Tripartite Motif Proteins - a Protein Family Strongly Linked to Cancer
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Educational Paper Ciliopathies
Eur J Pediatr (2012) 171:1285–1300 DOI 10.1007/s00431-011-1553-z REVIEW Educational paper Ciliopathies Carsten Bergmann Received: 11 June 2011 /Accepted: 3 August 2011 /Published online: 7 September 2011 # The Author(s) 2011. This article is published with open access at Springerlink.com Abstract Cilia are antenna-like organelles found on the (NPHP) . Ivemark syndrome . Meckel syndrome (MKS) . surface of most cells. They transduce molecular signals Joubert syndrome (JBTS) . Bardet–Biedl syndrome (BBS) . and facilitate interactions between cells and their Alstrom syndrome . Short-rib polydactyly syndromes . environment. Ciliary dysfunction has been shown to Jeune syndrome (ATD) . Ellis-van Crefeld syndrome (EVC) . underlie a broad range of overlapping, clinically and Sensenbrenner syndrome . Primary ciliary dyskinesia genetically heterogeneous phenotypes, collectively (Kartagener syndrome) . von Hippel-Lindau (VHL) . termed ciliopathies. Literally, all organs can be affected. Tuberous sclerosis (TSC) . Oligogenic inheritance . Modifier. Frequent cilia-related manifestations are (poly)cystic Mutational load kidney disease, retinal degeneration, situs inversus, cardiac defects, polydactyly, other skeletal abnormalities, and defects of the central and peripheral nervous Introduction system, occurring either isolated or as part of syn- dromes. Characterization of ciliopathies and the decisive Defective cellular organelles such as mitochondria, perox- role of primary cilia in signal transduction and cell isomes, and lysosomes are well-known -
Ciliopathiesneuromuscularciliopathies Disorders Disorders Ciliopathiesciliopathies
NeuromuscularCiliopathiesNeuromuscularCiliopathies Disorders Disorders CiliopathiesCiliopathies AboutAbout EGL EGL Genet Geneticsics EGLEGL Genetics Genetics specializes specializes in ingenetic genetic diagnostic diagnostic testing, testing, with with ne nearlyarly 50 50 years years of of clinical clinical experience experience and and board-certified board-certified labor laboratoryatory directorsdirectors and and genetic genetic counselors counselors reporting reporting out out cases. cases. EGL EGL Genet Geneticsics offers offers a combineda combined 1000 1000 molecular molecular genetics, genetics, biochemical biochemical genetics,genetics, and and cytogenetics cytogenetics tests tests under under one one roof roof and and custom custom test testinging for for all all medically medically relevant relevant genes, genes, for for domestic domestic andand international international clients. clients. EquallyEqually important important to to improving improving patient patient care care through through quality quality genetic genetic testing testing is is the the contribution contribution EGL EGL Genetics Genetics makes makes back back to to thethe scientific scientific and and medical medical communities. communities. EGL EGL Genetics Genetics is is one one of of only only a afew few clinical clinical diagnostic diagnostic laboratories laboratories to to openly openly share share data data withwith the the NCBI NCBI freely freely available available public public database database ClinVar ClinVar (>35,000 (>35,000 variants variants on on >1700 >1700 genes) genes) and and is isalso also the the only only laboratory laboratory with with a a frefree oen olinnlein dea dtabtaabsaes (eE m(EVmCVlaCslas)s,s f)e, afetuatruinrgin ag vaa vraiarniatn ctl acslasisfiscifiactiaotino sne saercahrc ahn adn rde rpeoprot rrte rqeuqeuset sint tinetrefarcfaec, ew, hwichhic fha cfailcitialiteatse rsa praidp id interactiveinteractive curation curation and and reporting reporting of of variants. -
Analysis of Trans Esnps Infers Regulatory Network Architecture
Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2014 Anat Kreimer All rights reserved ABSTRACT Analysis of trans eSNPs infers regulatory network architecture Anat Kreimer eSNPs are genetic variants associated with transcript expression levels. The characteristics of such variants highlight their importance and present a unique opportunity for studying gene regulation. eSNPs affect most genes and their cell type specificity can shed light on different processes that are activated in each cell. They can identify functional variants by connecting SNPs that are implicated in disease to a molecular mechanism. Examining eSNPs that are associated with distal genes can provide insights regarding the inference of regulatory networks but also presents challenges due to the high statistical burden of multiple testing. Such association studies allow: simultaneous investigation of many gene expression phenotypes without assuming any prior knowledge and identification of unknown regulators of gene expression while uncovering directionality. This thesis will focus on such distal eSNPs to map regulatory interactions between different loci and expose the architecture of the regulatory network defined by such interactions. We develop novel computational approaches and apply them to genetics-genomics data in human. We go beyond pairwise interactions to define network motifs, including regulatory modules and bi-fan structures, showing them to be prevalent in real data and exposing distinct attributes of such arrangements. We project eSNP associations onto a protein-protein interaction network to expose topological properties of eSNPs and their targets and highlight different modes of distal regulation. -
Functional Roles of Bromodomain Proteins in Cancer
cancers Review Functional Roles of Bromodomain Proteins in Cancer Samuel P. Boyson 1,2, Cong Gao 3, Kathleen Quinn 2,3, Joseph Boyd 3, Hana Paculova 3 , Seth Frietze 3,4,* and Karen C. Glass 1,2,4,* 1 Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; [email protected] 2 Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA; [email protected] 3 Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; [email protected] (C.G.); [email protected] (J.B.); [email protected] (H.P.) 4 University of Vermont Cancer Center, Burlington, VT 05405, USA * Correspondence: [email protected] (S.F.); [email protected] (K.C.G.) Simple Summary: This review provides an in depth analysis of the role of bromodomain-containing proteins in cancer development. As readers of acetylated lysine on nucleosomal histones, bromod- omain proteins are poised to activate gene expression, and often promote cancer progression. We examined changes in gene expression patterns that are observed in bromodomain-containing proteins and associated with specific cancer types. We also mapped the protein–protein interaction network for the human bromodomain-containing proteins, discuss the cellular roles of these epigenetic regu- lators as part of nine different functional groups, and identify bromodomain-specific mechanisms in cancer development. Lastly, we summarize emerging strategies to target bromodomain proteins in cancer therapy, including those that may be essential for overcoming resistance. Overall, this review provides a timely discussion of the different mechanisms of bromodomain-containing pro- Citation: Boyson, S.P.; Gao, C.; teins in cancer, and an updated assessment of their utility as a therapeutic target for a variety of Quinn, K.; Boyd, J.; Paculova, H.; cancer subtypes. -
Genome Wide Association Study of Response to Interval and Continuous Exercise Training: the Predict‑HIIT Study Camilla J
Williams et al. J Biomed Sci (2021) 28:37 https://doi.org/10.1186/s12929-021-00733-7 RESEARCH Open Access Genome wide association study of response to interval and continuous exercise training: the Predict-HIIT study Camilla J. Williams1†, Zhixiu Li2†, Nicholas Harvey3,4†, Rodney A. Lea4, Brendon J. Gurd5, Jacob T. Bonafglia5, Ioannis Papadimitriou6, Macsue Jacques6, Ilaria Croci1,7,20, Dorthe Stensvold7, Ulrik Wislof1,7, Jenna L. Taylor1, Trishan Gajanand1, Emily R. Cox1, Joyce S. Ramos1,8, Robert G. Fassett1, Jonathan P. Little9, Monique E. Francois9, Christopher M. Hearon Jr10, Satyam Sarma10, Sylvan L. J. E. Janssen10,11, Emeline M. Van Craenenbroeck12, Paul Beckers12, Véronique A. Cornelissen13, Erin J. Howden14, Shelley E. Keating1, Xu Yan6,15, David J. Bishop6,16, Anja Bye7,17, Larisa M. Haupt4, Lyn R. Grifths4, Kevin J. Ashton3, Matthew A. Brown18, Luciana Torquati19, Nir Eynon6 and Jef S. Coombes1* Abstract Background: Low cardiorespiratory ftness (V̇O2peak) is highly associated with chronic disease and mortality from all causes. Whilst exercise training is recommended in health guidelines to improve V̇O2peak, there is considerable inter-individual variability in the V̇O2peak response to the same dose of exercise. Understanding how genetic factors contribute to V̇O2peak training response may improve personalisation of exercise programs. The aim of this study was to identify genetic variants that are associated with the magnitude of V̇O2peak response following exercise training. Methods: Participant change in objectively measured V̇O2peak from 18 diferent interventions was obtained from a multi-centre study (Predict-HIIT). A genome-wide association study was completed (n 507), and a polygenic predictor score (PPS) was developed using alleles from single nucleotide polymorphisms= (SNPs) signifcantly associ- –5 ated (P < 1 10 ) with the magnitude of V̇O2peak response. -
Knock-In Mice Limits Responses to Muramyl Dipeptide in Alters
Blau Syndrome−Associated Nod2 Mutation Alters Expression of Full-Length NOD2 and Limits Responses to Muramyl Dipeptide in Knock-in Mice This information is current as of September 28, 2021. Jae Dugan, Eric Griffiths, Paige Snow, Holly Rosenzweig, Ellen Lee, Brieanna Brown, Daniel W. Carr, Carlos Rose, James Rosenbaum and Michael P. Davey J Immunol published online 26 November 2014 http://www.jimmunol.org/content/early/2014/11/26/jimmun Downloaded from ol.1402330 Supplementary http://www.jimmunol.org/content/suppl/2014/11/26/jimmunol.140233 http://www.jimmunol.org/ Material 0.DCSupplemental Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists by guest on September 28, 2021 • 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 © 2014 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Published November 26, 2014, doi:10.4049/jimmunol.1402330 The Journal of Immunology Blau Syndrome–Associated Nod2 Mutation Alters Expression of Full-Length NOD2 and Limits Responses to Muramyl Dipeptide in Knock-in Mice Jae Dugan,*,† Eric Griffiths,* Paige Snow,* Holly Rosenzweig,*,‡,x Ellen Lee,‡ Brieanna Brown,‡ Daniel W. -
Trim33 Is Essential for Macrophage and Neutrophil Mobilization To
© 2017. Published by The Company of Biologists Ltd | Journal of Cell Science (2017) 130, 2797-2807 doi:10.1242/jcs.203471 RESEARCH ARTICLE Trim33 is essential for macrophage and neutrophil mobilization to developmental or inflammatory cues Doris Lou Demy1,2,*, Muriel Tauzin1,2,‡, Mylenè Lancino1,2,Véronique Le Cabec3,4, Michael Redd5, Emi Murayama1,2, Isabelle Maridonneau-Parini3,4, Nikolaus Trede5 and Philippe Herbomel1,2,§ ABSTRACT first organs to become colonized in this way in mammalian and Macrophages infiltrate and establish in developing organs from an avian embryogenesis is the central nervous system (CNS) (Sorokin early stage, often before these have become vascularized. Similarly, et al., 1992; Cuadros et al., 1993), and at least in mammals, the leukocytes, in general, can quickly migrate through tissues to any site resulting resident macrophages then comprise the microglia for the of wounding. This unique capacity is rooted in their characteristic whole life of the animal (Kierdorf et al., 2015). The molecular and amoeboid motility, the genetic basis of which is poorly understood. cellular determinants of this early colonization are mostly unknown. Trim33 (also known as Tif1-γ), a nuclear protein that associates In the zebrafish embryo, primitive macrophages born in the yolk sac with specific DNA-binding transcription factors to modulate gene colonize the tissues of the embryo, notably the head, brain and expression, has been found to be mainly involved in hematopoiesis retina, in a pattern very similar to that seen in mammalian and avian and gene regulation mediated by TGF-β. Here, we have discovered embryos (Herbomel et al., 2001). The M-CSF/CSF-1 receptor that in Trim33-deficient zebrafish embryos, primitive macrophages are (CSF1-R) was found to be dispensable for the differentiation of unable to colonize the central nervous system to become microglia. -
Genome-Wide Analysis of Transcriptional Bursting-Induced Noise in Mammalian Cells
bioRxiv preprint doi: https://doi.org/10.1101/736207; this version posted August 15, 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. Title: Genome-wide analysis of transcriptional bursting-induced noise in mammalian cells Authors: Hiroshi Ochiai1*, Tetsutaro Hayashi2, Mana Umeda2, Mika Yoshimura2, Akihito Harada3, Yukiko Shimizu4, Kenta Nakano4, Noriko Saitoh5, Hiroshi Kimura6, Zhe Liu7, Takashi Yamamoto1, Tadashi Okamura4,8, Yasuyuki Ohkawa3, Itoshi Nikaido2,9* Affiliations: 1Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-0046, Japan 2Laboratory for Bioinformatics Research, RIKEN BDR, Wako, Saitama, 351-0198, Japan 3Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-0054, Japan 4Department of Animal Medicine, National Center for Global Health and Medicine (NCGM), Tokyo, 812-0054, Japan 5Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo, 135-8550, Japan 6Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan 7Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA 8Section of Animal Models, Department of Infectious Diseases, National Center for Global Health and Medicine (NCGM), Tokyo, 812-0054, Japan 9Bioinformatics Course, Master’s/Doctoral Program in Life Science Innovation (T-LSI), School of Integrative and Global Majors (SIGMA), University of Tsukuba, Wako, 351-0198, Japan *Corresponding authors Corresponding authors e-mail addresses Hiroshi Ochiai, [email protected] Itoshi Nikaido, [email protected] bioRxiv preprint doi: https://doi.org/10.1101/736207; this version posted August 15, 2019. -
Ciliopathies Gene Panel
Ciliopathies Gene Panel Contact details Introduction Molecular Genetics Service The ciliopathies are a heterogeneous group of conditions with considerable phenotypic overlap. Level 6, Barclay House These inherited diseases are caused by defects in cilia; hair-like projections present on most 37 Queen Square cells, with roles in key human developmental processes via their motility and signalling functions. Ciliopathies are often lethal and multiple organ systems are affected. Ciliopathies are London, WC1N 3BH united in being genetically heterogeneous conditions and the different subtypes can share T +44 (0) 20 7762 6888 many clinical features, predominantly cystic kidney disease, but also retinal, respiratory, F +44 (0) 20 7813 8578 skeletal, hepatic and neurological defects in addition to metabolic defects, laterality defects and polydactyly. Their clinical variability can make ciliopathies hard to recognise, reflecting the ubiquity of cilia. Gene panels currently offer the best solution to tackling mutational analysis of Samples required genetically heterogeneous conditions such as the ciliopathies. Ciliopathies affect approximately 5ml venous blood in plastic EDTA 1:2,000 births. bottles (>1ml from neonates) Ciliopathies are generally inherited in an autosomal recessive manner, with some autosomal Prenatal testing must be arranged dominant and X-linked exceptions. in advance, through a Clinical Genetics department if possible. Referrals Amniotic fluid or CV samples Patients presenting with a ciliopathy; due to the phenotypic variability this could be a diverse set should be sent to Cytogenetics for of features. For guidance contact the laboratory or Dr Hannah Mitchison dissecting and culturing, with ([email protected]) / Prof Phil Beales ([email protected]) instructions to forward the sample to the Regional Molecular Genetics Referrals will be accepted from clinical geneticists and consultants in nephrology, metabolic, laboratory for analysis respiratory and retinal diseases. -
Detection of TRIM32 Deletions in LGMD Patients Analyzed by a Combined Strategy of CGH Array and Massively Parallel Sequencing
European Journal of Human Genetics (2015) 23, 929–934 & 2015 Macmillan Publishers Limited All rights reserved 1018-4813/15 www.nature.com/ejhg ARTICLE Detection of TRIM32 deletions in LGMD patients analyzed by a combined strategy of CGH array and massively parallel sequencing Juliette Nectoux1,2,14, Rafael de Cid3,14,15, Sylvain Baulande4, France Leturcq1,5, Jon Andoni Urtizberea6, Isabelle Penisson-Besnier7, Aleksandra Nadaj-Pakleza7, Carinne Roudaut3, Audrey Criqui4, Lucie Orhant1, Delphine Peyroulan8, Raba Ben Yaou5, Isabelle Nelson5, Anna Maria Cobo6, Marie-Christine Arné-Bes9, Emmanuelle Uro-Coste9, Patrick Nitschke10, Mireille Claustres8,11, Gisèle Bonne5,12, Nicolas Lévy13, Jamel Chelly1,2, Isabelle Richard3 and Mireille Cossée*,8,11 Defects in TRIM32 were reported in limb-girdle muscular dystrophy type 2H (LGMD2H), sarcotubular myopathies (STM) and in Bardet-Biedl syndrome. Few cases have been described to date in LGMD2H/STM, but this gene is not systematically analysed because of the absence of specific signs and difficulties in protein analysis. By using high-throughput variants screening techniques, we identified variants in TRIM32 in two patients presenting nonspecific LGMD. We report the first case of total inactivation by homozygous deletion of the entire TRIM32 gene. Of interest, the deletion removes part of the ASTN2 gene, a large gene in which TRIM32 is nested. Despite the total TRIM32 gene inactivation, the patient does not present a more severe phenotype. However, he developed a mild progressive cognitive impairment that may be related to the loss of function of ASTN2 because association between ASTN2 heterozygous deletions and neurobehavioral disorders was previously reported. Regarding genomic characteristics at breakpoint of the deleted regions of TRIM32, we found a high density of repeated elements, suggesting a possible hotspot. -
TRIM68 Antibody (Monoclonal) (M01) Mouse Monoclonal Antibody Raised Against a Partial Recombinant TRIM68
10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 TRIM68 Antibody (monoclonal) (M01) Mouse monoclonal antibody raised against a partial recombinant TRIM68. Catalog # AT4362a Specification TRIM68 Antibody (monoclonal) (M01) - Product Information Application WB, E Primary Accession Q6AZZ1 Other Accession NM_018073 Reactivity Human Host mouse Clonality Monoclonal Isotype IgG2a Kappa Calculated MW 56259 TRIM68 Antibody (monoclonal) (M01) - Additional Information Antibody Reactive Against Recombinant Protein.Western Blot detection against Gene ID 55128 Immunogen (36.74 KDa) . Other Names E3 ubiquitin-protein ligase TRIM68, 632-, RING finger protein 137, SSA protein SS-56, SS-56, Tripartite motif-containing protein 68, TRIM68, GC109, RNF137, SS56 Target/Specificity TRIM68 (NP_060543, 181 a.a. ~ 280 a.a) partial recombinant protein with GST tag. MW of the GST tag alone is 26 KDa. Dilution Detection limit for recombinant GST tagged WB~~1:500~1000 TRIM68 is approximately 0.3ng/ml as a capture antibody. Format Clear, colorless solution in phosphate buffered saline, pH 7.2 . TRIM68 Antibody (monoclonal) (M01) - Background Storage Store at -20°C or lower. Aliquot to avoid The protein encoded by this gene contains a repeated freezing and thawing. RING finger domain, a motif present in a variety of functionally distinct proteins and Precautions known to be involved in protein-protein and TRIM68 Antibody (monoclonal) (M01) is for protein-DNA interactions. This gene is research use only and not for use in expressed in many cancer cell lines. Its diagnostic or therapeutic procedures. expression in normal tissues, however, was found to be restricted to prostate. -
TAZ-CAMTA1 and YAP-TFE3 Alter the TAZ/YAP Transcriptome By
RESEARCH ARTICLE TAZ-CAMTA1 and YAP-TFE3 alter the TAZ/YAP transcriptome by recruiting the ATAC histone acetyltransferase complex Nicole Merritt1†, Keith Garcia1,2†, Dushyandi Rajendran3, Zhen-Yuan Lin3, Xiaomeng Zhang4, Katrina A Mitchell4,5, Nicholas Borcherding6, Colleen Fullenkamp1, Michael S Chimenti7, Anne-Claude Gingras3, Kieran F Harvey4,5,8, Munir R Tanas1,2,9,10* 1Department of Pathology, University of Iowa, Iowa City, United States; 2Cancer Biology Graduate Program, University of Iowa, Iowa City, United States; 3Lunenfeld- Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, United States; 4Peter MacCallum Cancer Centre, Melbourne, Australia; 5Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Australia; 6Department of Pathology and Immunology, Washington University, St. Louis, United States; 7Iowa Institute of Human Genetics, Carver College of Medicine, University of Iowa, Iowa City, United States; 8Department of Anatomy and Developmental Biology and Biomedicine Discovery Institute, Monash University, Clayton, Australia; 9Holden Comprehensive Cancer Center, University of Iowa, Iowa City, United States; 10Pathology and Laboratory Medicine, Veterans Affairs Medical Center, Iowa City, United States *For correspondence: Abstract Epithelioid hemangioendothelioma (EHE) is a vascular sarcoma that metastasizes early [email protected] in its clinical course and lacks an effective medical therapy. The TAZ-CAMTA1 and YAP-TFE3 fusion proteins are chimeric transcription factors and initiating oncogenic drivers of EHE. A combined †These authors contributed proteomic/genetic screen in human cell lines identified YEATS2 and ZZZ3, components of the equally to this work Ada2a-containing histone acetyltransferase (ATAC) complex, as key interactors of both fusion Competing interests: The proteins despite the dissimilarity of the C terminal fusion partners CAMTA1 and TFE3.