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The BCR/ABL Oncogene Alters Interaction of the Adapter Proteins CRKL and CRK with Cellular Proteins N Uemura, R Salgia, J-L Li, E Pisick, M Sattler and JD Griffin
Leukemia (1997) 11, 376–385 1997 Stockton Press All rights reserved 0887-6924/97 $12.00 The BCR/ABL oncogene alters interaction of the adapter proteins CRKL and CRK with cellular proteins N Uemura, R Salgia, J-L Li, E Pisick, M Sattler and JD Griffin Division of Hematologic Malignancies, Dana-Farber Cancer Institute and Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA The Philadelphia chromosome translocation generates a chim- alternative splicing of the human CRK proto-oncogene.8,9 eric oncogene, BCR/ABL, which causes chronic myelogenous CRKL has the same overall organization as CRK II, consisting leukemia (CML). In primary leukemic neutrophils from patients of one N-terminal SH2 domain followed by two SH3 domains, with CML, the major tyrosine phosphorylated protein is CRKL, 9 an SH2-SH3-SH3 adapter protein which has an overall hom- and does not contain other known functional motifs. CRK I ology of 60% to CRK, the human homologue of the v-crk onco- lacks the C-terminal SH3 domain of CRK II and CRKL, and gene. In cell lines transformed by BCR/ABL, CRKL was tyrosine overexpression of CRK I, but not CRK II, leads to transform- phosphorylated, while CRK was not. We looked for changes in ation of mammalian fibroblasts.8 v-crk is the oncogene in the CRK- and CRKL-binding proteins in Ba/F3 hematopoietic cell avian retrovirus CT10, and relative to CRK, v-Crk has a lines which were transformed by BCR/ABL. Anti-CRK II or anti- deletion of the C-terminal SH3 domain and the major tyrosine CRKL immunoprecipitates were probed by far Western blotting 221 10 with CRK II- or CRKL-GST fusion proteins to display CRK- and phosphorylation site at tyr . -
Liquid-Like Protein Interactions Catalyze Assembly of Endocytic Vesicles
bioRxiv preprint doi: https://doi.org/10.1101/860684; this version posted December 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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. **This manuscript is being posted in tandem with a manuscript by M. Kozak and M. Kaksonen which reports complementary findings in budding yeast. Title Liquid-like protein interactions catalyze assembly of endocytic vesicles Authors Kasey J. Daya, Grace Kagob, Liping Wangc, J Blair Richterc, Carl C. Haydena, Eileen M. Laferc, Jeanne C. Stachowiaka,b,* Affiliations a Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA; b Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA; c Department of Biochemistry and Structural Biology, Center for Biomedical Neuroscience, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA * To whom correspondence should be addressed: [email protected]. 1 bioRxiv preprint doi: https://doi.org/10.1101/860684; this version posted December 2, 2019. 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. Abstract During clathrin-mediated endocytosis, dozens of proteins assemble into an interconnected network at the plasma membrane. As early initiators of endocytosis, Eps15 and Fcho1 are responsible for locally concentrating downstream components on the membrane surface. -
RNF11 at the Crossroads of Protein Ubiquitination
biomolecules Review RNF11 at the Crossroads of Protein Ubiquitination Anna Mattioni, Luisa Castagnoli and Elena Santonico * Department of Biology, University of Rome Tor Vergata, Via della ricerca scientifica, 00133 Rome, Italy; [email protected] (A.M.); [email protected] (L.C.) * Correspondence: [email protected] Received: 29 September 2020; Accepted: 8 November 2020; Published: 11 November 2020 Abstract: RNF11 (Ring Finger Protein 11) is a 154 amino-acid long protein that contains a RING-H2 domain, whose sequence has remained substantially unchanged throughout vertebrate evolution. RNF11 has drawn attention as a modulator of protein degradation by HECT E3 ligases. Indeed, the large number of substrates that are regulated by HECT ligases, such as ITCH, SMURF1/2, WWP1/2, and NEDD4, and their role in turning off the signaling by ubiquitin-mediated degradation, candidates RNF11 as the master regulator of a plethora of signaling pathways. Starting from the analysis of the primary sequence motifs and from the list of RNF11 protein partners, we summarize the evidence implicating RNF11 as an important player in modulating ubiquitin-regulated processes that are involved in transforming growth factor beta (TGF-β), nuclear factor-κB (NF-κB), and Epidermal Growth Factor (EGF) signaling pathways. This connection appears to be particularly significant, since RNF11 is overexpressed in several tumors, even though its role as tumor growth inhibitor or promoter is still controversial. The review highlights the different facets and peculiarities of this unconventional small RING-E3 ligase and its implication in tumorigenesis, invasion, neuroinflammation, and cancer metastasis. Keywords: Ring Finger Protein 11; HECT ligases; ubiquitination 1. -
Robust Identification of Somatic Mutations in Acute Myeloid Leukemia Using RNA-Seq
RNAmut: Robust Identification of Somatic Mutations in Acute Myeloid Leukemia Using RNA-seq Muxin Gu1,2, Maximillian Zwiebel1,3, Swee Hoe Ong4, Nick Boughton5, Josep Nomdedeu1,2,6, Faisal Basheer1,2,7, Yasuhito Nannya8, Pedro M. Quiros1,2, Seishi Ogawa8, Mario Cazzola9, Roland Rad3, Adam P. Butler4, MS Vijayabaskar1,2,* and George Vassiliou1,2,7,* 1. Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK 2. Wellcome Trust–MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK 3. German Consortium for Translational Cancer Research (DKTK), Partnering Site, Munich, 81377 Munich, Germany 4. Cancer Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridge, UK 5. Core Software Services, Wellcome Sanger Institute, Hinxton, Cambridge, UK 6. Hospital de la Santa Creu I Sant Pau, Barcelona, Spain 7. Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge, UK 8. Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan 9. Fondazione IRCCS Policlinico San Matteo and University of Pavia, 27100 Pavia, Italy *Correspondence to: [email protected] and [email protected] Acute myeloid leukemia (AML) is an aggressive malignancy of haematopoietic stem cells driven by a well-defined set of somatic mutations1, 2. Identifying the mutations driving individual cases is important for assigning the patient to a recognized WHO category, establishing prognostic risk and tailoring post-consolidation therapy3. As a result, AML research and diagnostic laboratories apply diverse methodologies to detect important mutations and many are introducing next generation sequencing approaches to study extended panels of genes in order to refine genomic classification and prognostic category1. -
Knowledge Management Enviroments for High Throughput Biology
Knowledge Management Enviroments for High Throughput Biology Abhey Shah A Thesis submitted for the degree of MPhil Biology Department University of York September 2007 Abstract With the growing complexity and scale of data sets in computational biology and chemoin- formatics, there is a need for novel knowledge processing tools and platforms. This thesis describes a newly developed knowledge processing platform that is different in its emphasis on architecture, flexibility, builtin facilities for datamining and easy cross platform usage. There exist thousands of bioinformatics and chemoinformatics databases, that are stored in many different forms with different access methods, this is a reflection of the range of data structures that make up complex biological and chemical data. Starting from a theoretical ba- sis, FCA (Formal Concept Analysis) an applied branch of lattice theory, is used in this thesis to develop a file system that automatically structures itself by it’s contents. The procedure of extracting concepts from data sets is examined. The system also finds appropriate labels for the discovered concepts by extracting data from ontological databases. A novel method for scaling non-binary data for use with the system is developed. Finally the future of integrative systems biology is discussed in the context of efficiently closed causal systems. Contents 1 Motivations and goals of the thesis 11 1.1 Conceptual frameworks . 11 1.2 Biological foundations . 12 1.2.1 Gene expression data . 13 1.2.2 Ontology . 14 1.3 Knowledge based computational environments . 15 1.3.1 Interfaces . 16 1.3.2 Databases and the character of biological data . -
Screening for Subtle Chromosomal Rearrangements in an Egyptian Sample of Children with Unexplained Mental Retardation
The Egyptian Journal of Medical Human Genetics (2011) 12, 63–68 Ain Shams University The Egyptian Journal of Medical Human Genetics www.ejmhg.eg.net www.sciencedirect.com ORIGINAL ARTICLE Screening for subtle chromosomal rearrangements in an Egyptian sample of children with unexplained mental retardation Rabah M. Shawky *, Farida El-Baz, Ezzat S. Elsobky, Solaf M. Elsayed, Eman Zaky, Riham M. El-Hossiny Faculty of Medicine, Ain Shams University, Cairo, Egypt Received 16 October 2010; accepted 5 December 2010 KEYWORDS Abstract Mental retardation is present in about 1–3% of individuals in the general population, but Idiopathic mental retarda- it can be explained in about half of the cases. A descriptive study was carried out to screen for subtle tion (IMR); chromosomal rearrangements in a group of Egyptian children with idiopathic mental retardation High resolution banding (IMR) to estimate its frequency if detected. The study enrolled 30 patients with IMR, with the per- (HRB); quisite criteria of being <18 years at referral, their IQ <70, and manifesting at least one of the cri- Fluorescent in situ hybrid- teria for selection of patients with subtelomeric abnormalities. Males were 63.3% and females were ization (FISH); 36.7%, with a mean age of 7.08 ± 4.22 years. Full history taking, thorough clinical examination, Subtelomeric chromosomal IQ, visual, and audiological assessment, brain CT scan, plasma aminogram, pelvi-abdominal ultra- rearrangement sonography, echocardiography, and cytogenetic evaluation using routine conventional karyotyp- ing, high resolution banding (HRB), and fluorescent in situ hybridization (FISH) technique with appropriate probes were carried out for all studied patients. All enrolled patients had apparently normal karyotypes within 450 bands resolution, except for one patient who had 46, XY, [del (18) (p11.2)]. -
Human Eps15 Antibody Recombinant Monoclonal Rabbit Igg Clone # 1261C Catalog Number: MAB8480
Human Eps15 Antibody Recombinant Monoclonal Rabbit IgG Clone # 1261C Catalog Number: MAB8480 DESCRIPTION Species Reactivity Human Specificity Detects human Eps15 in direct ELISAs and Western blots. Source Recombinant Monoclonal Rabbit IgG Clone # 1261C Purification Protein A or G purified from cell culture supernatant Immunogen E.coliderived recombinant human Eps15 Ala448Thr579 Accession # P42566 Formulation Lyophilized from a 0.2 μm filtered solution in PBS with Trehalose. See Certificate of Analysis for details. *Small pack size (SP) is supplied either lyophilized or as a 0.2 μm filtered solution in PBS. APPLICATIONS Please Note: Optimal dilutions should be determined by each laboratory for each application. General Protocols are available in the Technical Information section on our website. Recommended Sample Concentration Western Blot 0.1 µg/mL See Below Immunocytochemistry 125 µg/mL See Below Intracellular Staining by Flow Cytometry 0.25 µg/106 cells See Below Simple Western 1 µg/mL See Below DATA Western Blot Immunocytochemistry Detection of Human Eps15 by Western Eps15 in HeLa Human Cell Line. Eps15 Blot. Western blot shows lysates of HeLa was detected in immersion fixed HeLa human human cervical epithelial carcinoma cell line cervical epithelial carcinoma cell line using and A431 human epithelial carcinoma cell Rabbit AntiHuman Eps15 Monoclonal line. PVDF membrane was probed with Antibody (Catalog # MAB8480) at 1 µg/mL 0.1 µg/mL of Rabbit AntiHuman Eps15 for 3 hours at room temperature. Cells were Monoclonal Antibody (Catalog # MAB8480) stained using the NorthernLights™ 557 followed by HRPconjugated AntiRabbit IgG conjugated AntiRabbit IgG Secondary Secondary Antibody (Catalog # HAF008). -
Integrating Protein Copy Numbers with Interaction Networks to Quantify Stoichiometry in Mammalian Endocytosis
bioRxiv preprint doi: https://doi.org/10.1101/2020.10.29.361196; this version posted October 29, 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-ND 4.0 International license. Integrating protein copy numbers with interaction networks to quantify stoichiometry in mammalian endocytosis Daisy Duan1, Meretta Hanson1, David O. Holland2, Margaret E Johnson1* 1TC Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218. 2NIH, Bethesda, MD, 20892. *Corresponding Author: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2020.10.29.361196; this version posted October 29, 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-ND 4.0 International license. Abstract Proteins that drive processes like clathrin-mediated endocytosis (CME) are expressed at various copy numbers within a cell, from hundreds (e.g. auxilin) to millions (e.g. clathrin). Between cell types with identical genomes, copy numbers further vary significantly both in absolute and relative abundance. These variations contain essential information about each protein’s function, but how significant are these variations and how can they be quantified to infer useful functional behavior? Here, we address this by quantifying the stoichiometry of proteins involved in the CME network. We find robust trends across three cell types in proteins that are sub- vs super-stoichiometric in terms of protein function, network topology (e.g. -
Mammalian Eps15 Homology Domain 1 Potentiates Angiogenesis of Non
Wang et al. Journal of Experimental & Clinical Cancer Research (2019) 38:174 https://doi.org/10.1186/s13046-019-1162-7 RESEARCH Open Access Mammalian Eps15 homology domain 1 potentiates angiogenesis of non-small cell lung cancer by regulating β2AR signaling Ting Wang1†, Ying Xing1†, Qingwei Meng2, Hailing Lu1, Wei Liu1, Shi Yan1, Yang Song3, Xinyuan Xu1, Jian Huang1, Yue Cui1, Dexin Jia1 and Li Cai1* Abstract Background: Non-small cell lung cancer (NSCLC) is a devastating disease with a heterogeneous prognosis, and the molecular mechanisms underlying tumor progression remain elusive. Mammalian Eps15 homology domain 1 (EHD1) plays a promotive role in tumor progression, but its role in cancer angiogenesis remains unknown. This study thus explored the role of EHD1 in angiogenesis in NSCLC. Methods: The changes in angiogenesis were evaluated through human umbilical vein endothelial cell (HUVEC) proliferation, migration and tube formation assays. The impact of EHD1 on β2-adrenoceptor (β2AR) signaling was evaluated by Western blotting, quantitative real-time polymerase chain reaction (qRT-PCR) analysis, and enzyme- linked immunosorbent assay (ELISA). The interaction between EHD1 and β2AR was confirmed by immunofluorescence (IF) and coimmunoprecipitation (Co-IP) experiments, and confocal microscopy immunofluorescence studies revealed that β2AR colocalized with the recycling endosome marker Rab11, which indicated β2AR endocytosis. Xenograft tumor models were used to investigate the role of EHD1 in NSCLC tumor growth. Results: The microarray analysis revealed that EHD1 was significantly correlated with tumor angiogenesis, and loss- and gain-of-function experiments demonstrated that EHD1 potentiates HUVEC proliferation, migration and tube formation. EHD1 knockdown inhibited β2AR signaling activity, and EHD1 upregulation promoted vascular endothelial growth factor A (VEGFA) and β2AR expression. -
EPN1 Antibody Cat
EPN1 Antibody Cat. No.: 58-346 EPN1 Antibody Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Human HOMOLOGY: Predicted species reactivity based on immunogen sequence: Mouse, Rat This EPN1 antibody is generated from rabbits immunized with a KLH conjugated synthetic IMMUNOGEN: peptide between 203-232 amino acids from the Central region of human EPN1. TESTED APPLICATIONS: WB APPLICATIONS: For WB starting dilution is: 1:1000 PREDICTED MOLECULAR 60 kDa WEIGHT: Properties This antibody is purified through a protein A column, followed by peptide affinity PURIFICATION: purification. CLONALITY: Polyclonal ISOTYPE: Rabbit Ig CONJUGATE: Unconjugated October 1, 2021 1 https://www.prosci-inc.com/epn1-antibody-58-346.html PHYSICAL STATE: Liquid BUFFER: Supplied in PBS with 0.09% (W/V) sodium azide. CONCENTRATION: batch dependent Store at 4˚C for three months and -20˚C, stable for up to one year. As with all antibodies STORAGE CONDITIONS: care should be taken to avoid repeated freeze thaw cycles. Antibodies should not be exposed to prolonged high temperatures. Additional Info OFFICIAL SYMBOL: EPN1 ALTERNATE NAMES: Epsin-1, EH domain-binding mitotic phosphoprotein, EPS-15-interacting protein 1, EPN1 ACCESSION NO.: Q9Y6I3 PROTEIN GI NO.: 332278179 GENE ID: 29924 USER NOTE: Optimal dilutions for each application to be determined by the researcher. Background and References EPN1 is an endocytic accessory protein that interacts with EPS15 (MIM 600051), the alpha BACKGROUND: subunit of the clathrin adaptor AP2 (AP2A1; MIM 601026), and clathrin (see MIM 118960), as well as with other accessory proteins for the endocytosis of clathrin-coated vesicles. 1) Liu, Z., et al. J. Cell Biol. -
Eps15 Homology Domain-Containing Protein 3 Hypermethylation As a Prognostic and Predictive Marker for Colorectal Cancer
biomedicines Article Eps15 Homology Domain-Containing Protein 3 Hypermethylation as a Prognostic and Predictive Marker for Colorectal Cancer Yu-Han Wang 1,†, Shih-Ching Chang 2,† , Muhamad Ansar 3, Chin-Sheng Hung 4,5 and Ruo-Kai Lin 3,6,7,8,9,* 1 School of Medicine, Tzu Chi University, Hualien City 97071, Taiwan; [email protected] 2 Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan; [email protected] 3 Ph.D. Program in the Clinical Drug Development of Herbal Medicine, Taipei Medical University, Taipei 11031, Taiwan; [email protected] 4 Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan; [email protected] 5 Division of General Surgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, New Taipei City 23561, Taiwan 6 Graduate Institute of Pharmacognosy, Taipei Medical University, Taipei 11031, Taiwan 7 Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan 8 Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, Taipei 11031, Taiwan 9 Clinical Trial Center, Taipei Medical University Hospital, Taipei 11031, Taiwan * Correspondence: [email protected] † These authors are equal first authors in this work. Abstract: Colorectal cancer (CRC) arises from chromosomal instability, resulting from aberrant Citation: Wang, Y.-H.; Chang, S.-C.; hypermethylation in tumor suppressor genes. This study identified hypermethylated genes in Ansar, M.; Hung, C.-S.; Lin, R.-K. CRC and investigated how they affect clinical outcomes. Methylation levels of specific genes were Eps15 Homology Domain-Containing analyzed from The Cancer Genome Atlas dataset and 20 breast cancer, 16 esophageal cancer, 33 lung Protein 3 Hypermethylation as a cancer, 15 uterine cancer, 504 CRC, and 9 colon polyp tissues and 102 CRC plasma samples from a Prognostic and Predictive Marker for Colorectal Cancer. -
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Nieber et al. BMC Developmental Biology 2013, 13:36 http://www.biomedcentral.com/1471-213X/13/36 RESEARCH ARTICLE Open Access NumbL is essential for Xenopus primary neurogenesis Frank Nieber1,2, Marie Hedderich1,2, Olaf Jahn2,3, Tomas Pieler1,2 and Kristine A Henningfeld1,2* Abstract Background: Members of the vertebrate Numb family of cell fate determinants serve multiple functions throughout early embryogenesis, including an essential role in the development of the nervous system. The Numb proteins interact with various partner proteins and correspondingly participate in multiple cellular activities, including inhibition of the Notch pathway. Results: Here, we describe the expression characteristics of Numb and Numblike (NumbL) during Xenopus development and characterize the function of NumbL during primary neurogenesis. NumbL, in contrast to Numb,is expressed in the territories of primary neurogenesis and is positively regulated by the Neurogenin family of proneural transcription factors. Knockdown of NumbL afforded a complete loss of primary neurons and did not lead to an increase in Notch signaling in the open neural plate. Furthermore, we provide evidence that interaction of NumbL with the AP-2 complex is required for NumbL function during primary neurogenesis. Conclusion: We demonstrate an essential role of NumbL during Xenopus primary neurogenesis and provide evidence for a Notch-independent function of NumbL in this context. Keywords: Numb, Notch, Primary neurogenesis, Neurogenin, Neuronal differentiation, Xenopus Background In vertebrates, there are two closely related genes that Numb type proteins define an evolutionary conserved are homologues of Drosophila Numb, namely Numb and class of adaptor proteins that have been implicated in a Numblike (NumbL) [9-11].