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Heiman MG, Bülow HE. Dendrite morphogenesis in Caenorhabditis elegans. Genetics 2024:iyae056. [PMID: 38785371 DOI: 10.1093/genetics/iyae056] [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: 12/18/2023] [Accepted: 04/02/2024] [Indexed: 05/25/2024] Open
Abstract
Since the days of Ramón y Cajal, the vast diversity of neuronal and particularly dendrite morphology has been used to catalog neurons into different classes. Dendrite morphology varies greatly and reflects the different functions performed by different types of neurons. Significant progress has been made in our understanding of how dendrites form and the molecular factors and forces that shape these often elaborately sculpted structures. Here, we review work in the nematode Caenorhabditis elegans that has shed light on the developmental mechanisms that mediate dendrite morphogenesis with a focus on studies investigating ciliated sensory neurons and the highly elaborated dendritic trees of somatosensory neurons. These studies, which combine time-lapse imaging, genetics, and biochemistry, reveal an intricate network of factors that function both intrinsically in dendrites and extrinsically from surrounding tissues. Therefore, dendrite morphogenesis is the result of multiple tissue interactions, which ultimately determine the shape of dendritic arbors.
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Affiliation(s)
- Maxwell G Heiman
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Hannes E Bülow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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2
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Ghosh N, Treisman JE. Apical cell expansion maintained by Dusky-like establishes a scaffold for corneal lens morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.575959. [PMID: 38293108 PMCID: PMC10827211 DOI: 10.1101/2024.01.17.575959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The biconvex shape of the Drosophila corneal lens, which enables it to focus light onto the retina, arises by organized assembly of chitin and other apical extracellular matrix components. We show here that the Zona Pellucida domain-containing protein Dusky-like is essential for normal corneal lens morphogenesis. Dusky-like transiently localizes to the expanded apical surfaces of the corneal lens-secreting cells, and in its absence, these cells undergo apical constriction and apicobasal contraction. Dusky-like also controls the arrangement of two other Zona Pellucida-domain proteins, Dumpy and Piopio, external to the developing corneal lens. Loss of either dusky-like or dumpy delays chitin accumulation and disrupts the outer surface of the corneal lens. Artificially inducing apical constriction with constitutively active Myosin light chain kinase is sufficient to similarly alter chitin deposition and corneal lens morphology. These results demonstrate the importance of cell shape for the morphogenesis of overlying apical extracellular matrix structures.
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3
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Gredler ML, Zallen JA. Multicellular rosettes link mesenchymal-epithelial transition to radial intercalation in the mouse axial mesoderm. Dev Cell 2023:S1534-5807(23)00134-X. [PMID: 37080203 DOI: 10.1016/j.devcel.2023.03.018] [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: 06/15/2022] [Revised: 01/25/2023] [Accepted: 03/24/2023] [Indexed: 04/22/2023]
Abstract
Mesenchymal-epithelial transitions are fundamental drivers of development and disease, but how these behaviors generate epithelial structure is not well understood. Here, we show that mesenchymal-epithelial transitions promote epithelial organization in the mouse node and notochordal plate through the assembly and radial intercalation of three-dimensional rosettes. Axial mesoderm rosettes acquire junctional and apical polarity, develop a central lumen, and dynamically expand, coalesce, and radially intercalate into the surface epithelium, converting mesenchymal-epithelial transitions into higher-order tissue structure. In mouse Par3 mutants, axial mesoderm rosettes establish central tight junction polarity but fail to form an expanded apical domain and lumen. These defects are associated with altered rosette dynamics, delayed radial intercalation, and formation of a small, fragmented surface epithelial structure. These results demonstrate that three-dimensional rosette behaviors translate mesenchymal-epithelial transitions into collective radial intercalation and epithelial formation, providing a strategy for building epithelial sheets from individual self-organizing units in the mammalian embryo.
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Affiliation(s)
- Marissa L Gredler
- Howard Hughes Medical Institute and Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Jennifer A Zallen
- Howard Hughes Medical Institute and Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA.
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4
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Baraban M, Gordillo Pi C, Bonnet I, Gilles JF, Lejeune C, Cabrera M, Tep F, Breau MA. Actomyosin contractility in olfactory placode neurons opens the skin epithelium to form the zebrafish nostril. Dev Cell 2023; 58:361-375.e5. [PMID: 36841243 PMCID: PMC10023511 DOI: 10.1016/j.devcel.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/07/2022] [Accepted: 02/02/2023] [Indexed: 02/27/2023]
Abstract
Despite their barrier function, epithelia can locally lose their integrity to create physiological openings during morphogenesis. The mechanisms driving the formation of these epithelial breaks are only starting to be investigated. Here, we study the formation of the zebrafish nostril (the olfactory orifice), which opens in the skin epithelium to expose the olfactory neurons to external odorant cues. Combining live imaging, drug treatments, laser ablation, and tissue-specific functional perturbations, we characterize a mechanical interplay between olfactory placode neurons and the skin, which plays a crucial role in the formation of the orifice: the neurons pull on the overlying skin cells in an actomyosin-dependent manner which, in combination with a local reorganization of the skin epithelium, triggers the opening of the orifice. This work identifies an original mechanism to break an epithelial sheet, in which an adjacent group of cells mechanically assists the epithelium to induce its local rupture.
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Affiliation(s)
- Marion Baraban
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris-Seine (IBPS), Developmental Biology Laboratory, 75005 Paris, France; Laboratoire Jean Perrin, 75005 Paris, France.
| | - Clara Gordillo Pi
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris-Seine (IBPS), Developmental Biology Laboratory, 75005 Paris, France
| | - Isabelle Bonnet
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168, Laboratoire Physico Chimie Curie, 75005 Paris, France
| | | | - Camille Lejeune
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris-Seine (IBPS), Developmental Biology Laboratory, 75005 Paris, France
| | - Mélody Cabrera
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris-Seine (IBPS), Developmental Biology Laboratory, 75005 Paris, France
| | - Florian Tep
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris-Seine (IBPS), Developmental Biology Laboratory, 75005 Paris, France
| | - Marie Anne Breau
- Sorbonne Université, Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Paris-Seine (IBPS), Developmental Biology Laboratory, 75005 Paris, France; Laboratoire Jean Perrin, 75005 Paris, France; Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.
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5
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Rashid A, Tevlin M, Lu Y, Shaham S. A developmental pathway for epithelial-to-motoneuron transformation in C. elegans. Cell Rep 2022; 40:111414. [PMID: 36170838 PMCID: PMC9579992 DOI: 10.1016/j.celrep.2022.111414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 07/18/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022] Open
Abstract
Motoneurons and motoneuron-like pancreatic β cells arise from radial glia and ductal cells, respectively, both tube-lining progenitors that share molecular regulators. To uncover programs underlying motoneuron formation, we studied a similar, cell-division-independent transformation of the C. elegans tube-lining Y cell into the PDA motoneuron. We find that lin-12/Notch acts through ngn-1/Ngn and its regulator hlh-16/Olig to control transformation timing. lin-12 loss blocks transformation, while lin-12(gf) promotes precocious PDA formation. Early basal expression of ngn-1/Ngn and hlh-16/Olig depends on sem-4/Sall and egl-5/Hox. Later, coincident with Y cell morphological changes, ngn-1/Ngn expression is upregulated in a sem-4/Sall and egl-5/Hox-dependent but hlh-16/Olig-independent manner. Subsequently, Y cell retrograde extension forms an anchored process priming PDA axon extension. Extension requires ngn-1-dependent expression of the cytoskeleton organizers UNC-119, UNC-44/ANK, and UNC-33/CRMP, which also activate PDA terminal-gene expression. Our findings uncover cell-division-independent regulatory events leading to motoneuron generation, suggesting a conserved pathway for epithelial-to-motoneuron/motoneuron-like cell differentiation. Rashid et al. report on a conserved epithelial-to-motoneuron transformation pathway in C. elegans requiring ngn-1/Ngn and hlh-16/Olig. lin-12/Notch regulates transformation timing through these genes, while ngn-1/Ngn and hlh-16/Olig expression levels are regulated by sem-4/Sall and egl-5/Hox. Unexpectedly, the cytoskeleton organizers UNC-119, UNC-44, and UNC-33, which are ngn-1/Ngn targets, promote motoneuron terminal identity.
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Affiliation(s)
- Alina Rashid
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Maya Tevlin
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Yun Lu
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Shai Shaham
- Laboratory of Developmental Genetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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Xiao L, Fan D, Qi H, Cong Y, Du Z. Defect-buffering cellular plasticity increases robustness of metazoan embryogenesis. Cell Syst 2022; 13:615-630.e9. [PMID: 35882226 DOI: 10.1016/j.cels.2022.07.001] [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] [Received: 11/10/2021] [Revised: 04/14/2022] [Accepted: 06/30/2022] [Indexed: 01/26/2023]
Abstract
Developmental processes are intrinsically robust so as to preserve a normal-like state in response to genetic and environmental fluctuations. However, the robustness and potential phenotypic plasticity of individual developing cells under genetic perturbations remain to be systematically evaluated. Using large-scale gene perturbation, live imaging, lineage tracing, and single-cell phenomics, we quantified the phenotypic landscape of C. elegans embryogenesis in >2,000 embryos following individual knockdown of over 750 conserved genes. We observed that cellular genetic systems are not sufficiently robust to single-gene perturbations across all cells; rather, gene knockdowns frequently induced cellular defects. Dynamic phenotypic analyses revealed many cellular defects to be transient, with cells exhibiting phenotypic plasticity that serves to alleviate, correct, and accommodate the defects. Moreover, potential developmentally related cell modules may buffer the phenotypic effects of individual cell position changes. Our findings reveal non-negligible contributions of cellular plasticity and multicellularity as compensatory strategies to increase developmental robustness.
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Affiliation(s)
- Long Xiao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Duchangjiang Fan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huan Qi
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yulin Cong
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Du
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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7
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Ardiel EL, Lauziere A, Xu S, Harvey BJ, Christensen RP, Nurrish S, Kaplan JM, Shroff H. Stereotyped behavioral maturation and rhythmic quiescence in C.elegans embryos. eLife 2022; 11:76836. [PMID: 35929725 PMCID: PMC9448323 DOI: 10.7554/elife.76836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 08/01/2022] [Indexed: 11/18/2022] Open
Abstract
Systematic analysis of rich behavioral recordings is being used to uncover how circuits encode complex behaviors. Here, we apply this approach to embryos. What are the first embryonic behaviors and how do they evolve as early neurodevelopment ensues? To address these questions, we present a systematic description of behavioral maturation for Caenorhabditis elegans embryos. Posture libraries were built using a genetically encoded motion capture suit imaged with light-sheet microscopy and annotated using custom tracking software. Analysis of cell trajectories, postures, and behavioral motifs revealed a stereotyped developmental progression. Early movement is dominated by flipping between dorsal and ventral coiling, which gradually slows into a period of reduced motility. Late-stage embryos exhibit sinusoidal waves of dorsoventral bends, prolonged bouts of directed motion, and a rhythmic pattern of pausing, which we designate slow wave twitch (SWT). Synaptic transmission is required for late-stage motion but not for early flipping nor the intervening inactive phase. A high-throughput behavioral assay and calcium imaging revealed that SWT is elicited by the rhythmic activity of a quiescence-promoting neuron (RIS). Similar periodic quiescent states are seen prenatally in diverse animals and may play an important role in promoting normal developmental outcomes.
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Affiliation(s)
- Evan L Ardiel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
| | - Andrew Lauziere
- National Institute of Biomedical Imaging and Bioengineering, Bethesda, United States
| | - Stephen Xu
- National Institute of Biomedical Imaging and Bioengineering, Bethesda, United States
| | - Brandon J Harvey
- National Institute of Biomedical Imaging and Bioengineering, Bethesda, United States
| | | | - Stephen Nurrish
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
| | - Joshua M Kaplan
- Department of Molecular Biology, Massachusetts General Hospital, Boston, United States
| | - Hari Shroff
- National Institute of Biomedical Imaging and Bioengineering, Bethesda, United States
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8
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Santella A, Kolotuev I, Kizilyaprak C, Bao Z. Cross-modality synthesis of EM time series and live fluorescence imaging. eLife 2022; 11:77918. [PMID: 35666127 PMCID: PMC9213002 DOI: 10.7554/elife.77918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/05/2022] [Indexed: 11/13/2022] Open
Abstract
Analyses across imaging modalities allow the integration of complementary spatiotemporal information about brain development, structure, and function. However, systematic atlasing across modalities is limited by challenges to effective image alignment. We combine highly spatially resolved electron microscopy (EM) and highly temporally resolved time-lapse fluorescence microscopy (FM) to examine the emergence of a complex nervous system in Caenorhabditis elegans embryogenesis. We generate an EM time series at four classic developmental stages and create a landmark-based co-optimization algorithm for cross-modality image alignment, which handles developmental heterochrony among datasets to achieve accurate single-cell level alignment. Synthesis based on the EM series and time-lapse FM series carrying different cell-specific markers reveals critical dynamic behaviors across scales of identifiable individual cells in the emergence of the primary neuropil, the nerve ring, as well as a major sensory organ, the amphid. Our study paves the way for systematic cross-modality data synthesis in C. elegans and demonstrates a powerful approach that may be applied broadly.
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Affiliation(s)
- Anthony Santella
- Molecular Cytology Core, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Irina Kolotuev
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | | | - Zhirong Bao
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States
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9
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When is a neuron like an epithelial cell. Dev Biol 2022; 489:161-164. [DOI: 10.1016/j.ydbio.2022.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/18/2022] [Indexed: 11/30/2022]
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10
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Sengupta T, Koonce NL, Vázquez-Martínez N, Moyle MW, Duncan LH, Emerson SE, Han X, Shao L, Wu Y, Santella A, Fan L, Bao Z, Mohler W, Shroff H, Colón-Ramos DA. Differential adhesion regulates neurite placement via a retrograde zippering mechanism. eLife 2021; 10:71171. [PMID: 34783657 PMCID: PMC8843091 DOI: 10.7554/elife.71171] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
During development, neurites and synapses segregate into specific neighborhoods or layers within nerve bundles. The developmental programs guiding placement of neurites in specific layers, and hence their incorporation into specific circuits, are not well understood. We implement novel imaging methods and quantitative models to document the embryonic development of the C. elegans brain neuropil, and discover that differential adhesion mechanisms control precise placement of single neurites onto specific layers. Differential adhesion is orchestrated via developmentally-regulated expression of the IgCAM SYG-1, and its partner ligand SYG-2. Changes in SYG-1 expression across neuropil layers result in changes in adhesive forces, which sort SYG-2-expressing neurons. Sorting to layers occurs, not via outgrowth from the neurite tip, but via an alternate mechanism of retrograde zippering, involving interactions between neurite shafts. Our study indicates that biophysical principles from differential adhesion govern neurite placement and synaptic specificity in vivo in developing neuropil bundles.
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Affiliation(s)
- Titas Sengupta
- Yale University School of Medicine, New Haven, United States
| | - Noelle L Koonce
- Yale University School of Medicine, New Haven, United States
| | | | - Mark W Moyle
- Yale University School of Medicine, New Haven, United States
| | | | - Sarah E Emerson
- Yale University School of Medicine, New Haven, United States
| | - Xiaofei Han
- National Institutes of Health, Bethesda, United States
| | - Lin Shao
- Yale University School of Medicine, New Haven, United States
| | - Yicong Wu
- National Institutes of Health, Bethesda, United States
| | - Anthony Santella
- Developmental Biology Program, Molecular Cytology Core, Sloan-Kettering Institute, New York, United States
| | - Li Fan
- Helen and Robert Appel Alzheimer's Disease Institute, Weill Cornell Medicine, New York, United States
| | - Zhirong Bao
- Developmental Biology Program, Sloan-Kettering Institute, New York, United States
| | - William Mohler
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, United States
| | - Hari Shroff
- National Institutes of Health, Bethesda, United States
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Loss of the Extracellular Matrix Protein DIG-1 Causes Glial Fragmentation, Dendrite Breakage, and Dendrite Extension Defects. J Dev Biol 2021; 9:jdb9040042. [PMID: 34698211 PMCID: PMC8544517 DOI: 10.3390/jdb9040042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 12/03/2022] Open
Abstract
The extracellular matrix (ECM) guides and constrains the shape of the nervous system. In C. elegans, DIG-1 is a giant ECM component that is required for fasciculation of sensory dendrites during development and for maintenance of axon positions throughout life. We identified four novel alleles of dig-1 in three independent screens for mutants affecting disparate aspects of neuronal and glial morphogenesis. First, we find that disruption of DIG-1 causes fragmentation of the amphid sheath glial cell in larvae and young adults. Second, it causes severing of the BAG sensory dendrite from its terminus at the nose tip, apparently due to breakage of the dendrite as animals reach adulthood. Third, it causes embryonic defects in dendrite fasciculation in inner labial (IL2) sensory neurons, as previously reported, as well as rare defects in IL2 dendrite extension that are enhanced by loss of the apical ECM component DYF-7, suggesting that apical and basolateral ECM contribute separately to dendrite extension. Our results highlight novel roles for DIG-1 in maintaining the cellular integrity of neurons and glia, possibly by creating a barrier between structures in the nervous system.
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Lee J, Magescas J, Fetter RD, Feldman JL, Shen K. Inherited apicobasal polarity defines the key features of axon-dendrite polarity in a sensory neuron. Curr Biol 2021; 31:3768-3783.e3. [PMID: 34270949 DOI: 10.1016/j.cub.2021.06.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 05/05/2021] [Accepted: 06/14/2021] [Indexed: 11/25/2022]
Abstract
Neurons are highly polarized cells with morphologically and functionally distinct dendritic and axonal processes. The molecular mechanisms that establish axon-dendrite polarity in vivo are poorly understood. Here, we describe the initial polarization of posterior deirid (PDE), a ciliated mechanosensory neuron, during development in vivo through 4D live imaging with endogenously tagged proteins. PDE inherits and maintains apicobasal polarity from its epithelial precursor. Its apical domain is directly transformed into the ciliated dendritic tip through apical constriction, which is followed by axonal outgrowth from the opposite basal side of the cell. The apical Par complex and junctional proteins persistently localize at the developing dendritic domain throughout this transition. Consistent with their instructive role in axon-dendrite polarization, conditional depletion of the Par complex and junctional proteins results in robust defects in dendrite and axon formation. During apical constriction, a microtubule-organizing center (MTOC) containing the microtubule nucleator γ-tubulin ring complex (γ-TuRC) forms along the apical junction between PDE and its sister cell in a manner dependent on the Par complex and junctional proteins. This junctional MTOC patterns neuronal microtubule polarity and facilitate the dynein-dependent recruitment of the basal body for ciliogenesis. When non-ciliated neurons are genetically manipulated to obtain ciliated neuronal fate, inherited apicobasal polarity is required for generating ciliated dendritic tips. We propose that inherited apicobasal polarity, together with apical cell-cell interactions drive the morphological and cytoskeletal polarity in early neuronal differentiation.
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Affiliation(s)
- Joo Lee
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Jérémy Magescas
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Richard D Fetter
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | | | - Kang Shen
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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13
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Hong H, Chen H, Zhang Y, Wu Z, Zhang Y, Zhang Y, Hu Z, Zhang JV, Ling K, Hu J, Wei Q. DYF-4 regulates patched-related/DAF-6-mediated sensory compartment formation in C. elegans. PLoS Genet 2021; 17:e1009618. [PMID: 34115759 PMCID: PMC8221789 DOI: 10.1371/journal.pgen.1009618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 06/23/2021] [Accepted: 05/24/2021] [Indexed: 11/29/2022] Open
Abstract
Coordination of neurite extension with surrounding glia development is critical for neuronal function, but the underlying molecular mechanisms remain poorly understood. Through a genome-wide mutagenesis screen in C. elegans, we identified dyf-4 and daf-6 as two mutants sharing similar defects in dendrite extension. DAF-6 encodes a glia-specific patched-related membrane protein that plays vital roles in glial morphogenesis. We cloned dyf-4 and found that DYF-4 encodes a glia-secreted protein. Further investigations revealed that DYF-4 interacts with DAF-6 and functions in a same pathway as DAF-6 to regulate sensory compartment formation. Furthermore, we demonstrated that reported glial suppressors of daf-6 could also restore dendrite elongation and ciliogenesis in both dyf-4 and daf-6 mutants. Collectively, our data reveal that DYF-4 is a regulator for DAF-6 which promotes the proper formation of the glial channel and indirectly affects neurite extension and ciliogenesis. In C. elegans sensory organ, the ciliated neuronal endings are wrapped in a luminal channel formed by glial cells, forming a specialized sensory compartment critical for sensory activity. Coordination of glial channel formation, dendritic tip anchoring and ciliogenesis are critical for the formation of a functional sensory compartment. DAF-6, a patched-related glial membrane protein, was reported to play an important role in glial channel morphogenesis, but the molecular function and regulatory mechanism of DAF-6 remain poorly understood. Here, we found that DYF-4, a glia-secreted protein, interacts and colocalizes with DAF-6, and functions in a same pathway as DAF-6 to regulate sensory compartment formation. We propose that DYF-4 is a novel regulator for DAF-6 to control sensory compartment formation.
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Affiliation(s)
- Hui Hong
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Huicheng Chen
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China
| | - Yuxia Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Zhimao Wu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China
| | - Yingying Zhang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China
| | - Yingyi Zhang
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Zeng Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Jian V. Zhang
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China
| | - Kun Ling
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Jinghua Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Qing Wei
- Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences (CAS), Shenzhen, China
- * E-mail:
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14
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Yin C, Peterman E, Rasmussen JP, Parrish JZ. Transparent Touch: Insights From Model Systems on Epidermal Control of Somatosensory Innervation. Front Cell Neurosci 2021; 15:680345. [PMID: 34135734 PMCID: PMC8200473 DOI: 10.3389/fncel.2021.680345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 04/28/2021] [Indexed: 12/28/2022] Open
Abstract
Somatosensory neurons (SSNs) densely innervate our largest organ, the skin, and shape our experience of the world, mediating responses to sensory stimuli including touch, pressure, and temperature. Historically, epidermal contributions to somatosensation, including roles in shaping innervation patterns and responses to sensory stimuli, have been understudied. However, recent work demonstrates that epidermal signals dictate patterns of SSN skin innervation through a variety of mechanisms including targeting afferents to the epidermis, providing instructive cues for branching morphogenesis, growth control and structural stability of neurites, and facilitating neurite-neurite interactions. Here, we focus onstudies conducted in worms (Caenorhabditis elegans), fruit flies (Drosophila melanogaster), and zebrafish (Danio rerio): prominent model systems in which anatomical and genetic analyses have defined fundamental principles by which epidermal cells govern SSN development.
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Affiliation(s)
- Chang Yin
- Department of Biology, University of Washington, Seattle, WA, United States
| | - Eric Peterman
- Department of Biology, University of Washington, Seattle, WA, United States
| | | | - Jay Z Parrish
- Department of Biology, University of Washington, Seattle, WA, United States
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15
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Grimbert S, Mastronardi K, Richard V, Christensen R, Law C, Zardoui K, Fay D, Piekny A. Multi-tissue patterning drives anterior morphogenesis of the C. elegans embryo. Dev Biol 2021; 471:49-64. [PMID: 33309948 PMCID: PMC8597047 DOI: 10.1016/j.ydbio.2020.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 11/23/2022]
Abstract
Complex structures derived from multiple tissue types are challenging to study in vivo, and our knowledge of how cells from different tissues are coordinated is limited. Model organisms have proven invaluable for improving our understanding of how chemical and mechanical cues between cells from two different tissues can govern specific morphogenetic events. Here we used Caenorhabditis elegans as a model system to show how cells from three different tissues are coordinated to give rise to the anterior lumen. While some aspects of pharyngeal morphogenesis have been well-described, it is less clear how cells from the pharynx, epidermis and neuroblasts coordinate to define the location of the anterior lumen and supporting structures. Using various microscopy and software approaches, we define the movements and patterns of these cells during anterior morphogenesis. Projections from the anterior-most pharyngeal cells (arcade cells) provide the first visible markers for the location of the future lumen, and facilitate patterning of the surrounding neuroblasts. These neuroblast patterns control the rate of migration of the anterior epidermal cells, whereas the epidermal cells ultimately reinforce and control the position of the future lumen, as they must join with the pharyngeal cells for their epithelialization. Our studies are the first to characterize anterior morphogenesis in C. elegans in detail and should lay the framework for identifying how these different patterns are controlled at the molecular level.
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Affiliation(s)
- Stéphanie Grimbert
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, H4B 1R6, Canada
| | - Karina Mastronardi
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, H4B 1R6, Canada
| | - Victoria Richard
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, H4B 1R6, Canada
| | - Ryan Christensen
- Laboratory of High Resolution Optical Imaging, NIH/NIBIB, 13 South Drive, Bethesda, MD, 20892, USA
| | - Christopher Law
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, H4B 1R6, Canada
| | - Khashayar Zardoui
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, H4B 1R6, Canada
| | - David Fay
- Department of Molecular Biology, University of Wyoming, 1000 E. University Ave., Laramie, WY, 82071, USA
| | - Alisa Piekny
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montreal, Quebec, H4B 1R6, Canada.
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16
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Kunz P, Lehmann C, Pohl C. Differential Thresholds of Proteasome Activation Reveal Two Separable Mechanisms of Sensory Organ Polarization in C. elegans. Front Cell Dev Biol 2021; 9:619596. [PMID: 33634121 PMCID: PMC7900421 DOI: 10.3389/fcell.2021.619596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/19/2021] [Indexed: 01/01/2023] Open
Abstract
Cephalization is a major innovation of animal evolution and implies a synchronization of nervous system, mouth, and foregut polarization to align alimentary tract and sensomotoric system for effective foraging. However, the underlying integration of morphogenetic programs is poorly understood. Here, we show that invagination of neuroectoderm through de novo polarization and apical constriction creates the mouth opening in the Caenorhabditis elegans embryo. Simultaneously, all 18 juxta-oral sensory organ dendritic tips become symmetrically positioned around the mouth: While the two bilaterally symmetric amphid sensilla endings are towed to the mouth opening, labial and cephalic sensilla become positioned independently. Dendrite towing is enabled by the pre-polarized sensory amphid pores intercalating into the leading edge of the anteriorly migrating epidermal sheet, while apical constriction-mediated cell–cell re-arrangements mediate positioning of all other sensory organs. These two processes can be separated by gradual inactivation of the 26S proteasome activator, RPN-6.1. Moreover, RPN-6.1 also shows a dose-dependent requirement for maintenance of coordinated apical polarization of other organs with apical lumen, the pharynx, and the intestine. Thus, our data unveil integration of morphogenetic programs during the coordination of alimentary tract and sensory organ formation and suggest that this process requires tight control of ubiquitin-dependent protein degradation.
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Affiliation(s)
- Patricia Kunz
- Buchmann Institute for Molecular Life Sciences and Institute of Biochemistry II, Medical Faculty, Goethe University Frankfurt, Frankfurt, Germany
| | - Christina Lehmann
- Buchmann Institute for Molecular Life Sciences and Institute of Biochemistry II, Medical Faculty, Goethe University Frankfurt, Frankfurt, Germany
| | - Christian Pohl
- Buchmann Institute for Molecular Life Sciences and Institute of Biochemistry II, Medical Faculty, Goethe University Frankfurt, Frankfurt, Germany
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17
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Abstract
As multi-cellular organisms evolved from small clusters of cells to complex metazoans, biological tubes became essential for life. Tubes are typically thought of as mainly playing a role in transport, with the hollow space (lumen) acting as a conduit to distribute nutrients and waste, or for gas exchange. However, biological tubes also provide a platform for physiological, mechanical, and structural functions. Indeed, tubulogenesis is often a critical aspect of morphogenesis and organogenesis. C. elegans is made up of tubes that provide structural support and protection (the epidermis), perform the mechanical and enzymatic processes of digestion (the buccal cavity, pharynx, intestine, and rectum), transport fluids for osmoregulation (the excretory system), and execute the functions necessary for reproduction (the germline, spermatheca, uterus and vulva). Here we review our current understanding of the genetic regulation, molecular processes, and physical forces involved in tubulogenesis and morphogenesis of the epidermal, digestive and excretory systems in C. elegans.
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Affiliation(s)
- Daniel D Shaye
- Department of Physiology and Biophysics, University of Illinois at Chicago-College of Medicine, Chicago, IL, United States.
| | - Martha C Soto
- Department of Pathology and Laboratory Medicine, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, United States.
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18
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Nechipurenko I, Lavrentyeva S, Sengupta P. GRDN-1/Girdin regulates dendrite morphogenesis and cilium position in two specialized sensory neuron types in C. elegans. Dev Biol 2021; 472:38-51. [PMID: 33460640 DOI: 10.1016/j.ydbio.2020.12.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/18/2020] [Accepted: 12/22/2020] [Indexed: 10/22/2022]
Abstract
Primary cilia are located at the dendritic tips of sensory neurons and house the molecular machinery necessary for detection and transduction of sensory stimuli. The mechanisms that coordinate dendrite extension with cilium position during sensory neuron development are not well understood. Here, we show that GRDN-1, the Caenorhabditis elegans ortholog of the highly conserved scaffold and signaling protein Girdin/GIV, regulates both cilium position and dendrite extension in the postembryonic AQR and PQR gas-sensing neurons. Mutations in grdn-1 disrupt dendrite outgrowth and mislocalize cilia to the soma or proximal axonal segments in AQR, and to a lesser extent, in PQR. GRDN-1 is localized to the basal body and regulates localization of HMR-1/Cadherin to the distal AQR dendrite. However, knockdown of HMR-1 and/or loss of SAX-7/LICAM, molecules previously implicated in sensory dendrite development in C. elegans, do not alter AQR dendrite morphology or cilium position. We find that GRDN-1 localization in AQR is regulated by UNC-116/Kinesin-1, and that correspondingly, unc-116 mutants exhibit severe AQR dendrite outgrowth and cilium positioning defects. In contrast, GRDN-1 and cilium localization in PQR is modulated by LIN-44/Wnt signaling. Together, these findings identify upstream regulators of GRDN-1, and describe new cell-specific roles for this multifunctional protein in sensory neuron development.
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Affiliation(s)
- Inna Nechipurenko
- Department of Biology, Brandeis University, Waltham, MA, USA; Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA.
| | | | - Piali Sengupta
- Department of Biology, Brandeis University, Waltham, MA, USA.
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19
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Cohen JD, Sundaram MV. C. elegans Apical Extracellular Matrices Shape Epithelia. J Dev Biol 2020; 8:E23. [PMID: 33036165 PMCID: PMC7712855 DOI: 10.3390/jdb8040023] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023] Open
Abstract
Apical extracellular matrices (aECMs) coat exposed surfaces of epithelia to shape developing tissues and protect them from environmental insults. Despite their widespread importance for human health, aECMs are poorly understood compared to basal and stromal ECMs. The nematode Caenorhabditis elegans contains a variety of distinct aECMs, some of which share many of the same types of components (lipids, lipoproteins, collagens, zona pellucida domain proteins, chondroitin glycosaminoglycans and proteoglycans) with mammalian aECMs. These aECMs include the eggshell, a glycocalyx-like pre-cuticle, both collagenous and chitin-based cuticles, and other understudied aECMs of internal epithelia. C. elegans allows rapid genetic manipulations and live imaging of fluorescently-tagged aECM components, and is therefore providing new insights into aECM structure, trafficking, assembly, and functions in tissue shaping.
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Affiliation(s)
| | - Meera V. Sundaram
- Department of Genetics, University of Pennsylvania Perelman School of Medicine 415 Curie Blvd, Philadelphia, PA 19104-6145, USA;
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20
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Cebul ER, McLachlan IG, Heiman MG. Dendrites with specialized glial attachments develop by retrograde extension using SAX-7 and GRDN-1. Development 2020; 147:dev.180448. [PMID: 31988188 DOI: 10.1242/dev.180448] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 01/07/2020] [Indexed: 12/18/2022]
Abstract
Dendrites develop elaborate morphologies in concert with surrounding glia, but the molecules that coordinate dendrite and glial morphogenesis are mostly unknown. C. elegans offers a powerful model for identifying such factors. Previous work in this system examined dendrites and glia that develop within epithelia, similar to mammalian sense organs. Here, we focus on the neurons BAG and URX, which are not part of an epithelium but instead form membranous attachments to a single glial cell at the nose, reminiscent of dendrite-glia contacts in the mammalian brain. We show that these dendrites develop by retrograde extension, in which the nascent dendrite endings anchor to the presumptive nose and then extend by stretching during embryo elongation. Using forward genetic screens, we find that dendrite development requires the adhesion protein SAX-7/L1CAM and the cytoplasmic protein GRDN-1/CCDC88C to anchor dendrite endings at the nose. SAX-7 acts in neurons and glia, while GRDN-1 acts in glia to non-autonomously promote dendrite extension. Thus, this work shows how glial factors can help to shape dendrites, and identifies a novel molecular mechanism for dendrite growth by retrograde extension.
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Affiliation(s)
- Elizabeth R Cebul
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Ian G McLachlan
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Maxwell G Heiman
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
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21
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Bai X, Melesse M, Sorensen Turpin CG, Sloan DE, Chen CY, Wang WC, Lee PY, Simmons JR, Nebenfuehr B, Mitchell D, Klebanow LR, Mattson N, Betzig E, Chen BC, Cheerambathur D, Bembenek JN. Aurora B functions at the apical surface after specialized cytokinesis during morphogenesis in C. elegans. Development 2020; 147:dev.181099. [PMID: 31806662 PMCID: PMC6983721 DOI: 10.1242/dev.181099] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 11/26/2019] [Indexed: 12/18/2022]
Abstract
Although cytokinesis has been intensely studied, the way it is executed during development is not well understood, despite a long-standing appreciation that various aspects of cytokinesis vary across cell and tissue types. To address this, we investigated cytokinesis during the invariant Caenorhabditis elegans embryonic divisions and found several parameters that are altered at different stages in a reproducible manner. During early divisions, furrow ingression asymmetry and midbody inheritance is consistent, suggesting specific regulation of these events. During morphogenesis, we found several unexpected alterations to cytokinesis, including apical midbody migration in polarizing epithelial cells of the gut, pharynx and sensory neurons. Aurora B kinase, which is essential for several aspects of cytokinesis, remains apically localized in each of these tissues after internalization of midbody ring components. Aurora B inactivation disrupts cytokinesis and causes defects in apical structures, even if inactivated post-mitotically. Therefore, we demonstrate that cytokinesis is implemented in a specialized way during epithelial polarization and that Aurora B has a role in the formation of the apical surface.
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Affiliation(s)
- Xiaofei Bai
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Michael Melesse
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | | | - Dillon E. Sloan
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA,Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chin-Yi Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Wen-Cheng Wang
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Po-Yi Lee
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - James R. Simmons
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Benjamin Nebenfuehr
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Diana Mitchell
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lindsey R. Klebanow
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Nicholas Mattson
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Eric Betzig
- Janelia Research Campus, HHMI, Ashburn, VA 20147, USA
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan,Janelia Research Campus, HHMI, Ashburn, VA 20147, USA
| | - Dhanya Cheerambathur
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Joshua N. Bembenek
- Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA,Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA,Author for correspondence ()
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22
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Wang D, Lu Z, Xu Y, Wang ZI, Santella A, Bao Z. Cellular structure image classification with small targeted training samples. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2019; 7:148967-148974. [PMID: 32832309 PMCID: PMC7442139 DOI: 10.1109/access.2019.2940161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cell shapes provide crucial biological information on complex tissues. Different cell types often have distinct cell shapes, and collective shape changes usually indicate morphogenetic events and mechanisms. The identification and detection of collective cell shape changes in an extensive collection of 3D time-lapse images of complex tissues is an important step in assaying such mechanisms but is a tedious and time-consuming task. Machine learning provides new opportunities to automatically detect cell shape changes. However, it is challenging to generate sufficient training samples for pattern identification through deep learning because of a limited amount of images and annotations. We present a deep learning approach with minimal well-annotated training samples and apply it to identify multicellular rosettes from 3D live images of the Caenorhabditis elegans embryo with fluorescently labeled cell membranes. Our strategy is to combine two approaches, namely, feature transfer and generative adversarial networks (GANs), to boost image classification with small training samples. Specifically, we use a GAN framework and conduct an unsupervised training to capture the general characteristics of cell membrane images with 11,250 unlabelled images. We then transfer the structure of the GAN discriminator into a new Alex-style neural network for further learning with several dozen labeled samples. Our experiments showed that with 10-15 well-labeled rosette images and 30-40 randomly selected nonrosette images our approach can identify rosettes with more than 80% accuracy and capture more than 90% of the model accuracy achieved with a training data et that is five times larger. We also established a public benchmark dataset for rosette detection. This GAN-based transfer approach can be applied to the study of other cellular structures with minimal training samples.
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Affiliation(s)
- Dali Wang
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN 37934, USA
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Zheng Lu
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN 37934, USA
| | - Yichi Xu
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Z I Wang
- Department of Electrical Engineering and Computer Science, University of Tennessee, Knoxville, TN 37934, USA
| | - Anthony Santella
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Zhirong Bao
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
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23
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Low IIC, Williams CR, Chong MK, McLachlan IG, Wierbowski BM, Kolotuev I, Heiman MG. Morphogenesis of neurons and glia within an epithelium. Development 2019; 146:dev.171124. [PMID: 30683663 DOI: 10.1242/dev.171124] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 01/15/2019] [Indexed: 12/13/2022]
Abstract
To sense the outside world, some neurons protrude across epithelia, the cellular barriers that line every surface of our bodies. To study the morphogenesis of such neurons, we examined the C. elegans amphid, in which dendrites protrude through a glial channel at the nose. During development, amphid dendrites extend by attaching to the nose via DYF-7, a type of protein typically found in epithelial apical ECM. Here, we show that amphid neurons and glia exhibit epithelial properties, including tight junctions and apical-basal polarity, and develop in a manner resembling other epithelia. We find that DYF-7 is a fibril-forming apical ECM component that promotes formation of the tube-shaped glial channel, reminiscent of roles for apical ECM in other narrow epithelial tubes. We also identify a requirement for FRM-2, a homolog of EPBL15/moe/Yurt that promotes epithelial integrity in other systems. Finally, we show that other environmentally exposed neurons share a requirement for DYF-7. Together, our results suggest that these neurons and glia can be viewed as part of an epithelium continuous with the skin, and are shaped by mechanisms shared with other epithelia.
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Affiliation(s)
- Isabel I C Low
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Claire R Williams
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Megan K Chong
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Ian G McLachlan
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Bradley M Wierbowski
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
| | - Irina Kolotuev
- Université de Rennes 1, Plateforme microscopie électronique, 35043 Rennes, France
| | - Maxwell G Heiman
- Department of Genetics, Blavatnik Institute, Harvard Medical School and Boston Children's Hospital, Boston, MA 02115, USA
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