CARD10 Promotes the Progression of Renal Cell Carcinoma by Regulating the NF‑Κb Signaling Pathway
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NIH Public Access Author Manuscript Mol Psychiatry
NIH Public Access Author Manuscript Mol Psychiatry. Author manuscript; available in PMC 2014 July 01. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Mol Psychiatry. 2013 July ; 18(7): 781–787. doi:10.1038/mp.2013.24. Whole-exome sequencing and imaging genetics identify functional variants for rate of change in hippocampal volume in mild cognitive impairment K Nho1, JJ Corneveaux2, S Kim1,3, H Lin3, SL Risacher1, L Shen1,3, S Swaminathan1,4, VK Ramanan1,4, Y Liu3,4, T Foroud1,3,4, MH Inlow5, AL Siniard2, RA Reiman2, PS Aisen6, RC Petersen7, RC Green8, CR Jack7, MW Weiner9,10, CT Baldwin11, K Lunetta12, LA Farrer11,13, SJ Furney14,15,16, S Lovestone14,15,16, A Simmons14,15,16, P Mecocci17, B Vellas18, M Tsolaki19, I Kloszewska20, H Soininen21, BC McDonald1,22, MR Farlow22, B Ghetti23, MJ Huentelman2, and AJ Saykin1,3,4,22 for the Multi-Institutional Research on Alzheimer Genetic Epidemiology (MIRAGE) Study; for the AddNeuroMed Consortium; for the Indiana Memory and Aging Study; for the Alzheimer’s Disease Neuroimaging Initiative (ADNI)24 1Department of Radiology and Imaging Sciences, Center for Neuroimaging, Indiana University School of Medicine, Indianapolis, IN, USA 2Neurogenomics Division, The Translational Genomics Research Institute (TGen), Phoenix, AZ, USA 3Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, USA 4Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, -
An Integrated Analysis of Public Genomic Data Unveils a Possible
Kubota and Suyama BMC Medical Genomics (2020) 13:8 https://doi.org/10.1186/s12920-020-0662-9 RESEARCH ARTICLE Open Access An integrated analysis of public genomic data unveils a possible functional mechanism of psoriasis risk via a long- range ERRFI1 enhancer Naoto Kubota1,2 and Mikita Suyama1* Abstract Background: Psoriasis is a chronic inflammatory skin disease, for which genome-wide association studies (GWAS) have identified many genetic variants as risk markers. However, the details of underlying molecular mechanisms, especially which variants are functional, are poorly understood. Methods: We utilized a computational approach to survey psoriasis-associated functional variants that might affect protein functions or gene expression levels. We developed a pipeline by integrating publicly available datasets provided by GWAS Catalog, FANTOM5, GTEx, SNP2TFBS, and DeepBlue. To identify functional variants on exons or splice sites, we used a web-based annotation tool in the Ensembl database. To search for noncoding functional variants within promoters or enhancers, we used eQTL data calculated by GTEx. The data of variants lying on transcription factor binding sites provided by SNP2TFBS were used to predict detailed functions of the variants. Results: We discovered 22 functional variant candidates, of which 8 were in noncoding regions. We focused on the enhancer variant rs72635708 (T > C) in the 1p36.23 region; this variant is within the enhancer region of the ERRFI1 gene, which regulates lipid metabolism in the liver and skin morphogenesis via EGF signaling. Further analysis showed that the ERRFI1 promoter spatially contacts with the enhancer, despite the 170 kb distance between them. We found that this variant lies on the AP-1 complex binding motif and may modulate binding levels. -
Defining the Relevant Combinatorial Space of the PKC/CARD-CC Signal Transduction Nodes
bioRxiv preprint doi: https://doi.org/10.1101/228767; this version posted May 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Defining the relevant combinatorial space of the PKC/CARD-CC signal transduction nodes Jens Staal1,2,*, Yasmine Driege1,2, Mira Haegman1,2, Styliani Iliaki1,2, Domien Vanneste1,2, Inna Affonina1,2, Harald Braun1,2, Rudi Beyaert1,2 1 Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium, 2 VIB-UGent Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, VIB, Ghent, Belgium. * corresponding author: [email protected] Running title: PKC/CARD-CC signaling Abbreviations: Bcl10 = B Cell CLL/Lymphoma 10 CARD = Caspase activation and recruitment domain CC = Coiled-coil domain MALT1 = Mucosa-associated lymphoid tissue lymphoma translocation protein 1 PKC = protein kinase C Keywords: Inflammation, cancer, NF-kappaB, paracaspase Conflict of interests: The authors declare no conflict of interest. bioRxiv preprint doi: https://doi.org/10.1101/228767; this version posted May 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Abstract Biological signal transduction typically display a so-called bow-tie or hour glass topology: Multiple receptors lead to multiple cellular responses but the signals all pass through a narrow waist of central signaling nodes. -
Molecular Architecture and Regulation of BCL10-MALT1 Filaments
ARTICLE DOI: 10.1038/s41467-018-06573-8 OPEN Molecular architecture and regulation of BCL10-MALT1 filaments Florian Schlauderer1, Thomas Seeholzer2, Ambroise Desfosses3, Torben Gehring2, Mike Strauss 4, Karl-Peter Hopfner 1, Irina Gutsche3, Daniel Krappmann2 & Katja Lammens1 The CARD11-BCL10-MALT1 (CBM) complex triggers the adaptive immune response in lymphocytes and lymphoma cells. CARD11/CARMA1 acts as a molecular seed inducing 1234567890():,; BCL10 filaments, but the integration of MALT1 and the assembly of a functional CBM complex has remained elusive. Using cryo-EM we solved the helical structure of the BCL10- MALT1 filament. The structural model of the filament core solved at 4.9 Å resolution iden- tified the interface between the N-terminal MALT1 DD and the BCL10 caspase recruitment domain. The C-terminal MALT1 Ig and paracaspase domains protrude from this core to orchestrate binding of mediators and substrates at the filament periphery. Mutagenesis studies support the importance of the identified BCL10-MALT1 interface for CBM complex assembly, MALT1 protease activation and NF-κB signaling in Jurkat and primary CD4 T-cells. Collectively, we present a model for the assembly and architecture of the CBM signaling complex and how it functions as a signaling hub in T-lymphocytes. 1 Gene Center, Ludwig-Maximilians University, Feodor-Lynen-Str. 25, 81377 München, Germany. 2 Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz-Zentrum München - German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany. 3 University Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale IBS, F-38044 Grenoble, France. 4 Department of Anatomy and Cell Biology, McGill University, Montreal, Canada H3A 0C7. -
Analysis of CARD10 and CARD11 Somatic Mutations in Patients with Ovarian Endometriosis
ONCOLOGY LETTERS 16: 491-496, 2018 Analysis of CARD10 and CARD11 somatic mutations in patients with ovarian endometriosis YANG ZOU1,2, JIANG-YAN ZHOU1,3, FENG WANG1,2, ZI-YU ZHANG1,2, FA-YING LIU1,2, YONG LUO1,2, JUN TAN1,4, XIN ZENG1, XI-DI WAN1 and OU-PING HUANG1,3 1Key Laboratory of Women's Reproductive Health of Jiangxi Province; 2Central Laboratory; 3Department of Gynecology; 4Reproductive Medicine Center, Jiangxi Provincial Maternal and Child Health Hospital, Nanchang, Jiangxi 330006, P.R. China Received October 11, 2017; Accepted March 27, 2018 DOI: 10.3892/ol.2018.8659 Abstract. Endometriosis is a complex and heterogeneous amongst 101 cases of ovarian endometriosis for the first time, pre-malignant inflammatory disease harboring multiple these mutations may serve active roles in the development of gene mutations. Previous studies have suggested that caspase ovarian endometriosis. recruitment domain family member (CARD)10 and CARD11 mutations may exist in endometriosis. In the present study, Introduction a collection of endometriotic lesions and paired peripheral blood from 101 patients with ovarian endometriosis were Endometriosis is a heterogeneous estrogen-dependent chronic obtained, and the entire coding sequences of the CARD10 gynecological disease in women of reproductive age (1-3). The and CARD11 genes were sequenced. Evolutionary conserva- condition is characterized by endometrial tissues ectopically tion analysis and online prediction programs were applied implanting outside the uterine cavity, and is subdivided mainly to analyze the disease-causing potential of the identified into ovarian, peritoneal and deep infiltrating endometriosis mutations. A total of 4 novel somatic mutations were according to the different implant locations (4,5). -
Copy Number Variation at Chromosome 5Q21.2 Is Associated with Intraocular Pressure
Genetics Copy Number Variation at Chromosome 5q21.2 Is Associated With Intraocular Pressure Abhishek Nag,1 Cristina Venturini,2 Pirro G. Hysi,1 Matthew Arno,3 Estibaliz Aldecoa-Otalora Astarloa,3 Stuart MacGregor,4 Alex W. Hewitt,5,6 Terri L. Young,7 Paul Mitchell,8 Ananth C. Viswanathan,9 David A. Mackey,6 and Christopher J. Hammond1 1Department of Twin Research and Genetic Epidemiology, King’s College London, St. Thomas’ Hospital, London, United Kingdom 2UCL Institute of Ophthalmology, London, United Kingdom 3King’s Genomics Facilities, King’s College London, London, United Kingdom 4Queensland Institute of Medical Research, Statistical Genetics, Herston, Brisbane, Australia 5Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia 6University of Western Australia, Centre for Ophthalmology and Visual Science, Lions Eye Institute, Perth, Australia 7Center for Human Genetics, Duke University Medical Center, Durham, North Carolina 8Centre for Vision Research, Westmead Millennium Institute, University of Sydney, Sydney, Australia 9NIHR Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom Correspondence: Chris Hammond, PURPOSE. Glaucoma is a major cause of blindness in the world. Recent genome-wide Department of Twin Research and association studies (GWAS) have identified common genetic variants for glaucoma, but still a Genetic Epidemiology, St. Thomas’ significant heritability gap remains. We hypothesized -
UBAC1/KPC2 Regulates TLR3 Signaling in Human Keratinocytes Through Functional Interaction with the CARD14/Carma2sh-TANK Complex
International Journal of Molecular Sciences Article UBAC1/KPC2 Regulates TLR3 Signaling in Human Keratinocytes through Functional Interaction with the CARD14/CARMA2sh-TANK Complex Pellegrino Mazzone 1, Michele Congestrì 2, Ivan Scudiero 1, Immacolata Polvere 2,3, Serena Voccola 3, Lucrezia Zerillo 3, Gianluca Telesio 1, Pasquale Vito 2,3,*, Romania Stilo 2 and Tiziana Zotti 2,3 1 Biogem Consortium, Via Camporeale, 83031 Ariano Irpino (AV), Italy; [email protected] (P.M.); [email protected] (I.S.); [email protected] (G.T.) 2 Dipartimento di Scienze e Tecnologie, Università degli Studi del Sannio, Via Port’Arsa 11, 82100 Benevento, Italy; [email protected] (M.C.); [email protected] (I.P.); [email protected] (R.S.); [email protected] (T.Z.) 3 Genus Biotech, Università degli Studi del Sannio, Via Appia snc, 82030 Apollosa (BN), Italy; [email protected] (S.V.); [email protected] (L.Z.) * Correspondence: [email protected]; Tel.: +39-0824305105 Received: 8 November 2020; Accepted: 8 December 2020; Published: 9 December 2020 Abstract: CARD14/CARMA2 is a scaffold molecule whose genetic alterations are linked to human inherited inflammatory skin disorders. However, the mechanisms through which CARD14/CARMA2 controls innate immune response and chronic inflammation are not well understood. By means of a yeast two-hybrid screening, we identified the UBA Domain Containing 1 (UBAC1), the non-catalytic subunit of the E3 ubiquitin-protein ligase KPC complex, as an interactor of CARMA2sh, the CARD14/CARMA2 isoform mainly expressed in human keratinocytes. UBAC1 participates in the CARMA2sh/TANK complex and promotes K63-linked ubiquitination of TANK. -
Gene Section Short Communication
Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL INIST-CNRS Gene Section Short Communication CARD10 (caspase recruitment domain family, member 10) Gamze Ayaz, Mesut Muyan Department of Biological Sciences, Middle East Technical University, Ankara, Turkey (GA, MM) Published in Atlas Database: August 2014 Online updated version : http://AtlasGeneticsOncology.org/Genes/CARD10ID43187ch22q13.html Printable original version : http://documents.irevues.inist.fr/bitstream/handle/2042/62142/08-2014-CARD10ID43187ch22q13.pdf DOI: 10.4267/2042/62142 This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 2.0 France Licence. © 2015 Atlas of Genetics and Cytogenetics in Oncology and Haematology Abstract Pseudogene Caspase recruitment domain family, member 10, No reported pseudogene. CARD10 (also known as CARMA3 or Bimp1), is a member of the membrane-associated guanylate Protein kinase (MAGUK) superfamily proteins that act to Description organize signaling at the plasma membrane. This family of proteins contains Src-homology 3 (SH3), CARD10 (NP_055365) is a 1032 amino-acid long PDZ, GuK domains and caspase recruitment domain protein with a molecular mass of 116 kDa. (CARD). The amino-terminally located CARD of This protein consists of antiparallel alpha helices. CARD10 functions as an activator of BCL10 and CARD10 contains an N-terminal CARD domain, NF-kappaB (NF-kB) signaling critical for the followed by a central coiled-coil (CC) domain and a regulation of cellular survival and proliferation. C-terminal region encompassing a PDZ domain, a CARD10 (CARMA3) is reported to be over- SH3 domain and a GUK domain (Wang et al., 2001). expressed in various cancer types that include breast, The CARD domain has a hydrophobic core and a glioma, colon and non-small-cell lung cancers. -
An Evolutionary View
bioRxiv preprint doi: https://doi.org/10.1101/317719; this version posted May 9, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. How Much Information is Provided by Human Epigenomic Data? An Evolutionary View Brad Gulko1,2 and Adam Siepel2 1Graduate Field of Computer Science, Cornell University, Ithaca, NY, USA 2Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA ABSTRACT Here, we ask the question, “How much information do available epigenomic data sets provide about human genomic function, individually or in combination?” We measure genomic function by using signatures of natural selection as a proxy, and we measure information in terms of reductions in entropy derived from a probabilistic evolutionary model. Our analysis of the human genome considers measures of chromatin accessibility (DNase-seq), chromatin states (ChromHMM), RNA expression (RNA-seq), small RNAs, and DNA methylation across 115 cell types from the Roadmap Epigenomics project, together with gene annotations, splice sites, predicted transcription factor binding sites, and predicted DNA melting temperatures. Selective pressure is measured using patterns of genetic variation across ~50 modern humans and several nonhuman primates. We find that protein-coding gene annotations are most informative about genomic function, followed in decreasing order by RNA-seq, ChromHMM, splice sites, melting temperature, and DNase-seq. Several features exhibit clear synergy, meaning that they yield more information in combination than they do individually. -
Visualizing Spatiotemporal Dynamics of Apoptosis After G1 Arrest by Human T Cell Leukemia Virus Type 1 Tax and Insights Into
Arainga et al. BMC Genomics 2012, 13:275 http://www.biomedcentral.com/1471-2164/13/275 RESEARCH ARTICLE Open Access Visualizing spatiotemporal dynamics of apoptosis after G1 arrest by human T cell leukemia virus type 1 Tax and insights into gene expression changes using microarray-based gene expression analysis Mariluz Arainga1,2, Hironobu Murakami1,3 and Yoko Aida1,2* Abstract Background: Human T cell leukemia virus type 1 (HTLV-1) Tax is a potent activator of viral and cellular gene expression that interacts with a number of cellular proteins. Many reports show that Tax is capable of regulating cell cycle progression and apoptosis both positively and negatively. However, it still remains to understand why the Tax oncoprotein induces cell cycle arrest and apoptosis, or whether Tax-induced apoptosis is dependent upon its ability to induce G1 arrest. The present study used time-lapse imaging to explore the spatiotemporal patterns of cell cycle dynamics in Tax-expressing HeLa cells containing the fluorescent ubiquitination-based cell cycle indicator, Fucci2. A large-scale host cell gene profiling approach was also used to identify the genes involved in Tax-mediated cell signaling events related to cellular proliferation and apoptosis. Results: Tax-expressing apoptotic cells showed a rounded morphology and detached from the culture dish after cell cycle arrest at the G1 phase. Thus, it appears that Tax induces apoptosis through pathways identical to those involved in G1 arrest. To elucidate the mechanism(s) by which Tax induces cell cycle arrest and apoptosis, regulation of host cellular genes by Tax was analyzed using a microarray containing approximately 18,400 human mRNA transcripts. -
Rare Variants in Optic Disc Area Gene CARD10 Enriched in Primary Open‐
ORIGINAL ARTICLE Rare variants in optic disc area gene CARD10 enriched in primary open-angle glaucoma Tiger Zhou1, Emmanuelle Souzeau1, Shiwani Sharma1, Owen M. Siggs1, Ivan Goldberg2,3, Paul R. Healey2, Stuart Graham2, Alex W. Hewitt4, David A. Mackey5, Robert J. Casson6, John Landers1, Richard Mills1, Jonathan Ellis7, Paul Leo7, Matthew A. Brown7, Stuart MacGregor8, Kathryn P. Burdon1,4 & Jamie E. Craig1 1Department of Ophthalmology, Flinders University, Adelaide, SA, Australia 2Discipline of Ophthalmology, University of Sydney, Sydney, NSW, Australia 3Glaucoma Unit, Sydney Eye Hospital, Sydney, NSW, Australia 4Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia 5Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, WA, Australia 6Discipline of Ophthalmology & Visual Sciences, University of Adelaide, Adelaide, SA, Australia 7Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital, University of Queensland, Woolloongabba, QLD, Australia 8Statistical Genetics, QIMR Berghofer Medical Research Institute, Royal Brisbane Hospital, Brisbane, QLD, Australia Keywords Abstract CARD10, genome-wide association study, rare variants, whole exome sequencing Background Genome-wide association studies (GWAS) have identified association of com- Correspondence mon alleles with primary open-angle glaucoma (POAG) and its quantitative Tiger Zhou, Flinders Medical Centre, Flinders endophenotypes near numerous genes. This study aims to determine -
A Chromosome-Centric Human Proteome Project (C-HPP) To
computational proteomics Laboratory for Computational Proteomics www.FenyoLab.org E-mail: [email protected] Facebook: NYUMC Computational Proteomics Laboratory Twitter: @CompProteomics Perspective pubs.acs.org/jpr A Chromosome-centric Human Proteome Project (C-HPP) to Characterize the Sets of Proteins Encoded in Chromosome 17 † ‡ § ∥ ‡ ⊥ Suli Liu, Hogune Im, Amos Bairoch, Massimo Cristofanilli, Rui Chen, Eric W. Deutsch, # ¶ △ ● § † Stephen Dalton, David Fenyo, Susan Fanayan,$ Chris Gates, , Pascale Gaudet, Marina Hincapie, ○ ■ △ ⬡ ‡ ⊥ ⬢ Samir Hanash, Hoguen Kim, Seul-Ki Jeong, Emma Lundberg, George Mias, Rajasree Menon, , ∥ □ △ # ⬡ ▲ † Zhaomei Mu, Edouard Nice, Young-Ki Paik, , Mathias Uhlen, Lance Wells, Shiaw-Lin Wu, † † † ‡ ⊥ ⬢ ⬡ Fangfei Yan, Fan Zhang, Yue Zhang, Michael Snyder, Gilbert S. Omenn, , Ronald C. Beavis, † # and William S. Hancock*, ,$, † Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States ‡ Stanford University, Palo Alto, California, United States § Swiss Institute of Bioinformatics (SIB) and University of Geneva, Geneva, Switzerland ∥ Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States ⊥ Institute for System Biology, Seattle, Washington, United States ¶ School of Medicine, New York University, New York, United States $Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia ○ MD Anderson Cancer Center, Houston, Texas, United States ■ Yonsei University College of Medicine, Yonsei University,