Biomarker Discovery for Chronic Liver Diseases by Multi-Omics
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Complement Factor H Deficiency and Endocapillary Glomerulonephritis Due to Paternal Isodisomy and a Novel Factor H Mutation
Genes and Immunity (2011) 12, 90–99 & 2011 Macmillan Publishers Limited All rights reserved 1466-4879/11 www.nature.com/gene ORIGINAL ARTICLE Complement factor H deficiency and endocapillary glomerulonephritis due to paternal isodisomy and a novel factor H mutation L Schejbel1, IM Schmidt2, M Kirchhoff3, CB Andersen4, HV Marquart1, P Zipfel5 and P Garred1 1Department of Clinical Immunology, Laboratory of Molecular Medicine, Rigshospitalet, Copenhagen, Denmark; 2Department of Pediatrics, Rigshospitalet, Copenhagen, Denmark; 3Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark; 4Department of Pathology, Rigshospitalet, Copenhagen, Denmark and 5Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany Complement factor H (CFH) is a regulator of the alternative complement activation pathway. Mutations in the CFH gene are associated with atypical hemolytic uremic syndrome, membranoproliferative glomerulonephritis type II and C3 glomerulonephritis. Here, we report a 6-month-old CFH-deficient child presenting with endocapillary glomerulonephritis rather than membranoproliferative glomerulonephritis (MPGN) or C3 glomerulonephritis. Sequence analyses showed homozygosity for a novel CFH missense mutation (Pro139Ser) associated with severely decreased CFH plasma concentration (o6%) but normal mRNA splicing and expression. The father was heterozygous carrier of the mutation, but the mother was a non-carrier. Thus, a large deletion in the maternal CFH locus or uniparental isodisomy was suspected. Polymorphic markers across chromosome 1 showed homozygosity for the paternal allele in all markers and a lack of the maternal allele in six informative markers. This combined with a comparative genomic hybridization assay demonstrated paternal isodisomy. Uniparental isodisomy increases the risk of homozygous variations in other genes on the affected chromosome. -
Mitoxplorer, a Visual Data Mining Platform To
mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations Annie Yim, Prasanna Koti, Adrien Bonnard, Fabio Marchiano, Milena Dürrbaum, Cecilia Garcia-Perez, José Villaveces, Salma Gamal, Giovanni Cardone, Fabiana Perocchi, et al. To cite this version: Annie Yim, Prasanna Koti, Adrien Bonnard, Fabio Marchiano, Milena Dürrbaum, et al.. mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dy- namics and mutations. Nucleic Acids Research, Oxford University Press, 2020, 10.1093/nar/gkz1128. hal-02394433 HAL Id: hal-02394433 https://hal-amu.archives-ouvertes.fr/hal-02394433 Submitted on 4 Dec 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. Distributed under a Creative Commons Attribution| 4.0 International License Nucleic Acids Research, 2019 1 doi: 10.1093/nar/gkz1128 Downloaded from https://academic.oup.com/nar/advance-article-abstract/doi/10.1093/nar/gkz1128/5651332 by Bibliothèque de l'université la Méditerranée user on 04 December 2019 mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations Annie Yim1,†, Prasanna Koti1,†, Adrien Bonnard2, Fabio Marchiano3, Milena Durrbaum¨ 1, Cecilia Garcia-Perez4, Jose Villaveces1, Salma Gamal1, Giovanni Cardone1, Fabiana Perocchi4, Zuzana Storchova1,5 and Bianca H. -
A Bioinformatics Tool for Prioritizing Biological Leads from ‘Omics Data Using Literature Retrieval and Data Mining
International Journal of Molecular Sciences Article OmixLitMiner: A Bioinformatics Tool for Prioritizing Biological Leads from ‘Omics Data Using Literature Retrieval and Data Mining Pascal Steffen 1,2,3 , Jemma Wu 2, Shubhang Hariharan 1, Hannah Voss 3, Vijay Raghunath 4, Mark P. Molloy 1,2,* and Hartmut Schlüter 3,* 1 Bowel Cancer and Biomarker Research, Kolling Institute, The University of Sydney, Sydney 2065, Australia; pascal.steff[email protected] (P.S.); [email protected] (S.H.) 2 Department of Molecular Sciences, Macquarie University, Sydney 2109, Australia; [email protected] 3 Mass Spectrometric Proteomics Group, Department of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg 20246, Germany; [email protected] 4 Sydney Informatics Hub, The University of Sydney, Sydney 2008, Australia; [email protected] * Correspondence: [email protected] (M.P.M.); [email protected] (H.S.) Received: 7 November 2019; Accepted: 13 February 2020; Published: 19 February 2020 Abstract: Proteomics and genomics discovery experiments generate increasingly large result tables, necessitating more researcher time to convert the biological data into new knowledge. Literature review is an important step in this process and can be tedious for large scale experiments. An informed and strategic decision about which biomolecule targets should be pursued for follow-up experiments thus remains a considerable challenge. To streamline and formalise this process of literature retrieval and analysis of discovery based ‘omics data and as a decision-facilitating support tool for follow-up experiments we present OmixLitMiner, a package written in the computational language R. The tool automates the retrieval of literature from PubMed based on UniProt protein identifiers, gene names and their synonyms, combined with user defined contextual keyword search (i.e., gene ontology based). -
Supplementary Table 3: Genes Only Influenced By
Supplementary Table 3: Genes only influenced by X10 Illumina ID Gene ID Entrez Gene Name Fold change compared to vehicle 1810058M03RIK -1.104 2210008F06RIK 1.090 2310005E10RIK -1.175 2610016F04RIK 1.081 2610029K11RIK 1.130 381484 Gm5150 predicted gene 5150 -1.230 4833425P12RIK -1.127 4933412E12RIK -1.333 6030458P06RIK -1.131 6430550H21RIK 1.073 6530401D06RIK 1.229 9030607L17RIK -1.122 A330043C08RIK 1.113 A330043L12 1.054 A530092L01RIK -1.069 A630054D14 1.072 A630097D09RIK -1.102 AA409316 FAM83H family with sequence similarity 83, member H 1.142 AAAS AAAS achalasia, adrenocortical insufficiency, alacrimia 1.144 ACADL ACADL acyl-CoA dehydrogenase, long chain -1.135 ACOT1 ACOT1 acyl-CoA thioesterase 1 -1.191 ADAMTSL5 ADAMTSL5 ADAMTS-like 5 1.210 AFG3L2 AFG3L2 AFG3 ATPase family gene 3-like 2 (S. cerevisiae) 1.212 AI256775 RFESD Rieske (Fe-S) domain containing 1.134 Lipo1 (includes AI747699 others) lipase, member O2 -1.083 AKAP8L AKAP8L A kinase (PRKA) anchor protein 8-like -1.263 AKR7A5 -1.225 AMBP AMBP alpha-1-microglobulin/bikunin precursor 1.074 ANAPC2 ANAPC2 anaphase promoting complex subunit 2 -1.134 ANKRD1 ANKRD1 ankyrin repeat domain 1 (cardiac muscle) 1.314 APOA1 APOA1 apolipoprotein A-I -1.086 ARHGAP26 ARHGAP26 Rho GTPase activating protein 26 -1.083 ARL5A ARL5A ADP-ribosylation factor-like 5A -1.212 ARMC3 ARMC3 armadillo repeat containing 3 -1.077 ARPC5 ARPC5 actin related protein 2/3 complex, subunit 5, 16kDa -1.190 activating transcription factor 4 (tax-responsive enhancer element ATF4 ATF4 B67) 1.481 AU014645 NCBP1 nuclear cap -
New Functional and Structural Insights from Updated Mutational Databases for Complement Factor H, Factor I, Membrane Cofactor Protein and C3
Biosci. Rep. (2014) / 34 / art:e00146 / doi 10.1042/BSR20140117 New functional and structural insights from updated mutational databases for complement factor H, Factor I, membrane cofactor protein and C3 Elizabeth Rodriguez*1, Pavithra M. Rallapalli*1, Amy J. Osborne* and Stephen J. Perkins*2 *Department of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, U.K. Synopsis aHUS (atypical haemolytic uraemic syndrome), AMD (age-related macular degeneration) and other diseases are associated with defective AP (alternative pathway) regulation. CFH (complement factor H), CFI (complement factor I), MCP (membrane cofactor protein) and C3 exhibited the most disease-associated genetic alterations in the AP.Our interactive structural database for these was updated with a total of 324 genetic alterations. A consensus structure for the SCR (short complement regulator) domain showed that the majority (37 %) of SCR mutations occurred at its hypervariable loop and its four conserved Cys residues. Mapping 113 missense mutations onto the CFH structure showed that over half occurred in the C-terminal domains SCR-15 to -20. In particular, SCR-20 with the highest total of affected residues is associated with binding to C3d and heparin-like oligosaccharides. No clustering of 49 missense mutations in CFI was seen. In MCP, SCR-3 was the most affected by 23 missense mutations. In C3, the neighbouring thioester and MG (macroglobulin) domains exhibited most of 47 missense mutations. The mutations in the regulators CFH, CFI and MCP involve loss-of-function, whereas those for C3 involve gain-of-function. This combined update emphasizes the importance of the complement AP in inflammatory disease, clarifies the functionally important regions in these proteins, and will facilitate diagnosis and therapy. -
Epistatic Interactions of Genetic Loci Associated with Age-Related
www.nature.com/scientificreports OPEN Epistatic interactions of genetic loci associated with age‑related macular degeneration Christina Kiel1,3, Christoph A. Nebauer1,3, Tobias Strunz1,3, Simon Stelzl1 & Bernhard H. F. Weber 1,2* The currently largest genome‑wide association study (GWAS) for age‑related macular degeneration (AMD) defnes disease association with genome‑wide signifcance for 52 independent common and rare genetic variants across 34 chromosomal loci. Overall, these loci contain over 7200 variants and are enriched for genes with functions indicating several shared cellular processes. Still, the precise mechanisms leading to AMD pathology are largely unknown. Here, we exploit the phenomenon of epistatic interaction to identify seemingly independent AMD‑associated variants that reveal joint efects on gene expression. We focus on genetic variants associated with lipid metabolism, organization of extracellular structures, and innate immunity, specifcally the complement cascade. Multiple combinations of independent variants were used to generate genetic risk scores allowing gene expression in liver to be compared between low and high‑risk AMD. We identifed genetic variant combinations correlating signifcantly with expression of 26 genes, of which 19 have not been associated with AMD before. This study defnes novel targets and allows prioritizing further functional work into AMD pathobiology. A frst successful genome-wide association study (GWAS) was reported in 2005 and identifed with genome- wide signifcance genetic variants at the CFH locus associated with age-related macular degeneration (AMD), a complex disease which is a frequent cause of progressive vision loss in the elderly population 1. Since then, the list of AMD-associated genetic variation has grown exponentially, presently bringing the total to 52 independent common and rare variants across 34 chromosomal loci2. -
Whole Genome Sequencing of Familial Non-Medullary Thyroid Cancer Identifies Germline Alterations in MAPK/ERK and PI3K/AKT Signaling Pathways
biomolecules Article Whole Genome Sequencing of Familial Non-Medullary Thyroid Cancer Identifies Germline Alterations in MAPK/ERK and PI3K/AKT Signaling Pathways Aayushi Srivastava 1,2,3,4 , Abhishek Kumar 1,5,6 , Sara Giangiobbe 1, Elena Bonora 7, Kari Hemminki 1, Asta Försti 1,2,3 and Obul Reddy Bandapalli 1,2,3,* 1 Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany; [email protected] (A.S.); [email protected] (A.K.); [email protected] (S.G.); [email protected] (K.H.); [email protected] (A.F.) 2 Hopp Children’s Cancer Center (KiTZ), D-69120 Heidelberg, Germany 3 Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), D-69120 Heidelberg, Germany 4 Medical Faculty, Heidelberg University, D-69120 Heidelberg, Germany 5 Institute of Bioinformatics, International Technology Park, Bangalore 560066, India 6 Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104, India 7 S.Orsola-Malphigi Hospital, Unit of Medical Genetics, 40138 Bologna, Italy; [email protected] * Correspondence: [email protected]; Tel.: +49-6221-42-1709 Received: 29 August 2019; Accepted: 10 October 2019; Published: 13 October 2019 Abstract: Evidence of familial inheritance in non-medullary thyroid cancer (NMTC) has accumulated over the last few decades. However, known variants account for a very small percentage of the genetic burden. Here, we focused on the identification of common pathways and networks enriched in NMTC families to better understand its pathogenesis with the final aim of identifying one novel high/moderate-penetrance germline predisposition variant segregating with the disease in each studied family. -
Role and Regulation of the P53-Homolog P73 in the Transformation of Normal Human Fibroblasts
Role and regulation of the p53-homolog p73 in the transformation of normal human fibroblasts Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Bayerischen Julius-Maximilians-Universität Würzburg vorgelegt von Lars Hofmann aus Aschaffenburg Würzburg 2007 Eingereicht am Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Dr. Martin J. Müller Gutachter: Prof. Dr. Michael P. Schön Gutachter : Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am Erklärung Hiermit erkläre ich, dass ich die vorliegende Arbeit selbständig angefertigt und keine anderen als die angegebenen Hilfsmittel und Quellen verwendet habe. Diese Arbeit wurde weder in gleicher noch in ähnlicher Form in einem anderen Prüfungsverfahren vorgelegt. Ich habe früher, außer den mit dem Zulassungsgesuch urkundlichen Graden, keine weiteren akademischen Grade erworben und zu erwerben gesucht. Würzburg, Lars Hofmann Content SUMMARY ................................................................................................................ IV ZUSAMMENFASSUNG ............................................................................................. V 1. INTRODUCTION ................................................................................................. 1 1.1. Molecular basics of cancer .......................................................................................... 1 1.2. Early research on tumorigenesis ................................................................................. 3 1.3. Developing -
In This Table Protein Name, Uniprot Code, Gene Name P-Value
Supplementary Table S1: In this table protein name, uniprot code, gene name p-value and Fold change (FC) for each comparison are shown, for 299 of the 301 significantly regulated proteins found in both comparisons (p-value<0.01, fold change (FC) >+/-0.37) ALS versus control and FTLD-U versus control. Two uncharacterized proteins have been excluded from this list Protein name Uniprot Gene name p value FC FTLD-U p value FC ALS FTLD-U ALS Cytochrome b-c1 complex P14927 UQCRB 1.534E-03 -1.591E+00 6.005E-04 -1.639E+00 subunit 7 NADH dehydrogenase O95182 NDUFA7 4.127E-04 -9.471E-01 3.467E-05 -1.643E+00 [ubiquinone] 1 alpha subcomplex subunit 7 NADH dehydrogenase O43678 NDUFA2 3.230E-04 -9.145E-01 2.113E-04 -1.450E+00 [ubiquinone] 1 alpha subcomplex subunit 2 NADH dehydrogenase O43920 NDUFS5 1.769E-04 -8.829E-01 3.235E-05 -1.007E+00 [ubiquinone] iron-sulfur protein 5 ARF GTPase-activating A0A0C4DGN6 GIT1 1.306E-03 -8.810E-01 1.115E-03 -7.228E-01 protein GIT1 Methylglutaconyl-CoA Q13825 AUH 6.097E-04 -7.666E-01 5.619E-06 -1.178E+00 hydratase, mitochondrial ADP/ATP translocase 1 P12235 SLC25A4 6.068E-03 -6.095E-01 3.595E-04 -1.011E+00 MIC J3QTA6 CHCHD6 1.090E-04 -5.913E-01 2.124E-03 -5.948E-01 MIC J3QTA6 CHCHD6 1.090E-04 -5.913E-01 2.124E-03 -5.948E-01 Protein kinase C and casein Q9BY11 PACSIN1 3.837E-03 -5.863E-01 3.680E-06 -1.824E+00 kinase substrate in neurons protein 1 Tubulin polymerization- O94811 TPPP 6.466E-03 -5.755E-01 6.943E-06 -1.169E+00 promoting protein MIC C9JRZ6 CHCHD3 2.912E-02 -6.187E-01 2.195E-03 -9.781E-01 Mitochondrial 2- -
A Genome-Wide Association Study Identifies Key Modulators of Complement Factor H Binding to Malondialdehyde-Epitopes
A genome-wide association study identifies key modulators of complement factor H binding to malondialdehyde-epitopes Lejla Alica,b,c,1, Nikolina Papac-Milicevica,b,1,2, Darina Czamarad, Ramona B. Rudnicke, Maria Ozsvar-Kozmaa,b, Andrea Hartmanne, Michael Gurbisza, Gregor Hoermanna,f, Stefanie Haslinger-Huttera, Peter F. Zipfele,g, Christine Skerkae, Elisabeth B. Binderd, and Christoph J. Bindera,b,2 aDepartment of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; bResearch Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; cDepartment of Medical Biochemistry, Faculty of Medicine, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina; dDepartment of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany; eDepartment of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, 07745 Jena, Germany; fCentral Institute for Medical and Chemical Laboratory Diagnosis, University Hospital Innsbruck, 6020 Innsbruck, Austria; and gInstitute for Microbiology, Friedrich Schiller University, 07743 Jena, Germany Edited by Thaddeus Dryja, Harvard Medical School, Boston, MA, and approved March 17, 2020 (received for review August 12, 2019) Genetic variants within complement factor H (CFH), a major head-to-tail fashion. Moreover, its splice variant factor H-like alternative complement pathway regulator, are associated with protein 1 (FHL-1), consisting of the first seven SCRs of CFH, the development of age-related -
HMMR Acts in the PLK1-Dependent Spindle Positioning Pathway And
RESEARCH ARTICLE HMMR acts in the PLK1-dependent spindle positioning pathway and supports neural development Marisa Connell1†, Helen Chen1†, Jihong Jiang1, Chia-Wei Kuan2, Abbas Fotovati1, Tony LH Chu1, Zhengcheng He1, Tess C Lengyell3, Huaibiao Li4, Torsten Kroll4, Amanda M Li1, Daniel Goldowitz3,5, Lucien Frappart4, Aspasia Ploubidou4, Millan S Patel5, Linda M Pilarski6, Elizabeth M Simpson3,5, Philipp F Lange2,7, Douglas W Allan8, Christopher A Maxwell1,7* 1Department of Paediatrics, University of British Columbia, Vancouver, Canada; 2Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada; 3Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada; 4Leibniz Institute on Aging—Fritz Lipmann Institute, Beutenbergstrasse, Germany; 5Department of Medical Genetics, University of British Columbia, Vancouver, Canada; 6Cross Cancer Institute, Department of Oncology, University of Alberta, Edmonton, Canada; 7Michael Cuccione Childhood Cancer Research Program, BC Children’s Hospital, Vancouver, Canada; 8Department of Cellular and Physiological Sciences, Life Sciences Centre, University of British Columbia, Vancouver, Canada Abstract Oriented cell division is one mechanism progenitor cells use during development and to maintain tissue homeostasis. Common to most cell types is the asymmetric establishment and regulation of cortical NuMA-dynein complexes that position the mitotic spindle. Here, we discover *For correspondence: cmaxwell@ bcchr.ubc.ca that HMMR acts at centrosomes in a PLK1-dependent pathway that locates active Ran and modulates the cortical localization of NuMA-dynein complexes to correct mispositioned spindles. † These authors contributed This pathway was discovered through the creation and analysis of Hmmr-knockout mice, which equally to this work suffer neonatal lethality with defective neural development and pleiotropic phenotypes in multiple Competing interests: The tissues. -
Host Cell Factors Necessary for Influenza a Infection: Meta-Analysis of Genome Wide Studies
Host Cell Factors Necessary for Influenza A Infection: Meta-Analysis of Genome Wide Studies Juliana S. Capitanio and Richard W. Wozniak Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta Abstract: The Influenza A virus belongs to the Orthomyxoviridae family. Influenza virus infection occurs yearly in all countries of the world. It usually kills between 250,000 and 500,000 people and causes severe illness in millions more. Over the last century alone we have seen 3 global influenza pandemics. The great human and financial cost of this disease has made it the second most studied virus today, behind HIV. Recently, several genome-wide RNA interference studies have focused on identifying host molecules that participate in Influen- za infection. We used nine of these studies for this meta-analysis. Even though the overlap among genes identified in multiple screens was small, network analysis indicates that similar protein complexes and biological functions of the host were present. As a result, several host gene complexes important for the Influenza virus life cycle were identified. The biological function and the relevance of each identified protein complex in the Influenza virus life cycle is further detailed in this paper. Background and PA bound to the viral genome via nucleoprotein (NP). The viral core is enveloped by a lipid membrane derived from Influenza virus the host cell. The viral protein M1 underlies the membrane and anchors NEP/NS2. Hemagglutinin (HA), neuraminidase Viruses are the simplest life form on earth. They parasite host (NA), and M2 proteins are inserted into the envelope, facing organisms and subvert the host cellular machinery for differ- the viral exterior.