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Mukherjee N, Arathimos R, Chen S, Kheirkhah Rahimabad P, Han L, Zhang H, Holloway JW, Relton C, Henderson AJ, Arshad SH, Ewart S, Karmaus W. DNA methylation at birth is associated with lung function development until age 26 years. Eur Respir J 2021; 57:2003505. [PMID: 33214203 DOI: 10.1183/13993003.03505-2020] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022]
Abstract
Little is known about whether DNA methylation (DNAm) of cytosine-phosphate-guanine (CpG) sites at birth predicts patterns of lung function development. We used heel prick DNAm from the F1-generation of Isle of Wight birth cohort (IOWBC-F1) for discovery of CpGs associated with lung function trajectories (forced expiratory volume in 1 s, forced vital capacity, their ratio, and forced expiratory flow at 25-75% of forced vital capacity) over the first 26 years, stratified by sex. We replicated the findings in the Avon Longitudinal Study of Parents and Children (ALSPAC) using cord blood DNAm.Epigenome-wide screening was applied to identify CpGs associated with lung function trajectories in 396 boys and 390 girls of IOWBC-F1. Replication in ALSPAC focussed on lung function at ages 8, 15 and 24 years. Statistically significantly replicated CpGs were investigated for consistency in direction of association between cohorts, stability of DNAm over time in IOWBC-F1, relevant biological processes and for association with gene expression (n=161) in IOWBC F2-generation (IOWBC-F2).Differential DNAm of eight CpGs on genes GLUL, MYCN, HLX, LHX1, COBL, COL18A1, STRA6, and WNT11 involved in developmental processes, were significantly associated with lung function in the same direction in IOWBC-F1 and ALSPAC, and showed stable patterns at birth, aged 10 and 18 years between high and low lung function trajectories in IOWBC-F1. CpGs on LHX1 and COL18A1 were linked to gene expression in IOWBC-F2.In two large cohorts, novel DNAm at birth were associated with patterns of lung function in adolescence and early adulthood providing possible targets for preventative interventions against adverse pulmonary function development.
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Affiliation(s)
- Nandini Mukherjee
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Ryan Arathimos
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Social Genetic & Developmental Psychiatry Centre, Kings College London, London, UK
- NIHR Biomedical Research Centre for Mental Health, South London and Maudsley NHS Trust, London, UK
| | - Su Chen
- Dept of Mathematical Sciences, The University of Memphis, Memphis, TN, USA
| | - Parnian Kheirkhah Rahimabad
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Luhang Han
- Dept of Mathematical Sciences, The University of Memphis, Memphis, TN, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - John W Holloway
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - A John Henderson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- The David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
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2
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Choubey PK, Roy JK. Rab11 is required for tubulogenesis of Malpighian tubules in Drosophila melanogaster. Genesis 2017; 55. [PMID: 28653473 DOI: 10.1002/dvg.23045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 06/22/2017] [Accepted: 06/22/2017] [Indexed: 12/12/2022]
Abstract
Intracellular vesicular trafficking is one of the important tools in maintaining polarity, adhesion, and shape of epithelial cells. Rab11, a subfamily of the Ypt/Rab gene family of ubiquitously expressed GTPases and a molecular marker of recycling endosomes, transports different components of plasma membrane. Here, we report that Rab11 affects tubulogenesis of Malpighian tubules (MTs). MTs are simple polarized epithelial tubular structures, considered as functional analogue of human kidney. Rab11 has pleiotropic effects on MTs development as down-regulation of Rab11 in principal cells (PCs) of MTs from embryonic stages of development results in reduced endoreplication, clustering of cells, disorganized cytoskeleton, and disruption of polarity leading to shortening of MTs in third instar larvae. Rab11 is also required for proper localization of different transporters in PCs, essential for physiological activity of MTs. Collectively, our data suggest that Rab11 plays a key role in the process of tubulogenesis of MTs in Drosophila.
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Affiliation(s)
- Praween Kumar Choubey
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221 005, Uttar Pradesh, India
| | - Jagat Kumar Roy
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi, 221 005, Uttar Pradesh, India
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3
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Matsumoto S, Fujii S, Kikuchi A. Arl4c is a key regulator of tubulogenesis and tumourigenesis as a target gene of Wnt-β-catenin and growth factor-Ras signalling. J Biochem 2016; 161:27-35. [PMID: 28053143 DOI: 10.1093/jb/mvw069] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/13/2016] [Indexed: 12/19/2022] Open
Abstract
Epithelial tubular morphogenesis (tubulogenesis) is a fundamental morphogenetic process of many epithelial organs. In this developmental process, epithelial cells migrate, proliferate, polarize and differentiate towards surrounding mesenchymal tissue to form tubule structures. Although epithelial tissue structures are basically stable in the postnatal period, epithelial cells regain highly proliferative and invasive potentials within mesenchymal tissue during tumour formation (tumourigenesis). Therefore, there must be a common molecular basis orchestrating the cellular behaviours involved in both tubulogenesis and tumourigenesis. ADP-ribosylation factor (Arf)-like protein 4c (Arl4c), which belongs to the small GTP-binding protein family, is expressed by the simultaneous activation of Wnt-β-catenin and growth factor-Ras-mitogen-activated protein kinase signalling, was identified as an essential regulator of tubulogenesis. Arl4c expression was also involved in the tumour formation of colorectal and lung cancers. In this review, we focus on Arl4c as a novel Wnt signal target molecule that links epithelial tubulogenesis to tumourigenesis.
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Affiliation(s)
- Shinji Matsumoto
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shinsuke Fujii
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan.,Laboratory of Oral Pathology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Akira Kikuchi
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
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4
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Abstract
Transporting epithelia commonly consist of tubes that mediate between the body and its environment. Lumen formation is closely linked to epithelial morphogenesis, but an open question is how luminal symmetry is broken to generate tubes rather than hollow cysts. A report about the biomechanics of intercellular contacts might now provide some answers.
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Affiliation(s)
- Kenneth Wee
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Alpha S Yap
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
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5
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Kim HS, Nishiwaki K. Control of the basement membrane and cell migration by ADAMTS proteinases: Lessons from C. elegans genetics. Matrix Biol 2015; 44-46:64-9. [PMID: 25595837 DOI: 10.1016/j.matbio.2015.01.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 01/22/2023]
Abstract
The members of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) family of secreted proteins, MIG-17 and GON-1, play essential roles in Caenorhabditis elegans gonadogenesis. The genetic and molecular analyses of these proteinases uncovered novel molecular interactions regulating the basement membrane (BM) during the migration of the gonadal leader cells. MIG-17, which is localized to the gonadal BM recruits or activates fibulin-1 and type IV collagen, which then recruits nidogen, thereby inducing the remodeling of the BM that is required for directional control of leader cell migration. GON-1 acts antagonistically with fibulin-1 to regulate the levels of type IV collagen accumulation in the gonadal BM, which facilitates active migration of the leader cells. The cooperative action of MIG-17 and GON-1 represents an excellent model for understanding the mechanisms of organogenesis mediated by ADAMTS proteinases.
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Affiliation(s)
- Hon-Song Kim
- Department of Bioscience, Kwansei Gakuin University, 2-1 Gakuen, Sanda 669-1337, Japan
| | - Kiyoji Nishiwaki
- Department of Bioscience, Kwansei Gakuin University, 2-1 Gakuen, Sanda 669-1337, Japan.
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Ogden A, Rida PCG, Aneja R. Heading off with the herd: how cancer cells might maneuver supernumerary centrosomes for directional migration. Cancer Metastasis Rev 2013; 32:269-87. [PMID: 23114845 DOI: 10.1007/s10555-012-9413-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The complicity of centrosomes in carcinogenesis is unmistakable. Mounting evidence clearly implicates a robust correlation between centrosome amplification (CA) and malignant transformation in diverse tissue types. Furthermore, CA has been suggested as a marker of cancer aggressiveness, in particular the invasive phenotype, in breast and prostate cancers. One means by which CA promotes malignancy is through induction of transient spindle multipolarity during mitosis, which predisposes the cell to karyotypic changes arising from low-grade chromosome mis-segregation. It is well recognized that during cell migration in interphase, centrosome-mediated nucleation of a radial microtubule array is crucial for establishing a polarized Golgi apparatus, without which directionality is precluded. The question of how cancer cells maneuver their supernumerary centrosomes to achieve directionality during cell migration is virtually uncharted territory. Given that CA is a hallmark of cancers and has been correlated with cancer aggressiveness, malignant cells are presumably competent in managing their centrosome surfeit during directional migration, although the cellular logistics of this process remain unexplored. Another key angle worth pondering is whether an overabundance of centrosomes confers some advantage on cancer cells in terms of their migratory and invasive capabilities. Recent studies have uncovered a remarkable strategy that cancer cells employ to deal with the problem of excess centrosomes and ensure bipolar mitoses, viz., centrosome clustering. This review aims to change the narrative by exploring how an increased centrosome complement may, via aneuploidy-independent modulation of the microtubule cytoskeleton, enhance directional migration and invasion of malignant cells. We postulate that CA imbues cancer cells with cytoskeletal advantages that enhance cell polarization, Golgi-dependent vesicular trafficking, stromal invasion, and other aspects of metastatic progression. We also propose that centrosome declustering may represent a novel, cancer cell-specific antimetastatic strategy, as cancer cells may rely on centrosome clustering during migration as they do in mitosis. Elucidation of these details offers an exciting avenue for future research, as does investigating how CA may promote metastasis through enhanced directional migration.
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Affiliation(s)
- Angela Ogden
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
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7
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Abstract
Cell migration is fundamental to establishing and maintaining the proper organization of multicellular organisms. Morphogenesis can be viewed as a consequence, in part, of cell locomotion, from large-scale migrations of epithelial sheets during gastrulation, to the movement of individual cells during development of the nervous system. In an adult organism, cell migration is essential for proper immune response, wound repair, and tissue homeostasis, while aberrant cell migration is found in various pathologies. Indeed, as our knowledge of migration increases, we can look forward to, for example, abating the spread of highly malignant cancer cells, retarding the invasion of white cells in the inflammatory process, or enhancing the healing of wounds. This article is organized in two main sections. The first section is devoted to the single-cell migrating in isolation such as occurs when leukocytes migrate during the immune response or when fibroblasts squeeze through connective tissue. The second section is devoted to cells collectively migrating as part of multicellular clusters or sheets. This second type of migration is prevalent in development, wound healing, and in some forms of cancer metastasis.
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Affiliation(s)
- Xavier Trepat
- Institute for Bioengineering of Catalonia, Barcelona, Spain.
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Yates LL, Schnatwinkel C, Hazelwood L, Chessum L, Paudyal A, Hilton H, Romero MR, Wilde J, Bogani D, Sanderson J, Formstone C, Murdoch JN, Niswander LA, Greenfield A, Dean CH. Scribble is required for normal epithelial cell-cell contacts and lumen morphogenesis in the mammalian lung. Dev Biol 2012. [PMID: 23195221 PMCID: PMC3549499 DOI: 10.1016/j.ydbio.2012.11.012] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
During lung development, proper epithelial cell arrangements are critical for the formation of an arborized network of tubes. Each tube requires a lumen, the diameter of which must be tightly regulated to enable optimal lung function. Lung branching and lumen morphogenesis require close epithelial cell–cell contacts that are maintained as a result of adherens junctions, tight junctions and by intact apical–basal (A/B) polarity. However, the molecular mechanisms that maintain epithelial cohesion and lumen diameter in the mammalian lung are unknown. Here we show that Scribble, a protein implicated in planar cell polarity (PCP) signalling, is necessary for normal lung morphogenesis. Lungs of the Scrib mouse mutant Circletail (Crc) are abnormally shaped with fewer airways, and these airways often lack a visible, ‘open’ lumen. Mechanistically we show that Scrib genetically interacts with the core PCP gene Vangl2 in the developing lung and that the distribution of PCP pathway proteins and Rho mediated cytoskeletal modification is perturbed in ScribCrc/Crc lungs. However A/B polarity, which is disrupted in Drosophila Scrib mutants, is largely unaffected. Notably, we find that Scrib mediates functions not attributed to other PCP proteins in the lung. Specifically, Scrib localises to both adherens and tight junctions of lung epithelia and knockdown of Scrib in lung explants and organotypic cultures leads to reduced cohesion of lung epithelial cells. Live imaging of Scrib knockdown lungs shows that Scrib does not affect bud bifurcation, as previously shown for the PCP protein Celsr1, but is required to maintain epithelial cohesion. To understand the mechanism leading to reduced cell–cell association, we show that Scrib associates with β-catenin in embryonic lung and the sub-cellular distribution of adherens and tight junction proteins is perturbed in mutant lung epithelia. Our data reveal that Scrib is required for normal lung epithelial organisation and lumen morphogenesis by maintaining cell–cell contacts. Thus we reveal novel and important roles for Scrib in lung development operating via the PCP pathway, and in regulating junctional complexes and cell cohesion.
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Affiliation(s)
- Laura L Yates
- Mammalian Genetics Unit, Medical Research Council, Harwell, UK
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9
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Abstract
Cell migration is fundamental to establishing and maintaining the proper organization of multicellular organisms. Morphogenesis can be viewed as a consequence, in part, of cell locomotion, from large-scale migrations of epithelial sheets during gastrulation, to the movement of individual cells during development of the nervous system. In an adult organism, cell migration is essential for proper immune response, wound repair, and tissue homeostasis, while aberrant cell migration is found in various pathologies. Indeed, as our knowledge of migration increases, we can look forward to, for example, abating the spread of highly malignant cancer cells, retarding the invasion of white cells in the inflammatory process, or enhancing the healing of wounds. This article is organized in two main sections. The first section is devoted to the single-cell migrating in isolation such as occurs when leukocytes migrate during the immune response or when fibroblasts squeeze through connective tissue. The second section is devoted to cells collectively migrating as part of multicellular clusters or sheets. This second type of migration is prevalent in development, wound healing, and in some forms of cancer metastasis.
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Affiliation(s)
- Xavier Trepat
- Institute for Bioengineering of Catalonia, Barcelona, Spain.
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10
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Ghabrial AS, Levi BP, Krasnow MA. A systematic screen for tube morphogenesis and branching genes in the Drosophila tracheal system. PLoS Genet 2011; 7:e1002087. [PMID: 21750678 PMCID: PMC3131284 DOI: 10.1371/journal.pgen.1002087] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 04/05/2011] [Indexed: 01/10/2023] Open
Abstract
Many signaling proteins and transcription factors that induce and pattern organs have been identified, but relatively few of the downstream effectors that execute morphogenesis programs. Because such morphogenesis genes may function in many organs and developmental processes, mutations in them are expected to be pleiotropic and hence ignored or discarded in most standard genetic screens. Here we describe a systematic screen designed to identify all Drosophila third chromosome genes (∼40% of the genome) that function in development of the tracheal system, a tubular respiratory organ that provides a paradigm for branching morphogenesis. To identify potentially pleiotropic morphogenesis genes, the screen included analysis of marked clones of homozygous mutant tracheal cells in heterozygous animals, plus a secondary screen to exclude mutations in general “house-keeping” genes. From a collection including more than 5,000 lethal mutations, we identified 133 mutations representing ∼70 or more genes that subdivide the tracheal terminal branching program into six genetically separable steps, a previously established cell specification step plus five major morphogenesis and maturation steps: branching, growth, tubulogenesis, gas-filling, and maintenance. Molecular identification of 14 of the 70 genes demonstrates that they include six previously known tracheal genes, each with a novel function revealed by clonal analysis, and two well-known growth suppressors that establish an integral role for cell growth control in branching morphogenesis. The rest are new tracheal genes that function in morphogenesis and maturation, many through cytoskeletal and secretory pathways. The results suggest systematic genetic screens that include clonal analysis can elucidate the full organogenesis program and that over 200 patterning and morphogenesis genes are required to build even a relatively simple organ such as the Drosophila tracheal system. Elucidating the genetic programs that control formation and maintenance of body organs is a central goal of developmental biology, and understanding how these programs go awry in disease has important implications for medicine. Many such organogenesis genes have been identified, but most are early-acting “patterning genes” encoding signaling proteins and gene regulators that control expression of a poorly characterized set of downstream “morphogenesis genes,” which encode proteins that generate the remarkable organ forms and structures of the constituent cells. We screened ∼40% of the fruit fly Drosophila genome for mutations that affect tracheal (respiratory) system development. We included steps to bypass complexities from mutant effects on other tissues and steps to exclude mutations in general cell “housekeeping genes.” We isolated mutations in ∼70 genes that identify major steps in the organogenesis program including an integral cell growth control step. Many of the new tracheal genes are “morphogenesis genes” that encode proteins involved in cell structure or intracellular transport. The results suggest that genetic screens can elucidate a full organogenesis program and that over 200 patterning and morphogenesis genes are required to build even a relatively simple organ.
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Affiliation(s)
- Amin S. Ghabrial
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Cell and Developmental Biology, University Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (ASG); (MAK)
| | - Boaz P. Levi
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
| | - Mark A. Krasnow
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail: (ASG); (MAK)
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11
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Marrs JA. Branching morphogenesis: Rac signaling "PIX" tubulogenesis. Focus on "Pak1 regulates branching morphogenesis in 3D MDCK cell culture by a PIX and beta1-integrin-dependent mechanism". Am J Physiol Cell Physiol 2010; 299:C7-10. [PMID: 20427711 DOI: 10.1152/ajpcell.00145.2010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Miller RK, McCrea PD. Wnt to build a tube: contributions of Wnt signaling to epithelial tubulogenesis. Dev Dyn 2010; 239:77-93. [PMID: 19681164 DOI: 10.1002/dvdy.22059] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Epithelial tubes are crucial to the function of organ systems including the cardiovascular system, pulmonary system, gastrointestinal tract, reproductive organ systems, excretory system, and auditory system. Using a variety of animal model systems, recent studies have substantiated the role of Wnt signaling via the canonical/beta-catenin-mediated trajectory, the non-canonical Wnt trajectories, or both, in forming epithelial tubular tissues. This review focuses on the involvement of the Wnt pathways in the induction, specification, proliferation, and morphogenesis involved in tubulogenesis within tissues including the lungs, kidneys, ears, mammary glands, gut, and heart. The ultimate goal is to describe the developmental processes forming the various tubulogenic organ systems to determine the relationships between these processes.
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Affiliation(s)
- Rachel K Miller
- Department of Biochemistry and Molecular Biology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA.
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13
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Kim J, Cunningham R, James B, Wyder S, Gibson JD, Niehuis O, Zdobnov EM, Robertson HM, Robinson GE, Werren JH, Sinha S. Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances. PLoS Comput Biol 2010; 6:e1000652. [PMID: 20126523 PMCID: PMC2813253 DOI: 10.1371/journal.pcbi.1000652] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 12/18/2009] [Indexed: 11/19/2022] Open
Abstract
We address the problem of finding statistically significant associations between cis-regulatory motifs and functional gene sets, in order to understand the biological roles of transcription factors. We develop a computational framework for this task, whose features include a new statistical score for motif scanning, the use of different scores for predicting targets of different motifs, and new ways to deal with redundancies among significant motif–function associations. This framework is applied to the recently sequenced genome of the jewel wasp, Nasonia vitripennis, making use of the existing knowledge of motifs and gene annotations in another insect genome, that of the fruitfly. The framework uses cross-species comparison to improve the specificity of its predictions, and does so without relying upon non-coding sequence alignment. It is therefore well suited for comparative genomics across large evolutionary divergences, where existing alignment-based methods are not applicable. We also apply the framework to find motifs associated with socially regulated gene sets in the honeybee, Apis mellifera, using comparisons with Nasonia, a solitary species, to identify honeybee-specific associations. We develop a computational pipeline for predicting the functions of transcription factor motifs, through DNA sequence analysis. The pipeline is applied to the newly sequenced genome of the jewel wasp, Nasonia vitripennis. It exploits the wealth of molecular data available in another insect species, the fruitfly Drosophila melanogaster, and uses cross-species comparison to its advantage. Our main contribution is to show how this can be done despite the large evolutionary divergence between the two species. The methodology presented here may be applied more generally to other scenarios (genomes) where comparative regulatory genomics must deal with large evolutionary divergences.
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Affiliation(s)
- Jaebum Kim
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ryan Cunningham
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Brian James
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Stefan Wyder
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Joshua D. Gibson
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Oliver Niehuis
- Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Evgeny M. Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Hugh M. Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Gene E. Robinson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - John H. Werren
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Saurabh Sinha
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail:
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14
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Simonova OB, Burdina NV. Morphogenetic movement of cells in embryogenesis of Drosophila melanogaster: Mechanism and genetic control. Russ J Dev Biol 2009. [DOI: 10.1134/s1062360409050038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Harrington MJ, Hong E, Brewster R. Comparative analysis of neurulation: First impressions do not count. Mol Reprod Dev 2009; 76:954-65. [DOI: 10.1002/mrd.21085] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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16
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Abstract
The reorganization of epithelial sheets into tubes is a fundamental process in the formation of many organs, such as the lungs, kidneys, gut, and neural tube. This process involves the patterning of distinct cell types and the coordination of those cells during the shape changes and rearrangements that produce the tube. A better understanding of the cellular and genetic mechanisms that regulate tube formation is necessary for tissue engineers to develop functional organs in vitro. The Drosophila egg chamber has emerged as an outstanding model for studying tubulogenesis. Synthesis of the dorsal respiratory appendages by the follicular epithelium resembles primary neurulation in vertebrates. This review summarizes work on the patterning and morphogenesis of the dorsal-appendage tubes and highlights key areas where mathematical modeling could contribute to our understanding of these processes.
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Affiliation(s)
- Celeste A Berg
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195-5065, USA.
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17
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Development and morphogenesis of the Wolffian/epididymal duct, more twists and turns. Dev Biol 2008; 325:6-14. [PMID: 18992735 DOI: 10.1016/j.ydbio.2008.10.012] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 09/03/2008] [Accepted: 10/08/2008] [Indexed: 01/16/2023]
Abstract
The epididymis serves a critical function of preparing the male germ cells for fertilization. In order for the epididymis to carry out this role it must undergo a highly coordinated succession of molecular and morphogenic events during development. These events begin with the formation of the Wolffian or nephric duct, the embryonic precursor of the male reproductive system, and end with the three-dimensional coiled postnatal epididymis that is comprised of several distinctly functional segments. How the duct changes from a simple straight tube to a highly convoluted structure will be the focus of this article. In reviewing the literature's current understanding of epididymal morphogenesis, we will highlight some of the classic morphological studies and discuss some of the more recent genetic models that have all served to contribute to our understanding of this system. Where published information is scarce we will provide potential hypotheses that warrant further investigation and may open up new directions of exploration using the epididymis as a model for tubular morphogenesis.
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Finney L, Mandava S, Ursos L, Zhang W, Rodi D, Vogt S, Legnini D, Maser J, Ikpatt F, Olopade OI, Glesne D. X-ray fluorescence microscopy reveals large-scale relocalization and extracellular translocation of cellular copper during angiogenesis. Proc Natl Acad Sci U S A 2007; 104:2247-52. [PMID: 17283338 PMCID: PMC1892952 DOI: 10.1073/pnas.0607238104] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although copper has been reported to influence numerous proteins known to be important for angiogenesis, the enhanced sensitivity of this developmental process to copper bioavailability has remained an enigma, because copper metalloproteins are prevalent and essential throughout all cells. Recent developments in x-ray optics at third-generation synchrotron sources have provided a resource for highly sensitive visualization and quantitation of metalloproteins in biological samples. Here, we report the application of x-ray fluorescence microscopy (XFM) toin vitro models of angiogenesis and neurogenesis, revealing a surprisingly dramatic spatial relocalization specific to capillary formation of 80-90% of endogenous cellular copper stores from intracellular compartments to the tips of nascent endothelial cell filopodia and across the cell membrane. Although copper chelation had no effect on process formation, an almost complete ablation of network formation was observed. XFM of highly vascularized ductal carcinomas showed copper clustering in putative neoangiogenic areas. This use of XFM for the study of a dynamic developmental process not only sheds light on the copper requirement for endothelial tube formation but highlights the value of synchrotron-based facilities in biological research.
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Affiliation(s)
| | | | | | | | | | - Stefan Vogt
- Experimental Facilities Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439; and
| | - Daniel Legnini
- Experimental Facilities Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439; and
| | - Jorg Maser
- Experimental Facilities Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439; and
| | - Francis Ikpatt
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, 5841 South Maryland Avenue, MC 2115, Chicago, IL 60615
| | - Olufunmilayo I. Olopade
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, 5841 South Maryland Avenue, MC 2115, Chicago, IL 60615
| | - David Glesne
- *Biosciences Division and
- To whom correspondence should be addressed. E-mail:
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19
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Zeng G, Taylor SM, McColm JR, Kappas NC, Kearney JB, Williams LH, Hartnett ME, Bautch VL. Orientation of endothelial cell division is regulated by VEGF signaling during blood vessel formation. Blood 2006; 109:1345-52. [PMID: 17068148 PMCID: PMC1794069 DOI: 10.1182/blood-2006-07-037952] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
New blood vessel formation requires the coordination of endothelial cell division and the morphogenetic movements of vessel expansion, but it is not known how this integration occurs. Here, we show that endothelial cells regulate division orientation during the earliest stages of blood vessel formation, in response to morphogenetic cues. In embryonic stem (ES) cell-derived vessels that do not experience flow, the plane of endothelial cytokinesis was oriented perpendicular to the vessel long axis. We also demonstrated regulated cleavage orientation in vivo, in flow-exposed forming retinal vessels. Daughter nuclei moved away from the cleavage plane after division, suggesting that regulation of endothelial division orientation effectively extends vessel length in these developing vascular beds. A gain-of-function mutation in VEGF signaling increased randomization of endothelial division orientation, and this effect was rescued by a transgene, indicating that regulation of division orientation is a novel mechanism whereby VEGF signaling affects vessel morphogenesis. Thus, our findings show that endothelial cell division and morphogenesis are integrated in developing vessels by flow-independent mechanisms that involve VEGF signaling, and this cross talk is likely to be critical to proper vessel morphogenesis.
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Affiliation(s)
- Gefei Zeng
- Department of Biology, University of North Carolina at Chapel Hill 27599, USA
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20
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Abstract
Much progress has been made in recent years toward understanding mechanisms controlling branching morphogenesis, a fundamental aspect of development in a variety of invertebrate and vertebrate organs. To gain a deeper understanding of how branching morphogenesis occurs in the mammary gland, we compare and contrast the cellular and molecular events underlying this process in both invertebrate and vertebrate organs. Thus, in this review, we focus on the common themes that have emerged from such comparative analyses and discuss how they are implemented via a battery of signaling pathways to ensure proper branching morphogenesis in diverse systems.
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Affiliation(s)
- Pengfei Lu
- Department of Anatomy and Program in Developmental Biology, School of Medicine, University of California at San Francisco, San Francisco, CA 94143-0452, USA
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21
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Beis D, Stainier DYR. In vivo cell biology: following the zebrafish trend. Trends Cell Biol 2006; 16:105-12. [PMID: 16406520 DOI: 10.1016/j.tcb.2005.12.001] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Revised: 11/03/2005] [Accepted: 12/08/2005] [Indexed: 11/21/2022]
Abstract
A deeper understanding of the mechanisms of cell behavior is essential if we want to comprehend how an organism develops and functions. Changes in cellular processes, including the orientation of cell divisions, cell shape, polarity, differentiation and migration, account for tissue rearrangements during development and homeostasis. The in vivo relevance of in vitro findings is being constantly debated and the need for in vivo systems becoming more pressing. The zebrafish (Danio rerio) might become the vertebrate system of choice for a wide spectrum of biological questions that need to be investigated in vivo at cellular and subcellular resolutions. Here, we discuss some recent studies in which the zebrafish was used to gain insight into cell-biological mechanisms. Although this model system has been predominantly appreciated for its amenability to forward genetics, current advances in imaging technology and an increasing number of transgenic lines are bringing it closer to its full potential.
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Affiliation(s)
- Dimitris Beis
- Department of Biochemistry and Biophysics, Programs in Developmental Biology, Genetics and Human Genetics, Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94143-2711, USA.
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22
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Barka T, Gresik ES, Miyazaki Y. Differentiation of a mouse submandibular gland-derived cell line (SCA) grown on matrigel. Exp Cell Res 2005; 308:394-406. [PMID: 15922327 DOI: 10.1016/j.yexcr.2005.04.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2005] [Revised: 04/19/2005] [Accepted: 04/22/2005] [Indexed: 01/22/2023]
Abstract
SCA-9 cell line was developed from an induced tumor of mouse submandibular gland. We have studied some of the phenotypic characteristics of SCA cells cultured on different matrices. On plastic surface, the cells grow as a monolayer; on matrigel, they form branching structures and tubes, a phenomenon termed branching morphogenesis. EGF and HGF promoted cellular growth and branching morphogenesis which was inhibited by anti-EGF antibodies. We have performed RT-PCR and real-time quantitative RT-PCR of cells grown on plastic surface or on matrigel. Grown on plastic, the cells express EGF and renin 2, but no or only trace amounts of NGF. Growth on matrigel for 24 h resulted in a transient 21-fold increase in EGF mRNA and a 3371-fold increase in renin 2 mRNA. There was no change in NGF mRNA level. SCA-9 cells express mRNAs for receptors for the EGF family of ligands. On plastic, mainly ErbB1 and ErbB2 are expressed. Culture on matrigel resulted in 11-fold increase in mRNA levels for ErbB1 and ErbB2, and a 221-fold and 85-fold increase in the mRNA levels for ErbB3 and ErbB4, respectively. Small interfering RNAs siErbB3 and siErbB4 inhibited the growth of the cells grown on plastic or matrigel. Significant growth inhibition was seen also with siErbB1+siErbB3 and siErbB2+siErbB3. siErbB1 and siErbB2 also inhibited branching morphogenesis. Since SCA cells express EGF and receptors for EGF, EGF acts an autocrine regulator in promoting growth and branching morphogenesis. We conclude that SCA cells provide a useful model to analyze the mechanism of branching morphogenesis and the role of matrix in regulating expression of phenotypic characteristics of cultured cells.
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Affiliation(s)
- Tibor Barka
- Center for Anatomy and Functional Morphology and Department of Pathology, Mount Sinai School of Medicine, Box 1007, New York, NY 10029, USA.
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23
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Mai W, Chen D, Ding T, Kim I, Park S, Cho SY, Chu JSF, Liang D, Wang N, Wu D, Li S, Zhao P, Zent R, Wu G. Inhibition of Pkhd1 impairs tubulomorphogenesis of cultured IMCD cells. Mol Biol Cell 2005; 16:4398-409. [PMID: 15975909 PMCID: PMC1196347 DOI: 10.1091/mbc.e04-11-1019] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Fibrocystin/polyductin (FPC), the gene product of PKHD1, is responsible for autosomal recessive polycystic kidney disease (ARPKD). This disease is characterized by symmetrically large kidneys with ectasia of collecting ducts. In the kidney, FPC predominantly localizes to the apical domain of tubule cells, where it associates with the basal bodies/primary cilia; however, the functional role of this protein is still unknown. In this study, we established stable IMCD (mouse inner medullary collecting duct) cell lines, in which FPC was silenced by short hairpin RNA inhibition (shRNA). We showed that inhibition of FPC disrupted tubulomorphogenesis of IMCD cells grown in three-dimensional cultures. Pkhd1-silenced cells developed abnormalities in cell-cell contact, actin cytoskeleton organization, cell-ECM interactions, cell proliferation, and apoptosis, which may be mediated by dysregulation of extracellular-regulated kinase (ERK) and focal adhesion kinase (FAK) signaling. These alterations in cell function in vitro may explain the characteristics of ARPKD phenotypes in vivo.
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Affiliation(s)
- Weiyi Mai
- Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA
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24
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Dalpé G, Brown L, Culotti JG. Vulva morphogenesis involves attraction of plexin 1-expressing primordial vulva cells to semaphorin 1a sequentially expressed at the vulva midline. Development 2005; 132:1387-400. [PMID: 15716342 DOI: 10.1242/dev.01694] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Vulva development in C. elegans involves cell fate specification followed by a morphogenesis phase in which homologous mirror image pairs within a linear array of primordial vulva cells form a crescent shape as they move sequentially towards a midline position within the array. The homologous pairs from opposite half vulvae in fixed sequence fuse with one another at their leading tips to form ring-shaped (toroidal) cells stacked in precise alignment one atop the other. Here, we show that the semaphorin 1a SMP-1, and its plexin receptor PLX-1, are required for the movement of homologous pairs of vulva cells towards this midline position. SMP-1 is upregulated on the lumen membrane of each primordial vulva cell as it enters the forming vulva and apparently attracts the next flanking homologous PLX-1-expressing vulva cells towards the lumen surface of the ring. Consequently, a new ring-shaped cell forms immediately ventral to the previously formed ring. This smp-1- and plx-1-dependent process repeats until seven rings are stacked along the dorsoventral axis, creating a common vulva lumen. Ectopic expression of SMP-1 suggests it has an instructive role in vulva cell migration. At least two parallel acting pathways are required for vulva formation: one requires SMP-1, PLX-1 and CED-10; and another requires the MIG-2 Rac GTPase and its putative activator UNC-73.
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Affiliation(s)
- Gratien Dalpé
- Samuel Lunenfeld Research Institute of Mount Sinai Hospital, 600 University Avenue, Toronto M5G 1X5, Canada
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25
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Farooqui R, Fenteany G. Multiple rows of cells behind an epithelial wound edge extend cryptic lamellipodia to collectively drive cell-sheet movement. J Cell Sci 2004; 118:51-63. [PMID: 15585576 DOI: 10.1242/jcs.01577] [Citation(s) in RCA: 303] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mechanism by which epithelial, endothelial and other strongly cell-cell adhesive cells migrate collectively as continuous sheets is not clear, even though this process is crucial for embryonic development and tissue repair in virtually all multicellular animals. Wound closure in Madin-Darby canine kidney (MDCK) epithelial cell monolayers involves Rac GTPase-dependent migration of cells both at and behind the wound edge. We report here for the first time that cells behind the margin of wounded MDCK cell monolayers, even hundreds of microns from the edge, extend 'cryptic' lamellipodia against the substratum beneath cells in front of them, toward the wound, as determined by confocal, two-photon and transmission electron microscopy. These so-called submarginal cells nevertheless strictly maintain their more apical cell-cell contacts when they migrate as part of a coherent cell sheet, hiding their basal protrusions from conventional microscopy. The submarginal protrusions display the hallmarks of traditional lamellipodia based on morphology and dynamics. Cells behind the margin therefore actively crawl, instead of just moving passively when cells at the margin pull on them. The rate of migration is inversely proportional to the distance from the margin, and cells move co-ordinately, yet still in part autonomously, toward the wound area. We also clarify the ancillary role played by nonprotrusive contractile actin bundles that assemble in a Rho GTPase-dependent manner at the margin after wounding. In addition, some cell proliferation occurs at a delay after wounding but does not contribute to closure. Instead, it apparently serves to replace damaged cells so that intact spread cells can revert to their normal cuboidal morphology and the original cell density of the unbroken sheet can be restored.
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Affiliation(s)
- Rizwan Farooqui
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL 60607, USA
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