C. Elegans As a Model to Identify and Functionally Characterize Novel Genes Causing Rasopathies and Other Developmental Diseases
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Identification and Characterization of a Novel Human Testis-Specific
Biochemical and Biophysical Research Communications 285, 400–408 (2001) doi:10.1006/bbrc.2001.5165, available online at http://www.idealibrary.com on Identification and Characterization of a Novel Human Testis-Specific Kinase Substrate Gene Which Is Downregulated in Testicular Tumors Andreas Scorilas,*,† George M. Yousef,*,† Klaus Jung,‡ Ewa Rajpert-De Meyts,§ Stephan Carsten,‡ and Eleftherios P. Diamandis*,†,1 *Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada; †Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5G 1L5, Canada; ‡Department of Urology, University Hospital Charite, Humboldt University, Berlin, Germany; and §Department of Growth and Reproduction, Juliane Marie Centre, National University Hospital, Copenhagen, Denmark Received June 8, 2001 physiology, most probably in the process of spermato- By using the positional candidate gene approach, we genesis or spermiogenesis. © 2001 Academic Press identified a novel putative serine/threonine kinase Key Words: kinase substrates; testis-specific genes; substrate gene that maps to chromosome 19q13.3. gene mapping; gene characterization; TSKS; testis- Screening of expressed sequence tags and reverse specific kinase substrate; RRAS; IRF3; testicular transcription–polymerase chain reaction of total RNA cancer. from human tissues allowed us to establish the expres- sion of the gene and delineate its genomic organiza- tion (GenBank Accession No. AF200923). This gene (TSKS, for testis-specific kinase substrate) is com- Protein phosphorylation is the most common post- posed of 11 exons and 10 intervening introns and is translational protein modification in eukaryotes and a likely the human homolog of the mouse testis-specific fundamental mechanism for the direct or indirect con- serine kinase substrate gene. -
Nck Adaptor Proteins Link Nephrin at the Podocyte Slit Diaphragm to the Hippo Regulator WTIP
Nck Adaptor Proteins Link Nephrin at the Podocyte Slit Diaphragm to the Hippo Regulator WTIP by Ava Keyvani Chahi A Thesis presented to The University of Guelph In partial fulfilment of requirements for the degree of Master of Science in Molecular and Cellular Biology Guelph, Ontario, Canada © Ava Keyvani Chahi, December, 2014 ABSTRACT NCK ADAPTOR PROTEINS LINK NEPHRIN AT THE PODOCYTE SLIT DIAPHRAGM TO THE HIPPO REGULATOR WTIP Ava Keyvani Chahi Advisor: University of Guelph, 2014 Dr. Nina Jones Podocytes are specialized epithelial cells that contribute to the kidney blood filtration barrier. Their unique cytoskeletal architecture and other complex biological signals are largely maintained by a modified adherens junction known as the slit diaphragm (SD). A major component of the SD is the transmembrane protein nephrin, which upon tyrosine phosphorylation of the intracellular domain regulates actin remodeling and cell survival. Nck adaptor proteins are a critical component of the filtration barrier and connect nephrin to actin-remodeling proteins by binding phosphotyrosine residues and proline-rich motifs. Herein we identify a novel Nck binding partner, Wilm’s tumor interacting protein (WTIP). WTIP is a transcription regulator in podocytes, though Nck is not nuclear localized under conditions known to induce WTIP nuclear accumulation. However, we demonstrate that WTIP is recruited to nephrin, upon nephrin tyrosine phosphorylation by Src Family Kinases, in an Nck-dependent manner. WTIP is an evolutionarily conserved negative regulator of the Hippo kinase pathway, which inhibits the transcription factor Yap. Yap activity promotes podocyte survival. We show in mice that cannot recruit Nck to nephrin, and by extension WTIP, that Yap protein levels are downregulated. -
SHOC2–MRAS–PP1 Complex Positively Regulates RAF Activity and Contributes to Noonan Syndrome Pathogenesis
SHOC2–MRAS–PP1 complex positively regulates RAF activity and contributes to Noonan syndrome pathogenesis Lucy C. Younga,1, Nicole Hartiga,2, Isabel Boned del Ríoa, Sibel Saria, Benjamin Ringham-Terrya, Joshua R. Wainwrighta, Greg G. Jonesa, Frank McCormickb,3, and Pablo Rodriguez-Vicianaa,3 aUniversity College London Cancer Institute, University College London, London WC1E 6DD, United Kingdom; and bHelen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA 94158 Contributed by Frank McCormick, September 18, 2018 (sent for review November 22, 2017; reviewed by Deborah K. Morrison and Marc Therrien) Dephosphorylation of the inhibitory “S259” site on RAF kinases CRAF/RAF1 mutations are also frequently found in NS and (S259 on CRAF, S365 on BRAF) plays a key role in RAF activation. cluster around the S259 14-3-3 binding site, enhancing CRAF ac- The MRAS GTPase, a close relative of RAS oncoproteins, interacts tivity through disruption of 14-3-3 binding (8) and highlighting the with SHOC2 and protein phosphatase 1 (PP1) to form a heterotri- key role of this regulatory step in RAF–ERK pathway activation. meric holoenzyme that dephosphorylates this S259 RAF site. MRAS is a very close relative of the classical RAS oncoproteins MRAS and SHOC2 function as PP1 regulatory subunits providing (H-, N-, and KRAS, hereafter referred to collectively as “RAS”) the complex with striking specificity against RAF. MRAS also func- and shares most regulatory and effector interactions as well as tions as a targeting subunit as membrane localization is required transforming ability (9–11). However, MRAS also has specific for efficient RAF dephosphorylation and ERK pathway regulation functions of its own, and uniquely among RAS family GTPases, it in cells. -
DGCR8 Microprocessor Defect Characterizes Familial Multinodular Goiter with Schwannomatosis
The Journal of Clinical Investigation CLINICAL MEDICINE DGCR8 microprocessor defect characterizes familial multinodular goiter with schwannomatosis Barbara Rivera,1,2,3 Javad Nadaf,2,3 Somayyeh Fahiminiya,4 Maria Apellaniz-Ruiz,2,3,4,5 Avi Saskin,5,6 Anne-Sophie Chong,2,3 Sahil Sharma,7 Rabea Wagener,8 Timothée Revil,5,9 Vincenzo Condello,10 Zineb Harra,2,3 Nancy Hamel,4 Nelly Sabbaghian,2,3 Karl Muchantef,11,12 Christian Thomas,13 Leanne de Kock,2,3,5 Marie-Noëlle Hébert-Blouin,14 Angelia V. Bassenden,15 Hannah Rabenstein,8 Ozgur Mete,16,17 Ralf Paschke,18,19,20,21,22 Marc P. Pusztaszeri,23 Werner Paulus,13 Albert Berghuis,15 Jiannis Ragoussis,4,9 Yuri E. Nikiforov,10 Reiner Siebert,8 Steffen Albrecht,24 Robert Turcotte,25,26 Martin Hasselblatt,13 Marc R. Fabian,1,2,3,7,15 and William D. Foulkes1,2,3,4,5,6 1Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada. 2Lady Davis Institute for Medical Research and 3Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada. 4Cancer Research Program, McGill University Health Centre, Montreal, Quebec, Canada. 5Department of Human Genetics, McGill University, Montreal, Quebec, Canada. 6Division of Medical Genetics, Department of Medicine, McGill University Health Centre and Jewish General Hospital, Montreal, Quebec, Canada. 7Department of Experimental Medicine, McGill University, Montreal, Quebec, Canada. 8Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany. 9Génome Québec Innovation Centre, McGill University, Montreal, Quebec, Canada. 10Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA. 11Department of Diagnostic Radiology, McGill University, Montreal, Quebec, Canada. -
Identification of Transcriptional Mechanisms Downstream of Nf1 Gene Defeciency in Malignant Peripheral Nerve Sheath Tumors Daochun Sun Wayne State University
Wayne State University DigitalCommons@WayneState Wayne State University Dissertations 1-1-2012 Identification of transcriptional mechanisms downstream of nf1 gene defeciency in malignant peripheral nerve sheath tumors Daochun Sun Wayne State University, Follow this and additional works at: http://digitalcommons.wayne.edu/oa_dissertations Recommended Citation Sun, Daochun, "Identification of transcriptional mechanisms downstream of nf1 gene defeciency in malignant peripheral nerve sheath tumors" (2012). Wayne State University Dissertations. Paper 558. This Open Access Dissertation is brought to you for free and open access by DigitalCommons@WayneState. It has been accepted for inclusion in Wayne State University Dissertations by an authorized administrator of DigitalCommons@WayneState. IDENTIFICATION OF TRANSCRIPTIONAL MECHANISMS DOWNSTREAM OF NF1 GENE DEFECIENCY IN MALIGNANT PERIPHERAL NERVE SHEATH TUMORS by DAOCHUN SUN DISSERTATION Submitted to the Graduate School of Wayne State University, Detroit, Michigan in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY 2012 MAJOR: MOLECULAR BIOLOGY AND GENETICS Approved by: _______________________________________ Advisor Date _______________________________________ _______________________________________ _______________________________________ © COPYRIGHT BY DAOCHUN SUN 2012 All Rights Reserved DEDICATION This work is dedicated to my parents and my wife Ze Zheng for their continuous support and understanding during the years of my education. I could not achieve my goal without them. ii ACKNOWLEDGMENTS I would like to express tremendous appreciation to my mentor, Dr. Michael Tainsky. His guidance and encouragement throughout this project made this dissertation come true. I would also like to thank my committee members, Dr. Raymond Mattingly and Dr. John Reiners Jr. for their sustained attention to this project during the monthly NF1 group meetings and committee meetings, Dr. -
The Human Genome Project
TO KNOW OURSELVES ❖ THE U.S. DEPARTMENT OF ENERGY AND THE HUMAN GENOME PROJECT JULY 1996 TO KNOW OURSELVES ❖ THE U.S. DEPARTMENT OF ENERGY AND THE HUMAN GENOME PROJECT JULY 1996 Contents FOREWORD . 2 THE GENOME PROJECT—WHY THE DOE? . 4 A bold but logical step INTRODUCING THE HUMAN GENOME . 6 The recipe for life Some definitions . 6 A plan of action . 8 EXPLORING THE GENOMIC LANDSCAPE . 10 Mapping the terrain Two giant steps: Chromosomes 16 and 19 . 12 Getting down to details: Sequencing the genome . 16 Shotguns and transposons . 20 How good is good enough? . 26 Sidebar: Tools of the Trade . 17 Sidebar: The Mighty Mouse . 24 BEYOND BIOLOGY . 27 Instrumentation and informatics Smaller is better—And other developments . 27 Dealing with the data . 30 ETHICAL, LEGAL, AND SOCIAL IMPLICATIONS . 32 An essential dimension of genome research Foreword T THE END OF THE ROAD in Little has been rapid, and it is now generally agreed Cottonwood Canyon, near Salt that this international project will produce Lake City, Alta is a place of the complete sequence of the human genome near-mythic renown among by the year 2005. A skiers. In time it may well And what is more important, the value assume similar status among molecular of the project also appears beyond doubt. geneticists. In December 1984, a conference Genome research is revolutionizing biology there, co-sponsored by the U.S. Department and biotechnology, and providing a vital of Energy, pondered a single question: Does thrust to the increasingly broad scope of the modern DNA research offer a way of detect- biological sciences. -
S41467-021-24841-Y.Pdf
ARTICLE https://doi.org/10.1038/s41467-021-24841-y OPEN Integrative oncogene-dependency mapping identifies RIT1 vulnerabilities and synergies in lung cancer Athea Vichas1,10, Amanda K. Riley 1,2,10, Naomi T. Nkinsi1, Shriya Kamlapurkar1, Phoebe C. R. Parrish 1,3, April Lo1,3, Fujiko Duke4, Jennifer Chen4, Iris Fung4, Jacqueline Watson4, Matthew Rees 4, Austin M. Gabel 3,5,6,7, James D. Thomas 6,7, Robert K. Bradley 3,6,7, John K. Lee1, Emily M. Hatch 1,7, ✉ Marina K. Baine8, Natasha Rekhtman8, Marc Ladanyi8, Federica Piccioni4,9 & Alice H. Berger 1,3 1234567890():,; CRISPR-based cancer dependency maps are accelerating advances in cancer precision medicine, but adequate functional maps are limited to the most common oncogenes. To identify opportunities for therapeutic intervention in other rarer subsets of cancer, we investigate the oncogene-specific dependencies conferred by the lung cancer oncogene, RIT1. Here, genome-wide CRISPR screening in KRAS, EGFR, and RIT1-mutant isogenic lung cancer cells identifies shared and unique vulnerabilities of each oncogene. Combining this genetic data with small-molecule sensitivity profiling, we identify a unique vulnerability of RIT1- mutant cells to loss of spindle assembly checkpoint regulators. Oncogenic RIT1M90I weakens the spindle assembly checkpoint and perturbs mitotic timing, resulting in sensitivity to Aurora A inhibition. In addition, we observe synergy between mutant RIT1 and activation of YAP1 in multiple models and frequent nuclear overexpression of YAP1 in human primary RIT1-mutant lung tumors. These results provide a genome-wide atlas of oncogenic RIT1 functional inter- actions and identify components of the RAS pathway, spindle assembly checkpoint, and Hippo/YAP1 network as candidate therapeutic targets in RIT1-mutant lung cancer. -
Alterations of the Interactome of Bcl-2 Proteins in Breast Cancer at the Transcriptional, Mutational and Structural Level
RESEARCH ARTICLE Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level Simon Mathis Kønig1, Vendela Rissler1, Thilde Terkelsen1, Matteo Lambrughi1, 1,2 Elena PapaleoID * 1 Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark, a1111111111 2 Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark a1111111111 a1111111111 * [email protected] a1111111111 a1111111111 Abstract Apoptosis is an essential defensive mechanism against tumorigenesis. Proteins of the B- OPEN ACCESS cell lymphoma-2 (Bcl-2) family regulate programmed cell death by the mitochondrial apopto- sis pathway. In response to intracellular stress, the apoptotic balance is governed by inter- Citation: Kønig SM, Rissler V, Terkelsen T, Lambrughi M, Papaleo E (2019) Alterations of the actions of three distinct subgroups of proteins; the activator/sensitizer BH3 (Bcl-2 homology interactome of Bcl-2 proteins in breast cancer at 3)-only proteins, the pro-survival, and the pro-apoptotic executioner proteins. Changes in the transcriptional, mutational and structural level. expression levels, stability, and functional impairment of pro-survival proteins can lead to an PLoS Comput Biol 15(12): e1007485. https://doi. imbalance in tissue homeostasis. Their overexpression or hyperactivation can result in org/10.1371/journal.pcbi.1007485 oncogenic effects. Pro-survival Bcl-2 family members carry out their function by binding the Editor: Igor N. Berezovsky, A�STAR Singapore, BH3 short linear motif of pro-apoptotic proteins in a modular way, creating a complex net- SINGAPORE work of protein-protein interactions. Their dysfunction enables cancer cells to evade cell Received: July 8, 2019 death. -
Alterations of the Interactome of Bcl-2 Proteins in Breast Cancer at the Transcriptional, Mutational and Structural Level
Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level Konig, Simon Mathis; Rissler, Vendela; Terkelsen, Thilde; Lambrughi, Matteo; Papaleo, Elena Published in: P L o S One DOI: 10.1371/journal.pcbi.1007485 Publication date: 2019 Document version Publisher's PDF, also known as Version of record Citation for published version (APA): Konig, S. M., Rissler, V., Terkelsen, T., Lambrughi, M., & Papaleo, E. (2019). Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level. P L o S One, 15(12), [e1007485]. https://doi.org/10.1371/journal.pcbi.1007485 Download date: 25. sep.. 2021 RESEARCH ARTICLE Alterations of the interactome of Bcl-2 proteins in breast cancer at the transcriptional, mutational and structural level Simon Mathis Kønig1, Vendela Rissler1, Thilde Terkelsen1, Matteo Lambrughi1, 1,2 Elena PapaleoID * 1 Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark, a1111111111 2 Translational Disease Systems Biology, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research University of Copenhagen, Copenhagen, Denmark a1111111111 a1111111111 * [email protected] a1111111111 a1111111111 Abstract Apoptosis is an essential defensive mechanism against tumorigenesis. Proteins of the B- OPEN ACCESS cell lymphoma-2 (Bcl-2) family regulate programmed cell death by the mitochondrial apopto- sis pathway. In response to intracellular stress, the apoptotic balance is governed by inter- Citation: Kønig SM, Rissler V, Terkelsen T, Lambrughi M, Papaleo E (2019) Alterations of the actions of three distinct subgroups of proteins; the activator/sensitizer BH3 (Bcl-2 homology interactome of Bcl-2 proteins in breast cancer at 3)-only proteins, the pro-survival, and the pro-apoptotic executioner proteins. -
Human RRAS (1-215, His-Tag) - Purified
OriGene Technologies, Inc. OriGene Technologies GmbH 9620 Medical Center Drive, Ste 200 Schillerstr. 5 Rockville, MD 20850 32052 Herford UNITED STATES GERMANY Phone: +1-888-267-4436 Phone: +49-5221-34606-0 Fax: +1-301-340-8606 Fax: +49-5221-34606-11 [email protected] [email protected] AR09434PU-L Human RRAS (1-215, His-tag) - Purified Alternate names: R-Ras, Ras-related protein R-Ras Quantity: 0.25 mg Concentration: 0.5 mg/ml (determined by Bradford assay) Background: RRAS, also known as ras-related protein R-Ras, belongs to the Ras family which functions in signal transduction pathways. This protein has been shown to interact with RASSF5, NCK1, Bcl-2, ARAF and RALGDS. RRAS can bind GTP and GDP, and it has intrinsic GTPase activity. It also regulates the organization of the actin cytoskeleton. Uniprot ID: P10301 NCBI: NP_006261 GeneID: 6237 Species: Human Source: E. coli Format: State: Liquid purified protein Purity: >85% by SDS - PAGE Buffer System: 20 mM Tris-HCl buffer (pH 8.0) containing 10% glycerol, 0.1 M NaCl Description: Recombinant RRAS protein, fused to His-tag at N-terminus, was expressed in E.coli and purified by using conventional chromatography techniques. AA Sequence: MGSSHHHHHH SSGLVPRGSH MSSGAASGTG RGRPRGGGPG PGDPPPSETH KLVVVGGGGV GKSALTIQFI QSYFVSDYDP TIEDSYTKIC SVDGIPARLD ILDTAGQEEF GAMREQYMRA GHGFLLVFAI NDRQSFNEVG KLFTQILRVK DRDDFPVVLV GNKADLESQR QVPRSEASAF GASHHVAYFE ASAKLRLNVD EAFEQLVRAV RKYQEQELPP SPPSAPRKKG GGCPC Molecular weight: 25.3 kDa (235 aa), confirmed by MALDI-TOF Storage: Store undiluted at 2-8°C for up to two weeks or (in aliquots) at -20°C or -70°C for longer. Avoid repeated freezing and thawing. -
Connecting Myelin-Related and Synaptic Dysfunction In
www.nature.com/scientificreports OPEN Connecting myelin-related and synaptic dysfunction in schizophrenia with SNP-rich Received: 24 October 2016 Accepted: 27 February 2017 gene expression hubs Published: 07 April 2017 Hedi Hegyi Combining genome-wide mapping of SNP-rich regions in schizophrenics and gene expression data in all brain compartments across the human life span revealed that genes with promoters most frequently mutated in schizophrenia are expression hubs interacting with far more genes than the rest of the genome. We summed up the differentially methylated “expression neighbors” of genes that fall into one of 108 distinct schizophrenia-associated loci with high number of SNPs. Surprisingly, the number of expression neighbors of the genes in these loci were 35 times higher for the positively correlating genes (32 times higher for the negatively correlating ones) than for the rest of the ~16000 genes. While the genes in the 108 loci have little known impact in schizophrenia, we identified many more known schizophrenia-related important genes with a high degree of connectedness (e.g. MOBP, SYNGR1 and DGCR6), validating our approach. Both the most connected positive and negative hubs affected synapse-related genes the most, supporting the synaptic origin of schizophrenia. At least half of the top genes in both the correlating and anti-correlating categories are cancer-related, including oncogenes (RRAS and ALDOA), providing further insight into the observed inverse relationship between the two diseases. Gene expression correlation, protein-protein interaction and other high-throughput experiments in the post-genomic era have revealed that genes tend to form complex, scale-free networks where most genes have a few connections with others and a few have a high number of interactions, commonly referred to as “hubs”, estab- lishing them as important central genes in these gene networks1. -
The Human Gene Connectome As a Map of Short Cuts for Morbid Allele Discovery
The human gene connectome as a map of short cuts for morbid allele discovery Yuval Itana,1, Shen-Ying Zhanga,b, Guillaume Vogta,b, Avinash Abhyankara, Melina Hermana, Patrick Nitschkec, Dror Friedd, Lluis Quintana-Murcie, Laurent Abela,b, and Jean-Laurent Casanovaa,b,f aSt. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065; bLaboratory of Human Genetics of Infectious Diseases, Necker Branch, Paris Descartes University, Institut National de la Santé et de la Recherche Médicale U980, Necker Medical School, 75015 Paris, France; cPlateforme Bioinformatique, Université Paris Descartes, 75116 Paris, France; dDepartment of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; eUnit of Human Evolutionary Genetics, Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Institut Pasteur, F-75015 Paris, France; and fPediatric Immunology-Hematology Unit, Necker Hospital for Sick Children, 75015 Paris, France Edited* by Bruce Beutler, University of Texas Southwestern Medical Center, Dallas, TX, and approved February 15, 2013 (received for review October 19, 2012) High-throughput genomic data reveal thousands of gene variants to detect a single mutated gene, with the other polymorphic genes per patient, and it is often difficult to determine which of these being of less interest. This goes some way to explaining why, variants underlies disease in a given individual. However, at the despite the abundance of NGS data, the discovery of disease- population level, there may be some degree of phenotypic homo- causing alleles from such data remains somewhat limited. geneity, with alterations of specific physiological pathways under- We developed the human gene connectome (HGC) to over- come this problem.