DOCSLIB.ORG

PTK7) in Cancer Development and Cellular Fitness

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Characterizing the Role of Protein Tyrosine Kinase 7 (PTK7) in Cancer Development and Cellular Fitness by Sachin Anand Kumar A thesis submitted in conformity with the requirements for the degree of Master of Science Department of Molecular Genetics University of Toronto © Copyright by Sachin Anand Kumar (2015) Characterizing the Role of Protein Tyrosine Kinase 7 (PTK7) in Cancer Development and Cellular Fitness Sachin Anand Kumar Master of Science Department of Molecular Genetics University of Toronto 2015 Abstract Protein Tyrosine Kinase 7 has been recently affiliated with the development and progression of various cancers. Contradictory results about its expression, localization and processing across various cancer types has left a major gap in understanding its molecular mechanism and function. In my thesis, I utilized large data sets from essentiality screens and RNAseq, as well as antibody-related tools, to investigate the role of PTK7 in cellular fitness. I observed a negative correlation between PTK7 processing and its degree of essentiality. Furthermore, I demonstrated that the PTK7 intracellular domain (ICD) is integral to its function. Treatment of mouse xenografts with PTK7 antibodies, capable of blocking PTK7 processing, inhibited tumour growth in an ICD-expression dependent manner. Lastly, mRNA profiling of PTK7-knockdown cells and ICD over-expression cells provided a list of putative downstream gene targets under PTK7 regulation. Collectively, these findings implicate PTK7 in cellular transformation and provide insight into its signaling mechanism. II Acknowledgments First and foremost, I would like to thank my supervisor Dr. Jason Moffat. You gave me an opportunity to step outside of my comfort zone and partake in research that pushed the boundary of science, technology and discovery. Your mentorship and creativity have been an inspiration to me – teaching me how to be a critical scientist, think outside of the box and perseverant throughout the hardships of research. Thank you for always being candid with me about my capabilities, strengths and weaknesses and pushing me to achieve more than I knew I was capable of. From you I have learned the tools and foundation I need to pursue my dream career as a physician scientist. To my committee members Dr. Jeff Wrana and Dr. Igor Stagljar, thank you for your guidance, wealth of knowledge and constructive criticism. The rigorous perspective I have developed in my scientific questioning and approach were an integral part of my success, and will only flourish going forward. Thank you to my colleagues in the Moffat Lab, past and present. To Andrea, thank you for setting a rigorous example of what scientific questioning should be. Regardless of the ups and downs over the past years, what I have learned and taken away from this experience is invaluable. A special thank you to Peter Xu, who kept me motivated when the multi-day experiments failed and provided insight when I was out of ideas. The late night hours of lab work wouldn’t have been the same. To Megha, Kristin, Michael, Taras, Carly, Hayoung, Clara and Zvezden, thank you for providing countless memories and hilarious discussions – these are the moments that make graduate school a truly wonderful experience. Kevin and Traver, you always indulged my curiosity and pushed me to learn coding to test every single theory I had – you’ve made me a better scientist. Last but not least, to Patti and Christine, thank you for keeping our lab functioning. Whether ordering things last minute or rolling up your sleeves to help us get stuff done, I truly appreciate your commitment to our success and the wealth of knowledge you both have about pretty much every technique ever. To my friends and supporters (you know who you are), thank you for keeping my spirits high. Research finds unique ways to push you and test your limits. You were always there to help me push back. Last, but certainly not least, thank you to my family. To Mom & Dad, you never III really understood what I was working on, but let me bore you with the details anyways because you knew how passionate I was. That support is a huge factor in making me who I am, and where I am, today. To my brother Rishi, you always knew I could achieve anything I put my mind to. Some days that’s the only thing that kept me going. Thank you. IV Table of Contents Acknowledgments .......................................................................................................................... III Table of Contents ............................................................................................................................ V List of Tables ............................................................................................................................... VII List of Figures ............................................................................................................................. VIII List of Abbreviations ...................................................................................................................... X Chapter 1 Introduction .....................................................................................................................1 1.1 Signaling and activation of receptor tyrosine kinases ..........................................................1 1.2 Receptor tyrosine kinases in the development and progression of cancer ...........................5 1.3 Screening for genetic-based fitness defects in cancer ..........................................................6 1.4 Protein tyrosine kinase 7 (PTK7) .......................................................................................10 1.4.1 PTK7 in development and Wnt signaling ..............................................................11 1.4.2 Post-translational processing of PTK7 ...................................................................13 1.4.3 PTK7 as a prognostic biomarker in cancer ............................................................15 1.5 Thesis objectives ................................................................................................................15 Chapter 2 The intracellular domain of PTK7 is integral for proliferation .....................................17 2 Acknowledgements ...................................................................................................................17 2.1 Materials and Methods .......................................................................................................17 2.1.1 Cell Culture ............................................................................................................17 2.1.2 Effect of PTK7 knockdown on proliferation .........................................................18 2.1.3 Western Blot ..........................................................................................................19 2.1.4 Over-expression of PTK7 ......................................................................................20 2.1.5 Anchorage independent growth .............................................................................20 2.1.6 Immunofluorescence of PTK7 fragments ..............................................................21 2.1.7 ELISA and Cytometric Bead Array .......................................................................21 V 2.1.8 Tumour xenografts and antibody treatment ...........................................................23 2.1.9 Cleavage assessment of recombinant PTK7 protein ..............................................23 2.1.10 Cellular RNA isolation and sequencing .................................................................24 2.2 Results ................................................................................................................................25 2.2.1 PTK7 knockdown negatively affects cancer cell fitness .......................................25 2.2.2 PTK7 full-length rescues this proliferation defect .................................................28 2.2.3 PTK7 intracellular domain localizes to the nucleus ..............................................30 2.2.4 PTK7 intracellular domain is sufficient to partially rescue the fitness defect observed upon knockdown ....................................................................................32 2.2.5 Processing of PTK7 negatively-correlates to its essentiality .................................32 2.2.6 PTK7 antibodies demonstrate tumour growth inhibition potential in vivo ............34 2.2.7 PTK7 intracellular domain rescues the antibody effect in vivoError! Bookmark not defined. 2.2.8 Antibodies block cleavage of PTK7 in vitro and in vivo .......................................36 2.2.9 RNAseq of PTK7 knockdown and ICD over-expression identify putative targets for PTK7 associated function .....................................................................39 2.3 Discussion ..........................................................................................................................43 Chapter 3 Summary and Future Directions ...................................................................................49 3 Summary ...................................................................................................................................49 3.1 Future Directions ...............................................................................................................50 3.1.1 Determining protein interactors and transcriptional targets of the PTK7 intracellular domain ...............................................................................................50
Recommended publications
  • The Novel Mouse Mutant, Chuzhoi, Has Disruption of Ptk7 Protein and Exhibits Defects in Neural Tube, Heart and Lung Development

    The Novel Mouse Mutant, Chuzhoi, Has Disruption of Ptk7 Protein and Exhibits Defects in Neural Tube, Heart and Lung Development

    Paudyal et al. BMC Developmental Biology 2010, 10:87 http://www.biomedcentral.com/1471-213X/10/87 RESEARCH ARTICLE Open Access The novel mouse mutant, chuzhoi, has disruption of Ptk7 protein and exhibits defects in neural tube, heart and lung development and abnormal planar cell polarity in the ear Anju Paudyal1, Christine Damrau1, Victoria L Patterson1, Alexander Ermakov1,2, Caroline Formstone3, Zuzanna Lalanne1,4, Sara Wells5, Xiaowei Lu6, Dominic P Norris1, Charlotte H Dean1, Deborah J Henderson7, Jennifer N Murdoch1,8* Abstract Background: The planar cell polarity (PCP) signalling pathway is fundamental to a number of key developmental events, including initiation of neural tube closure. Disruption of the PCP pathway causes the severe neural tube defect of craniorachischisis, in which almost the entire brain and spinal cord fails to close. Identification of mouse mutants with craniorachischisis has proven a powerful way of identifying molecules that are components or regulators of the PCP pathway. In addition, identification of an allelic series of mutants, including hypomorphs and neomorphs in addition to complete nulls, can provide novel genetic tools to help elucidate the function of the PCP proteins. Results: We report the identification of a new N-ethyl-N-nitrosourea (ENU)-induced mutant with craniorachischisis, which we have named chuzhoi (chz). We demonstrate that chuzhoi mutant embryos fail to undergo initiation of neural tube closure, and have characteristics consistent with defective convergent extension. These characteristics include a broadened midline and reduced rate of increase of their length-to-width ratio. In addition, we demonstrate disruption in the orientation of outer hair cells in the inner ear, and defects in heart and lung development in chuzhoi mutants.
  • PTK7 Expression in Triple-Negative Breast Cancer

    PTK7 Expression in Triple-Negative Breast Cancer

    ANTICANCER RESEARCH 33: 3759-3764 (2013) PTK7 Expression in Triple-negative Breast Cancer BEYHAN ATASEVEN1,2, REGINA ANGERER1, RONALD KATES3, ANGELA GUNESCH1, PJOTR KNYAZEV4, BERNHARD HÖGEL5, CLEMENS BECKER5, WOLFGANG EIERMANN6 and NADIA HARBECK7 1Department of Gynecology and Obstetrics, Red Cross Women’s Hospital, Munich, Germany; 2Department of Gynecology and Gynecologic Oncology, Kliniken Essen-Mitte, Evangelische Huyssens-Stiftung, Essen, Germany; 3Breast Center, Department of Gynecology and Obstetrics Maistrasse Campus, Ludwig Maximilian University Munich, Munich, Germany; 4Department of Molecular Biology, Max Planck Institute of Biochemistry, Martinsried, Germany; 5Department of Pathology, Red Cross Women’s Hospital Munich, Munich, Germany; 6Department of Gynecology and Oncology, Interdiscipilnary Oncology Center Munich, Germany; 7Breast Center, Department of Gynecology and Obstetrics, Großhadern Campus, Ludwig Maximilian University Munich, Munich, Germany Abstract. Background: Protein tyrosine kinase-7 (PTK7) immunoglobulin-like loops, a transmenbrane domain and an plays an important role in cancer. Our aim was to evaluate inactive catalytic tyrosine kinase domain (2, 3). PTK7 seems PTK7 in triple-negative breast cancer (TNBC). Materials to be highly involved in the WNT (named after the Drosophilia and Methods: PTK7 Expression was assessed by Wingless (Wg) and the mouse Int-1 genes)-pathways (4), which immunohistochemistry (IHC) in 133 patients with TNBC. again represent key pathways for epithelial mesenchymal Expression levels were correlated with clinicopathological transition (EMT) and play important roles in cancer (5-8). A features and survival, taking chemotherapy into account. potential impact of PTK7 expression has been studied in Results: Positive PTK7 expression was detected in 28.6% of several malignancies, including colon, lung, gastric and breast tumors. In the total population, no significant difference was cancer, acute myeloid leukemia and liposarcoma (9-15).
  • Human Germ/Stem Cell-Specific Gene TEX19 Influences Cancer Cell

    Human Germ/Stem Cell-Specific Gene TEX19 Influences Cancer Cell

    Planells-Palop et al. Molecular Cancer (2017) 16:84 DOI 10.1186/s12943-017-0653-4 RESEARCH Open Access Human germ/stem cell-specific gene TEX19 influences cancer cell proliferation and cancer prognosis Vicente Planells-Palop1, Ali Hazazi1, Julia Feichtinger2,3, Jana Jezkova1, Gerhard Thallinger2,3, Naif O. Alsiwiehri1, Mikhlid Almutairi1,5, Lee Parry4, Jane A. Wakeman1 and Ramsay J. McFarlane1* Abstract Background: Cancer/testis (CT) genes have expression normally restricted to the testis, but become activated during oncogenesis, so they have excellent potential as cancer-specific biomarkers. Evidence is starting to emerge to indicate that they also provide function(s) in the oncogenic programme. Human TEX19 is a recently identified CT gene, but a functional role for TEX19 in cancer has not yet been defined. Methods: siRNA was used to deplete TEX19 levels in various cancer cell lines. This was extended using shRNA to deplete TEX19 in vivo. Western blotting, fluorescence activated cell sorting and immunofluorescence were used to study the effect of TEX19 depletion in cancer cells and to localize TEX19 in normal testis and cancer cells/tissues. RT-qPCR and RNA sequencing were employed to determine the changes to the transcriptome of cancer cells depleted for TEX19 and Kaplan-Meier plots were generated to explore the relationship between TEX19 expression and prognosis for a range of cancer types. Results: Depletion of TEX19 levels in a range of cancer cell lines in vitro and in vivo restricts cellular proliferation/ self-renewal/reduces tumour volume, indicating TEX19 is required for cancer cell proliferative/self-renewal potential. Analysis of cells depleted for TEX19 indicates they enter a quiescent-like state and have subtle defects in S-phase progression.
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
  • Supplementary Table 3 Complete List of RNA-Sequencing Analysis of Gene Expression Changed by ≥ Tenfold Between Xenograft and Cells Cultured in 10%O2

    Supplementary Table 3 Complete List of RNA-Sequencing Analysis of Gene Expression Changed by ≥ Tenfold Between Xenograft and Cells Cultured in 10%O2

    Supplementary Table 3 Complete list of RNA-Sequencing analysis of gene expression changed by ≥ tenfold between xenograft and cells cultured in 10%O2 Expr Log2 Ratio Symbol Entrez Gene Name (culture/xenograft) -7.182 PGM5 phosphoglucomutase 5 -6.883 GPBAR1 G protein-coupled bile acid receptor 1 -6.683 CPVL carboxypeptidase, vitellogenic like -6.398 MTMR9LP myotubularin related protein 9-like, pseudogene -6.131 SCN7A sodium voltage-gated channel alpha subunit 7 -6.115 POPDC2 popeye domain containing 2 -6.014 LGI1 leucine rich glioma inactivated 1 -5.86 SCN1A sodium voltage-gated channel alpha subunit 1 -5.713 C6 complement C6 -5.365 ANGPTL1 angiopoietin like 1 -5.327 TNN tenascin N -5.228 DHRS2 dehydrogenase/reductase 2 leucine rich repeat and fibronectin type III domain -5.115 LRFN2 containing 2 -5.076 FOXO6 forkhead box O6 -5.035 ETNPPL ethanolamine-phosphate phospho-lyase -4.993 MYO15A myosin XVA -4.972 IGF1 insulin like growth factor 1 -4.956 DLG2 discs large MAGUK scaffold protein 2 -4.86 SCML4 sex comb on midleg like 4 (Drosophila) Src homology 2 domain containing transforming -4.816 SHD protein D -4.764 PLP1 proteolipid protein 1 -4.764 TSPAN32 tetraspanin 32 -4.713 N4BP3 NEDD4 binding protein 3 -4.705 MYOC myocilin -4.646 CLEC3B C-type lectin domain family 3 member B -4.646 C7 complement C7 -4.62 TGM2 transglutaminase 2 -4.562 COL9A1 collagen type IX alpha 1 chain -4.55 SOSTDC1 sclerostin domain containing 1 -4.55 OGN osteoglycin -4.505 DAPL1 death associated protein like 1 -4.491 C10orf105 chromosome 10 open reading frame 105 -4.491
  • Ptk7-Deficient Mice Have Decreased Hematopoietic Stem Cell Pools As a Result of Deregulated Proliferation and Migration

    Ptk7-Deficient Mice Have Decreased Hematopoietic Stem Cell Pools As a Result of Deregulated Proliferation and Migration

    Ptk7-Deficient Mice Have Decreased Hematopoietic Stem Cell Pools as a Result of Deregulated Proliferation and Migration This information is current as Anne-Catherine Lhoumeau, Marie-Laure Arcangeli, Maria of September 24, 2021. De Grandis, Marilyn Giordano, Jean-Christophe Orsoni, Frédérique Lembo, Florence Bardin, Sylvie Marchetto, Michel Aurrand-Lions and Jean-Paul Borg J Immunol 2016; 196:4367-4377; Prepublished online 18 April 2016; Downloaded from doi: 10.4049/jimmunol.1500680 http://www.jimmunol.org/content/196/10/4367 Supplementary http://www.jimmunol.org/content/suppl/2016/04/16/jimmunol.150068 http://www.jimmunol.org/ Material 0.DCSupplemental References This article cites 55 articles, 24 of which you can access for free at: http://www.jimmunol.org/content/196/10/4367.full#ref-list-1 Why The JI? Submit online. by guest on September 24, 2021 • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright
  • Cellular and Molecular Signatures in the Disease Tissue of Early

    Cellular and Molecular Signatures in the Disease Tissue of Early

    Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of
  • A Single Wave of Monocytes Is Sufficient to Replenish the Long-Term

    A Single Wave of Monocytes Is Sufficient to Replenish the Long-Term

    bioRxiv preprint doi: https://doi.org/10.1101/617514; this version posted April 24, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. A single wave of monocytes is sufficient to replenish the long-term Langerhans cell network after immune injury Ivana R. Ferrer1,2,a, Heather C. West1,2,a, Stephen Henderson2, Dmitry S. Ushakov3, Pedro Santos e Sousa1,2, Jessica Strid4, Ronjon Chakraverty1,2, Andrew J. Yates5, and Clare L. Bennett1,2 1Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London NW3 2PF, UK 2Haematology, Division of Cancer Studies, University College London, London WC1E 6DD, UK. 3Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, New Hunt’s House, Newcomen St, London SE1 1UL, UK 4Division of Immunology and Inflammation, Imperial College London, Hammersmith campus, London W12 0NN, UK. 5Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY10032, USA. aThese authors contributed equally to this work Abstract • Immune injury and inefficient repopulation by Embryo-derived Langerhans cells (eLC) are maintained within monocyte-derived cells lead to a permanently altered the sealed epidermis without contribution from circulating cells. LC niche. When the network is perturbed by transient exposure to ultra- violet light, short-term LC are temporarily reconstituted from an initial wave of monocytes, but thought to be superseded by more permanent repopulation with undefined LC precur- sors. However, the extent to which this mechanism is relevant to immune-pathological processes that damage LC population integrity is not known.
  • Tex19 and Sectm1 Concordant Molecular

    Tex19 and Sectm1 Concordant Molecular

    Tex19 and Sectm1 concordant molecular phylogenies support co-evolution of both eutherian-specific genes Laurent Bianchetti, Yara Tarabay, Odile Lecompte, Roland Stote, Olivier Poch, Annick Dejaegere, Stéphane Viville To cite this version: Laurent Bianchetti, Yara Tarabay, Odile Lecompte, Roland Stote, Olivier Poch, et al.. Tex19 and Sectm1 concordant molecular phylogenies support co-evolution of both eutherian-specific genes. BMC Evolutionary Biology, BioMed Central, 2015, 15, pp.222. 10.1186/s12862-015-0506-y. inserm- 02057408 HAL Id: inserm-02057408 https://www.hal.inserm.fr/inserm-02057408 Submitted on 5 Mar 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Bianchetti et al. BMC Evolutionary Biology (2015) 15:222 DOI 10.1186/s12862-015-0506-y RESEARCH ARTICLE Open Access Tex19 and Sectm1 concordant molecular phylogenies support co-evolution of both eutherian-specific genes Laurent Bianchetti1*, Yara Tarabay2,5, Odile Lecompte3, Roland Stote1, Olivier Poch3, Annick Dejaegere1 and Stéphane Viville2,4 Abstract Background: Transposable elements (TE) have attracted much attention since they shape the genome and contribute to species evolution. Organisms have evolved mechanisms to control TE activity. Testis expressed 19 (Tex19) represses TE expression in mouse testis and placenta.
  • Ponatinib Shows Potent Antitumor Activity in Small Cell Carcinoma of the Ovary Hypercalcemic Type (SCCOHT) Through Multikinase Inhibition Jessica D

    Ponatinib Shows Potent Antitumor Activity in Small Cell Carcinoma of the Ovary Hypercalcemic Type (SCCOHT) Through Multikinase Inhibition Jessica D

    Published OnlineFirst February 9, 2018; DOI: 10.1158/1078-0432.CCR-17-1928 Cancer Therapy: Preclinical Clinical Cancer Research Ponatinib Shows Potent Antitumor Activity in Small Cell Carcinoma of the Ovary Hypercalcemic Type (SCCOHT) through Multikinase Inhibition Jessica D. Lang1,William P.D. Hendricks1, Krystal A. Orlando2, Hongwei Yin1, Jeffrey Kiefer1, Pilar Ramos1, Ritin Sharma3, Patrick Pirrotte3, Elizabeth A. Raupach1,3, Chris Sereduk1, Nanyun Tang1, Winnie S. Liang1, Megan Washington1, Salvatore J. Facista1, Victoria L. Zismann1, Emily M. Cousins4, Michael B. Major4, Yemin Wang5, Anthony N. Karnezis5, Aleksandar Sekulic1,6, Ralf Hass7, Barbara C. Vanderhyden8, Praveen Nair9, Bernard E. Weissman2, David G. Huntsman5,10, and Jeffrey M. Trent1 Abstract Purpose: Small cell carcinoma of the ovary, hypercalcemic type three SWI/SNF wild-type ovarian cancer cell lines. We further (SCCOHT) is a rare, aggressive ovarian cancer in young women identified ponatinib as the most effective clinically approved that is universally driven by loss of the SWI/SNF ATPase subunits RTK inhibitor. Reexpression of SMARCA4 was shown to confer SMARCA4 and SMARCA2. A great need exists for effective targeted a 1.7-fold increase in resistance to ponatinib. Subsequent therapies for SCCOHT. proteomic assessment of ponatinib target modulation in Experimental Design: To identify underlying therapeutic vul- SCCOHT cell models confirmed inhibition of nine known nerabilities in SCCOHT, we conducted high-throughput siRNA ponatinib target kinases alongside 77 noncanonical ponatinib and drug screens. Complementary proteomics approaches pro- targets in SCCOHT. Finally, ponatinib delayed tumor dou- filed kinases inhibited by ponatinib. Ponatinib was tested for bling time 4-fold in SCCOHT-1 xenografts while reducing efficacy in two patient-derived xenograft (PDX) models and one final tumor volumes in SCCOHT PDX models by 58.6% and cell-line xenograft model of SCCOHT.
  • Detecting Remote, Functional Conserved Domains in Entire Genomes by Combining Relaxed Sequence-Database Searches with Fold Recognition

    Detecting Remote, Functional Conserved Domains in Entire Genomes by Combining Relaxed Sequence-Database Searches with Fold Recognition

    HMMerThread: Detecting Remote, Functional Conserved Domains in Entire Genomes by Combining Relaxed Sequence-Database Searches with Fold Recognition Charles Richard Bradshaw1¤a, Vineeth Surendranath1, Robert Henschel2,3, Matthias Stefan Mueller2, Bianca Hermine Habermann1,4*¤b 1 Bioinformatics Laboratory, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony, Germany, 2 Center for Information Services and High Performance Computing (ZIH), Technical University, Dresden, Saxony, Germany, 3 High Performance Applications, Pervasive Technology Institute, Indiana University, Bloomington, Indiana, United States of America, 4 Bioinformatics Laboratory, Scionics c/o Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony, Germany Abstract Conserved domains in proteins are one of the major sources of functional information for experimental design and genome-level annotation. Though search tools for conserved domain databases such as Hidden Markov Models (HMMs) are sensitive in detecting conserved domains in proteins when they share sufficient sequence similarity, they tend to miss more divergent family members, as they lack a reliable statistical framework for the detection of low sequence similarity. We have developed a greatly improved HMMerThread algorithm that can detect remotely conserved domains in highly divergent sequences. HMMerThread combines relaxed conserved domain searches with fold recognition to eliminate false positive, sequence-based identifications. With an accuracy of 90%, our software is able to automatically predict highly divergent members of conserved domain families with an associated 3-dimensional structure. We give additional confidence to our predictions by validation across species. We have run HMMerThread searches on eight proteomes including human and present a rich resource of remotely conserved domains, which adds significantly to the functional annotation of entire proteomes.
  • Thai Hun Taiteit Ut La in Tutta Latoare

    Thai Hun Taiteit Ut La in Tutta Latoare

    THAI HUN TAITEIT US009970056B2UT LA IN TUTTA LATOARE (12 ) United States Patent ( 10 ) Patent No. : US 9 ,970 , 056 B2 Potashkin et al. ( 45 ) Date of Patent: May 15 , 2018 ( 54 ) METHODS AND KITS FOR DIAGNOSING , Aviles- Olmos , et al. “ Parkinson ' s Disease , Insulin Resistance and PROGNOSING AND MONITORING Novel Agents of Neuroprotection ” , Brain , 2013 , vol. 136 ( Pt 2 ) , pp . PARKINSON ' S DISEASE 37414 -- 384 .. Bassil, et al, “ Insulin , IGF - 1 and GLP - 1 Signaling in Neurodegenerative Disorders : Targets for Disease Modification ? ” , ( 71 ) Applicant: Rosalind Franklin University of Prog Neurobiol , Jul. 2014 , vol. 118 , pp . 1 - 18 . ( Abstract only ) . Medicine and Science , North Chicago , Bonnefond , et al. , “ The Emerging Genetics of Type 2 Diabetes ” , IL (US ) Trends Mol Med , Sep . 2010 , vol. 16 ( 9 ) , pp . 407 -416 . ( Abstract only ) . (72 ) Inventors : Judith Ann Potashkin , North Chicago , Cereda, et al. , “ Diabetes and Risk of Parkinson ' s Disease : A IL (US ) ; Jose Alfredo Santiago , North Systematic Review and Meta - Analysis ” , Diabetes Care, Dec . 2011 , Chicago , IL (US ) vol . 34 , pp . 2614 - 2623 . Cereda , et al. , “ Diabetes and Risk of Parkinson ' s Disease ” , Move ( 73 ) Assignee : Rosalind Franklin University of ment Disorders, 2013 , vol. 28 , pp . 257 - 261 ( Abstract only ) . Medicine and Science , North Chicago , Cereda , et al . , “ Clinical Features of Parkinson ' s Disease When Onset of Diabetes Came First: A Case - Control Study” , Neurology , IL (US ) May 8 , 2012 , vol . 78 ( 19 ), pp . 1507 - 1511 , doi: 10 .1212 /WNL . Ob013e3182553cc9 , Epub Apr. 25 , 2012 . ( Abstract only ) . ( * ) Notice : Subject to any disclaimer , the term of this Chen - Plotkin , et al. , “ Plasma Epidermal Growth Factor Levels patent is extended or adjusted under 35 Predict Cognitive Decline in Parkinson ' s Disease " , Ann Neurol , U .