Clinical and Genetic Studies in Inherited Cardiovascular

Total Page:16

File Type:pdf, Size:1020Kb

Load more

CLINICAL AND GENETIC STUDIES IN INHERITED CARDIOVASCULAR MALFORMATIONS CARDIOVASCULAR CLINICAL AND GENETIC STUDIES IN INHERITED MALFORMATIONS Ingrid van de Laar Financial support by the Dutch Heart Foundation and the J.E. Jurriaanse Stichting for the publication of this thesis is gratefully acknowledged. © Copyright: Ingrid van de Laar, Rotterdam, 2012 All rights reserved. No part of this thesis may be reproduced in any form or by any means, electronic, mechanical, photocopy, recording or otherwise, without prior permission from the holder of the copyright. The copyrights of the publications remain with the publisher. ISBN: 978-94-6169-259-7 Cover design: Esther van der Heijden Layout and printing: Optima Grafische Communicatie, Rotterdam, The Netherlands CLINICAL AND GENETIC STUDIES IN INHERITED CARDIOVAscULAR MALFORMATIONS Klinisch en Genetisch OnderZoek Van Erfelijke CardioVascUlaire Malformaties Proefschrift ter verkrijging van de graad van doctor aan de Erasmus Universiteit Rotterdam op gezag van de rector magnificus Prof.dr. H.G. Schmidt en volgens besluit van het College voor Promoties De openbare verdediging zal plaatsvinden op woensdag 27 juni 2012 om 13.30 uur door Ingrid Maria Bernadetta Henrica van de Laar geboren te Liempde Promotiecommissie Promotoren: Prof.dr. B.A. Oostra Prof.dr. J.W. Roos-Hesselink Overige leden: Prof.dr. W.A. Helbing Prof.dr. B.L. Loeys Dr. G. Pals Copromotoren: Dr. A.M. Bertoli-Avella Dr. M.W. Wessels Het onderzoek dat aan dit proefschrift ten grondslag ligt is mogelijk gemaakt door een subsidie van de Nederlandse Hartstichting (NHS-2006T006) TABLE OF CONTENTS Chapter 1 General introduction 13 1.1 15 1.1.1 Congenital heart malformations 15 1.1.1.1 Incidence 15 1.1.1.2 Classification and genetics 15 1.1.1.2.1 Non-syndromic CHM 16 1.1.1.2.2 Syndromic 16 CHM 1.1.1.3 Laterality disorders 21 1.1.1.3.1 Definition wand incidence 21 1.1.1.3.3 Pathophysiology 21 1.1.1.3.4 Genetics 22 1.1.1.4 Pulmonary vein anomalies 23 1.1.1.4.1 Definition and incidence 23 1.1.1.4.2 Pathophysiology 23 1.1.1.4.3 Genetics 24 1.1.1.5 Valvular 25 anomalies 1.1.1.5.1 Definition and 25 incidence 1.1.1.5.2 Pathophysiology 25 1.1.1.5.3 Genetics 25 1.1.2. Aortic aneurysms 26 1.1.2.1 Incidence 26 1.1.2.2 Classification and genetics 27 1.1.2.2.1 Abdominal aortic aneurysms 27 1.1.2.2.2 Thoracic aortic aneurysms 28 1.1.2.2.3 Non-syndromic aortic aneurysms 28 1.1.2.2.4 Syndromic aortic aneurysms 33 1.1.2.2.5 TGF-β signaling pathway 45 1.1.2.3. Aneurysms-osteoarthritis syndrome 49 1.1.2.3.1 Definition and incidence 49 1.1.2.3.3 Pathophysiology 52 1.1.2.3.4 Genetics 53 1.2 Aim and outline of the thesis 74 Chapter 2 NPHP4 genetic variants are associated with pleiotropic heart 77 malformations Circ Res. 2012, in press Chapter 3 First locus for primary pulmonary vein stenosis maps to chromosome 111 2q Eur Heart J. 2009; 30: 2485-92 Chapter 4 Autosomal dominant inheritance of cardiac valves anomalies in two families: extended spectrum of left-ventricular outflow tract obstruction 129 Am J Med Genet A. 2009; 149A: 216-25 Chapter 5 Mutations in SMAD3 cause a syndromic form of aortic aneurysms and dissections with early-onset osteoarthritis Nat Genet. 2011; 43: 151 121-6 Chapter 6 Phenotypic spectrum of the SMAD3-related aneurysms-osteoarthritis 175 syndrome J Med Genet. 2012; 49: 47-57 Chapter 7 Aggressive cardiovascular phenotype of aneurysms-osteoarthritis syndrome caused by pathogenic SMAD3 variants J Am Coll Cardiol. 199 2012, in press Chapter 8 Summary and discussion 225 Samenvatting 233 Curriculum Vitae 237 PhD Portfolio Summary 239 List of publications 243 List of affiliations by author 247 Dankwoord 253 ABBREVIATIONS AAA abdominal aortic aneurysm AF atrial fibrillation AI aortic valve insufficiency AOS aneurysms-osteoarthritis syndrome aPWV aortic pulse wave velocity ADCL autosomal dominant cutis laxa AR aortic valve regurgitation ARCL autosomal recessive cutis laxa AS aortic valve stenosis ASD atrial septal defect ATS arterial tortuosity syndrome AV atrioventricular AVSD atrioventricular septal defect BAV bicuspid aortic valve BSA body surface area CFC cardio-facio-cutaneous CHM congenital heart malformation CNV copy number variation CoA coarctation of the aorta CTA computed tomography angiography CTGF connective tissue growth factor CVM cardiovascular malformation DCM dilated cardiomyopathy DORV double outlet right ventricle EDS ehlers danlos syndrome ECG electocardiogram EMT endothelial-to-mesenchymal transdifferentiation FHF first heart field FTAAD familial thoracic aortic aneurysm-dissection GWAS genome wide association studies GWLA genome wide linkage analysis HAA hypoplastic aortic arch HCM hypertrophic cardiomyopathy Het heterozygous HLH hypoplastic left heart HLHS hypoplastic left heart syndrome HLV hypoplastic left ventricle Hom homozygous HRFC hepatorenal fibrocystic HRV hypoplastic right ventricle IAA interrupted aortic arch ICV inferior caval vein IFT intraflagellar transport KV kupffer’s vesicle LDS loeys-dietz syndrome LOD logarithm (base 10) of the odds LPM lateral plate mesoderm LPV left pulmonary vein LR left-right LVH left ventricular hypertrophy LVNC left ventricular noncompaction LVOTO left ventricular outflow tract obstruction Mb megabases MFS marfan syndrome MI mitral valve insufficiency MiRNA microRNA MO morpholino oligonucleotides MR mitral valve regurgitation MRA magnetic resonance angiography MRI magnetic resonance imaging MV mitral valve MS mitral valve stenosis MVP mitral valve prolapse NCCM noncompaction cardiomyopathy NGS next generation sequencing NPHP nephronophthisis NT-proBNP N-terminal probrain natriuretic peptide OA osteoarthritis OCD osteochondritis dissecans PA pulmonary atresia PAPVR partial anomalous pulmonary venous return PCD primary ciliary dyskinesia PCR polymerase chain reaction PDA persistent ductus arteriosus PPS peripheral pulmonary stenosis PS pulmonary valve stenosis PTA persistent truncus arteriosus PV pulmonary vein PVOD pulmonary veno-occlusive disease PVS pulmonary vein stenosis RPV right pulmonary vein SB stillbirth SB-MO splicing blocking morpholino SCV superior caval vein SLSN Senior-Loken syndrome SNP single nucleotide polymorphism SVAS supravalvular aortic stenosis TA tricuspid atresia TAA thoracic aortic aneurysm TAAD thoracic aortic aneurysm-dissection TAPVR total anomalous pulmonary venous return TB-MO translation blocking morpholino TGA transposition of the great arteries TGF transforming growth factor TOF tetralogy of Fallot TTE transthoracic echocardiography UTR untranslated region VSD ventricular septal defect VSMC vascular smooth muscle cells VUS variant of unknown significance WES whole exome sequencing GENERAL INTRODUCTION CHAPTER 1 1.1 CARDIOVASCULAR MALFORMATIONS Cardiovascular malformations comprise a broad spectrum of anomalies of the heart and blood vessels, including congenital heart malformations (CHM) and aortic aneurysms, the two main topics of this thesis. These conditions lead to significant morbidity and mortality both in infancy and adulthood. A substantial proportion of cardiovascular malformations have a genetic back- ground, including large chromosomal abnormalities, submicroscopic chromosome deletions or duplications, and single gene mutations. However, the majority of cardiovascular malformations is thought to be due to multifactorial inheritance, involving a multitude of mutations in susceptibility genes superposed on unfavorable environmental and life style factors. In the past decade, great progress has been made in the unravelling of genes involved in cardiovascular malformations. This made it possible to understand the genetic pathways and underlying pathophysiologic mechanisms, and develop therapeutic and preventive measures. It also led to the need for multidisciplinary cardiogenetic clinics in order to improve diagnosis and treatment of cardiovascular diseases. Such a multidisciplinary cardiogenetic clinic has been established in the (Paediatric) Cardiology Department of the Erasmus Medical Center in Rotterdam. In this setting most patients described in this thesis were studied. With the enthusiastic participation of these patients, their families and physicians, scientific studies were initiated to understand the genetic cause of cardiovascular malformations. 1.1.1 Congenital heart malformations 1.1.1.1 Incidence CHM are the most common birth defects, with an incidence ranging from 6 to 75 out of thousand live births.1 Accordingly, in the Netherlands every year around 1800 children are born with a CHM. The morbidity and mortality varies with the severity of the CHM, but overall, it is the leading cause of infant death in the Western countries.2 1.1.1.2 Classification and genetics CHM can be classified into syndromic and non-syndromic forms. Syndromic CHM, characterized by additional non-cardiac malformations, is present in about a quarter 15 of children with CHM.3 The majority of patients has non-syndromic CHM, not associ- 1 Chapter ated with other anomalies. In the past decade tremendous progress has been made in the elucidation of the molecular mechanisms involved in CHM.2 Monogenic inheritance can be autosomal dominant (most families), or autosomal recessive or X-linked (minority of families). Studies of monogenic CHM (both syndromic and non-syndromic) usually with auto- somal dominant inheritance have proven to be instrumental for the identification of genes involved in CHM. 1.1.1.2.1 Non-syndromic CHM Whereas monogenic mutations are responsible for many syndromic forms of CHM, mutations in these genes account for only a
Recommended publications
  • Long Non-Coding RNA Landscape in Prostate Cancer Molecular Subtypes: a Feature Selection Approach

    Long Non-Coding RNA Landscape in Prostate Cancer Molecular Subtypes: a Feature Selection Approach

    International Journal of Molecular Sciences Article Long Non-Coding RNA Landscape in Prostate Cancer Molecular Subtypes: A Feature Selection Approach Simona De Summa 1,* , Antonio Palazzo 2 , Mariapia Caputo 1, Rosa Maria Iacobazzi 3 , Brunella Pilato 1, Letizia Porcelli 3, Stefania Tommasi 1 , Angelo Virgilio Paradiso 4,† and Amalia Azzariti 3,† 1 Molecular Diagnostics and Pharmacogenetics Unit, IRCCS IstitutoTumori Giovanni Paolo II, 70124 Bari, Italy; [email protected] (M.C.); [email protected] (B.P.); [email protected] (S.T.) 2 Laboratory of Nanotechnology, IRCCS IstitutoTumori Giovanni Paolo II, 70124 Bari, Italy; [email protected] 3 Laboratory of Experimental Pharmacology, IRCCS Istituto Tumori Giovanni Paolo II, 70124 Bari, Italy; [email protected] (R.M.I.); [email protected] (L.P.); [email protected] (A.A.) 4 Scientific Directorate, IRCCS Istituto Tumori Giovanni Paolo II, 70124 Bari, Italy; [email protected] * Correspondence: [email protected] † Co-senior authors. Abstract: Prostate cancer is one of the most common malignancies in men. It is characterized by a high molecular genomic heterogeneity and, thus, molecular subtypes, that, to date, have not been used in clinical practice. In the present paper, we aimed to better stratify prostate cancer patients through the selection of robust long non-coding RNAs. To fulfill the purpose of the study, a bioinformatic approach focused on feature selection applied to a TCGA dataset was used. In such a way, LINC00668 and long non-coding(lnc)-SAYSD1-1, able to discriminate ERG/not-ERG subtypes, Citation: De Summa, S.; Palazzo, A.; were demonstrated to be positive prognostic biomarkers in ERG-positive patients.
  • A Genomics Approach Reveals Insights Into the Importance of Gene Losses for Mammalian Adaptations

    A Genomics Approach Reveals Insights Into the Importance of Gene Losses for Mammalian Adaptations

    Corrected: Publisher correction ARTICLE DOI: 10.1038/s41467-018-03667-1 OPEN A genomics approach reveals insights into the importance of gene losses for mammalian adaptations Virag Sharma1,2,3, Nikolai Hecker1,2,3, Juliana G. Roscito1,2,3, Leo Foerster1,2,3, Bjoern E. Langer1,2,3 & Michael Hiller1,2,3 1234567890():,; Identifying the genomic changes that underlie phenotypic adaptations is a key challenge in evolutionary biology and genomics. Loss of protein-coding genes is one type of genomic change with the potential to affect phenotypic evolution. Here, we develop a genomics approach to accurately detect gene losses and investigate their importance for adaptive evolution in mammals. We discover a number of gene losses that likely contributed to morphological, physiological, and metabolic adaptations in aquatic and flying mammals. These gene losses shed light on possible molecular and cellular mechanisms that underlie these adaptive phenotypes. In addition, we show that gene loss events that occur as a consequence of relaxed selection following adaptation provide novel insights into species’ biology. Our results suggest that gene loss is an evolutionary mechanism for adaptation that may be more widespread than previously anticipated. Hence, investigating gene losses has great potential to reveal the genomic basis underlying macroevolutionary changes. 1 Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany. 2 Max Planck Institute for the Physics of Complex Systems, Noethnitzer Str. 38, 01187 Dresden, Germany. 3 Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307 Dresden, Germany. Correspondence and requests for materials should be addressed to M.H. (email: [email protected]) NATURE COMMUNICATIONS | (2018) 9:1215 | DOI: 10.1038/s41467-018-03667-1 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-03667-1 ne of the most fascinating aspects of nature is the a b % conserved genes diversity of life.
  • Array Painting Reveals a High Frequency of Balanced Translocations in Breast Cancer Cell Lines That Break in Cancer-Relevant Genes

    Array Painting Reveals a High Frequency of Balanced Translocations in Breast Cancer Cell Lines That Break in Cancer-Relevant Genes

    Oncogene (2008) 27, 3345–3359 & 2008 Nature Publishing Group All rights reserved 0950-9232/08 $30.00 www.nature.com/onc ONCOGENOMICS Array painting reveals a high frequency of balanced translocations in breast cancer cell lines that break in cancer-relevant genes KD Howarth1, KA Blood1,BLNg2, JC Beavis1, Y Chua1, SL Cooke1, S Raby1, K Ichimura3, VP Collins3, NP Carter2 and PAW Edwards1 1Department of Pathology, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK; 2Wellcome Trust Sanger Institute, Cambridge, UK and 3Department of Pathology, Division of Molecular Histopathology, Addenbrookes Hospital, University of Cambridge, Cambridge, UK Chromosome translocations in the common epithelial tion and inversion, which can result in gene fusion, cancers are abundant, yet little is known about them. promoter insertion or gene inactivation. As is well They have been thought to be almost all unbalanced and known in haematopoietic tumours and sarcomas, therefore dismissed as mostly mediating tumour suppres- translocations and inversions can have powerful onco- sor loss. We present a comprehensive analysis by array genic effects on specific genes and play a central role in painting of the chromosome translocations of breast cancer development (Rowley, 1998). In the past there cancer cell lines HCC1806, HCC1187 and ZR-75-30. In has been an implicit assumption that such rearrange- array painting, chromosomes are isolated by flow ments are not significant players in the common cytometry, amplified and hybridized to DNA microarrays. epithelial
  • Supplementary Information

    Supplementary Information

    Supplementary Information A genomics approach reveals insights into the importance of gene losses for mammalian adaptations Sharma et al. The Supplementary Information contains - Supplementary Figures 1 - 35 - Supplementary Tables 1 - 8 - Supplementary Notes 1 - 8 1 A reference species with B annotated functional genes ? ? ? ? ? ? use Dollo parsimony ? ? to infer gene ancestry ? search for gene losses reference ? in query species ? ? ? ? ? non-ancestral branches Supplementary Figure 1: General framework for detecting gene losses in genome alignments. (A) Our approach considers all coding genes that are annotated and thus likely functional in a chosen reference species. We detect loss of a given gene in other query species by searching genome alignments for gene-inactivating mutations. Genome alignments are well-suited to detect gene losses for the following reasons. First, genome alignments can reveal the remnants of inactivated but not completely deleted genes, even if these genes are not expressed anymore and thus are not contained in a transcriptome or in mRNA/protein databases. Second, splice site mutations, which are one important class of inactivating mutations, can only be detected at the genomic but not at the mRNA/protein level. Third, information about missing sequence (assembly gaps, regions of low sequencing quality) are only visible by direct genome analysis. This is important as the absence of a gene in a gene/protein database or in a genomic BLAST run cannot distinguish between artifacts that perfectly mimic absence of a gene (such as large assembly gaps) and the complete deletion of a gene. Since gene loss in a query species requires that the common ancestor of the reference and this query species possessed the gene, we used Dollo parsimony to infer gene ancestry based on query species where the gene lacks any gene-inactivating mutations.
  • Detection of H3k4me3 Identifies Neurohiv Signatures, Genomic

    Detection of H3k4me3 Identifies Neurohiv Signatures, Genomic

    viruses Article Detection of H3K4me3 Identifies NeuroHIV Signatures, Genomic Effects of Methamphetamine and Addiction Pathways in Postmortem HIV+ Brain Specimens that Are Not Amenable to Transcriptome Analysis Liana Basova 1, Alexander Lindsey 1, Anne Marie McGovern 1, Ronald J. Ellis 2 and Maria Cecilia Garibaldi Marcondes 1,* 1 San Diego Biomedical Research Institute, San Diego, CA 92121, USA; [email protected] (L.B.); [email protected] (A.L.); [email protected] (A.M.M.) 2 Departments of Neurosciences and Psychiatry, University of California San Diego, San Diego, CA 92103, USA; [email protected] * Correspondence: [email protected] Abstract: Human postmortem specimens are extremely valuable resources for investigating trans- lational hypotheses. Tissue repositories collect clinically assessed specimens from people with and without HIV, including age, viral load, treatments, substance use patterns and cognitive functions. One challenge is the limited number of specimens suitable for transcriptional studies, mainly due to poor RNA quality resulting from long postmortem intervals. We hypothesized that epigenomic Citation: Basova, L.; Lindsey, A.; signatures would be more stable than RNA for assessing global changes associated with outcomes McGovern, A.M.; Ellis, R.J.; of interest. We found that H3K27Ac or RNA Polymerase (Pol) were not consistently detected by Marcondes, M.C.G. Detection of H3K4me3 Identifies NeuroHIV Chromatin Immunoprecipitation (ChIP), while the enhancer H3K4me3 histone modification was Signatures, Genomic Effects of abundant and stable up to the 72 h postmortem. We tested our ability to use H3K4me3 in human Methamphetamine and Addiction prefrontal cortex from HIV+ individuals meeting criteria for methamphetamine use disorder or not Pathways in Postmortem HIV+ Brain (Meth +/−) which exhibited poor RNA quality and were not suitable for transcriptional profiling.
  • Genomic Landscape of Human Allele-Specific DNA Methylation

    Genomic Landscape of Human Allele-Specific DNA Methylation

    Genomic landscape of human allele-specific DNA methylation Fang Fanga, Emily Hodgesb, Antoine Molarob, Matthew Deana, Gregory J. Hannonb, and Andrew D. Smitha,1 aMolecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California; and bHoward Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 Edited by Wing Hung Wong, Stanford University, Stanford, CA, and approved March 8, 2012 (received for review January 24, 2012) DNA methylation mediates imprinted gene expression by passing stages preceding the context in which they become active. Such an epigenomic state across generations and differentially marking methods have been successfully applied to identify unique im- specific regulatory regions on maternal and paternal alleles. Im- printed genes (14–17). printing has been tied to the evolution of the placenta in mammals Advances in DNA sequencing technology have been leveraged and defects of imprinting have been associated with human dis- for high-throughput identification of imprinted genes. The “BS- eases. Although recent advances in genome sequencing have revo- seq” technology couples bisulfite treatment with high-throughput lutionized the study of DNA methylation, existing methylome data short-read sequencing, and has enabled genome-wide profiling of remain largely untapped in the study of imprinting. We present a DNA methylation in mammalian genomes at single-CpG (cyto- statistical model to describe allele-specific methylation (ASM) in sine guanine dinucleotide) resolution (18). Li et al. (19) produced data from high-throughput short-read bisulfite sequencing. Simula- a methylome from peripheral blood of a single individual and tion results indicate technical specifications of existing methylome recognized the potential of using such data to profile ASM.
  • Adenosine Monophosphate Deaminase 3 Activation Shortens Erythrocyte Half-Life and Provides Malaria Resistance in Mice

    From www.bloodjournal.org by guest on January 20, 2017. For personal use only. Regular Article RED CELLS, IRON, AND ERYTHROPOIESIS Adenosine monophosphate deaminase 3 activation shortens erythrocyte half-life and provides malaria resistance in mice Elinor Hortle,1 Brunda Nijagal,2 Denis C. Bauer,3 Lora M. Jensen,1 Seong Beom Ahn,4 Ian A. Cockburn,1 Shelley Lampkin,1 Dedreia Tull,2 Malcolm J. McConville,5 Brendan J. McMorran,1 Simon J. Foote,1 and Gaetan Burgio1 1Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia; 2Metabolomics Australia, Bio21 Institute, University of Melbourne, Parkville, VIC, Australia; 3Commonwealth Scientific and Industrial Research Organization, Sydney, NSW, Australia; 4Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia; and 5Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia Key Points The factors that determine red blood cell (RBC) lifespan and the rate of RBC aging have not been fully elucidated. In several genetic conditions, including sickle cell disease, • AMPD3 activation reduces thalassemia, and G6PD deficiency, erythrocyte lifespan is significantly shortened. Many red blood cell half-life, which of these diseases are also associated with protection from severe malaria, suggesting is associated with increased a role for accelerated RBC senescence and clearance in malaria resistance. Here, we re- oxidative stress and port a novel, N-ethyl-N-nitrosourea–induced mutation that causes a gain of function in phosphatidylserine exposure. adenosine 59-monophosphate deaminase (AMPD3). Mice carrying the mutation exhibit • AMPD3 activation causes rapid RBC turnover, with increased erythropoiesis, dramatically shortened RBC lifespan, and signs of increased RBC senescence/eryptosis, suggesting a key role for AMPD3 in malaria resistance through determining RBC half-life.
  • Supporting Information

    Supporting Information

    Supporting Information Miller et al. 10.1073/pnas.0914257107 SI Materials and Methods files with 20 to 40 samples and 5,629 to 9,731 genes each and 20 Data Set Acquisition and Filtering. All data sets were downloaded mouse expression files with 18 and 44 samples and 5,176 to 6,157 from the GEO database, and consisted of experiments run on genes each. All preprocessed data files (as well as the resulting either mouse or human brain tissue (Fig. 1A). We filtered out all network data and some associated code and support files) are but a core collection of data sets that were similar enough for available at the WGCNA group Web site (www.genetics.ucla.edu/ useful bioinformatic comparison. First, we removed all data sets labs/horvath/CoexpressionNetwork/MouseHumanBrain). that were not run on an Affymetrix platform, leaving three From these preprocessed expression files we created a human platforms in human (HG-U95A, HG-U133A, HG-U133 Plus 2) and a mouse consensus network (method modified from ref. 4). and two in mouse (MG-U74A, MG-U430A). Second, we ex- For each consensus network we first created correlation matrices cluded all samples in each data set that were not taken from from each data set (obtained by calculating the Pearson correla- brain tissue (for example, in one expression atlas study, more tions between all variable probe sets across all subjects in each than 80% of the samples were excluded). Third, to make the data set), and then weighted them based on the number of sam- correlations between genes more comparable across studies, we ples used in that data set.
  • Masseter Muscle Gene Expression in Relation to Various Craniofacial Deformities: a Genotype-Phenotype Study

    Masseter Muscle Gene Expression in Relation to Various Craniofacial Deformities: a Genotype-Phenotype Study

    Masseter muscle gene expression in relation to various craniofacial deformities: A genotype-phenotype study Hadwah AbdelMatloub Moawad B.D.S Dental College/ King Saud University (Saudi Arabia) M.Sc in Orthodontics Eastman Dental Institute/ University of London (UK) A thesis submitted for the degree of Doctor of Philosophy Division of Craniofacial Developmental Sciences, Orthodontic Unit UCL Eastman Dental Institute, UK 2009 Dedication To my beloved parents My sisters: Ruba Anadel Ranad My brother: Mohamed You are the greatest treasure of my life and without your love, support and prayers I would have never produced this work ABSTRACT Craniofacial form is defined by a number of factors. A major contributor is the jaw musculature especially of the masseter muscle, as differences in transcription and translation of various genes have been documented from this tissue. Up to this point however, no reliable biological predictors of form have been identified. The aims of this study were therefore, to describe the transcriptome of the masseter muscle using microarray technology and to establish and correlate the expression levels of potential candidate and known “informative” genes in masseter muscle with selected clinical, radiographic and dental features of subjects with a variety of craniofacial morphologies. A total of 29 patients (18 deformity and 11 control) were selected from the orthodontic/orthognathic clinics at the Eastman Dental and Whipps Cross Hospitals, London, and Riyadh Military Hospital, Saudi Arabia. Microarray results indicated five “novel” genes not previously reported in relation to the masseter muscles of subjects with variable craniofacial morphologies. Two genes (KIAA1671 and DGCR6) were down-regulated in long face patients, one (SERGEF) was down-regulated in Class III patients and one (LOC730245) was up-regulated in Class II long faces and in all Class III subjects, compared to controls.
  • Genomic Landscape of Human Allele-Specific DNA Methylation

    Genomic Landscape of Human Allele-Specific DNA Methylation

    Genomic landscape of human allele-specific DNA methylation Fang Fanga, Emily Hodgesb, Antoine Molarob, Matthew Deana, Gregory J. Hannonb, and Andrew D. Smitha,1 aMolecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California; and bHoward Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724 Edited by Wing Hung Wong, Stanford University, Stanford, CA, and approved March 8, 2012 (received for review January 24, 2012) DNA methylation mediates imprinted gene expression by passing stages preceding the context in which they become active. Such an epigenomic state across generations and differentially marking methods have been successfully applied to identify unique im- specific regulatory regions on maternal and paternal alleles. Im- printed genes (14–17). printing has been tied to the evolution of the placenta in mammals Advances in DNA sequencing technology have been leveraged and defects of imprinting have been associated with human dis- for high-throughput identification of imprinted genes. The “BS- eases. Although recent advances in genome sequencing have revo- seq” technology couples bisulfite treatment with high-throughput lutionized the study of DNA methylation, existing methylome data short-read sequencing, and has enabled genome-wide profiling of remain largely untapped in the study of imprinting. We present a DNA methylation in mammalian genomes at single-CpG (cyto- statistical model to describe allele-specific methylation (ASM) in sine guanine dinucleotide) resolution (18). Li et al. (19) produced data from high-throughput short-read bisulfite sequencing. Simula- a methylome from peripheral blood of a single individual and tion results indicate technical specifications of existing methylome recognized the potential of using such data to profile ASM.
  • Clone : AMPD3/901)

    Clone : AMPD3/901)

    9853 Pacific Heights Blvd. Suite D. San Diego, CA 92121, USA Tel: 858-263-4982 Email: [email protected] 36-1185: Monoclonal Antibody to AMP Deaminase, Isoform E (AMPD3) (Erythroid Marker)(Clone : AMPD3/901) Clonality : Monoclonal Clone Name : AMPD3/901 Application : FACS,IF,IHC Reactivity : Human Gene : AMPD3 Gene ID : 272 Uniprot ID : Q01432 Format : Purified Alternative Name : AMPD3 Isotype : Mouse IgG2b Kappa Immunogen Information : Recombinant full-length human AMDP3 protein Description It recognizes a protein of ~90kDa, which is identified as Adenosine Monophosphate Deaminase, isoform E (AMPD3). It has 767 amino acids and is assigned an EC 3.5.4.6. It is a highly regulated enzyme that catalyzes the hydrolytic deamination of adenosine monophosphate to inosine monophosphate, a branch point in the adenylate catabolic pathway. AMPD3 gene encodes the erythrocyte (E) isoforms, whereas other family members encode isoforms that predominate in muscle (M) and liver (L) cells. This MAb shows reactivity with cells of the erythroid lineage at all stages of maturation in the peripheral blood, bone marrow, and fetal liver. Non-erythroid lineages are negative by flow cytometry. This MAb is useful in the diagnosis of erythroleukemia, identification of bone marrow erythroid precursors, gating erythroid nucleated precursor cells from malignant cells in bone marrow specimens. Product Info Amount : 100 µg Purification : Affinity Chromatography 100 µg in 500 µl PBS containing 0.05% BSA and 0.05% sodium azide. Sodium azide is highly Content : toxic. Store the antibody at 4°C; stable for 6 months. For long-term storage; store at -20°C. Avoid Storage condition : repeated freeze and thaw cycles.
  • An Investigation of the Antigastric Cancer Effect in Tumor Microenvironment of Radix Rhei Et Rhizome: a Network Pharmacology Study

    An Investigation of the Antigastric Cancer Effect in Tumor Microenvironment of Radix Rhei Et Rhizome: a Network Pharmacology Study

    Hindawi Evidence-Based Complementary and Alternative Medicine Volume 2021, Article ID 9913952, 9 pages https://doi.org/10.1155/2021/9913952 Research Article An Investigation of the Antigastric Cancer Effect in Tumor Microenvironment of Radix Rhei Et Rhizome: A Network Pharmacology Study Xinmiao Wang ,1 Guanghui Zhu ,1,2 Haoyu Yang ,1,2 Ruike Gao ,1 Zhe Wu ,1 Ying Zhang,1 Xiaoyu Zhu,1 Xiaoxiao Zhang,1 and Jie Li 1 1Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, China 2Beijing University of Traditional Chinese Medicine, Beijing 100029, China Correspondence should be addressed to Jie Li; [email protected] Received 27 March 2021; Revised 20 May 2021; Accepted 11 June 2021; Published 24 June 2021 Academic Editor: Yibin Feng Copyright © 2021 Xinmiao Wang et al. +is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Background. Tumor microenvironment (TME) takes a vital effect on the occurrence and development of cancer. Radix Rhei Et Rhizome (RRER, Da-Huang in pinyin), a classical Chinese herb, has been widely used in gastric cancer (GC) for many years in China. However, inadequate systematic studies have focused on the anti-GC effect of RRER in TME. +is study intended to uncover the mechanism of it by network pharmacology. Methods. We collected compounds and targets of RRER from traditional Chinese medicine system pharmacology database and analysis platform (TCMSP) and SwissTargetPrediction. GC targets were obtained from GeneCards. Protein- protein interaction (PPI) network and RRER-GC-target network were built by STRING and Cytoscape 3.2.1.