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Grossman EN, Giurumescu CA, Chisholm AD. Mechanisms of ephrin receptor protein kinase-independent signaling in amphid axon guidance in Caenorhabditis elegans. Genetics 2013; 195:899-913. [PMID: 23979582 PMCID: PMC3813872 DOI: 10.1534/genetics.113.154393] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/16/2013] [Indexed: 12/30/2022] Open
Abstract
Eph receptors and their ephrin ligands are key conserved regulators of axon guidance and can function in a variety of signaling modes. Here we analyze the genetic and cellular requirements for Eph signaling in a Caenorhabditis elegans axon guidance choice point, the ventral guidance of axons in the amphid commissure. The C. elegans Eph receptor EFN-1 has both kinase-dependent and kinase-independent roles in amphid ventral guidance. Of the four C. elegans ephrins, we find that only EFN-1 has a major role in amphid axon ventral guidance, and signals in both a receptor kinase-dependent and kinase-independent manner. Analysis of EFN-1 and EFN-1 expression and tissue-specific requirements is consistent with a model in which VAB-1 acts in amphid neurons, interacting with EFN-1 expressed on surrounding cells. Unexpectedly, left-hand neurons are more strongly affected than right-hand neurons by loss of Eph signaling, indicating a previously undetected left-right asymmetry in the requirement for Eph signaling. By screening candidate genes involved in Eph signaling, we find that the Eph kinase-independent pathway involves the ABL-1 nonreceptor tyrosine kinase and possibly the phosphatidylinositol 3-kinase pathway. Overexpression of ABL-1 is sufficient to rescue EFN-1 ventral guidance defects cell autonomously. Our results reveal new aspects of Eph signaling in a single axon guidance decision in vivo.
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Affiliation(s)
- Emily N. Grossman
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093
| | - Claudiu A. Giurumescu
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093
| | - Andrew D. Chisholm
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California 92093
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Giurumescu CA, Kang S, Planchon TA, Betzig E, Bloomekatz J, Yelon D, Cosman P, Chisholm AD. Quantitative semi-automated analysis of morphogenesis with single-cell resolution in complex embryos. Development 2012; 139:4271-9. [PMID: 23052905 DOI: 10.1242/dev.086256] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A quantitative understanding of tissue morphogenesis requires description of the movements of individual cells in space and over time. In transparent embryos, such as C. elegans, fluorescently labeled nuclei can be imaged in three-dimensional time-lapse (4D) movies and automatically tracked through early cleavage divisions up to ~350 nuclei. A similar analysis of later stages of C. elegans development has been challenging owing to the increased error rates of automated tracking of large numbers of densely packed nuclei. We present Nucleitracker4D, a freely available software solution for tracking nuclei in complex embryos that integrates automated tracking of nuclei in local searches with manual curation. Using these methods, we have been able to track >99% of all nuclei generated in the C. elegans embryo. Our analysis reveals that ventral enclosure of the epidermis is accompanied by complex coordinated migration of the neuronal substrate. We can efficiently track large numbers of migrating nuclei in 4D movies of zebrafish cardiac morphogenesis, suggesting that this approach is generally useful in situations in which the number, packing or dynamics of nuclei present challenges for automated tracking.
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Affiliation(s)
- Claudiu A Giurumescu
- Division of Biological Sciences, Section of Cell and Developmental Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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Abstract
Caenorhabditis elegans is uniquely suited to the analysis of cell lineage patterns. C. elegans has a small number of somatic cells whose position and morphology are almost invariant from animal to animal. Because C. elegans is virtually transparent, cells can be identified in live animals using a simple bright-field microscopy technique, Nomarski differential interference contrast (DIC), or by expression of transgenic fluorescent reporter genes. The small size and rapid development of C. elegans mean that animals can develop while under continuous observation, allowing cell lineages to be analyzed throughout embryonic and postembryonic development. Embryonic cell lineages can also be traced semiautomatically using timelapse imaging of GFP-labeled nuclei. Analysis of mutant cell lineages remains important for defining the roles of developmental control genes.
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Affiliation(s)
- Claudiu A Giurumescu
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
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Gotenstein JR, Swale RE, Fukuda T, Wu Z, Giurumescu CA, Goncharov A, Jin Y, Chisholm AD. The C. elegans peroxidasin PXN-2 is essential for embryonic morphogenesis and inhibits adult axon regeneration. Development 2010; 137:3603-13. [PMID: 20876652 PMCID: PMC2964093 DOI: 10.1242/dev.049189] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2010] [Indexed: 02/03/2023]
Abstract
Peroxidasins form a highly conserved family of extracellular peroxidases of unknown cellular function. We identified the C. elegans peroxidasin PXN-2 in screens for mutants defective in embryonic morphogenesis. We find that PXN-2 is essential for specific stages of embryonic morphogenesis and muscle-epidermal attachment, and is also required postembryonically for basement membrane integrity. The peroxidase catalytic activity of PXN-2 is necessary for these developmental roles. pxn-2 mutants display aberrant ultrastructure of the extracellular matrix, suggesting a role in basement membrane consolidation. PXN-2 affects specific axon guidance choice points in the developing nervous system but is dispensable for maintenance of process positions. In adults, loss of pxn-2 function promotes regrowth of axons after injury, providing the first evidence that C. elegans extracellular matrix can play an inhibitory role in axon regeneration. Loss of function in the closely related C. elegans peroxidasin pxn-1 does not cause overt developmental defects. Unexpectedly, pxn-2 mutant phenotypes are suppressed by loss of function in pxn-1 and exacerbated by overexpression of wild-type pxn-1, indicating that PXN-1 and PXN-2 have antagonistic functions. These results demonstrate that peroxidasins play crucial roles in development and reveal a new role for peroxidasins as extracellular inhibitors of axonal regeneration.
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Affiliation(s)
- Jennifer R. Gotenstein
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Ryann E. Swale
- Department of Molecular, Cell and Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA
| | - Tetsuko Fukuda
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Zilu Wu
- Howard Hughes Medical Institute
| | - Claudiu A. Giurumescu
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | | | - Yishi Jin
- Howard Hughes Medical Institute
- Section of Neurobiology, Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Andrew D. Chisholm
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Department of Molecular, Cell and Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, CA 95064, USA
- Section of Neurobiology, Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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Giurumescu CA, Sternberg PW, Asthagiri AR. Predicting phenotypic diversity and the underlying quantitative molecular transitions. PLoS Comput Biol 2009; 5:e1000354. [PMID: 19360093 PMCID: PMC2661366 DOI: 10.1371/journal.pcbi.1000354] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Accepted: 03/10/2009] [Indexed: 11/19/2022] Open
Abstract
During development, signaling networks control the formation of multicellular
patterns. To what extent quantitative fluctuations in these complex networks may
affect multicellular phenotype remains unclear. Here, we describe a
computational approach to predict and analyze the phenotypic diversity that is
accessible to a developmental signaling network. Applying this framework to
vulval development in C. elegans, we demonstrate that
quantitative changes in the regulatory network can render ∼500
multicellular phenotypes. This phenotypic capacity is an order-of-magnitude
below the theoretical upper limit for this system but yet is large enough to
demonstrate that the system is not restricted to a select few outcomes. Using
metrics to gauge the robustness of these phenotypes to parameter perturbations,
we identify a select subset of novel phenotypes that are the most promising for
experimental validation. In addition, our model calculations provide a layout of
these phenotypes in network parameter space. Analyzing this landscape of
multicellular phenotypes yielded two significant insights. First, we show that
experimentally well-established mutant phenotypes may be rendered using
non-canonical network perturbations. Second, we show that the predicted
multicellular patterns include not only those observed in C.
elegans, but also those occurring exclusively in other species of the
Caenorhabditis genus. This result demonstrates that
quantitative diversification of a common regulatory network is indeed
demonstrably sufficient to generate the phenotypic differences observed across
three major species within the Caenorhabditis genus. Using our
computational framework, we systematically identify the quantitative changes
that may have occurred in the regulatory network during the evolution of these
species. Our model predictions show that significant phenotypic diversity may be
sampled through quantitative variations in the regulatory network without
overhauling the core network architecture. Furthermore, by comparing the
predicted landscape of phenotypes to multicellular patterns that have been
experimentally observed across multiple species, we systematically trace the
quantitative regulatory changes that may have occurred during the evolution of
the Caenorhabditis genus. The diversity of metazoan life forms that we experience today arose as
multicellular systems continually sampled new phenotypes that withstood ever
changing selective pressures. This phenotypic diversification is driven by
variations in the underlying regulatory network that instructs cells to form
multicellular patterns and structures. Here, we computationally construct the
phenotypic diversity that may be accessible through quantitative tuning of the
regulatory network that drives multicellular patterning during C.
elegans vulval development. We show that significant phenotypic
diversity may be sampled through quantitative variations without overhauling the
core regulatory network architecture. Furthermore, by comparing the predicted
landscape of phenotypes to multicellular patterns that have been experimentally
observed across multiple species, we systematically deduce the quantitative
molecular changes that may have transpired during the evolution of the
Caenorhabditis genus.
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Affiliation(s)
- Claudiu A. Giurumescu
- Division of Chemistry and Chemical Engineering, California Institute of
Technology, Pasadena, California, United States of America
| | - Paul W. Sternberg
- Division of Biology, California Institute of Technology, Pasadena,
California, United States of America
| | - Anand R. Asthagiri
- Division of Chemistry and Chemical Engineering, California Institute of
Technology, Pasadena, California, United States of America
- * E-mail:
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Abstract
Developing design strategies for tissue engineering and regenerative medicine is limited by our nascent understanding of how cell populations "self-organize" into multicellular structures on synthetic scaffolds. Mechanistic insights can be gleaned from the quantitative analysis of biomolecular signals that drive multicellular patterning during the natural processes of embryonic and adult development. This review describes three critical layers of signal processing that govern multicellular patterning: spatiotemporal presentation of extracellular cues, intracellular signaling networks that mediate crosstalk among extracellular cues, and finally, intranuclear signal integration at the level of transcriptional regulation. At every level in this hierarchy, the quantitative attributes of signals have a profound impact on patterning. We discuss how experiments and mathematical models are being used to uncover these quantitative features and their impact on multicellular phenotype.
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Affiliation(s)
- Claudiu A Giurumescu
- Division of Chemistry and Chemical Engineering, The Jacobs Institute for Molecular Engineering for Medicine, California Institute of Technology, Pasadena, California 91125, USA
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Giurumescu CA, Sternberg PW, Asthagiri AR. Intercellular coupling amplifies fate segregation during Caenorhabditis elegans vulval development. Proc Natl Acad Sci U S A 2006; 103:1331-6. [PMID: 16432231 PMCID: PMC1360524 DOI: 10.1073/pnas.0506476103] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
During vulval development in Caenorhabditis elegans, six precursor cells acquire a spatial pattern of distinct cell fates. This process is guided by a gradient in the soluble factor, LIN-3, and by direct interactions between neighboring cells mediated by the Notch-like receptor, LIN-12. Genetic evidence has revealed that these two extracellular signals are coupled: lateral cell-cell interactions inhibit LIN-3-mediated signaling, whereas LIN-3 regulates the extent of lateral signaling. To elucidate the quantitative implications of this coupled network topology for cell patterning during vulval development, we developed a mathematical model of LIN-3/LIN-12-mediated signaling in the vulval precursor cell array. Our analysis reveals that coupling LIN-3 and LIN-12 amplifies cellular perception of the LIN-3 gradient and polarizes lateral signaling, both of which enhance fate segregation beyond that achievable by an uncoupled system.
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Affiliation(s)
- Claudiu A Giurumescu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, CA 91125, USA
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