we uncovered CIH-dependent altered patterns of diffusible intercellular signaling. These insights offer a comprehensive transcriptomic cellular atlas of the pons-medulla and provide a fundamental resource for the analysis of molecular adaptations triggered by CIH.NEW & NOTEWORTHY This study on chronic intermittent hypoxia (CIH) from pons-medulla provides initial insights into the molecular effects on excitatory neurons, inhibitory neurons, and oligodendrocytes, highlighting our unbiased approach, in comparison with earlier studies focusing on single target genes. Our findings reveal that CIH affects cell classes distinctly, and the dysregulated genes in distinct cell classes are associated with synaptic transmission, ion channels, inflammation, oxidative stress, and intercellular signaling, advancing our understanding of CIH-induced molecular responses.
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Affiliation(s)
- Hemalatha Bhagavan
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, United States
| | - Aguan D Wei
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, United States
| | - Luiz M Oliveira
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, United States
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, United States
- Department of Pediatrics, University of Washington, Seattle, Washington, United States
- Department of Neurology, University of Washington, Seattle, Washington, United States
| | - Jan-Marino Ramirez
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, United States
- Department of Pediatrics, University of Washington, Seattle, Washington, United States
- Department of Neurological Surgery, University of Washington, Seattle, Washington, United States
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3
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Aitken K, Campagnola L, Garrett ME, Olsen SR, Mihalas S. Simple synaptic modulations implement diverse novelty computations. Cell Rep 2024; 43:114188. [PMID: 38713584 DOI: 10.1016/j.celrep.2024.114188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/09/2024] [Accepted: 04/17/2024] [Indexed: 05/09/2024] Open
Abstract
Detecting novelty is ethologically useful for an organism's survival. Recent experiments characterize how different types of novelty over timescales from seconds to weeks are reflected in the activity of excitatory and inhibitory neuron types. Here, we introduce a learning mechanism, familiarity-modulated synapses (FMSs), consisting of multiplicative modulations dependent on presynaptic or pre/postsynaptic neuron activity. With FMSs, network responses that encode novelty emerge under unsupervised continual learning and minimal connectivity constraints. Implementing FMSs within an experimentally constrained model of a visual cortical circuit, we demonstrate the generalizability of FMSs by simultaneously fitting absolute, contextual, and omission novelty effects. Our model also reproduces functional diversity within cell subpopulations, leading to experimentally testable predictions about connectivity and synaptic dynamics that can produce both population-level novelty responses and heterogeneous individual neuron signals. Altogether, our findings demonstrate how simple plasticity mechanisms within a cortical circuit structure can produce qualitatively distinct and complex novelty responses.
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Affiliation(s)
- Kyle Aitken
- Center for Data-Driven Discovery for Biology, Allen Institute, Seattle, WA 98109, USA.
| | | | | | - Shawn R Olsen
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Stefan Mihalas
- Center for Data-Driven Discovery for Biology, Allen Institute, Seattle, WA 98109, USA; Applied Mathematics, University of Washington, Seattle, WA 98195, USA
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4
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Buchan MJ, Gothard G, Mahfooz K, van Rheede JJ, Avery SV, Vourvoukelis A, Demby A, Ellender TJ, Newey SE, Akerman CJ. Higher-order thalamocortical circuits are specified by embryonic cortical progenitor types in the mouse brain. Cell Rep 2024; 43:114157. [PMID: 38678557 DOI: 10.1016/j.celrep.2024.114157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 02/14/2024] [Accepted: 04/10/2024] [Indexed: 05/01/2024] Open
Abstract
The sensory cortex receives synaptic inputs from both first-order and higher-order thalamic nuclei. First-order inputs relay simple stimulus properties from the periphery, whereas higher-order inputs relay more complex response properties, provide contextual feedback, and modulate plasticity. Here, we reveal that a cortical neuron's higher-order input is determined by the type of progenitor from which it is derived during embryonic development. Within layer 4 (L4) of the mouse primary somatosensory cortex, neurons derived from intermediate progenitors receive stronger higher-order thalamic input and exhibit greater higher-order sensory responses. These effects result from differences in dendritic morphology and levels of the transcription factor Lhx2, which are specified by the L4 neuron's progenitor type. When this mechanism is disrupted, cortical circuits exhibit altered higher-order responses and sensory-evoked plasticity. Therefore, by following distinct trajectories, progenitor types generate diversity in thalamocortical circuitry and may provide a general mechanism for differentially routing information through the cortex.
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Affiliation(s)
| | - Gemma Gothard
- Department of Pharmacology, Mansfield Road, OX1 3QT Oxford, UK
| | - Kashif Mahfooz
- Department of Pharmacology, Mansfield Road, OX1 3QT Oxford, UK
| | | | - Sophie V Avery
- Department of Pharmacology, Mansfield Road, OX1 3QT Oxford, UK
| | | | - Alexander Demby
- Department of Pharmacology, Mansfield Road, OX1 3QT Oxford, UK
| | - Tommas J Ellender
- Department of Pharmacology, Mansfield Road, OX1 3QT Oxford, UK; Experimental Neurobiology Unit, Universiteitsplein, 2610 Antwerp, Belgium
| | - Sarah E Newey
- Department of Pharmacology, Mansfield Road, OX1 3QT Oxford, UK
| | - Colin J Akerman
- Department of Pharmacology, Mansfield Road, OX1 3QT Oxford, UK.
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5
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Liu Y, Zhang J, Jiang Z, Qin M, Xu M, Zhang S, Ma G. Organization of corticocortical and thalamocortical top-down inputs in the primary visual cortex. Nat Commun 2024; 15:4495. [PMID: 38802410 PMCID: PMC11130321 DOI: 10.1038/s41467-024-48924-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
Unified visual perception requires integration of bottom-up and top-down inputs in the primary visual cortex (V1), yet the organization of top-down inputs in V1 remains unclear. Here, we used optogenetics-assisted circuit mapping to identify how multiple top-down inputs from higher-order cortical and thalamic areas engage V1 excitatory and inhibitory neurons. Top-down inputs overlap in superficial layers yet segregate in deep layers. Inputs from the medial secondary visual cortex (V2M) and anterior cingulate cortex (ACA) converge on L6 Pyrs, whereas ventrolateral orbitofrontal cortex (ORBvl) and lateral posterior thalamic nucleus (LP) inputs are processed in parallel in Pyr-type-specific subnetworks (Pyr←ORBvl and Pyr←LP) and drive mutual inhibition between them via local interneurons. Our study deepens understanding of the top-down modulation mechanisms of visual processing and establishes that V2M and ACA inputs in L6 employ integrated processing distinct from the parallel processing of LP and ORBvl inputs in L5.
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Affiliation(s)
- Yanmei Liu
- Songjiang Hospital and Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jiahe Zhang
- Songjiang Hospital and Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhishan Jiang
- Songjiang Hospital and Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Meiling Qin
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Min Xu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Siyu Zhang
- Songjiang Hospital and Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China.
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Guofen Ma
- Songjiang Hospital and Songjiang Research Institute, Shanghai Key Laboratory of Emotions and Affective Disorders, Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, China.
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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6
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Lee EJ, Suh M, Choi H, Choi Y, Hwang DW, Bae S, Lee DS. Spatial transcriptomic brain imaging reveals the effects of immunomodulation therapy on specific regional brain cells in a mouse dementia model. BMC Genomics 2024; 25:516. [PMID: 38796425 PMCID: PMC11128132 DOI: 10.1186/s12864-024-10434-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024] Open
Abstract
Increasing evidence of brain-immune crosstalk raises expectations for the efficacy of novel immunotherapies in Alzheimer's disease (AD), but the lack of methods to examine brain tissues makes it difficult to evaluate therapeutics. Here, we investigated the changes in spatial transcriptomic signatures and brain cell types using the 10x Genomics Visium platform in immune-modulated AD models after various treatments. To proceed with an analysis suitable for barcode-based spatial transcriptomics, we first organized a workflow for segmentation of neuroanatomical regions, establishment of appropriate gene combinations, and comprehensive review of altered brain cell signatures. Ultimately, we investigated spatial transcriptomic changes following administration of immunomodulators, NK cell supplements and an anti-CD4 antibody, which ameliorated behavior impairment, and designated brain cells and regions showing probable associations with behavior changes. We provided the customized analytic pipeline into an application named STquantool. Thus, we anticipate that our approach can help researchers interpret the real action of drug candidates by simultaneously investigating the dynamics of all transcripts for the development of novel AD therapeutics.
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Affiliation(s)
- Eun Ji Lee
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Minseok Suh
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Institute of Radiation Medicine, Medical Research Center, Seoul National University, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Hongyoon Choi
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Yoori Choi
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Cliniclal Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Do Won Hwang
- Research and Development Center, THERABEST Inc., Seocho-daero 40-gil, Seoul, 06657, Republic of Korea
| | - Sungwoo Bae
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Institute of Radiation Medicine, Medical Research Center, Seoul National University, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
| | - Dong Soo Lee
- Department of Nuclear Medicine, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea.
- Department of Nuclear Medicine, Seoul National University Hospital, Seoul, Republic of Korea.
- Institute of Radiation Medicine, Medical Research Center, Seoul National University, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Medical Science and Engineering, School of Convergence Science and Technology, POSTECH, Pohang, Republic of Korea.
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7
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Roux de Bézieux H, Street K, Fischer S, Van den Berge K, Chance R, Risso D, Gillis J, Ngai J, Purdom E, Dudoit S. Improving replicability in single-cell RNA-Seq cell type discovery with Dune. BMC Bioinformatics 2024; 25:198. [PMID: 38789920 PMCID: PMC11127396 DOI: 10.1186/s12859-024-05814-6] [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: 09/14/2023] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
BACKGROUND Single-cell transcriptome sequencing (scRNA-Seq) has allowed new types of investigations at unprecedented levels of resolution. Among the primary goals of scRNA-Seq is the classification of cells into distinct types. Many approaches build on existing clustering literature to develop tools specific to single-cell. However, almost all of these methods rely on heuristics or user-supplied parameters to control the number of clusters. This affects both the resolution of the clusters within the original dataset as well as their replicability across datasets. While many recommendations exist, in general, there is little assurance that any given set of parameters will represent an optimal choice in the trade-off between cluster resolution and replicability. For instance, another set of parameters may result in more clusters that are also more replicable. RESULTS Here, we propose Dune, a new method for optimizing the trade-off between the resolution of the clusters and their replicability. Our method takes as input a set of clustering results-or partitions-on a single dataset and iteratively merges clusters within each partitions in order to maximize their concordance between partitions. As demonstrated on multiple datasets from different platforms, Dune outperforms existing techniques, that rely on hierarchical merging for reducing the number of clusters, in terms of replicability of the resultant merged clusters as well as concordance with ground truth. Dune is available as an R package on Bioconductor: https://www.bioconductor.org/packages/release/bioc/html/Dune.html . CONCLUSIONS Cluster refinement by Dune helps improve the robustness of any clustering analysis and reduces the reliance on tuning parameters. This method provides an objective approach for borrowing information across multiple clusterings to generate replicable clusters most likely to represent common biological features across multiple datasets.
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Affiliation(s)
- Hector Roux de Bézieux
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Kelly Street
- Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Koen Van den Berge
- Department of Statistics, University of California, Berkeley, CA, USA
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Rebecca Chance
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Davide Risso
- Department of Statistical Sciences, University of Padova, Padova, Italy
| | - Jesse Gillis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - John Ngai
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Sandrine Dudoit
- Department of Statistics, University of California, Berkeley, CA, USA.
- Division of Biostatistics, School of Public Health, University of California, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, CA, USA.
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8
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Gonzalez-Ferrer J, Lehrer J, O'Farrell A, Paten B, Teodorescu M, Haussler D, Jonsson VD, Mostajo-Radji MA. SIMS: A deep-learning label transfer tool for single-cell RNA sequencing analysis. CELL GENOMICS 2024:100581. [PMID: 38823397 DOI: 10.1016/j.xgen.2024.100581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/03/2024]
Abstract
Cell atlases serve as vital references for automating cell labeling in new samples, yet existing classification algorithms struggle with accuracy. Here we introduce SIMS (scalable, interpretable machine learning for single cell), a low-code data-efficient pipeline for single-cell RNA classification. We benchmark SIMS against datasets from different tissues and species. We demonstrate SIMS's efficacy in classifying cells in the brain, achieving high accuracy even with small training sets (<3,500 cells) and across different samples. SIMS accurately predicts neuronal subtypes in the developing brain, shedding light on genetic changes during neuronal differentiation and postmitotic fate refinement. Finally, we apply SIMS to single-cell RNA datasets of cortical organoids to predict cell identities and uncover genetic variations between cell lines. SIMS identifies cell-line differences and misannotated cell lineages in human cortical organoids derived from different pluripotent stem cell lines. Altogether, we show that SIMS is a versatile and robust tool for cell-type classification from single-cell datasets.
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Affiliation(s)
- Jesus Gonzalez-Ferrer
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Julian Lehrer
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Applied Mathematics, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Ash O'Farrell
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Benedict Paten
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Mircea Teodorescu
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Electrical and Computer Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - David Haussler
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA
| | - Vanessa D Jonsson
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Applied Mathematics, University of California, Santa Cruz, Santa Cruz, CA 95060, USA.
| | - Mohammed A Mostajo-Radji
- Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Live Cell Biotechnology Discovery Lab, University of California, Santa Cruz, Santa Cruz, CA 95060, USA.
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9
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Rastogi M, Bartolucci M, Nanni M, Aloisio M, Vozzi D, Petretto A, Contestabile A, Cancedda L. Integrative multi-omic analysis reveals conserved cell-projection deficits in human Down syndrome brains. Neuron 2024:S0896-6273(24)00329-5. [PMID: 38810652 DOI: 10.1016/j.neuron.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/17/2024] [Accepted: 05/01/2024] [Indexed: 05/31/2024]
Abstract
Down syndrome (DS) is the most common genetic cause of cognitive disability. However, it is largely unclear how triplication of a small gene subset may impinge on diverse aspects of DS brain physiopathology. Here, we took a multi-omic approach and simultaneously analyzed by RNA-seq and proteomics the expression signatures of two diverse regions of human postmortem DS brains. We found that the overexpression of triplicated genes triggered global expression dysregulation, differentially affecting transcripts, miRNAs, and proteins involved in both known and novel biological candidate pathways. Among the latter, we observed an alteration in RNA splicing, specifically modulating the expression of genes involved in cytoskeleton and axonal dynamics in DS brains. Accordingly, we found an alteration in axonal polarization in neurons from DS human iPSCs and mice. Thus, our study provides an integrated multilayer expression database capable of identifying new potential targets to aid in designing future clinical interventions for DS.
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Affiliation(s)
- Mohit Rastogi
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - Martina Bartolucci
- Core Facilities - Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, Genova 16147, Italy
| | - Marina Nanni
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy
| | | | - Diego Vozzi
- Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova 16152, Italy
| | - Andrea Petretto
- Core Facilities - Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, Genova 16147, Italy
| | - Andrea Contestabile
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy.
| | - Laura Cancedda
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy; Dulbecco Telethon Institute, Rome 00185, Italy.
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10
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Sharifi O, Haghani V, Neier KE, Fraga KJ, Korf I, Hakam SM, Quon G, Johansen N, Yasui DH, LaSalle JM. Sex-specific single cell-level transcriptomic signatures of Rett syndrome disease progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.16.594595. [PMID: 38798575 PMCID: PMC11118571 DOI: 10.1101/2024.05.16.594595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Dominant X-linked diseases are uncommon due to female X chromosome inactivation (XCI). While random XCI usually protects females against X-linked mutations, Rett syndrome (RTT) is a female neurodevelopmental disorder caused by heterozygous MECP2 mutation. After 6-18 months of typical neurodevelopment, RTT girls undergo poorly understood regression. We performed longitudinal snRNA-seq on cerebral cortex in a construct-relevant Mecp2e1 mutant mouse model of RTT, revealing transcriptional effects of cell type, mosaicism, and sex on progressive disease phenotypes. Across cell types, we observed sex differences in the number of differentially expressed genes (DEGs) with 6x more DEGs in mutant females than males. Unlike males, female DEGs emerged prior to symptoms, were enriched for homeostatic gene pathways in distinct cell types over time, and correlated with disease phenotypes and human RTT cortical cell transcriptomes. Non-cell-autonomous effects were prominent and dynamic across disease progression of Mecp2e1 mutant females, indicating wild-type-expressing cells normalizing transcriptional homeostasis. These results improve understanding of RTT progression and treatment.
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Affiliation(s)
- Osman Sharifi
- Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616
- Genome Center, University of California, Davis, CA 95616
- MIND Institute, University of California, Davis, CA 95616
| | - Viktoria Haghani
- Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616
- Genome Center, University of California, Davis, CA 95616
- MIND Institute, University of California, Davis, CA 95616
| | - Kari E. Neier
- Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616
- Genome Center, University of California, Davis, CA 95616
- MIND Institute, University of California, Davis, CA 95616
| | - Keith J. Fraga
- Cellular and Molecular Biology, College of Biological Sciences, University of California, Davis, CA 95616
- Genome Center, University of California, Davis, CA 95616
| | - Ian Korf
- Cellular and Molecular Biology, College of Biological Sciences, University of California, Davis, CA 95616
- Genome Center, University of California, Davis, CA 95616
| | - Sophia M. Hakam
- Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616
- Genome Center, University of California, Davis, CA 95616
- MIND Institute, University of California, Davis, CA 95616
| | - Gerald Quon
- Cellular and Molecular Biology, College of Biological Sciences, University of California, Davis, CA 95616
- Genome Center, University of California, Davis, CA 95616
| | - Nelson Johansen
- Cellular and Molecular Biology, College of Biological Sciences, University of California, Davis, CA 95616
- Genome Center, University of California, Davis, CA 95616
| | - Dag H. Yasui
- Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616
- Genome Center, University of California, Davis, CA 95616
- MIND Institute, University of California, Davis, CA 95616
| | - Janine M. LaSalle
- Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616
- Genome Center, University of California, Davis, CA 95616
- MIND Institute, University of California, Davis, CA 95616
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11
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Steyn C, Mishi R, Fillmore S, Verhoog MB, More J, Rohlwink UK, Melvill R, Butler J, Enslin JMN, Jacobs M, Sauka-Spengler T, Greco M, Quiñones S, Dulla CG, Raimondo JV, Figaji A, Hockman D. Cell type-specific gene expression dynamics during human brain maturation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.29.560114. [PMID: 37808657 PMCID: PMC10557738 DOI: 10.1101/2023.09.29.560114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The human brain undergoes protracted post-natal maturation, guided by dynamic changes in gene expression. Most studies exploring these processes have used bulk tissue analyses, which mask cell type-specific gene expression dynamics. Here, using single nucleus (sn)RNA-seq on temporal lobe tissue, including samples of African ancestry, we build a joint paediatric and adult atlas of 75 cell subtypes, which we verify with spatial transcriptomics. We explore the differences between paediatric and adult cell types, revealing the genes and pathways that change during brain maturation. Our results highlight excitatory neuron subtypes, including the LTK and FREM subtypes, that show elevated expression of genes associated with cognition and synaptic plasticity in paediatric tissue. The new resources we present here improve our understanding of the brain during its development and contribute to global efforts to build an inclusive brain cell map.
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Affiliation(s)
- Christina Steyn
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Ruvimbo Mishi
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Stephanie Fillmore
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Matthijs B Verhoog
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Jessica More
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Ursula K Rohlwink
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - Roger Melvill
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - James Butler
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Johannes M N Enslin
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - Muazzam Jacobs
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Immunology, Department of Pathology University of Cape Town
- National Health Laboratory Service, South Africa
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Maria Greco
- Single Cell Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Sadi Quiñones
- Department of Neuroscience, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
- Graduate School of Biomedical Science, Tufts University School of Medicine, Boston, MA, USA
| | - Chris G Dulla
- Department of Neuroscience, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
| | - Joseph V Raimondo
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Anthony Figaji
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Division of Neurosurgery, Department of Surgery, University of Cape Town, Cape Town, South Africa
| | - Dorit Hockman
- Division of Cell Biology, Department of Human Biology, University of Cape Town, Cape Town, South Africa
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
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12
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Burman RJ, Diviney T, Călin A, Gothard G, Jouhanneau JSM, Poulet JFA, Sen A, Akerman CJ. Optogenetic Determination of Dynamic and Cell-Type-Specific Inhibitory Reversal Potentials. J Neurosci 2024; 44:e1392232024. [PMID: 38604778 PMCID: PMC11097265 DOI: 10.1523/jneurosci.1392-23.2024] [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: 07/24/2023] [Revised: 03/31/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024] Open
Abstract
The reversal potential refers to the membrane potential at which the net current flow through a channel reverses direction. The reversal potential is determined by transmembrane ion gradients and, in turn, determines how the channel's activity will affect the membrane potential. Traditional investigation into the reversal potential of inhibitory ligand-gated ion channels (EInh) has relied upon the activation of endogenous receptors, such as the GABA-A receptor (GABAAR). There are, however, challenges associated with activating endogenous receptors, including agonist delivery, isolating channel responses, and the effects of receptor saturation and desensitization. Here, we demonstrate the utility of using a light-gated anion channel, stGtACR2, to probe EInh in the rodent brain. Using mice of both sexes, we demonstrate that the properties of this optically activated channel make it a suitable proxy for studying GABAAR receptor-mediated inhibition. We validate this agonist-independent optogenetic strategy in vitro and in vivo and further show how it can accurately capture differences in EInh dynamics following manipulations of endogenous ion fluxes. This allows us to explore distinct resting EInh differences across genetically defined neuronal subpopulations. Using this approach to challenge ion homeostasis mechanisms in neurons, we uncover cell-specific EInh dynamics that are supported by the differential expression of endogenous ion handling mechanisms. Our findings therefore establish an effective optical strategy for revealing novel aspects of inhibitory reversal potentials and thereby expand the repertoire of optogenetics.
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Affiliation(s)
- Richard J Burman
- Department of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom
- Oxford Epilepsy Research Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Tara Diviney
- Department of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom
| | - Alexandru Călin
- Department of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom
| | - Gemma Gothard
- Department of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom
| | - Jean-Sébastien M Jouhanneau
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin 13125, Germany
- Neuroscience Research Center, Charité-Universitätsmedizin, Berlin 10117, Germany
| | - James F A Poulet
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin 13125, Germany
- Neuroscience Research Center, Charité-Universitätsmedizin, Berlin 10117, Germany
| | - Arjune Sen
- Oxford Epilepsy Research Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Colin J Akerman
- Department of Pharmacology, University of Oxford, Oxford OX1 3QT, United Kingdom
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13
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Zheng X, Wu B, Liu Y, Simmons SK, Kim K, Clarke GS, Ashiq A, Park J, Li J, Wang Z, Tong L, Wang Q, Rajamani KT, Muñoz-Castañeda R, Mu S, Qi T, Zhang Y, Ngiam ZC, Ohte N, Hanashima C, Wu Z, Xu X, Levin JZ, Jin X. Massively parallel in vivo Perturb-seq reveals cell-type-specific transcriptional networks in cortical development. Cell 2024:S0092-8674(24)00476-8. [PMID: 38772369 DOI: 10.1016/j.cell.2024.04.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/30/2023] [Accepted: 04/30/2024] [Indexed: 05/23/2024]
Abstract
Leveraging AAVs' versatile tropism and labeling capacity, we expanded the scale of in vivo CRISPR screening with single-cell transcriptomic phenotyping across embryonic to adult brains and peripheral nervous systems. Through extensive tests of 86 vectors across AAV serotypes combined with a transposon system, we substantially amplified labeling efficacy and accelerated in vivo gene delivery from weeks to days. Our proof-of-principle in utero screen identified the pleiotropic effects of Foxg1, highlighting its tight regulation of distinct networks essential for cell fate specification of Layer 6 corticothalamic neurons. Notably, our platform can label >6% of cerebral cells, surpassing the current state-of-the-art efficacy at <0.1% by lentivirus, to achieve analysis of over 30,000 cells in one experiment and enable massively parallel in vivo Perturb-seq. Compatible with various phenotypic measurements (single-cell or spatial multi-omics), it presents a flexible approach to interrogate gene function across cell types in vivo, translating gene variants to their causal function.
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Affiliation(s)
- Xinhe Zheng
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Boli Wu
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Yuejia Liu
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Sean K Simmons
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kwanho Kim
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Grace S Clarke
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Abdullah Ashiq
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Joshua Park
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Jiwen Li
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Zhilin Wang
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Liqi Tong
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA 92617, USA
| | - Qizhao Wang
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA 92617, USA
| | - Keerthi T Rajamani
- Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Rodrigo Muñoz-Castañeda
- Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Shang Mu
- Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Tianbo Qi
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Yunxiao Zhang
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA
| | - Zi Chao Ngiam
- Center for Advanced Biomedical Sciences, Waseda University, Tokyo 162-8480, Japan
| | - Naoto Ohte
- Center for Advanced Biomedical Sciences, Waseda University, Tokyo 162-8480, Japan
| | - Carina Hanashima
- Center for Advanced Biomedical Sciences, Waseda University, Tokyo 162-8480, Japan
| | - Zhuhao Wu
- Appel Alzheimer's Disease Research Institute, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA
| | - Xiangmin Xu
- Center for Neural Circuit Mapping, Department of Anatomy and Neurobiology, University of California, Irvine, Irvine, CA 92617, USA
| | - Joshua Z Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xin Jin
- Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA 92037, USA.
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14
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Di Bella DJ, Domínguez-Iturza N, Brown JR, Arlotta P. Making Ramón y Cajal proud: Development of cell identity and diversity in the cerebral cortex. Neuron 2024:S0896-6273(24)00282-4. [PMID: 38754415 DOI: 10.1016/j.neuron.2024.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/28/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024]
Abstract
Since the beautiful images of Santiago Ramón y Cajal provided a first glimpse into the immense diversity and complexity of cell types found in the cerebral cortex, neuroscience has been challenged and inspired to understand how these diverse cells are generated and how they interact with each other to orchestrate the development of this remarkable tissue. Some fundamental questions drive the field's quest to understand cortical development: what are the mechanistic principles that govern the emergence of neuronal diversity? How do extrinsic and intrinsic signals integrate with physical forces and activity to shape cell identity? How do the diverse populations of neurons and glia influence each other during development to guarantee proper integration and function? The advent of powerful new technologies to profile and perturb cortical development at unprecedented resolution and across a variety of modalities has offered a new opportunity to integrate past knowledge with brand new data. Here, we review some of this progress using cortical excitatory projection neurons as a system to draw out general principles of cell diversification and the role of cell-cell interactions during cortical development.
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Affiliation(s)
- Daniela J Di Bella
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Nuria Domínguez-Iturza
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Juliana R Brown
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Paola Arlotta
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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15
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Obert DP, Killing D, Happe T, Tamas P, Altunkaya A, Dragovic SZ, Kreuzer M, Schneider G, Fenzl T. Substance specific EEG patterns in mice undergoing slow anesthesia induction. BMC Anesthesiol 2024; 24:167. [PMID: 38702608 PMCID: PMC11067159 DOI: 10.1186/s12871-024-02552-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/26/2024] [Indexed: 05/06/2024] Open
Abstract
The exact mechanisms and the neural circuits involved in anesthesia induced unconsciousness are still not fully understood. To elucidate them valid animal models are necessary. Since the most commonly used species in neuroscience are mice, we established a murine model for commonly used anesthetics/sedatives and evaluated the epidural electroencephalographic (EEG) patterns during slow anesthesia induction and emergence. Forty-four mice underwent surgery in which we inserted a central venous catheter and implanted nine intracranial electrodes above the prefrontal, motor, sensory, and visual cortex. After at least one week of recovery, mice were anesthetized either by inhalational sevoflurane or intravenous propofol, ketamine, or dexmedetomidine. We evaluated the loss and return of righting reflex (LORR/RORR) and recorded the electrocorticogram. For spectral analysis we focused on the prefrontal and visual cortex. In addition to analyzing the power spectral density at specific time points we evaluated the changes in the spectral power distribution longitudinally. The median time to LORR after start anesthesia ranged from 1080 [1st quartile: 960; 3rd quartile: 1080]s under sevoflurane anesthesia to 1541 [1455; 1890]s with ketamine. Around LORR sevoflurane as well as propofol induced a decrease in the theta/alpha band and an increase in the beta/gamma band. Dexmedetomidine infusion resulted in a shift towards lower frequencies with an increase in the delta range. Ketamine induced stronger activity in the higher frequencies. Our results showed substance-specific changes in EEG patterns during slow anesthesia induction. These patterns were partially identical to previous observations in humans, but also included significant differences, especially in the low frequencies. Our study emphasizes strengths and limitations of murine models in neuroscience and provides an important basis for future studies investigating complex neurophysiological mechanisms.
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Affiliation(s)
- David P Obert
- School of Medicine and Health, Department of Anesthesiology and Intensive Care, Technical University of Munich, 81675, Munich, Germany
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts's General Hospital, Boston, MA, 02114, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - David Killing
- School of Medicine and Health, Department of Anesthesiology and Intensive Care, Technical University of Munich, 81675, Munich, Germany
| | - Tom Happe
- School of Medicine and Health, Department of Anesthesiology and Intensive Care, Technical University of Munich, 81675, Munich, Germany
| | - Philipp Tamas
- School of Medicine and Health, Department of Anesthesiology and Intensive Care, Technical University of Munich, 81675, Munich, Germany
| | - Alp Altunkaya
- School of Medicine and Health, Department of Anesthesiology and Intensive Care, Technical University of Munich, 81675, Munich, Germany
| | - Srdjan Z Dragovic
- School of Medicine and Health, Department of Anesthesiology and Intensive Care, Technical University of Munich, 81675, Munich, Germany
| | - Matthias Kreuzer
- School of Medicine and Health, Department of Anesthesiology and Intensive Care, Technical University of Munich, 81675, Munich, Germany
| | - Gerhard Schneider
- School of Medicine and Health, Department of Anesthesiology and Intensive Care, Technical University of Munich, 81675, Munich, Germany
| | - Thomas Fenzl
- School of Medicine and Health, Department of Anesthesiology and Intensive Care, Technical University of Munich, 81675, Munich, Germany.
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16
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Vornholt E, Liharska LE, Cheng E, Hashemi A, Park YJ, Ziafat K, Wilkins L, Silk H, Linares LM, Thompson RC, Sullivan B, Moya E, Nadkarni GN, Sebra R, Schadt EE, Kopell BH, Charney AW, Beckmann ND. Characterizing cell type specific transcriptional differences between the living and postmortem human brain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.01.24306590. [PMID: 38746297 PMCID: PMC11092720 DOI: 10.1101/2024.05.01.24306590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Single-nucleus RNA sequencing (snRNA-seq) is often used to define gene expression patterns characteristic of brain cell types as well as to identify cell type specific gene expression signatures of neurological and mental illnesses in postmortem human brains. As methods to obtain brain tissue from living individuals emerge, it is essential to characterize gene expression differences associated with tissue originating from either living or postmortem subjects using snRNA-seq, and to assess whether and how such differences may impact snRNA-seq studies of brain tissue. To address this, human prefrontal cortex single nuclei gene expression was generated and compared between 31 samples from living individuals and 21 postmortem samples. The same cell types were consistently identified in living and postmortem nuclei, though for each cell type, a large proportion of genes were differentially expressed between samples from postmortem and living individuals. Notably, estimation of cell type proportions by cell type deconvolution of pseudo-bulk data was found to be more accurate in samples from living individuals. To allow for future integration of living and postmortem brain gene expression, a model was developed that quantifies from gene expression data the probability a human brain tissue sample was obtained postmortem. These probabilities are established as a means to statistically account for the gene expression differences between samples from living and postmortem individuals. Together, the results presented here provide a deep characterization of both differences between snRNA-seq derived from samples from living and postmortem individuals, as well as qualify and account for their effect on common analyses performed on this type of data.
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17
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Lukomska A, Frost MP, Theune WC, Xing J, Gupta M, Trakhtenberg EF. Nfe2l3 promotes neuroprotection and long-distance axon regeneration after injury in vivo. Exp Neurol 2024; 375:114741. [PMID: 38395216 PMCID: PMC10981571 DOI: 10.1016/j.expneurol.2024.114741] [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: 11/11/2023] [Revised: 01/22/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
Nuclear factor erythroid 2 like (Nfe2l) gene family members 1-3 mediate cellular response to oxidative stress, including in the central nervous system (CNS). However, neuronal functions of Nfe2l3 are unknown. Here, we comparatively evaluated expression of Nfe2l1, Nfe2l2, and Nfe2l3 in singe cell RNA-seq (scRNA-seq)-profiled cortical and retinal ganglion cell (RGC) CNS projection neurons, investigated whether Nfe2l3 regulates neuroprotection and axon regeneration after CNS injury in vivo, and characterized a gene network associated with Nfe2l3 in neurons. We showed that, Nfe2l3 expression transiently peaks in developing immature cortical and RGC projection neurons, but is nearly abolished in adult neurons and is not upregulated after injury. Furthermore, within the retina, Nfe2l3 is enriched in RGCs, primarily neonatally, and not upregulated in injured RGCs, whereas Nfe2l1 and Nfe2l2 are expressed robustly in other retinal cell types as well and are upregulated in injured RGCs. We also found that, expressing Nfe2l3 in injured RGCs through localized intralocular viral vector delivery promotes neuroprotection and long-distance axon regeneration after optic nerve injury in vivo. Moreover, Nfe2l3 provided a similar extent of neuroprotection and axon regeneration as viral vector-targeting of Pten and Klf9, which are prominent regulators of neuroprotection and long-distance axon regeneration. Finally, we bioinformatically characterized a gene network associated with Nfe2l3 in neurons, which predicted the association of Nfe2l3 with established mechanisms of neuroprotection and axon regeneration. Thus, Nfe2l3 is a novel neuroprotection and axon regeneration-promoting factor with a therapeutic potential for treating CNS injury and disease.
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Affiliation(s)
- Agnieszka Lukomska
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Matthew P Frost
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - William C Theune
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Jian Xing
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Mahit Gupta
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
| | - Ephraim F Trakhtenberg
- Department of Neuroscience, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA.
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18
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Chung C, Yang X, Hevner RF, Kennedy K, Vong KI, Liu Y, Patel A, Nedunuri R, Barton ST, Noel G, Barrows C, Stanley V, Mittal S, Breuss MW, Schlachetzki JCM, Kingsmore SF, Gleeson JG. Cell-type-resolved mosaicism reveals clonal dynamics of the human forebrain. Nature 2024; 629:384-392. [PMID: 38600385 DOI: 10.1038/s41586-024-07292-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 03/11/2024] [Indexed: 04/12/2024]
Abstract
Debate remains around the anatomical origins of specific brain cell subtypes and lineage relationships within the human forebrain1-7. Thus, direct observation in the mature human brain is critical for a complete understanding of its structural organization and cellular origins. Here we utilize brain mosaic variation within specific cell types as distinct indicators for clonal dynamics, denoted as cell-type-specific mosaic variant barcode analysis. From four hemispheres and two different human neurotypical donors, we identified 287 and 780 mosaic variants, respectively, that were used to deconvolve clonal dynamics. Clonal spread and allele fractions within the brain reveal that local hippocampal excitatory neurons are more lineage-restricted than resident neocortical excitatory neurons or resident basal ganglia GABAergic inhibitory neurons. Furthermore, simultaneous genome transcriptome analysis at both a cell-type-specific and a single-cell level suggests a dorsal neocortical origin for a subgroup of DLX1+ inhibitory neurons that disperse radially from an origin shared with excitatory neurons. Finally, the distribution of mosaic variants across 17 locations within one parietal lobe reveals that restriction of clonal spread in the anterior-posterior axis precedes restriction in the dorsal-ventral axis for both excitatory and inhibitory neurons. Thus, cell-type-resolved somatic mosaicism can uncover lineage relationships governing the development of the human forebrain.
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Affiliation(s)
- Changuk Chung
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Robert F Hevner
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
- Department of Pathology, UC San Diego School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Keng Ioi Vong
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Yang Liu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Arzoo Patel
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Rahul Nedunuri
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Scott T Barton
- Division of Medical Education, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Geoffroy Noel
- Division of Anatomy, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Chelsea Barrows
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Valentina Stanley
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Swapnil Mittal
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Martin W Breuss
- Department of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO, USA
| | - Johannes C M Schlachetzki
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Joseph G Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
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19
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Mao X, Staiger JF. Multimodal cortical neuronal cell type classification. Pflugers Arch 2024; 476:721-733. [PMID: 38376567 PMCID: PMC11033238 DOI: 10.1007/s00424-024-02923-2] [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: 11/24/2023] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/21/2024]
Abstract
Since more than a century, neuroscientists have distinguished excitatory (glutamatergic) neurons with long-distance projections from inhibitory (GABAergic) neurons with local projections and established layer-dependent schemes for the ~ 80% excitatory (principal) cells as well as the ~ 20% inhibitory neurons. Whereas, in the early days, mainly morphological criteria were used to define cell types, later supplemented by electrophysiological and neurochemical properties, nowadays. single-cell transcriptomics is the method of choice for cell type classification. Bringing recent insight together, we conclude that despite all established layer- and area-dependent differences, there is a set of reliably identifiable cortical cell types that were named (among others) intratelencephalic (IT), extratelencephalic (ET), and corticothalamic (CT) for the excitatory cells, which altogether comprise ~ 56 transcriptomic cell types (t-types). By the same means, inhibitory neurons were subdivided into parvalbumin (PV), somatostatin (SST), vasoactive intestinal polypeptide (VIP), and "other (i.e. Lamp5/Sncg)" subpopulations, which altogether comprise ~ 60 t-types. The coming years will show which t-types actually translate into "real" cell types that show a common set of multimodal features, including not only transcriptome but also physiology and morphology as well as connectivity and ultimately function. Only with the better knowledge of clear-cut cell types and experimental access to them, we will be able to reveal their specific functions, a task which turned out to be difficult in a part of the brain being so much specialized for cognition as the cerebral cortex.
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Affiliation(s)
- Xiaoyi Mao
- Institute for Neuroanatomy, University Medical Center Göttingen, Georg-August-University, Kreuzbergring 36, 37075, Göttingen, Germany
| | - Jochen F Staiger
- Institute for Neuroanatomy, University Medical Center Göttingen, Georg-August-University, Kreuzbergring 36, 37075, Göttingen, Germany.
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20
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Enkavi G, Girych M, Moliner R, Vattulainen I, Castrén E. TrkB transmembrane domain: bridging structural understanding with therapeutic strategy. Trends Biochem Sci 2024; 49:445-456. [PMID: 38433044 DOI: 10.1016/j.tibs.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/19/2024] [Accepted: 02/09/2024] [Indexed: 03/05/2024]
Abstract
TrkB (neuronal receptor tyrosine kinase-2, NTRK2) is the receptor for brain-derived neurotrophic factor (BDNF) and is a critical regulator of activity-dependent neuronal plasticity. The past few years have witnessed an increasing understanding of the structure and function of TrkB, including its transmembrane domain (TMD). TrkB interacts with membrane cholesterol, which bidirectionally regulates TrkB signaling. Additionally, TrkB has recently been recognized as a binding target of antidepressant drugs. A variety of different antidepressants, including typical and rapid-acting antidepressants, as well as psychedelic compounds, act as allosteric potentiators of BDNF signaling through TrkB. This suggests that TrkB is the common target of different antidepressant compounds. Although more research is needed, current knowledge suggests that TrkB is a promising target for further drug development.
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Affiliation(s)
- Giray Enkavi
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Mykhailo Girych
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Rafael Moliner
- Neuroscience Center/HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland.
| | - Eero Castrén
- Neuroscience Center/HiLIFE, University of Helsinki, Helsinki, Finland.
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21
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Wei C, Jiang W, Wang R, Zhong H, He H, Gao X, Zhong S, Yu F, Guo Q, Zhang L, Schiffelers LDJ, Zhou B, Trepel M, Schmidt FI, Luo M, Shao F. Brain endothelial GSDMD activation mediates inflammatory BBB breakdown. Nature 2024; 629:893-900. [PMID: 38632402 DOI: 10.1038/s41586-024-07314-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/14/2024] [Indexed: 04/19/2024]
Abstract
The blood-brain barrier (BBB) protects the central nervous system from infections or harmful substances1; its impairment can lead to or exacerbate various diseases of the central nervous system2-4. However, the mechanisms of BBB disruption during infection and inflammatory conditions5,6 remain poorly defined. Here we find that activation of the pore-forming protein GSDMD by the cytosolic lipopolysaccharide (LPS) sensor caspase-11 (refs. 7-9), but not by TLR4-induced cytokines, mediates BBB breakdown in response to circulating LPS or during LPS-induced sepsis. Mice deficient in the LBP-CD14 LPS transfer and internalization pathway10-12 resist BBB disruption. Single-cell RNA-sequencing analysis reveals that brain endothelial cells (bECs), which express high levels of GSDMD, have a prominent response to circulating LPS. LPS acting on bECs primes Casp11 and Cd14 expression and induces GSDMD-mediated plasma membrane permeabilization and pyroptosis in vitro and in mice. Electron microscopy shows that this features ultrastructural changes in the disrupted BBB, including pyroptotic endothelia, abnormal appearance of tight junctions and vasculature detachment from the basement membrane. Comprehensive mouse genetic analyses, combined with a bEC-targeting adeno-associated virus system, establish that GSDMD activation in bECs underlies BBB disruption by LPS. Delivery of active GSDMD into bECs bypasses LPS stimulation and opens the BBB. In CASP4-humanized mice, Gram-negative Klebsiella pneumoniae infection disrupts the BBB; this is blocked by expression of a GSDMD-neutralizing nanobody in bECs. Our findings outline a mechanism for inflammatory BBB breakdown, and suggest potential therapies for diseases of the central nervous system associated with BBB impairment.
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Affiliation(s)
- Chao Wei
- Chinese Institute for Brain Research, Beijing, P. R. China
| | - Wei Jiang
- National Institute of Biological Sciences, Beijing, P. R. China
- Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing, P. R. China
| | - Ruiyu Wang
- National Institute of Biological Sciences, Beijing, P. R. China
| | - Haoyu Zhong
- National Institute of Biological Sciences, Beijing, P. R. China
| | - Huabin He
- National Institute of Biological Sciences, Beijing, P. R. China
- Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing, P. R. China
| | - Xinwei Gao
- Chinese Institute for Brain Research, Beijing, P. R. China
| | - Shilin Zhong
- National Institute of Biological Sciences, Beijing, P. R. China
| | - Fengting Yu
- Chinese Institute for Brain Research, Beijing, P. R. China
| | - Qingchun Guo
- Chinese Institute for Brain Research, Beijing, P. R. China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, P. R. China
| | - Lisa D J Schiffelers
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Bin Zhou
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Martin Trepel
- Department of Hematology and Medical Oncology, University Medical Center Augsburg, Augsburg, Germany
| | - Florian I Schmidt
- Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Minmin Luo
- Chinese Institute for Brain Research, Beijing, P. R. China.
- National Institute of Biological Sciences, Beijing, P. R. China.
- Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing, P. R. China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, P. R. China.
- New Cornerstone Science Laboratory, Shenzhen, P. R. China.
| | - Feng Shao
- National Institute of Biological Sciences, Beijing, P. R. China.
- Research Unit of Pyroptosis and Immunity, Chinese Academy of Medical Sciences and National Institute of Biological Sciences, Beijing, P. R. China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, P. R. China.
- New Cornerstone Science Laboratory, Shenzhen, P. R. China.
- Changping Laboratory, Beijing, P. R. China.
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22
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MacDonald A, Hebling A, Wei XP, Yackle K. The breath shape controls intonation of mouse vocalizations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.16.562597. [PMID: 37904912 PMCID: PMC10614923 DOI: 10.1101/2023.10.16.562597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Intonation in speech is the control of vocal pitch to layer expressive meaning to communication, like increasing pitch to indicate a question. Also, stereotyped patterns of pitch are used to create distinct sounds with different denotations, like in tonal languages and, perhaps, the ten sounds in the murine lexicon. A basic tone is created by exhalation through a constricted laryngeal voice box, and it is thought that more complex utterances are produced solely by dynamic changes in laryngeal tension. But perhaps, the shifting pitch also results from altering the swiftness of exhalation. Consistent with the latter model, we describe that intonation in most vocalization types follows deviations in exhalation that appear to be generated by the re-activation of the cardinal breathing muscle for inspiration. We also show that the brainstem vocalization central pattern generator, the iRO, can create this breath pattern. Consequently, ectopic activation of the iRO not only induces phonation, but also the pitch patterns that compose most of the vocalizations in the murine lexicon. These results reveal a novel brainstem mechanism for intonation.
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Affiliation(s)
- Alastair MacDonald
- Department of Physiology, University of California-San Francisco, San Francisco, CA 94143
| | - Alina Hebling
- Neuroscience Graduate Program, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Xin Paul Wei
- Department of Physiology, University of California-San Francisco, San Francisco, CA 94143
- Biomedical Sciences Graduate Program, University of California-San Francisco, San Francisco, CA 94143, USA
| | - Kevin Yackle
- Department of Physiology, University of California-San Francisco, San Francisco, CA 94143
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23
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Yang L, Liu F, Hahm H, Okuda T, Li X, Zhang Y, Kalyanaraman V, Heitmeier MR, Samineni VK. Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590975. [PMID: 38712231 PMCID: PMC11071495 DOI: 10.1101/2024.04.24.590975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Single-cell multiomic techniques have sparked immense interest in developing a comprehensive multi-modal map of diverse neuronal cell types and their brain wide projections. However, investigating the spatial organization, transcriptional and epigenetic landscapes of brain wide projection neurons is hampered by the lack of efficient and easily adoptable tools. Here we introduce Projection-TAGs, a retrograde AAV platform that allows multiplex tagging of projection neurons using RNA barcodes. By using Projection-TAGs, we performed multiplex projection tracing of the mouse cortex and high-throughput single-cell profiling of the transcriptional and epigenetic landscapes of the cortical projection neurons. Projection-TAGs can be leveraged to obtain a snapshot of activity-dependent recruitment of distinct projection neurons and their molecular features in the context of a specific stimulus. Given its flexibility, usability, and compatibility, we envision that Projection-TAGs can be readily applied to build a comprehensive multi-modal map of brain neuronal cell types and their projections.
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Affiliation(s)
- Lite Yang
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
- Neuroscience Graduate Program, Division of Biology & Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, United States
| | - Fang Liu
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Hannah Hahm
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Takao Okuda
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Xiaoyue Li
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Yufen Zhang
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Vani Kalyanaraman
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Monique R. Heitmeier
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Vijay K. Samineni
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
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24
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Chen X, Fischer S, Rue MCP, Zhang A, Mukherjee D, Kanold PO, Gillis J, Zador AM. Whole-cortex in situ sequencing reveals input-dependent area identity. Nature 2024:10.1038/s41586-024-07221-6. [PMID: 38658747 DOI: 10.1038/s41586-024-07221-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 02/22/2024] [Indexed: 04/26/2024]
Abstract
The cerebral cortex is composed of neuronal types with diverse gene expression that are organized into specialized cortical areas. These areas, each with characteristic cytoarchitecture1,2, connectivity3,4 and neuronal activity5,6, are wired into modular networks3,4,7. However, it remains unclear whether these spatial organizations are reflected in neuronal transcriptomic signatures and how such signatures are established in development. Here we used BARseq, a high-throughput in situ sequencing technique, to interrogate the expression of 104 cell-type marker genes in 10.3 million cells, including 4,194,658 cortical neurons over nine mouse forebrain hemispheres, at cellular resolution. De novo clustering of gene expression in single neurons revealed transcriptomic types consistent with previous single-cell RNA sequencing studies8,9. The composition of transcriptomic types is highly predictive of cortical area identity. Moreover, areas with similar compositions of transcriptomic types, which we defined as cortical modules, overlap with areas that are highly connected, suggesting that the same modular organization is reflected in both transcriptomic signatures and connectivity. To explore how the transcriptomic profiles of cortical neurons depend on development, we assessed cell-type distributions after neonatal binocular enucleation. Notably, binocular enucleation caused the shifting of the cell-type compositional profiles of visual areas towards neighbouring cortical areas within the same module, suggesting that peripheral inputs sharpen the distinct transcriptomic identities of areas within cortical modules. Enabled by the high throughput, low cost and reproducibility of BARseq, our study provides a proof of principle for the use of large-scale in situ sequencing to both reveal brain-wide molecular architecture and understand its development.
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Affiliation(s)
- Xiaoyin Chen
- Allen Institute for Brain Science, Seattle, WA, USA.
| | - Stephan Fischer
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Mara C P Rue
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Aixin Zhang
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Didhiti Mukherjee
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Patrick O Kanold
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Jesse Gillis
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada.
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25
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Chamberland S, Grant G, Machold R, Nebet ER, Tian G, Stich J, Hanani M, Kullander K, Tsien RW. Functional specialization of hippocampal somatostatin-expressing interneurons. Proc Natl Acad Sci U S A 2024; 121:e2306382121. [PMID: 38640347 PMCID: PMC11047068 DOI: 10.1073/pnas.2306382121] [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: 04/23/2023] [Accepted: 02/27/2024] [Indexed: 04/21/2024] Open
Abstract
Hippocampal somatostatin-expressing (Sst) GABAergic interneurons (INs) exhibit considerable anatomical and functional heterogeneity. Recent single-cell transcriptome analyses have provided a comprehensive Sst-IN subpopulations census, a plausible molecular ground truth of neuronal identity whose links to specific functionality remain incomplete. Here, we designed an approach to identify and access subpopulations of Sst-INs based on transcriptomic features. Four mouse models based on single or combinatorial Cre- and Flp- expression differentiated functionally distinct subpopulations of CA1 hippocampal Sst-INs that largely tiled the morpho-functional parameter space of the Sst-INs superfamily. Notably, the Sst;;Tac1 intersection revealed a population of bistratified INs that preferentially synapsed onto fast-spiking interneurons (FS-INs) and were sufficient to interrupt their firing. In contrast, the Ndnf;;Nkx2-1 intersection identified a population of oriens lacunosum-moleculare INs that predominantly targeted CA1 pyramidal neurons, avoiding FS-INs. Overall, our results provide a framework to translate neuronal transcriptomic identity into discrete functional subtypes that capture the diverse specializations of hippocampal Sst-INs.
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Affiliation(s)
- Simon Chamberland
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Gariel Grant
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Robert Machold
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Erica R. Nebet
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Guoling Tian
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Joshua Stich
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Monica Hanani
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Department of Neuroscience and Physiology, New York University, New York, NY10016
| | - Klas Kullander
- Developmental Genetics, Department of Neuroscience, Uppsala University, Uppsala, Uppsala län752 37, Sweden
| | - Richard W. Tsien
- New York University Neuroscience Institute, New York University Grossman School of Medicine, New York University, New York, NY10016
- Center for Neural Science, New York University, New York, NY10003
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26
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Ozkan A, Padmanabhan HK, Shipman SL, Azim E, Kumar P, Sadegh C, Basak AN, Macklis JD. Directed differentiation of functional corticospinal-like neurons from endogenous SOX6+/NG2+ cortical progenitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.21.590488. [PMID: 38712174 PMCID: PMC11071355 DOI: 10.1101/2024.04.21.590488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Corticospinal neurons (CSN) centrally degenerate in amyotrophic lateral sclerosis (ALS), along with spinal motor neurons, and loss of voluntary motor function in spinal cord injury (SCI) results from damage to CSN axons. For functional regeneration of specifically affected neuronal circuitry in vivo , or for optimally informative disease modeling and/or therapeutic screening in vitro , it is important to reproduce the type or subtype of neurons involved. No such appropriate in vitro models exist with which to investigate CSN selective vulnerability and degeneration in ALS, or to investigate routes to regeneration of CSN circuitry for ALS or SCI, critically limiting the relevance of much research. Here, we identify that the HMG-domain transcription factor Sox6 is expressed by a subset of NG2+ endogenous cortical progenitors in postnatal and adult cortex, and that Sox6 suppresses a latent neurogenic program by repressing inappropriate proneural Neurog2 expression by progenitors. We FACS-purify these genetically accessible progenitors from postnatal mouse cortex and establish a pure culture system to investigate their potential for directed differentiation into CSN. We then employ a multi-component construct with complementary and differentiation-sharpening transcriptional controls (activating Neurog2, Fezf2 , while antagonizing Olig2 with VP16:Olig2 ). We generate corticospinal-like neurons from SOX6+/NG2+ cortical progenitors, and find that these neurons differentiate with remarkable fidelity compared with corticospinal neurons in vivo . They possess appropriate morphological, molecular, transcriptomic, and electrophysiological characteristics, without characteristics of the alternate intracortical or other neuronal subtypes. We identify that these critical specifics of differentiation are not reproduced by commonly employed Neurog2 -driven differentiation. Neurons induced by Neurog2 instead exhibit aberrant multi-axon morphology and express molecular hallmarks of alternate cortical projection subtypes, often in mixed form. Together, this developmentally-based directed differentiation from genetically accessible cortical progenitors sets a precedent and foundation for in vitro mechanistic and therapeutic disease modeling, and toward regenerative neuronal repopulation and circuit repair.
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27
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Courcelles EJ, Kjelsberg K, Convertino L, Nair RR, Witter MP, Nigro MJ. Association cortical areas in the mouse contain a large population of fast-spiking GABAergic neurons that do not express parvalbumin. Eur J Neurosci 2024. [PMID: 38643976 DOI: 10.1111/ejn.16341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024]
Abstract
GABAergic neurons represent 10-15% of the neuronal population of the cortex but exert a powerful control over information flow in cortical circuits. The largest GABAergic class in the neocortex is represented by the parvalbumin-expressing fast-spiking neurons, which provide powerful somatic inhibition to their postsynaptic targets. Recently, the density of parvalbumin interneurons has been shown to be lower in associative areas of the mouse cortex as compared with sensory and motor areas. Modelling work based on these quantifications linked the low-density of parvalbumin interneurons with specific computations of associative cortices. However, it is still unknown whether the total GABAergic population of association cortices is smaller or whether another GABAergic type can compensate for the low density of parvalbumin interneurons. In the present study, we investigated these hypotheses using a combination of neuroanatomy, mouse genetics and neurophysiology. We found that the GABAergic population of association areas is comparable with that of primary sensory areas, and it is enriched of fast-spiking neurons that do not express parvalbumin and were not accounted for by previous quantifications. We developed an intersectional viral strategy to demonstrate that the population of fast-spiking neurons is comparable across cortical regions. Our results provide quantifications of the density of fast-spiking GABAergic neurons and offers new biological constrains to refine current models of cortical computations.
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Affiliation(s)
- Erik Justin Courcelles
- Kavli Institute for Systems Neuroscience, Center for Algorithms in the Cortex, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kasper Kjelsberg
- Kavli Institute for Systems Neuroscience, Center for Algorithms in the Cortex, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, Norwegian University of Science and Technology, Trondheim, Norway
| | - Laura Convertino
- Kavli Institute for Systems Neuroscience, Center for Algorithms in the Cortex, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, Norwegian University of Science and Technology, Trondheim, Norway
| | - Rajeevkumar Raveendran Nair
- Kavli Institute for Systems Neuroscience, Center for Algorithms in the Cortex, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, Norwegian University of Science and Technology, Trondheim, Norway
| | - Menno P Witter
- Kavli Institute for Systems Neuroscience, Center for Algorithms in the Cortex, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, Norwegian University of Science and Technology, Trondheim, Norway
| | - Maximiliano José Nigro
- Kavli Institute for Systems Neuroscience, Center for Algorithms in the Cortex, Egil and Pauline Braathen and Fred Kavli Center for Cortical Microcircuits, Norwegian University of Science and Technology, Trondheim, Norway
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28
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Aydin AG, Lemenze A, Bieszczad KM. Functional diversities within neurons and astrocytes in the adult rat auditory cortex revealed by single-nucleus RNA sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589831. [PMID: 38659766 PMCID: PMC11042262 DOI: 10.1101/2024.04.16.589831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The mammalian cerebral cortex is composed of a rich diversity of cell types. Cortical cells are organized into networks that rely on their functional diversity to ultimately carry out a variety of sophisticated cognitive functions. To investigate the breadth of transcriptional diverse cell types in the sensory cortex, we have used single-nucleus RNA sequencing (snRNA-seq) in the auditory cortex of the adult rat. A variety of unique excitatory and inhibitory neuron types were identified. In addition, we report for the first time a diversity of astrocytes in the auditory cortex that may represent functionally unique subtypes. Together, these results pave the way for building models of how neurons in the sensory cortex work in concert with astrocytes at synapses to fulfill high-cognitive functions like learning and memory.
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29
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Dummer PD, Lee DI, Hossain S, Wang R, Evard A, Newman G, Ho C, Schneider-Mizell CM, Menon V, Au E. Multidimensional analysis of cortical interneuron synaptic features reveals underlying synaptic heterogeneity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586340. [PMID: 38659827 PMCID: PMC11042224 DOI: 10.1101/2024.03.22.586340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Cortical interneurons represent a diverse set of neuronal subtypes characterized in part by their striking degree of synaptic specificity. However, little is known about the extent of synaptic diversity because of the lack of unbiased methods to extract synaptic features among interneuron subtypes. Here, we develop an approach to aggregate image features from fluorescent confocal images of interneuron synapses and their post-synaptic targets, in order to characterize the heterogeneity of synapses at fine scale. We started by training a model that recognizes pre- and post-synaptic compartments and then determines the target of each genetically-identified interneuron synapse in vitro and in vivo. Our model extracts hundreds of spatial and intensity features from each analyzed synapse, constructing a multidimensional data set, consisting of millions of synapses, which allowed us to perform an unsupervised analysis on this dataset, uncovering novel synaptic subgroups. The subgroups were spatially distributed in a highly structured manner that revealed the local underlying topology of the postsynaptic environment. Dendrite-targeting subgroups were clustered onto subdomains of the dendrite along the proximal to distal axis. Soma-targeting subgroups were enriched onto different postsynaptic cell types. We also find that the two main subclasses of interneurons, basket cells and somatostatin interneurons, utilize distinct strategies to enact inhibitory coverage. Thus, our analysis of multidimensional synaptic features establishes a conceptual framework for studying interneuron synaptic diversity.
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Affiliation(s)
- Patrick D. Dummer
- Department of Pathology and Cell Biology, Columbia Irving Medical Center, New York NY, 10032
| | - Dylan I. Lee
- Department of Neurology, Columbia Irving Medical Center, New York NY, 10032
| | - Sakib Hossain
- Department of Pathology and Cell Biology, Columbia Irving Medical Center, New York NY, 10032
| | - Runsheng Wang
- Department of Pathology and Cell Biology, Columbia Irving Medical Center, New York NY, 10032
| | - Andre Evard
- Department of Pathology and Cell Biology, Columbia Irving Medical Center, New York NY, 10032
| | - Gabriel Newman
- Department of Pathology and Cell Biology, Columbia Irving Medical Center, New York NY, 10032
| | - Claire Ho
- Department of Pathology and Cell Biology, Columbia Irving Medical Center, New York NY, 10032
| | | | - Vilas Menon
- Department of Neurology, Columbia Irving Medical Center, New York NY, 10032
| | - Edmund Au
- Department of Pathology and Cell Biology, Columbia Irving Medical Center, New York NY, 10032
- Columbia Translation Neuroscience Initiative Fellow, Columbia Irving Medical Center, New York NY, 10032
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30
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Burbridge TJ, Ratliff JM, Dwivedi D, Vrudhula U, Alvarado-Huerta F, Sjulson L, Ibrahim LA, Cheadle L, Fishell G, Batista-Brito R. Disruption of Cholinergic Retinal Waves Alters Visual Cortex Development and Function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588143. [PMID: 38644996 PMCID: PMC11030223 DOI: 10.1101/2024.04.05.588143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Retinal waves represent an early form of patterned spontaneous neural activity in the visual system. These waves originate in the retina before eye-opening and propagate throughout the visual system, influencing the assembly and maturation of subcortical visual brain regions. However, because it is technically challenging to ablate retina-derived cortical waves without inducing compensatory activity, the role these waves play in the development of the visual cortex remains unclear. To address this question, we used targeted conditional genetics to disrupt cholinergic retinal waves and their propagation to select regions of primary visual cortex, which largely prevented compensatory patterned activity. We find that loss of cholinergic retinal waves without compensation impaired the molecular and synaptic maturation of excitatory neurons located in the input layers of visual cortex, as well as layer 1 interneurons. These perinatal molecular and synaptic deficits also relate to functional changes observed at later ages. We find that the loss of perinatal cholinergic retinal waves causes abnormal visual cortex retinotopy, mirroring changes in the retinotopic organization of gene expression, and additionally impairs the processing of visual information. We further show that retinal waves are necessary for higher order processing of sensory information by impacting the state-dependent activity of layer 1 interneurons, a neuronal type that shapes neocortical state-modulation, as well as for state-dependent gain modulation of visual responses of excitatory neurons. Together, these results demonstrate that a brief targeted perinatal disruption of patterned spontaneous activity alters early cortical gene expression as well as synaptic and physiological development, and compromises both fundamental and, notably, higher-order functions of visual cortex after eye-opening.
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Affiliation(s)
- Timothy J Burbridge
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave., Boston, MA 02115
| | - Jacob M Ratliff
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Deepanjali Dwivedi
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave., Boston, MA 02115
| | - Uma Vrudhula
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | | | - Lucas Sjulson
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
- Department of Psychiatry and Behavioral Sciences, Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
| | - Leena Ali Ibrahim
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955–6900, KSA
| | - Lucas Cheadle
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724
| | - Gordon Fishell
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave., Boston, MA 02115
| | - Renata Batista-Brito
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
- Department of Psychiatry and Behavioral Sciences, Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
- Department of Genetics, Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
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31
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Wei Y, Lei J, Peng Y, Chang H, Luo T, Tang Y, Wang L, Wen H, Volpe G, Liu L, Han L. Expression characteristics and potential function of non-coding RNA in mouse cortical cells. Front Mol Neurosci 2024; 17:1365978. [PMID: 38660385 PMCID: PMC11040102 DOI: 10.3389/fnmol.2024.1365978] [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: 01/05/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
Non-coding RNAs (ncRNAs) play essential regulatory functions in various physiological and pathological processes in the brain. To systematically characterize the ncRNA profile in cortical cells, we downloaded single-cell SMART-Seq v4 data of mouse cerebral cortex. Our results revealed that the ncRNAs alone are sufficient to define the identity of most cortical cell types. We identified 1,600 ncRNAs that exhibited cell type specificity, even yielding to distinguish microglia from perivascular macrophages with ncRNA. Moreover, we characterized cortical layer and region specific ncRNAs, in line with the results by spatial transcriptome (ST) data. By constructing a co-expression network of ncRNAs and protein-coding genes, we predicted the function of ncRNAs. By integrating with genome-wide association studies data, we established associations between cell type-specific ncRNAs and traits related to neurological disorders. Collectively, our study identified differentially expressed ncRNAs at multiple levels and provided the valuable resource to explore the functions and dysfunctions of ncRNAs in cortical cells.
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Affiliation(s)
- Yanrong Wei
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Research, Hangzhou, China
| | - Junjie Lei
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Research, Hangzhou, China
| | | | | | | | - Yuanchun Tang
- BGI Research, Hangzhou, China
- BGI College & Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | | | - Huiying Wen
- BGI Research, Hangzhou, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Giacomo Volpe
- Hematology and Cell Therapy Unit, IRCCS–Istituto Tumori ‘Giovanni Paolo II’, Bari, Italy
| | - Longqi Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Research, Hangzhou, China
| | - Lei Han
- BGI Research, Hangzhou, China
- BGI Research, Shenzhen, China
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Yaghmaeian Salmani B, Lahti L, Gillberg L, Jacobsen JK, Mantas I, Svenningsson P, Perlmann T. Transcriptomic atlas of midbrain dopamine neurons uncovers differential vulnerability in a Parkinsonism lesion model. eLife 2024; 12:RP89482. [PMID: 38587883 PMCID: PMC11001297 DOI: 10.7554/elife.89482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
Midbrain dopamine (mDA) neurons comprise diverse cells with unique innervation targets and functions. This is illustrated by the selective sensitivity of mDA neurons of the substantia nigra compacta (SNc) in patients with Parkinson's disease, while those in the ventral tegmental area (VTA) are relatively spared. Here, we used single nuclei RNA sequencing (snRNA-seq) of approximately 70,000 mouse midbrain cells to build a high-resolution atlas of mouse mDA neuron diversity at the molecular level. The results showed that differences between mDA neuron groups could best be understood as a continuum without sharp differences between subtypes. Thus, we assigned mDA neurons to several 'territories' and 'neighborhoods' within a shifting gene expression landscape where boundaries are gradual rather than discrete. Based on the enriched gene expression patterns of these territories and neighborhoods, we were able to localize them in the adult mouse midbrain. Moreover, because the underlying mechanisms for the variable sensitivities of diverse mDA neurons to pathological insults are not well understood, we analyzed surviving neurons after partial 6-hydroxydopamine (6-OHDA) lesions to unravel gene expression patterns that correlate with mDA neuron vulnerability and resilience. Together, this atlas provides a basis for further studies on the neurophysiological role of mDA neurons in health and disease.
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Affiliation(s)
| | - Laura Lahti
- Department of Cell and Molecular Biology, Karolinska InstitutetStockholmSweden
| | - Linda Gillberg
- Department of Cell and Molecular Biology, Karolinska InstitutetStockholmSweden
| | - Jesper Kjaer Jacobsen
- Department of Cell and Molecular Biology, Karolinska InstitutetStockholmSweden
- Department of Neurology, Karolinska University HospitalStockholmSweden
| | - Ioannis Mantas
- Department of Clinical Neuroscience, Karolinska InstitutetStockholmSweden
| | - Per Svenningsson
- Department of Clinical Neuroscience, Karolinska InstitutetStockholmSweden
| | - Thomas Perlmann
- Department of Cell and Molecular Biology, Karolinska InstitutetStockholmSweden
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Wang H, Flores RJ, Yarur HE, Limoges A, Bravo-Rivera H, Casello SM, Loomba N, Enriquez-Traba J, Arenivar M, Wang Q, Ganley R, Ramakrishnan C, Fenno LE, Kim Y, Deisseroth K, Or G, Dong C, Hoon MA, Tian L, Tejeda HA. Prefrontal cortical dynorphin peptidergic transmission constrains threat-driven behavioral and network states. Neuron 2024:S0896-6273(24)00193-4. [PMID: 38614102 DOI: 10.1016/j.neuron.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 01/19/2024] [Accepted: 03/13/2024] [Indexed: 04/15/2024]
Abstract
Prefrontal cortical (PFC) circuits provide top-down control of threat reactivity. This includes ventromedial PFC (vmPFC) circuitry, which plays a role in suppressing fear-related behavioral states. Dynorphin (Dyn) has been implicated in mediating negative affect and maladaptive behaviors induced by severe threats and is expressed in limbic circuits, including the vmPFC. However, there is a critical knowledge gap in our understanding of how vmPFC Dyn-expressing neurons and Dyn transmission detect threats and regulate expression of defensive behaviors. Here, we demonstrate that Dyn cells are broadly activated by threats and release Dyn locally in the vmPFC to limit passive defensive behaviors. We further demonstrate that vmPFC Dyn-mediated signaling promotes a switch of vmPFC networks to a fear-related state. In conclusion, we reveal a previously unknown role of vmPFC Dyn neurons and Dyn neuropeptidergic transmission in suppressing defensive behaviors in response to threats via state-driven changes in vmPFC networks.
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Affiliation(s)
- Huikun Wang
- Neuromodulation and Synaptic Integration Unit, National Institute of Mental Health Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Rodolfo J Flores
- Neuromodulation and Synaptic Integration Unit, National Institute of Mental Health Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Hector E Yarur
- Neuromodulation and Synaptic Integration Unit, National Institute of Mental Health Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Aaron Limoges
- Neuromodulation and Synaptic Integration Unit, National Institute of Mental Health Intramural Research Program, National Institutes of Health, Bethesda, MD, USA; Columbia University - NIH Graduate Partnership Program, National Institutes of Health, Bethesda, MD, USA
| | - Hector Bravo-Rivera
- Neuromodulation and Synaptic Integration Unit, National Institute of Mental Health Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Sanne M Casello
- Neuromodulation and Synaptic Integration Unit, National Institute of Mental Health Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Niharika Loomba
- Neuromodulation and Synaptic Integration Unit, National Institute of Mental Health Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Juan Enriquez-Traba
- Neuromodulation and Synaptic Integration Unit, National Institute of Mental Health Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Miguel Arenivar
- Neuromodulation and Synaptic Integration Unit, National Institute of Mental Health Intramural Research Program, National Institutes of Health, Bethesda, MD, USA; Brown University - NIH Graduate Partnership Program, National Institutes of Health, Bethesda, MD, USA
| | - Queenie Wang
- Neuromodulation and Synaptic Integration Unit, National Institute of Mental Health Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Robert Ganley
- Molecular Genetics Section, Laboratory of Sensory Biology, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Charu Ramakrishnan
- Departments of Bioengineering and Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Lief E Fenno
- Departments of Bioengineering and Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Yoon Kim
- Departments of Bioengineering and Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Karl Deisseroth
- Departments of Bioengineering and Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Grace Or
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
| | - Chunyang Dong
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
| | - Mark A Hoon
- Molecular Genetics Section, Laboratory of Sensory Biology, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Lin Tian
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA; Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
| | - Hugo A Tejeda
- Neuromodulation and Synaptic Integration Unit, National Institute of Mental Health Intramural Research Program, National Institutes of Health, Bethesda, MD, USA.
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Co M, O'Brien GK, Wright KM, O'Roak BJ. Detailed phenotyping of Tbr1-2A-CreER knock-in mice demonstrates significant impacts on TBR1 protein levels and axon development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588147. [PMID: 38617321 PMCID: PMC11014564 DOI: 10.1101/2024.04.04.588147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Spatiotemporal control of Cre-mediated recombination has been an invaluable tool for understanding key developmental processes. For example, knock-in of Cre into cell type marker gene loci drives Cre expression under endogenous promoter and enhancer sequences, greatly facilitating the study of diverse neuronal subtypes in the cerebral cortex. However, insertion of exogenous DNA into the genome can have unintended effects on local gene regulation or protein function that must be carefully considered. Here, we analyze a recently generated Tbr1-2A-CreER knock-in mouse line, where a 2A-CreER cassette was inserted in-frame just before the stop codon of the transcription factor gene Tbr1 . Heterozygous TBR1 mutations in humans and mice are known to cause autism or autism-like behavioral phenotypes accompanied by structural brain malformations, most frequently a reduction of the anterior commissure. Thus, it is critical for modified versions of Tbr1 to exhibit true wild-type-like activity. We evaluated the Tbr1-2A-CreER allele for its potential impact on Tbr1 function and complementation to Tbr1 loss-of-function alleles. In mice with one copy of the Tbr1-2A-CreER allele, we identified reduction of TBR1 protein in early postnatal cortex along with thinning of the anterior commissure, suggesting hypersensitivity of this structure to TBR1 dosage. Comparing Tbr1-2A-CreER and Tbr1 -null heterozygous and homozygous mice to Tbr1 -null complementation crosses showed reductions of TBR1 dosage ranging from 28.4% to 95.9%. Using these combinatorial genotypes, we found that low levels of TBR1 protein (∼16%) are sufficient to establish cortical layer positioning, while greater levels (>50%) are required for normal suppression of layer 5 identity. In total, these results strongly support the conclusion that Tbr1-2A-CreER is a hypomorphic allele. We advise caution when interpreting experiments using this allele, such as transcriptomic studies, considering the sensitivity of various corticogenic processes to TBR1 dosage and the association of heterozygous TBR1 mutations with complex neurodevelopmental disorders.
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35
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Qu G, Merchant JP, Clatot J, DeFlitch LM, Frederick DJ, Tang S, Salvatore M, Zhang X, Li J, Anderson SA, Goldberg EM. Targeted blockade of aberrant sodium current in a stem cell-derived neuron model of SCN3A encephalopathy. Brain 2024; 147:1247-1263. [PMID: 37935051 PMCID: PMC10994535 DOI: 10.1093/brain/awad376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/30/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023] Open
Abstract
Missense variants in SCN3A encoding the voltage-gated sodium (Na+) channel α subunit Nav1.3 are associated with SCN3A-related neurodevelopmental disorder (SCN3A-NDD), a spectrum of disease that includes epilepsy and malformation of cortical development. How genetic variation in SCN3A leads to pathology remains unclear, as prior electrophysiological work on disease-associated variants has been performed exclusively in heterologous cell systems. To further investigate the mechanisms of SCN3A-NDD pathogenesis, we used CRISPR/Cas9 gene editing to modify a control human induced pluripotent stem cell (iPSC) line to express the recurrent de novo missense variant SCN3A c.2624T>C (p.Ile875Thr). With the established Ngn2 rapid induction protocol, we generated glutamatergic forebrain-like neurons (iNeurons), which we showed to express SCN3A mRNA and Nav1.3-mediated Na+ currents. We performed detailed whole-cell patch clamp recordings to determine the effect of the SCN3A-p.Ile875Thr variant on endogenous Na+ currents in, and intrinsic excitability of, human neurons. Compared to control iNeurons, variant-expressing iNeurons exhibit markedly increased slowly-inactivating/persistent Na+ current, abnormal firing patterns with paroxysmal bursting and plateau-like potentials with action potential failure, and a hyperpolarized voltage threshold for action potential generation. We then validated these findings using a separate iPSC line generated from a patient harbouring the SCN3A-p.Ile875Thr variant compared to a corresponding CRISPR-corrected isogenic control line. Finally, we found that application of the Nav1.3-selective blocker ICA-121431 normalizes action potential threshold and aberrant firing patterns in SCN3A-p.Ile1875Thr iNeurons; in contrast, consistent with action as a Na+ channel blocker, ICA-121431 decreases excitability of control iNeurons. Our findings demonstrate that iNeurons can model the effects of genetic variation in SCN3A yet reveal a complex relationship between gain-of-function at the level of the ion channel versus impact on neuronal excitability. Given the transient expression of SCN3A in the developing human nervous system, selective blockade or suppression of Nav1.3-containing Na+ channels could represent a therapeutic approach towards SCN3A-NDD.
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Affiliation(s)
- Guojie Qu
- Division of Neurology, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Julie P Merchant
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Jérôme Clatot
- Division of Neurology, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Leah M DeFlitch
- Division of Neurology, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Danny J Frederick
- Department of Child and Adolescent Psychiatry, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sheng Tang
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Madeleine Salvatore
- Department of Child and Adolescent Psychiatry, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Xiaohong Zhang
- Division of Neurology, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Jianping Li
- Department of Child and Adolescent Psychiatry, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Stewart A Anderson
- The Epilepsy NeuroGenetics Initiative, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Child and Adolescent Psychiatry, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Ethan M Goldberg
- Division of Neurology, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
- The Epilepsy NeuroGenetics Initiative, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Neurology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA
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Zhou Y, He W, Hou W, Zhu Y. Pianno: a probabilistic framework automating semantic annotation for spatial transcriptomics. Nat Commun 2024; 15:2848. [PMID: 38565531 DOI: 10.1038/s41467-024-47152-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
Spatial transcriptomics has revolutionized the study of gene expression within tissues, while preserving spatial context. However, annotating spatial spots' biological identity remains a challenge. To tackle this, we introduce Pianno, a Bayesian framework automating structural semantics annotation based on marker genes. Comprehensive evaluations underscore Pianno's remarkable prowess in precisely annotating a wide array of spatial semantics, ranging from diverse anatomical structures to intricate tumor microenvironments, as well as in estimating cell type distributions, across data generated from various spatial transcriptomics platforms. Furthermore, Pianno, in conjunction with clustering approaches, uncovers a region- and species-specific excitatory neuron subtype in the deep layer 3 of the human neocortex, shedding light on cellular evolution in the human neocortex. Overall, Pianno equips researchers with a robust and efficient tool for annotating diverse biological structures, offering new perspectives on spatial transcriptomics data.
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Affiliation(s)
- Yuqiu Zhou
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Wei He
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Weizhen Hou
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Ying Zhu
- State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science and Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.
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37
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Kumar P, Goettemoeller AM, Espinosa-Garcia C, Tobin BR, Tfaily A, Nelson RS, Natu A, Dammer EB, Santiago JV, Malepati S, Cheng L, Xiao H, Duong DD, Seyfried NT, Wood LB, Rowan MJM, Rangaraju S. Native-state proteomics of Parvalbumin interneurons identifies unique molecular signatures and vulnerabilities to early Alzheimer's pathology. Nat Commun 2024; 15:2823. [PMID: 38561349 PMCID: PMC10985119 DOI: 10.1038/s41467-024-47028-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
Dysfunction in fast-spiking parvalbumin interneurons (PV-INs) may represent an early pathophysiological perturbation in Alzheimer's Disease (AD). Defining early proteomic alterations in PV-INs can provide key biological and translationally-relevant insights. We used cell-type-specific in-vivo biotinylation of proteins (CIBOP) coupled with mass spectrometry to obtain native-state PV-IN proteomes. PV-IN proteomic signatures include high metabolic and translational activity, with over-representation of AD-risk and cognitive resilience-related proteins. In bulk proteomes, PV-IN proteins were associated with cognitive decline in humans, and with progressive neuropathology in humans and the 5xFAD mouse model of Aβ pathology. PV-IN CIBOP in early stages of Aβ pathology revealed signatures of increased mitochondria and metabolism, synaptic and cytoskeletal disruption and decreased mTOR signaling, not apparent in whole-brain proteomes. Furthermore, we demonstrated pre-synaptic defects in PV-to-excitatory neurotransmission, validating our proteomic findings. Overall, in this study we present native-state proteomes of PV-INs, revealing molecular insights into their unique roles in cognitive resiliency and AD pathogenesis.
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Affiliation(s)
- Prateek Kumar
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Annie M Goettemoeller
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Neuroscience Graduate Program, Laney Graduate School, Emory University, Atlanta, USA
| | - Claudia Espinosa-Garcia
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Brendan R Tobin
- Georgia W. Woodruff School of Mechanical Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, and Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Ali Tfaily
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Ruth S Nelson
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Aditya Natu
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Eric B Dammer
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Juliet V Santiago
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Neuroscience Graduate Program, Laney Graduate School, Emory University, Atlanta, USA
| | - Sneha Malepati
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Lihong Cheng
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
| | - Hailian Xiao
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
| | - Duc D Duong
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Nicholas T Seyfried
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Levi B Wood
- Georgia W. Woodruff School of Mechanical Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, and Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30322, USA
- School of Chemical and Biological Engineering, GeoInsrgia titute of Technology, Atlanta, GA, 30322, USA
| | - Matthew J M Rowan
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA.
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Srikant Rangaraju
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, USA.
- 3 Department of Neurology, Yale University School of Medicine, New Haven, CT, 06510, USA.
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Shen Y, Shao M, Hao ZZ, Huang M, Xu N, Liu S. Multimodal Nature of the Single-cell Primate Brain Atlas: Morphology, Transcriptome, Electrophysiology, and Connectivity. Neurosci Bull 2024; 40:517-532. [PMID: 38194157 PMCID: PMC11003949 DOI: 10.1007/s12264-023-01160-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/23/2023] [Indexed: 01/10/2024] Open
Abstract
Primates exhibit complex brain structures that augment cognitive function. The neocortex fulfills high-cognitive functions through billions of connected neurons. These neurons have distinct transcriptomic, morphological, and electrophysiological properties, and their connectivity principles vary. These features endow the primate brain atlas with a multimodal nature. The recent integration of next-generation sequencing with modified patch-clamp techniques is revolutionizing the way to census the primate neocortex, enabling a multimodal neuronal atlas to be established in great detail: (1) single-cell/single-nucleus RNA-seq technology establishes high-throughput transcriptomic references, covering all major transcriptomic cell types; (2) patch-seq links the morphological and electrophysiological features to the transcriptomic reference; (3) multicell patch-clamp delineates the principles of local connectivity. Here, we review the applications of these technologies in the primate neocortex and discuss the current advances and tentative gaps for a comprehensive understanding of the primate neocortex.
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Affiliation(s)
- Yuhui Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Mingting Shao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, 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, 510060, China
| | - Mengyao Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, 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, 510060, China
| | - Sheng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China.
- Guangdong Province Key Laboratory of Brain Function and Disease, Guangzhou, 510080, China.
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39
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Sherman J, Bortz E, Antonio ES, Tseng HA, Raiff L, Han X. Ultrasound pulse repetition frequency preferentially activates different neuron populations independent of cell type. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586645. [PMID: 38585918 PMCID: PMC10996595 DOI: 10.1101/2024.03.25.586645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Transcranial ultrasound activates mechanosensitive cellular signaling and modulates neural dynamics. Given that intrinsic neuronal activity is limited to a couple hundred hertz and often exhibits frequency preference, we examined whether pulsing ultrasound at physiologic pulse repetition frequencies (PRFs) could selectively influence neuronal activity in the mammalian brain. We performed calcium imaging of individual motor cortex neurons, while delivering 0.35 MHz ultrasound at PRFs of 10, 40, and 140 Hz in awake mice. We found that most neurons were preferentially activated by only one of the three PRFs, highlighting unique cellular effects of physiologic PRFs. Further, ultrasound evoked responses were similar between excitatory neurons and parvalbumin positive interneurons regardless of PRFs, indicating that individual cell sensitivity dominates ultrasound-evoked effects, consistent with the heterogeneous mechanosensitive channel expression we found across single neurons in mice and humans. These results highlight the feasibility of tuning ultrasound neuromodulation effects through varying PRFs.
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40
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Li K, Li J, Tao Y, Wang F. stDiff: a diffusion model for imputing spatial transcriptomics through single-cell transcriptomics. Brief Bioinform 2024; 25:bbae171. [PMID: 38628114 PMCID: PMC11021815 DOI: 10.1093/bib/bbae171] [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: 01/05/2024] [Revised: 03/11/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024] Open
Abstract
Spatial transcriptomics (ST) has become a powerful tool for exploring the spatial organization of gene expression in tissues. Imaging-based methods, though offering superior spatial resolutions at the single-cell level, are limited in either the number of imaged genes or the sensitivity of gene detection. Existing approaches for enhancing ST rely on the similarity between ST cells and reference single-cell RNA sequencing (scRNA-seq) cells. In contrast, we introduce stDiff, which leverages relationships between gene expression abundance in scRNA-seq data to enhance ST. stDiff employs a conditional diffusion model, capturing gene expression abundance relationships in scRNA-seq data through two Markov processes: one introducing noise to transcriptomics data and the other denoising to recover them. The missing portion of ST is predicted by incorporating the original ST data into the denoising process. In our comprehensive performance evaluation across 16 datasets, utilizing multiple clustering and similarity metrics, stDiff stands out for its exceptional ability to preserve topological structures among cells, positioning itself as a robust solution for cell population identification. Moreover, stDiff's enhancement outcomes closely mirror the actual ST data within the batch space. Across diverse spatial expression patterns, our model accurately reconstructs them, delineating distinct spatial boundaries. This highlights stDiff's capability to unify the observed and predicted segments of ST data for subsequent analysis. We anticipate that stDiff, with its innovative approach, will contribute to advancing ST imputation methodologies.
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Affiliation(s)
- Kongming Li
- Shanghai Key Lab of Intelligent Information Processing, Handan Street, 200433 Shanghai, China
- School of Computer Science and Technology, Fudan UniversityHandan Street, 200433 Shanghai, China
| | - Jiahao Li
- Shanghai Key Lab of Intelligent Information Processing, Handan Street, 200433 Shanghai, China
- School of Computer Science and Technology, Fudan UniversityHandan Street, 200433 Shanghai, China
| | - Yuhao Tao
- Shanghai Key Lab of Intelligent Information Processing, Handan Street, 200433 Shanghai, China
- School of Computer Science and Technology, Fudan UniversityHandan Street, 200433 Shanghai, China
| | - Fei Wang
- Shanghai Key Lab of Intelligent Information Processing, Handan Street, 200433 Shanghai, China
- School of Computer Science and Technology, Fudan UniversityHandan Street, 200433 Shanghai, China
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41
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Wang H, Dey O, Lagos WN, Behnam N, Callaway EM, Stafford BK. Parallel pathways carrying direction-and orientation-selective retinal signals to layer 4 of the mouse visual cortex. Cell Rep 2024; 43:113830. [PMID: 38386556 PMCID: PMC11111173 DOI: 10.1016/j.celrep.2024.113830] [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: 09/25/2023] [Revised: 12/14/2023] [Accepted: 02/03/2024] [Indexed: 02/24/2024] Open
Abstract
Parallel visual pathways from the retina to the primary visual cortex (V1) via the lateral geniculate nucleus are common to many mammalian species, including mice, carnivores, and primates. However, it remains unclear which visual features present in both retina and V1 may be inherited from parallel pathways versus extracted by V1 circuits in the mouse. Here, using calcium imaging and rabies circuit tracing, we explore the relationships between tuning of layer 4 (L4) V1 neurons and their retinal ganglion cell (RGC) inputs. We find that subpopulations of L4 V1 neurons differ in their tuning for direction, orientation, spatial frequency, temporal frequency, and speed. Furthermore, we find that direction-tuned L4 V1 neurons receive input from direction-selective RGCs, whereas orientation-tuned L4 V1 neurons receive input from orientation-selective RGCs. These results suggest that direction and orientation tuning of V1 neurons may be partly inherited from parallel pathways originating in the retina.
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Affiliation(s)
- Helen Wang
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Neurosciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA; Medical Scientist Training Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Oyshi Dey
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Willian N Lagos
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Noor Behnam
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Edward M Callaway
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Neurosciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
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42
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Raudales R, Kim G, Kelly SM, Hatfield J, Guan W, Zhao S, Paul A, Qian Y, Li B, Huang ZJ. Specific and comprehensive genetic targeting reveals brain-wide distribution and synaptic input patterns of GABAergic axo-axonic interneurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.07.566059. [PMID: 37986757 PMCID: PMC10659298 DOI: 10.1101/2023.11.07.566059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Axo-axonic cells (AACs), also called chandelier cells (ChCs) in the cerebral cortex, are the most distinctive type of GABAergic interneurons described in the neocortex, hippocampus, and basolateral amygdala (BLA). AACs selectively innervate glutamatergic projection neurons (PNs) at their axon initial segment (AIS), thus may exert decisive control over PN spiking and regulate PN functional ensembles. However, the brain-wide distribution, synaptic connectivity, and circuit function of AACs remains poorly understood, largely due to the lack of specific and reliable experimental tools. Here, we have established an intersectional genetic strategy that achieves specific and comprehensive targeting of AACs throughout the mouse brain based on their lineage (Nkx2.1) and molecular (Unc5b, Pthlh) markers. We discovered that AACs are deployed across essentially all the pallium-derived brain structures, including not only the dorsal pallium-derived neocortex and medial pallium-derived hippocampal formation, but also the lateral pallium-derived claustrum-insular complex, and the ventral pallium-derived extended amygdaloid complex and olfactory centers. AACs are also abundant in anterior olfactory nucleus, taenia tecta and lateral septum. AACs show characteristic variations in density across neocortical areas and layers and across subregions of the hippocampal formation. Neocortical AACs comprise multiple laminar subtypes with distinct dendritic and axonal arborization patterns. Retrograde monosynaptic tracing from AACs across neocortical, hippocampal and BLA regions reveal shared as well as distinct patterns of synaptic input. Specific and comprehensive targeting of AACs facilitates the study of their developmental genetic program and circuit function across brain structures, providing a ground truth platform for understanding the conservation and variation of a bona fide cell type across brain regions and species.
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Affiliation(s)
- Ricardo Raudales
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Program in Neurobiology, Stony Brook University, NY, 11794, USA
| | - Gukhan Kim
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sean M Kelly
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Program in Neurobiology, Stony Brook University, NY, 11794, USA
| | - Joshua Hatfield
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Department of Neurobiology, Duke University, Durham, NC 27710, USA
| | - Wuqiang Guan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Shengli Zhao
- Department of Neurobiology, Duke University, Durham, NC 27710, USA
| | - Anirban Paul
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Department of Neural and Behavioral Sciences, Penn State College of Medicine, Hershey, PA, 17033
| | - Yongjun Qian
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Department of Neurobiology, Duke University, Durham, NC 27710, USA
| | - Bo Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Z Josh Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
- Department of Neurobiology, Duke University, Durham, NC 27710, USA
- Department of Biomedical Engineering, Duke University, Durham, NC 27710, USA
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43
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Nakata S, Iwasaki K, Funato H, Yanagisawa M, Ozaki H. Neuronal subtype-specific transcriptomic changes in the cerebral neocortex associated with sleep pressure. Neurosci Res 2024:S0168-0102(24)00042-7. [PMID: 38537682 DOI: 10.1016/j.neures.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/07/2024]
Abstract
Sleep is homeostatically regulated by sleep pressure, which increases during wakefulness and dissipates during sleep. Recent studies have suggested that the cerebral neocortex, a six-layered structure composed of various layer- and projection-specific neuronal subtypes, is involved in the representation of sleep pressure governed by transcriptional regulation. Here, we examined the transcriptomic changes in neuronal subtypes in the neocortex upon increased sleep pressure using single-nucleus RNA sequencing datasets and predicted the putative intracellular and intercellular molecules involved in transcriptome alterations. We revealed that sleep deprivation (SD) had the greatest effect on the transcriptome of layer 2 and 3 intratelencephalic (L2/3 IT) neurons among the neocortical glutamatergic neuronal subtypes. The expression of mutant SIK3 (SLP), which is known to increase sleep pressure, also induced profound changes in the transcriptome of L2/3 IT neurons. We identified Junb as a candidate transcription factor involved in the alteration of the L2/3 IT neuronal transcriptome by SD and SIK3 (SLP) expression. Finally, we inferred putative intercellular ligands, including BDNF, LSAMP, and PRNP, which may be involved in SD-induced alteration of the transcriptome of L2/3 IT neurons. We suggest that the transcriptome of L2/3 IT neurons is most impacted by increased sleep pressure among neocortical glutamatergic neuronal subtypes and identify putative molecules involved in such transcriptional alterations.
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Affiliation(s)
- Shinya Nakata
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kanako Iwasaki
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hiromasa Funato
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan; Department of Anatomy, Graduate School of Medicine, Toho University, Tokyo, Japan
| | - Masashi Yanagisawa
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan; Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA; Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Ibaraki, Japan.
| | - Haruka Ozaki
- Bioinformatics Laboratory, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan; Center for Artificial Intelligence Research, University of Tsukuba, Tsukuba, Ibaraki, Japan.
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44
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Yang F, Beltran-Lobo P, Sung K, Goldrick C, Croft CL, Nishimura A, Hedges E, Mahiddine F, Troakes C, Golde TE, Perez-Nievas BG, Hanger DP, Noble W, Jimenez-Sanchez M. Reactive astrocytes secrete the chaperone HSPB1 to mediate neuroprotection. SCIENCE ADVANCES 2024; 10:eadk9884. [PMID: 38507480 PMCID: PMC10954207 DOI: 10.1126/sciadv.adk9884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/14/2024] [Indexed: 03/22/2024]
Abstract
Molecular chaperones are protective in neurodegenerative diseases by preventing protein misfolding and aggregation, such as extracellular amyloid plaques and intracellular tau neurofibrillary tangles in Alzheimer's disease (AD). In addition, AD is characterized by an increase in astrocyte reactivity. The chaperone HSPB1 has been proposed as a marker for reactive astrocytes; however, its astrocytic functions in neurodegeneration remain to be elucidated. Here, we identify that HSPB1 is secreted from astrocytes to exert non-cell-autonomous protective functions. We show that in human AD brain, HSPB1 levels increase in astrocytes that cluster around amyloid plaques, as well as in the adjacent extracellular space. Moreover, in conditions that mimic an inflammatory reactive response, astrocytes increase HSPB1 secretion. Concomitantly, astrocytes and neurons can uptake astrocyte-secreted HSPB1, which is accompanied by an attenuation of the inflammatory response in reactive astrocytes and reduced pathological tau inclusions. Our findings highlight a protective mechanism in disease conditions that encompasses the secretion of a chaperone typically regarded as intracellular.
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Affiliation(s)
- Fangjia Yang
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 5 Cutcombe Road, London SE5 9RX, UK
| | - Paula Beltran-Lobo
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 5 Cutcombe Road, London SE5 9RX, UK
| | - Katherine Sung
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 5 Cutcombe Road, London SE5 9RX, UK
| | - Caoimhe Goldrick
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 5 Cutcombe Road, London SE5 9RX, UK
| | - Cara L. Croft
- UK Dementia Research Institute, UCL Institute of Neurology, University College London, London, UK
- Centre for Neuroscience, Surgery and Trauma, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Agnes Nishimura
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 5 Cutcombe Road, London SE5 9RX, UK
| | - Erin Hedges
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 5 Cutcombe Road, London SE5 9RX, UK
| | - Farah Mahiddine
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 5 Cutcombe Road, London SE5 9RX, UK
| | - Claire Troakes
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 5 Cutcombe Road, London SE5 9RX, UK
- London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Todd E. Golde
- Department of Neuroscience, College of Medicine, University of Florida, Gainesville, FL, USA
- Center for Translational Research in Neurodegenerative Disease, College of Medicine, University of Florida, Gainesville, FL, USA
- McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL, USA
- Department of Pharmacology and Chemical Biology, Department of Neurology, Emory Center for Neurodegenerative Disease, Emory University, Atlanta, GA, USA
| | - Beatriz G. Perez-Nievas
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 5 Cutcombe Road, London SE5 9RX, UK
| | - Diane P. Hanger
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 5 Cutcombe Road, London SE5 9RX, UK
| | - Wendy Noble
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 5 Cutcombe Road, London SE5 9RX, UK
- Department of Biomedical and Clinical Sciences, University of Exeter, Exeter, UK
| | - Maria Jimenez-Sanchez
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 5 Cutcombe Road, London SE5 9RX, UK
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45
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Shimogori T, Onishi K, Hoshino T, Nakanishi M. Molecular architecture of primate specific neural circuit formation. RESEARCH SQUARE 2024:rs.3.rs-4082064. [PMID: 38562839 PMCID: PMC10984012 DOI: 10.21203/rs.3.rs-4082064/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The mammalian cortex is a highly evolved brain region, but we still lack a comprehensive understanding of the molecular mechanisms underlying primate-specific neural circuits formation. In this study, we employed spatial transcriptomics to assess gene expression dynamics in the marmoset cortex during development, focusing on key regions and time points. Spatial transcriptomics identified genes that are sexually, spatially, and temporally differentially expressed in the developing marmoset cortex. Our detailed analysis of the visual cortex unveiled dynamic changes in gene expression across layers with distinct projections and functions. Notably, we discovered numerous axon guidance molecules with spatiotemporal expression patterns unique to the developing marmoset prefrontal cortex (PFC), which control PFC neuronal circuits. Among these molecules, PRSS12 (Protease, Serine, 12 (neurotrypsin, motopsin), when ectopically expressed in the mouse prelimbic cortex, caused similar changes in connectivity as observed in the marmoset A32 area. Furthermore, PRSS12 showed similar expression patterns in both marmoset and human PFC during development, suggesting parallels between marmoset and human brain development. The differential expression of axon guidance molecules in the developing PFC, varying by region, likely contributes to the formation of unique circuits observed in primates.
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Affiliation(s)
- Tomomi Shimogori
- Molecular Mechanisms of Brain Development, Center for Brain Science (CBS), RIKEN
| | - Kohei Onishi
- Molecular Mechanisms of Brain Development, Center for Brain Science (CBS), RIKEN
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46
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Pressl C, Mätlik K, Kus L, Darnell P, Luo JD, Paul MR, Weiss AR, Liguore W, Carroll TS, Davis DA, McBride J, Heintz N. Selective vulnerability of layer 5a corticostriatal neurons in Huntington's disease. Neuron 2024; 112:924-941.e10. [PMID: 38237588 DOI: 10.1016/j.neuron.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/18/2023] [Accepted: 12/13/2023] [Indexed: 01/30/2024]
Abstract
The properties of the cell types that are selectively vulnerable in Huntington's disease (HD) cortex, the nature of somatic CAG expansions of mHTT in these cells, and their importance in CNS circuitry have not been delineated. Here, we employed serial fluorescence-activated nuclear sorting (sFANS), deep molecular profiling, and single-nucleus RNA sequencing (snRNA-seq) of motor-cortex samples from thirteen predominantly early stage, clinically diagnosed HD donors and selected samples from cingulate, visual, insular, and prefrontal cortices to demonstrate loss of layer 5a pyramidal neurons in HD. Extensive mHTT CAG expansions occur in vulnerable layer 5a pyramidal cells, and in Betz cells, layers 6a and 6b neurons that are resilient in HD. Retrograde tracing experiments in macaque brains identify layer 5a neurons as corticostriatal pyramidal cells. We propose that enhanced somatic mHTT CAG expansion and altered synaptic function act together to cause corticostriatal disconnection and selective neuronal vulnerability in HD cerebral cortex.
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Affiliation(s)
- Christina Pressl
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Kert Mätlik
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Laura Kus
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Paul Darnell
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Matthew R Paul
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - Alison R Weiss
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, USA
| | - William Liguore
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, USA
| | - Thomas S Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, USA
| | - David A Davis
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jodi McBride
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR, USA
| | - Nathaniel Heintz
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY, USA.
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47
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Zhou X, Seow WY, Ha N, Cheng TH, Jiang L, Boonruangkan J, Goh JJL, Prabhakar S, Chou N, Chen KH. Highly sensitive spatial transcriptomics using FISHnCHIPs of multiple co-expressed genes. Nat Commun 2024; 15:2342. [PMID: 38491027 PMCID: PMC10943009 DOI: 10.1038/s41467-024-46669-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
High-dimensional, spatially resolved analysis of intact tissue samples promises to transform biomedical research and diagnostics, but existing spatial omics technologies are costly and labor-intensive. We present Fluorescence In Situ Hybridization of Cellular HeterogeneIty and gene expression Programs (FISHnCHIPs) for highly sensitive in situ profiling of cell types and gene expression programs. FISHnCHIPs achieves this by simultaneously imaging ~2-35 co-expressed genes (clustered into modules) that are spatially co-localized in tissues, resulting in similar spatial information as single-gene Fluorescence In Situ Hybridization (FISH), but with ~2-20-fold higher sensitivity. Using FISHnCHIPs, we image up to 53 modules from the mouse kidney and mouse brain, and demonstrate high-speed, large field-of-view profiling of a whole tissue section. FISHnCHIPs also reveals spatially restricted localizations of cancer-associated fibroblasts in a human colorectal cancer biopsy. Overall, FISHnCHIPs enables fast, robust, and scalable cell typing of tissues with normal physiology or undergoing pathogenesis.
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Affiliation(s)
- Xinrui Zhou
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Wan Yi Seow
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Norbert Ha
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Teh How Cheng
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Lingfan Jiang
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Jeeranan Boonruangkan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Jolene Jie Lin Goh
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Shyam Prabhakar
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore
| | - Nigel Chou
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore.
| | - Kok Hao Chen
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Singapore, 138672, Singapore.
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48
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Shi Y, Wang G. Protocol to study microcircuits in the medial entorhinal cortex in mice using multiple patch-clamp recordings and morphological reconstruction. STAR Protoc 2024; 5:102917. [PMID: 38421863 PMCID: PMC10910315 DOI: 10.1016/j.xpro.2024.102917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/30/2024] [Accepted: 02/09/2024] [Indexed: 03/02/2024] Open
Abstract
Multiple patch-clamp recordings and morphological reconstruction are powerful approaches for neuronal microcircuitry dissection and cell type classification but are challenging due to the sophisticated expertise needed. Here, we present a protocol for applying these techniques to neurons in the medial entorhinal cortex (MEC) of mice. We detail steps to prepare brain slices containing MEC and perform simultaneous multiple whole-cell recordings, followed by procedures of histological staining and neuronal reconstruction. We then describe how we analyze morphological and electrophysiological features. For complete details on the use and execution of this protocol, please refer to Shi et al.1.
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Affiliation(s)
- Yuying Shi
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Guangfu Wang
- HIT Center for Life Sciences, School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China.
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49
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Burg MF, Zenkel T, Vystrčilová M, Oesterle J, Höfling L, Willeke KF, Lause J, Müller S, Fahey PG, Ding Z, Restivo K, Sridhar S, Gollisch T, Berens P, Tolias AS, Euler T, Bethge M, Ecker AS. Most discriminative stimuli for functional cell type clustering. ARXIV 2024:arXiv:2401.05342v2. [PMID: 38560735 PMCID: PMC10980086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Identifying cell types and understanding their functional properties is crucial for unraveling the mechanisms underlying perception and cognition. In the retina, functional types can be identified by carefully selected stimuli, but this requires expert domain knowledge and biases the procedure towards previously known cell types. In the visual cortex, it is still unknown what functional types exist and how to identify them. Thus, for unbiased identification of the functional cell types in retina and visual cortex, new approaches are needed. Here we propose an optimization-based clustering approach using deep predictive models to obtain functional clusters of neurons using Most Discriminative Stimuli (MDS). Our approach alternates between stimulus optimization with cluster reassignment akin to an expectation-maximization algorithm. The algorithm recovers functional clusters in mouse retina, marmoset retina and macaque visual area V4. This demonstrates that our approach can successfully find discriminative stimuli across species, stages of the visual system and recording techniques. The resulting most discriminative stimuli can be used to assign functional cell types fast and on the fly, without the need to train complex predictive models or show a large natural scene dataset, paving the way for experiments that were previously limited by experimental time. Crucially, MDS are interpretable: they visualize the distinctive stimulus patterns that most unambiguously identify a specific type of neuron.
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Affiliation(s)
- Max F Burg
- International Max Planck Research School for Intelligent Systems, Tübingen, Germany
- Institute of Computer Science and Campus Institute Data Science, University of Göttingen, Germany
- Tübingen AI Center, University of Tübingen, Germany
| | - Thomas Zenkel
- Institute of Ophthalmic Research, University of Tübingen, Germany
- Centre for Integrative Neuroscience, University of Tübingen, Germany
| | - Michaela Vystrčilová
- Institute of Computer Science and Campus Institute Data Science, University of Göttingen, Germany
| | - Jonathan Oesterle
- Institute of Ophthalmic Research, University of Tübingen, Germany
- Centre for Integrative Neuroscience, University of Tübingen, Germany
| | - Larissa Höfling
- Institute of Ophthalmic Research, University of Tübingen, Germany
- Centre for Integrative Neuroscience, University of Tübingen, Germany
| | - Konstantin F Willeke
- International Max Planck Research School for Intelligent Systems, Tübingen, Germany
- Institute of Computer Science and Campus Institute Data Science, University of Göttingen, Germany
- Institute for Bioinformatics and Medical Informatics, Tübingen University, Germany
| | - Jan Lause
- Tübingen AI Center, University of Tübingen, Germany
- Hertie Institute for AI in Brain Health, University of Tübingen, Germany
| | - Sarah Müller
- International Max Planck Research School for Intelligent Systems, Tübingen, Germany
- Tübingen AI Center, University of Tübingen, Germany
- Hertie Institute for AI in Brain Health, University of Tübingen, Germany
| | - Paul G Fahey
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
| | - Zhiwei Ding
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
| | - Kelli Restivo
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
| | - Shashwat Sridhar
- University Medical Center Göttingen, Department of Ophthalmology, Germany
- Bernstein Center for Computational Neuroscience Göttingen, Germany
| | - Tim Gollisch
- University Medical Center Göttingen, Department of Ophthalmology, Germany
- Bernstein Center for Computational Neuroscience Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Germany
| | - Philipp Berens
- Tübingen AI Center, University of Tübingen, Germany
- Hertie Institute for AI in Brain Health, University of Tübingen, Germany
| | - Andreas S Tolias
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Center for Neuroscience and Artificial Intelligence, Baylor College of Medicine, Houston, TX, USA
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, USA
| | - Thomas Euler
- Institute of Ophthalmic Research, University of Tübingen, Germany
- Centre for Integrative Neuroscience, University of Tübingen, Germany
| | - Matthias Bethge
- Tübingen AI Center, University of Tübingen, Germany
- Centre for Integrative Neuroscience, University of Tübingen, Germany
| | - Alexander S Ecker
- Institute of Computer Science and Campus Institute Data Science, University of Göttingen, Germany
- Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
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50
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Günther DM, Batiuk MY, Petukhov V, De Oliveira R, Wunderle T, Buchholz CJ, Fries P, Khodosevich K. Heterogeneity of layer 4 in visual areas of rhesus macaque cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584345. [PMID: 38559123 PMCID: PMC10979896 DOI: 10.1101/2024.03.11.584345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Recently, single-cell RNA-sequencing (scRNA-seq) has enabled unprecedented insights to the cellular landscape of the brains of many different species, among them the rhesus macaque as a key animal model. Building on previous, broader surveys of the macaque brain, we closely examined five immediately neighboring areas within the visual cortex of the rhesus macaque: V1, V2, V4, MT and TEO. To facilitate this, we first devised a novel pipeline for brain spatial archive - the BrainSPACE - which enabled robust archiving and sampling from the whole unfixed brain. SnRNA-sequencing of ~100,000 nuclei from visual areas V1 and V4 revealed conservation within the GABAergic neuron subtypes, while seven and one distinct principle neuron subtypes were detected in V1 and V4, respectively, all most likely located in layer 4. Moreover, using small molecule fluorescence in situ hybridization, we identified cell type density gradients across V1, V2, V4, MT, and TEO appearing to reflect the visual hierarchy. These findings demonstrate an association between the clear areal specializations among neighboring areas with the hierarchical levels within the visual cortex of the rhesus macaque.
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Affiliation(s)
- Dorothee M. Günther
- Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, 60528 Frankfurt, Germany
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 EN Nijmegen, the Netherlands
- Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Mykhailo Y. Batiuk
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Viktor Petukhov
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Romain De Oliveira
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Thomas Wunderle
- Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, 60528 Frankfurt, Germany
| | - Christian J. Buchholz
- Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, 63225 Langen, Germany
| | - Pascal Fries
- Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, 60528 Frankfurt, Germany
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 EN Nijmegen, the Netherlands
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
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