L7 Interaction Genes
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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. -
NUFIP1 Sirna (H): Sc-105367
SANTA CRUZ BIOTECHNOLOGY, INC. NUFIP1 siRNA (h): sc-105367 BACKGROUND STORAGE AND RESUSPENSION NUFIP1 (nuclear fragile X mental retardation-interacting protein 1) is a 495 Store lyophilized siRNA duplex at -20° C with desiccant. Stable for at least amino acid protein that localizes to the nucleus and can interact with FMR1 one year from the date of shipment. Once resuspended, store at -20° C, (fragile X mental retardation protein) and BRCA1, a breast and ovarian-specific avoid contact with RNAses and repeated freeze thaw cycles. tumor suppressor. Through its interaction with FMR1, NUFIP1 is thought to Resuspend lyophilized siRNA duplex in 330 µl of the RNAse-free water shuttle specific mRNPs to active neuronal synapses, thereby regulating the provided. Resuspension of the siRNA duplex in 330 µl of RNAse-free water translation of synaptic plasticity-related mRNA. The close interaction of makes a 10 µM solution in a 10 µM Tris-HCl, pH 8.0, 20 mM NaCl, 1 mM NUFIP1 with FMR1, a protein that is essential for proper dendritic spine matu- EDTA buffered solution. ration, suggests close involvement in neuronal development. Interaction of NUFIP1 with BRCA1 results in the formation of a complex which binds the APPLICATIONS positive elongation factor P-TEFb, thus stimulating RNA polymerase II (pol II) transcription. When associated with BRAC1, NUFIP1 acts as a transcriptional NUFIP1 siRNA (h) is recommended for the inhibition of NUFIP1 expression in activator contributing to tumor suppressor gene expression. NUFIP1 contains human cells. one C2H2-type zinc finger and is expressed throughout the body. SUPPORT REAGENTS REFERENCES For optimal siRNA transfection efficiency, Santa Cruz Biotechnology’s 1. -
Detection of Aneuploidies by Paralogous Sequence Quantification S Deutsch, U Choudhury, G Merla, C Howald, a Sylvan, S E Antonarakis
908 J Med Genet: first published as 10.1136/jmg.2004.023184 on 9 December 2004. Downloaded from ORIGINAL ARTICLE Detection of aneuploidies by paralogous sequence quantification S Deutsch, U Choudhury, G Merla, C Howald, A Sylvan, S E Antonarakis ............................................................................................................................... J Med Genet 2004;41:908–915. doi: 10.1136/jmg.2004.023184 Background: Chromosomal aneuploidies are a common cause of congenital disorders associated with cognitive impairment and multiple dysmorphic features. Pre-natal diagnosis of aneuploidies is most See end of article for commonly performed by the karyotyping of fetal cells obtained by amniocentesis or chorionic villus authors’ affiliations sampling, but this method is labour intensive and requires about 14 days to complete. ....................... Methods: We have developed a PCR based method for the detection of targeted chromosome number Correspondence to: abnormalities termed paralogous sequence quantification (PSQ), based on the use of paralogous genes. Professor Stylianos E Paralogous sequences have a high degree of sequence identity, but accumulate nucleotide substitutions in Antonarakis, Department a locus specific manner. These sequence differences, which we term paralogous sequence mismatches of Genetic Medicine and Development, University of (PSMs), can be quantified using pyrosequencing technology, to estimate the relative dosage between Geneva Medical School, different chromosomes. We designed 10 assays for the detection of trisomies of chromosomes 13, 18, and GE 1211, Geneva, 21 and sex chromosome aneuploidies. Switzerland; Stylianos. antonarakis@medecine. Results: We evaluated the performance of this method on 175 DNAs, highly enriched for abnormal unige.ch samples. A correct and unambiguous diagnosis was given for 119 out of 120 aneuploid samples as well as for all the controls. -
Upregulation of Cyclin T1/CDK9 Complexes During T Cell Activation
Oncogene (1998) 17, 3093 ± 3102 ã 1998 Stockton Press All rights reserved 0950 ± 9232/98 $12.00 http://www.stockton-press.co.uk/onc Upregulation of cyclin T1/CDK9 complexes during T cell activation Judit Garriga1,2, Junmin Peng4, Matilde ParrenÄ o1,2, David H Price4, Earl E Henderson1,3 and Xavier GranÄ a*,1,2 1Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, 3307 North Broad Street, Philadelphia, Pennsylvania 19140, USA; 2Department of Biochemistry, Temple University School of Medicine, 3307 North Broad Street, Philadelphia, Pennsylvania 19140, USA; 3Microbiology and Immunology, Temple University School of Medicine, 3420 North Broad Street, Philadelphia, Pennsylvania 19140, USA and 4Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242, USA Cyclin T1 has been identi®ed recently as a regulatory date in response to intracellular or extracellular signals subunit of CDK9 and as a component of the transcrip- in mammalian cells, although it has been shown that tion elongation factor P-TEFb. Cyclin T1/CDK9 com- the levels of cyclin C mRNA are stimulated by serum plexes phosphorylate the carboxy terminal domain and cytokines (Lew et al., 1991; Liu et al., 1998). All (CTD) of RNA polymerase II (RNAP II) in vitro. Here cyclin/CDK pairs involved in transcription are able to we report that the levels of cyclin T1 are dramatically phosphorylate the C-terminal domain (CTD) of RNA upregulated by two independent signaling pathways polymerase II (RNAP II) in vitro. Multiple kinases triggered respectively by PMA and PHA in primary seem to phosphorylate the CTD of RNAP II in vivo in human peripheral blood lymphocytes (PBLs). -
Identification and Characterization of Novel Fusion Genes with Potential
International Journal of Molecular Sciences Article Identification and Characterization of Novel Fusion Genes with Potential Clinical Applications in Mexican Children with Acute Lymphoblastic Leukemia Minerva Mata-Rocha 1,2 , Angelica Rangel-López 3 , Elva Jiménez-Hernández 4,5, Blanca Angélica Morales-Castillo 6, Carolina González-Torres 7, Javier Gaytan-Cervantes 7, Enrique Álvarez-Olmos 6, Juan Carlos Núñez-Enríquez 6 , Arturo Fajardo-Gutiérrez 6, Jorge Alfonso Martín-Trejo 8, Karina Anastacia Solís-Labastida 8, Aurora Medina-Sansón 9, Janet Flores-Lujano 6, Omar Alejandro Sepúlveda-Robles 1,2 , José Gabriel Peñaloza-González 10, Laura Eugenia Espinoza-Hernández 4, Nora Nancy Núñez-Villegas 4, Rosa Martha Espinosa-Elizondo 11, Beatriz Cortés-Herrera 11, José Refugio Torres-Nava 5, Luz Victoria Flores-Villegas 12, Laura Elizabeth Merino-Pasaye 12, Vilma Carolina Bekker-Méndez 13, Martha Margarita Velázquez-Aviña 10, María Luisa Pérez-Saldívar 6, Benito Alejandro Bautista-Martínez 8, Raquel Amador-Sánchez 14, Ana Itamar González-Avila 14, Silvia Jiménez-Morales 15 , David Aldebarán Duarte-Rodríguez 6, Jessica Denisse Santillán-Juárez 16, Alejandra Jimena García-Velázquez 16, Haydeé Rosas-Vargas 2,* and Juan Manuel Mejía-Aranguré 17,* 1 CONACyT-Unidad de Investigacion Medica en Epidemiologia Clinica, Hospital de Pediatria, Centro Medico Siglo XXI, IMSS, 06720 Mexico City, Mexico; [email protected] (M.M.-R.); [email protected] (O.A.S.-R.) 2 Unidad de Investigacion Medica en Genética Humana, Hospital de Pediatria, Centro Medico Nacional -
Integrative Genomics Analyses Reveal Molecularly Distinct Subgroups of B-Cell Chronic Lymphocytic Leukemia Patients with 13Q14 Deletion
Published OnlineFirst October 14, 2010; DOI: 10.1158/1078-0432.CCR-10-0151 Clinical Cancer Human Cancer Biology Research Integrative Genomics Analyses Reveal Molecularly Distinct Subgroups of B-Cell Chronic Lymphocytic Leukemia Patients with 13q14 Deletion Laura Mosca1, Sonia Fabris1, Marta Lionetti1, Katia Todoerti1, Luca Agnelli1, Fortunato Morabito2, Giovanna Cutrona3, Adrian Andronache1, Serena Matis3, Francesco Ferrari4, Massimo Gentile2, Mauro Spriano5, Vincenzo Callea6, Gianluca Festini7, Stefano Molica8, Giorgio Lambertenghi Deliliers1, Silvio Bicciato4, Manlio Ferrarini3,9, and Antonino Neri1 Abstract Purpose: Chromosome 13q14 deletion occurs in a substantial number of chronic lymphocytic leukemia (CLL) patients and it is believed to play a pathogenetic role. The exact mechanisms involved in this lesion have not yet been fully elucidated because of its heterogeneity and the imprecise knowledge of the implicated genes. This study was addressed to further contribute to the molecular definition of this lesion in CLL. Experimental Design: We applied single-nucleotide polymorphism (SNP)-array technology and gene expression profiling data to investigate the 13q14 deletion occurring in a panel of 100 untreated, early-stage (Binet A) patients representative of the major genetics, molecular, and biological features of the disease. Results: Concordantly with FISH analysis, SNP arrays identified 44 patients with del(13)(q14) including 11 cases with a biallelic deletion. The shorter monoallelic deletion was 635-kb long. The loss of the miR-15a/16-1 cluster occurred in all del(13)(q14) cases except in 2 patients with a monoallelic deletion, who retained both copies. MiR-15a/16 expression was significantly downregulated only in patients with the biallelic loss of the miRNA cluster compared to 13q normal cases. -
HIV-1 Tat: Its Dependence on Host Factors Is Crystal Clear
Viruses 2010, 2, 2226-2234; doi:10.3390/v2102226 OPEN ACCESS viruses ISSN 1999-4915 www.mdpi.com/journal/viruses Commentary HIV-1 Tat: Its Dependence on Host Factors is Crystal Clear Iván D’Orso and Alan D. Frankel * Department of Biochemistry and Biophysics, University of California, 600 16th Street, San Francisco, CA 94158-2280, USA; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-415-476-9994; Fax: +1-415-514-4112. Received: 2 September 2010; in revised form: 1 October 2010 / Accepted: 1 October 2010 / Published: 6 October 2010 Abstract: HIV-1 transcription is regulated at the level of elongation by the viral Tat protein together with the cellular elongation factor P-TEFb, which is composed of cyclin T1 and Cdk9 subunits. The crystal structure of a Tat:P-TEFb complex (Tahirov, T.H.; Babayeva, N.D.; Varzavand, K.; Cooper, J.J.; Sedore, S.C.; and Price, D.H. Crystal structure of HIV-1 Tat complexed with human P-TEFb. Nature 2010, 465, 747-751.) reveals molecular details of Tat and its interactions that have eluded investigators for more than two decades and provides provocative insights into the mechanism of Tat activation. Keywords: HIV-1; Tat; transcription; P-TEFb; retroviruses HIV-1, like many viruses, co-opts the cellular machinery to orchestrate its life cycle, including its transcriptional program, and the recent crystal structure of a viral-host protein complex has revealed new facets of this interplay [1]. In this case, the virally encoded Tat protein recruits the host factor positive transcription elongation factor b (P-TEFb) to an RNA hairpin formed at the 5’-end of nascent viral RNAs (TAR) to activate a switch to transcription elongation [2]. -
Supplementary Table 1
Supplementary Table 1. 492 genes are unique to 0 h post-heat timepoint. The name, p-value, fold change, location and family of each gene are indicated. Genes were filtered for an absolute value log2 ration 1.5 and a significance value of p ≤ 0.05. Symbol p-value Log Gene Name Location Family Ratio ABCA13 1.87E-02 3.292 ATP-binding cassette, sub-family unknown transporter A (ABC1), member 13 ABCB1 1.93E-02 −1.819 ATP-binding cassette, sub-family Plasma transporter B (MDR/TAP), member 1 Membrane ABCC3 2.83E-02 2.016 ATP-binding cassette, sub-family Plasma transporter C (CFTR/MRP), member 3 Membrane ABHD6 7.79E-03 −2.717 abhydrolase domain containing 6 Cytoplasm enzyme ACAT1 4.10E-02 3.009 acetyl-CoA acetyltransferase 1 Cytoplasm enzyme ACBD4 2.66E-03 1.722 acyl-CoA binding domain unknown other containing 4 ACSL5 1.86E-02 −2.876 acyl-CoA synthetase long-chain Cytoplasm enzyme family member 5 ADAM23 3.33E-02 −3.008 ADAM metallopeptidase domain Plasma peptidase 23 Membrane ADAM29 5.58E-03 3.463 ADAM metallopeptidase domain Plasma peptidase 29 Membrane ADAMTS17 2.67E-04 3.051 ADAM metallopeptidase with Extracellular other thrombospondin type 1 motif, 17 Space ADCYAP1R1 1.20E-02 1.848 adenylate cyclase activating Plasma G-protein polypeptide 1 (pituitary) receptor Membrane coupled type I receptor ADH6 (includes 4.02E-02 −1.845 alcohol dehydrogenase 6 (class Cytoplasm enzyme EG:130) V) AHSA2 1.54E-04 −1.6 AHA1, activator of heat shock unknown other 90kDa protein ATPase homolog 2 (yeast) AK5 3.32E-02 1.658 adenylate kinase 5 Cytoplasm kinase AK7 -
Genotype-Phenotype Correlations in Patients with Retinoblastoma And
Genotype-phenotype correlations in patients with Retinoblastoma and an interstitial 13q deletion Diana Mitter, Reinhard Ullmann, Artur Muradyan, Ludger Klein-Hitpaß, Deniz Kanber, Dietmar R Lohmann, Katrin Ounap, Marc Kaulisch To cite this version: Diana Mitter, Reinhard Ullmann, Artur Muradyan, Ludger Klein-Hitpaß, Deniz Kanber, et al.. Genotype-phenotype correlations in patients with Retinoblastoma and an interstitial 13q deletion. European Journal of Human Genetics, Nature Publishing Group, 2011, 10.1038/ejhg.2011.58. hal- 00633984 HAL Id: hal-00633984 https://hal.archives-ouvertes.fr/hal-00633984 Submitted on 20 Oct 2011 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. 1 Genotype-phenotype correlations in patients with Retinoblastoma and interstitial 13q deletions 1, *Diana Mitter, 2Reinhard Ullmann, 2Artur Muradyan, 3Ludger Klein-Hitpaß, 1Deniz Kanber, 4Katrin Õunap, 5Marc Kaulisch, 1Dietmar Lohmann 1Institut für Humangenetik, Universitätsklinikum Essen, Germany; 2Max-Planck- Institute of Molecular Genetic, Berlin, Germany; 3Institute for Cell Biology (Tumor Research), University of Duisburg-Essen, Germany; 4Department of Genetics, United Laboratories, Tartu University Hospital, Estonia; 5Institute for Research Information and Quality Assurance, Germany. *Correspondence and present address: Diana Mitter, Institut für Humangenetik, Universitätsklinikum Leipzig, Philipp-Rosenthal-Str. -
Massively Parallel Sequencing Reveals an Accumulation of De Novo Mutations and an Activating Mutation of LPAR1 in a Patient with Metastatic Neuroblastoma
Massively Parallel Sequencing Reveals an Accumulation of De Novo Mutations and an Activating Mutation of LPAR1 in a Patient with Metastatic Neuroblastoma Jun S. Wei1*, Peter Johansson1, Li Chen1, Young K. Song1, Catherine Tolman1, Samuel Li1, Laura Hurd1, Rajesh Patidar1, Xinyu Wen1,2, Thomas C. Badgett1, Adam T. C. Cheuk1, Jean-Claude Marshall3, Patricia S. Steeg3, José P. Vaqué Díez4, Yanlin Yu5, J. Silvio Gutkind4, Javed Khan1* 1 Oncogenomics Section, Pediatric Oncology Branch, Advanced Technology Center, National Cancer Institute, Bethesda, Maryland, United States of America, 2 The Advanced Biomedical Computing Center, SAIC-Frederick, Inc., National Cancer Institute, Frederick, Frederick, Maryland, United States of America, 3 Women’s Cancers Section, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America, 4 Cell Growth Regulation Section, National Institute of Dental and Craniofacial Research, Bethesda, Maryland, United States of America, 5 Cancer Modeling Section, Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America Abstract Neuroblastoma is one of the most genomically heterogeneous childhood malignances studied to date, and the molecular events that occur during the course of the disease are not fully understood. Genomic studies in neuroblastoma have showed only a few recurrent mutations and a low somatic mutation burden. However, none of these studies has examined the mutations arising during the course of disease, nor have they systemically examined the expression of mutant genes. Here we performed genomic analyses on tumors taken during a 3.5 years disease course from a neuroblastoma patient (bone marrow biopsy at diagnosis, adrenal primary tumor taken at surgical resection, and a liver metastasis at autopsy). -
Whole Genome Sequencing Identifies Homozygous BRCA2 Deletion Guiding Treatment in De-Differentiated Prostate Cancer
Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Whole Genome Sequencing identifies homozygous BRCA2 deletion guiding treatment in de-differentiated prostate cancer Karin Purshouse1~, Anna Schuh2~, Benjamin P Fairfax1, 5, Sam Knight3, Pavlos Antoniou2, Helene Dreau2, Niko Popitsch3, Kevin Gatter4, Ian Roberts5, Lisa Browning6, Zoe Traill7, David Kerr1, Clare Verrill6, Mark Tuthill1, Jenny C Taylor2,3*, Andrew Protheroe1* ~ joint first authors * Joint senior authors 1 - Oxford Cancer and Haematology Centre, Churchill Hospital, Headington, Oxford, OX3 7LE, UK. 2- Oxford National Institute for Health Research, Biomedical Research Centre/NHS Translational Diagnostics Centre, The Joint Research Office, Block 60, The Churchill Hospital, Old Road, Headington, Oxford, OX3 7LE, UK 3- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK 4- Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK. 5- Molecular Oncology and Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, OX3 9DS, UK 6- Department of Cellular Pathology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK. 7- Department of Radiology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 9DU, UK. Downloaded from molecularcasestudies.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Abstract Whole genome sequencing (WGS) has transformed the understanding of the genetic drivers of cancer and is increasingly being used in cancer medicine to identify personalised therapies. Here we describe a case where the application of WGS identified a tumoural BRCA2 deletion in a patient with aggressive dedifferentiated prostate cancer that was repeat biopsied after disease progression. -
Establishment and Characterisation of a New Breast Cancer Xenograft Obtained from a Woman Carrying a Germline BRCA2 Mutation
British Journal of Cancer (2010) 103, 1192 – 1200 & 2010 Cancer Research UK All rights reserved 0007 – 0920/10 www.bjcancer.com Establishment and characterisation of a new breast cancer xenograft obtained from a woman carrying a germline BRCA2 mutation 1 ´ 2 1 1 1 2 2,3 L de Plater , A Lauge , C Guyader , M-F Poupon , F Assayag , P de Cremoux , A Vincent-Salomon , 2,3,4 2 5 6 6 6 1,7 D Stoppa-Lyonnet , B Sigal-Zafrani , J-J Fontaine , R Brough , CJ Lord , A Ashworth , P Cottu , 1,7 *,1 D Decaudin and E Marangoni 1 Preclinical Investigation Unit, Institut Curie – Translational Research Department, Hoˆpital St Louis, Quadrilate`re historique, Porte 13, 1, Ave Claude 2 3 4 Vellefaux, Paris 75010, France; Department of Tumor Biology, Institut Curie, Paris, France; INSERM U830, Institut Curie, Paris, France; University Paris Translational Therapeutics 5 6 Descartes, Paris, France; National Veterinary School of Maisons Alfort, Maisons-Alfort, France; Gene Function Laboratory, The Breakthrough Breast 7 Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK; Department of Medical Oncology, Institut Curie, Paris, France BACKGROUND: The BRCA2 gene is responsible for a high number of hereditary breast and ovarian cancers, and studies of the BRCA2 biological functions are limited by the lack of models that resemble the patient’s tumour features. The aim of this study was to establish and characterise a new human breast carcinoma xenograft obtained from a woman carrying a germline BRCA2 mutation. METHODS: A transplantable xenograft was obtained by grafting a breast cancer sample into nude mice.