1
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Sabin KZ, Chen S, Hill EM, Weaver KJ, Yonke J, Kirkman M, Redwine WB, Klompen AML, Zhao X, Guo F, McKinney MC, Dewey JL, Gibson MC. Graded FGF activity patterns distinct cell types within the apical sensory organ of the sea anemone Nematostella vectensis. Dev Biol 2024; 510:50-65. [PMID: 38521499 DOI: 10.1016/j.ydbio.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/25/2024]
Abstract
Bilaterian animals have evolved complex sensory organs comprised of distinct cell types that function coordinately to sense the environment. Each sensory unit has a defined architecture built from component cell types, including sensory cells, non-sensory support cells, and dedicated sensory neurons. Whether this characteristic cellular composition is present in the sensory organs of non-bilaterian animals is unknown. Here, we interrogate the cell type composition and gene regulatory networks controlling development of the larval apical sensory organ in the sea anemone Nematostella vectensis. Using single cell RNA sequencing and imaging approaches, we reveal two unique cell types in the Nematostella apical sensory organ, GABAergic sensory cells and a putative non-sensory support cell population. Further, we identify the paired-like (PRD) homeodomain gene prd146 as a specific sensory cell marker and show that Prd146+ sensory cells become post-mitotic after gastrulation. Genetic loss of function approaches show that Prd146 is essential for apical sensory organ development. Using a candidate gene knockdown approach, we place prd146 downstream of FGF signaling in the apical sensory organ gene regulatory network. Further, we demonstrate that an aboral FGF activity gradient coordinately regulates the specification of both sensory and support cells. Collectively, these experiments define the genetic basis for apical sensory organ development in a non-bilaterian animal and reveal an unanticipated degree of complexity in a prototypic sensory structure.
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Affiliation(s)
- Keith Z Sabin
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Shiyuan Chen
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Eric M Hill
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Kyle J Weaver
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Jacob Yonke
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | | | | | - Xia Zhao
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Fengli Guo
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | | | - Matthew C Gibson
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA.
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2
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Yang Y, Li S, Luo L. Responses of organ precursors to correct and incorrect inductive signals. Trends Cell Biol 2024; 34:484-495. [PMID: 37739814 DOI: 10.1016/j.tcb.2023.08.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/24/2023]
Abstract
During embryonic development, the inductive molecules produced by local origins normally arrive at their target tissues in a nondirectional, diffusion manner. The target organ precursor cells must correctly interpret these inductive signals to ensure proper specification/differentiation, which is dependent on two prerequisites: (i) obtaining cell-intrinsic competence; and (ii) receiving correct inductive signals while resisting incorrect ones. Gain of intrinsic competence could avoid a large number of misinductions because the incompetent cells are nonresponsive to inductive signals. However, in cases of different precursor cells with similar competence and located in close proximity, resistance to incorrect inductive signals is essential for accurate determination of cell fate. Here we outline the mechanisms of how organ precursors respond to correct and incorrect inductive signals.
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Affiliation(s)
- Yun Yang
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China
| | - Shuang Li
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China
| | - Lingfei Luo
- Institute of Development Biology and Regenerative Medicine, Southwest University, Chongqing, China; School of Life Sciences, Fudan University, Shanghai, China.
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3
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Recouvreux P, Pai P, Dunsing V, Torro R, Ludanyi M, Mélénec P, Boughzala M, Bertrand V, Lenne PF. Transfer of polarity information via diffusion of Wnt ligands in C. elegans embryos. Curr Biol 2024; 34:1853-1865.e6. [PMID: 38604167 DOI: 10.1016/j.cub.2024.03.030] [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: 01/18/2023] [Revised: 10/26/2023] [Accepted: 03/18/2024] [Indexed: 04/13/2024]
Abstract
Different signaling mechanisms concur to ensure robust tissue patterning and cell fate instruction during animal development. Most of these mechanisms rely on signaling proteins that are produced, transported, and detected. The spatiotemporal dynamics of signaling molecules are largely unknown, yet they determine signal activity's spatial range and time frame. Here, we use the Caenorhabditis elegans embryo to study how Wnt ligands, an evolutionarily conserved family of signaling proteins, dynamically organize to establish cell polarity in a developing tissue. We identify how Wnt ligands, produced in the posterior half of the embryos, spread extracellularly to transmit information to distant target cells in the anterior half. With quantitative live imaging and fluorescence correlation spectroscopy, we show that Wnt ligands diffuse through the embryo over a timescale shorter than the cell cycle, in the intercellular space, and outside the tissue below the eggshell. We extracted diffusion coefficients of Wnt ligands and their receptor Frizzled and characterized their co-localization. Integrating our different measurements and observations in a simple computational framework, we show how fast diffusion in the embryo can polarize individual cells through a time integration of the arrival of the ligands at the target cells. The polarity established at the tissue level by a posterior Wnt source can be transferred to the cellular level. Our results support a diffusion-based long-range Wnt signaling, which is consistent with the dynamics of developing processes.
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Affiliation(s)
- Pierre Recouvreux
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France.
| | - Pritha Pai
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Valentin Dunsing
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Rémy Torro
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Monika Ludanyi
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Pauline Mélénec
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Mariem Boughzala
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Vincent Bertrand
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Pierre-François Lenne
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
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4
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Mii Y. Understanding and manipulating extracellular behaviors of Wnt ligands. In Vitro Cell Dev Biol Anim 2024; 60:441-448. [PMID: 38379096 DOI: 10.1007/s11626-024-00856-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/17/2024] [Indexed: 02/22/2024]
Abstract
Wnt, a family of secreted signaling proteins, serves diverse functions in embryogenesis, organogenesis, cancer, and stem cell functions. In the context of development, Wnt has been considered a representative morphogen, forming concentration gradients to give positional information to cells or tissues. However, although gradients are often illustrated in schemata, the reality of concentration gradients, or in other words, actual spatial distribution of Wnt ligands, and their behaviors in the extracellular space still remain poorly known. To understand extracellular behavior of Wnt ligands, quantitative analyses such as fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP) are highly informative because Wnt dispersal involves physical and biochemical processes, such as diffusion and binding to or dissociation from cell surface molecules, including heparan sulfate proteoglycans (HSPGs). Here, I briefly discuss representative methods to quantify morphogen dynamics. In addition, I discuss molecular manipulations of morphogens, mainly focusing on use of protein binders, and synthetic biology of morphogens as indicators of current and future directions in this field.
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Affiliation(s)
- Yusuke Mii
- National Institute for Basic Biology (NIBB) and Exploratory Research Center On Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
- The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, 444-8787, Japan.
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5
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McNamara HM, Jia BZ, Guyer A, Parot VJ, Dobbs C, Schier AF, Cohen AE, Lord ND. Optogenetic control of Nodal signaling patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.588875. [PMID: 38645239 PMCID: PMC11030342 DOI: 10.1101/2024.04.11.588875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
A crucial step in early embryogenesis is the establishment of spatial patterns of signaling activity. Tools to perturb morphogen signals with high resolution in space and time can help reveal how embryonic cells decode these signals to make appropriate fate decisions. Here, we present new optogenetic reagents and an experimental pipeline for creaHng designer Nodal signaling patterns in live zebrafish embryos. Nodal receptors were fused to the light-sensitive heterodimerizing pair Cry2/CIB1N, and the Type II receptor was sequestered to the cytosol. The improved optoNodal2 reagents eliminate dark activity and improve response kinetics, without sacrificing dynamic range. We adapted an ultra-widefield microscopy platform for parallel light patterning in up to 36 embryos and demonstrated precise spatial control over Nodal signaling activity and downstream gene expression. Patterned Nodal activation drove precisely controlled internalization of endodermal precursors. Further, we used patterned illumination to generate synthetic signaling patterns in Nodal signaling mutants, rescuing several characteristic developmental defects. This study establishes an experimental toolkit for systematic exploration of Nodal signaling patterns in live embryos.
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Affiliation(s)
| | - Bill Z. Jia
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Alison Guyer
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vicente J. Parot
- Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Caleb Dobbs
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Adam E. Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Nathan D. Lord
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, USA
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6
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Athilingam T, Nelanuthala AVS, Breen C, Karedla N, Fritzsche M, Wohland T, Saunders TE. Long-range formation of the Bicoid gradient requires multiple dynamic modes that spatially vary across the embryo. Development 2024; 151:dev202128. [PMID: 38345326 PMCID: PMC10911119 DOI: 10.1242/dev.202128] [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: 06/26/2023] [Accepted: 01/03/2024] [Indexed: 02/15/2024]
Abstract
Morphogen gradients provide essential positional information to gene networks through their spatially heterogeneous distribution, yet how they form is still hotly contested, with multiple models proposed for different systems. Here, we focus on the transcription factor Bicoid (Bcd), a morphogen that forms an exponential gradient across the anterior-posterior (AP) axis of the early Drosophila embryo. Using fluorescence correlation spectroscopy we find there are spatial differences in Bcd diffusivity along the AP axis, with Bcd diffusing more rapidly in the posterior. We establish that such spatially varying differences in Bcd dynamics are sufficient to explain how Bcd can have a steep exponential gradient in the anterior half of the embryo and yet still have an observable fraction of Bcd near the posterior pole. In the nucleus, we demonstrate that Bcd dynamics are impacted by binding to DNA. Addition of the Bcd homeodomain to eGFP::NLS qualitatively replicates the Bcd concentration profile, suggesting this domain regulates Bcd dynamics. Our results reveal how a long-range gradient can form while retaining a steep profile through much of its range.
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Affiliation(s)
- Thamarailingam Athilingam
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
- Mechanobiology Institute, National University of Singapore, Singapore117411
| | - Ashwin V. S. Nelanuthala
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore117558
| | | | - Narain Karedla
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7LF, UK
| | - Marco Fritzsche
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7LF, UK
| | - Thorsten Wohland
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore117558
- Department of Chemistry, National University of Singapore, Singapore117558
| | - Timothy E. Saunders
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
- Mechanobiology Institute, National University of Singapore, Singapore117411
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore117558
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7
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Cooper EJ, Scholpp S. Transport and gradient formation of Wnt and Fgf in the early zebrafish gastrula. Curr Top Dev Biol 2023; 157:125-153. [PMID: 38556457 DOI: 10.1016/bs.ctdb.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Within embryonic development, the occurrence of gastrulation is critical in the formation of multiple germ layers with many differentiative abilities. These cells are instructed through exposure to signalling molecules called morphogens. The secretion of morphogens from a source tissue creates a concentration gradient that allows distinct pattern formation in the receiving tissue. This review focuses on the morphogens Wnt and Fgf in zebrafish development. Wnt has been shown to have critical roles throughout gastrulation, including in anteroposterior patterning and neural posterisation. Fgf is also a vital signal, contributing to involution and mesodermal specification. Both morphogens have also been found to work in finely balanced synergy for processes such as neural induction. Thus, the signalling range of Wnts and Fgfs must be strictly controlled to target the correct target cells. Fgf and Wnts signal to local cells as well as to cells in the distance in a highly regulated way, requiring specific dissemination mechanisms that allow efficient and precise signalling over short and long distances. Multiple transportation mechanisms have been discovered to aid in producing a stable morphogen gradient, including short-range diffusion, filopodia-like extensions called cytonemes and extracellular vesicles, mainly exosomes. These mechanisms are specific to the morphogen that they transport and the intended signalling range. This review article discusses how spreading mechanisms in these two morphogenetic systems differ and the consequences on paracrine signalling, hence tissue patterning.
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Affiliation(s)
- Emma J Cooper
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Steffen Scholpp
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom.
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8
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Mederacke M, Conrad L, Doumpas N, Vetter R, Iber D. Geometric effects position renal vesicles during kidney development. Cell Rep 2023; 42:113526. [PMID: 38060445 DOI: 10.1016/j.celrep.2023.113526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 07/25/2023] [Accepted: 11/15/2023] [Indexed: 12/30/2023] Open
Abstract
During kidney development, reciprocal signaling between the epithelium and the mesenchyme coordinates nephrogenesis with branching morphogenesis of the collecting ducts. The mechanism that positions the renal vesicles, and thus the nephrons, relative to the branching ureteric buds has remained elusive. By combining computational modeling and experiments, we show that geometric effects concentrate the key regulator, WNT9b, at the junctions between parent and daughter branches where renal vesicles emerge, even when uniformly expressed in the ureteric epithelium. This curvature effect might be a general paradigm to create non-uniform signaling in development.
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Affiliation(s)
- Malte Mederacke
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Lisa Conrad
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland; Department for BioMedical Research (DBMR), University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland
| | - Nikolaos Doumpas
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Roman Vetter
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Dagmar Iber
- Department of Biosystems Science and Engineering, ETH Zürich, Schanzenstrasse 44, 4056 Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058 Basel, Switzerland.
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9
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Kendall JJ, Ledoux C, Marques FC, Boaretti D, Schulte FA, Morgan EF, Müller R. An in silico micro-multiphysics agent-based approach for simulating bone regeneration in a mouse femur defect model. Front Bioeng Biotechnol 2023; 11:1289127. [PMID: 38164405 PMCID: PMC10757951 DOI: 10.3389/fbioe.2023.1289127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
Bone defects represent a challenging clinical problem as they can lead to non-union. In silico models are well suited to study bone regeneration under varying conditions by linking both cellular and systems scales. This paper presents an in silico micro-multiphysics agent-based (micro-MPA) model for bone regeneration following an osteotomy. The model includes vasculature, bone, and immune cells, as well as their interaction with the local environment. The model was calibrated by time-lapsed micro-computed tomography data of femoral osteotomies in C57Bl/6J mice, and the differences between predicted bone volume fractions and the longitudinal in vivo measurements were quantitatively evaluated using root mean square error (RMSE). The model performed well in simulating bone regeneration across the osteotomy gap, with no difference (5.5% RMSE, p = 0.68) between the in silico and in vivo groups for the 5-week healing period - from the inflammatory phase to the remodelling phase - in the volume spanning the osteotomy gap. Overall, the proposed micro-MPA model was able to simulate the influence of the local mechanical environment on bone regeneration, and both this environment and cytokine concentrations were found to be key factors in promoting bone regeneration. Further, the validated model matched clinical observations that larger gap sizes correlate with worse healing outcomes and ultimately simulated non-union. This model could help design and guide future experimental studies in bone repair, by identifying which are the most critical in vivo experiments to perform.
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Affiliation(s)
- Jack J. Kendall
- Institute for Biomechanics, ETH Zurich, Zurich, Switzerland
- Center for Multiscale and Translational Mechanobiology, Boston University, Boston, MA, United States
| | - Charles Ledoux
- Institute for Biomechanics, ETH Zurich, Zurich, Switzerland
| | | | | | | | - Elise F. Morgan
- Center for Multiscale and Translational Mechanobiology, Boston University, Boston, MA, United States
| | - Ralph Müller
- Institute for Biomechanics, ETH Zurich, Zurich, Switzerland
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10
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Oikonomou P, Cirne HC, Nerurkar NL. A chemo-mechanical model of endoderm movements driving elongation of the amniote hindgut. Development 2023; 150:dev202010. [PMID: 37840469 PMCID: PMC10690059 DOI: 10.1242/dev.202010] [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: 05/22/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023]
Abstract
Although mechanical and biochemical descriptions of development are each essential, integration of upstream morphogenic cues with downstream tissue mechanics remains understudied during vertebrate morphogenesis. Here, we developed a two-dimensional chemo-mechanical model to investigate how mechanical properties of the endoderm and transport properties of fibroblast growth factor (FGF) regulate avian hindgut morphogenesis in a coordinated manner. Posterior endoderm cells convert a gradient of FGF ligands into a contractile force gradient, leading to a force imbalance that drives collective cell movements that elongate the forming hindgut tube. We formulated a 2D reaction-diffusion-advection model describing the formation of an FGF protein gradient as a result of posterior displacement of cells transcribing unstable Fgf8 mRNA during axis elongation, coupled with translation, diffusion and degradation of FGF protein. The endoderm was modeled as an active viscous fluid that generates contractile stresses in proportion to FGF concentration. With parameter values constrained by experimental data, the model replicates key aspects of hindgut morphogenesis, suggests that graded isotropic contraction is sufficient to generate large anisotropic cell movements, and provides new insight into how chemo-mechanical coupling across the mesoderm and endoderm coordinates hindgut elongation with axis elongation.
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Affiliation(s)
- Panagiotis Oikonomou
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| | - Helena C. Cirne
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
| | - Nandan L. Nerurkar
- Department of Biomedical Engineering, Columbia University, 351 Engineering Terrace, 1210 Amsterdam Avenue, New York, NY 10027, USA
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11
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Harish RK, Brand M. The people behind the papers - Rohit Krishnan Harish and Michael Brand. Development 2023; 150:dev202337. [PMID: 37787121 DOI: 10.1242/dev.202337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The growth factor Fgf8a has been suggested to act as a morphogen during zebrafish gastrulation, spreading from a localized source to form a concentration gradient and impart positional information to cells along a tissue field. In a new paper in Development, Michael Brand and colleagues directly visualize the endogenous Fgf8a gradient in the developing zebrafish embryo. We caught up with the first author Rohit Krishnan Harish, and his PhD supervisor Michael Brand, Professor at the Center for Regenerative Therapies (CRTD) at TU Dresden.
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12
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Harish RK, Gupta M, Zöller D, Hartmann H, Gheisari A, Machate A, Hans S, Brand M. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development 2023; 150:dev201559. [PMID: 37665167 PMCID: PMC10565248 DOI: 10.1242/dev.201559] [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: 01/04/2023] [Accepted: 08/29/2023] [Indexed: 09/05/2023]
Abstract
Morphogen gradients impart positional information to cells in a homogenous tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act as a morphogen during zebrafish gastrulation. However, technical limitations have so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation of its morphogenic activity. Here, we monitor Fgf8a propagation in the developing neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a locus. By combining sensitive imaging with single-molecule fluorescence correlation spectroscopy, we demonstrate that Fgf8a, which is produced at the embryonic margin, propagates by diffusion through the extracellular space and forms a graded distribution towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles of its downstream targets determines the precise input-output relationship of Fgf8a-mediated patterning. Manipulation of the extracellular Fgf8a levels alters the signaling outcome, thus establishing Fgf8a as a bona fide morphogen during zebrafish gastrulation. Furthermore, by hindering Fgf8a diffusion, we demonstrate that extracellular diffusion of the protein from the source is crucial for it to achieve its morphogenic potential.
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Affiliation(s)
- Rohit Krishnan Harish
- CRTD – Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
- PoL – Cluster of Excellence Physics of Life, Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Mansi Gupta
- CRTD – Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
- PoL – Cluster of Excellence Physics of Life, Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Daniela Zöller
- CRTD – Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
- PoL – Cluster of Excellence Physics of Life, Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Hella Hartmann
- CRTD – Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
- CMCB Technology Platform, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Ali Gheisari
- CRTD – Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
- CMCB Technology Platform, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Anja Machate
- CRTD – Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
- PoL – Cluster of Excellence Physics of Life, Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Stefan Hans
- CRTD – Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
- PoL – Cluster of Excellence Physics of Life, Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Michael Brand
- CRTD – Center for Regenerative Therapies TU Dresden, Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
- PoL – Cluster of Excellence Physics of Life, Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany
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13
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Sankaran J, Wohland T. Current capabilities and future perspectives of FCS: super-resolution microscopy, machine learning, and in vivo applications. Commun Biol 2023; 6:699. [PMID: 37419967 PMCID: PMC10328937 DOI: 10.1038/s42003-023-05069-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023] Open
Abstract
Fluorescence correlation spectroscopy (FCS) is a single molecule sensitive tool for the quantitative measurement of biomolecular dynamics and interactions. Improvements in biology, computation, and detection technology enable real-time FCS experiments with multiplexed detection even in vivo. These new imaging modalities of FCS generate data at the rate of hundreds of MB/s requiring efficient data processing tools to extract information. Here, we briefly review FCS's capabilities and limitations before discussing recent directions that address these limitations with a focus on imaging modalities of FCS, their combinations with super-resolution microscopy, new evaluation strategies, especially machine learning, and applications in vivo.
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Affiliation(s)
- Jagadish Sankaran
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138632, Singapore.
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
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14
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Thompson MJ, Young CA, Munnamalai V, Umulis DM. Early radial positional information in the cochlea is optimized by a precise linear BMP gradient and enhanced by SOX2. Sci Rep 2023; 13:8567. [PMID: 37237002 PMCID: PMC10219982 DOI: 10.1038/s41598-023-34725-4] [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: 01/23/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
Positional information encoded in signaling molecules is essential for early patterning in the prosensory domain of the developing cochlea. The sensory epithelium, the organ of Corti, contains an exquisite repeating pattern of hair cells and supporting cells. This requires precision in the morphogen signals that set the initial radial compartment boundaries, but this has not been investigated. To measure gradient formation and morphogenetic precision in developing cochlea, we developed a quantitative image analysis procedure measuring SOX2 and pSMAD1/5/9 profiles in mouse embryos at embryonic day (E)12.5, E13.5, and E14.5. Intriguingly, we found that the pSMAD1/5/9 profile forms a linear gradient up to the medial ~ 75% of the PSD from the pSMAD1/5/9 peak in the lateral edge during E12.5 and E13.5. This is a surprising activity readout for a diffusive BMP4 ligand secreted from a tightly constrained lateral region since morphogens typically form exponential or power-law gradient shapes. This is meaningful for gradient interpretation because while linear profiles offer the theoretically highest information content and distributed precision for patterning, a linear morphogen gradient has not yet been observed. Furthermore, this is unique to the cochlear epithelium as the pSMAD1/5/9 gradient is exponential in the surrounding mesenchyme. In addition to the information-optimized linear profile, we found that while pSMAD1/5/9 is stable during this timeframe, an accompanying gradient of SOX2 shifts dynamically. Last, through joint decoding maps of pSMAD1/5/9 and SOX2, we see that there is a high-fidelity mapping between signaling activity and position in the regions that will become Kölliker's organ and the organ of Corti. Mapping is ambiguous in the prosensory domain precursory to the outer sulcus. Altogether, this research provides new insights into the precision of early morphogenetic patterning cues in the radial cochlea prosensory domain.
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Affiliation(s)
- Matthew J Thompson
- Weldon School of Biomedical Engineering, Purdue University, 206 S Martin Jischke Dr, West Lafayette, IN, 47907, USA
| | - Caryl A Young
- University of Maine, 168 College Ave, Orono, ME, 04469, USA
| | - Vidhya Munnamalai
- University of Maine, 168 College Ave, Orono, ME, 04469, USA.
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA.
| | - David M Umulis
- Weldon School of Biomedical Engineering, Purdue University, 206 S Martin Jischke Dr, West Lafayette, IN, 47907, USA.
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15
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Oikonomou P, Cirne HC, Nerurkar NL. A chemo-mechanical model of endoderm movements driving elongation of the amniote hindgut. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541363. [PMID: 37292966 PMCID: PMC10245718 DOI: 10.1101/2023.05.18.541363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
While mechanical and biochemical descriptions of development are each essential, integration of upstream morphogenic cues with downstream tissue mechanics remains understudied in many contexts during vertebrate morphogenesis. A posterior gradient of Fibroblast Growth Factor (FGF) ligands generates a contractile force gradient in the definitive endoderm, driving collective cell movements to form the hindgut. Here, we developed a two-dimensional chemo-mechanical model to investigate how mechanical properties of the endoderm and transport properties of FGF coordinately regulate this process. We began by formulating a 2-D reaction-diffusion-advection model that describes the formation of an FGF protein gradient due to posterior displacement of cells transcribing unstable Fgf8 mRNA during axis elongation, coupled with translation, diffusion, and degradation of FGF protein. This was used together with experimental measurements of FGF activity in the chick endoderm to inform a continuum model of definitive endoderm as an active viscous fluid that generates contractile stresses in proportion to FGF concentration. The model replicated key aspects of hindgut morphogenesis, confirms that heterogeneous - but isotropic - contraction is sufficient to generate large anisotropic cell movements, and provides new insight into how chemo-mechanical coupling across the mesoderm and endoderm coordinates hindgut elongation with outgrowth of the tailbud.
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Affiliation(s)
| | - Helena C. Cirne
- Department of Biomedical Engineering, Columbia University, New York NY 10027
| | - Nandan L. Nerurkar
- Department of Biomedical Engineering, Columbia University, New York NY 10027
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16
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Koh I, Hagiwara M. Gradient to sectioning CUBE workflow for the generation and imaging of organoids with localized differentiation. Commun Biol 2023; 6:299. [PMID: 36944757 PMCID: PMC10030548 DOI: 10.1038/s42003-023-04694-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/10/2023] [Indexed: 03/23/2023] Open
Abstract
Advancements in organoid culture have led to various in vitro mini-organs that mimic native tissues in many ways. Yet, the bottleneck remains to generate complex organoids with body axis patterning, as well as keeping the orientation of organoids during post-experiment analysis processes. Here, we present a workflow for culturing organoids with morphogen gradient using a CUBE culture device, followed by sectioning samples with the CUBE to retain information on gradient direction. We show that hiPSC spheroids cultured with two separated differentiation media on opposing ends of the CUBE resulted in localized expressions of the respective differentiation markers, in contrast to homogeneous distribution of markers in controls. We also describe the processes for cryo and paraffin sectioning of spheroids in CUBE to retain gradient orientation information. This workflow from gradient culture to sectioning with CUBE can provide researchers with a convenient tool to generate increasingly complex organoids and study their developmental processes in vitro.
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Affiliation(s)
- Isabel Koh
- Cluster for Pioneering Research, RIKEN, Saitama, 351-0198, Japan
| | - Masaya Hagiwara
- Cluster for Pioneering Research, RIKEN, Saitama, 351-0198, Japan.
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17
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Hedgehog is relayed through dynamic heparan sulfate interactions to shape its gradient. Nat Commun 2023; 14:758. [PMID: 36765094 PMCID: PMC9918555 DOI: 10.1038/s41467-023-36450-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 01/27/2023] [Indexed: 02/12/2023] Open
Abstract
Cellular differentiation is directly determined by concentration gradients of morphogens. As a central model for gradient formation during development, Hedgehog (Hh) morphogens spread away from their source to direct growth and pattern formation in Drosophila wing and eye discs. What is not known is how extracellular Hh spread is achieved and how it translates into precise gradients. Here we show that two separate binding areas located on opposite sides of the Hh molecule can interact directly and simultaneously with two heparan sulfate (HS) chains to temporarily cross-link the chains. Mutated Hh lacking one fully functional binding site still binds HS but shows reduced HS cross-linking. This, in turn, impairs Hhs ability to switch between both chains in vitro and results in striking Hh gradient hypomorphs in vivo. The speed and propensity of direct Hh switching between HS therefore shapes the Hh gradient, revealing a scalable design principle in morphogen-patterned tissues.
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18
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Sharma A, Meer M, Dapkunas A, Ihermann-Hella A, Kuure S, Vainio SJ, Iber D, Naillat F. FGF8 induces chemokinesis and regulates condensation of mouse nephron progenitor cells. Development 2022; 149:277149. [DOI: 10.1242/dev.201012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022]
Abstract
ABSTRACT
Kidneys develop via iterative branching of the ureteric epithelial tree and subsequent nephrogenesis at the branch points. Nephrons form in the cap mesenchyme as the metanephric mesenchyme (MM) condenses around the epithelial ureteric buds (UBs). Previous work has demonstrated that FGF8 is important for the survival of nephron progenitor cells (NPCs), and early deletion of Fgf8 leads to the cessation of nephron formation, which results in post-natal lethality. We now reveal a previously unreported function of FGF8. By combining transgenic mouse models, quantitative imaging assays and data-driven computational modelling, we show that FGF8 has a strong chemokinetic effect and that this chemokinetic effect is important for the condensation of NPCs to the UB. The computational model shows that the motility must be lower close to the UB to achieve NPC attachment. We conclude that the FGF8 signalling pathway is crucial for the coordination of NPC condensation at the UB. Chemokinetic effects have also been described for other FGFs and may be generally important for the formation of mesenchymal condensates.
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Affiliation(s)
- Abhishek Sharma
- University of Oulu 1 Faculty of Biochemistry and Molecular Medicine , , Oulu 90220, Finland
- Biocenter Oulu 2 , Oulu 90220, Finland
| | - Marco Meer
- ETH Zürich 3 Department of Biosystems, Science and Engineering , , Zürich 04058, Switzerland
- Swiss Institute of Bioinformatics 4 , Lausanne 1015 , Switzerland
| | - Arvydas Dapkunas
- University of Helsinki 5 HiLIFE and Research Programs Unit, Faculty of Medicine , , Helsinki 00014, Finland
| | - Anneliis Ihermann-Hella
- University of Helsinki 5 HiLIFE and Research Programs Unit, Faculty of Medicine , , Helsinki 00014, Finland
| | - Satu Kuure
- University of Helsinki 5 HiLIFE and Research Programs Unit, Faculty of Medicine , , Helsinki 00014, Finland
- LAC/HiLIFE, and Medicum, University of Helsinki 6 GM-Unit , , Helsinki 00014, Finland
| | - Seppo J. Vainio
- University of Oulu 1 Faculty of Biochemistry and Molecular Medicine , , Oulu 90220, Finland
- Biocenter Oulu 2 , Oulu 90220, Finland
- Infotech Oulu 7 , Oulu 90200, Finland
- Borealis Biobank 8 , Oulu 90200, Finland
- Kvantum Institute, University of Oulu 9 , Oulu 90200, Finland
| | - Dagmar Iber
- ETH Zürich 3 Department of Biosystems, Science and Engineering , , Zürich 04058, Switzerland
- Swiss Institute of Bioinformatics 4 , Lausanne 1015 , Switzerland
| | - Florence Naillat
- University of Oulu 1 Faculty of Biochemistry and Molecular Medicine , , Oulu 90220, Finland
- Biocenter Oulu 2 , Oulu 90220, Finland
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19
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Kuhn T, Landge AN, Mörsdorf D, Coßmann J, Gerstenecker J, Čapek D, Müller P, Gebhardt JCM. Single-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model. Nat Commun 2022; 13:6101. [PMID: 36243734 PMCID: PMC9569377 DOI: 10.1038/s41467-022-33704-z] [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: 04/15/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022] Open
Abstract
The hindered diffusion model postulates that the movement of a signaling molecule through an embryo is affected by tissue geometry and binding-mediated hindrance, but these effects have not been directly demonstrated in vivo. Here, we visualize extracellular movement and binding of individual molecules of the activator-inhibitor signaling pair Nodal and Lefty in live developing zebrafish embryos using reflected light-sheet microscopy. We observe that diffusion coefficients of molecules are high in extracellular cavities, whereas mobility is reduced and bound fractions are high within cell-cell interfaces. Counterintuitively, molecules nevertheless accumulate in cavities, which we attribute to the geometry of the extracellular space by agent-based simulations. We further find that Nodal has a larger bound fraction than Lefty and shows a binding time of tens of seconds. Together, our measurements and simulations provide direct support for the hindered diffusion model and yield insights into the nanometer-to-micrometer-scale mechanisms that lead to macroscopic signal dispersal.
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Affiliation(s)
- Timo Kuhn
- grid.6582.90000 0004 1936 9748Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Amit N. Landge
- grid.9811.10000 0001 0658 7699University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - David Mörsdorf
- grid.418026.90000 0004 0492 0357Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, Germany ,grid.10420.370000 0001 2286 1424University of Vienna, Department of Neurosciences and Developmental Biology, Djerassiplatz 1, 1030 Vienna, Austria
| | - Jonas Coßmann
- grid.6582.90000 0004 1936 9748Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Johanna Gerstenecker
- grid.6582.90000 0004 1936 9748Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Daniel Čapek
- grid.9811.10000 0001 0658 7699University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Patrick Müller
- grid.9811.10000 0001 0658 7699University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany ,grid.418026.90000 0004 0492 0357Friedrich Miescher Laboratory of the Max Planck Society, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - J. Christof M. Gebhardt
- grid.6582.90000 0004 1936 9748Institute of Biophysics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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20
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Abstract
Metazoan embryos develop from a single cell into three-dimensional structured organisms while groups of genetically identical cells attain specialized identities. Cells of the developing embryo both create and accurately interpret morphogen gradients to determine their positions and make specific decisions in response. Here, we first cover intellectual roots of morphogen and positional information concepts. Focusing on animal embryos, we then provide a review of current understanding on how morphogen gradients are established and how their spans are controlled. Lastly, we cover how gradients evolve in time and space during development, and how they encode information to control patterning. In sum, we provide a list of patterning principles for morphogen gradients and review recent advances in quantitative methodologies elucidating information provided by morphogens.
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Affiliation(s)
- M. Fethullah Simsek
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ertuğrul M. Özbudak
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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21
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Dickmann JEM, Rink JC, Jülicher F. Long-range morphogen gradient formation by cell-to-cell signal propagation. Phys Biol 2022; 19. [PMID: 35921820 DOI: 10.1088/1478-3975/ac86b4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/03/2022] [Indexed: 11/12/2022]
Abstract
Morphogen gradients are a central concept in developmental biology. Their formation often involves the secretion of morphogens from a local source, that spread by diffusion in the cell field, where molecules eventually get degraded. This implies limits to both the time and length scales over which morphogen gradients can form which are set by diffusion coefficients and degradation rates. Towards the goal of identifying plausible mechanisms capable of extending the gradient range, we here use theory to explore properties of a cell-to-cell signaling relay. Inspired by the millimeter-scale Wnt-expression and signaling gradients in flatworms, we consider morphogen-mediated morphogen production in the cell field. We show that such a relay can generate stable morphogen and signaling gradients that are oriented by a local, morphogen-independent source of morphogen at a boundary. This gradient formation can be related to an effective diffusion and an effective degradation that result from morphogen production due to signaling relay. If the secretion of morphogen produced in response to the relay is polarized, it further gives rise to an effective drift. We find that signaling relay can generate long-ranged gradients in relevant times without relying on extreme choices of diffusion coefficients or degradation rates, thus exceeding the limits set by physiological diffusion coefficients and degradation rates. A signaling relay is hence an attractive principle to conceptualize long-range gradient formation by slowly diffusing morphogens that are relevant for patterning in adult contexts such as regeneration and tissue turn-over.
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Affiliation(s)
- Johanna E M Dickmann
- Max-Planck-Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, Dresden, Sachsen, 01187, GERMANY
| | - Jochen C Rink
- Max Planck Institute for Multidisciplinary Sciences, Am Faßberg 11, Gottingen, Niedersachsen, 37077, GERMANY
| | - Frank Jülicher
- Max-Planck-Institut fuer Physik komplexer Systeme, Nöthnitzer Strasse 38, 01187 Dresden, Dresden, 01187, GERMANY
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22
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Stapornwongkul KS, Briscoe J. In preprints: morphogens in motion. Development 2022; 149:276010. [DOI: 10.1242/dev.201066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Kristina S. Stapornwongkul
- Tissue Biology and Disease Modelling, European Molecular Biology Laboratory (EMBL) Barcelona 1 , Dr. Aiguader 88, 08003 Barcelona , Spain
| | - James Briscoe
- Developmental Dynamics, The Francis Crick Institute 2 , 1 Midland Road, London, NW1 1AT , UK
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23
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Zheng W, Xie R, Liang X, Liang Q. Fabrication of Biomaterials and Biostructures Based On Microfluidic Manipulation. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2105867. [PMID: 35072338 DOI: 10.1002/smll.202105867] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Biofabrication technologies are of importance for the construction of organ models and functional tissue replacements. Microfluidic manipulation, a promising biofabrication technique with micro-scale resolution, can not only help to realize the fabrication of specific microsized structures but also build biomimetic microenvironments for biofabricated tissues. Therefore, microfluidic manipulation has attracted attention from researchers in the manipulation of particles and cells, biochemical analysis, tissue engineering, disease diagnostics, and drug discovery. Herein, biofabrication based on microfluidic manipulation technology is reviewed. The application of microfluidic manipulation technology in the manufacturing of biomaterials and biostructures with different dimensions and the control of the microenvironment is summarized. Finally, current challenges are discussed and a prospect of microfluidic manipulation technology is given. The authors hope this review can provide an overview of microfluidic manipulation technologies used in biofabrication and thus steer the current efforts in this field.
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Affiliation(s)
- Wenchen Zheng
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Ruoxiao Xie
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Xiaoping Liang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangdong, 510006, China
| | - Qionglin Liang
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
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24
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Vetter R, Iber D. Precision of morphogen gradients in neural tube development. Nat Commun 2022; 13:1145. [PMID: 35241686 PMCID: PMC8894346 DOI: 10.1038/s41467-022-28834-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 02/15/2022] [Indexed: 12/19/2022] Open
Abstract
Morphogen gradients encode positional information during development. How high patterning precision is achieved despite natural variation in both the morphogen gradients and in the readout process, is still largely elusive. Here, we show that the positional error of gradients in the mouse neural tube has previously been overestimated, and that the reported accuracy of the central progenitor domain boundaries in the mouse neural tube can be achieved with a single gradient, rather than requiring the simultaneous readout of opposing gradients. Consistently and independently, numerical simulations based on measured molecular noise levels likewise result in lower gradient variabilities than reported. Finally, we show that the patterning mechanism yields progenitor cell numbers with even greater precision than boundary positions, as gradient amplitude changes do not affect interior progenitor domain sizes. We conclude that single gradients can yield the observed developmental precision, which provides prospects for tissue engineering.
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Affiliation(s)
- Roman Vetter
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland.
- Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058, Basel, Switzerland.
| | - Dagmar Iber
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058, Basel, Switzerland.
- Swiss Institute of Bioinformatics, Mattenstrasse 26, 4058, Basel, Switzerland.
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25
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Fgf8 dynamics and critical slowing down may account for the temperature independence of somitogenesis. Commun Biol 2022; 5:113. [PMID: 35132142 PMCID: PMC8821593 DOI: 10.1038/s42003-022-03053-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 12/29/2021] [Indexed: 12/17/2022] Open
Abstract
Somitogenesis, the segmentation of the antero-posterior axis in vertebrates, is thought to result from the interactions between a genetic oscillator and a posterior-moving determination wavefront. The segment (somite) size is set by the product of the oscillator period and the velocity of the determination wavefront. Surprisingly, while the segmentation period can vary by a factor three between 20 °C and 32 °C, the somite size is constant. How this temperature independence is achieved is a mystery that we address in this study. Using RT-qPCR we show that the endogenous fgf8 mRNA concentration decreases during somitogenesis and correlates with the exponent of the shrinking pre-somitic mesoderm (PSM) size. As the temperature decreases, the dynamics of fgf8 and many other gene transcripts, as well as the segmentation frequency and the PSM shortening and tail growth rates slows down as T-Tc (with Tc = 14.4 °C). This behavior characteristic of a system near a critical point may account for the temperature independence of somitogenesis in zebrafish.
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26
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Abstract
Embryonic development hinges on effective coordination of molecular events across space and time. Waves have recently emerged as constituting an ubiquitous mechanism that ensures rapid spreading of regulatory signals across embryos, as well as reliable control of their patterning, namely, for the emergence of body plan structures. In this article, we review a selection of recent quantitative work on signaling waves and present an overview of the theory of waves. Our aim is to provide a succinct yet comprehensive guiding reference for the theoretical frameworks by which signaling waves can arise in embryos. We start, then, from reaction-diffusion systems, both static and time dependent; move to excitable dynamics; and conclude with systems of coupled oscillators. We link these theoretical models to molecular mechanisms recently elucidated for the control of mitotic waves in early embryos, patterning of the vertebrate body axis, micropattern cultures, and bone regeneration. Our goal is to inspire experimental work that will advance theory in development and connect its predictions to quantitative biological observations. Expected final online publication date for the Annual Review of Biophysics, Volume 51 is May 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Stefano Di Talia
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, USA
| | - Massimo Vergassola
- Laboratoire de physique de l'École Normale Supérieure, CNRS, PSL Research University, Sorbonne Université, Paris, France; .,Department of Physics, University of California, San Diego, California, USA
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27
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Daly CA, Hall ET, Ogden SK. Regulatory mechanisms of cytoneme-based morphogen transport. Cell Mol Life Sci 2022; 79:119. [PMID: 35119540 PMCID: PMC8816744 DOI: 10.1007/s00018-022-04148-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/05/2022] [Accepted: 01/12/2022] [Indexed: 01/07/2023]
Abstract
During development and tissue homeostasis, cells must communicate with their neighbors to ensure coordinated responses to instructional cues. Cues such as morphogens and growth factors signal at both short and long ranges in temporal- and tissue-specific manners to guide cell fate determination, provide positional information, and to activate growth and survival responses. The precise mechanisms by which such signals traverse the extracellular environment to ensure reliable delivery to their intended cellular targets are not yet clear. One model for how this occurs suggests that specialized filopodia called cytonemes extend between signal-producing and -receiving cells to function as membrane-bound highways along which information flows. A growing body of evidence supports a crucial role for cytonemes in cell-to-cell communication. Despite this, the molecular mechanisms by which cytonemes are initiated, how they grow, and how they deliver specific signals are only starting to be revealed. Herein, we discuss recent advances toward improved understanding of cytoneme biology. We discuss similarities and differences between cytonemes and other types of cellular extensions, summarize what is known about how they originate, and discuss molecular mechanisms by which their activity may be controlled in development and tissue homeostasis. We conclude by highlighting important open questions regarding cytoneme biology, and comment on how a clear understanding of their function may provide opportunities for treating or preventing disease.
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Affiliation(s)
- Christina A Daly
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl. MS340, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, MS 1500, Memphis, TN, 38105, USA
| | - Eric T Hall
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl. MS340, Memphis, TN, 38105, USA
| | - Stacey K Ogden
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl. MS340, Memphis, TN, 38105, USA.
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28
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Ceccarelli AS, Borges A, Chara O. Size matters: tissue size as a marker for a transition between reaction-diffusion regimes in spatio-temporal distribution of morphogens. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211112. [PMID: 35116146 PMCID: PMC8790355 DOI: 10.1098/rsos.211112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
The reaction-diffusion model constitutes one of the most influential mathematical models to study distribution of morphogens in tissues. Despite its widespread use, the effect of finite tissue size on model-predicted spatio-temporal morphogen distributions has not been completely elucidated. In this study, we analytically investigated the spatio-temporal distributions of morphogens predicted by a reaction-diffusion model in a finite one-dimensional domain, as a proxy for a biological tissue, and compared it with the solution of the infinite-domain model. We explored the reduced parameter, the tissue length in units of a characteristic reaction-diffusion length, and identified two reaction-diffusion regimes separated by a crossover tissue size estimated in approximately three characteristic reaction-diffusion lengths. While above this crossover the infinite-domain model constitutes a good approximation, it breaks below this crossover, whereas the finite-domain model faithfully describes the entire parameter space. We evaluated whether the infinite-domain model renders accurate estimations of diffusion coefficients when fitted to finite spatial profiles, a procedure typically followed in fluorescence recovery after photobleaching (FRAP) experiments. We found that the infinite-domain model overestimates diffusion coefficients when the domain is smaller than the crossover tissue size. Thus, the crossover tissue size may be instrumental in selecting the suitable reaction-diffusion model to study tissue morphogenesis.
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Affiliation(s)
- Alberto S. Ceccarelli
- Systems Biology Group (SysBio), Institute of Physics of Liquids and Biological Systems (IFLySIB), National Scientific and Technical Research Council (CONICET), University of La Plata, La Plata, Argentina
| | - Augusto Borges
- Systems Biology Group (SysBio), Institute of Physics of Liquids and Biological Systems (IFLySIB), National Scientific and Technical Research Council (CONICET), University of La Plata, La Plata, Argentina
- Research Unit of Sensory Biology & Organogenesis, Helmholtz Zentrum München, Munich, Germany
- Graduate School of Quantitative Biosciences (QBM), Munich, Germany
| | - Osvaldo Chara
- Systems Biology Group (SysBio), Institute of Physics of Liquids and Biological Systems (IFLySIB), National Scientific and Technical Research Council (CONICET), University of La Plata, La Plata, Argentina
- Center for Information Services and High Performance Computing (ZIH), Technische Universität Dresden, Dresden, Germany
- Instituto de Tecnología, Universidad Argentina de la Empresa (UADE), Buenos Aires, Argentina
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29
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Jones WD, Mullins MC. Cell signaling pathways controlling an axis organizing center in the zebrafish. Curr Top Dev Biol 2022; 150:149-209. [DOI: 10.1016/bs.ctdb.2022.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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30
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Song Y, Hyeon C. Cost-precision trade-off relation determines the optimal morphogen gradient for accurate biological pattern formation. eLife 2021; 10:70034. [PMID: 34402427 PMCID: PMC8457829 DOI: 10.7554/elife.70034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/13/2021] [Indexed: 01/05/2023] Open
Abstract
Spatial boundaries formed during animal development originate from the pre-patterning of tissues by signaling molecules, called morphogens. The accuracy of boundary location is limited by the fluctuations of morphogen concentration that thresholds the expression level of target gene. Producing more morphogen molecules, which gives rise to smaller relative fluctuations, would better serve to shape more precise target boundaries; however, it incurs more thermodynamic cost. In the classical diffusion-depletion model of morphogen profile formation, the morphogen molecules synthesized from a local source display an exponentially decaying concentration profile with a characteristic length λ. Our theory suggests that in order to attain a precise profile with the minimal cost, λ should be roughly half the distance to the target boundary position from the source. Remarkably, we find that the profiles of morphogens that pattern the Drosophila embryo and wing imaginal disk are formed with nearly optimal λ. Our finding underscores the cost-effectiveness of precise morphogen profile formation in Drosophila development.
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Affiliation(s)
- Yonghyun Song
- Korea Institute for Advanced Study, Seoul, Republic of Korea
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul, Republic of Korea
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31
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Kühn S, Freyse J, Atallah P, Rademann J, Freudenberg U, Werner C. Tuning the network charge of biohybrid hydrogel matrices to modulate the release of SDF-1. Biol Chem 2021; 402:1453-1464. [PMID: 34218538 DOI: 10.1515/hsz-2021-0175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 06/10/2021] [Indexed: 11/15/2022]
Abstract
The delivery of chemotactic signaling molecules via customized biomaterials can effectively guide the migration of cells to improve the regeneration of damaged or diseased tissues. Here, we present a novel biohybrid hydrogel system containing two different sulfated glycosaminoglycans (sGAG)/sGAG derivatives, namely either a mixture of short heparin polymers (Hep-Mal) or structurally defined nona-sulfated tetrahyaluronans (9s-HA4-SH), to precisely control the release of charged signaling molecules. The polymer networks are described in terms of their negative charge, i.e. the anionic sulfate groups on the saccharides, using two parameters, the integral density of negative charge and the local charge distribution (clustering) within the network. The modulation of both parameters was shown to govern the release characteristics of the chemotactic signaling molecule SDF-1 and allows for seamless transitions between burst and sustained release conditions as well as the precise control over the total amount of delivered protein. The obtained hydrogels with well-adjusted release profiles effectively promote MSC migration in vitro and emerge as promising candidates for new treatment modalities in the context of bone repair and wound healing.
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Affiliation(s)
- Sebastian Kühn
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Str. 6, D-01069Dresden, Germany
| | - Joanna Freyse
- Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, D-14195Berlin, Germany
| | - Passant Atallah
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Str. 6, D-01069Dresden, Germany
| | - Jörg Rademann
- Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, D-14195Berlin, Germany
| | - Uwe Freudenberg
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Str. 6, D-01069Dresden, Germany
| | - Carsten Werner
- Leibniz Institute of Polymer Research Dresden (IPF), Max Bergmann Center of Biomaterials Dresden (MBC), Hohe Str. 6, D-01069Dresden, Germany.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Fetscherstraße 105, D-01307Dresden, Germany
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32
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Douek AM, Amiri Khabooshan M, Henry J, Stamatis SA, Kreuder F, Ramm G, Änkö ML, Wlodkowic D, Kaslin J. An Engineered sgsh Mutant Zebrafish Recapitulates Molecular and Behavioural Pathobiology of Sanfilippo Syndrome A/MPS IIIA. Int J Mol Sci 2021; 22:ijms22115948. [PMID: 34073041 PMCID: PMC8197930 DOI: 10.3390/ijms22115948] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 12/29/2022] Open
Abstract
Mucopolysaccharidosis IIIA (MPS IIIA, Sanfilippo syndrome type A), a paediatric neurological lysosomal storage disease, is caused by impaired function of the enzyme N-sulfoglucosamine sulfohydrolase (SGSH) resulting in impaired catabolism of heparan sulfate glycosaminoglycan (HS GAG) and its accumulation in tissues. MPS IIIA represents a significant proportion of childhood dementias. This condition generally leads to patient death in the teenage years, yet no effective therapy exists for MPS IIIA and a complete understanding of the mechanisms of MPS IIIA pathogenesis is lacking. Here, we employ targeted CRISPR/Cas9 mutagenesis to generate a model of MPS IIIA in the zebrafish, a model organism with strong genetic tractability and amenity for high-throughput screening. The sgshΔex5-6 zebrafish mutant exhibits a complete absence of Sgsh enzymatic activity, leading to progressive accumulation of HS degradation products with age. sgshΔex5-6 zebrafish faithfully recapitulate diverse CNS-specific features of MPS IIIA, including neuronal lysosomal overabundance, complex behavioural phenotypes, and profound, lifelong neuroinflammation. We further demonstrate that neuroinflammation in sgshΔex5-6 zebrafish is largely dependent on interleukin-1β and can be attenuated via the pharmacological inhibition of Caspase-1, which partially rescues behavioural abnormalities in sgshΔex5-6 mutant larvae in a context-dependent manner. We expect the sgshΔex5-6 zebrafish mutant to be a valuable resource in gaining a better understanding of MPS IIIA pathobiology towards the development of timely and effective therapeutic interventions.
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Affiliation(s)
- Alon M. Douek
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; (A.M.D.); (M.A.K.); (S.-A.S.); (F.K.)
| | - Mitra Amiri Khabooshan
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; (A.M.D.); (M.A.K.); (S.-A.S.); (F.K.)
| | - Jason Henry
- Neurotoxicology Lab, School of Science (Biosciences), RMIT University, Bundoora, VIC 3083, Australia; (J.H.); (D.W.)
| | - Sebastian-Alexander Stamatis
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; (A.M.D.); (M.A.K.); (S.-A.S.); (F.K.)
| | - Florian Kreuder
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; (A.M.D.); (M.A.K.); (S.-A.S.); (F.K.)
| | - Georg Ramm
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC 3800, Australia;
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Minna-Liisa Änkö
- Centre for Reproductive Health and Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia;
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Donald Wlodkowic
- Neurotoxicology Lab, School of Science (Biosciences), RMIT University, Bundoora, VIC 3083, Australia; (J.H.); (D.W.)
| | - Jan Kaslin
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia; (A.M.D.); (M.A.K.); (S.-A.S.); (F.K.)
- Correspondence: ; Tel.: +61-3-9902-9613; Fax: +61-3-9902-9729
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33
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Lord ND, Carte AN, Abitua PB, Schier AF. The pattern of nodal morphogen signaling is shaped by co-receptor expression. eLife 2021; 10:e54894. [PMID: 34036935 PMCID: PMC8266389 DOI: 10.7554/elife.54894] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 05/26/2021] [Indexed: 12/13/2022] Open
Abstract
Embryos must communicate instructions to their constituent cells over long distances. These instructions are often encoded in the concentration of signals called morphogens. In the textbook view, morphogen molecules diffuse from a localized source to form a concentration gradient, and target cells adopt fates by measuring the local morphogen concentration. However, natural patterning systems often incorporate numerous co-factors and extensive signaling feedback, suggesting that embryos require additional mechanisms to generate signaling patterns. Here, we examine the mechanisms of signaling pattern formation for the mesendoderm inducer Nodal during zebrafish embryogenesis. We find that Nodal signaling activity spans a normal range in the absence of signaling feedback and relay, suggesting that diffusion is sufficient for Nodal gradient formation. We further show that the range of endogenous Nodal ligands is set by the EGF-CFC co-receptor Oep: in the absence of Oep, Nodal activity spreads to form a nearly uniform distribution throughout the embryo. In turn, increasing Oep levels sensitizes cells to Nodal ligands. We recapitulate these experimental results with a computational model in which Oep regulates the diffusive spread of Nodal ligands by setting the rate of capture by target cells. This model predicts, and we confirm in vivo, the surprising observation that a failure to replenish Oep transforms the Nodal signaling gradient into a travelling wave. These results reveal that patterns of Nodal morphogen signaling are shaped by co-receptor-mediated restriction of ligand spread and sensitization of responding cells.
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Affiliation(s)
- Nathan D Lord
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Adam N Carte
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
- Systems, Synthetic, and Quantitative Biology PhD Program, Harvard UniversityCambridgeUnited States
- Biozentrum, University of BaselBaselSwitzerland
| | - Philip B Abitua
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
- Biozentrum, University of BaselBaselSwitzerland
- Allen Discovery Center for Cell Lineage Tracing, University of WashingtonSeattleUnited States
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34
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Mii Y, Nakazato K, Pack CG, Ikeda T, Sako Y, Mochizuki A, Taira M, Takada S. Quantitative analyses reveal extracellular dynamics of Wnt ligands in Xenopus embryos. eLife 2021; 10:55108. [PMID: 33904408 PMCID: PMC8139832 DOI: 10.7554/elife.55108] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/23/2021] [Indexed: 12/11/2022] Open
Abstract
The mechanism of intercellular transport of Wnt ligands is still a matter of debate. To better understand this issue, we examined the distribution and dynamics of Wnt8 in Xenopus embryos. While Venus-tagged Wnt8 was found on the surfaces of cells close to Wnt-producing cells, we also detected its dispersal over distances of 15 cell diameters. A combination of fluorescence correlation spectroscopy and quantitative imaging suggested that only a small proportion of Wnt8 ligands diffuses freely, whereas most Wnt8 molecules are bound to cell surfaces. Fluorescence decay after photoconversion showed that Wnt8 ligands bound on cell surfaces decrease exponentially, suggesting a dynamic exchange of bound forms of Wnt ligands. Mathematical modeling based on this exchange recapitulates a graded distribution of bound, but not free, Wnt ligands. Based on these results, we propose that Wnt distribution in tissues is controlled by a dynamic exchange of its abundant bound and rare free populations.
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Affiliation(s)
- Yusuke Mii
- National Institute for Basic Biology and Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan.,Japan Science and Technology Agency (JST), PRESTO, Kawaguchi, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | | | - Chan-Gi Pack
- Cellular Informatics Laboratory, RIKEN, Wako, Japan.,ASAN Institute for Life Sciences, ASAN Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Takafumi Ikeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yasushi Sako
- Cellular Informatics Laboratory, RIKEN, Wako, Japan
| | - Atsushi Mochizuki
- Theoretical Biology Laboratory, RIKEN, Wako, Japan.,Laboratory of Mathematical Biology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Masanori Taira
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Shinji Takada
- National Institute for Basic Biology and Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan.,The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
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35
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Chen P, Chen X, Hepfer RG, Damon BJ, Shi C, Yao JJ, Coombs MC, Kern MJ, Ye T, Yao H. A noninvasive fluorescence imaging-based platform measures 3D anisotropic extracellular diffusion. Nat Commun 2021; 12:1913. [PMID: 33772014 PMCID: PMC7997923 DOI: 10.1038/s41467-021-22221-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 03/03/2021] [Indexed: 12/21/2022] Open
Abstract
Diffusion is a major molecular transport mechanism in biological systems. Quantifying direction-dependent (i.e., anisotropic) diffusion is vitally important to depicting how the three-dimensional (3D) tissue structure and composition affect the biochemical environment, and thus define tissue functions. However, a tool for noninvasively measuring the 3D anisotropic extracellular diffusion of biorelevant molecules is not yet available. Here, we present light-sheet imaging-based Fourier transform fluorescence recovery after photobleaching (LiFT-FRAP), which noninvasively determines 3D diffusion tensors of various biomolecules with diffusivities up to 51 µm2 s-1, reaching the physiological diffusivity range in most biological systems. Using cornea as an example, LiFT-FRAP reveals fundamental limitations of current invasive two-dimensional diffusion measurements, which have drawn controversial conclusions on extracellular diffusion in healthy and clinically treated tissues. Moreover, LiFT-FRAP demonstrates that tissue structural or compositional changes caused by diseases or scaffold fabrication yield direction-dependent diffusion changes. These results demonstrate LiFT-FRAP as a powerful platform technology for studying disease mechanisms, advancing clinical outcomes, and improving tissue engineering.
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Affiliation(s)
- Peng Chen
- Clemson-MUSC Joint Bioengineering Program, Department of Bioengineering, Clemson University, Clemson, SC, USA
| | - Xun Chen
- Clemson-MUSC Joint Bioengineering Program, Department of Bioengineering, Clemson University, Clemson, SC, USA
| | - R Glenn Hepfer
- Clemson-MUSC Joint Bioengineering Program, Department of Bioengineering, Clemson University, Clemson, SC, USA
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Brooke J Damon
- Clemson-MUSC Joint Bioengineering Program, Department of Bioengineering, Clemson University, Clemson, SC, USA
| | - Changcheng Shi
- Clemson-MUSC Joint Bioengineering Program, Department of Bioengineering, Clemson University, Clemson, SC, USA
- Ningbo Institute of Industrial Technology, Chinese Academy of Sciences, Ningbo, Zhejiang, China
| | - Jenny J Yao
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Matthew C Coombs
- Clemson-MUSC Joint Bioengineering Program, Department of Bioengineering, Clemson University, Clemson, SC, USA
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Michael J Kern
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Tong Ye
- Clemson-MUSC Joint Bioengineering Program, Department of Bioengineering, Clemson University, Clemson, SC, USA.
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA.
| | - Hai Yao
- Clemson-MUSC Joint Bioengineering Program, Department of Bioengineering, Clemson University, Clemson, SC, USA.
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, SC, USA.
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36
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Stapornwongkul KS, Vincent JP. Generation of extracellular morphogen gradients: the case for diffusion. Nat Rev Genet 2021; 22:393-411. [PMID: 33767424 DOI: 10.1038/s41576-021-00342-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2021] [Indexed: 02/07/2023]
Abstract
Cells within developing tissues rely on morphogens to assess positional information. Passive diffusion is the most parsimonious transport model for long-range morphogen gradient formation but does not, on its own, readily explain scaling, robustness and planar transport. Here, we argue that diffusion is sufficient to ensure robust morphogen gradient formation in a variety of tissues if the interactions between morphogens and their extracellular binders are considered. A current challenge is to assess how the affinity for extracellular binders, as well as other biophysical and cell biological parameters, determines gradient dynamics and shape in a diffusion-based transport system. Technological advances in genome editing, tissue engineering, live imaging and in vivo biophysics are now facilitating measurement of these parameters, paving the way for mathematical modelling and a quantitative understanding of morphogen gradient formation and modulation.
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37
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Vaahtomeri K, Moussion C, Hauschild R, Sixt M. Shape and Function of Interstitial Chemokine CCL21 Gradients Are Independent of Heparan Sulfates Produced by Lymphatic Endothelium. Front Immunol 2021; 12:630002. [PMID: 33717158 PMCID: PMC7946817 DOI: 10.3389/fimmu.2021.630002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/20/2021] [Indexed: 12/30/2022] Open
Abstract
Gradients of chemokines and growth factors guide migrating cells and morphogenetic processes. Migration of antigen-presenting dendritic cells from the interstitium into the lymphatic system is dependent on chemokine CCL21, which is secreted by endothelial cells of the lymphatic capillary, binds heparan sulfates and forms gradients decaying into the interstitium. Despite the importance of CCL21 gradients, and chemokine gradients in general, the mechanisms of gradient formation are unclear. Studies on fibroblast growth factors have shown that limited diffusion is crucial for gradient formation. Here, we used the mouse dermis as a model tissue to address the necessity of CCL21 anchoring to lymphatic capillary heparan sulfates in the formation of interstitial CCL21 gradients. Surprisingly, the absence of lymphatic endothelial heparan sulfates resulted only in a modest decrease of CCL21 levels at the lymphatic capillaries and did neither affect interstitial CCL21 gradient shape nor dendritic cell migration toward lymphatic capillaries. Thus, heparan sulfates at the level of the lymphatic endothelium are dispensable for the formation of a functional CCL21 gradient.
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Affiliation(s)
- Kari Vaahtomeri
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria.,Wihuri Research Institute and Translational Cancer Medicine Research Program, University of Helsinki, Biomedicum Helsinki, Helsinki, Finland
| | - Christine Moussion
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Robert Hauschild
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Michael Sixt
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
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38
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Duran-Nebreda S, Pla J, Vidiella B, Piñero J, Conde-Pueyo N, Solé R. Synthetic Lateral Inhibition in Periodic Pattern Forming Microbial Colonies. ACS Synth Biol 2021; 10:277-285. [PMID: 33449631 PMCID: PMC8486170 DOI: 10.1021/acssynbio.0c00318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Multicellular entities are characterized by intricate spatial patterns, intimately related to the functions they perform. These patterns are often created from isotropic embryonic structures, without external information cues guiding the symmetry breaking process. Mature biological structures also display characteristic scales with repeating distributions of signals or chemical species across space. Many candidate patterning modules have been used to explain processes during development and typically include a set of interacting and diffusing chemicals or agents known as morphogens. Great effort has been put forward to better understand the conditions in which pattern-forming processes can occur in the biological domain. However, evidence and practical knowledge allowing us to engineer symmetry-breaking is still lacking. Here we follow a different approach by designing a synthetic gene circuit in E. coli that implements a local activation long-range inhibition mechanism. The synthetic gene network implements an artificial differentiation process that changes the physicochemical properties of the agents. Using both experimental results and modeling, we show that the proposed system is capable of symmetry-breaking leading to regular spatial patterns during colony growth. Studying how these patterns emerge is fundamental to further our understanding of the evolution of biocomplexity and the role played by self-organization. The artificial system studied here and the engineering perspective on embryogenic processes can help validate developmental theories and identify universal properties underpinning biological pattern formation, with special interest for the area of synthetic developmental biology.
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Affiliation(s)
- Salva Duran-Nebreda
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Evolution of Technology Lab, Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
| | - Jordi Pla
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Blai Vidiella
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Jordi Piñero
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Nuria Conde-Pueyo
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Ricard Solé
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico 87501, United States
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39
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Isthmin1, a secreted signaling protein, acts downstream of diverse embryonic patterning centers in development. Cell Tissue Res 2020; 383:987-1002. [PMID: 33367974 PMCID: PMC7960586 DOI: 10.1007/s00441-020-03318-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/06/2020] [Indexed: 11/25/2022]
Abstract
Extracellular signals play essential roles during embryonic patterning by providing positional information in a concentration-dependent manner, and many such signals, like Wnt, fibroblast growth factor (FGF), Hedgehog (Hh), and retinoic acid, act by being secreted into the extracellular space, thereby triggering receptor-mediated responses in other cells. Isthmin1 (ism1) is a secreted protein whose gene expression pattern coincides with that of early dorsal determinants, nodal ligand genes like sqt and cyc, and with fgf8 during various phases of zebrafish development. Ism1 functions in early embryonic patterning and development are poorly understood; however, it has recently been shown to interact with nodal pathway genes to control organ asymmetry in chicken. Here, we show that misexpression of ism1 deletion constructs disrupts embryonic patterning in zebrafish and exhibits genetic interactions with both Fgf and nodal signaling. Unlike Fgf and nodal pathway mutants, CRISPR/Cas9-engineered ism1 mutants did not show obvious developmental defects. Further, in vivo single molecule fluorescence correlation spectroscopy (FCCS) showed that Ism1 diffuses freely in the extra-cellular space, with a diffusion coefficient similar to that of Fgf8a; however, our measurements do not support direct molecular interactions between Ism1 and either nodal ligands or Fgf8a in the developing zebrafish embryo. Together, data from gain- and loss-of-function experiments suggest that zebrafish Ism1 plays a complex role in regulating extracellular signals during early embryonic development.
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40
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Veerapathiran S, Teh C, Zhu S, Kartigayen I, Korzh V, Matsudaira PT, Wohland T. Wnt3 distribution in the zebrafish brain is determined by expression, diffusion and multiple molecular interactions. eLife 2020; 9:e59489. [PMID: 33236989 PMCID: PMC7725503 DOI: 10.7554/elife.59489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/23/2020] [Indexed: 12/19/2022] Open
Abstract
Wnt3 proteins are lipidated and glycosylated signaling molecules that play an important role in zebrafish neural patterning and brain development. However, the transport mechanism of lipid-modified Wnts through the hydrophilic extracellular environment for long-range action remains unresolved. Here we determine how Wnt3 accomplishes long-range distribution in the zebrafish brain. First, we characterize the Wnt3-producing source and Wnt3-receiving target regions. Subsequently, we analyze Wnt3 mobility at different length scales by fluorescence correlation spectroscopy and fluorescence recovery after photobleaching. We demonstrate that Wnt3 spreads extracellularly and interacts with heparan sulfate proteoglycans (HSPG). We then determine the binding affinity of Wnt3 to its receptor, Frizzled1 (Fzd1), using fluorescence cross-correlation spectroscopy and show that the co-receptor, low-density lipoprotein receptor-related protein 5 (Lrp5), is required for Wnt3-Fzd1 interaction. Our results are consistent with the extracellular distribution of Wnt3 by a diffusive mechanism that is modified by tissue morphology, interactions with HSPG, and Lrp5-mediated receptor binding, to regulate zebrafish brain development.
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Affiliation(s)
- Sapthaswaran Veerapathiran
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Cathleen Teh
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Shiwen Zhu
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Indira Kartigayen
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Vladimir Korzh
- International Institute of Molecular and Cell Biology in WarsawWarsawPoland
| | - Paul T Matsudaira
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Thorsten Wohland
- Department of Biological Sciences, National University of SingaporeSingaporeSingapore
- Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
- Department of Chemistry, National University of SingaporeSingaporeSingapore
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41
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Simon CS, Rahman S, Raina D, Schröter C, Hadjantonakis AK. Live Visualization of ERK Activity in the Mouse Blastocyst Reveals Lineage-Specific Signaling Dynamics. Dev Cell 2020; 55:341-353.e5. [PMID: 33091370 PMCID: PMC7658048 DOI: 10.1016/j.devcel.2020.09.030] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/05/2020] [Accepted: 09/28/2020] [Indexed: 01/16/2023]
Abstract
FGF/ERK signaling is crucial for the patterning and proliferation of cell lineages that comprise the mouse blastocyst. However, ERK signaling dynamics have never been directly visualized in live embryos. To address whether differential signaling is associated with particular cell fates and states, we generated a targeted mouse line expressing an ERK-kinase translocation reporter (KTR) that enables live quantification of ERK activity at single-cell resolution. 3D time-lapse imaging of this biosensor in embryos revealed spatially graded ERK activity in the trophectoderm prior to overt polar versus mural differentiation. Within the inner cell mass (ICM), all cells relayed FGF/ERK signals with varying durations and magnitude. Primitive endoderm cells displayed higher overall levels of ERK activity, while pluripotent epiblast cells exhibited lower basal activity with sporadic pulses. These results constitute a direct visualization of signaling events during mammalian pre-implantation development and reveal the existence of spatial and temporal lineage-specific dynamics.
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Affiliation(s)
- Claire S Simon
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Shahadat Rahman
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dhruv Raina
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Christian Schröter
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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42
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Dawes ML, Soeller C, Scholpp S. Studying molecular interactions in the intact organism: fluorescence correlation spectroscopy in the living zebrafish embryo. Histochem Cell Biol 2020; 154:507-519. [PMID: 33067656 PMCID: PMC7609432 DOI: 10.1007/s00418-020-01930-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2020] [Indexed: 02/07/2023]
Abstract
Cell behaviour and function is determined through the interactions of a multitude of molecules working in concert. To observe these molecular dynamics, biophysical studies have been developed that track single interactions. Fluorescence correlation spectroscopy (FCS) is an optical biophysical technique that non-invasively resolves single molecules through recording the signal intensity at the femtolitre scale. However, recording the behaviour of these biomolecules using in vitro-based assays often fails to recapitulate the full range of variables in vivo that directly confer dynamics. Therefore, there has been an increasing interest in observing the state of these biomolecules within living organisms such as the zebrafish Danio rerio. In this review, we explore the advancements of FCS within the zebrafish and compare and contrast these findings to those found in vitro.
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Affiliation(s)
- Michael L Dawes
- Living Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Christian Soeller
- Living Systems Institute, College of Engineering, Mathematics, and Physical Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Steffen Scholpp
- Living Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK.
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43
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York HM, Coyle J, Arumugam S. To be more precise: the role of intracellular trafficking in development and pattern formation. Biochem Soc Trans 2020; 48:2051-2066. [PMID: 32915197 PMCID: PMC7609031 DOI: 10.1042/bst20200223] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 02/07/2023]
Abstract
Living cells interpret a variety of signals in different contexts to elucidate functional responses. While the understanding of signalling molecules, their respective receptors and response at the gene transcription level have been relatively well-explored, how exactly does a single cell interpret a plethora of time-varying signals? Furthermore, how their subsequent responses at the single cell level manifest in the larger context of a developing tissue is unknown. At the same time, the biophysics and chemistry of how receptors are trafficked through the complex dynamic transport network between the plasma membrane-endosome-lysosome-Golgi-endoplasmic reticulum are much more well-studied. How the intracellular organisation of the cell and inter-organellar contacts aid in orchestrating trafficking, as well as signal interpretation and modulation by the cells are beginning to be uncovered. In this review, we highlight the significant developments that have strived to integrate endosomal trafficking, signal interpretation in the context of developmental biology and relevant open questions with a few chosen examples. Furthermore, we will discuss the imaging technologies that have been developed in the recent past that have the potential to tremendously accelerate knowledge gain in this direction while shedding light on some of the many challenges.
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Affiliation(s)
- Harrison M. York
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Joanne Coyle
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Senthil Arumugam
- Monash Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC 3800, Australia
- European Molecular Biological Laboratory Australia (EMBL Australia), Monash University, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
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44
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Stapornwongkul KS, de Gennes M, Cocconi L, Salbreux G, Vincent JP. Patterning and growth control in vivo by an engineered GFP gradient. Science 2020; 370:321-327. [PMID: 33060356 PMCID: PMC7611032 DOI: 10.1126/science.abb8205] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Accepted: 08/21/2020] [Indexed: 02/06/2023]
Abstract
Morphogen gradients provide positional information during development. To uncover the minimal requirements for morphogen gradient formation, we have engineered a synthetic morphogen in Drosophila wing primordia. We show that an inert protein, green fluorescent protein (GFP), can form a detectable diffusion-based gradient in the presence of surface-associated anti-GFP nanobodies, which modulate the gradient by trapping the ligand and limiting leakage from the tissue. We next fused anti-GFP nanobodies to the receptors of Dpp, a natural morphogen, to render them responsive to extracellular GFP. In the presence of these engineered receptors, GFP could replace Dpp to organize patterning and growth in vivo. Concomitant expression of glycosylphosphatidylinositol (GPI)-anchored nonsignaling receptors further improved patterning, to near-wild-type quality. Theoretical arguments suggest that GPI anchorage could be important for these receptors to expand the gradient length scale while at the same time reducing leakage.
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Affiliation(s)
| | - Marc de Gennes
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Luca Cocconi
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Imperial College, Department of Mathematics, London, UK
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45
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Fancher S, Mugler A. Diffusion vs. direct transport in the precision of morphogen readout. eLife 2020; 9:58981. [PMID: 33051001 PMCID: PMC7641583 DOI: 10.7554/elife.58981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/13/2020] [Indexed: 01/14/2023] Open
Abstract
Morphogen profiles allow cells to determine their position within a developing organism, but not all morphogen profiles form by the same mechanism. Here, we derive fundamental limits to the precision of morphogen concentration sensing for two canonical mechanisms: the diffusion of morphogen through extracellular space and the direct transport of morphogen from source cell to target cell, for example, via cytonemes. We find that direct transport establishes a morphogen profile without adding noise in the process. Despite this advantage, we find that for sufficiently large values of profile length, the diffusion mechanism is many times more precise due to a higher refresh rate of morphogen molecules. We predict a profile lengthscale below which direct transport is more precise, and above which diffusion is more precise. This prediction is supported by data from a wide variety of morphogens in developing Drosophila and zebrafish.
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Affiliation(s)
- Sean Fancher
- Department of Physics and Astronomy, Purdue University, West Lafayette, United States.,Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, United States
| | - Andrew Mugler
- Department of Physics and Astronomy, Purdue University, West Lafayette, United States.,Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, United States
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46
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Corbeil D, Santos MF, Karbanová J, Kurth T, Rappa G, Lorico A. Uptake and Fate of Extracellular Membrane Vesicles: Nucleoplasmic Reticulum-Associated Late Endosomes as a New Gate to Intercellular Communication. Cells 2020; 9:cells9091931. [PMID: 32825578 PMCID: PMC7563309 DOI: 10.3390/cells9091931] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
Extracellular membrane vesicles (EVs) are emerging as new vehicles in intercellular communication, but how the biological information contained in EVs is shared between cells remains elusive. Several mechanisms have been described to explain their release from donor cells and the initial step of their uptake by recipient cells, which triggers a cellular response. Yet, the intracellular routes and subcellular fate of EV content upon internalization remain poorly characterized. This is particularly true for EV-associated proteins and nucleic acids that shuttle to the nucleus of host cells. In this review, we will describe and discuss the release of EVs from donor cells, their uptake by recipient cells, and the fate of their cargoes, focusing on a novel intracellular route wherein small GTPase Rab7+ late endosomes containing endocytosed EVs enter into nuclear envelope invaginations and deliver their cargo components to the nucleoplasm of recipient cells. A tripartite protein complex composed of (VAMP)-associated protein A (VAP-A), oxysterol-binding protein (OSBP)-related protein-3 (ORP3), and Rab7 is essential for the transfer of EV-derived components to the nuclear compartment by orchestrating the particular localization of late endosomes in the nucleoplasmic reticulum.
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Affiliation(s)
- Denis Corbeil
- Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany; (J.K.)
- Correspondence: (D.C.); (A.L.); Tel.: +49-(0)351-463-40118 (D.C.); +1-(702)-777-3942 (A.L.); Fax: +49-(0)351-463-40244 (D.C.); +1-(702)-777-1758 (A.L.)
| | - Mark F. Santos
- College of Osteopathic Medicine, Touro University Nevada, 874 American Pacific Drive, Henderson, NV 89014, USA; (M.F.S.); (G.R.)
| | - Jana Karbanová
- Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany; (J.K.)
| | - Thomas Kurth
- Center for Regenerative Therapies Dresden and CMCB, Technische Universität Dresden, Fetscherstraße 105, 01307 Dresden, Germany; (T.K.)
| | - Germana Rappa
- College of Osteopathic Medicine, Touro University Nevada, 874 American Pacific Drive, Henderson, NV 89014, USA; (M.F.S.); (G.R.)
| | - Aurelio Lorico
- College of Osteopathic Medicine, Touro University Nevada, 874 American Pacific Drive, Henderson, NV 89014, USA; (M.F.S.); (G.R.)
- Mediterranean Institute of Oncology, Via Penninazzo, 11, 95029 Viagrande, Italy
- Correspondence: (D.C.); (A.L.); Tel.: +49-(0)351-463-40118 (D.C.); +1-(702)-777-3942 (A.L.); Fax: +49-(0)351-463-40244 (D.C.); +1-(702)-777-1758 (A.L.)
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47
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Wnt/β-catenin Signaling in Tissue Self-Organization. Genes (Basel) 2020; 11:genes11080939. [PMID: 32823838 PMCID: PMC7464740 DOI: 10.3390/genes11080939] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
Across metazoans, animal body structures and tissues exist in robust patterns that arise seemingly out of stochasticity of a few early cells in the embryo. These patterns ensure proper tissue form and function during early embryogenesis, development, homeostasis, and regeneration. Fundamental questions are how these patterns are generated and maintained during tissue homeostasis and regeneration. Though fascinating scientists for generations, these ideas remain poorly understood. Today, it is apparent that the Wnt/β-catenin pathway plays a central role in tissue patterning. Wnt proteins are small diffusible morphogens which are essential for cell type specification and patterning of tissues. In this review, we highlight several mechanisms described where the spatial properties of Wnt/β-catenin signaling are controlled, allowing them to work in combination with other diffusible molecules to control tissue patterning. We discuss examples of this self-patterning behavior during development and adult tissues' maintenance. The combination of new physiological culture systems, mathematical approaches, and synthetic biology will continue to fuel discoveries about how tissues are patterned. These insights are critical for understanding the intricate interplay of core patterning signals and how they become disrupted in disease.
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48
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Karkaria BD, Treloar NJ, Barnes CP, Fedorec AJH. From Microbial Communities to Distributed Computing Systems. Front Bioeng Biotechnol 2020; 8:834. [PMID: 32793576 PMCID: PMC7387671 DOI: 10.3389/fbioe.2020.00834] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022] Open
Abstract
A distributed biological system can be defined as a system whose components are located in different subpopulations, which communicate and coordinate their actions through interpopulation messages and interactions. We see that distributed systems are pervasive in nature, performing computation across all scales, from microbial communities to a flock of birds. We often observe that information processing within communities exhibits a complexity far greater than any single organism. Synthetic biology is an area of research which aims to design and build synthetic biological machines from biological parts to perform a defined function, in a manner similar to the engineering disciplines. However, the field has reached a bottleneck in the complexity of the genetic networks that we can implement using monocultures, facing constraints from metabolic burden and genetic interference. This makes building distributed biological systems an attractive prospect for synthetic biology that would alleviate these constraints and allow us to expand the applications of our systems into areas including complex biosensing and diagnostic tools, bioprocess control and the monitoring of industrial processes. In this review we will discuss the fundamental limitations we face when engineering functionality with a monoculture, and the key areas where distributed systems can provide an advantage. We cite evidence from natural systems that support arguments in favor of distributed systems to overcome the limitations of monocultures. Following this we conduct a comprehensive overview of the synthetic communities that have been built to date, and the components that have been used. The potential computational capabilities of communities are discussed, along with some of the applications that these will be useful for. We discuss some of the challenges with building co-cultures, including the problem of competitive exclusion and maintenance of desired community composition. Finally, we assess computational frameworks currently available to aide in the design of microbial communities and identify areas where we lack the necessary tools.
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Affiliation(s)
- Behzad D. Karkaria
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Neythen J. Treloar
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Chris P. Barnes
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Alex J. H. Fedorec
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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49
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Fuentes R, Tajer B, Kobayashi M, Pelliccia JL, Langdon Y, Abrams EW, Mullins MC. The maternal coordinate system: Molecular-genetics of embryonic axis formation and patterning in the zebrafish. Curr Top Dev Biol 2020; 140:341-389. [PMID: 32591080 DOI: 10.1016/bs.ctdb.2020.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Axis specification of the zebrafish embryo begins during oogenesis and relies on proper formation of well-defined cytoplasmic domains within the oocyte. Upon fertilization, maternally-regulated cytoplasmic flow and repositioning of dorsal determinants establish the coordinate system that will build the structure and developmental body plan of the embryo. Failure of specific genes that regulate the embryonic coordinate system leads to catastrophic loss of body structures. Here, we review the genetic principles of axis formation and discuss how maternal factors orchestrate axis patterning during zebrafish early embryogenesis. We focus on the molecular identity and functional contribution of genes controlling critical aspects of oogenesis, egg activation, blastula, and gastrula stages. We examine how polarized cytoplasmic domains form in the oocyte, which set off downstream events such as animal-vegetal polarity and germ line development. After gametes interact and form the zygote, cytoplasmic segregation drives the animal-directed reorganization of maternal determinants through calcium- and cell cycle-dependent signals. We also summarize how maternal genes control dorsoventral, anterior-posterior, mesendodermal, and left-right cell fate specification and how signaling pathways pattern these axes and tissues during early development to instruct the three-dimensional body plan. Advances in reverse genetics and phenotyping approaches in the zebrafish model are revealing positional patterning signatures at the single-cell level, thus enhancing our understanding of genotype-phenotype interactions in axis formation. Our emphasis is on the genetic interrogation of novel and specific maternal regulatory mechanisms of axis specification in the zebrafish.
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Affiliation(s)
- Ricardo Fuentes
- Departamento de Biología Celular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile.
| | - Benjamin Tajer
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, United States
| | - Manami Kobayashi
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, United States
| | - Jose L Pelliccia
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, United States
| | | | - Elliott W Abrams
- Department of Biology, Purchase College, State University of New York, Harrison, NY, United States
| | - Mary C Mullins
- Department of Cell and Developmental Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, United States.
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50
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Cui KW, Engel L, Dundes CE, Nguyen TC, Loh KM, Dunn AR. Spatially controlled stem cell differentiation via morphogen gradients: A comparison of static and dynamic microfluidic platforms. JOURNAL OF VACUUM SCIENCE & TECHNOLOGY. A, VACUUM, SURFACES, AND FILMS : AN OFFICIAL JOURNAL OF THE AMERICAN VACUUM SOCIETY 2020; 38:033205. [PMID: 32255900 PMCID: PMC7093209 DOI: 10.1116/1.5142012#suppl] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 05/30/2023]
Abstract
The ability to harness the processes by which complex tissues arise during embryonic development would improve the ability to engineer complex tissuelike constructs in vitro-a longstanding goal of tissue engineering and regenerative medicine. In embryos, uniform populations of stem cells are exposed to spatial gradients of diffusible extracellular signaling proteins, known as morphogens. Varying levels of these signaling proteins induce stem cells to differentiate into distinct cell types at different positions along the gradient, thus creating spatially patterned tissues. Here, the authors describe two straightforward and easy-to-adopt microfluidic strategies to expose human pluripotent stem cells in vitro to spatial gradients of desired differentiation-inducing extracellular signals. Both approaches afford a high degree of control over the distribution of extracellular signals, while preserving the viability of the cultured stem cells. The first microfluidic platform is commercially available and entails static culture, whereas the second microfluidic platform requires fabrication and dynamic fluid exchange. In each platform, the authors first computationally modeled the spatial distribution of differentiation-inducing extracellular signals. Then, the authors used each platform to expose human pluripotent stem cells to a gradient of these signals (in this case, inducing a cell type known as the primitive streak), resulting in a regionalized culture with differentiated primitive streak cells predominately localized on one side and undifferentiated stem cells at the other side of the device. By combining this approach with a fluorescent reporter for differentiated cells and live-cell fluorescence imaging, the authors characterized the spatial and temporal dynamics of primitive streak differentiation within the induced signaling gradients. Microfluidic approaches to create precisely controlled morphogen gradients will add to the stem cell and developmental biology toolkit, and may eventually pave the way to create increasingly spatially patterned tissuelike constructs in vitro.
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Affiliation(s)
- Kiara W Cui
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
| | - Leeya Engel
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
| | - Carolyn E Dundes
- Department of Developmental Biology, Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305
| | - Tina C Nguyen
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
| | - Kyle M Loh
- Department of Developmental Biology, Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305
| | - Alexander R Dunn
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
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