1
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Ahmed M, Rajagopalan AE, Pan Y, Li Y, Williams DL, Pedersen EA, Thakral M, Previero A, Close KC, Christoforou CP, Cai D, Turner GC, Clowney EJ. Input density tunes Kenyon cell sensory responses in the Drosophila mushroom body. Curr Biol 2023; 33:2742-2760.e12. [PMID: 37348501 PMCID: PMC10529417 DOI: 10.1016/j.cub.2023.05.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 05/02/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023]
Abstract
The ability to discriminate sensory stimuli with overlapping features is thought to arise in brain structures called expansion layers, where neurons carrying information about sensory features make combinatorial connections onto a much larger set of cells. For 50 years, expansion coding has been a prime topic of theoretical neuroscience, which seeks to explain how quantitative parameters of the expansion circuit influence sensory sensitivity, discrimination, and generalization. Here, we investigate the developmental events that produce the quantitative parameters of the arthropod expansion layer, called the mushroom body. Using Drosophila melanogaster as a model, we employ genetic and chemical tools to engineer changes to circuit development. These allow us to produce living animals with hypothesis-driven variations on natural expansion layer wiring parameters. We then test the functional and behavioral consequences. By altering the number of expansion layer neurons (Kenyon cells) and their dendritic complexity, we find that input density, but not cell number, tunes neuronal odor selectivity. Simple odor discrimination behavior is maintained when the Kenyon cell number is reduced and augmented by Kenyon cell number expansion. Animals with increased input density to each Kenyon cell show increased overlap in Kenyon cell odor responses and become worse at odor discrimination tasks.
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Affiliation(s)
- Maria Ahmed
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Adithya E Rajagopalan
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yijie Pan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ye Li
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48104, USA
| | - Donnell L Williams
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erik A Pedersen
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Manav Thakral
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Angelica Previero
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kari C Close
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | | | - Dawen Cai
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48104, USA; Biophysics LS&A, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Neuroscience Institute Affiliate, University of Michigan, Ann Arbor, MI 48109, USA
| | - Glenn C Turner
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - E Josephine Clowney
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Neuroscience Institute Affiliate, University of Michigan, Ann Arbor, MI 48109, USA.
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2
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Salavaty A, Azadian E, Naik SH, Currie PD. Clonal selection parallels between normal and cancer tissues. Trends Genet 2023; 39:358-380. [PMID: 36842901 DOI: 10.1016/j.tig.2023.01.007] [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: 07/27/2022] [Revised: 01/12/2023] [Accepted: 01/26/2023] [Indexed: 02/28/2023]
Abstract
Clonal selection and drift drive both normal tissue and cancer development. However, the biological mechanisms and environmental conditions underpinning these processes remain to be elucidated. Clonal selection models are centered in Darwinian evolutionary theory, where some clones with the fittest features are selected and populate the tissue or tumor. We suggest that different subclasses of stem cells, each of which is responsible for a distinct feature of the selection process, share common features between normal and cancer conditions. While active stem cells populate the tissue, dormant cells account for tissue replenishment/regeneration in both normal and cancerous tissues. We also discuss potential mechanisms that drive clonal drift, their interactions with clonal selection, and their similarities during normal and cancer tissue development.
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Affiliation(s)
- Adrian Salavaty
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; Systems Biology Institute Australia, Monash University, Clayton, VIC 3800, Australia.
| | - Esmaeel Azadian
- Immunology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Shalin H Naik
- Immunology Division, Walter and Eliza Hall Institute, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia; Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; EMBL Australia, Monash University, Clayton, VIC 3800, Australia.
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3
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Ahmed M, Rajagopalan AE, Pan Y, Li Y, Williams DL, Pedersen EA, Thakral M, Previero A, Close KC, Christoforou CP, Cai D, Turner GC, Clowney EJ. Hacking brain development to test models of sensory coding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525425. [PMID: 36747712 PMCID: PMC9900841 DOI: 10.1101/2023.01.25.525425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Animals can discriminate myriad sensory stimuli but can also generalize from learned experience. You can probably distinguish the favorite teas of your colleagues while still recognizing that all tea pales in comparison to coffee. Tradeoffs between detection, discrimination, and generalization are inherent at every layer of sensory processing. During development, specific quantitative parameters are wired into perceptual circuits and set the playing field on which plasticity mechanisms play out. A primary goal of systems neuroscience is to understand how material properties of a circuit define the logical operations-computations--that it makes, and what good these computations are for survival. A cardinal method in biology-and the mechanism of evolution--is to change a unit or variable within a system and ask how this affects organismal function. Here, we make use of our knowledge of developmental wiring mechanisms to modify hard-wired circuit parameters in the Drosophila melanogaster mushroom body and assess the functional and behavioral consequences. By altering the number of expansion layer neurons (Kenyon cells) and their dendritic complexity, we find that input number, but not cell number, tunes odor selectivity. Simple odor discrimination performance is maintained when Kenyon cell number is reduced and augmented by Kenyon cell expansion.
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Affiliation(s)
- Maria Ahmed
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Adithya E. Rajagopalan
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yijie Pan
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ye Li
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48104, USA
| | - Donnell L. Williams
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erik A. Pedersen
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Manav Thakral
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Angelica Previero
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kari C. Close
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | | | - Dawen Cai
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48104, USA
- Biophysics LS&A, University of Michigan, Ann Arbor, MI 48109, United States
- Michigan Neuroscience Institute Affiliate
| | - Glenn C. Turner
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
| | - E. Josephine Clowney
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Michigan Neuroscience Institute Affiliate
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4
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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: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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5
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Chen S, Loper J, Zhou P, Paninski L. Blind demixing methods for recovering dense neuronal morphology from barcode imaging data. PLoS Comput Biol 2022; 18:e1009991. [PMID: 35395020 PMCID: PMC9020678 DOI: 10.1371/journal.pcbi.1009991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 04/20/2022] [Accepted: 03/07/2022] [Indexed: 11/19/2022] Open
Abstract
Cellular barcoding methods offer the exciting possibility of 'infinite-pseudocolor' anatomical reconstruction-i.e., assigning each neuron its own random unique barcoded 'pseudocolor,' and then using these pseudocolors to trace the microanatomy of each neuron. Here we use simulations, based on densely-reconstructed electron microscopy microanatomy, with signal structure matched to real barcoding data, to quantify the feasibility of this procedure. We develop a new blind demixing approach to recover the barcodes that label each neuron, and validate this method on real data with known barcodes. We also develop a neural network which uses the recovered barcodes to reconstruct the neuronal morphology from the observed fluorescence imaging data, 'connecting the dots' between discontiguous barcode amplicon signals. We find that accurate recovery should be feasible, provided that the barcode signal density is sufficiently high. This study suggests the possibility of mapping the morphology and projection pattern of many individual neurons simultaneously, at high resolution and at large scale, via conventional light microscopy.
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Affiliation(s)
- Shuonan Chen
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, New York, United States of America
- Department of Statistics, Columbia University, New York, New York, United States of America
- Center for Theoretical Neuroscience, Columbia University, New York, New York, United States of America
- Grossman Center for the Statistics of Mind, Columbia University, New York, New York, United States of America
- Department of Neuroscience, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - Jackson Loper
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, New York, United States of America
- Department of Statistics, Columbia University, New York, New York, United States of America
- Center for Theoretical Neuroscience, Columbia University, New York, New York, United States of America
- Grossman Center for the Statistics of Mind, Columbia University, New York, New York, United States of America
- Department of Neuroscience, Columbia University, New York, New York, United States of America
- Data Science Institute, Columbia University, New York, New York, United States of America
| | - Pengcheng Zhou
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Liam Paninski
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, New York, United States of America
- Department of Statistics, Columbia University, New York, New York, United States of America
- Center for Theoretical Neuroscience, Columbia University, New York, New York, United States of America
- Grossman Center for the Statistics of Mind, Columbia University, New York, New York, United States of America
- Department of Neuroscience, Columbia University, New York, New York, United States of America
- Data Science Institute, Columbia University, New York, New York, United States of America
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6
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Aydin O, Passaro AP, Raman R, Spellicy SE, Weinberg RP, Kamm RD, Sample M, Truskey GA, Zartman J, Dar RD, Palacios S, Wang J, Tordoff J, Montserrat N, Bashir R, Saif MTA, Weiss R. Principles for the design of multicellular engineered living systems. APL Bioeng 2022; 6:010903. [PMID: 35274072 PMCID: PMC8893975 DOI: 10.1063/5.0076635] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/02/2022] [Indexed: 12/14/2022] Open
Abstract
Remarkable progress in bioengineering over the past two decades has enabled the formulation of fundamental design principles for a variety of medical and non-medical applications. These advancements have laid the foundation for building multicellular engineered living systems (M-CELS) from biological parts, forming functional modules integrated into living machines. These cognizant design principles for living systems encompass novel genetic circuit manipulation, self-assembly, cell-cell/matrix communication, and artificial tissues/organs enabled through systems biology, bioinformatics, computational biology, genetic engineering, and microfluidics. Here, we introduce design principles and a blueprint for forward production of robust and standardized M-CELS, which may undergo variable reiterations through the classic design-build-test-debug cycle. This Review provides practical and theoretical frameworks to forward-design, control, and optimize novel M-CELS. Potential applications include biopharmaceuticals, bioreactor factories, biofuels, environmental bioremediation, cellular computing, biohybrid digital technology, and experimental investigations into mechanisms of multicellular organisms normally hidden inside the "black box" of living cells.
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Affiliation(s)
| | - Austin P. Passaro
- Regenerative Bioscience Center, University of Georgia, Athens, Georgia 30602, USA
| | - Ritu Raman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | | | - Robert P. Weinberg
- School of Pharmacy, Massachusetts College of Pharmacy and Health Sciences, Boston, Massachusetts 02115, USA
| | | | - Matthew Sample
- Center for Ethics and Law in the Life Sciences, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - George A. Truskey
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA
| | - Jeremiah Zartman
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Roy D. Dar
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Sebastian Palacios
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Jason Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jesse Tordoff
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Nuria Montserrat
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | | | - M. Taher A. Saif
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ron Weiss
- Author to whom correspondence should be addressed:
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7
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Multicolor strategies for investigating clonal expansion and tissue plasticity. Cell Mol Life Sci 2022; 79:141. [PMID: 35187598 PMCID: PMC8858928 DOI: 10.1007/s00018-021-04077-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/27/2021] [Accepted: 10/14/2021] [Indexed: 12/20/2022]
Abstract
Understanding the generation of complexity in living organisms requires the use of lineage tracing tools at a multicellular scale. In this review, we describe the different multicolor strategies focusing on mouse models expressing several fluorescent reporter proteins, generated by classical (MADM, Brainbow and its multiple derivatives) or acute (StarTrack, CLoNe, MAGIC Markers, iOn, viral vectors) transgenesis. After detailing the multi-reporter genetic strategies that serve as a basis for the establishment of these multicolor mouse models, we briefly mention other animal and cellular models (zebrafish, chicken, drosophila, iPSC) that also rely on these constructs. Then, we highlight practical applications of multicolor mouse models to better understand organogenesis at single progenitor scale (clonal analyses) in the brain and briefly in several other tissues (intestine, skin, vascular, hematopoietic and immune systems). In addition, we detail the critical contribution of multicolor fate mapping strategies in apprehending the fine cellular choreography underlying tissue morphogenesis in several models with a particular focus on brain cytoarchitecture in health and diseases. Finally, we present the latest technological advances in multichannel and in-depth imaging, and automated analyses that enable to better exploit the large amount of data generated from multicolored tissues.
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8
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Li Y, Walker LA, Zhao Y, Edwards EM, Michki NS, Cheng HPJ, Ghazzi M, Chen TY, Chen M, Roossien DH, Cai D. Bitbow Enables Highly Efficient Neuronal Lineage Tracing and Morphology Reconstruction in Single Drosophila Brains. Front Neural Circuits 2021; 15:732183. [PMID: 34744636 PMCID: PMC8564373 DOI: 10.3389/fncir.2021.732183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/14/2021] [Indexed: 12/15/2022] Open
Abstract
Identifying the cellular origins and mapping the dendritic and axonal arbors of neurons have been century old quests to understand the heterogeneity among these brain cells. Current Brainbow based transgenic animals take the advantage of multispectral labeling to differentiate neighboring cells or lineages, however, their applications are limited by the color capacity. To improve the analysis throughput, we designed Bitbow, a digital format of Brainbow which exponentially expands the color palette to provide tens of thousands of spectrally resolved unique labels. We generated transgenic Bitbow Drosophila lines, established statistical tools, and streamlined sample preparation, image processing, and data analysis pipelines to conveniently mapping neural lineages, studying neuronal morphology and revealing neural network patterns with unprecedented speed, scale, and resolution.
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Affiliation(s)
- Ye Li
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Logan A Walker
- Biophysics LS&A, University of Michigan, Ann Arbor, MI, United States
| | - Yimeng Zhao
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Erica M Edwards
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Nigel S Michki
- Biophysics LS&A, University of Michigan, Ann Arbor, MI, United States
| | - Hon Pong Jimmy Cheng
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Marya Ghazzi
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Tiffany Y Chen
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Maggie Chen
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Douglas H Roossien
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Dawen Cai
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, United States.,Biophysics LS&A, University of Michigan, Ann Arbor, MI, United States.,Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, United States
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9
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Michki NS, Li Y, Sanjasaz K, Zhao Y, Shen FY, Walker LA, Cao W, Lee CY, Cai D. The molecular landscape of neural differentiation in the developing Drosophila brain revealed by targeted scRNA-seq and multi-informatic analysis. Cell Rep 2021; 35:109039. [PMID: 33909998 PMCID: PMC8139287 DOI: 10.1016/j.celrep.2021.109039] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/19/2021] [Accepted: 04/06/2021] [Indexed: 01/16/2023] Open
Abstract
The Drosophila type II neuroblast lineages present an attractive model to investigate the neurogenesis and differentiation process as they adapt to a process similar to that in the human outer subventricular zone. We perform targeted single-cell mRNA sequencing in third instar larval brains to study this process of the type II NB lineage. Combining prior knowledge, in silico analyses, and in situ validation, our multi-informatic investigation describes the molecular landscape from a single developmental snapshot. 17 markers are identified to differentiate distinct maturation stages. 30 markers are identified to specify the stem cell origin and/or cell division numbers of INPs, and at least 12 neuronal subtypes are identified. To foster future discoveries, we provide annotated tables of pairwise gene-gene correlation in single cells and MiCV, a web tool for interactively analyzing scRNA-seq datasets. Taken together, these resources advance our understanding of the neural differentiation process at the molecular level.
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Affiliation(s)
- Nigel S Michki
- Biophysics LS&A, University of Michigan, Ann Arbor, MI, USA
| | - Ye Li
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kayvon Sanjasaz
- Molecular, Cellular, and Developmental Biology LS&A, University of Michigan, Ann Arbor, MI, USA
| | - Yimeng Zhao
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Fred Y Shen
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Logan A Walker
- Biophysics LS&A, University of Michigan, Ann Arbor, MI, USA
| | - Wenjia Cao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Cheng-Yu Lee
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Dawen Cai
- Biophysics LS&A, University of Michigan, Ann Arbor, MI, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA; Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, USA.
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10
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Figueres-Oñate M, Sánchez-González R, López-Mascaraque L. Deciphering neural heterogeneity through cell lineage tracing. Cell Mol Life Sci 2021; 78:1971-1982. [PMID: 33151389 PMCID: PMC7966193 DOI: 10.1007/s00018-020-03689-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/10/2020] [Accepted: 10/20/2020] [Indexed: 12/21/2022]
Abstract
Understanding how an adult brain reaches an appropriate size and cell composition from a pool of progenitors that proliferates and differentiates is a key question in Developmental Neurobiology. Not only the control of final size but also, the proper arrangement of cells of different embryonic origins is fundamental in this process. Each neural progenitor has to produce a precise number of sibling cells that establish clones, and all these clones will come together to form the functional adult nervous system. Lineage cell tracing is a complex and challenging process that aims to reconstruct the offspring that arise from a single progenitor cell. This tracing can be achieved through strategies based on genetically modified organisms, using either genetic tracers, transfected viral vectors or DNA constructs, and even single-cell sequencing. Combining different reporter proteins and the use of transgenic mice revolutionized clonal analysis more than a decade ago and now, the availability of novel genome editing tools and single-cell sequencing techniques has vastly improved the capacity of lineage tracing to decipher progenitor potential. This review brings together the strategies used to study cell lineages in the brain and the role they have played in our understanding of the functional clonal relationships among neural cells. In addition, future perspectives regarding the study of cell heterogeneity and the ontogeny of different cell lineages will also be addressed.
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Affiliation(s)
- María Figueres-Oñate
- Department of Molecular, Cellular and Development Neurobiology, Instituto Cajal-CSIC, 28002, Madrid, Spain
- Max Planck Research Unit for Neurogenetics, 60438, Frankfurt am Main, Germany
| | - Rebeca Sánchez-González
- Department of Molecular, Cellular and Development Neurobiology, Instituto Cajal-CSIC, 28002, Madrid, Spain
| | - Laura López-Mascaraque
- Department of Molecular, Cellular and Development Neurobiology, Instituto Cajal-CSIC, 28002, Madrid, Spain.
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Shen FY, Harrington MM, Walker LA, Cheng HPJ, Boyden ES, Cai D. Light microscopy based approach for mapping connectivity with molecular specificity. Nat Commun 2020; 11:4632. [PMID: 32934230 PMCID: PMC7493953 DOI: 10.1038/s41467-020-18422-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/21/2020] [Indexed: 11/28/2022] Open
Abstract
Mapping neuroanatomy is a foundational goal towards understanding brain function. Electron microscopy (EM) has been the gold standard for connectivity analysis because nanoscale resolution is necessary to unambiguously resolve synapses. However, molecular information that specifies cell types is often lost in EM reconstructions. To address this, we devise a light microscopy approach for connectivity analysis of defined cell types called spectral connectomics. We combine multicolor labeling (Brainbow) of neurons with multi-round immunostaining Expansion Microscopy (miriEx) to simultaneously interrogate morphology, molecular markers, and connectivity in the same brain section. We apply this strategy to directly link inhibitory neuron cell types with their morphologies. Furthermore, we show that correlative Brainbow and endogenous synaptic machinery immunostaining can define putative synaptic connections between neurons, as well as map putative inhibitory and excitatory inputs. We envision that spectral connectomics can be applied routinely in neurobiology labs to gain insights into normal and pathophysiological neuroanatomy.
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Affiliation(s)
- Fred Y Shen
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Margaret M Harrington
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Logan A Walker
- LS & A, Program in Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Hon Pong Jimmy Cheng
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Edward S Boyden
- McGovern Institute, Koch Institute, Department of Media Arts and Sciences, Department of Biological Engineering, and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Dawen Cai
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA.
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
- LS & A, Program in Biophysics, University of Michigan, Ann Arbor, MI, USA.
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