Ryanodine Receptors: Structure, Expression, Molecular Details, and Function in Calcium Release
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Surface Glycoproteomic Analysis of Hepatocellular Carcinoma Cells by Affinity Enrichment and Mass Spectrometric Identification
Glycoconj J (2012) 29:411–424 DOI 10.1007/s10719-012-9420-3 Surface glycoproteomic analysis of hepatocellular carcinoma cells by affinity enrichment and mass spectrometric identification Wei Mi & Wei Jia & Zhaobin Zheng & Jinglan Wang & Yun Cai & Wantao Ying & Xiaohong Qian Received: 14 April 2012 /Revised: 5 June 2012 /Accepted: 12 June 2012 /Published online: 1 July 2012 # Springer Science+Business Media, LLC 2012 Abstract Cell surface glycoproteins are one of the most surface-capturing (CSC) technique was an approach specif- frequently observed phenomena correlated with malignant ically targeted at membrane glycoproteins involving the growth. Hepatocellular carcinoma (HCC) is one of the most affinity capture of membrane glycoproteins using glycan malignant tumors in the world. The majority of hepatocel- biotinylation labeling on intact cell surfaces. To characterize lular carcinoma cell surface proteins are modified by glyco- the cell surface glycoproteome and probe the mechanism of sylation in the process of tumor invasion and metastasis. tumor invasion and metastasis of HCC, we have modified Therefore, characterization of cell surface glycoproteins can and evaluated the cell surface-capturing strategy, and ap- provide important information for diagnosis and treatment plied it for surface glycoproteomic analysis of hepatocellu- of liver cancer, and also represent a promising source of lar carcinoma cells. In total, 119 glycosylation sites on 116 potential diagnostic biomarkers and therapeutic targets for unique glycopeptides were identified, corresponding to 79 hepatocellular carcinoma. However, cell surface glycopro- different protein species. Of these, 65 (54.6 %) new pre- teins of HCC have been seldom identified by proteomics dicted glycosylation sites were identified that had not pre- approaches because of their hydrophobic nature, poor solu- viously been determined experimentally. -
Microarchitecture of the Dyad
Cardiovascular Research (2013) 98, 169–176 SPOTLIGHT REVIEW doi:10.1093/cvr/cvt025 Microarchitecture of the dyad David R.L. Scriven, Parisa Asghari, and Edwin D.W. Moore* Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, Canada V6T 1Z3 Received 12 December 2012; revised 2 February 2013; accepted 4 February 2013; online publish-ahead-of-print 11 February 2013 Downloaded from https://academic.oup.com/cardiovascres/article/98/2/169/278625 by guest on 23 September 2021 Abstract This review highlights recent and ongoing discoveries that are transforming the previously held view of dyad structure and function. New data show that dyads vary greatly in both structure and in their associated molecules. Dyads can contain varying numbers of type 2 ryanodine receptor (RYR2) clusters that range in size from one to hundreds of tetramers and they can adopt numerous orientations other than the expected checkerboard. The association of Cav1.2 with RYR2, which defines the couplon, is not absolute, leading to a number of scenarios such as dyads without couplons and those in which only a fraction of the clusters are in couplons. Different dyads also vary in the transporters and exchangers with which they are associated producing functional differences that amplify their structural diversity. The essential role of proteins, such as junctophilin-2, calsequestrin, triadin, and junctin that main- tain both the functional and structural integrity of the dyad have recently been elucidated giving a new mechanistic understanding of heart diseases, such as arrhythmias, hypertension, failure, and sudden cardiac death. -
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. -
The Inactive X Chromosome Is Epigenetically Unstable and Transcriptionally Labile in Breast Cancer
Supplemental Information The inactive X chromosome is epigenetically unstable and transcriptionally labile in breast cancer Ronan Chaligné1,2,3,8, Tatiana Popova1,4, Marco-Antonio Mendoza-Parra5, Mohamed-Ashick M. Saleem5 , David Gentien1,6, Kristen Ban1,2,3,8, Tristan Piolot1,7, Olivier Leroy1,7, Odette Mariani6, Hinrich Gronemeyer*5, Anne Vincent-Salomon*1,4,6,8, Marc-Henri Stern*1,4,6 and Edith Heard*1,2,3,8 Extended Experimental Procedures Cell Culture Human Mammary Epithelial Cells (HMEC, Invitrogen) were grown in serum-free medium (HuMEC, Invitrogen). WI- 38, ZR-75-1, SK-BR-3 and MDA-MB-436 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen) containing 10% fetal bovine serum (FBS). DNA Methylation analysis. We bisulfite-treated 2 µg of genomic DNA using Epitect bisulfite kit (Qiagen). Bisulfite converted DNA was amplified with bisulfite primers listed in Table S3. All primers incorporated a T7 promoter tag, and PCR conditions are available upon request. We analyzed PCR products by MALDI-TOF mass spectrometry after in vitro transcription and specific cleavage (EpiTYPER by Sequenom®). For each amplicon, we analyzed two independent DNA samples and several CG sites in the CpG Island. Design of primers and selection of best promoter region to assess (approx. 500 bp) were done by a combination of UCSC Genome Browser (http://genome.ucsc.edu) and MethPrimer (http://www.urogene.org). All the primers used are listed (Table S3). NB: MAGEC2 CpG analysis have been done with a combination of two CpG island identified in the gene core. Analysis of RNA allelic expression profiles (based on Human SNP Array 6.0) DNA and RNA hybridizations were normalized by Genotyping console. -
Multiple Actions of Φ-LITX-Lw1a on Ryanodine Receptors Reveal a Functional Link Between Scorpion DDH and ICK Toxins
Multiple actions of φ-LITX-Lw1a on ryanodine receptors reveal a functional link between scorpion DDH and ICK toxins Jennifer J. Smitha, Irina Vettera, Richard J. Lewisa, Steve Peigneurb, Jan Tytgatb, Alexander Lamc, Esther M. Gallantc, Nicole A. Beardd, Paul F. Alewooda,1,2, and Angela F. Dulhuntyc,1,2 aChemical and Structural Biology, Institute for Molecular Biosciences, University of Queensland, St. Lucia, QLD 4072, Australia; bLaboratory of Toxicology, University of Leuven, 3000 Leuven, Belgium; cDepartment of Molecular Bioscience, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia; and dDiscipline of Biomedical Sciences, Faculty of Education, Science, Technology and Mathematics, University of Canberra, Canberra, ACT 2601, Australia Edited by Clara Franzini-Armstrong, University of Pennsylvania Medical Center, Philadelphia, PA, and approved April 23, 2013 (received for review August 26, 2012) We recently reported the isolation of a scorpion toxin named U1- mutations, atypical posttranslational modifications of RyRs, liotoxin-Lw1a (U1-LITX-Lw1a) that adopts an unusual 3D fold termed including hyperphosphorylation and S-nitrosylation, have been the disulfide-directed hairpin (DDH) motif, which is the proposed implicated in heart failure and pathologic muscle fatigue (10– evolutionary structural precursor of the three-disulfide-containing 12). Because of their wide distribution, there is mounting evidence inhibitor cystine knot (ICK) motif found widely in animals and plants. to suggest that dysregulation of RyRs also plays a role in a plethora Here we reveal that U1-LITX-Lw1a targets and activates the mam- of other disease states, including chronic pain, neurodegenerative malian ryanodine receptor intracellular calcium release channel (RyR) disorders such as Alzheimer’s disease, and intellectual deficit (13– with high (fM) potency and provides a functional link between DDH 15). -
Absence of Triadin, a Protein of the Calcium Release Complex, Is Responsible for Cardiac Arrhythmia with Sudden Death in Human
Absence of triadin, a protein of the calcium release complex, is responsible for cardiac arrhythmia with sudden death in human. Nathalie Roux-Buisson, Marine Cacheux, Anne Fourest-Lieuvin, J. Fauconnier, Julie Brocard, Isabelle Denjoy, Philippe Durand, Pascale Guicheney, Florence Kyndt, Antoine Leenhardt, et al. To cite this version: Nathalie Roux-Buisson, Marine Cacheux, Anne Fourest-Lieuvin, J. Fauconnier, Julie Brocard, et al.. Absence of triadin, a protein of the calcium release complex, is responsible for cardiac arrhythmia with sudden death in human.. Human Molecular Genetics, Oxford University Press (OUP), 2012, 21 (12), pp.2759-67. 10.1093/hmg/dds104. inserm-00763211 HAL Id: inserm-00763211 https://www.hal.inserm.fr/inserm-00763211 Submitted on 10 Dec 2012 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. HMG Advance Access published March 29, 2012 Human Molecular Genetics, 2012 1–9 doi:10.1093/hmg/dds104 Absence of triadin, a protein of the calcium release complex, is responsible for cardiac arrhythmia with sudden death in human Nathalie Roux-Buisson1,2,3,4,{, Marine Cacheux1,4,{, Anne Fourest-Lieuvin1,4,5, Jeremy Fauconnier6,7,8,9, Julie Brocard1,4, Isabelle Denjoy10, Philippe Durand11, Pascale Guicheney12,13, Florence Kyndt14,15,16, Antoine Leenhardt10, Herve´ Le Marec14,16,17, Vincent Lucet18, Philippe Mabo19, Vincent Probst14,16,17, Nicole Monnier1,2, Pierre F. -
Triadin, a Linker for Calsequestrin and the Ryanodine Receptor
Triadin, a Linker for Calsequestrin and the Ryanodine Receptor Wei Guo,* Annelise 0. Jorgensen,' and Kevin P. Campbell* *Howard Hughes Medical Institute, Department of Physiology and Biophysics, University of Iowa College of Medicine, Iowa City, Iowa 52242, and *Departmentof Anatomy and Cell Biology, University of Toronto, Toronto, Ontario, Canada M5S 1A8 Introduction Protein components of the triad junction play essential roles in muscle excitation- contraction coupling (EC coupling). Considerable research has been performed on the identification and characterization of proteins that regulate calcium storage and release from the sarcoplasmic reticulum (McPherson and Campbell, 1993; Franzini- Armstrong and Jorgensen, 1994). Key proteins characterized include the dihydro- pyridine receptor; the voltage sensor and L-type calcium channel in t-tubules; the ryanodine receptor/Ca2+-releasechannel in the terminal cisternae of the sarcoplas- mic reticulum; and calsequestrin, a moderate-affinity, high-capacity calcium-bind- ing protein located in the lumen of the junctional sarcoplasmic reticulum. Study of these proteins has been instrumental to our understanding of the molecular mecha- nisms of EC coupling. Recent research from our laboratory has focused on triadin, an abundant transmembrane protein in the junctional sarcoplasmic reticulum. Here, we briefly review recent results on the structure of triadin and its interactions with other protein components of the junctional complex in skeletal and cardiac muscle. Identification of Triadin Using purified skeletal muscle triads, we generated a library of monoclonal anti- bodies against different proteins of the junctional sarcoplasmic reticulum (Camp- bell et al., 1987). Several monoclonal antibodies recognize a protein of 94 kD (now called triadin) on reducing SDS-PAGE (Fig. -
Cldn19 Clic2 Clmp Cln3
NewbornDx™ Advanced Sequencing Evaluation When time to diagnosis matters, the NewbornDx™ Advanced Sequencing Evaluation from Athena Diagnostics delivers rapid, 5- to 7-day results on a targeted 1,722-genes. A2ML1 ALAD ATM CAV1 CLDN19 CTNS DOCK7 ETFB FOXC2 GLUL HOXC13 JAK3 AAAS ALAS2 ATP1A2 CBL CLIC2 CTRC DOCK8 ETFDH FOXE1 GLYCTK HOXD13 JUP AARS2 ALDH18A1 ATP1A3 CBS CLMP CTSA DOK7 ETHE1 FOXE3 GM2A HPD KANK1 AASS ALDH1A2 ATP2B3 CC2D2A CLN3 CTSD DOLK EVC FOXF1 GMPPA HPGD K ANSL1 ABAT ALDH3A2 ATP5A1 CCDC103 CLN5 CTSK DPAGT1 EVC2 FOXG1 GMPPB HPRT1 KAT6B ABCA12 ALDH4A1 ATP5E CCDC114 CLN6 CUBN DPM1 EXOC4 FOXH1 GNA11 HPSE2 KCNA2 ABCA3 ALDH5A1 ATP6AP2 CCDC151 CLN8 CUL4B DPM2 EXOSC3 FOXI1 GNAI3 HRAS KCNB1 ABCA4 ALDH7A1 ATP6V0A2 CCDC22 CLP1 CUL7 DPM3 EXPH5 FOXL2 GNAO1 HSD17B10 KCND2 ABCB11 ALDOA ATP6V1B1 CCDC39 CLPB CXCR4 DPP6 EYA1 FOXP1 GNAS HSD17B4 KCNE1 ABCB4 ALDOB ATP7A CCDC40 CLPP CYB5R3 DPYD EZH2 FOXP2 GNE HSD3B2 KCNE2 ABCB6 ALG1 ATP8A2 CCDC65 CNNM2 CYC1 DPYS F10 FOXP3 GNMT HSD3B7 KCNH2 ABCB7 ALG11 ATP8B1 CCDC78 CNTN1 CYP11B1 DRC1 F11 FOXRED1 GNPAT HSPD1 KCNH5 ABCC2 ALG12 ATPAF2 CCDC8 CNTNAP1 CYP11B2 DSC2 F13A1 FRAS1 GNPTAB HSPG2 KCNJ10 ABCC8 ALG13 ATR CCDC88C CNTNAP2 CYP17A1 DSG1 F13B FREM1 GNPTG HUWE1 KCNJ11 ABCC9 ALG14 ATRX CCND2 COA5 CYP1B1 DSP F2 FREM2 GNS HYDIN KCNJ13 ABCD3 ALG2 AUH CCNO COG1 CYP24A1 DST F5 FRMD7 GORAB HYLS1 KCNJ2 ABCD4 ALG3 B3GALNT2 CCS COG4 CYP26C1 DSTYK F7 FTCD GP1BA IBA57 KCNJ5 ABHD5 ALG6 B3GAT3 CCT5 COG5 CYP27A1 DTNA F8 FTO GP1BB ICK KCNJ8 ACAD8 ALG8 B3GLCT CD151 COG6 CYP27B1 DUOX2 F9 FUCA1 GP6 ICOS KCNK3 ACAD9 ALG9 -
Dual Copy Number Variants Involving 16P11 and 6Q22 in a Case
European Journal of Human Genetics (2013) 21, 361–366 & 2013 Macmillan Publishers Limited All rights reserved 1018-4813/13 www.nature.com/ejhg LETTERS 32 duplications, 0.78%). A detailed review of 18 patients found Dual copy number variants that the most consistent clinical manifestations in these individuals were intellectual impairment and speech and language delays.8 involving 16p11 and These findings were supported by a similar study that included 7400 patients who had undergone array comparative genomic 6q22inacaseof hybridisation (array-CGH) testing in a clinical context, 45 of whom carried 16p11.2 anomalies (27 deletions, 18 duplications, 0.6%).3 childhood apraxia of Phenotypic characterisation of 27 individuals also found that all had speech and language delays and cognitive impairment.3 Other predomi- nant features of 16p11.2 syndrome include dysmorphism, macrocephaly speech and pervasive and autistic disorders.3,4,8,14 However, all of these features have been disputed and it is likely that ascertainment bias will affect the developmental disorder conclusions of many studies, particularly those that focus upon single cases. Thus, the characterisation of the relationships between genetic aberration and clinical presentation is ongoing and will require European Journal of Human Genetics (2013) 21, 361–365; further, more refined, studies with detailed investigations of this doi:10.1038/ejhg.2012.166; published online 22 August 2012 chromosome region and consistent phenotyping of affected individuals. The child described here was originally assessed for the presence of In this issue, Raca et al1 present two cases of childhood apraxia of FOXP2 (OMIM #605317) mutations and rearrangements, as part of 15 speech (CAS) arising from microdeletions of chromosome 16p11.2. -
Application of Microrna Database Mining in Biomarker Discovery and Identification of Therapeutic Targets for Complex Disease
Article Application of microRNA Database Mining in Biomarker Discovery and Identification of Therapeutic Targets for Complex Disease Jennifer L. Major, Rushita A. Bagchi * and Julie Pires da Silva * Department of Medicine, Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; [email protected] * Correspondence: [email protected] (R.A.B.); [email protected] (J.P.d.S.) Supplementary Tables Methods Protoc. 2021, 4, 5. https://doi.org/10.3390/mps4010005 www.mdpi.com/journal/mps Methods Protoc. 2021, 4, 5. https://doi.org/10.3390/mps4010005 2 of 25 Table 1. List of all hsa-miRs identified by Human microRNA Disease Database (HMDD; v3.2) analysis. hsa-miRs were identified using the term “genetics” and “circulating” as input in HMDD. Targets CAD hsa-miR-1 Targets IR injury hsa-miR-423 Targets Obesity hsa-miR-499 hsa-miR-146a Circulating Obesity Genetics CAD hsa-miR-423 hsa-miR-146a Circulating CAD hsa-miR-149 hsa-miR-499 Circulating IR Injury hsa-miR-146a Circulating Obesity hsa-miR-122 Genetics Stroke Circulating CAD hsa-miR-122 Circulating Stroke hsa-miR-122 Genetics Obesity Circulating Stroke hsa-miR-26b hsa-miR-17 hsa-miR-223 Targets CAD hsa-miR-340 hsa-miR-34a hsa-miR-92a hsa-miR-126 Circulating Obesity Targets IR injury hsa-miR-21 hsa-miR-423 hsa-miR-126 hsa-miR-143 Targets Obesity hsa-miR-21 hsa-miR-223 hsa-miR-34a hsa-miR-17 Targets CAD hsa-miR-223 hsa-miR-92a hsa-miR-126 Targets IR injury hsa-miR-155 hsa-miR-21 Circulating CAD hsa-miR-126 hsa-miR-145 hsa-miR-21 Targets Obesity hsa-mir-223 hsa-mir-499 hsa-mir-574 Targets IR injury hsa-mir-21 Circulating IR injury Targets Obesity hsa-mir-21 Targets CAD hsa-mir-22 hsa-mir-133a Targets IR injury hsa-mir-155 hsa-mir-21 Circulating Stroke hsa-mir-145 hsa-mir-146b Targets Obesity hsa-mir-21 hsa-mir-29b Methods Protoc. -
Generation of a Triadin Knockout Syndrome Zebrafish Model
International Journal of Molecular Sciences Article Generation of a Triadin KnockOut Syndrome Zebrafish Model Vanilla Martina Vecchi 1,†, Marco Spreafico 1,† , Alessia Brix 1, Anna Santoni 2, Simone Sala 3 , Anna Pistocchi 1,* , Anna Marozzi 1,† and Chiara Di Resta 2,† 1 Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, LITA, Segrate, 20090 Milan, Italy; [email protected] (V.M.V.); marco.spreafi[email protected] (M.S.); [email protected] (A.B.); [email protected] (A.M.) 2 UOC Clinical Genomics, IRCCS San Raffaele Hospital, 20132 Milan, Italy; [email protected] (A.S.); [email protected] (C.D.R.) 3 Department of Cardiac Electrophysiology and Arrhythmology, IRCCS San Raffaele Hospital, 20132 Milan, Italy; [email protected] * Correspondence: [email protected] † These authors contributed equally to the work. Abstract: Different forms of sudden cardiac death have been described, including a recently identified form of genetic arrhythmogenic disorder, named “Triadin KnockOut Syndrome” (TKOS). TKOS is associated with recessive mutations in the TRDN gene, encoding for TRIADIN, but the pathogenic mechanism underlying the malignant phenotype has yet to be completely defined. Moreover, patients with TKOS are often refractory to conventional treatment, substantiating the need to identify new therapeutic strategies in order to prevent or treat cardiac events. The zebrafish (Danio rerio) heart is highly comparable to the human heart in terms of functions, signal pathways and ion channels, representing a good model to study cardiac disorders. In this work, we generated the first zebrafish model for trdn loss-of-function, by means of trdn morpholino injections, and characterized Citation: Vecchi, V.M.; Spreafico, M.; its phenotype. -
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European Review for Medical and Pharmacological Sciences 2019; 23: 1710-1721 Next-generation sequencing identifies a homozygous mutation in ACADVL associated with pediatric familial dilated cardiomyopathy S.J. CARLUS1, I.S. ALMUZAINI2, M. KARTHIKEYAN3, L. LOGANATHAN3, G.S. AL-HARBI1, A.M. ABDALLAH4, K.M. AL-HARBI1 1Pediatrics Department, Cardiogenetics Unit, College of Medicine, Taibah University, Al-Madinah, Kingdom of Saudi Arabia 2Department of Pediatric Cardiology, Al-Madinah Maternity and Children Hospital (MMCH), Al-Madinah, Kingdom of Saudi Arabia 3Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India 4West Midlands Regional Genetics Laboratory, Birmingham Women’s NHS Foundation Trust, Birmingham, United Kingdom Abstract. – OBJECTIVE: Pediatric familial di- Key Words lated cardiomyopathy (DCM) is a rare and se- Pediatric familial dilated cardiomyopathy, Targeted vere heart disease. The genetics of familial DCM gene sequencing, ACADVL, Saudi Arabia, Consanguinity, are complex and include over 100 known dis- Molecular docking, Molecular dynamics. ease-causing genes, but many causative genes are unknown. We aimed to identify the causative gene for DCM in a consanguineous Saudi Ara- bian family with affected family members and a history of sudden death. Introduction PATIENTS AND METHODS: Affected (two chil- dren) and unaffected (one sibling and the mother) Dilated cardiomyopathy (DCM) is a heart family members were screened by next-gener- ation sequencing (NGS) for 181 candidate DCM disease characterized by ventricular dilation and genes and underwent metabolic screening. Fif- impaired myocardial contractility. DCM affects ty-seven clinically annotated controls and 46 DCM 1 in 2500 of the general population and is one of cases were then tested for the identified mutation.