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The Proximal Signaling Network of the BCR-ABL1 Oncogene Shows a Modular Organization
Oncogene (2010) 29, 5895–5910 & 2010 Macmillan Publishers Limited All rights reserved 0950-9232/10 www.nature.com/onc ORIGINAL ARTICLE The proximal signaling network of the BCR-ABL1 oncogene shows a modular organization B Titz, T Low, E Komisopoulou, SS Chen, L Rubbi and TG Graeber Crump Institute for Molecular Imaging, Institute for Molecular Medicine, Jonsson Comprehensive Cancer Center, California NanoSystems Institute, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, USA BCR-ABL1 is a fusion tyrosine kinase, which causes signaling effects of BCR-ABL1 toward leukemic multiple types of leukemia. We used an integrated transformation. proteomic approach that includes label-free quantitative Oncogene (2010) 29, 5895–5910; doi:10.1038/onc.2010.331; protein complex and phosphorylation profiling by mass published online 9 August 2010 spectrometry to systematically characterize the proximal signaling network of this oncogenic kinase. The proximal Keywords: adaptor protein; BCR-ABL1; phospho- BCR-ABL1 signaling network shows a modular and complex; quantitative mass spectrometry; signaling layered organization with an inner core of three leukemia network; systems biology transformation-relevant adaptor protein complexes (Grb2/Gab2/Shc1 complex, CrkI complex and Dok1/ Dok2 complex). We introduced an ‘interaction direction- ality’ analysis, which annotates static protein networks Introduction with information on the directionality of phosphorylation- dependent interactions. In this analysis, the observed BCR-ABL1 is a constitutively active oncogenic fusion network structure was consistent with a step-wise kinase that arises through a chromosomal translocation phosphorylation-dependent assembly of the Grb2/Gab2/ and causes multiple types of leukemia. It is found in Shc1 and the Dok1/Dok2 complexes on the BCR-ABL1 many cases (B25%) of adult acute lymphoblastic core. -
Mutation-Specific and Common Phosphotyrosine Signatures of KRAS G12D and G13D Alleles Anticipated Graduation August 1St, 2018
MUTATION-SPECIFIC AND COMMON PHOSPHOTYROSINE SIGNATURES OF KRAS G12D AND G13D ALLELES by Raiha Tahir A dissertation submitted to The Johns Hopkins University in conformity with the requirement of the degree of Doctor of Philosophy Baltimore, MD August 2018 © 2018 Raiha Tahir All Rights Reserved ABSTRACT KRAS is one of the most frequently mutated genes across all cancer subtypes. Two of the most frequent oncogenic KRAS mutations observed in patients result in glycine to aspartic acid substitution at either codon 12 (G12D) or 13 (G13D). Although the biochemical differences between these two predominant mutations are not fully understood, distinct clinical features of the resulting tumors suggest involvement of disparate signaling mechanisms. When we compared the global phosphotyrosine proteomic profiles of isogenic colorectal cancer cell lines bearing either G12D or G13D KRAS mutations, we observed both shared as well as unique signaling events induced by the two KRAS mutations. Remarkably, while the G12D mutation led to an increase in membrane proximal and adherens junction signaling, the G13D mutation led to activation of signaling molecules such as non-receptor tyrosine kinases, MAPK kinases and regulators of metabolic processes. The importance of one of the cell surface molecules, MPZL1, which found to be hyperphosphorylated in G12D cells, was confirmed by cellular assays as its knockdown led to a decrease in proliferation of G12D but not G13D expressing cells. Overall, our study reveals important signaling differences across two common KRAS mutations and highlights the utility of our approach to systematically dissect the subtle differences between related oncogenic mutants and potentially lead to individualized treatments. -
Defining Functional Interactions During Biogenesis of Epithelial Junctions
ARTICLE Received 11 Dec 2015 | Accepted 13 Oct 2016 | Published 6 Dec 2016 | Updated 5 Jan 2017 DOI: 10.1038/ncomms13542 OPEN Defining functional interactions during biogenesis of epithelial junctions J.C. Erasmus1,*, S. Bruche1,*,w, L. Pizarro1,2,*, N. Maimari1,3,*, T. Poggioli1,w, C. Tomlinson4,J.Lees5, I. Zalivina1,w, A. Wheeler1,w, A. Alberts6, A. Russo2 & V.M.M. Braga1 In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell–cell contacts. This unexpected result reflects a more dynamic and mobile junctional actin in EEF1A-depleted cells. A partner for EEF1A in cadherin contact maintenance is the formin DIAPH2, which interacts with EEF1A. In contrast, depletion of either the endocytic regulator TRIP10 or the Rho GTPase activator VAV2 reduces E-cadherin levels at junctions. TRIP10 binds to and requires VAV2 function for its junctional localization. Overall, we present new conceptual insights on junction stabilization, which integrate known and novel pathways with impact for epithelial morphogenesis, homeostasis and diseases. 1 National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. 2 Computing Department, Imperial College London, London SW7 2AZ, UK. 3 Bioengineering Department, Faculty of Engineering, Imperial College London, London SW7 2AZ, UK. 4 Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. -
The Contributions of Microglial Vps35 to Adult Hippocampal Neurogenesis and Neurodegenerative Disorders
THE CONTRIBUTIONS OF MICROGLIAL VPS35 TO ADULT HIPPOCAMPAL NEUROGENESIS AND NEURODEGENERATIVE DISORDERS By Joanna Ruth Erion Submitted to the Faculty of the Graduate School of Augusta University in partial fulfillment of the Requirements of the Degree of Doctor of Philosophy April 2017 COPYRIGHT© 2017 by Joanna Ruth Erion THE CONTRIBUTIONS OF MICROGLIAL VPS35 TO ADULT HIPPOCAMPAL NEUROGENESIS AND NEURODEGENERATIVE DISORDERS This thesis/dissertation is submitted by Joanna Ruth Erion and has been examined and approved by an appointed committee of the faculty of the Graduate School of Augusta University. The signatures which appear below verify the fact that all required changes have been incorporated and that the thesis/dissertation has received final approval with reference to content, form and accuracy of presentation. This thesis/dissertation is therefore in partial fulfillment of the requirements for the degree of Doctor of Philosophy). ___________________ __________________________________ Date Major Advisor __________________________________ Departmental Chairperson __________________________________ Dean, Graduate School ACKNOWLEDGEMENTS I will be forever grateful to my mentor, Dr. Wen-Cheng Xiong, for welcoming me into her laboratory and providing me with the honor and opportunity to work under her astute leadership. I have learned many valuable lessons under her guidance, all of which have enabled me to grow as both a student and a scientist. It was with her erudite guidance and suggestions that I was able to examine aspects of my investigations that I had yet to consider and ask questions that would not have otherwise occurred to me. I would also like to thank Dr. Lin Mei for contributing not only his laboratory and resources to my endeavors, but also his guidance and input into my investigations, providing me with additional avenues for directing my efforts. -
Yuri Gagarin Is Required for Actin, Tubulin and Basal Body Functions in Drosophila Spermatogenesis
1926 Research Article yuri gagarin is required for actin, tubulin and basal body functions in Drosophila spermatogenesis Michael J. Texada, Rebecca A. Simonette, Cassidy B. Johnson, William J. Deery and Kathleen M. Beckingham* Department of Biochemistry and Cell Biology, MS-140, Rice University, 6100 South Main Street, Houston, TX 77005, USA *Author for correspondence (e-mail: [email protected]) Accepted 20 March 2008 Journal of Cell Science 121, 1926-1936 Published by The Company of Biologists 2008 doi:10.1242/jcs.026559 Summary Males of the genus Drosophila produce sperm of remarkable the yuri mutant, late clusters of syncytial nuclei are deformed length. Investigation of giant sperm production in Drosophila and disorganized. The basal bodies are also mispositioned on melanogaster has demonstrated that specialized actin and the nuclei, and the association of a specialized structure, the microtubule structures play key roles. The gene yuri gagarin centriolar adjunct (CA), with the basal body is lost. Some of (yuri) encodes a novel protein previously identified through its these nuclear defects might underlie a further unexpected role in gravitaxis. A male-sterile mutation of yuri has revealed abnormality: sperm nuclei occasionally locate to the wrong ends roles for Yuri in the functions of the actin and tubulin structures of the spermatid cysts. The structure of the axonemes that grow of spermatogenesis. Yuri is a component of the motile actin cones out from the basal bodies is affected in the yuri mutant, that individualize the spermatids and is essential for their suggesting a possible role for the CA in axoneme formation. formation. Furthermore, Yuri is required for actin accumulation in the dense complex, a microtubule-rich structure on the sperm Key words: Drosophila, Spermatogenesis, Actin, Tubulin, Basal nuclei thought to strengthen the nuclei during elongation. -
CD93 and Dystroglycan Cooperation in Human Endothelial Cell Adhesion and Migration
www.impactjournals.com/oncotarget/ Oncotarget, Vol. 7, No. 9 CD93 and dystroglycan cooperation in human endothelial cell adhesion and migration Federico Galvagni1,*, Federica Nardi1,*, Marco Maida1, Giulia Bernardini1, Silvia Vannuccini2, Felice Petraglia2, Annalisa Santucci1, Maurizio Orlandini1 1 Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 2-53100 Siena, Italy 2 Department of Molecular and Developmental Medicine, Obstetrics and Gynecology, University of Siena, 53100 Siena, Italy *These authors contributed equally to this work Correspondence to: Maurizio Orlandini, e-mail: [email protected] Keywords: angiogenesis, signal transduction, C1qRp, Src, Cbl Received: June 29, 2015 Accepted: January 22, 2016 Published: February 02, 2016 ABSTRACT CD93 is a transmembrane glycoprotein predominantly expressed in endothelial cells. Although CD93 displays proangiogenic activity, its molecular function in angiogenesis still needs to be clarified. To get molecular insight into the biological role of CD93 in the endothelium, we performed proteomic analyses to examine changes in the protein profile of endothelial cells after CD93 silencing. Among differentially expressed proteins, we identified dystroglycan, a laminin-binding protein involved in angiogenesis, whose expression is increased in vascular endothelial cells within malignant tumors. Using immunofluorescence, FRET, and proximity ligation analyses, we observed a close interaction between CD93 and β-dystroglycan. Moreover, silencing experiments showed that CD93 and dystroglycan promoted endothelial cell migration and organization into capillary-like structures. CD93 proved to be phosphorylated on tyrosine 628 and 644 following cell adhesion on laminin through dystroglycan. This phosphorylation was shown to be necessary for a proper endothelial migratory phenotype. Moreover, we showed that during cell spreading phosphorylated CD93 recruited the signaling protein Cbl, which in turn was phosphorylated on tyrosine 774. -
Parkinson's Disease Causative Mutation in Vps35 Disturbs Tetherin
cells Article Parkinson’s Disease Causative Mutation in Vps35 Disturbs Tetherin Trafficking to Cell Surfaces and Facilitates Virus Spread Yingzhuo Ding 1,†, Yan Li 1,† , Gaurav Chhetri 1 , Xiaoxin Peng 1, Jing Wu 1, Zejian Wang 1, Bo Zhao 1 , Wenjuan Zhao 1 and Xueyi Li 1,2,* 1 School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; [email protected] (Y.D.); [email protected] (Y.L.); [email protected] (G.C.); [email protected] (X.P.); [email protected] (J.W.); [email protected] (Z.W.); [email protected] (B.Z.); [email protected] (W.Z.) 2 Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA * Correspondence: [email protected] or [email protected] † These authors contributed equally to this work. Abstract: Parkinson’s disease (PD) is the most common neurodegenerative movement disorder, characterized by progressive loss of dopaminergic neurons in the substantia nigra, intraneuronal deposition of misfolded proteins known as Lewy bodies, and chronic neuroinflammation. PD can arise from monogenic mutations, but in most cases, the etiology is unclear. Viral infection is gaining increasing attentions as a trigger of PD. In this study, we investigated whether the PD-causative Citation: Ding, Y.; Li, Y.; Chhetri, G.; 620 aspartate (D) to asparagine (N) mutation in the vacuolar protein sorting 35 ortholog (Vps35) Peng, X.; Wu, J.; Wang, Z.; Zhao, B.; precipitated herpes simplex virus (HSV) infection. We observed that ectopic expression of Vps35 Zhao, W.; Li, X. Parkinson’s Disease significantly reduced the proliferation and release of HSV-1 virions; the D620N mutation rendered Causative Mutation in Vps35 Vps35 a partial loss of such inhibitory effects. -
Retromer Deficiency Observed in Alzheimer's Disease Causes
Retromer deficiency observed in Alzheimer’s disease causes hippocampal dysfunction, neurodegeneration, and A accumulation Alim Muhammad*, Ingrid Flores*, Hong Zhang*†, Rui Yu*, Agnieszka Staniszewski*†, Emmanuel Planel*†, Mathieu Herman*†, Lingling Ho‡, Robert Kreber‡, Lawrence S. Honig*§, Barry Ganetzky‡¶, Karen Duff*†, Ottavio Arancio*†, and Scott A. Small*§¶ *Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, and Departments of §Neurology and †Pathology, Columbia University College of Physicians and Surgeons, New York, NY 10032; and ‡Laboratory of Genetics, University of Wisconsin, Madison, WI 53706-1580 Contributed by Barry Ganetzky, March 13, 2008 (sent for review December 2, 2007) Although deficiencies in the retromer sorting pathway have been ␥-secretase, it was important to investigate retromer deficiency linked to late-onset Alzheimer’s disease, whether these deficien- on a nonmutated genetic background. To determine whether cies underlie the disease remains unknown. Here we characterized retromer deficiency causes hippocampal dysfunction, a key two genetically modified animal models to test separate but clinical feature of Alzheimer’s disease, we began by investigating related questions about the effects that retromer deficiency has on retromer deficiency in genetically modified mice. Our results the brain. First, testing for cognitive defects, we investigated suggest that retromer deficiency causes hippocampal dysfunction retromer-deficient mice and found that they develop hippocampal- by elevating concentrations of endogenous A peptide. dependent memory and synaptic dysfunction, which was associ- Although APP and BACE are highly homologous across species, ated with elevations in endogenous A peptide. Second, testing important sequence differences do exist, and these differences can for neurodegeneration and amyloid deposits, we investigated affect their intracellular transport, APP processing, and the neu- retromer-deficient flies expressing human wild-type amyloid pre- rotoxicity of APP end products (12). -
Cytoskeleton Cytoskeleton
CYTOSKELETON CYTOSKELETON The cytoskeleton is composed of three principal types of protein filaments: actin filaments, intermediate filaments, and microtubules, which are held together and linked to subcellular organelles and the plasma membrane by a variety of accessory proteins Muscle Contraction • Skeletal muscles are bundles of muscle fibers • Most of the cytoplasm consists of myofibrils, which are cylindrical bundles of two types of filaments: thick filaments of myosin (about 15 run in diameter) and thin filaments of actin (about 7 nm in diameter). • Each myofibril is organized as a chain of contractile units called sarcomeres, which are responsible for the striated appearance of skeletal and cardiac muscle. Structure of muscle cells Sarcomere • The ends of each sarcomere are defined by the Z disc. • Within each sarcomere, dark bands (called A bands because they are anisotropic when viewed with polarized light) alternate with light bands (called I bands for isotropic). • The I bands contain only thin (actin) filaments, whereas the A bands contain thick (myosin) filaments. • The myosin and actin filaments overlap in peripheral regions of the A band, whereas a middle region (called the H zone) contains only myosin. Muscle contraction • The basis for understanding muscle contraction is the sliding filament model, first proposed in 1954 both by Andrew Huxley and Ralph Niedergerke and by Hugh Huxley and Jean Hanson • During muscle contraction each sarcomere shortens, bringing the Z discs closer together. • There is no change in the width of the A band, but both the I bands and the H zone almost completely disappear. • These changes are explained by the actin and myosin filaments sliding past one another so that the actin filaments move into the A band and H zone. -
Myosin-Driven Actin-Microtubule Networks Exhibit Self-Organized Contractile Dynamics Gloria Lee1, Michael J
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.11.146662; this version posted June 12, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Myosin-driven actin-microtubule networks exhibit self-organized contractile dynamics Gloria Lee1, Michael J. Rust2, Moumita Das3, Ryan J. McGorty1, Jennifer L. Ross4, Rae M. Robertson-Anderson1* 1Department of Physics and Biophysics, University of San Diego, San Diego, CA 92110, USA 2Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA 3School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY 14623, USA 4Department of Physics, Syracuse University, Syracuse, NY 13244, USA Abstract The cytoskeleton is a dynamic network of proteins, including actin, microtubules, and myosin, that enables essential cellular processes such as motility, division, mechanosensing, and growth. While actomyosin networks are extensively studied, how interactions between actin and microtubules, ubiquitous in the cytoskeleton, influence actomyosin activity remains an open question. Here, we create a network of co-entangled actin and microtubules driven by myosin II. We combine dynamic differential microscopy, particle image velocimetry and particle-tracking to show that both actin and microtubules in the network undergo ballistic contraction with surprisingly indistinguishable characteristics. This controlled contractility is distinct from the faster turbulent motion and rupturing that active actin networks exhibit. Our results suggest that microtubules can enable self-organized myosin-driven contraction by providing flexural rigidity and enhanced connectivity to actin networks. -
NCK1 Antibody (Monoclonal) (M01) Mouse Monoclonal Antibody Raised Against a Partial Recombinant NCK1
10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 NCK1 Antibody (monoclonal) (M01) Mouse monoclonal antibody raised against a partial recombinant NCK1. Catalog # AT2980a Specification NCK1 Antibody (monoclonal) (M01) - Product Information Application WB, E Primary Accession P16333 Other Accession BC006403 Reactivity Human Host mouse Clonality Monoclonal Isotype IgG1 Kappa Calculated MW 42864 NCK1 Antibody (monoclonal) (M01) - Additional Information Antibody Reactive Against Recombinant Protein.Western Blot detection against Gene ID 4690 Immunogen (37.73 KDa) . Other Names Cytoplasmic protein NCK1, NCK adaptor protein 1, Nck-1, SH2/SH3 adaptor protein NCK-alpha, NCK1, NCK Target/Specificity NCK1 (AAH06403, 185 a.a. ~ 294 a.a) partial recombinant protein with GST tag. MW of the GST tag alone is 26 KDa. Dilution WB~~1:500~1000 Format Clear, colorless solution in phosphate NCK1 monoclonal antibody (M01), clone 1A1 buffered saline, pH 7.2 . Western Blot analysis of NCK1 expression in Hela S3 NE ( (Cat # AT2980a ) Storage Store at -20°C or lower. Aliquot to avoid repeated freezing and thawing. Precautions NCK1 Antibody (monoclonal) (M01) is for research use only and not for use in diagnostic or therapeutic procedures. NCK1 Antibody (monoclonal) (M01) - Protocols Page 1/3 10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 Provided below are standard protocols that you may find useful for product applications. • Western Blot • Blocking Peptides • Dot Blot • Immunohistochemistry • Immunofluorescence • Immunoprecipitation • Flow Cytomety • Cell Culture Western Blot analysis of NCK1 expression in transfected 293T cell line by NCK1 monoclonal antibody (M01), clone 1A1. -
Ciliary Dyneins and Dynein Related Ciliopathies
cells Review Ciliary Dyneins and Dynein Related Ciliopathies Dinu Antony 1,2,3, Han G. Brunner 2,3 and Miriam Schmidts 1,2,3,* 1 Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Mathildenstrasse 1, 79106 Freiburg, Germany; [email protected] 2 Genome Research Division, Human Genetics Department, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 KL Nijmegen, The Netherlands; [email protected] 3 Radboud Institute for Molecular Life Sciences (RIMLS), Geert Grooteplein Zuid 10, 6525 KL Nijmegen, The Netherlands * Correspondence: [email protected]; Tel.: +49-761-44391; Fax: +49-761-44710 Abstract: Although ubiquitously present, the relevance of cilia for vertebrate development and health has long been underrated. However, the aberration or dysfunction of ciliary structures or components results in a large heterogeneous group of disorders in mammals, termed ciliopathies. The majority of human ciliopathy cases are caused by malfunction of the ciliary dynein motor activity, powering retrograde intraflagellar transport (enabled by the cytoplasmic dynein-2 complex) or axonemal movement (axonemal dynein complexes). Despite a partially shared evolutionary developmental path and shared ciliary localization, the cytoplasmic dynein-2 and axonemal dynein functions are markedly different: while cytoplasmic dynein-2 complex dysfunction results in an ultra-rare syndromal skeleto-renal phenotype with a high lethality, axonemal dynein dysfunction is associated with a motile cilia dysfunction disorder, primary ciliary dyskinesia (PCD) or Kartagener syndrome, causing recurrent airway infection, degenerative lung disease, laterality defects, and infertility. In this review, we provide an overview of ciliary dynein complex compositions, their functions, clinical disease hallmarks of ciliary dynein disorders, presumed underlying pathomechanisms, and novel Citation: Antony, D.; Brunner, H.G.; developments in the field.