James Sharpe

Institut Marqués, Spain, Barcelona, Barcino, Catalonia, Spain

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Publications (114)613.8 Total impact

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    ABSTRACT: Reactive lymph nodes (LNs) are sites where pMHC-loaded dendritic cells (DCs) interact with rare cognate T cells, leading to their clonal expansion. While DC interactions with T cell subsets critically shape the ensuing immune response, surprisingly little is known on their spatial orchestration at physiologically T cell low precursor frequencies. Light sheet fluorescence microscopy and one of its implementations, selective plane illumination microscopy (SPIM), is a powerful method to obtain precise spatial information of entire organs of 0.5–10 mm diameter, the size range of murine LNs. Yet, its usefulness for immunological research has thus far not been comprehensively explored. Here, we have tested and defined protocols that preserve fluorescent protein function during lymphoid tissue clearing required for SPIM. Reconstructions of SPIM-generated 3D data sets revealed that calibrated numbers of adoptively transferred T cells and DCs are successfully detected at a single cell level within optically cleared murine LNs. Finally, we define parameters to quantify specific interactions between antigen-specific T cells and pMHC-bearing DCs in murine LNs. In sum, our studies describe the successful application of light sheet fluorescence microscopy to immunologically relevant tissues.
    No preview · Article · Feb 2016 · Journal of immunological methods
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    ABSTRACT: During somitogenesis in embryos, a posteriorly moving differentiation front arrests the oscillations of “segmentation clock” genes, leaving behind a frozen, periodic pattern of expression stripes. Both mathematical theories and experimental observations have invoked a “clock and wavefront” model to explain this phenomenon, in which long-range molecular gradients control the movement of the front and therefore the placement of the stripes in the embryo. Here, we develop a fundamentally different model—a progressive oscillatory reaction-diffusion (PORD) system driven by short-range interactions. In this model, posterior movement of the front is a local, emergent phenomenon that, in contrast to the clock and wavefront model, is not controlled by global positional information. The PORD model explains important features of somitogenesis, such as size regulation, that previous reaction-diffusion models could not explain. Moreover, the PORD and clock and wavefront models make different predictions about the results of FGF-inhibition and tissue-cutting experiments, and we demonstrate that the results of these experiments favor the PORD model.
    No preview · Article · Oct 2015
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    ABSTRACT: How the genotype translates into the phenotype through development is critical to fully understand the evolution of phenotypes. We propose a novel approach to directly assess how changes in gene expression patterns are associated with changes in morphology using the limb as a case example. Our method combines molecular biology techniques, such as whole-mount in situ hybridization, with image and shape analysis, extending the use of Geometric Morphometrics to the analysis of non-anatomical shapes, such as gene expression domains. Elliptical Fourier and Procrustes-based semilandmark analyses were used to analyze the variation and covariation patterns of the limb bud shape with the expression patterns of two relevant genes for limb morphogenesis, Hoxa11 and Hoxa13. We devised a multiple thresholding method to semiautomatically segment gene domains at several expression levels in large samples of limb buds from C57Bl6 mouse embryos between 10 and 12 post-fertilization days. Besides providing an accurate phenotyping tool to quantify the spatiotemporal dynamics of gene expression patterns within developing structures, our morphometric analyses revealed high, non-random and gene-specific variation undergoing canalization during limb development. Our results demonstrate that Hoxa11 and Hoxa13, despite being paralogs with analogous functions in limb patterning, show clearly distinct dynamic patterns, both in shape and size, and are associated differently with the limb bud shape. The correspondence between our results and already well-established molecular processes underlying limb development confirms that this morphometric approach is a powerful tool to extract features of development regulating morphogenesis. Such multilevel analyses are promising in systems where not so much molecular information is available and will advance our understanding of the genotype-phenotype map. In systematics, this knowledge will increase our ability to infer how evolution modified a common developmental pattern to generate a wide diversity of morphologies, as in the vertebrate limb.
    Full-text · Article · Sep 2015 · Systematic Biology
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    Manu Uzkudun · Luciano Marcon · James Sharpe
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    ABSTRACT: Parameter optimization coupled with model selection is a convenient approach to infer gene regulatory networks from experimental gene expression data, but so far it has been limited to single cells or static tissues where growth is not significant. Here, we present a computational study in which we determine an optimal gene regulatory network from the spatiotemporal dynamics of gene expression patterns in a complex 2D growing tissue (non-isotropic and heterogeneous growth rates). We use this method to predict the regulatory mechanisms that underlie proximodistal (PD) patterning of the developing limb bud. First, we map the expression patterns of the PD markers Meis1, Hoxa11 and Hoxa13 into a dynamic description of the tissue movements that drive limb morphogenesis. Secondly, we use reverse-engineering to test how different gene regulatory networks can interpret the opposing gradients of fibroblast growth factors (FGF) and retinoic acid (RA) to pattern the PD markers. Finally, we validate and extend the best model against various previously published manipulative experiments, including exogenous application of RA, surgical removal of the FGF source and genetic ectopic expression of Meis1. Our approach identifies the most parsimonious gene regulatory network that can correctly pattern the PD markers downstream of FGF and RA. This network reveals a new model of PD regulation which we call the "crossover model", because the proximal morphogen (RA) controls the distal boundary of Hoxa11, while conversely the distal morphogens (FGFs) control the proximal boundary. © 2015 The Authors. Published under the terms of the CC BY 4.0 license.
    Full-text · Article · Jul 2015 · Molecular Systems Biology
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    ABSTRACT: Biological tissues must generate forces to shape organs and achieve proper development. Such forces often result from the contraction of an apical acto-myosin meshwork. Here we describe an alternative mechanism for tissue contraction, based on individual cell volume change. We show that during Drosophila dorsal closure (DC), a wound healing-related process, the contraction of the amnioserosa (AS) is associated with a major reduction of the volume of its cells, triggered by caspase activation at the onset of the apoptotic program of AS cells. Cell volume decrease results in a contractile force that promotes tissue shrinkage. Estimating mechanical tensions with laser dissection and using 3D biophysical modeling, we show that the cell volume decrease acts together with the contraction of the actin cable surrounding the tissue to govern DC kinetics. Our study identifies a mechanism by which tissues generate forces and movements by modulating individual cell volume during development. Copyright © 2015 Elsevier Inc. All rights reserved.
    Full-text · Article · May 2015 · Developmental Cell
  • Jeremy B. A. Green · James Sharpe
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    ABSTRACT: One of the most fundamental questions in biology is that of biological pattern: how do the structures and shapes of organisms arise? Undoubtedly, the two most influential ideas in this area are those of Alan Turing's 'reaction-diffusion' and Lewis Wolpert's 'positional information'. Much has been written about these two concepts but some confusion still remains, in particular about the relationship between them. Here, we address this relationship and propose a scheme of three distinct ways in which these two ideas work together to shape biological form.
    No preview · Article · Mar 2015 · Development
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    Alba Jiménez · Andreea Munteanu · James Sharpe
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    ABSTRACT: To what extent does the dynamical mechanism producing a specific biological phenotype bias the ability to evolve into novel phenotypes? We use the interpretation of a morphogen gradient into a single stripe of gene expression as a model phenotype. Although there are thousands of three-gene circuit topologies that can robustly develop a stripe of gene expression, the vast majority of these circuits use one of just six fundamentally different dynamical mechanisms. Here we explore the potential for gene circuits that use each of these six mechanisms to evolve novel phenotypes such as multiple stripes, inverted stripes, and gradients of gene expression. Through a comprehensive and systematic analysis, we find that circuits that use alternative mechanisms differ in the likelihood of reaching novel phenotypes through mutation. We characterize the phenotypic transitions and identify key ingredients of the evolutionary potential, such as sensitive interactions and phenotypic hubs. Finally, we provide an intuitive understanding on how the modular design of a particular mechanism favors the access to novel phenotypes. Our work illustrates how the dynamical mechanism by which an organism develops constrains how it can evolve. It is striking that these dynamical mechanisms and their impact on evolvability can be observed even for such an apparently simple patterning task, performed by just three-node circuits.
    Preview · Article · Feb 2015 · Proceedings of the National Academy of Sciences
  • James Sharpe
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    ABSTRACT: Gradients of fibroblast growth factors often induce cells to adopt different fates. A study in zebrafish embryos reveals another, unexpected role when the factors are trapped in small spaces by a special arrangement of cells. SEE LETTER P.120
    No preview · Article · Oct 2014 · Nature
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    ABSTRACT: Highlights ENU-induced mutation of mouse ESCRT-II/Vps25 causes polydactyly Vps25 hypomorphic mutants survive until late gestation unlike ESCRT LOF embryos ESCRT-II constrains digit number by endosome-mediated mod-ulation of FGF signaling Mutations in ESCRT reveal a mechanism underlying congenital limb defects In Brief Using a polydactylous mouse line car-rying a hypomorphic mutation in the Vps25 subunit of the ESCRT-II complex, Handschuh et al. now establish that ubiq-uitously expressed machineries that sort signaling proteins preferentially regulate, or are rate limiting for, select signaling pathways in different contexts of the developing embryo.
    Full-text · Article · Oct 2014 · Cell Reports
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    ABSTRACT: Apert syndrome is a rare congenital disorder characterized by cranial, neural, limb and visceral malformations. Over 98% of Apert cases are caused by two FGFR2 mutations, Ser252Trp and Pro253Arg, which alter the ligand-binding specificity of the receptors. Patients carrying the P253R mutation show more severe limb malformations, such as syndactyly and symphalangism. Here we explored limb morphogenesis in early development using an inbred mouse model of Apert syndrome, Fgfr2+/P253R, to assess whether the P253R mutation induces changes in the expression pattern of Dusp6, a downstream gene of the FGF/FGFR signaling pathway, and whether these genetic changes can be associated with limb malformations in mutant littermates. We performed Geometric Morphometric (GM) analyses of 3D landmark-based data recorded on optical projection tomography (OPT) images of 11.5 embryonic day (E11.5) embryos labeled for Dusp6 expression using whole-mount in situ hybridization. Comparative quantitative analysis of large samples of limbs and their corresponding Dusp6 gene expression pattern show differences in limb size and shape between mutant and unaffected littermates. At E11.5, mutant mice are significantly smaller and appear underdeveloped in comparison with unaffected littermates. Results show that size explains more than 80% of limb shape variation, but when this allometric effect is minimized the limbs of mutant mice, especially hindlimbs, remain different from the limbs of unaffected littermates. Shape differences are also found at the gene expression level, suggesting that altered FGF/FGFR signaling due to the FGFR2 mutation alters Dusp6 gene expression patterns and contributes to limb malformations as early as E11.5. Our morphometric assessment of gene expression patterns by combining OPT and GM is a novel and useful tool to compare normal and disease-altered patterns of variation. Precise embryo phenotyping of Apert syndrome mice will allow us to identify the origins of abnormal processes that can have a damaging effect on the developing limbs.
    No preview · Conference Paper · Oct 2014
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    ABSTRACT: Synthetic biology is a promising tool to study the function and properties of gene regulatory networks. Gene circuits with predefined behaviours have been successfully built and modelled, but largely on a case-by-case basis. Here we go beyond individual networks and explore both computationally and synthetically the design space of possible dynamical mechanisms for 3-node stripe-forming networks. First, we computationally test every possible 3-node network for stripe formation in a morphogen gradient. We discover four different dynamical mechanisms to form a stripe and identify the minimal network of each group. Next, with the help of newly established engineering criteria we build these four networks synthetically and show that they indeed operate with four fundamentally distinct mechanisms. Finally, this close match between theory and experiment allows us to infer and subsequently build a 2-node network that represents the archetype of the explored design space.
    Full-text · Article · Sep 2014 · Nature Communications
  • J Raspopovic · L Marcon · L Russo · J Sharpe
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    ABSTRACT: During limb development, digits emerge from the undifferentiated mesenchymal tissue that constitutes the limb bud. It has been proposed that this process is controlled by a self-organizing Turing mechanism, whereby diffusible molecules interact to produce a periodic pattern of digital and interdigital fates. However, the identities of the molecules remain unknown. By combining experiments and modeling, we reveal evidence that a Turing network implemented by Bmp, Sox9, and Wnt drives digit specification. We develop a realistic two-dimensional simulation of digit patterning and show that this network, when modulated by morphogen gradients, recapitulates the expression patterns of Sox9 in the wild type and in perturbation experiments. Our systems biology approach reveals how a combination of growth, morphogen gradients, and a self-organizing Turing network can achieve robust and reproducible pattern formation.
    No preview · Article · Aug 2014 · Science
  • Niamh C Nowlan · Vikesh Chandaria · James Sharpe
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    ABSTRACT: We have almost no understanding of how our joints take on their range of distinctive shapes, despite the clinical relevance of joint morphogenesis to postnatal skeletal malformations such as developmental dysplasia of the hip (DDH). In this study, we investigate the role of spontaneous prenatal movements in joint morphogenesis using pharmacological immobilization of developing chicks, and assess the system as a suitable model for early-onset hip dysplasia. We show that, prior to joint cavitation, the lack of dynamic muscle contractions has little impact on the shape of the hip joint. However, after the timepoint at which cavitation occurs, a dramatic effect on hip joint morphogenesis was observed. Effects in the immobilized chicks included flattening of the proximal femur, abnormal orientation of the pelvis relative to the femur and abnormal placement and coverage of the acetabulum. Although many clinical case studies have identified reduced or restricted movement as a risk factor for DDH, this study provides the first experimental evidence of the role of prenatal movements in early hip joint development. We propose that the immobilized chick embryo serves as a suitable model system for the type of early-onset DDH which arises due to neuromuscular conditions such as spinal muscular atrophy. © 2014 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res.
    No preview · Article · Jun 2014 · Journal of Orthopaedic Research
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    ABSTRACT: Interpreting a morphogen gradient into a single stripe of gene-expression is a fundamental unit of patterning in early embryogenesis. From both experimental data and computational studies the feed-forward motifs stand out as minimal networks capable of this patterning function. Positive feedback within gene networks has been hypothesised to enhance the sharpness and precision of gene-expression borders, however a systematic analysis has not yet been reported. Here we set out to assess this hypothesis, and find an unexpected result. The addition of positive-feedback can have different effects on two different designs of feed-forward motif- it increases the parametric robustness of one design, while being neutral or detrimental to the other. These results shed light on the abundance of the former motif and especially of mutual-inhibition positive feedback in developmental networks.
    Preview · Article · May 2014 · Scientific Reports

  • No preview · Article · May 2014 · Mycoses
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    ABSTRACT: Mesoscopic 3D imaging has become a widely used optical imaging technique to visualize intact biological specimens. Selective plane illumination microscopy (SPIM) visualizes samples up to a centimeter in size with micrometer resolution by 3D data stitching but is limited to fluorescent contrast. Optical projection tomography (OPT) works with fluorescent and nonfluorescent contrasts, but its resolution is limited in large samples. We present a hybrid setup (OPTiSPIM) combining the advantages of each technique. The combination of fluorescent and nonfluorescent high-resolution 3D data into integrated datasets enables a more extensive representation of mesoscopic biological samples. The modular concept of the OPTiSPIM facilitates incorporation of the transmission OPT modality into already established light sheet based imaging setups.
    Full-text · Article · Feb 2014 · Optics Letters
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    Niamh C Nowlan · James Sharpe
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    ABSTRACT: The biology and mechanobiology of joint cavitation have undergone extensive investigation, but we have almost no understanding of the development of joint shape. Joint morphogenesis, the development of shape, has been identified as the 'least understood aspect of joint formation' (2005, Birth Defects Res C Embryo Today 75, 237), despite the clinical relevance of shape morphogenesis to postnatal skeletal malformations such as developmental dysplasia of the hip. In this study, we characterise development of early hip joint shape in the embryonic chick using direct capture 3D imaging. Contrary to formerly held assumptions that cavitation precedes morphogenesis in joint development, we have found that the major anatomical features of the adult hip are present at Hamburger Hamilton (HH)32, a full day prior to cavitation of the joint at HH34. We also reveal that the pelvis undergoes significant changes in orientation with respect to the femur, despite the lack of a joint cavity between the rudiments. Furthermore, we have identified the appearance of the ischium and pubis several developmental stages earlier than was previously reported, illustrating the value and importance of direct capture 3D imaging.
    Preview · Article · Nov 2013 · Journal of Anatomy
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    ABSTRACT: Senescence is a form of cell-cycle arrest linked to tumor suppression and aging. However, it remains controversial and has not been documented in nonpathologic states. Here we describe senescence as a normal developmental mechanism found throughout the embryo, including the apical ectodermal ridge (AER) and the neural roof plate, two signaling centers in embryonic patterning. Embryonic senescent cells are nonproliferative and share features with oncogene-induced senescence (OIS), including expression of p21, p15, and mediators of the senescence-associated secretory phenotype (SASP). Interestingly, mice deficient in p21 have defects in embryonic senescence, AER maintenance, and patterning. Surprisingly, the underlying mesenchyme was identified as a source for senescence instruction in the AER, whereas the ultimate fate of these senescent cells is apoptosis and macrophage-mediated clearance. We propose that senescence is a normal programmed mechanism that plays instructive roles in development, and that OIS is an evolutionarily adapted reactivation of a developmental process.
    Full-text · Article · Nov 2013 · Cell
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    ABSTRACT: Direct videomicroscopic visualization of organ formation and regeneration in toto is a powerful strategy to study cellular processes that often cannot be replicated in vitro. Intravital imaging aims at quantifying changes in tissue architecture or subcellular organization over time during organ development, regeneration or degeneration. A general feature of this approach is its reliance on the optical isolation of defined cell types in the whole animals by transgenic expression of fluorescent markers. Here we describe a simple and robust method to analyze sensory hair-cell development and regeneration in the zebrafish lateral line by high-resolution intravital imaging using laser-scanning confocal microscopy (LSCM) and selective plane illumination microscopy (SPIM). The main advantage of studying hair-cell regeneration in the lateral line is that it occurs throughout the life of the animal, which allows its study in the most natural context. We detail protocols to achieve continuous videomicroscopy for up to 68 hours, enabling direct observation of cellular behavior, which can provide a sensitive assay for the quantitative classification of cellular phenotypes and cell-lineage reconstruction. Modifications to this protocol should facilitate pharmacogenetic assays to identify or validate otoprotective or reparative drugs for future clinical strategies aimed at preserving aural function in humans.
    Full-text · Article · Oct 2013 · Frontiers in Neuroanatomy
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    ABSTRACT: Growth and Differentiation Factor 5 (GDF5) is a secreted growth factor that belongs to the Bone Morphogenetic Protein (BMP) family and plays a pivotal role during limb development. GDF5 is a susceptibility gene for osteoarthritis (OA) and mutations in GDF5 are associated with a wide variety of skeletal malformations ranging from complex syndromes such as acromesomelic chondrodysplasias to isolated forms of brachydactylies or multiple synostoses syndrome 2 (SYNS2). Here, we report on a family with an autosomal dominant inherited combination of SYNS2 and additional brachydactyly type A1 (BDA1) caused by a single point mutation in GDF5 (p.W414R). Functional studies, including chondrogenesis assays with primary mesenchymal cells, luciferase reporter gene assays and Surface Plasmon Resonance analysis, of the GDF5(W414R) variant in comparison to other GDF5 mutations associated with isolated BDA1 (p.R399C) or SYNS2 (p.E491K) revealed a dual pathomechanism characterized by a gain- and loss-of-function at the same time. On the one hand insensitivity to the main GDF5 antagonist NOGGIN (NOG) leads to a GDF5 gain of function and subsequent SYNS2 phenotype. Whereas on the other hand, a reduced signaling activity, specifically via the BMP receptor type IA (BMPR1A), is likely responsible for the BDA1 phenotype. These results demonstrate that one mutation in the overlapping interface of antagonist and receptor binding site in GDF5 can lead to a GDF5 variant with pathophysiological relevance for both, BDA1 and SYNS2 development. Consequently, our study assembles another part of the molecular puzzle of how loss and gain of function mutations in GDF5 affect bone development in hands and feet resulting in specific types of brachydactyly and SYNS2. These novel insights into the biology of GDF5 might also provide further clues on the pathophysiology of OA.
    Full-text · Article · Oct 2013 · PLoS Genetics

Publication Stats

3k Citations
613.80 Total Impact Points

Institutions

  • 2010-2015
    • Institut Marqués, Spain, Barcelona
      Barcino, Catalonia, Spain
  • 2008-2015
    • University Pompeu Fabra
      • Center for Genomic Regulation (CRG)
      Barcino, Catalonia, Spain
  • 2008-2014
    • Catalan Institution for Research and Advanced Studies
      Barcino, Catalonia, Spain
  • 2007-2013
    • CRG Centre for Genomic Regulation
      Barcino, Catalonia, Spain
  • 2011
    • Stanford University
      • Department of Developmental Biology
      Stanford, California, United States
  • 2001-2009
    • Western General Hospital
      Edinburgh, Scotland, United Kingdom
  • 1996-1999
    • MRC National Institute for Medical Research
      • Division of Developmental Neurobiology
      Londinium, England, United Kingdom