A Child with Multiple Congenital Anomalies Due to Partial Trisomy
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Modes of Interaction of KMT2 Histone H3 Lysine 4 Methyltransferase/COMPASS Complexes with Chromatin
cells Review Modes of Interaction of KMT2 Histone H3 Lysine 4 Methyltransferase/COMPASS Complexes with Chromatin Agnieszka Bochy ´nska,Juliane Lüscher-Firzlaff and Bernhard Lüscher * ID Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, Pauwelsstrasse 30, 52057 Aachen, Germany; [email protected] (A.B.); jluescher-fi[email protected] (J.L.-F.) * Correspondence: [email protected]; Tel.: +49-241-8088850; Fax: +49-241-8082427 Received: 18 January 2018; Accepted: 27 February 2018; Published: 2 March 2018 Abstract: Regulation of gene expression is achieved by sequence-specific transcriptional regulators, which convey the information that is contained in the sequence of DNA into RNA polymerase activity. This is achieved by the recruitment of transcriptional co-factors. One of the consequences of co-factor recruitment is the control of specific properties of nucleosomes, the basic units of chromatin, and their protein components, the core histones. The main principles are to regulate the position and the characteristics of nucleosomes. The latter includes modulating the composition of core histones and their variants that are integrated into nucleosomes, and the post-translational modification of these histones referred to as histone marks. One of these marks is the methylation of lysine 4 of the core histone H3 (H3K4). While mono-methylation of H3K4 (H3K4me1) is located preferentially at active enhancers, tri-methylation (H3K4me3) is a mark found at open and potentially active promoters. Thus, H3K4 methylation is typically associated with gene transcription. The class 2 lysine methyltransferases (KMTs) are the main enzymes that methylate H3K4. KMT2 enzymes function in complexes that contain a necessary core complex composed of WDR5, RBBP5, ASH2L, and DPY30, the so-called WRAD complex. -
S41467-020-18249-3.Pdf
ARTICLE https://doi.org/10.1038/s41467-020-18249-3 OPEN Pharmacologically reversible zonation-dependent endothelial cell transcriptomic changes with neurodegenerative disease associations in the aged brain Lei Zhao1,2,17, Zhongqi Li 1,2,17, Joaquim S. L. Vong2,3,17, Xinyi Chen1,2, Hei-Ming Lai1,2,4,5,6, Leo Y. C. Yan1,2, Junzhe Huang1,2, Samuel K. H. Sy1,2,7, Xiaoyu Tian 8, Yu Huang 8, Ho Yin Edwin Chan5,9, Hon-Cheong So6,8, ✉ ✉ Wai-Lung Ng 10, Yamei Tang11, Wei-Jye Lin12,13, Vincent C. T. Mok1,5,6,14,15 &HoKo 1,2,4,5,6,8,14,16 1234567890():,; The molecular signatures of cells in the brain have been revealed in unprecedented detail, yet the ageing-associated genome-wide expression changes that may contribute to neurovas- cular dysfunction in neurodegenerative diseases remain elusive. Here, we report zonation- dependent transcriptomic changes in aged mouse brain endothelial cells (ECs), which pro- minently implicate altered immune/cytokine signaling in ECs of all vascular segments, and functional changes impacting the blood–brain barrier (BBB) and glucose/energy metabolism especially in capillary ECs (capECs). An overrepresentation of Alzheimer disease (AD) GWAS genes is evident among the human orthologs of the differentially expressed genes of aged capECs, while comparative analysis revealed a subset of concordantly downregulated, functionally important genes in human AD brains. Treatment with exenatide, a glucagon-like peptide-1 receptor agonist, strongly reverses aged mouse brain EC transcriptomic changes and BBB leakage, with associated attenuation of microglial priming. We thus revealed tran- scriptomic alterations underlying brain EC ageing that are complex yet pharmacologically reversible. -
Human Lectins, Their Carbohydrate Affinities and Where to Find Them
biomolecules Review Human Lectins, Their Carbohydrate Affinities and Where to Review HumanFind Them Lectins, Their Carbohydrate Affinities and Where to FindCláudia ThemD. Raposo 1,*, André B. Canelas 2 and M. Teresa Barros 1 1, 2 1 Cláudia D. Raposo * , Andr1 é LAQVB. Canelas‐Requimte,and Department M. Teresa of Chemistry, Barros NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829‐516 Caparica, Portugal; [email protected] 12 GlanbiaLAQV-Requimte,‐AgriChemWhey, Department Lisheen of Chemistry, Mine, Killoran, NOVA Moyne, School E41 of ScienceR622 Co. and Tipperary, Technology, Ireland; canelas‐ [email protected] NOVA de Lisboa, 2829-516 Caparica, Portugal; [email protected] 2* Correspondence:Glanbia-AgriChemWhey, [email protected]; Lisheen Mine, Tel.: Killoran, +351‐212948550 Moyne, E41 R622 Tipperary, Ireland; [email protected] * Correspondence: [email protected]; Tel.: +351-212948550 Abstract: Lectins are a class of proteins responsible for several biological roles such as cell‐cell in‐ Abstract:teractions,Lectins signaling are pathways, a class of and proteins several responsible innate immune for several responses biological against roles pathogens. such as Since cell-cell lec‐ interactions,tins are able signalingto bind to pathways, carbohydrates, and several they can innate be a immuneviable target responses for targeted against drug pathogens. delivery Since sys‐ lectinstems. In are fact, able several to bind lectins to carbohydrates, were approved they by canFood be and a viable Drug targetAdministration for targeted for drugthat purpose. delivery systems.Information In fact, about several specific lectins carbohydrate were approved recognition by Food by andlectin Drug receptors Administration was gathered for that herein, purpose. plus Informationthe specific organs about specific where those carbohydrate lectins can recognition be found by within lectin the receptors human was body. -
Get.Com Oncotarget, 2018, Vol
www.oncotarget.com Oncotarget, 2018, Vol. 9, (No. 35), pp: 24122-24139 Research Paper Etoposide-induced DNA damage affects multiple cellular pathways in addition to DNA damage response Fengxiang Wei1, Peng Hao2, Xiangzhong Zhang3, Haiyan Hu4, Dan Jiang5, Aihua Yin6, Lijuan Wen1,7, Lihong Zheng8, Jeffrey Zheru He9, Wenjuan Mei10,12, Hui Zeng11,12 and Damu Tang12 1The Genetics Laboratory, Shenzhen Longgang District Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, PR China 2Division of Nephrology, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, PR China 3Department of Hematology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, PR China 4Department of Obstetrics and Gynecology, Shenzhen Maternal and Child Healthcare Hospital, Southern Medical University, Shenzhen, Guangdong, PR China 5Shenzhen Hua Da Clinical Laboratory Center Co., Ltd., Shenzhen, Guangdong, PR China 6Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, PR China 7Zunyi Medical University, Zunyi, Guizhou, PR China 8Department of Biogenetics, Qiqihar Medical University, Qiqihar, Heilongjiang, PR China 9Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA 10Department of Nephrology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, PR China 11Department of Thoracic Surgery, Fourth Hospital of Hebei Medical University, Shijiazhuang City, Hebei, PR China 12Division of Nephrology, Department of Medicine, McMaster -
Investigation of Differentially Expressed Genes in Nasopharyngeal Carcinoma by Integrated Bioinformatics Analysis
916 ONCOLOGY LETTERS 18: 916-926, 2019 Investigation of differentially expressed genes in nasopharyngeal carcinoma by integrated bioinformatics analysis ZhENNING ZOU1*, SIYUAN GAN1*, ShUGUANG LIU2, RUjIA LI1 and jIAN hUANG1 1Department of Pathology, Guangdong Medical University, Zhanjiang, Guangdong 524023; 2Department of Pathology, The Eighth Affiliated hospital of Sun Yat‑sen University, Shenzhen, Guangdong 518033, P.R. China Received October 9, 2018; Accepted April 10, 2019 DOI: 10.3892/ol.2019.10382 Abstract. Nasopharyngeal carcinoma (NPC) is a common topoisomerase 2α and TPX2 microtubule nucleation factor), malignancy of the head and neck. The aim of the present study 8 modules, and 14 TFs were identified. Modules analysis was to conduct an integrated bioinformatics analysis of differ- revealed that cyclin-dependent kinase 1 and exportin 1 were entially expressed genes (DEGs) and to explore the molecular involved in the pathway of Epstein‑Barr virus infection. In mechanisms of NPC. Two profiling datasets, GSE12452 and summary, the hub genes, key modules and TFs identified in GSE34573, were downloaded from the Gene Expression this study may promote our understanding of the pathogenesis Omnibus database and included 44 NPC specimens and of NPC and require further in-depth investigation. 13 normal nasopharyngeal tissues. R software was used to identify the DEGs between NPC and normal nasopharyngeal Introduction tissues. Distributions of DEGs in chromosomes were explored based on the annotation file and the CYTOBAND database Nasopharyngeal carcinoma (NPC) is a common malignancy of DAVID. Gene ontology (GO) and Kyoto Encyclopedia of occurring in the head and neck. It is prevalent in the eastern Genes and Genomes (KEGG) pathway enrichment analysis and southeastern parts of Asia, especially in southern China, were applied. -
Open Data for Differential Network Analysis in Glioma
International Journal of Molecular Sciences Article Open Data for Differential Network Analysis in Glioma , Claire Jean-Quartier * y , Fleur Jeanquartier y and Andreas Holzinger Holzinger Group HCI-KDD, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz 2/V, 8036 Graz, Austria; [email protected] (F.J.); [email protected] (A.H.) * Correspondence: [email protected] These authors contributed equally to this work. y Received: 27 October 2019; Accepted: 3 January 2020; Published: 15 January 2020 Abstract: The complexity of cancer diseases demands bioinformatic techniques and translational research based on big data and personalized medicine. Open data enables researchers to accelerate cancer studies, save resources and foster collaboration. Several tools and programming approaches are available for analyzing data, including annotation, clustering, comparison and extrapolation, merging, enrichment, functional association and statistics. We exploit openly available data via cancer gene expression analysis, we apply refinement as well as enrichment analysis via gene ontology and conclude with graph-based visualization of involved protein interaction networks as a basis for signaling. The different databases allowed for the construction of huge networks or specified ones consisting of high-confidence interactions only. Several genes associated to glioma were isolated via a network analysis from top hub nodes as well as from an outlier analysis. The latter approach highlights a mitogen-activated protein kinase next to a member of histondeacetylases and a protein phosphatase as genes uncommonly associated with glioma. Cluster analysis from top hub nodes lists several identified glioma-associated gene products to function within protein complexes, including epidermal growth factors as well as cell cycle proteins or RAS proto-oncogenes. -
Deletions of Chromosome 7Q Affect Nuclear Organization And
cancers Article Deletions of Chromosome 7q Affect Nuclear Organization and HLXB9Gene Expression in Hematological Disorders Concetta Federico 1 , Temitayo Owoka 2, Denise Ragusa 2, Valentina Sturiale 1, Domenica Caponnetto 1, Claudia Giovanna Leotta 1, Francesca Bruno 1 , Helen A. Foster 3,5, Silvia Rigamonti 4, Giovanni Giudici 4, Giovanni Cazzaniga 4, Joanna M. Bridger 2, Cristina Sisu 5 , Salvatore Saccone 1,* and Sabrina Tosi 2,* 1 Department of Biological, Geological and Environmental Sciences, University of Catania, via Androne 81, 95124 Catania CT, Italy; [email protected] (C.F.); [email protected] (V.S.); [email protected] (D.C.); [email protected] (C.G.L.); [email protected] (F.B.) 2 Genome Engineering and Maintenance Network, Institute of Environment, Health and Societies, Brunel University London, Kingston Lane UB8 3PH, UK; [email protected] (T.O.); [email protected] (D.R.); [email protected] (J.M.B.) 3 Department of Biological and Environmental Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK; [email protected] 4 Associazione Italiana Ematologia Oncologia Pediatrica (AIEOP), Centro Ricerca Tettamanti, Pediatric Department, University of Milano-Bicocca, 20900 Monza, Italy; [email protected] (S.R.); [email protected] (G.G.); [email protected] (G.C.) 5 College of Health and Life Science, Brunel University London, Kingston Lane UB8 3PH, UK; [email protected] * Correspondence: [email protected] (S.S.); [email protected] (S.T.) Received: 12 March 2019; Accepted: 19 April 2019; Published: 25 April 2019 Abstract: The radial spatial positioning of individual gene loci within interphase nuclei has been associated with up- and downregulation of their expression. -
Genetic Variation Regulates Opioid-Induced Respiratory Depression in Mice
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.15.152249; this version posted June 15, 2020. 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-NC-ND 4.0 International license. 1 Genetic Variation Regulates Opioid-Induced Respiratory Depression in Mice 2 3 4 5 6 Jason A. Bubier1, Hao He1, Vivek M. Philip1, Tyler Roy, Christian Monroy Hernandez, Kevin D. 7 Donohue2,3 Bruce F. O’Hara2,4, Elissa J. Chesler1* 8 1The Jackson Laboratory, Bar Harbor ME 04605; 9 2Signal Solutions, LLC, Lexington, KY; 10 3Electrical and Computer Engineering Department, University of Kentucky, Lexington, KY; 11 4Department of Biology, University of Kentucky, Lexington KY 12 *Corresponding author [email protected] 13 RUNNING TITLE: 14 KEY WORDS: 15 16 Specs-Scientific Reports (4.122, preprint ok) 17 Title (20 Words) 18 Abstract (200 words) 19 Introduction (4500 words with Results and Discussion) (3473 as of 4/28) 20 Results (with subheadings) 21 Discussion (without subheadings) 22 Methods (Methods section to 1,500 words) (1050 words) 23 Figure legends are limited to 350 words; no more than 8 display items 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.15.152249; this version posted June 15, 2020. 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-NC-ND 4.0 International license. -
Genetic Variation Regulates Opioid-Induced Respiratory
www.nature.com/scientificreports OPEN Genetic variation regulates opioid‑induced respiratory depression in mice Jason A. Bubier1*, Hao He1, Vivek M. Philip1, Tyler Roy1, Christian Monroy Hernandez1, Rebecca Bernat2, Kevin D. Donohue2,3, Bruce F. O’Hara2,4 & Elissa J. Chesler1 In the U.S., opioid prescription for treatment of pain nearly quadrupled from 1999 to 2014. The diversion and misuse of prescription opioids along with increased use of drugs like heroin and fentanyl, has led to an epidemic in addiction and overdose deaths. The most common cause of opioid overdose and death is opioid‑induced respiratory depression (OIRD), a life‑threatening depression in respiratory rate thought to be caused by stimulation of opioid receptors in the inspiratory‑generating regions of the brain. Studies in mice have revealed that variation in opiate lethality is associated with strain diferences, suggesting that sensitivity to OIRD is genetically determined. We frst tested the hypothesis that genetic variation in inbred strains of mice infuences the innate variability in opioid- induced responses in respiratory depression, recovery time and survival time. Using the founders of the advanced, high‑diversity mouse population, the Diversity Outbred (DO), we found substantial sex and genetic efects on respiratory sensitivity and opiate lethality. We used DO mice treated with morphine to map quantitative trait loci for respiratory depression, recovery time and survival time. Trait mapping and integrative functional genomic analysis in GeneWeaver has allowed us to implicate Galnt11, an N‑acetylgalactosaminyltransferase, as a gene that regulates OIRD. An estimated 4 to 6% of patients who misuse prescription opioids switch to illicit drugs such as heroin1,2 and about 80% of people who use heroin had frst misused prescription opioids 1,2. -
Characterizing Genomic Duplication in Autism Spectrum Disorder by Edward James Higginbotham a Thesis Submitted in Conformity
Characterizing Genomic Duplication in Autism Spectrum Disorder by Edward James Higginbotham A thesis submitted in conformity with the requirements for the degree of Master of Science Graduate Department of Molecular Genetics University of Toronto © Copyright by Edward James Higginbotham 2020 i Abstract Characterizing Genomic Duplication in Autism Spectrum Disorder Edward James Higginbotham Master of Science Graduate Department of Molecular Genetics University of Toronto 2020 Duplication, the gain of additional copies of genomic material relative to its ancestral diploid state is yet to achieve full appreciation for its role in human traits and disease. Challenges include accurately genotyping, annotating, and characterizing the properties of duplications, and resolving duplication mechanisms. Whole genome sequencing, in principle, should enable accurate detection of duplications in a single experiment. This thesis makes use of the technology to catalogue disease relevant duplications in the genomes of 2,739 individuals with Autism Spectrum Disorder (ASD) who enrolled in the Autism Speaks MSSNG Project. Fine-mapping the breakpoint junctions of 259 ASD-relevant duplications identified 34 (13.1%) variants with complex genomic structures as well as tandem (193/259, 74.5%) and NAHR- mediated (6/259, 2.3%) duplications. As whole genome sequencing-based studies expand in scale and reach, a continued focus on generating high-quality, standardized duplication data will be prerequisite to addressing their associated biological mechanisms. ii Acknowledgements I thank Dr. Stephen Scherer for his leadership par excellence, his generosity, and for giving me a chance. I am grateful for his investment and the opportunities afforded me, from which I have learned and benefited. I would next thank Drs. -
Decreased DNA Methylation at Promoters and Gene-Specific Neuronal
medRxiv preprint doi: https://doi.org/10.1101/2020.12.10.20246405; this version posted December 11, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license . Decreased DNA methylation at promoters and gene-specific neuronal hypermethylation in the prefrontal cortex of patients with bipolar disorder Miki Bundo1†, Junko Ueda1,2†, Yutaka Nakachi1, Kiyoto Kasai3,4, Tadafumi Kato2,5#, Kazuya Iwamoto1# 1Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Japan 2Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Japan 3Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Japan 4The International Research Center for Neurointelligence (WPI-IRCN) at The University of Tokyo Institutes for Advanced Study (UTIAS), 5Department of Psychiatry and Behavioral Science, Graduate School of Medicine, Juntendo University †contributed equally to this work #corresponding authors: Kazuya Iwamoto Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University. 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan [email protected] Tadadumi Kato Department of Psychiatry and Behavioral Science, Graduate School of Medicine, Juntendo University. 2-1-1 Hongo, Bunkyo, Tokyo 113-8421, Japan [email protected]. Running title: DNA methylation analysis in bipolar disorder 1 NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.10.20246405; this version posted December 11, 2020. -
Broad and Thematic Remodeling of the Surfaceome and Glycoproteome on Isogenic Cells Transformed with Driving Proliferative Oncogenes
Broad and thematic remodeling of the surfaceome and glycoproteome on isogenic cells transformed with driving proliferative oncogenes Kevin K. Leunga,1 , Gary M. Wilsonb,c,1, Lisa L. Kirkemoa, Nicholas M. Rileyb,c,d , Joshua J. Coonb,c, and James A. Wellsa,2 aDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143; bDepartment of Chemistry, University of Wisconsin–Madison, Madison, WI 53706; cDepartment of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, WI 53706; and dDepartment of Chemistry, Stanford University, Stanford, CA 94305 Edited by Benjamin F. Cravatt, Scripps Research Institute, La Jolla, CA, and approved February 24, 2020 (received for review October 14, 2019) The cell surface proteome, the surfaceome, is the interface for tumors. For example, lung cancer patients with oncogenic EGFR engaging the extracellular space in normal and cancer cells. Here mutations seldom harbor oncogenic KRAS or BRAF mutations we apply quantitative proteomics of N-linked glycoproteins to and vice versa (9). Also, recent evidence shows that oncogene reveal how a collection of some 700 surface proteins is dra- coexpression can induce synthetic lethality or oncogene-induced matically remodeled in an isogenic breast epithelial cell line senescence, further reinforcing that activation of one oncogene stably expressing any of six of the most prominent prolifera- without the others is preferable in cancer (10, 11). tive oncogenes, including the receptor tyrosine kinases, EGFR There is also substantial