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Kohn KW, Zeeberg BR, Reinhold WC, Sunshine M, Luna A, Pommier Y. Gene expression profiles of the NCI-60 human tumor cell lines define molecular interaction networks governing cell migration processes. PLoS One 2012; 7:e35716. [PMID: 22570691 PMCID: PMC3343048 DOI: 10.1371/journal.pone.0035716] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 03/20/2012] [Indexed: 12/14/2022] Open
Abstract
Although there is extensive information on gene expression and molecular interactions in various cell types, integrating those data in a functionally coherent manner remains challenging. This study explores the premise that genes whose expression at the mRNA level is correlated over diverse cell lines are likely to function together in a network of molecular interactions. We previously derived expression-correlated gene clusters from the database of the NCI-60 human tumor cell lines and associated each cluster with function categories of the Gene Ontology (GO) database. From a cluster rich in genes associated with GO categories related to cell migration, we extracted 15 genes that were highly cross-correlated; prominent among them were RRAS, AXL, ADAM9, FN14, and integrin-beta1. We then used those 15 genes as bait to identify other correlated genes in the NCI-60 database. A survey of current literature disclosed, not only that many of the expression-correlated genes engaged in molecular interactions related to migration, invasion, and metastasis, but that highly cross-correlated subsets of those genes engaged in specific cell migration processes. We assembled this information in molecular interaction maps (MIMs) that depict networks governing 3 cell migration processes: degradation of extracellular matrix, production of transient focal complexes at the leading edge of the cell, and retraction of the rear part of the cell. Also depicted are interactions controlling the release and effects of calcium ions, which may regulate migration in a spaciotemporal manner in the cell. The MIMs and associated text comprise a detailed and integrated summary of what is currently known or surmised about the role of the expression cross-correlated genes in molecular networks governing those processes.
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Affiliation(s)
- Kurt W Kohn
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA.
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202
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Purevjav E, Arimura T, Augustin S, Huby AC, Takagi K, Nunoda S, Kearney DL, Taylor MD, Terasaki F, Bos JM, Ommen SR, Shibata H, Takahashi M, Itoh-Satoh M, McKenna WJ, Murphy RT, Labeit S, Yamanaka Y, Machida N, Park JE, Alexander PM, Weintraub RG, Kitaura Y, Ackerman MJ, Kimura A, Towbin JA. Molecular basis for clinical heterogeneity in inherited cardiomyopathies due to myopalladin mutations. Hum Mol Genet 2012; 21:2039-53. [PMID: 22286171 PMCID: PMC3315208 DOI: 10.1093/hmg/dds022] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 01/23/2012] [Indexed: 01/07/2023] Open
Abstract
Abnormalities in Z-disc proteins cause hypertrophic (HCM), dilated (DCM) and/or restrictive cardiomyopathy (RCM), but disease-causing mechanisms are not fully understood. Myopalladin (MYPN) is a Z-disc protein expressed in striated muscle and functions as a structural, signaling and gene expression regulating molecule in response to muscle stress. MYPN was genetically screened in 900 patients with HCM, DCM and RCM, and disease-causing mechanisms were investigated using comparative immunohistochemical analysis of the patient myocardium and neonatal rat cardiomyocytes expressing mutant MYPN. Cardiac-restricted transgenic (Tg) mice were generated and protein-protein interactions were evaluated. Two nonsense and 13 missense MYPN variants were identified in subjects with DCM, HCM and RCM with the average cardiomyopathy prevalence of 1.66%. Functional studies were performed on two variants (Q529X and Y20C) associated with variable clinical phenotypes. Humans carrying the Y20C-MYPN variant developed HCM or DCM, whereas Q529X-MYPN was found in familial RCM. Disturbed myofibrillogenesis with disruption of α-actinin2, desmin and cardiac ankyrin repeat protein (CARP) was evident in rat cardiomyocytes expressing MYPN(Q529X). Cardiac-restricted MYPN(Y20C) Tg mice developed HCM and disrupted intercalated discs, with disturbed expression of desmin, desmoplakin, connexin43 and vinculin being evident. Failed nuclear translocation and reduced binding of Y20C-MYPN to CARP were demonstrated using in vitro and in vivo systems. MYPN mutations cause various forms of cardiomyopathy via different protein-protein interactions. Q529X-MYPN causes RCM via disturbed myofibrillogenesis, whereas Y20C-MYPN perturbs MYPN nuclear shuttling and leads to abnormal assembly of terminal Z-disc within the cardiac transitional junction and intercalated disc.
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MESH Headings
- Animals
- Animals, Newborn
- Cardiomyopathy, Dilated/genetics
- Cardiomyopathy, Dilated/pathology
- Cardiomyopathy, Dilated/physiopathology
- Cardiomyopathy, Hypertrophic, Familial/genetics
- Cardiomyopathy, Hypertrophic, Familial/pathology
- Cardiomyopathy, Hypertrophic, Familial/physiopathology
- Case-Control Studies
- Codon, Nonsense
- Female
- Humans
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Microscopy, Electron, Transmission
- Muscle Proteins/chemistry
- Muscle Proteins/genetics
- Muscle Proteins/metabolism
- Muscle Proteins/physiology
- Mutant Proteins/chemistry
- Mutant Proteins/genetics
- Mutant Proteins/physiology
- Mutation
- Mutation, Missense
- Myocardium/pathology
- Myocytes, Cardiac/ultrastructure
- Nuclear Proteins/metabolism
- Pedigree
- Phenotype
- Protein Binding
- Rats
- Rats, Mutant Strains
- Rats, Sprague-Dawley
- Repressor Proteins/metabolism
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Affiliation(s)
- Enkhsaikhan Purevjav
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Takuro Arimura
- Department of Molecular Pathogenesis, Medical Research Institute and Laboratory of Genome Diversity, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sibylle Augustin
- Department of Medicine
- Department of Pediatrics and
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Anne-Cecile Huby
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ken Takagi
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Shinichi Nunoda
- Department of Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Debra L. Kearney
- Department of Pediatrics, Section of Pathology, Baylor College of Medicine, Houston, TX, USA
| | - Michael D. Taylor
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Fumio Terasaki
- Third Department of Medicine, Osaka Medical College, Takatsuki, Japan
| | - Johan M. Bos
- Department of Medicine
- Department of Pediatrics and
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Steve R. Ommen
- Department of Medicine
- Department of Pediatrics and
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Hiroki Shibata
- Department of Molecular Pathogenesis, Medical Research Institute and Laboratory of Genome Diversity, Tokyo Medical and Dental University, Tokyo, Japan
| | - Megumi Takahashi
- Department of Molecular Pathogenesis, Medical Research Institute and Laboratory of Genome Diversity, Tokyo Medical and Dental University, Tokyo, Japan
| | - Manatsu Itoh-Satoh
- Department of Molecular Pathogenesis, Medical Research Institute and Laboratory of Genome Diversity, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Ross T. Murphy
- Department of Cardiology, The Heart Hospital, London, UK
| | - Siegfried Labeit
- Department of Experimental Medicine, Klinikum Mannheim, Mannheim, Germany
| | - Yoichi Yamanaka
- Department of Veterinary Pathology, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Noboru Machida
- Department of Veterinary Pathology, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Jeong-Euy Park
- Division of Cardiology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Peta M.A. Alexander
- Department of Cardiology, The Royal Children's Hospital, Melbourne, Australia and
| | - Robert G. Weintraub
- Department of Cardiology, The Royal Children's Hospital, Melbourne, Australia and
- Murdoch Children's Research Institute, Melbourne, Australia
| | - Yasushi Kitaura
- Third Department of Medicine, Osaka Medical College, Takatsuki, Japan
| | - Michael J. Ackerman
- Department of Medicine
- Department of Pediatrics and
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Akinori Kimura
- Department of Molecular Pathogenesis, Medical Research Institute and Laboratory of Genome Diversity, Tokyo Medical and Dental University, Tokyo, Japan
| | - Jeffrey A. Towbin
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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203
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Wang P, Ballestrem C, Streuli CH. The C terminus of talin links integrins to cell cycle progression. ACTA ACUST UNITED AC 2012; 195:499-513. [PMID: 22042621 PMCID: PMC3206343 DOI: 10.1083/jcb.201104128] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Talin recruits and activates focal adhesion proteins required for cell cycle progression. Integrins are cell adhesion receptors that sense the extracellular matrix (ECM) environment. One of their functions is to regulate cell fate decisions, although the question of how integrins initiate intracellular signaling is not fully resolved. In this paper, we examine the role of talin, an adapter protein at cell–matrix attachment sites, in outside-in signaling. We used lentiviral small hairpin ribonucleic acid to deplete talin in mammary epithelial cells. These cells still attached to the ECM in an integrin-dependent manner and spread. They had a normal actin cytoskeleton, but vinculin, paxillin, focal adhesion kinase (FAK), and integrin-linked kinase were not recruited to adhesion sites. Talin-deficient cells showed proliferation defects, and reexpressing a tail portion of the talin rod, but not its head domain, restored integrin-mediated FAK phosphorylation, suppressed p21 expression, and rescued cell cycle. Thus, talin recruits and activates focal adhesion proteins required for proliferation via the C terminus of its rod domain. Our study reveals a new function for talin, which is to link integrin adhesions with cell cycle progression.
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Affiliation(s)
- Pengbo Wang
- Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester M13 9PT, England, UK
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204
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Abstract
This chapter discusses the biochemical and functional links between classical cadherin adhesion systems and the cytoskeleton. Cadherins are best understood to cooperate with the actin cytoskeleton, but there is increasing evidence for the role of junctional microtubules in regulating cadherin biology. Cadherin adhesions and the junctional cytoskeleton are both highly dynamic systems that undergo continual assembly, turnover and remodeling, and yet maintain steady state structures necessary for intercellular adhesion. This requires the functional coordination of cadherins and cadherin-binding proteins, actin regulatory proteins, organizers of microtubule assembly and structure, and signaling pathways. These components act in concert to regulate junctional organization in response to extracellular forces and changing cellular contexts, which is essential for intercellular cohesion and tissue integrity.
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Affiliation(s)
- Siew Ping Han
- Division of Molecular Cell Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, 4072, Brisbane, Queensland, Australia
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205
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Chervin-Pétinot A, Courçon M, Almagro S, Nicolas A, Grichine A, Grunwald D, Prandini MH, Huber P, Gulino-Debrac D. Epithelial protein lost in neoplasm (EPLIN) interacts with α-catenin and actin filaments in endothelial cells and stabilizes vascular capillary network in vitro. J Biol Chem 2011; 287:7556-72. [PMID: 22194609 DOI: 10.1074/jbc.m111.328682] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Adherens junctions are required for vascular endothelium integrity. These structures are formed by the clustering of the homophilic adhesive protein VE-cadherin, which recruits intracellular partners, such as β- and α-catenins, vinculin, and actin filaments. The dogma according to which α-catenin bridges cadherin·β-catenin complexes to the actin cytoskeleton has been challenged during the past few years, and the link between the VE-cadherin·catenin complex and the actin cytoskeleton remains unclear. Recently, epithelial protein lost in neoplasm (EPLIN) has been proposed as a possible bond between the E-cadherin·catenin complex and actin in epithelial cells. Herein, we show that EPLIN is expressed at similar levels in endothelial and epithelial cells and is located at interendothelial junctions in confluent cells. Co-immunoprecipitation and GST pulldown experiments provided evidence that EPLIN interacts directly with α-catenin and tethers the VE-cadherin·catenin complex to the actin cytoskeleton. In the absence of EPLIN, vinculin was delocalized from the junctions. Furthermore, suppression of actomyosin tension using blebbistatin triggered a similar vinculin delocalization from the junctions. In a Matrigel assay, EPLIN-depleted endothelial cells exhibited a reduced capacity to form pseudocapillary networks because of numerous breakage events. In conclusion, we propose a model in which EPLIN establishes a link between the cadherin·catenin complex and actin that is independent of actomyosin tension. This link acts as a mechanotransmitter, allowing vinculin binding to α-catenin and formation of a secondary molecular bond between the adherens complex and the cytoskeleton through vinculin. In addition, we provide evidence that the EPLIN clutch is necessary for stabilization of capillary structures in an angiogenesis model.
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206
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Shen K, Tolbert CE, Guilluy C, Swaminathan VS, Berginski ME, Burridge K, Superfine R, Campbell SL. The vinculin C-terminal hairpin mediates F-actin bundle formation, focal adhesion, and cell mechanical properties. J Biol Chem 2011; 286:45103-15. [PMID: 22052910 DOI: 10.1074/jbc.m111.244293] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Vinculin is an essential and highly conserved cell adhesion protein, found at both focal adhesions and adherens junctions, where it couples integrins or cadherins to the actin cytoskeleton. Vinculin is involved in controlling cell shape, motility, and cell survival, and has more recently been shown to play a role in force transduction. The tail domain of vinculin (Vt) contains determinants necessary for binding and bundling of actin filaments. Actin binding to Vt has been proposed to induce formation of a Vt dimer that is necessary for cross-linking actin filaments. Results from this study provide additional support for actin-induced Vt self-association. Moreover, the actin-induced Vt dimer appears distinct from the dimer formed in the absence of actin. To better characterize the role of the Vt strap and carboxyl terminus (CT) in actin binding, Vt self-association, and actin bundling, we employed smaller amino-terminal (NT) and CT deletions that do not perturb the structural integrity of Vt. Although both NT and CT deletions retain actin binding, removal of the CT hairpin (1061-1066) selectively impairs actin bundling in vitro. Moreover, expression of vinculin lacking the CT hairpin in vinculin knock-out murine embryonic fibroblasts affects the number of focal adhesions formed, cell spreading as well as cellular stiffening in response to mechanical force.
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Affiliation(s)
- Kai Shen
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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207
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Balanis N, Yoshigi M, Wendt MK, Schiemann WP, Carlin CR. β3 integrin-EGF receptor cross-talk activates p190RhoGAP in mouse mammary gland epithelial cells. Mol Biol Cell 2011; 22:4288-301. [PMID: 21937717 PMCID: PMC3216655 DOI: 10.1091/mbc.e10-08-0700] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Active RhoA localizes to plasma membrane, where it stimulates formation of focal adhesions and stress fibers. RhoA activity is inhibited by p190RhoGAP following integrin-mediated cell attachment to allow sampling of new adhesive environments. p190RhoGAP is itself activated by Src-dependent tyrosine phosphorylation, which facilitates complex formation with p120RasGAP. This complex then translocates to the cell surface, where p190RhoGAP down-regulates RhoA. Here we demonstrate that the epidermal growth factor receptor (EGFR) cooperates with β3 integrin to regulate p190RhoGAP activity in mouse mammary gland epithelial cells. Adhesion to fibronectin stimulates tyrosine phosphorylation of the EGFR in the absence of receptor ligands. Use of a dominant inhibitory EGFR mutant demonstrates that fibronectin-activated EGFR recruits p120RasGAP to the cell periphery. Expression of an inactive β3 integrin subunit abolishes p190RhoGAP tyrosine phosphorylation, demonstrating a mechanistic link between β3 integrin-activated Src and EGFR regulation of the RhoA inhibitor. The β3 integrin/EGFR pathway also has a positive role in formation of filopodia. Together our data suggest that EGFR constitutes an important intrinsic migratory cue since fibronectin is a key component of the microenvironment in normal mammary gland development and breast cancer. Our data also suggest that EGFR expressed at high levels has a role in eliciting cell shape changes associated with epithelial-to-mesenchymal transition.
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Affiliation(s)
- Nikolas Balanis
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH 44106, USA
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208
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Gomez GA, McLachlan RW, Yap AS. Productive tension: force-sensing and homeostasis of cell-cell junctions. Trends Cell Biol 2011; 21:499-505. [PMID: 21763139 DOI: 10.1016/j.tcb.2011.05.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 05/25/2011] [Accepted: 05/26/2011] [Indexed: 12/22/2022]
Abstract
Cell-cell contacts are major determinants of tissue organization in both health and disease. Adhesive interactions, especially those mediated by classical cadherin receptors, influence cell-cell recognition and tissue patterning during development. Conversely, cadherin dysfunction promotes tumor progression to invasion and metastasis. Over the past three decades, we have learnt a great deal about the molecular mechanisms responsible for cadherin-based cell-cell interactions. Yet our knowledge remains incomplete. The intersection between cell biology and mechanical forces has long been suspected to be an important missing factor in understanding cadherin biology. However, tangible evidence remained elusive until recently, when several reports began to elucidate the role of cadherins and the cytoskeleton in mechanotransduction. In this review, we examine these advances and discuss their implications.
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Affiliation(s)
- Guillermo A Gomez
- Division of Molecular Cell Biology, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, Queensland, Australia 4072
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209
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New insights into vinculin function and regulation. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2011; 287:191-231. [PMID: 21414589 DOI: 10.1016/b978-0-12-386043-9.00005-0] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Vinculin is a cytoplasmic actin-binding protein enriched in focal adhesions and adherens junctions that is essential for embryonic development. Much is now known regarding the role of vinculin in governing cell-matrix adhesion. In the past decade that the crystal structure of vinculin and the molecular details for how vinculin regulates adhesion events have emerged. The recent data suggests a critical function for vinculin in regulating integrin clustering, force generation, and strength of adhesion. In addition to an important role in cell-matrix adhesion, vinculin is also emerging as a regulator of apoptosis, Shigella entry into host cells, and cadherin-based cell-cell adhesion. A close inspection of this work reveals that there are similarities between vinculin's role in focal adhesions and these processes and also some intriguing differences.
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210
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Siu MK, Wong CH, Xia W, Mruk DD, Lee WM, Cheng CY. The β1-integrin-p-FAK-p130Cas-DOCK180-RhoA-vinculin is a novel regulatory protein complex at the apical ectoplasmic specialization in adult rat testes. SPERMATOGENESIS 2011; 1:73-86. [PMID: 21866278 DOI: 10.4161/spmg.1.1.15452] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2001] [Revised: 02/11/2011] [Accepted: 03/11/2011] [Indexed: 12/21/2022]
Abstract
During spermatogenesis, step 1 spermatids (round spermatids) derive from spermatocytes following meiosis I and II at stage XIV of the epithelial cycle begin a series of morphological transformation and differentiation via 19 steps in rats to form spermatozoa. This process is known as spermiogenesis, which is marked by condensation of the genetic material in the spermatid head, formation of the acrosome and elongation of the tail. Since developing spermatids are lacking the robust protein synthesis and transcriptional activity, the cellular, molecular and morphological changes associated with spermiogenesis rely on the Sertoli cell in the seminiferous epithelium via desmosome and gap junction between Sertoli cells and step 1-7 spermatids. Interestingly, a unique anchoring junction type arises at the interface of step 8 spermatid and Sertoli cell known as apical ectoplasmic specialization (apical ES). Once it appears, apical ES is the only anchoring device restricted to the interface of step 8-19 spermatids and Sertoli cells to confer spermatid polarity, adhesion, signal communication and structural support, and to provide nutritional support during spermiogenesis, replacing desmosome and gap junction. While the adhesion protein complexes that constitute the apical ES are known, the signaling protein complexes that regulate apical ES dynamics, however, remain largely unknown. Herein we report the presence of a FAK (focal adhesion kinase)-p130Cas (p130 Crk-associated substrate)-DOCK180 (Dedicator of cytokinesis 180)-RhoA (Ras homolog gene family, member A)-vinculin signaling protein complex at the apical ES, which is also an integrated component of the β1-integrin-based adhesion protein complex based on co-immunoprecipitation experiment. It was also shown that besides p-FAK-Tyr(397) and p-FAK-Tyr(576), β1-integrin, p130Cas, RhoA and vinculin displayed stage-specific expression in the seminiferous epithelium during the epithelial cycle with predominant localization at the apical ES as demonstrated by immunohistochemistry. Based on these findings, functional studies can now be performed to assess the role of this β1-integrin-p-FAK-p130Cas-DOCK180-RhoA-vinculin protein complex in apical ES dynamics during spermiogenesis.
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Affiliation(s)
- Michelle Ky Siu
- Center for Biomedical Research; The Population Council; New York, NY USA
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