Noncoding Microdeletion in Mouse Hgf Disrupts Neural Crest Migration Into the Stria Vascularis, Reduces the Endocochlear Potenti
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Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
Predicting Gene Ontology Biological Process from Temporal Gene Expression Patterns Astrid Lægreid,1,4 Torgeir R
Methods Predicting Gene Ontology Biological Process From Temporal Gene Expression Patterns Astrid Lægreid,1,4 Torgeir R. Hvidsten,2 Herman Midelfart,2 Jan Komorowski,2,3,4 and Arne K. Sandvik1 1Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489 Trondheim, Norway; 2Department of Information and Computer Science, Norwegian University of Science and Technology, N-7491 Trondheim, Norway; 3The Linnaeus Centre for Bioinformatics, Uppsala University, SE-751 24 Uppsala, Sweden The aim of the present study was to generate hypotheses on the involvement of uncharacterized genes in biological processes. To this end,supervised learning was used to analyz e microarray-derived time-series gene expression data. Our method was objectively evaluated on known genes using cross-validation and provided high-precision Gene Ontology biological process classifications for 211 of the 213 uncharacterized genes in the data set used. In addition,new roles in biological process were hypothesi zed for known genes. Our method uses biological knowledge expressed by Gene Ontology and generates a rule model associating this knowledge with minimal characteristic features of temporal gene expression profiles. This model allows learning and classification of multiple biological process roles for each gene and can predict participation of genes in a biological process even though the genes of this class exhibit a wide variety of gene expression profiles including inverse coregulation. A considerable number of the hypothesized new roles for known genes were confirmed by literature search. In addition,many biological process roles hypothesi zed for uncharacterized genes were found to agree with assumptions based on homology information. -
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. -
TBC1D24-Related Disorders
NLM Citation: Mucha BE, Hennekam RCM, Sisodiya S, et al. TBC1D24- Related Disorders. 2015 Feb 26 [Updated 2017 Dec 7]. In: Adam MP, Ardinger HH, Pagon RA, et al., editors. GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2020. Bookshelf URL: https://www.ncbi.nlm.nih.gov/books/ TBC1D24-Related Disorders Bettina E Mucha, MD,1 Raoul CM Hennekam, MD, PhD,2 Sanjay Sisodiya, MD, PhD,3 and Philippe M Campeau, MD1 Created: February 26, 2015; Updated: December 7, 2017. Summary Clinical characteristics TBC1D24-related disorders comprise a continuum of features that were originally described as distinct, recognized phenotypes: • DOORS syndrome (deafness, onychodystrophy, osteodystrophy, mental retardation, and seizures). Profound sensorineural hearing loss, onychodystrophy, osteodystrophy, intellectual disability / developmental delay, and seizures • Familial infantile myoclonic epilepsy (FIME). Early-onset myoclonic seizures, focal epilepsy, dysarthria, and mild-to-moderate intellectual disability • Progressive myoclonus epilepsy (PME). Action myoclonus, tonic-clonic seizures, progressive neurologic decline, and ataxia • Early-infantile epileptic encephalopathy 16 (EIEE16). Epileptiform EEG abnormalities which themselves are believed to contribute to progressive disturbance in cerebral function • Autosomal recessive nonsyndromic hearing loss, DFNB86. Profound prelingual deafness • Autosomal dominant nonsyndromic hearing loss, DFNA65. Slowly progressive deafness with onset in the third decade, initially affecting the -
A Novel Scoring System for Gastric Cancer Risk Assessment Based on the Expression of Three CLIP4 DNA Methylation-Associated Genes
INTERNATIONAL JOURNAL OF ONCOLOGY 53: 633-643, 2018 A novel scoring system for gastric cancer risk assessment based on the expression of three CLIP4 DNA methylation-associated genes CHENGGONG HU, YONGFANG ZHOU, CHANG LIU and YAN KANG Department of Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, P.R. China Received January 19, 2018; Accepted April 26, 2018 DOI: 10.3892/ijo.2018.4433 Abstract. Gastric cancer (GC) is the fifth most common cancer CLIP4 DNA methylation, and three prognostic signature genes, and the third leading cause of cancer-associated mortality claudin-11 (CLDN11), apolipoprotein D (APOD), and chordin worldwide. In the current study, comprehensive bioinformatic like 1 (CHRDL1), were used to establish a risk assessment analyses were performed to develop a novel scoring system system. The prognostic scoring system exhibited efficiency in for GC risk assessment based on CAP-Gly domain containing classifying patients with different prognoses, where the low- linker protein family member 4 (CLIP4) DNA methylation risk groups had significantly longer overall survival times than status. Two GC datasets with methylation sequencing informa- those in the high-risk groups. CLDN11, APOD and CHRDL1 tion and mRNA expression profiling were downloaded from exhibited reduced expression in the hypermethylation and low- the The Cancer Genome Atlas and Gene Expression Omnibus risk groups compare with the hypomethylation and high-risk databases. Differentially expressed genes (DEGs) between groups, respectively. Multivariate Cox analysis indicated that the CLIP4 hypermethylation and CLIP4 hypomethylation risk value could be used as an independent prognostic factor. groups were screened using the limma package in R 3.3.1, In functional analysis, six functional gene ontology terms and and survival analysis of these DEGs was performed using the five GSEA pathways were associated with CLDN11, APOD survival package. -
Université De Montréal Clarification of the Role of the TBC1D24 Gene In
Université de Montréal Clarification of the role of the TBC1D24 gene in human genetic conditions Par Bettina E. Mucha-Le Ny Programme des sciences biomédicales Faculté de Médecine Mémoire présenté à la Faculté des études supérieures en vue de l’obtention du grade de maîtrise en Sciences biomédicale, option médecine expérimental Mai 4 2020 © Bettina E. Mucha-Le Ny, 2020 Université de Montréal Programme des sciences biomédicales, Faculté de Médecine Ce mémoire intitulé Clarification of the role of the TBC1D24 gene in human genetic conditions Présenté par Bettina E. Mucha-L eNy A été évaluée par un jury composé des personnes suivantes Dr Sébastien Jacquemont Président-rapporteur Philippe. Campeau Directeur de recherche Myriam Srour Membre du jury Résumé Des variants pathogéniques du gène TBC1D24 sont associés à des maladies génétiques dont la majorité sont transmises d’une façon autosomique récessive. Les phénotypes sont variables en termes de présentation clinique et de sévérité. Les formes les plus sévères causent une encéphalopathie épileptique (EIEE16) ou le syndrome DOORS qui est marqué par une surdité, des anomalies des ongles et des doigts, un déficit intellectuel et des convulsions qui sont souvent difficiles à contrôler. D’autres formes d’épilepsie incluent EPRPDC (Rolandic epilepsy with paroxysmal exercise-induce dystonia and writer's cramp), FIME (familial infantile myoclonic epilepsy), et PME (progressive myoclonus epilepsy). Une variant faux-sens spécifique est associée à une surdité autosomique dominante (DFNA65) qui se développe à l’âge adulte. Nous avons écrit un guide de pratique clinique qui inclut une revue de la littérature sur les phénotypes publiés chez les individus avec des variantes pathogénique du gène TBC1D24 avec de recommandations pour le suivi clinique de ces patients. -
Integrative Analysis of Disease Signatures Shows Inflammation Disrupts Juvenile Experience-Dependent Cortical Plasticity
New Research Development Integrative Analysis of Disease Signatures Shows Inflammation Disrupts Juvenile Experience- Dependent Cortical Plasticity Milo R. Smith1,2,3,4,5,6,7,8, Poromendro Burman1,3,4,5,8, Masato Sadahiro1,3,4,5,6,8, Brian A. Kidd,2,7 Joel T. Dudley,2,7 and Hirofumi Morishita1,3,4,5,8 DOI:http://dx.doi.org/10.1523/ENEURO.0240-16.2016 1Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 2Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 3Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 4Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 5Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 6Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, 7Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, and 8Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029 Visual Abstract Throughout childhood and adolescence, periods of heightened neuroplasticity are critical for the development of healthy brain function and behavior. Given the high prevalence of neurodevelopmental disorders, such as autism, identifying disruptors of developmental plasticity represents an essential step for developing strategies for prevention and intervention. Applying a novel computational approach that systematically assessed connections between 436 transcriptional signatures of disease and multiple signatures of neuroplasticity, we identified inflammation as a common pathological process central to a diverse set of diseases predicted to dysregulate Significance Statement During childhood and adolescence, heightened neuroplasticity allows the brain to reorganize and adapt to its environment. -
Recessive TBC1D24 Mutations Are Frequent in Moroccan Non-Syndromic Hearing Loss Pedigrees
RESEARCH ARTICLE Recessive TBC1D24 Mutations Are Frequent in Moroccan Non-Syndromic Hearing Loss Pedigrees Amina Bakhchane1, Majida Charif1,3,4, Sara Salime1,3, Redouane Boulouiz1, Halima Nahili1, Rachida Roky2, Guy Lenaers3,4☯, Abdelhamid Barakat1☯* 1 Laboratoire de Génétique Moléculaire Humaine, Département de Recherche Scientifique, Institut Pasteur du Maroc, Casablanca, Morocco, 2 Université Hassan II Ain Chock, Laboratoire de Physiologie et génétique moléculaire, Km 8 Route d'El Jadida, B.P 5366 Maarif, Casablanca, 20100, Morocco, 3 Institut des Neurosciences de Montpellier, U1051 de l’INSERM, Université de Montpellier, BP 74103, 34091 Montpellier cedex 05, France, 4 PREMMi, Mitochondrial Medicine Research Centre, Université d'Angers, CHU Bât IRIS/ IBS, Rue des Capucins, 49933 Angers cedex 9, France ☯ These authors contributed equally to this work. * [email protected] OPEN ACCESS Abstract Citation: Bakhchane A, Charif M, Salime S, Boulouiz R, Nahili H, Roky R, et al. (2015) Recessive Mutations in the TBC1D24 gene are responsible for four neurological presentations: infan- TBC1D24 Mutations Are Frequent in Moroccan Non- tile epileptic encephalopathy, infantile myoclonic epilepsy, DOORS (deafness, onychody- Syndromic Hearing Loss Pedigrees. PLoS ONE 10 strophy, osteodystrophy, mental retardation and seizures) and NSHL (non-syndromic (9): e0138072. doi:10.1371/journal.pone.0138072 hearing loss). For the latter, two recessive (DFNB86) and one dominant (DFNA65) muta- Editor: Dror Sharon, Hadassah-Hebrew University tions have so far been identified in consanguineous Pakistani and European/Chinese fami- Medical Center, ISRAEL lies, respectively. Here we report the results of a genetic study performed on a large Received: May 8, 2015 Moroccan cohort of deaf patients that identified three families with compound heterozygote Accepted: August 26, 2015 mutations in TBC1D24. -
The Phenotypic Landscape of a Tbc1d24 Mutant Mouse Title Includes Convulsive Seizures Resembling Human Early Infantile Epileptic Encephalopathy( Dissertation 全文 )
The Phenotypic Landscape of a Tbc1d24 Mutant Mouse Title Includes Convulsive Seizures Resembling Human Early Infantile Epileptic Encephalopathy( Dissertation_全文 ) Author(s) Tona, Risa Citation 京都大学 Issue Date 2019-03-25 URL https://doi.org/10.14989/doctor.k21664 許諾条件により本文は2020-01-02に公開; This is a pre- copyedited, author-produced version of an article accepted for Right publication in Human Molecular Genetics peer review.The version of record is available oline. Type Thesis or Dissertation Textversion ETD Kyoto University Human Molecular Genetics General Article The Phenotypic Landscape of a Tbc1d24 Mutant Mouse Includes Convulsive Seizures Resembling Human Early Infantile Epileptic Encephalopathy Risa Tona1, 2, Wenqian Chen1, Yoko Nakano3, Laura D. Reyes4, Ronald S. Petralia5, Ya-Xian Wang5, Matthew F. Starost6, Talah T. Wafa7, Robert J. Morell8, Kevin D. Cravedi9, Johann du Hoffmann9, Takushi Miyoshi1, Jeeva P. Munasinghe10, Tracy S. Fitzgerald7, Yogita Chudasama9, 11, Koichi Omori2, Carlo Pierpaoli4, Botond Banfi3, Lijin Dong12, Inna A. Belyantseva1, Thomas B. Friedman1,* 1Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, Porter Neuroscience Research Center, National Institutes of Health, Bethesda, Maryland 20892, USA 2Department of Otolaryngology, Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto City, Kyoto 606-8507, Japan 3Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA 4Quantitative Medical -
A New Microdeletion Syndrome Involving TBC1D24, ATP6V0C and PDPK1 Causes Epilepsy, Microcephaly and Developmental Delay. Bettina
Manuscript (All Manuscript Text Pages, including Title Page, References and Figure Legends) A new microdeletion syndrome involving TBC1D24, ATP6V0C and PDPK1 causes epilepsy, microcephaly and developmental delay. Bettina E Mucha1, Siddhart Banka2, Norbert Fonya Ajeawung3, Sirinart Molidperee3, Gary G Chen4, Mary Kay Koenig5, Rhamat B Adejumo5, Marianne Till6, Michael Harbord7, Renee Perrier8, Emmanuelle Lemyre9, Renee-Myriam Boucher10, Brian G Skotko11, Jessica L Waxler11, Mary Ann Thomas8, Jennelle C Hodge12, Jozef Gecz13, Jillian Nicholl14, Lesley McGregor14, Tobias Linden15, Sanjay M Sisodiya16, Damien Sanlaville6, Sau W Cheung17, Carl Ernst4, Philippe M Campeau9 1. Division of Medical Genetics, Department of Specialized Medicine, McGill University Health Centre, Montreal, QC, Canada. 2. Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PL, Manchester, UK. 3. Centre de Recherche du CHU Sainte-Justine, Montreal, QC, Canada 4. Department of Psychiatry, McGill University, Montreal, Canada. 5. Department of Pediatrics, Division of Child & Adolescent Neurology, The University of Texas McGovern Medical School, Houston, Texas, USA. 6. Service de Génétique CHU de Lyon-GH Est, Lyon, France. 7. Department of Pediatrics, Flinders Medical Centre, Bedford Park, South Australia, Australia. ___________________________________________________________________ This is the author's manuscript of the article published in final edited form as: Mucha, B. E., Banka, S., Ajeawung, N. F., Molidperee, S., Chen, G. G., Koenig, M. K., … Campeau, P. M. (2018). A new microdeletion syndrome involving TBC1D24, ATP6V0C , and PDPK1 causes epilepsy, microcephaly, and developmental delay. Genetics in Medicine, 1. https://doi.org/10.1038/s41436-018-0290-3 8. Department of Medical Genetics, University of Calgary, Calgary, AB, Canada. -
Genome-Scale Analysis of DNA Methylation in Lung Adenocarcinoma and Integration with Mrna Expression
Downloaded from genome.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press Research Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression Suhaida A. Selamat,1 Brian S. Chung,1 Luc Girard,2 Wei Zhang,2 Ying Zhang,3 Mihaela Campan,1 Kimberly D. Siegmund,3 Michael N. Koss,4 Jeffrey A. Hagen,5 Wan L. Lam,6 Stephen Lam,6 Adi F. Gazdar,2 and Ite A. Laird-Offringa1,7 1Department of Surgery, Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California 90089-9176, USA; 2The Hamon Center for Therapeutic Oncology Research and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; 3Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90089-9176, USA; 4Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California 90089-9176, USA; 5Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, California 90089-9176, USA; 6BC Cancer Research Center, BC Cancer Agency, Vancouver, BC V521L3, Canada Lung cancer is the leading cause of cancer death worldwide, and adenocarcinoma is its most common histological subtype. Clinical and molecular evidence indicates that lung adenocarcinoma is a heterogeneous disease, which has important implications for treatment. Here we performed genome-scale DNA methylation profiling using the Illumina Infinium HumanMethylation27 platform on 59 matched lung adenocarcinoma/non-tumor lung pairs, with genome-scale verifi- cation on an independent set of tissues. -
TBC1D24 Gene TBC1 Domain Family Member 24
TBC1D24 gene TBC1 domain family member 24 Normal Function The TBC1D24 gene provides instructions for making a protein whose specific function in the cell is unclear. Studies suggest the protein may have several roles in cells. The TBC1D24 protein belongs to a group of proteins that are involved in the movement ( transport) of vesicles, which are small sac-like structures that transport proteins and other materials within cells. Research suggests that the TBC1D24 protein may also help cells respond to oxidative stress. Oxidative stress occurs when unstable molecules called free radicals accumulate to levels that can damage or kill cells. Studies indicate that the TBC1D24 protein is active in a variety of organs and tissues; it is particularly active in the brain and likely plays an important role in normal brain development. The TBC1D24 protein is also active in specialized structures called stereocilia. In the inner ear, stereocilia project from certain cells called hair cells. The stereocilia bend in response to sound waves, which is critical for converting sound waves to nerve impulses. Health Conditions Related to Genetic Changes DOORS syndrome At least 10 mutations in the TBC1D24 gene have been identified in people with DOORS syndrome, a disorder involving multiple abnormalities that are present from birth ( congenital). "DOORS" is an abbreviation for the major features of the disorder including deafness; short or absent nails (onychodystrophy); short fingers and toes ( osteodystrophy); developmental delay and intellectual disability (previously called mental retardation); and seizures. Some people with DOORS syndrome do not have all of these features. Most of the TBC1D24 gene mutations that cause DOORS syndrome change single protein building blocks (amino acids) in the TBC1D24 protein sequence.