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Ricquebourg R, Konstantinides N. [A temporal mechanism for the generation of neuronal diversity]. Med Sci (Paris) 2024; 40:251-257. [PMID: 38520100 DOI: 10.1051/medsci/2024012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024] Open
Abstract
One of the greatest challenges in neuroscience is to understand how a complex structure, such as the brain, is built. Spatial and temporal patternings of neuronal progenitors are responsible for the generation of most of the neuronal diversity observed in the brain. This review focuses on the temporal patterning of neuronal progenitors, i.e. the sequential expression of transcription factors that changes the capacity of stem cells to generate different neuronal types, and which is conserved in animals. Recent papers have offered a near complete understanding of the mechanism of temporal patterning in the developing visual system of Drosophila, and of how this contributes to the specification of diverse neuronal identities, which are then maintained by the sustained expression of downstream transcription factors. The insect visual system provides a unique model to study the evolution of neuronal cell types, as well as the evolution of neurodevelopmental mechanisms that generate them.
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2
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Osaka J, Ishii A, Wang X, Iwanaga R, Kawamura H, Akino S, Sugie A, Hakeda-Suzuki S, Suzuki T. Complex formation of immunoglobulin superfamily molecules Side-IV and Beat-IIb regulates synaptic specificity. Cell Rep 2024; 43:113798. [PMID: 38381608 DOI: 10.1016/j.celrep.2024.113798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/03/2023] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
Neurons establish specific synapses based on the adhesive properties of cell-surface proteins while also retaining the ability to form synapses in a relatively non-selective manner. However, comprehensive understanding of the underlying mechanism reconciling these opposing characteristics remains incomplete. Here, we have identified Side-IV/Beat-IIb, members of the Drosophila immunoglobulin superfamily, as a combination of cell-surface recognition molecules inducing synapse formation. The Side-IV/Beat-IIb combination transduces bifurcated signaling with Side-IV's co-receptor, Kirre, and a synaptic scaffold protein, Dsyd-1. Genetic experiments and subcellular protein localization analyses showed the Side-IV/Beat-IIb/Kirre/Dsyd-1 complex to have two essential functions. First, it narrows neuronal binding specificity through Side-IV/Beat-IIb extracellular interactions. Second, it recruits synapse formation factors, Kirre and Dsyd-1, to restrict synaptic loci and inhibit miswiring. This dual function explains how the combinations of cell-surface molecules enable the ranking of preferred interactions among neuronal pairs to achieve synaptic specificity in complex circuits in vivo.
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Affiliation(s)
- Jiro Osaka
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan; Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Arisa Ishii
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Xu Wang
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Riku Iwanaga
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Hinata Kawamura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Shogo Akino
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Atsushi Sugie
- Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Satoko Hakeda-Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan; Research Initiatives and Promotion Organization, Yokohama National University, Yokohama 240-8501, Japan
| | - Takashi Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan.
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Simon F, Holguera I, Chen YC, Malin J, Valentino P, Erclik T, Desplan C. High-throughput identification of the spatial origins of Drosophila optic lobe neurons using single-cell mRNA-sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.578975. [PMID: 38370610 PMCID: PMC10871188 DOI: 10.1101/2024.02.05.578975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The medulla is the largest neuropil of the Drosophila optic lobe. It contains about 100 neuronal types that have been comprehensively characterized morphologically and molecularly. These neuronal types are specified from a larval neuroepithelium called the Outer Proliferation Center (OPC) via the integration of temporal, spatial, and Notch-driven mechanisms. Although we recently characterized the temporal windows of origin of all medulla neurons, as well as their Notch status, their spatial origins remained unknown. Here, we isolated cells from different OPC spatial domains and performed single-cell mRNA-sequencing to identify the neuronal types produced in these domains. This allowed us to characterize in a high-throughput manner the spatial origins of all medulla neurons and to identify two new spatial subdivisions of the OPC. Moreover, our work shows that the most abundant neuronal types are produced from epithelial domains of different sizes despite being present in a similar number of copies. Combined with our previously published scRNA-seq developmental atlas of the optic lobe, our work opens the door for further studies on how specification factor expression in progenitors impacts gene expression in developing and adult neurons.
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Affiliation(s)
- Félix Simon
- Department of Biology, New York University, New York, NY 10003, USA
| | - Isabel Holguera
- Department of Biology, New York University, New York, NY 10003, USA
| | - Yen-Chung Chen
- Department of Biology, New York University, New York, NY 10003, USA
| | - Jennifer Malin
- Department of Biology, New York University, New York, NY 10003, USA
| | - Priscilla Valentino
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Ted Erclik
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Claude Desplan
- Department of Biology, New York University, New York, NY 10003, USA
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Sun C, Shao Y, Iqbal J. Insect Insights at the Single-Cell Level: Technologies and Applications. Cells 2023; 13:91. [PMID: 38201295 PMCID: PMC10777908 DOI: 10.3390/cells13010091] [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: 11/22/2023] [Revised: 12/23/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Single-cell techniques are a promising way to unravel the complexity and heterogeneity of transcripts at the cellular level and to reveal the composition of different cell types and functions in a tissue or organ. In recent years, advances in single-cell RNA sequencing (scRNA-seq) have further changed our view of biological systems. The application of scRNA-seq in insects enables the comprehensive characterization of both common and rare cell types and cell states, the discovery of new cell types, and revealing how cell types relate to each other. The recent application of scRNA-seq techniques to insect tissues has led to a number of exciting discoveries. Here we provide an overview of scRNA-seq and its application in insect research, focusing on biological applications, current challenges, and future opportunities to make new discoveries with scRNA-seq in insects.
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Affiliation(s)
- Chao Sun
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou 310058, China;
| | - Yongqi Shao
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Junaid Iqbal
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
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Lago-Baldaia I, Cooper M, Seroka A, Trivedi C, Powell GT, Wilson SW, Ackerman SD, Fernandes VM. A Drosophila glial cell atlas reveals a mismatch between transcriptional and morphological diversity. PLoS Biol 2023; 21:e3002328. [PMID: 37862379 PMCID: PMC10619882 DOI: 10.1371/journal.pbio.3002328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 11/01/2023] [Accepted: 09/08/2023] [Indexed: 10/22/2023] Open
Abstract
Morphology is a defining feature of neuronal identity. Like neurons, glia display diverse morphologies, both across and within glial classes, but are also known to be morphologically plastic. Here, we explored the relationship between glial morphology and transcriptional signature using the Drosophila central nervous system (CNS), where glia are categorised into 5 main classes (outer and inner surface glia, cortex glia, ensheathing glia, and astrocytes), which show within-class morphological diversity. We analysed and validated single-cell RNA sequencing data of Drosophila glia in 2 well-characterised tissues from distinct developmental stages, containing distinct circuit types: the embryonic ventral nerve cord (VNC) (motor) and the adult optic lobes (sensory). Our analysis identified a new morphologically and transcriptionally distinct surface glial population in the VNC. However, many glial morphological categories could not be distinguished transcriptionally, and indeed, embryonic and adult astrocytes were transcriptionally analogous despite differences in developmental stage and circuit type. While we did detect extensive within-class transcriptomic diversity for optic lobe glia, this could be explained entirely by glial residence in the most superficial neuropil (lamina) and an associated enrichment for immune-related gene expression. In summary, we generated a single-cell transcriptomic atlas of glia in Drosophila, and our extensive in vivo validation revealed that glia exhibit more diversity at the morphological level than was detectable at the transcriptional level. This atlas will serve as a resource for the community to probe glial diversity and function.
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Affiliation(s)
- Inês Lago-Baldaia
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Maia Cooper
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Austin Seroka
- Institute of Neuroscience, Howard Hughes Medical Institute, University of Oregon, Eugene, Oregon, United States of America
| | - Chintan Trivedi
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Gareth T. Powell
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Stephen W. Wilson
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Sarah D. Ackerman
- Department of Pathology and Immunology, Brain Immunology and Glia Center, Washington University School of Medicine, Saint Louis, Missouri, United States of America
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, Missouri, United States of America
| | - Vilaiwan M. Fernandes
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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Ferreira AAG, Desplan C. An Atlas of the Developing Drosophila Visual System Glia and Subcellular mRNA Localization of Transcripts in Single Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.06.552169. [PMID: 37609218 PMCID: PMC10441313 DOI: 10.1101/2023.08.06.552169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Glial cells are essential for proper nervous system development and function. To understand glial development and function, we comprehensively annotated glial cells in a single-cell mRNA-sequencing (scRNAseq) atlas of the developing Drosophila visual system. This allowed us to study their developmental trajectories, from larval to adult stages, and to understand how specific types of glia diversify during development. For example, neuropil glia that are initially transcriptionally similar in larvae, split into ensheathing and astrocyte-like glia during pupal stages. Other glial types, such as chiasm glia change gradually during development without splitting into two cell types. The analysis of scRNA-seq allowed us to discover that the transcriptome of glial cell bodies can be distinguished from that of their broken processes. The processes contain distinct enriched mRNAs that were validated in vivo. Therefore, we have identified most glial types in the developing optic lobe and devised a computational approach to identify mRNA species that are localized to cell bodies or cellular processes.
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Affiliation(s)
| | - Claude Desplan
- Department of Biology, New York University, New York, NY, USA
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Palmateer CM, Artikis C, Brovero SG, Friedman B, Gresham A, Arbeitman MN. Single-cell transcriptome profiles of Drosophila fruitless-expressing neurons from both sexes. eLife 2023; 12:e78511. [PMID: 36724009 PMCID: PMC9891730 DOI: 10.7554/elife.78511] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 01/08/2023] [Indexed: 02/02/2023] Open
Abstract
Drosophila melanogaster reproductive behaviors are orchestrated by fruitless neurons. We performed single-cell RNA-sequencing on pupal neurons that produce sex-specifically spliced fru transcripts, the fru P1-expressing neurons. Uniform Manifold Approximation and Projection (UMAP) with clustering generates an atlas containing 113 clusters. While the male and female neurons overlap in UMAP space, more than half the clusters have sex differences in neuron number, and nearly all clusters display sex-differential expression. Based on an examination of enriched marker genes, we annotate clusters as circadian clock neurons, mushroom body Kenyon cell neurons, neurotransmitter- and/or neuropeptide-producing, and those that express doublesex. Marker gene analyses also show that genes that encode members of the immunoglobulin superfamily of cell adhesion molecules, transcription factors, neuropeptides, neuropeptide receptors, and Wnts have unique patterns of enriched expression across the clusters. In vivo spatial gene expression links to the clusters are examined. A functional analysis of fru P1 circadian neurons shows they have dimorphic roles in activity and period length. Given that most clusters are comprised of male and female neurons indicates that the sexes have fru P1 neurons with common gene expression programs. Sex-specific expression is overlaid on this program, to build the potential for vastly different sex-specific behaviors.
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Affiliation(s)
- Colleen M Palmateer
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
| | - Catherina Artikis
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
| | - Savannah G Brovero
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
| | - Benjamin Friedman
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
| | - Alexis Gresham
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
| | - Michelle N Arbeitman
- Department of Biomedical Sciences, Florida State University, College of MedicineTallahasseeUnited States
- Program of Neuroscience, Florida State UniversityTallahasseeUnited States
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Sato M, Suzuki T. Cutting edge technologies expose the temporal regulation of neurogenesis in the Drosophila nervous system. Fly (Austin) 2022; 16:222-232. [PMID: 35549651 PMCID: PMC9116403 DOI: 10.1080/19336934.2022.2073158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 04/28/2022] [Accepted: 04/28/2022] [Indexed: 11/23/2022] Open
Abstract
During the development of the central nervous system (CNS), extremely large numbers of neurons are produced in a regular fashion to form precise neural circuits. During this process, neural progenitor cells produce different neurons over time due to their intrinsic gene regulatory mechanisms as well as extrinsic mechanisms. The Drosophila CNS has played an important role in elucidating the temporal mechanisms that control neurogenesis over time. It has been shown that a series of temporal transcription factors are sequentially expressed in neural progenitor cells and regulate the temporal specification of neurons in the embryonic CNS. Additionally, similar mechanisms are found in the developing optic lobe and central brain in the larval CNS. However, it is difficult to elucidate the function of numerous molecules in many different cell types solely by molecular genetic approaches. Recently, omics analysis using single-cell RNA-seq and other methods has been used to study the Drosophila nervous system on a large scale and is making a significant contribution to the understanding of the temporal mechanisms of neurogenesis. In this article, recent findings on the temporal patterning of neurogenesis and the contributions of cutting-edge technologies will be reviewed.
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Affiliation(s)
- Makoto Sato
- Mathematical Neuroscience Unit, Institute for Frontier Science Initiative,Laboratory of Developmental Neurobiology, Graduate School of Medical Sciences, Kanazawa University, Ishikawa, Japan
| | - Takumi Suzuki
- College of Science, Department of Science, Ibaraki University, Ibaraki, Japan
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Wang Y, Lobb-Rabe M, Ashley J, Chatterjee P, Anand V, Bellen HJ, Kanca O, Carrillo RA. Systematic expression profiling of Dpr and DIP genes reveals cell surface codes in Drosophila larval motor and sensory neurons. Development 2022; 149:dev200355. [PMID: 35502740 PMCID: PMC9188756 DOI: 10.1242/dev.200355] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/20/2022] [Indexed: 07/26/2023]
Abstract
In complex nervous systems, neurons must identify their correct partners to form synaptic connections. The prevailing model to ensure correct recognition posits that cell-surface proteins (CSPs) in individual neurons act as identification tags. Thus, knowing what cells express which CSPs would provide insights into neural development, synaptic connectivity, and nervous system evolution. Here, we investigated expression of Dpr and DIP genes, two CSP subfamilies belonging to the immunoglobulin superfamily, in Drosophila larval motor neurons (MNs), muscles, glia and sensory neurons (SNs) using a collection of GAL4 driver lines. We found that Dpr genes are more broadly expressed than DIP genes in MNs and SNs, and each examined neuron expresses a unique combination of Dpr and DIP genes. Interestingly, many Dpr and DIP genes are not robustly expressed, but are found instead in gradient and temporal expression patterns. In addition, the unique expression patterns of Dpr and DIP genes revealed three uncharacterized MNs. This study sets the stage for exploring the functions of Dpr and DIP genes in Drosophila MNs and SNs and provides genetic access to subsets of neurons.
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Affiliation(s)
- Yupu Wang
- Department of Molecular Genetics & Cellular Biology, University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, University of Chicago, Chicago, IL 60637, USA
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Meike Lobb-Rabe
- Department of Molecular Genetics & Cellular Biology, University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, University of Chicago, Chicago, IL 60637, USA
- Program in Cell and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - James Ashley
- Department of Molecular Genetics & Cellular Biology, University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, University of Chicago, Chicago, IL 60637, USA
| | - Purujit Chatterjee
- Department of Molecular Genetics & Cellular Biology, University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, University of Chicago, Chicago, IL 60637, USA
| | - Veera Anand
- Department of Molecular Genetics & Cellular Biology, University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, University of Chicago, Chicago, IL 60637, USA
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics and Jan and Dan Duncan Neurobiological Research Institute, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Department of Neuroscience and Howard Hughes Medical Institute, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics and Jan and Dan Duncan Neurobiological Research Institute, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Robert A. Carrillo
- Department of Molecular Genetics & Cellular Biology, University of Chicago, Chicago, IL 60637, USA
- Neuroscience Institute, University of Chicago, Chicago, IL 60637, USA
- Committee on Development, Regeneration, and Stem Cell Biology, University of Chicago, Chicago, IL 60637, USA
- Program in Cell and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
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Yousefian S, Musillo MJ, Bageritz J. Analysis of Single-Cell Transcriptome Data in Drosophila. Methods Mol Biol 2022; 2540:93-111. [PMID: 35980574 DOI: 10.1007/978-1-0716-2541-5_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The fly Drosophila is a versatile model organism that has led to fascinating biological discoveries. In the past few years, Drosophila researchers have used single-cell RNA-sequencing (scRNA-seq) to gain insights into the cellular composition, and developmental processes of various tissues and organs. Given the success of single-cell technologies a variety of computational tools and software packages were developed to enable and facilitate the analysis of scRNA-seq data. In this book chapter we want to give guidance on analyzing droplet-based scRNA-seq data from Drosophila. We will initially describe the preprocessing commonly done for Drosophila, point out possible downstream analyses, and finally highlight computational methods developed using Drosophila scRNA-seq data.
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Affiliation(s)
- Schayan Yousefian
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Maria Jelena Musillo
- Centre for Organismal Studies Heidelberg (COS), Universität Heidelberg, Heidelberg, Germany
| | - Josephine Bageritz
- Centre for Organismal Studies Heidelberg (COS), Universität Heidelberg, Heidelberg, Germany.
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