1
|
Zehtabian A, Fuchs J, Eickholt BJ, Ewers H. Automated Analysis of Neuronal Morphology in 2D Fluorescence Micrographs through an Unsupervised Semantic Segmentation of Neurons. Neuroscience 2024; 551:333-344. [PMID: 38838980 DOI: 10.1016/j.neuroscience.2024.05.024] [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: 12/19/2023] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024]
Abstract
Brain function emerges from a highly complex network of specialized cells that are interlinked by billions of synapses. The synaptic connectivity between neurons is established between the elongated processes of their axons and dendrites or, together, neurites. To establish these connections, cellular neurites have to grow in highly specialized, cell-type dependent patterns covering extensive distances and connecting with thousands of other neurons. The outgrowth and branching of neurites are tightly controlled during development and are a commonly used functional readout of imaging in the neurosciences. Manual analysis of neuronal morphology from microscopy images, however, is very time intensive and prone to bias. Most automated analyses of neurons rely on reconstruction of the neuron as a whole without a semantic analysis of each neurite. A fully-automated classification of all neurites still remains unavailable in open-source software. Here we present a standalone, GUI-based software for batch-quantification of neuronal morphology in two-dimensional fluorescence micrographs of cultured neurons with minimal requirements for user interaction. Single neurons are first reconstructed into binarized images using a Hessian-based segmentation algorithm to detect thin neurite structures combined with intensity- and shape-based reconstruction of the cell body. Neurites are then classified into axon, dendrites and their branches of increasing order using a geodesic distance transform of the cell skeleton. The software was benchmarked against a published dataset and reproduced the phenotype observed after manual annotation. Our tool promises accelerated and improved morphometric studies of neuronal morphology by allowing for consistent and automated analysis of large datasets.
Collapse
Affiliation(s)
- Amin Zehtabian
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany.
| | - Joachim Fuchs
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Molecular Biology and Biochemistry, Virchowweg 6, 10117 Berlin, Germany
| | - Britta J Eickholt
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Molecular Biology and Biochemistry, Virchowweg 6, 10117 Berlin, Germany
| | - Helge Ewers
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany
| |
Collapse
|
2
|
Yang R, Xiao T, Cheng Y, Li A, Qu J, Liang R, Bao S, Wang X, Wang J, Suo J, Luo Q, Dai Q. Sharing massive biomedical data at magnitudes lower bandwidth using implicit neural function. Proc Natl Acad Sci U S A 2024; 121:e2320870121. [PMID: 38959033 PMCID: PMC11252806 DOI: 10.1073/pnas.2320870121] [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: 11/28/2023] [Accepted: 05/21/2024] [Indexed: 07/04/2024] Open
Abstract
Efficient storage and sharing of massive biomedical data would open up their wide accessibility to different institutions and disciplines. However, compressors tailored for natural photos/videos are rapidly limited for biomedical data, while emerging deep learning-based methods demand huge training data and are difficult to generalize. Here, we propose to conduct Biomedical data compRession with Implicit nEural Function (BRIEF) by representing the target data with compact neural networks, which are data specific and thus have no generalization issues. Benefiting from the strong representation capability of implicit neural function, BRIEF achieves 2[Formula: see text]3 orders of magnitude compression on diverse biomedical data at significantly higher fidelity than existing techniques. Besides, BRIEF is of consistent performance across the whole data volume, and supports customized spatially varying fidelity. BRIEF's multifold advantageous features also serve reliable downstream tasks at low bandwidth. Our approach will facilitate low-bandwidth data sharing and promote collaboration and progress in the biomedical field.
Collapse
Affiliation(s)
- Runzhao Yang
- Department of Automation, Tsinghua University, Beijing100084, China
- Institute of Brain and Cognitive Sciences, Tsinghua University, Beijing100084, China
- Shanghai Artificial Intelligence Laboratory, Shanghai200232, China
| | - Tingxiong Xiao
- Department of Automation, Tsinghua University, Beijing100084, China
| | - Yuxiao Cheng
- Department of Automation, Tsinghua University, Beijing100084, China
| | - Anan Li
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan430074, China
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou215123, China
| | - Jinyuan Qu
- Department of Automation, Tsinghua University, Beijing100084, China
| | - Rui Liang
- School of Biomedical Engineering, Hainan University, Haikou570228, China
| | - Shengda Bao
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan430074, China
| | - Xiaofeng Wang
- Britton Chance Center and MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan430074, China
| | - Jue Wang
- Department of Automation, Tsinghua University, Beijing100084, China
| | - Jinli Suo
- Department of Automation, Tsinghua University, Beijing100084, China
- Institute of Brain and Cognitive Sciences, Tsinghua University, Beijing100084, China
- Shanghai Artificial Intelligence Laboratory, Shanghai200232, China
| | - Qingming Luo
- School of Biomedical Engineering, Hainan University, Haikou570228, China
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing100084, China
- Institute of Brain and Cognitive Sciences, Tsinghua University, Beijing100084, China
| |
Collapse
|
3
|
Leite J, Nhoatto F, Jacob A, Santana R, Lobato F. Computational Tools for Neuronal Morphometric Analysis: A Systematic Search and Review. Neuroinformatics 2024:10.1007/s12021-024-09674-6. [PMID: 38922389 DOI: 10.1007/s12021-024-09674-6] [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] [Accepted: 06/08/2024] [Indexed: 06/27/2024]
Abstract
Morphometry is fundamental for studying and correlating neuronal morphology with brain functions. With increasing computational power, it is possible to extract morphometric characteristics automatically, including features such as length, volume, and number of neuron branches. However, to the best of our knowledge, there is no mapping of morphometric tools yet. In this context, we conducted a systematic search and review to identify and analyze tools within the scope of neuron analysis. Thus, the work followed a well-defined protocol and sought to answer the following research questions: What open-source tools are available for neuronal morphometric analysis? What morphometric characteristics are extracted by these tools? For this, aiming for greater robustness and coverage, the study was based on the paper analysis as well as the study of documentation and tests with the tools available in repositories. We analyzed 1,586 papers and mapped 23 tools, where NeuroM, L-Measure, and NeuroMorphoVis extract the most features. Furthermore, we contribute to the body of knowledge with the unprecedented presentation of 150 unique morphometric features whose terminologies were categorized and standardized. Overall, the study contributes to advancing the understanding of the complex mechanisms underlying the brain.
Collapse
Affiliation(s)
- Jéssica Leite
- Institute of Engineering and Geosciences, Federal University of Western Pará, Santarém, Pará, Brazil
| | - Fabiano Nhoatto
- Institute of Engineering and Geosciences, Federal University of Western Pará, Santarém, Pará, Brazil
| | - Antonio Jacob
- Department of Computer Engineering, State University of Maranhão, São Luís, Maranhão, Brazil
| | - Roberto Santana
- Department of Computer Science and Artificial Intelligence, University of the Basque Country, Donostia/San Sebastián, Guipúzcoa, Spain
| | - Fábio Lobato
- Institute of Engineering and Geosciences, Federal University of Western Pará, Santarém, Pará, Brazil.
| |
Collapse
|
4
|
Checcucci C, Wicinski B, Mazzamuto G, Scardigli M, Ramazzotti J, Brady N, Pavone FS, Hof PR, Costantini I, Frasconi P. Deep learning-based localization algorithms on fluorescence human brain 3D reconstruction: a comparative study using stereology as a reference. Sci Rep 2024; 14:14629. [PMID: 38918523 PMCID: PMC11199592 DOI: 10.1038/s41598-024-65092-3] [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: 01/22/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024] Open
Abstract
3D reconstruction of human brain volumes at high resolution is now possible thanks to advancements in tissue clearing methods and fluorescence microscopy techniques. Analyzing the massive data produced with these approaches requires automatic methods able to perform fast and accurate cell counting and localization. Recent advances in deep learning have enabled the development of various tools for cell segmentation. However, accurate quantification of neurons in the human brain presents specific challenges, such as high pixel intensity variability, autofluorescence, non-specific fluorescence and very large size of data. In this paper, we provide a thorough empirical evaluation of three techniques based on deep learning (StarDist, CellPose and BCFind-v2, an updated version of BCFind) using a recently introduced three-dimensional stereological design as a reference for large-scale insights. As a representative problem in human brain analysis, we focus on a 4 -cm 3 portion of the Broca's area. We aim at helping users in selecting appropriate techniques depending on their research objectives. To this end, we compare methods along various dimensions of analysis, including correctness of the predicted density and localization, computational efficiency, and human annotation effort. Our results suggest that deep learning approaches are very effective, have a high throughput providing each cell 3D location, and obtain results comparable to the estimates of the adopted stereological design.
Collapse
Affiliation(s)
- Curzio Checcucci
- Department of Information Engineering, University of Florence, 50100, Firenze, FI, Italy.
| | - Bridget Wicinski
- Nash Family Department of Neuroscience, Friedman Brain Institute and Center for Discovery and Innovation, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
| | - Giacomo Mazzamuto
- European Laboratory for Non-Linear Spectroscopy (LENS), 50019, Sesto Fiorentino, FI, Italy
- National Research Council, National Institute of Optics (CNR-INO), 50019, Sesto Fiorentino, FI, Italy
- Department of Physics, University of Florence, 50019, Sesto Fiorentino, FI, Italy
| | - Marina Scardigli
- European Laboratory for Non-Linear Spectroscopy (LENS), 50019, Sesto Fiorentino, FI, Italy
- Department of Experimental and Clinical Medicine, University of Florence, 50100, Firenze, FI, Italy
| | - Josephine Ramazzotti
- European Laboratory for Non-Linear Spectroscopy (LENS), 50019, Sesto Fiorentino, FI, Italy
| | - Niamh Brady
- European Laboratory for Non-Linear Spectroscopy (LENS), 50019, Sesto Fiorentino, FI, Italy
| | - Francesco S Pavone
- European Laboratory for Non-Linear Spectroscopy (LENS), 50019, Sesto Fiorentino, FI, Italy
- National Research Council, National Institute of Optics (CNR-INO), 50019, Sesto Fiorentino, FI, Italy
- Department of Physics, University of Florence, 50019, Sesto Fiorentino, FI, Italy
| | - Patrick R Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute and Center for Discovery and Innovation, Icahn School of Medicine at Mount Sinai, New York, NY, 10019, USA
| | - Irene Costantini
- European Laboratory for Non-Linear Spectroscopy (LENS), 50019, Sesto Fiorentino, FI, Italy
- National Research Council, National Institute of Optics (CNR-INO), 50019, Sesto Fiorentino, FI, Italy
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, FI, Italy
| | - Paolo Frasconi
- Department of Information Engineering, University of Florence, 50100, Firenze, FI, Italy
- European Laboratory for Non-Linear Spectroscopy (LENS), 50019, Sesto Fiorentino, FI, Italy
| |
Collapse
|
5
|
Garcia SB, Schlotter AP, Pereira D, Polleux F, Hammond LA. RESPAN: an accurate, unbiased and automated pipeline for analysis of dendritic morphology and dendritic spine mapping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597812. [PMID: 38895232 PMCID: PMC11185717 DOI: 10.1101/2024.06.06.597812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Accurate and unbiased reconstructions of neuronal morphology, including quantification of dendritic spine morphology and distribution, are widely used in neuroscience but remain a major roadblock for large-scale analysis. Traditionally, spine analysis has required labor-intensive manual annotation, which is prone to human error and impractical for large 3D datasets. Previous automated tools for reconstructing neuronal morphology and quantitative dendritic spine analysis face challenges in generating accurate results and, following close inspection, often require extensive manual correction. While recent tools leveraging deep learning approaches have substantially increased accuracy, they lack functionality and useful outputs, necessitating additional tools to perform a complete analysis and limiting their utility. In this paper, we describe Restoration Enhanced SPine And Neuron (RESPAN) analysis, a new comprehensive pipeline developed as an open-source, easily deployable solution that harnesses recent advances in deep learning and GPU processing. Our approach demonstrates high accuracy and robustness, validated extensively across a range of imaging modalities for automated dendrite and spine mapping. It also offers extensive visual and tabulated data outputs, including detailed morphological and spatial metrics, dendritic spine classification, and 3D renderings. Additionally, RESPAN includes tools for validating results, ensuring scientific rigor and reproducibility.
Collapse
Affiliation(s)
- Sergio B. Garcia
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Alexa P. Schlotter
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Daniela Pereira
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon 1400-038, Portugal
| | - Franck Polleux
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Luke A. Hammond
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| |
Collapse
|
6
|
Buccino AP, Damart T, Bartram J, Mandge D, Xue X, Zbili M, Gänswein T, Jaquier A, Emmenegger V, Markram H, Hierlemann A, Van Geit W. A Multimodal Fitting Approach to Construct Single-Neuron Models With Patch Clamp and High-Density Microelectrode Arrays. Neural Comput 2024; 36:1286-1331. [PMID: 38776965 DOI: 10.1162/neco_a_01672] [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: 03/15/2023] [Accepted: 02/20/2024] [Indexed: 05/25/2024]
Abstract
In computational neuroscience, multicompartment models are among the most biophysically realistic representations of single neurons. Constructing such models usually involves the use of the patch-clamp technique to record somatic voltage signals under different experimental conditions. The experimental data are then used to fit the many parameters of the model. While patching of the soma is currently the gold-standard approach to build multicompartment models, several studies have also evidenced a richness of dynamics in dendritic and axonal sections. Recording from the soma alone makes it hard to observe and correctly parameterize the activity of nonsomatic compartments. In order to provide a richer set of data as input to multicompartment models, we here investigate the combination of somatic patch-clamp recordings with recordings of high-density microelectrode arrays (HD-MEAs). HD-MEAs enable the observation of extracellular potentials and neural activity of neuronal compartments at subcellular resolution. In this work, we introduce a novel framework to combine patch-clamp and HD-MEA data to construct multicompartment models. We first validate our method on a ground-truth model with known parameters and show that the use of features extracted from extracellular signals, in addition to intracellular ones, yields models enabling better fits than using intracellular features alone. We also demonstrate our procedure using experimental data by constructing cell models from in vitro cell cultures. The proposed multimodal fitting procedure has the potential to augment the modeling efforts of the computational neuroscience community and provide the field with neuronal models that are more realistic and can be better validated.
Collapse
Affiliation(s)
- Alessio Paolo Buccino
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
| | - Tanguy Damart
- Blue Brain Project, École polytechnique fédérale de Lausanne, Campus Biotech, 1202 Geneva, Switzerland
| | - Julian Bartram
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
| | - Darshan Mandge
- Blue Brain Project, École polytechnique fédérale de Lausanne, Campus Biotech, 1202 Geneva, Switzerland
| | - Xiaohan Xue
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
| | - Mickael Zbili
- Blue Brain Project, École polytechnique fédérale de Lausanne, Campus Biotech, 1202 Geneva, Switzerland
| | - Tobias Gänswein
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
| | - Aurélien Jaquier
- Blue Brain Project, École polytechnique fédérale de Lausanne, Campus Biotech, 1202 Geneva, Switzerland
| | - Vishalini Emmenegger
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
| | - Henry Markram
- Blue Brain Project, École polytechnique fédérale de Lausanne, Campus Biotech, 1202 Geneva, Switzerland
| | - Andreas Hierlemann
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
| | - Werner Van Geit
- Blue Brain Project, École polytechnique fédérale de Lausanne, Campus Biotech, 1202 Geneva, Switzerland Present address: Foundation for Research on Information Technologies in Society (IT'IS), Zurich 8004, Switzerland
| |
Collapse
|
7
|
Choi YK, Feng L, Jeong WK, Kim J. Connecto-informatics at the mesoscale: current advances in image processing and analysis for mapping the brain connectivity. Brain Inform 2024; 11:15. [PMID: 38833195 DOI: 10.1186/s40708-024-00228-9] [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: 03/29/2024] [Accepted: 05/08/2024] [Indexed: 06/06/2024] Open
Abstract
Mapping neural connections within the brain has been a fundamental goal in neuroscience to understand better its functions and changes that follow aging and diseases. Developments in imaging technology, such as microscopy and labeling tools, have allowed researchers to visualize this connectivity through high-resolution brain-wide imaging. With this, image processing and analysis have become more crucial. However, despite the wealth of neural images generated, access to an integrated image processing and analysis pipeline to process these data is challenging due to scattered information on available tools and methods. To map the neural connections, registration to atlases and feature extraction through segmentation and signal detection are necessary. In this review, our goal is to provide an updated overview of recent advances in these image-processing methods, with a particular focus on fluorescent images of the mouse brain. Our goal is to outline a pathway toward an integrated image-processing pipeline tailored for connecto-informatics. An integrated workflow of these image processing will facilitate researchers' approach to mapping brain connectivity to better understand complex brain networks and their underlying brain functions. By highlighting the image-processing tools available for fluroscent imaging of the mouse brain, this review will contribute to a deeper grasp of connecto-informatics, paving the way for better comprehension of brain connectivity and its implications.
Collapse
Affiliation(s)
- Yoon Kyoung Choi
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, South Korea
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea
| | | | - Won-Ki Jeong
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea
| | - Jinhyun Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, South Korea.
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea.
- KIST-SKKU Brain Research Center, SKKU Institute for Convergence, Sungkyunkwan University, Suwon, South Korea.
| |
Collapse
|
8
|
Hong J, Hnatyshyn R, Santos EAD, Maciejewski R, Isenberg T. A Survey of Designs for Combined 2D+3D Visual Representations. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2024; 30:2888-2902. [PMID: 38648152 DOI: 10.1109/tvcg.2024.3388516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
We examine visual representations of data that make use of combinations of both 2D and 3D data mappings. Combining 2D and 3D representations is a common technique that allows viewers to understand multiple facets of the data with which they are interacting. While 3D representations focus on the spatial character of the data or the dedicated 3D data mapping, 2D representations often show abstract data properties and take advantage of the unique benefits of mapping to a plane. Many systems have used unique combinations of both types of data mappings effectively. Yet there are no systematic reviews of the methods in linking 2D and 3D representations. We systematically survey the relationships between 2D and 3D visual representations in major visualization publications-IEEE VIS, IEEE TVCG, and EuroVis-from 2012 to 2022. We closely examined 105 articles where 2D and 3D representations are connected visually, interactively, or through animation. These approaches are designed based on their visual environment, the relationships between their visual representations, and their possible layouts. Through our analysis, we introduce a design space as well as provide design guidelines for effectively linking 2D and 3D visual representations.
Collapse
|
9
|
Cauzzo S, Bruno E, Boulet D, Nazac P, Basile M, Callara AL, Tozzi F, Ahluwalia A, Magliaro C, Danglot L, Vanello N. A modular framework for multi-scale tissue imaging and neuronal segmentation. Nat Commun 2024; 15:4102. [PMID: 38778027 PMCID: PMC11111705 DOI: 10.1038/s41467-024-48146-y] [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: 04/20/2023] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
The development of robust tools for segmenting cellular and sub-cellular neuronal structures lags behind the massive production of high-resolution 3D images of neurons in brain tissue. The challenges are principally related to high neuronal density and low signal-to-noise characteristics in thick samples, as well as the heterogeneity of data acquired with different imaging methods. To address this issue, we design a framework which includes sample preparation for high resolution imaging and image analysis. Specifically, we set up a method for labeling thick samples and develop SENPAI, a scalable algorithm for segmenting neurons at cellular and sub-cellular scales in conventional and super-resolution STimulated Emission Depletion (STED) microscopy images of brain tissues. Further, we propose a validation paradigm for testing segmentation performance when a manual ground-truth may not exhaustively describe neuronal arborization. We show that SENPAI provides accurate multi-scale segmentation, from entire neurons down to spines, outperforming state-of-the-art tools. The framework will empower image processing of complex neuronal circuitries.
Collapse
Affiliation(s)
- Simone Cauzzo
- Research Center "E. Piaggio", University of Pisa, Pisa, Italy.
- Parkinson's Disease and Movement Disorders Unit, Center for Rare Neurological Diseases (ERN-RND), Department of Neurosciences, University of Padova, Padova, Italy.
| | - Ester Bruno
- Research Center "E. Piaggio", University of Pisa, Pisa, Italy
- Dipartimento di Ingegneria dell'Informazione, University of Pisa, Pisa, Italy
| | - David Boulet
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, NeurImag Core Facility, 75014, Paris, France
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Membrane traffic and diseased brain, 75014, Paris, France
| | - Paul Nazac
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Membrane traffic and diseased brain, 75014, Paris, France
| | - Miriam Basile
- Dipartimento di Ingegneria dell'Informazione, University of Pisa, Pisa, Italy
| | - Alejandro Luis Callara
- Research Center "E. Piaggio", University of Pisa, Pisa, Italy
- Dipartimento di Ingegneria dell'Informazione, University of Pisa, Pisa, Italy
| | - Federico Tozzi
- Research Center "E. Piaggio", University of Pisa, Pisa, Italy
- Dipartimento di Ingegneria dell'Informazione, University of Pisa, Pisa, Italy
| | - Arti Ahluwalia
- Research Center "E. Piaggio", University of Pisa, Pisa, Italy
- Dipartimento di Ingegneria dell'Informazione, University of Pisa, Pisa, Italy
| | - Chiara Magliaro
- Research Center "E. Piaggio", University of Pisa, Pisa, Italy
- Dipartimento di Ingegneria dell'Informazione, University of Pisa, Pisa, Italy
| | - Lydia Danglot
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, NeurImag Core Facility, 75014, Paris, France.
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Membrane traffic and diseased brain, 75014, Paris, France.
| | - Nicola Vanello
- Research Center "E. Piaggio", University of Pisa, Pisa, Italy.
- Dipartimento di Ingegneria dell'Informazione, University of Pisa, Pisa, Italy.
| |
Collapse
|
10
|
Zeng Y, Wang Y. Complete Neuron Reconstruction Based on Branch Confidence. Brain Sci 2024; 14:396. [PMID: 38672045 PMCID: PMC11047972 DOI: 10.3390/brainsci14040396] [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: 03/04/2024] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
In the past few years, significant advancements in microscopic imaging technology have led to the production of numerous high-resolution images capturing brain neurons at the micrometer scale. The reconstructed structure of neurons from neuronal images can serve as a valuable reference for research in brain diseases and neuroscience. Currently, there lacks an accurate and efficient method for neuron reconstruction. Manual reconstruction remains the primary approach, offering high accuracy but requiring significant time investment. While some automatic reconstruction methods are faster, they often sacrifice accuracy and cannot be directly relied upon. Therefore, the primary goal of this paper is to develop a neuron reconstruction tool that is both efficient and accurate. The tool aids users in reconstructing complete neurons by calculating the confidence of branches during the reconstruction process. The method models the neuron reconstruction as multiple Markov chains, and calculates the confidence of the connections between branches by simulating the reconstruction artifacts in the results. Users iteratively modify low-confidence branches to ensure precise and efficient neuron reconstruction. Experiments on both the publicly accessible BigNeuron dataset and a self-created Whole-Brain dataset demonstrate that the tool achieves high accuracy similar to manual reconstruction, while significantly reducing reconstruction time.
Collapse
Affiliation(s)
- Ying Zeng
- School of Computer Science and Technology, Shanghai University, Shanghai 200444, China;
- Guangdong Institute of Intelligence Science and Technology, Zhuhai 519031, China
| | - Yimin Wang
- Guangdong Institute of Intelligence Science and Technology, Zhuhai 519031, China
| |
Collapse
|
11
|
Takeshita N, Sakaki S, Saba R, Inoue S, Nishikawa K, Ueyama A, Nakajima Y, Matsuo K, Shigeta M, Kobayashi D, Yamazaki H, Yamada K, Iehara T, Yashiro K. Acto3D: an open-source user-friendly volume rendering software for high-resolution 3D fluorescence imaging in biology. Development 2024; 151:dev202550. [PMID: 38657972 DOI: 10.1242/dev.202550] [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: 11/16/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024]
Abstract
Advances in fluorescence microscopy and tissue-clearing have revolutionised 3D imaging of fluorescently labelled tissues, organs and embryos. However, the complexity and high cost of existing software and computing solutions limit their widespread adoption, especially by researchers with limited resources. Here, we present Acto3D, an open-source software, designed to streamline the generation and analysis of high-resolution 3D images of targets labelled with multiple fluorescent probes. Acto3D provides an intuitive interface for easy 3D data import and visualisation. Although Acto3D offers straightforward 3D viewing, it performs all computations explicitly, giving users detailed control over the displayed images. Leveraging an integrated graphics processing unit, Acto3D deploys all pixel data to system memory, reducing visualisation latency. This approach facilitates accurate image reconstruction and efficient data processing in 3D, eliminating the need for expensive high-performance computers and dedicated graphics processing units. We have also introduced a method for efficiently extracting lumen structures in 3D. We have validated Acto3D by imaging mouse embryonic structures and by performing 3D reconstruction of pharyngeal arch arteries while preserving fluorescence information. Acto3D is a cost-effective and efficient platform for biological research.
Collapse
Affiliation(s)
- Naoki Takeshita
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Shinichiro Sakaki
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Rie Saba
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
- Department of Radiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Satoshi Inoue
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Kosuke Nishikawa
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Atsuko Ueyama
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Yoshiro Nakajima
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Kazuhiko Matsuo
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Masaki Shigeta
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Daisuke Kobayashi
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Hideya Yamazaki
- Department of Radiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Kei Yamada
- Department of Radiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Tomoko Iehara
- Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| | - Kenta Yashiro
- Division of Anatomy and Developmental Biology, Department of Anatomy, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, 602-8566, Japan
| |
Collapse
|
12
|
Walsh CL, Berg M, West H, Holroyd NA, Walker-Samuel S, Shipley RJ. Reconstructing microvascular network skeletons from 3D images: What is the ground truth? Comput Biol Med 2024; 171:108140. [PMID: 38422956 DOI: 10.1016/j.compbiomed.2024.108140] [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: 10/18/2023] [Revised: 01/29/2024] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
Structural changes to microvascular networks are increasingly highlighted as markers of pathogenesis in a wide range of disease, e.g. Alzheimer's disease, vascular dementia and tumour growth. This has motivated the development of dedicated 3D imaging techniques, alongside the creation of computational modelling frameworks capable of using 3D reconstructed networks to simulate functional behaviours such as blood flow or transport processes. Extraction of 3D networks from imaging data broadly consists of two image processing steps: segmentation followed by skeletonisation. Much research effort has been devoted to segmentation field, and there are standard and widely-applied methodologies for creating and assessing gold standards or ground truths produced by manual annotation or automated algorithms. The Skeletonisation field, however, lacks widely applied, simple to compute metrics for the validation or optimisation of the numerous algorithms that exist to extract skeletons from binary images. This is particularly problematic as 3D imaging datasets increase in size and visual inspection becomes an insufficient validation approach. In this work, we first demonstrate the extent of the problem by applying 4 widely-used skeletonisation algorithms to 3 different imaging datasets. In doing so we show significant variability between reconstructed skeletons of the same segmented imaging dataset. Moreover, we show that such a structural variability propagates to simulated metrics such as blood flow. To mitigate this variability we introduce a new, fast and easy to compute super metric that compares the volume, connectivity, medialness, bifurcation point identification and homology of the reconstructed skeletons to the original segmented data. We then show that such a metric can be used to select the best performing skeletonisation algorithm for a given dataset, as well as to optimise its parameters. Finally, we demonstrate that the super metric can also be used to quickly identify how a particular skeletonisation algorithm could be improved, becoming a powerful tool in understanding the complex implication of small structural changes in a network.
Collapse
Affiliation(s)
- Claire L Walsh
- Department of Mechanical Engineering, University College London, United Kingdom
| | - Maxime Berg
- Department of Mechanical Engineering, University College London, United Kingdom.
| | - Hannah West
- Department of Mechanical Engineering, University College London, United Kingdom
| | - Natalie A Holroyd
- Centre for Computational Medicine, Division of Medicine, University College London, United Kingdom
| | - Simon Walker-Samuel
- Centre for Computational Medicine, Division of Medicine, University College London, United Kingdom
| | - Rebecca J Shipley
- Department of Mechanical Engineering, University College London, United Kingdom; Centre for Computational Medicine, Division of Medicine, University College London, United Kingdom
| |
Collapse
|
13
|
Velasco I, Garcia-Cantero JJ, Brito JP, Bayona S, Pastor L, Mata S. NeuroEditor: a tool to edit and visualize neuronal morphologies. Front Neuroanat 2024; 18:1342762. [PMID: 38425804 PMCID: PMC10902916 DOI: 10.3389/fnana.2024.1342762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/22/2024] [Indexed: 03/02/2024] Open
Abstract
The digital extraction of detailed neuronal morphologies from microscopy data is an essential step in the study of neurons. Ever since Cajal's work, the acquisition and analysis of neuron anatomy has yielded invaluable insight into the nervous system, which has led to our present understanding of many structural and functional aspects of the brain and the nervous system, well beyond the anatomical perspective. Obtaining detailed anatomical data, though, is not a simple task. Despite recent progress, acquiring neuron details still involves using labor-intensive, error prone methods that facilitate the introduction of inaccuracies and mistakes. In consequence, getting reliable morphological tracings usually needs the completion of post-processing steps that require user intervention to ensure the extracted data accuracy. Within this framework, this paper presents NeuroEditor, a new software tool for visualization, editing and correction of previously reconstructed neuronal tracings. This tool has been developed specifically for alleviating the burden associated with the acquisition of detailed morphologies. NeuroEditor offers a set of algorithms that can automatically detect the presence of potential errors in tracings. The tool facilitates users to explore an error with a simple mouse click so that it can be corrected manually or, where applicable, automatically. In some cases, this tool can also propose a set of actions to automatically correct a particular type of error. Additionally, this tool allows users to visualize and compare the original and modified tracings, also providing a 3D mesh that approximates the neuronal membrane. The approximation of this mesh is computed and recomputed on-the-fly, reflecting any instantaneous changes during the tracing process. Moreover, NeuroEditor can be easily extended by users, who can program their own algorithms in Python and run them within the tool. Last, this paper includes an example showing how users can easily define a customized workflow by applying a sequence of editing operations. The edited morphology can then be stored, together with the corresponding 3D mesh that approximates the neuronal membrane.
Collapse
Affiliation(s)
- Ivan Velasco
- Department of Computer Science, Universidad Rey Juan Carlos (URJC), Tulipan, Madrid, Spain
| | - Juan J. Garcia-Cantero
- Department of Computer Science, Universidad Rey Juan Carlos (URJC), Tulipan, Madrid, Spain
- Center for Computational Simulation, Universidad Politecnica de Madrid, Madrid, Spain
| | - Juan P. Brito
- Center for Computational Simulation, Universidad Politecnica de Madrid, Madrid, Spain
- DLSIIS, ETSIINF, Universidad Politecnica de Madrid, Madrid, Spain
| | - Sofia Bayona
- Department of Computer Science, Universidad Rey Juan Carlos (URJC), Tulipan, Madrid, Spain
- Center for Computational Simulation, Universidad Politecnica de Madrid, Madrid, Spain
| | - Luis Pastor
- Department of Computer Science, Universidad Rey Juan Carlos (URJC), Tulipan, Madrid, Spain
- Center for Computational Simulation, Universidad Politecnica de Madrid, Madrid, Spain
| | - Susana Mata
- Department of Computer Science, Universidad Rey Juan Carlos (URJC), Tulipan, Madrid, Spain
- Center for Computational Simulation, Universidad Politecnica de Madrid, Madrid, Spain
| |
Collapse
|
14
|
Yi Y, Li Y, Zhang S, Men Y, Wang Y, Jing D, Ding J, Zhu Q, Chen Z, Chen X, Li JL, Wang Y, Wang J, Peng H, Zhang L, Luo W, Feng JQ, He Y, Ge WP, Zhao H. Mapping of individual sensory nerve axons from digits to spinal cord with the transparent embedding solvent system. Cell Res 2024; 34:124-139. [PMID: 38168640 PMCID: PMC10837210 DOI: 10.1038/s41422-023-00867-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/07/2023] [Indexed: 01/05/2024] Open
Abstract
Achieving uniform optical resolution for a large tissue sample is a major challenge for deep imaging. For conventional tissue clearing methods, loss of resolution and quality in deep regions is inevitable due to limited transparency. Here we describe the Transparent Embedding Solvent System (TESOS) method, which combines tissue clearing, transparent embedding, sectioning and block-face imaging. We used TESOS to acquire volumetric images of uniform resolution for an adult mouse whole-body sample. The TESOS method is highly versatile and can be combined with different microscopy systems to achieve uniformly high resolution. With a light sheet microscope, we imaged the whole body of an adult mouse, including skin, at a uniform 0.8 × 0.8 × 3.5 μm3 voxel resolution within 120 h. With a confocal microscope and a 40×/1.3 numerical aperture objective, we achieved a uniform sub-micron resolution in the whole sample to reveal a complete projection of individual nerve axons within the central or peripheral nervous system. Furthermore, TESOS allowed the first mesoscale connectome mapping of individual sensory neuron axons spanning 5 cm from adult mouse digits to the spinal cord at a uniform sub-micron resolution.
Collapse
Affiliation(s)
- Yating Yi
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Chinese Institute for Brain Research, Beijing, China
| | - Youqi Li
- Chinese Institute for Brain Research, Beijing, China
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Shiwen Zhang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yi Men
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yuhong Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Dian Jing
- Department of Orthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology, Shanghai, China
| | - Jiayi Ding
- Chinese Institute for Brain Research, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Qingjie Zhu
- Chinese Institute for Brain Research, Beijing, China
| | - Zexi Chen
- Chinese Institute for Brain Research, Beijing, China
| | - Xingjun Chen
- Chinese Institute for Brain Research, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jun-Liszt Li
- Chinese Institute for Brain Research, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yilong Wang
- Chinese Institute for Brain Research, Beijing, China
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jun Wang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Hanchuan Peng
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu, China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, China
| | | | - Jian Q Feng
- Texas A&M University, College of Dentistry, Dallas, TX, USA
| | - Yongwen He
- Qujing Medical College, Qujing, Yunnan, China.
| | - Woo-Ping Ge
- Chinese Institute for Brain Research, Beijing, China.
| | - Hu Zhao
- Chinese Institute for Brain Research, Beijing, China.
| |
Collapse
|
15
|
Roudot P, Legant WR, Zou Q, Dean KM, Isogai T, Welf ES, David AF, Gerlich DW, Fiolka R, Betzig E, Danuser G. u-track3D: Measuring, navigating, and validating dense particle trajectories in three dimensions. CELL REPORTS METHODS 2023; 3:100655. [PMID: 38042149 PMCID: PMC10783629 DOI: 10.1016/j.crmeth.2023.100655] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/10/2023] [Accepted: 11/09/2023] [Indexed: 12/04/2023]
Abstract
We describe u-track3D, a software package that extends the versatile u-track framework established in 2D to address the specific challenges of 3D particle tracking. First, we present the performance of the new package in quantifying a variety of intracellular dynamics imaged by multiple 3D microcopy platforms and on the standard 3D test dataset of the particle tracking challenge. These analyses indicate that u-track3D presents a tracking solution that is competitive to both conventional and deep-learning-based approaches. We then present the concept of dynamic region of interest (dynROI), which allows an experimenter to interact with dynamic 3D processes in 2D views amenable to visual inspection. Third, we present an estimator of trackability that automatically defines a score for every trajectory, thereby overcoming the challenges of trajectory validation by visual inspection. With these combined strategies, u-track3D provides a complete framework for unbiased studies of molecular processes in complex volumetric sequences.
Collapse
Affiliation(s)
- Philippe Roudot
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA; Aix Marseille University, CNRS, Centrale Marseille, I2M, Turing Centre for Living Systems, Marseille, France.
| | - Wesley R Legant
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, USA; Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Qiongjing Zou
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Kevin M Dean
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Tadamoto Isogai
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Erik S Welf
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ana F David
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Reto Fiolka
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Eric Betzig
- Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
16
|
Kaya Z, Belder N, Sever-Bahcekapili M, Donmez-Demir B, Erdener ŞE, Bozbeyoglu N, Bagci C, Eren-Kocak E, Yemisci M, Karatas H, Erdemli E, Gursel I, Dalkara T. Vesicular HMGB1 release from neurons stressed with spreading depolarization enables confined inflammatory signaling to astrocytes. J Neuroinflammation 2023; 20:295. [PMID: 38082296 PMCID: PMC10712196 DOI: 10.1186/s12974-023-02977-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
The role of high mobility group box 1 (HMGB1) in inflammation is well characterized in the immune system and in response to tissue injury. More recently, HMGB1 was also shown to initiate an "inflammatory signaling cascade" in the brain parenchyma after a mild and brief disturbance, such as cortical spreading depolarization (CSD), leading to headache. Despite substantial evidence implying a role for inflammatory signaling in prevalent neuropsychiatric disorders such as migraine and depression, how HMGB1 is released from healthy neurons and how inflammatory signaling is initiated in the absence of apparent cell injury are not well characterized. We triggered a single cortical spreading depolarization by optogenetic stimulation or pinprick in naïve Swiss albino or transgenic Thy1-ChR2-YFP and hGFAP-GFP adult mice. We evaluated HMGB1 release in brain tissue sections prepared from these mice by immunofluorescent labeling and immunoelectron microscopy. EzColocalization and Costes thresholding algorithms were used to assess the colocalization of small extracellular vesicles (sEVs) carrying HMGB1 with astrocyte or microglia processes. sEVs were also isolated from the brain after CSD, and neuron-derived sEVs were captured by CD171 (L1CAM). sEVs were characterized with flow cytometry, scanning electron microscopy, nanoparticle tracking analysis, and Western blotting. We found that HMGB1 is released mainly within sEVs from the soma of stressed neurons, which are taken up by surrounding astrocyte processes. This creates conditions for selective communication between neurons and astrocytes bypassing microglia, as evidenced by activation of the proinflammatory transcription factor NF-ĸB p65 in astrocytes but not in microglia. Transmission immunoelectron microscopy data illustrated that HMGB1 was incorporated into sEVs through endosomal mechanisms. In conclusion, proinflammatory mediators released within sEVs can induce cell-specific inflammatory signaling in the brain without activating transmembrane receptors on other cells and causing overt inflammation.
Collapse
Affiliation(s)
- Zeynep Kaya
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Sıhhiye, Ankara, Turkey
| | - Nevin Belder
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Sıhhiye, Ankara, Turkey
- Biotechnology Institute, Ankara University, Ankara, Turkey
| | - Melike Sever-Bahcekapili
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Sıhhiye, Ankara, Turkey
| | - Buket Donmez-Demir
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Sıhhiye, Ankara, Turkey
| | - Şefik Evren Erdener
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Sıhhiye, Ankara, Turkey
| | - Naz Bozbeyoglu
- Department of Molecular Biology and Genetics, Science Faculty, Bilkent University, Ankara, Turkey
| | - Canan Bagci
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Sıhhiye, Ankara, Turkey
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Bahçeşehir University, Istanbul, Turkey
| | - Emine Eren-Kocak
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Sıhhiye, Ankara, Turkey
| | - Muge Yemisci
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Sıhhiye, Ankara, Turkey
| | - Hulya Karatas
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Sıhhiye, Ankara, Turkey
| | - Esra Erdemli
- Department of Histology and Embryology, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - Ihsan Gursel
- Department of Molecular Biology and Genetics, Science Faculty, Bilkent University, Ankara, Turkey
- Izmir Biomedicine and Genome Center, Dokuz Eylul University, İzmir, Turkey
| | - Turgay Dalkara
- Institute of Neurological Sciences and Psychiatry, Hacettepe University, Sıhhiye, Ankara, Turkey.
| |
Collapse
|
17
|
Studtmann C, Ladislav M, Safari M, Khondaker R, Chen Y, Vaughan GA, Topolski MA, Tomović E, Balík A, Swanger SA. Ventral posterolateral and ventral posteromedial thalamocortical neurons have distinct physiological properties. J Neurophysiol 2023; 130:1492-1507. [PMID: 37937368 PMCID: PMC11068404 DOI: 10.1152/jn.00525.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 10/09/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023] Open
Abstract
Somatosensory information is propagated from the periphery to the cerebral cortex by two parallel pathways through the ventral posterolateral (VPL) and ventral posteromedial (VPM) thalamus. VPL and VPM neurons receive somatosensory signals from the body and head, respectively. VPL and VPM neurons may also receive cell type-specific GABAergic input from the reticular nucleus of the thalamus. Although VPL and VPM neurons have distinct connectivity and physiological roles, differences in their functional properties remain unclear as they are often studied as one ventrobasal thalamus neuron population. Here, we directly compared synaptic and intrinsic properties of VPL and VPM neurons in C57Bl/6J mice of both sexes aged P25-P32. VPL neurons showed greater depolarization-induced spike firing and spike frequency adaptation than VPM neurons. VPL and VPM neurons fired similar numbers of spikes during hyperpolarization rebound bursts, but VPM neurons exhibited shorter burst latency compared with VPL neurons, which correlated with larger sag potential. VPM neurons had larger membrane capacitance and more complex dendritic arbors. Recordings of spontaneous and evoked synaptic transmission suggested that VPL neurons receive stronger excitatory synaptic input, whereas inhibitory synapse strength was stronger in VPM neurons. This work indicates that VPL and VPM thalamocortical neurons have distinct intrinsic and synaptic properties. The observed functional differences could have important implications for their specific physiological and pathophysiological roles within the somatosensory thalamocortical network.NEW & NOTEWORTHY This study revealed that somatosensory thalamocortical neurons in the VPL and VPM have substantial differences in excitatory synaptic input and intrinsic firing properties. The distinct properties suggest that VPL and VPM neurons could process somatosensory information differently and have selective vulnerability to disease. This work improves our understanding of nucleus-specific neuron function in the thalamus and demonstrates the critical importance of studying these parallel somatosensory pathways separately.
Collapse
Affiliation(s)
- Carleigh Studtmann
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, Virginia, United States
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, Virginia, United States
| | - Marek Ladislav
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, Virginia, United States
| | - Mona Safari
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, Virginia, United States
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, Virginia, United States
| | - Rabeya Khondaker
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, Virginia, United States
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, Virginia, United States
| | - Yang Chen
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, Virginia, United States
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Tech, Blacksburg, Virginia, United States
| | - Grace A Vaughan
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, Virginia, United States
- Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, Virginia, United States
| | - Mackenzie A Topolski
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, Virginia, United States
| | - Eni Tomović
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, Virginia, United States
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Aleš Balík
- Institute of Physiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Sharon A Swanger
- Fralin Biomedical Research Institute at Virginia Tech Carilion, Roanoke, Virginia, United States
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, United States
- Department of Internal Medicine, Virginia Tech Carilion School of Medicine, Roanoke, Virginia, United States
| |
Collapse
|
18
|
Vanherle S, Guns J, Loix M, Mingneau F, Dierckx T, Wouters F, Kuipers K, Vangansewinkel T, Wolfs E, Lins PP, Bronckaers A, Lambrichts I, Dehairs J, Swinnen JV, Verberk SGS, Haidar M, Hendriks JJA, Bogie JFJ. Extracellular vesicle-associated cholesterol supports the regenerative functions of macrophages in the brain. J Extracell Vesicles 2023; 12:e12394. [PMID: 38124258 PMCID: PMC10733568 DOI: 10.1002/jev2.12394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 11/15/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Macrophages play major roles in the pathophysiology of various neurological disorders, being involved in seemingly opposing processes such as lesion progression and resolution. Yet, the molecular mechanisms that drive their harmful and benign effector functions remain poorly understood. Here, we demonstrate that extracellular vesicles (EVs) secreted by repair-associated macrophages (RAMs) enhance remyelination ex vivo and in vivo by promoting the differentiation of oligodendrocyte precursor cells (OPCs). Guided by lipidomic analysis and applying cholesterol depletion and enrichment strategies, we find that EVs released by RAMs show markedly elevated cholesterol levels and that cholesterol abundance controls their reparative impact on OPC maturation and remyelination. Mechanistically, EV-associated cholesterol was found to promote OPC differentiation predominantly through direct membrane fusion. Collectively, our findings highlight that EVs are essential for cholesterol trafficking in the brain and that changes in cholesterol abundance support the reparative impact of EVs released by macrophages in the brain, potentially having broad implications for therapeutic strategies aimed at promoting repair in neurodegenerative disorders.
Collapse
Affiliation(s)
- Sam Vanherle
- Department of Immunology and Infection, Biomedical Research InstituteHasselt UniversityDiepenbeekBelgium
- University MS Center HasseltPeltBelgium
| | - Jeroen Guns
- Department of Immunology and Infection, Biomedical Research InstituteHasselt UniversityDiepenbeekBelgium
- University MS Center HasseltPeltBelgium
| | - Melanie Loix
- Department of Immunology and Infection, Biomedical Research InstituteHasselt UniversityDiepenbeekBelgium
- University MS Center HasseltPeltBelgium
| | - Fleur Mingneau
- Department of Immunology and Infection, Biomedical Research InstituteHasselt UniversityDiepenbeekBelgium
- University MS Center HasseltPeltBelgium
| | - Tess Dierckx
- Department of Immunology and Infection, Biomedical Research InstituteHasselt UniversityDiepenbeekBelgium
- University MS Center HasseltPeltBelgium
| | - Flore Wouters
- Department of Immunology and Infection, Biomedical Research InstituteHasselt UniversityDiepenbeekBelgium
- University MS Center HasseltPeltBelgium
| | - Koen Kuipers
- Department of Immunology and Infection, Biomedical Research InstituteHasselt UniversityDiepenbeekBelgium
- University MS Center HasseltPeltBelgium
| | - Tim Vangansewinkel
- Department of Cardio and Organs Systems, Biomedical Research InstituteHasselt UniversityDiepenbeekBelgium
- VIB, Center for Brain & Disease Research, Laboratory of NeurobiologyUniversity of LeuvenLeuvenBelgium
| | - Esther Wolfs
- Department of Cardio and Organs Systems, Biomedical Research InstituteHasselt UniversityDiepenbeekBelgium
| | - Paula Pincela Lins
- Department of Cardio and Organs Systems, Biomedical Research InstituteHasselt UniversityDiepenbeekBelgium
- Health DepartmentFlemish Institute for Technological ResearchMolBelgium
| | - Annelies Bronckaers
- Department of Cardio and Organs Systems, Biomedical Research InstituteHasselt UniversityDiepenbeekBelgium
| | - Ivo Lambrichts
- Department of Cardio and Organs Systems, Biomedical Research InstituteHasselt UniversityDiepenbeekBelgium
| | - Jonas Dehairs
- Department of Oncology, Laboratory of Lipid Metabolism and Cancer, Leuven Cancer InstituteUniversity of LeuvenLeuvenBelgium
| | - Johannes V. Swinnen
- Department of Oncology, Laboratory of Lipid Metabolism and Cancer, Leuven Cancer InstituteUniversity of LeuvenLeuvenBelgium
| | - Sanne G. S. Verberk
- Department of Immunology and Infection, Biomedical Research InstituteHasselt UniversityDiepenbeekBelgium
- University MS Center HasseltPeltBelgium
| | - Mansour Haidar
- Department of Immunology and Infection, Biomedical Research InstituteHasselt UniversityDiepenbeekBelgium
- University MS Center HasseltPeltBelgium
| | - Jerome J. A. Hendriks
- Department of Immunology and Infection, Biomedical Research InstituteHasselt UniversityDiepenbeekBelgium
- University MS Center HasseltPeltBelgium
| | - Jeroen F. J. Bogie
- Department of Immunology and Infection, Biomedical Research InstituteHasselt UniversityDiepenbeekBelgium
- University MS Center HasseltPeltBelgium
| |
Collapse
|
19
|
Sorensen SA, Gouwens NW, Wang Y, Mallory M, Budzillo A, Dalley R, Lee B, Gliko O, Kuo HC, Kuang X, Mann R, Ahmadinia L, Alfiler L, Baftizadeh F, Baker K, Bannick S, Bertagnolli D, Bickley K, Bohn P, Brown D, Bomben J, Brouner K, Chen C, Chen K, Chvilicek M, Collman F, Daigle T, Dawes T, de Frates R, Dee N, DePartee M, Egdorf T, El-Hifnawi L, Enstrom R, Esposito L, Farrell C, Gala R, Glomb A, Gamlin C, Gary A, Goldy J, Gu H, Hadley K, Hawrylycz M, Henry A, Hill D, Hirokawa KE, Huang Z, Johnson K, Juneau Z, Kebede S, Kim L, Lee C, Lesnar P, Li A, Glomb A, Li Y, Liang E, Link K, Maxwell M, McGraw M, McMillen DA, Mukora A, Ng L, Ochoa T, Oldre A, Park D, Pom CA, Popovich Z, Potekhina L, Rajanbabu R, Ransford S, Reding M, Ruiz A, Sandman D, Siverts L, Smith KA, Stoecklin M, Sulc J, Tieu M, Ting J, Trinh J, Vargas S, Vumbaco D, Walker M, Wang M, Wanner A, Waters J, Williams G, Wilson J, Xiong W, Lein E, Berg J, Kalmbach B, Yao S, Gong H, Luo Q, Ng L, Sümbül U, Jarsky T, Yao Z, Tasic B, Zeng H. Connecting single-cell transcriptomes to projectomes in mouse visual cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.25.568393. [PMID: 38168270 PMCID: PMC10760188 DOI: 10.1101/2023.11.25.568393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The mammalian brain is composed of diverse neuron types that play different functional roles. Recent single-cell RNA sequencing approaches have led to a whole brain taxonomy of transcriptomically-defined cell types, yet cell type definitions that include multiple cellular properties can offer additional insights into a neuron's role in brain circuits. While the Patch-seq method can investigate how transcriptomic properties relate to the local morphological and electrophysiological properties of cell types, linking transcriptomic identities to long-range projections is a major unresolved challenge. To address this, we collected coordinated Patch-seq and whole brain morphology data sets of excitatory neurons in mouse visual cortex. From the Patch-seq data, we defined 16 integrated morpho-electric-transcriptomic (MET)-types; in parallel, we reconstructed the complete morphologies of 300 neurons. We unified the two data sets with a multi-step classifier, to integrate cell type assignments and interrogate cross-modality relationships. We find that transcriptomic variations within and across MET-types correspond with morphological and electrophysiological phenotypes. In addition, this variation, along with the anatomical location of the cell, can be used to predict the projection targets of individual neurons. We also shed new light on infragranular cell types and circuits, including cell-type-specific, interhemispheric projections. With this approach, we establish a comprehensive, integrated taxonomy of excitatory neuron types in mouse visual cortex and create a system for integrated, high-dimensional cell type classification that can be extended to the whole brain and potentially across species.
Collapse
Affiliation(s)
| | | | - Yun Wang
- Allen Institute for Brain Science
| | | | | | | | | | | | | | - Xiuli Kuang
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | | | | | | | | | | | | | | | | | | | | | | | - Chao Chen
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Kai Chen
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | | | | | | | | | - Nick Dee
- Allen Institute for Brain Science
| | | | | | | | | | | | | | | | | | | | | | | | - Hong Gu
- Allen Institute for Brain Science
| | | | | | | | | | | | - Zili Huang
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | | | | | - Lisa Kim
- Allen Institute for Brain Science
| | | | | | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | | | - Yaoyao Li
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | | | | | | | | | | | | | | | | | | | | | - Zoran Popovich
- University of Washington, Dept. of Computer Science and Engineering
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Wei Xiong
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Ed Lein
- Allen Institute for Brain Science
| | - Jim Berg
- Allen Institute for Brain Science
| | | | | | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Qingming Luo
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, China
| | - Lydia Ng
- Allen Institute for Brain Science
| | | | | | | | | | | |
Collapse
|
20
|
Morrison LM, Huang H, Handler HP, Fu M, Bushart DD, Pappas SS, Orr HT, Shakkottai VG. Increased intrinsic membrane excitability is associated with hypertrophic olivary degeneration in spinocerebellar ataxia type 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563657. [PMID: 37961407 PMCID: PMC10634770 DOI: 10.1101/2023.10.23.563657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
One of the characteristic areas of brainstem degeneration across multiple spinocerebellar ataxias (SCAs) is the inferior olive (IO), a medullary nucleus that plays a key role in motor learning. In addition to its vulnerability in SCAs, the IO is also susceptible to a distinct pathology known as hypertrophic olivary degeneration (HOD). Clinically, HOD has been exclusively observed after lesions in the brainstem disrupt inhibitory afferents to the IO. Here, for the first time, we describe HOD in another context: spinocerebellar ataxia type 1 (SCA1). Using the genetically-precise SCA1 knock-in mouse model (SCA1-KI; both sexes used), we assessed SCA1-associated changes in IO neuron structure and function. Concurrent with degeneration, we found that SCA1-KI IO neurons are hypertrophic, exhibiting early dendrite lengthening and later somatic expansion. Unlike in previous descriptions of HOD, we observed no clear loss of IO inhibitory innervation; nevertheless, patch-clamp recordings from brainstem slices reveal that SCA1-KI IO neurons are hyperexcitable. Rather than synaptic disinhibition, we identify increases in intrinsic membrane excitability as the more likely mechanism underlying this novel SCA1 phenotype. Specifically, transcriptome analysis indicates that SCA1-KI IO hyperexcitability is associated with a reduced medullary expression of ion channels responsible for spike afterhyperpolarization (AHP) in IO neurons - a result that has a functional consequence, as SCA1-KI IO neuron spikes exhibit a diminished AHP. These results reveal membrane excitability as a potential link between disparate causes of IO degeneration, suggesting that HOD can result from any cause, intrinsic or extrinsic, that increases excitability of the IO neuron membrane.
Collapse
Affiliation(s)
- Logan M. Morrison
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Haoran Huang
- Medical Scientist Training Program, The Ohio State University, Columbus, OH 43210 USA
- College of Medicine, The Ohio State University, Columbus, OH 43210 USA
| | - Hillary P. Handler
- Molecular Diagnostics Laboratory, University of Minnesota Fairview Medical Center, Minneapolis, MN 55455, USA
| | - Min Fu
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David D. Bushart
- College of Medicine, The Ohio State University, Columbus, OH 43210 USA
| | - Samuel S. Pappas
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Harry T. Orr
- Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Vikram G. Shakkottai
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
21
|
Chartrand T, Dalley R, Close J, Goriounova NA, Lee BR, Mann R, Miller JA, Molnar G, Mukora A, Alfiler L, Baker K, Bakken TE, Berg J, Bertagnolli D, Braun T, Brouner K, Casper T, Csajbok EA, Dee N, Egdorf T, Enstrom R, Galakhova AA, Gary A, Gelfand E, Goldy J, Hadley K, Heistek TS, Hill D, Jorstad N, Kim L, Kocsis AK, Kruse L, Kunst M, Leon G, Long B, Mallory M, McGraw M, McMillen D, Melief EJ, Mihut N, Ng L, Nyhus J, Oláh G, Ozsvár A, Omstead V, Peterfi Z, Pom A, Potekhina L, Rajanbabu R, Rozsa M, Ruiz A, Sandle J, Sunkin SM, Szots I, Tieu M, Toth M, Trinh J, Vargas S, Vumbaco D, Williams G, Wilson J, Yao Z, Barzo P, Cobbs C, Ellenbogen RG, Esposito L, Ferreira M, Gouwens NW, Grannan B, Gwinn RP, Hauptman JS, Jarsky T, Keene CD, Ko AL, Koch C, Ojemann JG, Patel A, Ruzevick J, Silbergeld DL, Smith K, Sorensen SA, Tasic B, Ting JT, Waters J, de Kock CPJ, Mansvelder HD, Tamas G, Zeng H, Kalmbach B, Lein ES. Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex. Science 2023; 382:eadf0805. [PMID: 37824667 DOI: 10.1126/science.adf0805] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 09/09/2023] [Indexed: 10/14/2023]
Abstract
Neocortical layer 1 (L1) is a site of convergence between pyramidal-neuron dendrites and feedback axons where local inhibitory signaling can profoundly shape cortical processing. Evolutionary expansion of human neocortex is marked by distinctive pyramidal neurons with extensive L1 branching, but whether L1 interneurons are similarly diverse is underexplored. Using Patch-seq recordings from human neurosurgical tissue, we identified four transcriptomic subclasses with mouse L1 homologs, along with distinct subtypes and types unmatched in mouse L1. Subclass and subtype comparisons showed stronger transcriptomic differences in human L1 and were correlated with strong morphoelectric variability along dimensions distinct from mouse L1 variability. Accompanied by greater layer thickness and other cytoarchitecture changes, these findings suggest that L1 has diverged in evolution, reflecting the demands of regulating the expanded human neocortical circuit.
Collapse
Affiliation(s)
| | | | - Jennie Close
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Natalia A Goriounova
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, Netherlands
| | - Brian R Lee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Gabor Molnar
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Jim Berg
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Eva Adrienn Csajbok
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Anna A Galakhova
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, Netherlands
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Tim S Heistek
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, Netherlands
| | - DiJon Hill
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nik Jorstad
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Agnes Katalin Kocsis
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Brian Long
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Erica J Melief
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Norbert Mihut
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Gáspár Oláh
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Attila Ozsvár
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | | | - Zoltan Peterfi
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Alice Pom
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Marton Rozsa
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | | | - Joanna Sandle
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | | | - Ildiko Szots
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Martin Toth
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | | | - Sara Vargas
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Julia Wilson
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Pal Barzo
- Department of Neurosurgery, University of Szeged, Szeged, Hungary
| | | | | | | | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Benjamin Grannan
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Jason S Hauptman
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Anoop Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Jacob Ruzevick
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Daniel L Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | | | | | | | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
- Washington National Primate Research Center, University of Washington, Seattle, WA, USA
| | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Christiaan P J de Kock
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, Netherlands
| | - Huib D Mansvelder
- Center for Neurogenomics and Cognitive Research, Vrije Universiteit, Amsterdam, Netherlands
| | - Gabor Tamas
- Research Group for Cortical Microcircuits of the Hungarian Academy of Science, University of Szeged, Szeged, Hungary
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| |
Collapse
|
22
|
Lee BR, Dalley R, Miller JA, Chartrand T, Close J, Mann R, Mukora A, Ng L, Alfiler L, Baker K, Bertagnolli D, Brouner K, Casper T, Csajbok E, Donadio N, Driessens SLW, Egdorf T, Enstrom R, Galakhova AA, Gary A, Gelfand E, Goldy J, Hadley K, Heistek TS, Hill D, Hou WH, Johansen N, Jorstad N, Kim L, Kocsis AK, Kruse L, Kunst M, León G, Long B, Mallory M, Maxwell M, McGraw M, McMillen D, Melief EJ, Molnar G, Mortrud MT, Newman D, Nyhus J, Opitz-Araya X, Ozsvár A, Pham T, Pom A, Potekhina L, Rajanbabu R, Ruiz A, Sunkin SM, Szöts I, Taskin N, Thyagarajan B, Tieu M, Trinh J, Vargas S, Vumbaco D, Waleboer F, Walling-Bell S, Weed N, Williams G, Wilson J, Yao S, Zhou T, Barzó P, Bakken T, Cobbs C, Dee N, Ellenbogen RG, Esposito L, Ferreira M, Gouwens NW, Grannan B, Gwinn RP, Hauptman JS, Hodge R, Jarsky T, Keene CD, Ko AL, Korshoej AR, Levi BP, Meier K, Ojemann JG, Patel A, Ruzevick J, Silbergeld DL, Smith K, Sørensen JC, Waters J, Zeng H, Berg J, Capogna M, Goriounova NA, Kalmbach B, de Kock CPJ, Mansvelder HD, Sorensen SA, Tamas G, Lein ES, Ting JT. Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex. Science 2023; 382:eadf6484. [PMID: 37824669 DOI: 10.1126/science.adf6484] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 09/08/2023] [Indexed: 10/14/2023]
Abstract
Human cortex transcriptomic studies have revealed a hierarchical organization of γ-aminobutyric acid-producing (GABAergic) neurons from subclasses to a high diversity of more granular types. Rapid GABAergic neuron viral genetic labeling plus Patch-seq (patch-clamp electrophysiology plus single-cell RNA sequencing) sampling in human brain slices was used to reliably target and analyze GABAergic neuron subclasses and individual transcriptomic types. This characterization elucidated transitions between PVALB and SST subclasses, revealed morphological heterogeneity within an abundant transcriptomic type, identified multiple spatially distinct types of the primate-specialized double bouquet cells (DBCs), and shed light on cellular differences between homologous mouse and human neocortical GABAergic neuron types. These results highlight the importance of multimodal phenotypic characterization for refinement of emerging transcriptomic cell type taxonomies and for understanding conserved and specialized cellular properties of human brain cell types.
Collapse
Affiliation(s)
- Brian R Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rachel Dalley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Thomas Chartrand
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Jennie Close
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rusty Mann
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Alice Mukora
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lindsay Ng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lauren Alfiler
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Krissy Brouner
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tamara Casper
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Eva Csajbok
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, 6726 Szeged, Hungary
| | | | - Stan L W Driessens
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rachel Enstrom
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Anna A Galakhova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Emily Gelfand
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kristen Hadley
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tim S Heistek
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | - Dijon Hill
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Wen-Hsien Hou
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | | | - Nik Jorstad
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lisa Kim
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Agnes Katalin Kocsis
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, 6726 Szeged, Hungary
| | - Lauren Kruse
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Michael Kunst
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Gabriela León
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Brian Long
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Erica J Melief
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Gabor Molnar
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, 6726 Szeged, Hungary
| | | | - Dakota Newman
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Julie Nyhus
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Attila Ozsvár
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | | | - Alice Pom
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Ram Rajanbabu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Augustin Ruiz
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ildikó Szöts
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, 6726 Szeged, Hungary
| | - Naz Taskin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jessica Trinh
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Sara Vargas
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - David Vumbaco
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Femke Waleboer
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | | | - Natalie Weed
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Grace Williams
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Julia Wilson
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Shenqin Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Thomas Zhou
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Pál Barzó
- Department of Neurosurgery, University of Szeged, 6725 Szeged, Hungary
| | - Trygve Bakken
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Charles Cobbs
- Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Richard G Ellenbogen
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Luke Esposito
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Manuel Ferreira
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | | | - Benjamin Grannan
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Ryder P Gwinn
- Swedish Neuroscience Institute, Seattle, WA 98122, USA
| | - Jason S Hauptman
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Rebecca Hodge
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Andrew L Ko
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | | | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kaare Meier
- Department of Neurosurgery, Aarhus University Hospital, 8200 Aarhus, Denmark
- Department of Anesthesiology, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Anoop Patel
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Jacob Ruzevick
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Daniel L Silbergeld
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Kimberly Smith
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jens Christian Sørensen
- Department of Neurosurgery, Aarhus University Hospital, 8200 Aarhus, Denmark
- Center for Experimental Neuroscience, Aarhus University Hospital, 8200 Aarhus, Denmark
| | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jim Berg
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Allen Institute for Neural Dynamics, Seattle, WA 98109, USA
| | - Marco Capogna
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
| | - Natalia A Goriounova
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| | - Christiaan P J de Kock
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | - Huib D Mansvelder
- Department of Integrative Neurophysiology, Center for Neurogenomics and Cognitive Research (CNCR), Vrije Universiteit, Amsterdam, 1081 HV, Netherlands
| | | | - Gabor Tamas
- MTA-SZTE Research Group for Cortical Microcircuits, Department of Physiology, Anatomy, and Neuroscience, University of Szeged, 6726 Szeged, Hungary
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Jonathan T Ting
- Allen Institute for Brain Science, Seattle, WA 98109, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
23
|
Andrade López JM, Pani AM, Wu M, Gerhart J, Lowe CJ. Molecular characterization of nervous system organization in the hemichordate acorn worm Saccoglossus kowalevskii. PLoS Biol 2023; 21:e3002242. [PMID: 37725784 PMCID: PMC10508912 DOI: 10.1371/journal.pbio.3002242] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/11/2023] [Indexed: 09/21/2023] Open
Abstract
Hemichordates are an important group for investigating the evolution of bilaterian nervous systems. As the closest chordate outgroup with a bilaterally symmetric adult body plan, hemichordates are particularly informative for exploring the origins of chordates. Despite the importance of hemichordate neuroanatomy for testing hypotheses on deuterostome and chordate evolution, adult hemichordate nervous systems have not been comprehensively described using molecular techniques, and classic histological descriptions disagree on basic aspects of nervous system organization. A molecular description of hemichordate nervous system organization is important for both anatomical comparisons across phyla and for attempts to understand how conserved gene regulatory programs for ectodermal patterning relate to morphological evolution in deep time. Here, we describe the basic organization of the adult hemichordate Saccoglossus kowalevskii nervous system using immunofluorescence, in situ hybridization, and transgenic reporters to visualize neurons, neuropil, and key neuronal cell types. Consistent with previous descriptions, we found the S. kowalevskii nervous system consists of a pervasive nerve plexus concentrated in the anterior, along with nerve cords on both the dorsal and ventral side. Neuronal cell types exhibited clear anteroposterior and dorsoventral regionalization in multiple areas of the body. We observed spatially demarcated expression patterns for many genes involved in synthesis or transport of neurotransmitters and neuropeptides but did not observe clear distinctions between putatively centralized and decentralized portions of the nervous system. The plexus shows regionalized structure and is consistent with the proboscis base as a major site for information processing rather than the dorsal nerve cord. In the trunk, there is a clear division of cell types between the dorsal and ventral cords, suggesting differences in function. The absence of neural processes crossing the basement membrane into muscle and extensive axonal varicosities suggest that volume transmission may play an important role in neural function. These data now facilitate more informed neural comparisons between hemichordates and other groups, contributing to broader debates on the origins and evolution of bilaterian nervous systems.
Collapse
Affiliation(s)
- José M. Andrade López
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Ariel M. Pani
- Departments of Biology and Cell Biology, University of Virginia, Charlottesville, Virginia, Unites States of America
| | - Mike Wu
- Department of Molecular and Cell Biology, University of California, Berkeley, California, Unites States of America
| | - John Gerhart
- Department of Molecular and Cell Biology, University of California, Berkeley, California, Unites States of America
| | - Christopher J. Lowe
- Department of Biology, Stanford University, Stanford, California, United States of America
| |
Collapse
|
24
|
Franceschini A, Mazzamuto G, Checcucci C, Chicchi L, Fanelli D, Costantini I, Passani MB, Silva BA, Pavone FS, Silvestri L. Brain-wide neuron quantification toolkit reveals strong sexual dimorphism in the evolution of fear memory. Cell Rep 2023; 42:112908. [PMID: 37516963 DOI: 10.1016/j.celrep.2023.112908] [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: 02/14/2023] [Revised: 06/07/2023] [Accepted: 07/14/2023] [Indexed: 08/01/2023] Open
Abstract
Fear responses are functionally adaptive behaviors that are strengthened as memories. Indeed, detailed knowledge of the neural circuitry modulating fear memory could be the turning point for the comprehension of this emotion and its pathological states. A comprehensive understanding of the circuits mediating memory encoding, consolidation, and retrieval presents the fundamental technological challenge of analyzing activity in the entire brain with single-neuron resolution. In this context, we develop the brain-wide neuron quantification toolkit (BRANT) for mapping whole-brain neuronal activation at micron-scale resolution, combining tissue clearing, high-resolution light-sheet microscopy, and automated image analysis. The robustness and scalability of this method allow us to quantify the evolution of activity patterns across multiple phases of memory in mice. This approach highlights a strong sexual dimorphism in recruited circuits, which has no counterpart in the behavior. The methodology presented here paves the way for a comprehensive characterization of the evolution of fear memory.
Collapse
Affiliation(s)
- Alessandra Franceschini
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy; Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy.
| | - Giacomo Mazzamuto
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy; Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy; National Institute of Optics - National Research Council (CNR-INO), Sesto Fiorentino, Italy
| | - Curzio Checcucci
- Department of Information Engineering (DINFO), University of Florence, Florence, Italy
| | - Lorenzo Chicchi
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
| | - Duccio Fanelli
- Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
| | - Irene Costantini
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy; Department of Biology, University of Florence, Florence, Italy
| | | | - Bianca Ambrogina Silva
- National Research Council of Italy, Institute of Neuroscience, Milan, Italy; IRCCS Humanitas Research Hospital, Lab of Circuits Neuroscience, Rozzano, Milan, Italy
| | - Francesco Saverio Pavone
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy; Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy; National Institute of Optics - National Research Council (CNR-INO), Sesto Fiorentino, Italy
| | - Ludovico Silvestri
- European Laboratory for Non-linear Spectroscopy (LENS), University of Florence, Sesto Fiorentino, Italy; Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy; National Institute of Optics - National Research Council (CNR-INO), Sesto Fiorentino, Italy.
| |
Collapse
|
25
|
Keto L, Manninen T. CellRemorph: A Toolkit for Transforming, Selecting, and Slicing 3D Cell Structures on the Road to Morphologically Detailed Astrocyte Simulations. Neuroinformatics 2023; 21:483-500. [PMID: 37133688 PMCID: PMC10406679 DOI: 10.1007/s12021-023-09627-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2023] [Indexed: 05/04/2023]
Abstract
Understanding functions of astrocytes can be greatly enhanced by building and simulating computational models that capture their morphological details. Novel computational tools enable utilization of existing morphological data of astrocytes and building models that have appropriate level of details for specific simulation purposes. In addition to analyzing existing computational tools for constructing, transforming, and assessing astrocyte morphologies, we present here the CellRemorph toolkit implemented as an add-on for Blender, a 3D modeling platform increasingly recognized for its utility for manipulating 3D biological data. To our knowledge, CellRemorph is the first toolkit for transforming astrocyte morphologies from polygonal surface meshes into adjustable surface point clouds and vice versa, precisely selecting nanoprocesses, and slicing morphologies into segments with equal surface areas or volumes. CellRemorph is an open-source toolkit under the GNU General Public License and easily accessible via an intuitive graphical user interface. CellRemorph will be a valuable addition to other Blender add-ons, providing novel functionality that facilitates the creation of realistic astrocyte morphologies for different types of morphologically detailed simulations elucidating the role of astrocytes both in health and disease.
Collapse
Affiliation(s)
- Laura Keto
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
| | - Tiina Manninen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
| |
Collapse
|
26
|
Ding L, Zhao X, Guo S, Liu Y, Liu L, Wang Y, Peng H. SNAP: a structure-based neuron morphology reconstruction automatic pruning pipeline. Front Neuroinform 2023; 17:1174049. [PMID: 37388757 PMCID: PMC10303825 DOI: 10.3389/fninf.2023.1174049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/22/2023] [Indexed: 07/01/2023] Open
Abstract
Background Neuron morphology analysis is an essential component of neuron cell-type definition. Morphology reconstruction represents a bottleneck in high-throughput morphology analysis workflow, and erroneous extra reconstruction owing to noise and entanglements in dense neuron regions restricts the usability of automated reconstruction results. We propose SNAP, a structure-based neuron morphology reconstruction pruning pipeline, to improve the usability of results by reducing erroneous extra reconstruction and splitting entangled neurons. Methods For the four different types of erroneous extra segments in reconstruction (caused by noise in the background, entanglement with dendrites of close-by neurons, entanglement with axons of other neurons, and entanglement within the same neuron), SNAP incorporates specific statistical structure information into rules for erroneous extra segment detection and achieves pruning and multiple dendrite splitting. Results Experimental results show that this pipeline accomplishes pruning with satisfactory precision and recall. It also demonstrates good multiple neuron-splitting performance. As an effective tool for post-processing reconstruction, SNAP can facilitate neuron morphology analysis.
Collapse
Affiliation(s)
- Liya Ding
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Xuan Zhao
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Shuxia Guo
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Yufeng Liu
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Lijuan Liu
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Yimin Wang
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
- Guangdong Institute of Intelligence Science and Technology, Zhuhai, China
| | - Hanchuan Peng
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| |
Collapse
|
27
|
Schepers M, Malheiro A, Gamardo AS, Hellings N, Prickaerts J, Moroni L, Vanmierlo T, Wieringa P. Phosphodiesterase (PDE) 4 inhibition boosts Schwann cell myelination in a 3D regeneration model. Eur J Pharm Sci 2023; 185:106441. [PMID: 37004962 DOI: 10.1016/j.ejps.2023.106441] [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: 11/16/2022] [Revised: 03/14/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023]
Abstract
Phosphodiesterase 4 (PDE4) inhibitors have been extensively researched for their anti-inflammatory and neuroregenerative properties. Despite the known neuroplastic and myelin regenerative properties of nonselective PDE4 inhibitors on the central nervous system, the direct impact on peripheral remyelination and subsequent neuroregeneration has not yet been investigated. Therefore, to examine the possible therapeutic effect of PDE4 inhibition on peripheral glia, we assessed the differentiation of primary rat Schwann cells exposed in vitro to the PDE4 inhibitor roflumilast. To further investigate the differentiation promoting effects of roflumilast, we developed a 3D model of rat Schwann cell myelination that closely resembles the in vivo situation. Using these in vitro models, we demonstrated that pan-PDE4 inhibition using roflumilast significantly promoted differentiation of Schwann cells towards a myelinating phenotype, as indicated by the upregulation of myelin proteins, including MBP and MAG. Additionally, we created a unique regenerative model comprised of a 3D co-culture of rat Schwann cells and human iPSC-derived neurons. Schwann cells treated with roflumilast enhanced axonal outgrowth of iPSC-derived nociceptive neurons, which was accompanied by an accelerated myelination speed, thereby showing not only phenotypic but also functional changes of roflumilast-treated Schwann cells. Taken together, the PDE4 inhibitor roflumilast possesses a therapeutic benefit to stimulate Schwann cell differentiation and, subsequently myelination, as demonstrated in the biologically relevant in vitro platform used in this study. These results can aid in the development of novel PDE4 inhibition-based therapies in the advancement of peripheral regenerative medicine.
Collapse
Affiliation(s)
- Melissa Schepers
- Department Psychiatry and Neuropsychology, European Graduate School of Neuroscience, School for Mental Health and Neuroscience, Maastricht University, Maastricht, MD 6200, the Netherlands; Biomedical Research Institute, Hasselt University, Hasselt 3500, Belgium; University MS Center (UMSC) Hasselt-Pelt, Hasselt, Belgium
| | - Afonso Malheiro
- MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, the Netherlands
| | - Adrián Seijas Gamardo
- MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, the Netherlands
| | - Niels Hellings
- Biomedical Research Institute, Hasselt University, Hasselt 3500, Belgium; University MS Center (UMSC) Hasselt-Pelt, Hasselt, Belgium
| | - Jos Prickaerts
- Department Psychiatry and Neuropsychology, European Graduate School of Neuroscience, School for Mental Health and Neuroscience, Maastricht University, Maastricht, MD 6200, the Netherlands
| | - Lorenzo Moroni
- MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, the Netherlands
| | - Tim Vanmierlo
- Department Psychiatry and Neuropsychology, European Graduate School of Neuroscience, School for Mental Health and Neuroscience, Maastricht University, Maastricht, MD 6200, the Netherlands; Biomedical Research Institute, Hasselt University, Hasselt 3500, Belgium; University MS Center (UMSC) Hasselt-Pelt, Hasselt, Belgium.
| | - Paul Wieringa
- University MS Center (UMSC) Hasselt-Pelt, Hasselt, Belgium
| |
Collapse
|
28
|
Kim MH, Radaelli C, Thomsen ER, Monet D, Chartrand T, Jorstad NL, Mahoney JT, Taormina MJ, Long B, Baker K, Bakken TE, Campagnola L, Casper T, Clark M, Dee N, D'Orazi F, Gamlin C, Kalmbach BE, Kebede S, Lee BR, Ng L, Trinh J, Cobbs C, Gwinn RP, Keene CD, Ko AL, Ojemann JG, Silbergeld DL, Sorensen SA, Berg J, Smith KA, Nicovich PR, Jarsky T, Zeng H, Ting JT, Levi BP, Lein E. Target cell-specific synaptic dynamics of excitatory to inhibitory neuron connections in supragranular layers of human neocortex. eLife 2023; 12:e81863. [PMID: 37249212 PMCID: PMC10332811 DOI: 10.7554/elife.81863] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 05/29/2023] [Indexed: 05/31/2023] Open
Abstract
Rodent studies have demonstrated that synaptic dynamics from excitatory to inhibitory neuron types are often dependent on the target cell type. However, these target cell-specific properties have not been well investigated in human cortex, where there are major technical challenges in reliably obtaining healthy tissue, conducting multiple patch-clamp recordings on inhibitory cell types, and identifying those cell types. Here, we take advantage of newly developed methods for human neurosurgical tissue analysis with multiple patch-clamp recordings, post-hoc fluorescent in situ hybridization (FISH), machine learning-based cell type classification and prospective GABAergic AAV-based labeling to investigate synaptic properties between pyramidal neurons and PVALB- vs. SST-positive interneurons. We find that there are robust molecular differences in synapse-associated genes between these neuron types, and that individual presynaptic pyramidal neurons evoke postsynaptic responses with heterogeneous synaptic dynamics in different postsynaptic cell types. Using molecular identification with FISH and classifiers based on transcriptomically identified PVALB neurons analyzed by Patch-seq, we find that PVALB neurons typically show depressing synaptic characteristics, whereas other interneuron types including SST-positive neurons show facilitating characteristics. Together, these data support the existence of target cell-specific synaptic properties in human cortex that are similar to rodent, thereby indicating evolutionary conservation of local circuit connectivity motifs from excitatory to inhibitory neurons and their synaptic dynamics.
Collapse
Affiliation(s)
- Mean-Hwan Kim
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | - Deja Monet
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | | | | | - Brian Long
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | | | - Tamara Casper
- Allen Institute for Brain ScienceSeattleUnited States
| | - Michael Clark
- Allen Institute for Brain ScienceSeattleUnited States
| | - Nick Dee
- Allen Institute for Brain ScienceSeattleUnited States
| | | | - Clare Gamlin
- Allen Institute for Brain ScienceSeattleUnited States
| | - Brian E Kalmbach
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Physiology & Biophysics, School of Medicine, University of WashingtonSeattleUnited States
| | - Sara Kebede
- Allen Institute for Brain ScienceSeattleUnited States
| | - Brian R Lee
- Allen Institute for Brain ScienceSeattleUnited States
| | - Lindsay Ng
- Allen Institute for Brain ScienceSeattleUnited States
| | - Jessica Trinh
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | - C Dirk Keene
- Department of Laboratory Medicine & Pathology, School of Medicine, University of WashingtonSeattleUnited States
| | - Andrew L Ko
- Department of Neurological Surgery, School of Medicine, University of WashingtonSeattleUnited States
| | - Jeffrey G Ojemann
- Department of Neurological Surgery, School of Medicine, University of WashingtonSeattleUnited States
| | - Daniel L Silbergeld
- Department of Neurological Surgery, School of Medicine, University of WashingtonSeattleUnited States
| | | | - Jim Berg
- Allen Institute for Brain ScienceSeattleUnited States
| | | | | | - Tim Jarsky
- Allen Institute for Brain ScienceSeattleUnited States
| | - Hongkui Zeng
- Allen Institute for Brain ScienceSeattleUnited States
| | - Jonathan T Ting
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Physiology & Biophysics, School of Medicine, University of WashingtonSeattleUnited States
| | - Boaz P Levi
- Allen Institute for Brain ScienceSeattleUnited States
| | - Ed Lein
- Allen Institute for Brain ScienceSeattleUnited States
- Department of Laboratory Medicine & Pathology, School of Medicine, University of WashingtonSeattleUnited States
- Department of Neurological Surgery, School of Medicine, University of WashingtonSeattleUnited States
| |
Collapse
|
29
|
Yasuhiko O, Takeuchi K. In-silico clearing approach for deep refractive index tomography by partial reconstruction and wave-backpropagation. LIGHT, SCIENCE & APPLICATIONS 2023; 12:101. [PMID: 37105955 PMCID: PMC10140380 DOI: 10.1038/s41377-023-01144-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 03/08/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Refractive index (RI) is considered to be a fundamental physical and biophysical parameter in biological imaging, as it governs light-matter interactions and light propagation while reflecting cellular properties. RI tomography enables volumetric visualization of RI distribution, allowing biologically relevant analysis of a sample. However, multiple scattering (MS) and sample-induced aberration (SIA) caused by the inhomogeneity in RI distribution of a thick sample make its visualization challenging. This paper proposes a deep RI tomographic approach to overcome MS and SIA and allow the enhanced reconstruction of thick samples compared to that enabled by conventional linear-model-based RI tomography. The proposed approach consists of partial RI reconstruction using multiple holograms acquired with angular diversity and their backpropagation using the reconstructed partial RI map, which unambiguously reconstructs the next partial volume. Repeating this operation efficiently reconstructs the entire RI tomogram while suppressing MS and SIA. We visualized a multicellular spheroid of diameter 140 µm within minutes of reconstruction, thereby demonstrating the enhanced deep visualization capability and computational efficiency of the proposed method compared to those of conventional RI tomography. Furthermore, we quantified the high-RI structures and morphological changes inside multicellular spheroids, indicating that the proposed method can retrieve biologically relevant information from the RI distribution. Benefitting from the excellent biological interpretability of RI distributions, the label-free deep visualization capability of the proposed method facilitates a noninvasive understanding of the architecture and time-course morphological changes of thick multicellular specimens.
Collapse
Affiliation(s)
- Osamu Yasuhiko
- Central Research Laboratory, Hamamatsu Photonics K.K, 5000 Hirakuchi, Hamakita-ku, Hamamatsu, 434-8601, Shizuoka, Japan.
| | - Kozo Takeuchi
- Central Research Laboratory, Hamamatsu Photonics K.K, 5000 Hirakuchi, Hamakita-ku, Hamamatsu, 434-8601, Shizuoka, Japan.
| |
Collapse
|
30
|
Guo C, Zhang Y, Shuai S, Sigbessia A, Hao S, Xie P, Jiang X, Luo Z, Lin C. The super elongation complex (SEC) mediates phase transition of SPT5 during transcriptional pause release. EMBO Rep 2023; 24:e55699. [PMID: 36629390 PMCID: PMC9986819 DOI: 10.15252/embr.202255699] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 01/12/2023] Open
Abstract
Release of promoter-proximally paused RNA Pol II into elongation is a tightly regulated and rate-limiting step in metazoan gene transcription. However, the biophysical mechanism underlying pause release remains unclear. Here, we demonstrate that the pausing and elongation regulator SPT5 undergoes phase transition during transcriptional pause release. SPT5 per se is prone to form clusters. The disordered domain in SPT5 is required for pause release and gene activation. During early elongation, the super elongation complex (SEC) induces SPT5 transition into elongation droplets. Depletion of SEC increases SPT5 pausing clusters. Furthermore, disease-associated SEC mutations impair phase properties of elongation droplets and transcription. Our study suggests that SEC-mediated SPT5 phase transition might be essential for pause release and early elongation and that aberrant phase properties could contribute to transcription abnormality in diseases.
Collapse
Affiliation(s)
- Chenghao Guo
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
- Co‐innovation Center of NeuroregenerationNantong UniversityNantongChina
| | - Yadi Zhang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Shimin Shuai
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Abire Sigbessia
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Shaohua Hao
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Peng Xie
- Southeast University‐Allen Institute Joint Center, Institute for Brain and IntelligenceSoutheast UniversityNanjingChina
| | - Xu Jiang
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Zhuojuan Luo
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
- Co‐innovation Center of NeuroregenerationNantong UniversityNantongChina
- Shenzhen Research InstituteSoutheast UniversityShenzhenChina
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Life Science and TechnologySoutheast UniversityNanjingChina
| | - Chengqi Lin
- Key Laboratory of Developmental Genes and Human Disease, School of Life Science and TechnologySoutheast UniversityNanjingChina
- Co‐innovation Center of NeuroregenerationNantong UniversityNantongChina
- Shenzhen Research InstituteSoutheast UniversityShenzhenChina
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, School of Life Science and TechnologySoutheast UniversityNanjingChina
- Key Laboratory of Technical Evaluation of Fertility Regulation of Non‐human primate, Fujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| |
Collapse
|
31
|
Schepers M, Paes D, Tiane A, Rombaut B, Piccart E, van Veggel L, Gervois P, Wolfs E, Lambrichts I, Brullo C, Bruno O, Fedele E, Ricciarelli R, Ffrench-Constant C, Bechler ME, van Schaik P, Baron W, Lefevere E, Wasner K, Grünewald A, Verfaillie C, Baeten P, Broux B, Wieringa P, Hellings N, Prickaerts J, Vanmierlo T. Selective PDE4 subtype inhibition provides new opportunities to intervene in neuroinflammatory versus myelin damaging hallmarks of multiple sclerosis. Brain Behav Immun 2023; 109:1-22. [PMID: 36584795 DOI: 10.1016/j.bbi.2022.12.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/17/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system (CNS) characterized by focal inflammatory lesions and prominent demyelination. Even though the currently available therapies are effective in treating the initial stages of disease, they are unable to halt or reverse disease progression into the chronic progressive stage. Thus far, no repair-inducing treatments are available for progressive MS patients. Hence, there is an urgent need for the development of new therapeutic strategies either targeting the destructive immunological demyelination or boosting endogenous repair mechanisms. Using in vitro, ex vivo, and in vivo models, we demonstrate that selective inhibition of phosphodiesterase 4 (PDE4), a family of enzymes that hydrolyzes and inactivates cyclic adenosine monophosphate (cAMP), reduces inflammation and promotes myelin repair. More specifically, we segregated the myelination-promoting and anti-inflammatory effects into a PDE4D- and PDE4B-dependent process respectively. We show that inhibition of PDE4D boosts oligodendrocyte progenitor cells (OPC) differentiation and enhances (re)myelination of both murine OPCs and human iPSC-derived OPCs. In addition, PDE4D inhibition promotes in vivo remyelination in the cuprizone model, which is accompanied by improved spatial memory and reduced visual evoked potential latency times. We further identified that PDE4B-specific inhibition exerts anti-inflammatory effects since it lowers in vitro monocytic nitric oxide (NO) production and improves in vivo neurological scores during the early phase of experimental autoimmune encephalomyelitis (EAE). In contrast to the pan PDE4 inhibitor roflumilast, the therapeutic dose of both the PDE4B-specific inhibitor A33 and the PDE4D-specific inhibitor Gebr32a did not trigger emesis-like side effects in rodents. Finally, we report distinct PDE4D isoform expression patterns in human area postrema neurons and human oligodendroglia lineage cells. Using the CRISPR-Cas9 system, we confirmed that pde4d1/2 and pde4d6 are the key targets to induce OPC differentiation. Collectively, these data demonstrate that gene specific PDE4 inhibitors have potential as novel therapeutic agents for targeting the distinct disease processes of MS.
Collapse
Affiliation(s)
- Melissa Schepers
- Department of Neuroscience, Biomedical Research Institute, Faculty of Medicine and Life Sciences, Hasselt University, Diepenbeek, Belgium; Department Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands; University MS Center (UMSC) Hasselt-Pelt, Hasselt, Belgium
| | - Dean Paes
- Department of Neuroscience, Biomedical Research Institute, Faculty of Medicine and Life Sciences, Hasselt University, Diepenbeek, Belgium; Department Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Assia Tiane
- Department of Neuroscience, Biomedical Research Institute, Faculty of Medicine and Life Sciences, Hasselt University, Diepenbeek, Belgium; Department Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands; University MS Center (UMSC) Hasselt-Pelt, Hasselt, Belgium
| | - Ben Rombaut
- Department of Neuroscience, Biomedical Research Institute, Faculty of Medicine and Life Sciences, Hasselt University, Diepenbeek, Belgium; Department Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Elisabeth Piccart
- Department of Neuroscience, Biomedical Research Institute, Faculty of Medicine and Life Sciences, Hasselt University, Diepenbeek, Belgium
| | - Lieve van Veggel
- Department of Neuroscience, Biomedical Research Institute, Faculty of Medicine and Life Sciences, Hasselt University, Diepenbeek, Belgium; Department Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands; University MS Center (UMSC) Hasselt-Pelt, Hasselt, Belgium
| | - Pascal Gervois
- Department of Cardio and Organ Systems, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Esther Wolfs
- Department of Cardio and Organ Systems, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Ivo Lambrichts
- Department of Cardio and Organ Systems, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Chiara Brullo
- Department of Pharmacy, Section of Medicinal Chemistry, University of Genoa, Genova, Italy
| | - Olga Bruno
- Department of Pharmacy, Section of Medicinal Chemistry, University of Genoa, Genova, Italy
| | - Ernesto Fedele
- Department of Pharmacy, Section of Pharmacology and Toxicology, University of Genova, Genova, Italy; IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Roberta Ricciarelli
- IRCCS Ospedale Policlinico San Martino, Genova, Italy; Department of Experimental Medicine, Section of General Pathology, University of Genova, Genova, Italy
| | - Charles Ffrench-Constant
- MRC Centre for Regenerative Medicine and MS Society Edinburgh Centre, Edinburgh bioQuarter, University of Edinburgh, Edinburgh, UK
| | - Marie E Bechler
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Pauline van Schaik
- Department of Biomedical Sciences of Cells and Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Wia Baron
- Department of Biomedical Sciences of Cells and Systems, Section Molecular Neurobiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Evy Lefevere
- Rewind Therapeutics NV, Gaston Geenslaan 2, B-3001, Leuven, Belgium
| | - Kobi Wasner
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Anne Grünewald
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Catherine Verfaillie
- Stem Cell Institute, Department of Development and Regeneration, KU Leuven, Belgium
| | - Paulien Baeten
- University MS Center (UMSC) Hasselt-Pelt, Hasselt, Belgium; Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Bieke Broux
- University MS Center (UMSC) Hasselt-Pelt, Hasselt, Belgium; Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Paul Wieringa
- MERLN Institute for Technology-Inspired Regenerative Medicine, Complex Tissue Regeneration department, Maastricht University, Maastricht, the Netherlands
| | - Niels Hellings
- University MS Center (UMSC) Hasselt-Pelt, Hasselt, Belgium; Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Jos Prickaerts
- Department Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Tim Vanmierlo
- Department of Neuroscience, Biomedical Research Institute, Faculty of Medicine and Life Sciences, Hasselt University, Diepenbeek, Belgium; Department Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University, Maastricht, Netherlands; University MS Center (UMSC) Hasselt-Pelt, Hasselt, Belgium.
| |
Collapse
|
32
|
Wills JW, Robertson J, Tourlomousis P, Gillis CM, Barnes CM, Miniter M, Hewitt RE, Bryant CE, Summers HD, Powell JJ, Rees P. Label-free cell segmentation of diverse lymphoid tissues in 2D and 3D. CELL REPORTS METHODS 2023; 3:100398. [PMID: 36936072 PMCID: PMC10014308 DOI: 10.1016/j.crmeth.2023.100398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 10/14/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
Unlocking and quantifying fundamental biological processes through tissue microscopy requires accurate, in situ segmentation of all cells imaged. Currently, achieving this is complex and requires exogenous fluorescent labels that occupy significant spectral bandwidth, increasing the duration and complexity of imaging experiments while limiting the number of channels remaining to address the study's objectives. We demonstrate that the excitation light reflected during routine confocal microscopy contains sufficient information to achieve accurate, label-free cell segmentation in 2D and 3D. This is achieved using a simple convolutional neural network trained to predict the probability that reflected light pixels belong to either nucleus, cytoskeleton, or background classifications. We demonstrate the approach across diverse lymphoid tissues and provide video tutorials demonstrating deployment in Python and MATLAB or via standalone software for Windows.
Collapse
Affiliation(s)
- John W. Wills
- Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
- Department of Biomedical Engineering, Swansea University, Fabian Way, Crymlyn Burrows, Swansea SA1 8EN, Wales, UK
| | - Jack Robertson
- Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | - Pani Tourlomousis
- Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | - Clare M.C. Gillis
- Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | - Claire M. Barnes
- Department of Biomedical Engineering, Swansea University, Fabian Way, Crymlyn Burrows, Swansea SA1 8EN, Wales, UK
| | - Michelle Miniter
- Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | - Rachel E. Hewitt
- Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | - Clare E. Bryant
- Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | - Huw D. Summers
- Department of Biomedical Engineering, Swansea University, Fabian Way, Crymlyn Burrows, Swansea SA1 8EN, Wales, UK
| | - Jonathan J. Powell
- Department of Veterinary Medicine, Cambridge University, Madingley Road, Cambridge CB3 0ES, UK
| | - Paul Rees
- Department of Biomedical Engineering, Swansea University, Fabian Way, Crymlyn Burrows, Swansea SA1 8EN, Wales, UK
- Imaging Platform, Broad Institute of MIT and Harvard, 415 Main Street, Boston, Cambridge, MA 02142, USA
| |
Collapse
|
33
|
Wei X, Liu Q, Liu M, Wang Y, Meijering E. 3D Soma Detection in Large-Scale Whole Brain Images via a Two-Stage Neural Network. IEEE TRANSACTIONS ON MEDICAL IMAGING 2023; 42:148-157. [PMID: 36103445 DOI: 10.1109/tmi.2022.3206605] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
3D soma detection in whole brain images is a critical step for neuron reconstruction. However, existing soma detection methods are not suitable for whole mouse brain images with large amounts of data and complex structure. In this paper, we propose a two-stage deep neural network to achieve fast and accurate soma detection in large-scale and high-resolution whole mouse brain images (more than 1TB). For the first stage, a lightweight Multi-level Cross Classification Network (MCC-Net) is proposed to filter out images without somas and generate coarse candidate images by combining the advantages of the multi convolution layer's feature extraction ability. It can speed up the detection of somas and reduce the computational complexity. For the second stage, to further obtain the accurate locations of somas in the whole mouse brain images, the Scale Fusion Segmentation Network (SFS-Net) is developed to segment soma regions from candidate images. Specifically, the SFS-Net captures multi-scale context information and establishes a complementary relationship between encoder and decoder by combining the encoder-decoder structure and a 3D Scale-Aware Pyramid Fusion (SAPF) module for better segmentation performance. The experimental results on three whole mouse brain images verify that the proposed method can achieve excellent performance and provide the reconstruction of neurons with beneficial information. Additionally, we have established a public dataset named WBMSD, including 798 high-resolution and representative images ( 256 ×256 ×256 voxels) from three whole mouse brain images, dedicated to the research of soma detection, which will be released along with this paper.
Collapse
|
34
|
IMAGE-IN: Interactive web-based multidimensional 3D visualizer for multi-modal microscopy images. PLoS One 2022; 17:e0279825. [PMID: 36584152 PMCID: PMC9803232 DOI: 10.1371/journal.pone.0279825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/14/2022] [Indexed: 12/31/2022] Open
Abstract
Advances in microscopy hardware and storage capabilities lead to increasingly larger multidimensional datasets. The multiple dimensions are commonly associated with space, time, and color channels. Since "seeing is believing", it is important to have easy access to user-friendly visualization software. Here we present IMAGE-IN, an interactive web-based multidimensional (N-D) viewer designed specifically for confocal laser scanning microscopy (CLSM) and focused ion beam scanning electron microscopy (FIB-SEM) data, with the goal of assisting biologists in their visualization and analysis tasks and promoting digital workflows. This new visualization platform includes intuitive multidimensional opacity fine-tuning, shading on/off, multiple blending modes for volume viewers, and the ability to handle multichannel volumetric data in volume and surface views. The software accepts a sequence of image files or stacked 3D images as input and offers a variety of viewing options ranging from 3D volume/surface rendering to multiplanar reconstruction approaches. We evaluate the performance by comparing the loading and rendering timings of a heterogeneous dataset of multichannel CLSM and FIB-SEM images on two devices with installed graphic cards, as well as comparing rendered image quality between ClearVolume (the ImageJ open-source desktop viewer), Napari (the Python desktop viewer), Imaris (the closed-source desktop viewer), and our proposed IMAGE-IN web viewer.
Collapse
|
35
|
Liu Y, Wang G, Ascoli GA, Zhou J, Liu L. Neuron tracing from light microscopy images: automation, deep learning and bench testing. Bioinformatics 2022; 38:5329-5339. [PMID: 36303315 PMCID: PMC9750132 DOI: 10.1093/bioinformatics/btac712] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/19/2022] [Accepted: 10/26/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Large-scale neuronal morphologies are essential to neuronal typing, connectivity characterization and brain modeling. It is widely accepted that automation is critical to the production of neuronal morphology. Despite previous survey papers about neuron tracing from light microscopy data in the last decade, thanks to the rapid development of the field, there is a need to update recent progress in a review focusing on new methods and remarkable applications. RESULTS This review outlines neuron tracing in various scenarios with the goal to help the community understand and navigate tools and resources. We describe the status, examples and accessibility of automatic neuron tracing. We survey recent advances of the increasingly popular deep-learning enhanced methods. We highlight the semi-automatic methods for single neuron tracing of mammalian whole brains as well as the resulting datasets, each containing thousands of full neuron morphologies. Finally, we exemplify the commonly used datasets and metrics for neuron tracing bench testing.
Collapse
Affiliation(s)
- Yufeng Liu
- School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Gaoyu Wang
- School of Computer Science and Engineering, Southeast University, Nanjing, China
| | - Giorgio A Ascoli
- Center for Neural Informatics, Structures, & Plasticity, Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, USA
| | - Jiangning Zhou
- Institute of Brain Science, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lijuan Liu
- School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| |
Collapse
|
36
|
Yayon N, Amsalem O, Zorbaz T, Yakov O, Dubnov S, Winek K, Dudai A, Adam G, Schmidtner AK, Tessier‐Lavigne M, Renier N, Habib N, Segev I, London M, Soreq H. High-throughput morphometric and transcriptomic profiling uncovers composition of naïve and sensory-deprived cortical cholinergic VIP/CHAT neurons. EMBO J 2022; 42:e110565. [PMID: 36377476 PMCID: PMC9811618 DOI: 10.15252/embj.2021110565] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 10/03/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Cortical neuronal networks control cognitive output, but their composition and modulation remain elusive. Here, we studied the morphological and transcriptional diversity of cortical cholinergic VIP/ChAT interneurons (VChIs), a sparse population with a largely unknown function. We focused on VChIs from the whole barrel cortex and developed a high-throughput automated reconstruction framework, termed PopRec, to characterize hundreds of VChIs from each mouse in an unbiased manner, while preserving 3D cortical coordinates in multiple cleared mouse brains, accumulating thousands of cells. We identified two fundamentally distinct morphological types of VChIs, bipolar and multipolar that differ in their cortical distribution and general morphological features. Following mild unilateral whisker deprivation on postnatal day seven, we found after three weeks both ipsi- and contralateral dendritic arborization differences and modified cortical depth and distribution patterns in the barrel fields alone. To seek the transcriptomic drivers, we developed NuNeX, a method for isolating nuclei from fixed tissues, to explore sorted VChIs. This highlighted differentially expressed neuronal structural transcripts, altered exitatory innervation pathways and established Elmo1 as a key regulator of morphology following deprivation.
Collapse
Affiliation(s)
- Nadav Yayon
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael,The Department of Biological Chemistry, The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael
| | - Oren Amsalem
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael,The Department of Neurobiology, The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael
| | - Tamara Zorbaz
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael,The Department of Biological Chemistry, The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael,Biochemistry and Organic Analytical Chemistry UnitThe Institute of Medical Research and Occupational HealthZagrebCroatia
| | - Or Yakov
- The Department of Biological Chemistry, The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael
| | - Serafima Dubnov
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael,The Department of Biological Chemistry, The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael
| | - Katarzyna Winek
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael,The Department of Biological Chemistry, The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael
| | - Amir Dudai
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael,The Department of Neurobiology, The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael
| | - Gil Adam
- The Department of Biological Chemistry, The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael
| | - Anna K Schmidtner
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael
| | | | - Nicolas Renier
- Sorbonne Université, Paris Brain Institute ‐ ICM, INSERM, CNRS, AP‐HP, Hôpital de la Pitié SalpêtrièreParisFrance
| | - Naomi Habib
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael,The Department of Neurobiology, The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael
| | - Idan Segev
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael,The Department of Neurobiology, The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael
| | - Michael London
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael,The Department of Neurobiology, The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael
| | - Hermona Soreq
- The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael,The Department of Biological Chemistry, The Life Sciences InstituteThe Hebrew University of JerusalemJerusalemIsrael
| |
Collapse
|
37
|
Vanherle S, Jorissen W, Dierckx T, Loix M, Grajchen E, Mingneau F, Guns J, Gervois P, Lambrichts I, Dehairs J, Swinnen JV, Mulder MT, Remaley AT, Haidar M, Hendriks JJ, Bogie JJ. The ApoA-I mimetic peptide 5A enhances remyelination by promoting clearance and degradation of myelin debris. Cell Rep 2022; 41:111591. [DOI: 10.1016/j.celrep.2022.111591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/09/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022] Open
|
38
|
Zhou W, Ke S, Li W, Yuan J, Li X, Jin R, Jia X, Jiang T, Dai Z, He G, Fang Z, Shi L, Zhang Q, Gong H, Luo Q, Sun W, Li A, Li P. Mapping the Function of Whole-Brain Projection at the Single Neuron Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2202553. [PMID: 36228099 PMCID: PMC9685445 DOI: 10.1002/advs.202202553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/18/2022] [Indexed: 06/16/2023]
Abstract
Axonal projection conveys neural information. The divergent and diverse projections of individual neurons imply the complexity of information flow. It is necessary to investigate the relationship between the projection and functional information at the single neuron level for understanding the rules of neural circuit assembly, but a gap remains due to a lack of methods to map the function to whole-brain projection. Here an approach is developed to bridge two-photon calcium imaging in vivo with high-resolution whole-brain imaging based on sparse labeling with the genetically encoded calcium indicator GCaMP6. Reliable whole-brain projections are captured by the high-definition fluorescent micro-optical sectioning tomography (HD-fMOST). A cross-modality cell matching is performed and the functional annotation of whole-brain projection at the single-neuron level (FAWPS) is obtained. Applying it to the layer 2/3 (L2/3) neurons in mouse visual cortex, the relationship is investigated between functional preferences and axonal projection features. The functional preference of projection motifs and the correlation between axonal length in MOs and neuronal orientation selectivity, suggest that projection motif-defined neurons form a functionally specific information flow, and the projection strength in specific targets relates to the information clarity. This pipeline provides a new way to understand the principle of neuronal information transmission.
Collapse
Affiliation(s)
- Wei Zhou
- Britton Chance Center and MoE Key Laboratory for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and ImagingChinese Academy of Medical SciencesHUST‐Suzhou Institute for BrainsmaticsJITRISuzhou215100China
| | - Shanshan Ke
- Britton Chance Center and MoE Key Laboratory for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and ImagingChinese Academy of Medical SciencesHUST‐Suzhou Institute for BrainsmaticsJITRISuzhou215100China
| | - Wenwei Li
- Britton Chance Center and MoE Key Laboratory for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and ImagingChinese Academy of Medical SciencesHUST‐Suzhou Institute for BrainsmaticsJITRISuzhou215100China
| | - Jing Yuan
- Britton Chance Center and MoE Key Laboratory for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and ImagingChinese Academy of Medical SciencesHUST‐Suzhou Institute for BrainsmaticsJITRISuzhou215100China
| | - Xiangning Li
- Britton Chance Center and MoE Key Laboratory for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and ImagingChinese Academy of Medical SciencesHUST‐Suzhou Institute for BrainsmaticsJITRISuzhou215100China
| | - Rui Jin
- Britton Chance Center and MoE Key Laboratory for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and ImagingChinese Academy of Medical SciencesHUST‐Suzhou Institute for BrainsmaticsJITRISuzhou215100China
| | - Xueyan Jia
- Research Unit of Multimodal Cross Scale Neural Signal Detection and ImagingChinese Academy of Medical SciencesHUST‐Suzhou Institute for BrainsmaticsJITRISuzhou215100China
| | - Tao Jiang
- Research Unit of Multimodal Cross Scale Neural Signal Detection and ImagingChinese Academy of Medical SciencesHUST‐Suzhou Institute for BrainsmaticsJITRISuzhou215100China
| | - Zimin Dai
- Britton Chance Center and MoE Key Laboratory for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and ImagingChinese Academy of Medical SciencesHUST‐Suzhou Institute for BrainsmaticsJITRISuzhou215100China
| | - Guannan He
- Britton Chance Center and MoE Key Laboratory for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and ImagingChinese Academy of Medical SciencesHUST‐Suzhou Institute for BrainsmaticsJITRISuzhou215100China
| | - Zhiwei Fang
- Britton Chance Center and MoE Key Laboratory for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and ImagingChinese Academy of Medical SciencesHUST‐Suzhou Institute for BrainsmaticsJITRISuzhou215100China
| | - Liang Shi
- Britton Chance Center and MoE Key Laboratory for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and ImagingChinese Academy of Medical SciencesHUST‐Suzhou Institute for BrainsmaticsJITRISuzhou215100China
| | - Qi Zhang
- Britton Chance Center and MoE Key Laboratory for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
| | - Hui Gong
- Britton Chance Center and MoE Key Laboratory for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and ImagingChinese Academy of Medical SciencesHUST‐Suzhou Institute for BrainsmaticsJITRISuzhou215100China
| | - Qingming Luo
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical EngineeringHainan UniversityHaikou570228China
| | - Wenzhi Sun
- Chinese Institute for Brain ResearchBeijing102206China
- School of Basic Medical SciencesCapital Medical UniversityBeijing100069China
| | - Anan Li
- Britton Chance Center and MoE Key Laboratory for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and ImagingChinese Academy of Medical SciencesHUST‐Suzhou Institute for BrainsmaticsJITRISuzhou215100China
| | - Pengcheng Li
- Britton Chance Center and MoE Key Laboratory for Biomedical PhotonicsWuhan National Laboratory for OptoelectronicsHuazhong University of Science and TechnologyWuhan430074China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and ImagingChinese Academy of Medical SciencesHUST‐Suzhou Institute for BrainsmaticsJITRISuzhou215100China
| |
Collapse
|
39
|
Haidar M, Loix M, Vanherle S, Dierckx T, Vangansewinkel T, Gervois P, Wolfs E, Lambrichts I, Bogie JFJ, Hendriks JJA. Targeting lipophagy in macrophages improves repair in multiple sclerosis. Autophagy 2022; 18:2697-2710. [PMID: 35282773 PMCID: PMC9629102 DOI: 10.1080/15548627.2022.2047343] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Foamy macrophages containing abundant intracellular myelin remnants are an important pathological hallmark of multiple sclerosis. Reducing the intracellular lipid burden in foamy macrophages is considered a promising therapeutic strategy to induce a phagocyte phenotype that promotes central nervous system repair. Recent research from our group showed that sustained intracellular accumulation of myelin-derived lipids skews these phagocytes toward a disease-promoting and more inflammatory phenotype. Our data now demonstrate that disturbed lipophagy, a selective form of autophagy that helps with the degradation of lipid droplets, contributes to the induction of this phenotype. Stimulating autophagy using the natural disaccharide trehalose reduced the lipid load and inflammatory phenotype of myelin-laden macrophages. Importantly, trehalose was able to boost remyelination in the ex vivo brain slice model and the in vivo cuprizone-induced demyelination model. In summary, our results provide a molecular rationale for impaired metabolism of myelin-derived lipids in macrophages, and identify lipophagy induction as a promising treatment strategy to promote remyelination.Abbreviations: Baf: bafilomycin a1; BMDM: bone marrow-derived macrophage; CD68: CD68 antigen; CNS: central nervous system; LD: lipid droplet; LIPE/HSL: lipase, hormone sensitive; LPS: lipopolysaccharide; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MBP: myelin basic protein; MGLL: monoglyceride lipase; MS: multiple sclerosis; NO: nitric oxide; NOS2/iNOS: nitric oxide synthase 2, inducible; ORO: oil red o; PNPLA2: patatin-like phospholipase domain containing 2; PLIN2: perilipin 2; TEM: transmission electron microscopy; TFEB: transcription factor EB; TOH: trehalose.
Collapse
Affiliation(s)
- Mansour Haidar
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Melanie Loix
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Sam Vanherle
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Tess Dierckx
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Tim Vangansewinkel
- Department of Cardio and Organs Systems, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Pascal Gervois
- Department of Cardio and Organs Systems, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Esther Wolfs
- Department of Cardio and Organs Systems, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Ivo Lambrichts
- Department of Cardio and Organs Systems, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Jeroen F J Bogie
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Jerome J A Hendriks
- Department of Immunology and Infection, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| |
Collapse
|
40
|
Nandi A, Chartrand T, Van Geit W, Buchin A, Yao Z, Lee SY, Wei Y, Kalmbach B, Lee B, Lein E, Berg J, Sümbül U, Koch C, Tasic B, Anastassiou CA. Single-neuron models linking electrophysiology, morphology, and transcriptomics across cortical cell types. Cell Rep 2022; 40:111176. [PMID: 35947954 PMCID: PMC9793758 DOI: 10.1016/j.celrep.2022.111176] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 01/28/2022] [Accepted: 07/18/2022] [Indexed: 12/30/2022] Open
Abstract
Which cell types constitute brain circuits is a fundamental question, but establishing the correspondence across cellular data modalities is challenging. Bio-realistic models allow probing cause-and-effect and linking seemingly disparate modalities. Here, we introduce a computational optimization workflow to generate 9,200 single-neuron models with active conductances. These models are based on 230 in vitro electrophysiological experiments followed by morphological reconstruction from the mouse visual cortex. We show that, in contrast to current belief, the generated models are robust representations of individual experiments and cortical cell types as defined via cellular electrophysiology or transcriptomics. Next, we show that differences in specific conductances predicted from the models reflect differences in gene expression supported by single-cell transcriptomics. The differences in model conductances, in turn, explain electrophysiological differences observed between the cortical subclasses. Our computational effort reconciles single-cell modalities that define cell types and enables causal relationships to be examined.
Collapse
Affiliation(s)
- Anirban Nandi
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Thomas Chartrand
- Allen Institute for Brain Science, Seattle, WA 98109, USA,These authors contributed equally
| | - Werner Van Geit
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Campus Biotech, Geneva 1202, Switzerland,These authors contributed equally
| | - Anatoly Buchin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Soo Yeun Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Yina Wei
- Allen Institute for Brain Science, Seattle, WA 98109, USA,Zhejiang Lab, Hangzhou City, Zhejiang Province 311121, China
| | - Brian Kalmbach
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Brian Lee
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jim Berg
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Uygar Sümbül
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Christof Koch
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Costas A. Anastassiou
- Allen Institute for Brain Science, Seattle, WA 98109, USA,Department of Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA,Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA,Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA,Center for Neural Science and Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA,Lead contact,Correspondence:
| |
Collapse
|
41
|
nGauge: Integrated and Extensible Neuron Morphology Analysis in Python. Neuroinformatics 2022; 20:755-764. [PMID: 35247136 PMCID: PMC9720862 DOI: 10.1007/s12021-022-09573-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2022] [Indexed: 12/31/2022]
Abstract
The study of neuron morphology requires robust and comprehensive methods to quantify the differences between neurons of different subtypes and animal species. Several software packages have been developed for the analysis of neuron tracing results stored in the standard SWC format. The packages, however, provide relatively simple quantifications and their non-extendable architecture prohibit their use for advanced data analysis and visualization. We developed nGauge, a Python toolkit to support the parsing and analysis of neuron morphology data. As an application programming interface (API), nGauge can be referenced by other popular open-source software to create custom informatics analysis pipelines and advanced visualizations. nGauge defines an extendable data structure that handles volumetric constructions (e.g. soma), in addition to the SWC linear reconstructions, while remaining lightweight. This greatly extends nGauge's data compatibility.
Collapse
|
42
|
Three-Dimensional Imaging of Circular Array Synthetic Aperture Sonar for Unmanned Surface Vehicle. SENSORS 2022; 22:s22103797. [PMID: 35632206 PMCID: PMC9147049 DOI: 10.3390/s22103797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/13/2022] [Accepted: 05/15/2022] [Indexed: 02/01/2023]
Abstract
Synthetic aperture sonar (SAS) and interferometric synthetic aperture sonar (InSAS) have a range layover phenomenon during underwater observation, the AUV-mounted circular synthetic aperture sonar (CSAS) system, that insonifies targets using multiple circular scans that vary in height and can eliminate the layover phenomenon. However, this observation method is time-consuming and difficult to compensate. To solve this problem, the circular array synthetic aperture sonar (CASAS) based on the equivalent phase center was established for unmanned surface vehicles. Corresponding to the echo signal model of circular array synthetic aperture sonar, a novel three-dimensional imaging algorithm was derived. Firstly, the echo datacube was processed by signal calibration with near-field to far-field transformation and grid interpolation. Then, the sparse recover method was adopted to achieve the scattering coefficient in the height direction by sparse Bayesian learning. Thirdly, the Fourier slice theorem was adopted to obtain the 2D image of the ground plane. After the reconstruction of all height slice cells was accomplished, the final 3D image was obtained. Numerical simulations and experiments using the USV-mounted CASAS system were performed. The imaging results verify the effectiveness of the 3D imaging algorithm for the proposed model and validate the feasibility of CASAS applied in underwater target imaging and detection.
Collapse
|
43
|
Chen W, Liu M, Du H, Radojevic M, Wang Y, Meijering E. Deep-Learning-Based Automated Neuron Reconstruction From 3D Microscopy Images Using Synthetic Training Images. IEEE TRANSACTIONS ON MEDICAL IMAGING 2022; 41:1031-1042. [PMID: 34847022 DOI: 10.1109/tmi.2021.3130934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Digital reconstruction of neuronal structures from 3D microscopy images is critical for the quantitative investigation of brain circuits and functions. It is a challenging task that would greatly benefit from automatic neuron reconstruction methods. In this paper, we propose a novel method called SPE-DNR that combines spherical-patches extraction (SPE) and deep-learning for neuron reconstruction (DNR). Based on 2D Convolutional Neural Networks (CNNs) and the intensity distribution features extracted by SPE, it determines the tracing directions and classifies voxels into foreground or background. This way, starting from a set of seed points, it automatically traces the neurite centerlines and determines when to stop tracing. To avoid errors caused by imperfect manual reconstructions, we develop an image synthesizing scheme to generate synthetic training images with exact reconstructions. This scheme simulates 3D microscopy imaging conditions as well as structural defects, such as gaps and abrupt radii changes, to improve the visual realism of the synthetic images. To demonstrate the applicability and generalizability of SPE-DNR, we test it on 67 real 3D neuron microscopy images from three datasets. The experimental results show that the proposed SPE-DNR method is robust and competitive compared with other state-of-the-art neuron reconstruction methods.
Collapse
|
44
|
Petabyte-Scale Multi-Morphometry of Single Neurons for Whole Brains. Neuroinformatics 2022; 20:525-536. [PMID: 35182359 DOI: 10.1007/s12021-022-09569-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2022] [Indexed: 01/04/2023]
Abstract
Recent advances in brain imaging allow producing large amounts of 3-D volumetric data from which morphometry data is reconstructed and measured. Fine detailed structural morphometry of individual neurons, including somata, dendrites, axons, and synaptic connectivity based on digitally reconstructed neurons, is essential for cataloging neuron types and their connectivity. To produce quality morphometry at large scale, it is highly desirable but extremely challenging to efficiently handle petabyte-scale high-resolution whole brain imaging database. Here, we developed a multi-level method to produce high quality somatic, dendritic, axonal, and potential synaptic morphometry, which was made possible by utilizing necessary petabyte hardware and software platform to optimize both the data and workflow management. Our method also boosts data sharing and remote collaborative validation. We highlight a petabyte application dataset involving 62 whole mouse brains, from which we identified 50,233 somata of individual neurons, profiled the dendrites of 11,322 neurons, reconstructed the full 3-D morphology of 1,050 neurons including their dendrites and full axons, and detected 1.9 million putative synaptic sites derived from axonal boutons. Analysis and simulation of these data indicate the promise of this approach for modern large-scale morphology applications.
Collapse
|
45
|
Winfree S, Al Hasan M, El-Achkar TM. Profiling Immune Cells in the Kidney Using Tissue Cytometry and Machine Learning. KIDNEY360 2022; 3:968-978. [PMID: 36128490 PMCID: PMC9438423 DOI: 10.34067/kid.0006802020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/09/2021] [Indexed: 01/10/2023]
Abstract
The immune system governs key functions that maintain renal homeostasis through various effector cells that reside in or infiltrate the kidney. These immune cells play an important role in shaping adaptive or maladaptive responses to local or systemic stress and injury. We increasingly recognize that microenvironments within the kidney are characterized by a unique distribution of immune cells, the function of which depends on this unique spatial localization. Therefore, quantitative profiling of immune cells in intact kidney tissue becomes essential, particularly at a scale and resolution that allow the detection of differences between the various "nephro-ecosystems" in health and disease. In this review, we discuss advancements in tissue cytometry of the kidney, performed through multiplexed confocal imaging and analysis using the Volumetric Tissue Exploration and Analysis (VTEA) software. We highlight how this tool has improved our understanding of the role of the immune system in the kidney and its relevance in the pathobiology of renal disease. We also discuss how the field is increasingly incorporating machine learning to enhance the analytic potential of imaging data and provide unbiased methods to explore and visualize multidimensional data. Such novel analytic methods could be particularly relevant when applied to profiling immune cells. Furthermore, machine-learning approaches applied to cytometry could present venues for nonexhaustive exploration and classification of cells from existing data and improving tissue economy. Therefore, tissue cytometry is transforming what used to be a qualitative assessment of the kidney into a highly quantitative, imaging-based "omics" assessment that complements other advanced molecular interrogation technologies.
Collapse
Affiliation(s)
- Seth Winfree
- Division of Nephrology, Department of Medicine, Indiana University, Indianapolis, Indiana
| | - Mohammad Al Hasan
- Department of Computer Science, Indiana University–Purdue University, Indianapolis, Indiana
| | - Tarek M. El-Achkar
- Division of Nephrology, Department of Medicine, Indiana University, Indianapolis, Indiana,Indianapolis Veterans Affairs Medical Center, Indianapolis, Indiana,Correspondence: Dr. Tarek M. El-Achkar (Ashkar), Division of Nephrology, Department of Medicine, Indiana University, 950 W Walnut St., R2-202, Indianapolis, IN 46202.
| |
Collapse
|
46
|
Wu J, Turner N, Bae JA, Vishwanathan A, Seung HS. RealNeuralNetworks.jl: An Integrated Julia Package for Skeletonization, Morphological Analysis, and Synaptic Connectivity Analysis of Terabyte-Scale 3D Neural Segmentations. Front Neuroinform 2022; 16:828169. [PMID: 35311003 PMCID: PMC8924549 DOI: 10.3389/fninf.2022.828169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/10/2022] [Indexed: 11/30/2022] Open
Abstract
Benefiting from the rapid development of electron microscopy imaging and deep learning technologies, an increasing number of brain image datasets with segmentation and synapse detection are published. Most of the automated segmentation methods label voxels rather than producing neuron skeletons directly. A further skeletonization step is necessary for quantitative morphological analysis. Currently, several tools are published for skeletonization as well as morphological and synaptic connectivity analysis using different computer languages and environments. Recently the Julia programming language, notable for elegant syntax and high performance, has gained rapid adoption in the scientific computing community. Here, we present a Julia package, called RealNeuralNetworks.jl, for efficient sparse skeletonization, morphological analysis, and synaptic connectivity analysis. Based on a large-scale Zebrafish segmentation dataset, we illustrate the software features by performing distributed skeletonization in Google Cloud, clustering the neurons using the NBLAST algorithm, combining morphological similarity and synaptic connectivity to study their relationship. We demonstrate that RealNeuralNetworks.jl is suitable for use in terabyte-scale electron microscopy image segmentation datasets.
Collapse
Affiliation(s)
- Jingpeng Wu
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States
- *Correspondence: Jingpeng Wu,
| | - Nicholas Turner
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States
- Department of Computer Science, Princeton University, Princeton, NJ, United States
| | - J. Alexander Bae
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States
- Department of Electrical and Computer Engineering, Princeton University, Princeton, NJ, United States
| | - Ashwin Vishwanathan
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States
| | - H. Sebastian Seung
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, United States
- Department of Computer Science, Princeton University, Princeton, NJ, United States
| |
Collapse
|
47
|
Perelsman O, Asano S, Freifeld L. Expansion Microscopy of Larval Zebrafish Brains and Zebrafish Embryos. Methods Mol Biol 2022; 2440:211-222. [PMID: 35218542 DOI: 10.1007/978-1-0716-2051-9_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Since its introduction in 2015, expansion microscopy (ExM) allowed imaging a broad variety of biological structures in many models, at nanoscale resolution. Here, we describe in detail a protocol for application of ExM in whole-brains of zebrafish larvae and intact embryos, and discuss the considerations involved in the imaging of nonflat, whole-organ or organism samples, more broadly.
Collapse
Affiliation(s)
- Ory Perelsman
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Shoh Asano
- Internal Medicine Research Unit, Pfizer, Cambridge, MA, USA
| | - Limor Freifeld
- Department of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa, Israel.
| |
Collapse
|
48
|
Huber N, Hoffmann D, Giniatullina R, Rostalski H, Leskelä S, Takalo M, Natunen T, Solje E, Remes AM, Giniatullin R, Hiltunen M, Haapasalo A. C9orf72 hexanucleotide repeat expansion leads to altered neuronal and dendritic spine morphology and synaptic dysfunction. Neurobiol Dis 2021; 162:105584. [PMID: 34915153 DOI: 10.1016/j.nbd.2021.105584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/26/2021] [Accepted: 12/11/2021] [Indexed: 12/14/2022] Open
Abstract
Frontotemporal lobar degeneration (FTLD) comprises a heterogenous group of progressive neurodegenerative syndromes. To date, no validated biomarkers or effective disease-modifying therapies exist for the different clinical or genetic subtypes of FTLD. The most common genetic cause underlying FTLD and amyotrophic lateral sclerosis (ALS) is a hexanucleotide repeat expansion in the C9orf72 gene (C9-HRE). FTLD is accompanied by changes in several neurotransmitter systems, including the glutamatergic, GABAergic, dopaminergic, and serotonergic systems and many clinical symptoms can be explained by disturbances in these systems. Here, we aimed to elucidate the effects of the C9-HRE on synaptic function, molecular composition of synapses, and dendritic spine morphology. We overexpressed the pathological C9-HRE in cultured E18 mouse primary hippocampal neurons and characterized the pathological, morphological, and functional changes by biochemical methods, confocal microscopy, and live cell calcium imaging. The C9-HRE-expressing neurons were confirmed to display the pathological RNA foci and DPR proteins. C9-HRE expression led to significant changes in dendritic spine morphologies, as indicated by decreased number of mushroom-type spines and increased number of stubby and thin spines, as well as diminished neuronal branching. These morphological changes were accompanied by concomitantly enhanced susceptibility of the neurons to glutamate-induced excitotoxicity as well as augmented and prolonged responses to excitatory stimuli by glutamate and depolarizing potassium chloride as compared to control neurons. Mechanistically, the hyperexcitation phenotype in the C9-HRE-expressing neurons was found to be underlain by increased activity of extrasynaptic GluN2B-containing N-methyl-d-aspartate (NMDA) receptors. Our results are in accordance with the idea suggesting that C9-HRE is associated with enhanced excitotoxicity and synaptic dysfunction. Thus, therapeutic interventions targeted to alleviate synaptic disturbances might offer efficient avenues for the treatment of patients with C9-HRE-associated FTLD.
Collapse
Affiliation(s)
- Nadine Huber
- Molecular Neurodegeneration group, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland.
| | - Dorit Hoffmann
- Molecular Neurodegeneration group, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland.
| | - Raisa Giniatullina
- Molecular Pain Research group, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland.
| | - Hannah Rostalski
- Molecular Neurodegeneration group, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland.
| | - Stina Leskelä
- Molecular Neurodegeneration group, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland.
| | - Mari Takalo
- Institute of Biomedicine, University of Eastern Finland, Yliopistonranta 1E, 70211 Kuopio, Finland.
| | - Teemu Natunen
- Institute of Biomedicine, University of Eastern Finland, Yliopistonranta 1E, 70211 Kuopio, Finland.
| | - Eino Solje
- Institute of Clinical Medicine - Neurology, University of Eastern Finland, Yliopistonranta 1 C, 70211 Kuopio, Finland; Neuro Center, Neurology, Kuopio University Hospital, P. O. Box 100, FI-70029 KYS, Finland.
| | - Anne M Remes
- Medical Research Center, Oulu University Hospital, P. O. Box 8000, FI-90014 University of Oulu, Finland; Unit of Clinical Neuroscience, Neurology, University of Oulu, P. O. Box 8000, FI-90014 University of Oulu, Finland.
| | - Rashid Giniatullin
- Molecular Pain Research group, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland.
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Yliopistonranta 1E, 70211 Kuopio, Finland.
| | - Annakaisa Haapasalo
- Molecular Neurodegeneration group, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Neulaniementie 2, 70211 Kuopio, Finland.
| |
Collapse
|
49
|
Xu F, Shen Y, Ding L, Yang CY, Tan H, Wang H, Zhu Q, Xu R, Wu F, Xiao Y, Xu C, Li Q, Su P, Zhang LI, Dong HW, Desimone R, Xu F, Hu X, Lau PM, Bi GQ. High-throughput mapping of a whole rhesus monkey brain at micrometer resolution. Nat Biotechnol 2021; 39:1521-1528. [PMID: 34312500 DOI: 10.1038/s41587-021-00986-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 06/14/2021] [Indexed: 02/06/2023]
Abstract
Whole-brain mesoscale mapping in primates has been hindered by large brain sizes and the relatively low throughput of available microscopy methods. Here, we present an approach that combines primate-optimized tissue sectioning and clearing with ultrahigh-speed fluorescence microscopy implementing improved volumetric imaging with synchronized on-the-fly-scan and readout technique, and is capable of completing whole-brain imaging of a rhesus monkey at 1 × 1 × 2.5 µm3 voxel resolution within 100 h. We also developed a highly efficient method for long-range tracing of sparse axonal fibers in datasets numbering hundreds of terabytes. This pipeline, which we call serial sectioning and clearing, three-dimensional microscopy with semiautomated reconstruction and tracing (SMART), enables effective connectome-scale mapping of large primate brains. With SMART, we were able to construct a cortical projection map of the mediodorsal nucleus of the thalamus and identify distinct turning and routing patterns of individual axons in the cortical folds while approaching their arborization destinations.
Collapse
Affiliation(s)
- Fang Xu
- Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, China.,CAS Key Laboratory of Brain Connectome and Manipulation, Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China
| | - Yan Shen
- CAS Key Laboratory of Brain Function and Disease, and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Lufeng Ding
- CAS Key Laboratory of Brain Function and Disease, and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Chao-Yu Yang
- CAS Key Laboratory of Brain Function and Disease, and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Heng Tan
- Key Laboratory of Animal Models and Human Disease Mechanism, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Department of Pathology and Pathophysiology, Kunming Medical University, Kunming, China
| | - Hao Wang
- Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, China.,Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Qingyuan Zhu
- Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Rui Xu
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fengyi Wu
- CAS Key Laboratory of Brain Connectome and Manipulation, Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China
| | - Yanyang Xiao
- CAS Key Laboratory of Brain Connectome and Manipulation, Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China
| | - Cheng Xu
- Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Qianwei Li
- Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Peng Su
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| | - Li I Zhang
- Zilkha Neurogenetic Institute, Center for Neural Circuits & Sensory Processing Disorders, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hong-Wei Dong
- UCLA Brain Research & Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Robert Desimone
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fuqiang Xu
- CAS Key Laboratory of Brain Connectome and Manipulation, Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China.,State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai, China
| | - Xintian Hu
- Key Laboratory of Animal Models and Human Disease Mechanism, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai, China
| | - Pak-Ming Lau
- Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, China. .,CAS Key Laboratory of Brain Connectome and Manipulation, Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China. .,CAS Key Laboratory of Brain Function and Disease, and School of Life Sciences, University of Science and Technology of China, Hefei, China. .,Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China.
| | - Guo-Qiang Bi
- Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, China. .,CAS Key Laboratory of Brain Connectome and Manipulation, Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China. .,Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology, Shanghai, China.
| |
Collapse
|
50
|
Settell ML, Skubal AC, Chen RCH, Kasole M, Knudsen BE, Nicolai EN, Huang C, Zhou C, Trevathan JK, Upadhye A, Kolluru C, Shoffstall AJ, Williams JC, Suminski AJ, Grill WM, Pelot NA, Chen S, Ludwig KA. In vivo Visualization of Pig Vagus Nerve "Vagotopy" Using Ultrasound. Front Neurosci 2021; 15:676680. [PMID: 34899151 PMCID: PMC8660563 DOI: 10.3389/fnins.2021.676680] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 11/01/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Placement of the clinical vagus nerve stimulating cuff is a standard surgical procedure based on anatomical landmarks, with limited patient specificity in terms of fascicular organization or vagal anatomy. As such, the therapeutic effects are generally limited by unwanted side effects of neck muscle contractions, demonstrated by previous studies to result from stimulation of (1) motor fibers near the cuff in the superior laryngeal and (2) motor fibers within the cuff projecting to the recurrent laryngeal. Objective: Conventional non-invasive ultrasound, where the transducer is placed on the surface of the skin, has been previously used to visualize the vagus with respect to other landmarks such as the carotid and internal jugular vein. However, it lacks sufficient resolution to provide details about the vagus fascicular organization, or detail about smaller neural structures such as the recurrent and superior laryngeal branch responsible for therapy limiting side effects. Here, we characterize the use of ultrasound with the transducer placed in the surgical pocket to improve resolution without adding significant additional risk to the surgical procedure in the pig model. Methods: Ultrasound images were obtained from a point of known functional organization at the nodose ganglia to the point of placement of stimulating electrodes within the surgical window. Naïve volunteers with minimal training were then asked to use these ultrasound videos to trace afferent groupings of fascicles from the nodose to their location within the surgical window where a stimulating cuff would normally be placed. Volunteers were asked to select a location for epineural electrode placement away from the fascicles containing efferent motor nerves responsible for therapy limiting side effects. 2-D and 3-D reconstructions of the ultrasound were directly compared to post-mortem histology in the same animals. Results: High-resolution ultrasound from the surgical pocket enabled 2-D and 3-D reconstruction of the cervical vagus and surrounding structures that accurately depicted the functional vagotopy of the pig vagus nerve as confirmed via histology. Although resolution was not sufficient to match specific fascicles between ultrasound and histology 1 to 1, it was sufficient to trace fascicle groupings from a point of known functional organization at the nodose ganglia to their locations within the surgical window at stimulating electrode placement. Naïve volunteers were able place an electrode proximal to the sensory afferent grouping of fascicles and away from the motor nerve efferent grouping of fascicles in each subject (n = 3). Conclusion: The surgical pocket itself provides a unique opportunity to obtain higher resolution ultrasound images of neural targets responsible for intended therapeutic effect and limiting off-target effects. We demonstrate the increase in resolution is sufficient to aid patient-specific electrode placement to optimize outcomes. This simple technique could be easily adopted for multiple neuromodulation targets to better understand how patient specific anatomy impacts functional outcomes.
Collapse
Affiliation(s)
- Megan L. Settell
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Institute of Neuroengineering (WITNe), University of Wisconsin-Madison, Madison, WI, United States
| | - Aaron C. Skubal
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Institute of Neuroengineering (WITNe), University of Wisconsin-Madison, Madison, WI, United States
| | - Rex C. H. Chen
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Institute of Neuroengineering (WITNe), University of Wisconsin-Madison, Madison, WI, United States
| | - Maïsha Kasole
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Institute of Neuroengineering (WITNe), University of Wisconsin-Madison, Madison, WI, United States
| | - Bruce E. Knudsen
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Institute of Neuroengineering (WITNe), University of Wisconsin-Madison, Madison, WI, United States
| | - Evan N. Nicolai
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Institute of Neuroengineering (WITNe), University of Wisconsin-Madison, Madison, WI, United States
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, United States
| | - Chengwu Huang
- Department of Radiology, Mayo Clinic, Rochester, MN, United States
| | - Chenyun Zhou
- Department of Radiology, Mayo Clinic, Rochester, MN, United States
- Department of Ultrasound, West China Hospital of Sichuan University, Chengdu, China
| | - James K. Trevathan
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Institute of Neuroengineering (WITNe), University of Wisconsin-Madison, Madison, WI, United States
| | - Aniruddha Upadhye
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, United States
- Louis Stokes Cleveland VA Medical Center, Cleveland, OH, United States
| | - Chaitanya Kolluru
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, United States
- Louis Stokes Cleveland VA Medical Center, Cleveland, OH, United States
| | - Andrew J. Shoffstall
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, United States
- Louis Stokes Cleveland VA Medical Center, Cleveland, OH, United States
| | - Justin C. Williams
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Institute of Neuroengineering (WITNe), University of Wisconsin-Madison, Madison, WI, United States
- Department of Neurosurgery, University of Wisconsin-Madison, Madison, WI, United States
| | - Aaron J. Suminski
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Institute of Neuroengineering (WITNe), University of Wisconsin-Madison, Madison, WI, United States
- Department of Neurosurgery, University of Wisconsin-Madison, Madison, WI, United States
| | - Warren M. Grill
- Department of Biomedical Engineering, Duke University, Durham, NC, United States
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, United States
- Department of Neurobiology, Duke University, Durham, NC, United States
- Department of Neurosurgery, Duke University, Durham, NC, United States
| | - Nicole A. Pelot
- Department of Biomedical Engineering, Duke University, Durham, NC, United States
| | - Shigao Chen
- Department of Radiology, Mayo Clinic, Rochester, MN, United States
| | - Kip A. Ludwig
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
- Wisconsin Institute of Neuroengineering (WITNe), University of Wisconsin-Madison, Madison, WI, United States
- Department of Neurosurgery, University of Wisconsin-Madison, Madison, WI, United States
| |
Collapse
|