DOCSLIB.ORG

Increased Expression of the Frontotemporal Dementia Risk Factor Tmem106b Causes C9orf72-Dependent Alterations in Lysosomes

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Increased Expression of the Frontotemporal Dementia Risk Factor Tmem106b Causes C9orf72-Dependent Alterations in Lysosomes University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2016 Increased Expression of Frontotemporal Dementia Risk Factor Tmem106b Alters Lysosomal and Autophagosomal Pathways Johanna Irene Busch University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Cell Biology Commons, and the Neuroscience and Neurobiology Commons Recommended Citation Busch, Johanna Irene, "Increased Expression of Frontotemporal Dementia Risk Factor Tmem106b Alters Lysosomal and Autophagosomal Pathways" (2016). Publicly Accessible Penn Dissertations. 1630. https://repository.upenn.edu/edissertations/1630 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1630 For more information, please contact [email protected]. Increased Expression of Frontotemporal Dementia Risk Factor Tmem106b Alters Lysosomal and Autophagosomal Pathways Abstract Frontotemporal lobar degeneration (FTLD) is an important cause of dementia in individuals under age 65. Common variants in the TMEM106B gene were previously discovered by genome-wide association (GWAS) to confer genetic risk for FTLD-TDP, the largest neuropathological subset of FTLD (p=1x10-11, OR=1.6). Prior to its discovery in the GWAS, TMEM106B, or Transmembrane Protein 106B, was uncharacterized. To further understand the role of TMEM106B in disease pathogenesis, we used immortalized as well as primary neurons to assess the cell biological effects of disease-relevant levels of TMEM106B overexpression and the interaction of TMEM106B with additional disease-associated proteins. We also employed immunostaining to assess its expression pattern in human brain from controls and FTLD cases. We discovered that TMEM106B is a highly glycosylated, Type II late endosomal/lysosomal transmembrane protein. We found that it is expressed by neurons, glia, and peri-vascular cells in disease- affected and unaffected regions of human brain from normal controls in a cytoplasmic, perikaryal distribution. In brain from FTLD patients, we discovered a striking loss of subcellular localization with highly disordered TMEM106B immunostaining patterns in a subset of FTLD-TDP cases. Evidence suggests that TMEM106B variants increase risk for developing FTLD-TDP by increasing TMEM106B mRNA and protein expression levels. We therefore investigated the cell biological effects of increased TMEM106B expression. Increased TMEM106B results in a decrease in the average number of late endosomes/lysosomes per cell, loss of lysosomal acidification, and impaired lysosomal degradation. In addition, lysosomal deficits are accompanied by the appearance of enlarged organelles (>2-3μm) demonstrating ultrastructural characteristics of late autophagic vacuoles (autolysosomes/amphisomes). We observed these effects in both immortalized cell lines and in primary neurons overexpressing TMEM106B. Furthermore, we show that the effects of increased TMEM106B expression can be abrogated by (1) a single point mutation to a lysosomal sorting motif in TMEM106B newly identified here, or (2) knockdown of C9orf72 protein. In sum, our results suggest that TMEM106B exerts its effects on FTLD-TDP disease risk through alterations of lysosomal and autophagic pathways and that TMEM106B and C9orf72 may interact in disease pathophysiology. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Alice Chen-Plotkin Keywords C9orf72, Frontotemporal dementia, FTD, FTLD, Lysosome, TMEM106B Subject Categories Cell Biology | Neuroscience and Neurobiology This dissertation is available at ScholarlyCommons: https://repository.upenn.edu/edissertations/1630 INCREASED EXPRESSION OF FRONTOTEMPORAL DEMENTIA RISK FACTOR TMEM106B ALTERS LYSOSOMAL AND AUTOPHAGOSOMAL PATHWAYS Johanna I. Busch A DISSERTATION in Cell and Molecular Biology Presented to the Faculties of the University of Pennsylvania in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy 2016 Supervisor of Dissertation _________________ Alice Chen-Plotkin, M.D. Assistant Professor of Neurology Graduate Group Chairperson _________________ Daniel S. Kessler, Ph.D. Associate Professor of Cell and Developmental Biology Dissertation Committee Erika L. F. Holzbaur, Ph.D., Professor of Physiology (Chair) Robert W. Doms, M.D., Ph.D., Professor of Pathology and Laboratory Medicine Virginia M.-Y. Lee, Ph.D., John H. Ware 3rd Endowed Professor in Alzheimer’s Research, Professor of Pathology and Laboratory Medicine Michael S. Marks, Ph.D., Professor of Pathology and Laboratory Medicine ACKNOWLEDGMENT I would like to thank my mentor, Dr. Alice Chen-Plotkin, for giving me the opportunity to study the exciting new world of TMEM106B and for providing me with advice, mentorship, and scientific discourse throughout the past few years. I would also like to thank the members of the lab and the members of my thesis committee for their insights and support throughout. I also thank my family and those who are like family to me for their emotional support and for the fun, both inside and outside the lab, we have had over the past years. I thank Margie Maronski and the "Neurons R Us" core facility for providing primary murine neurons, the Electron Microscopy Resource Laboratory for processing and assistance with electron microscopy, Dr. Fenghua Hu for providing the GFP-TMEM106B construct, Robert Arauz Perez, Emily Bill, Nimansha Jain, Jordan Mak, Tyler Skrinak, and Travis Unger for their assistance, and Dr. Mickey Marks for his input and advice regarding lysosomal targeting motifs. Finally, I would like to thank the patients and their families, whose contributions and dedication to understanding this disease make this work possible. ii ABSTRACT INCREASED EXPRESSION OF FRONTOTEMPORAL DEMENTIA RISK FACTOR TMEM106B ALTERS LYSOSOMAL AND AUTOPHAGOSOMAL PATHWAY Johanna Busch Dr. Alice Chen-Plotkin Frontotemporal lobar degeneration (FTLD) is an important cause of dementia in individuals under age 65. Common variants in the TMEM106B gene were previously discovered by genome-wide association (GWAS) to confer genetic risk for FTLD-TDP, the largest neuropathological subset of FTLD (p=1x10-11, OR=1.6). Prior to its discovery in the GWAS, TMEM106B, or Transmembrane Protein 106B, was uncharacterized. To further understand the role of TMEM106B in disease pathogenesis, we used immortalized as well as primary neurons to assess the cell biological effects of disease-relevant levels of TMEM106B overexpression and the interaction of TMEM106B with additional disease-associated proteins. We also employed immunostaining to assess its expression pattern in human brain from controls and FTLD cases. We discovered that TMEM106B is a highly glycosylated, Type II late endosomal/lysosomal transmembrane protein. We found that it is expressed by neurons, glia, and peri-vascular cells in disease-affected and unaffected regions of human brain from normal controls in a cytoplasmic, perikaryal distribution. In brain from FTLD patients, we discovered a striking loss of subcellular localization with highly disordered TMEM106B immunostaining patterns in a subset of FTLD-TDP cases. Evidence suggests that TMEM106B variants increase risk for developing FTLD-TDP by increasing TMEM106B mRNA and protein expression levels. We therefore investigated the cell biological effects of increased TMEM106B expression. Increased TMEM106B results in a decrease in the average number of late endosomes/lysosomes per cell, loss of lysosomal acidification, and impaired lysosomal degradation. In addition, lysosomal deficits are accompanied by the appearance of enlarged organelles (>2-3μm) demonstrating ultrastructural characteristics of late autophagic vacuoles iii (autolysosomes/amphisomes). We observed these effects in both immortalized cell lines and in primary neurons overexpressing TMEM106B. Furthermore, we show that the effects of increased TMEM106B expression can be abrogated by (1) a single point mutation to a lysosomal sorting motif in TMEM106B newly identified here, or (2) knockdown of C9orf72 protein. In sum, our results suggest that TMEM106B exerts its effects on FTLD-TDP disease risk through alterations of lysosomal and autophagic pathways and that TMEM106B and C9orf72 may interact in disease pathophysiology. iv TABLE OF CONTENTS ACKNOWLEDGMENT .................................................................................................................... II ABSTRACT .................................................................................................................................... III TABLE OF CONTENTS .................................................................................................................. V LIST OF TABLES .......................................................................................................................... VII LIST OF ILLUSTRATIONS........................................................................................................... VIII CHAPTER 1: INTRODUCTION ....................................................................................................... 1 1.1 PART I: Frontotemporal dementia and disease-associated mutations ........................... 1 1.1.1 Frontotemporal Lobar Degeneration ........................................................................ 1 1.1.2 Epidemiology ...........................................................................................................
Load more

Recommended publications
  • Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model
    Downloaded from http://www.jimmunol.org/ by guest on September 25, 2021 T + is online at: average * The Journal of Immunology , 34 of which you can access for free at: 2016; 197:1477-1488; Prepublished online 1 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600589 http://www.jimmunol.org/content/197/4/1477 Molecular Profile of Tumor-Specific CD8 Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A. Waugh, Sonia M. Leach, Brandon L. Moore, Tullia C. Bruno, Jonathan D. Buhrman and Jill E. Slansky J Immunol cites 95 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html http://www.jimmunol.org/content/suppl/2016/07/01/jimmunol.160058 9.DCSupplemental This article http://www.jimmunol.org/content/197/4/1477.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 25, 2021. The Journal of Immunology Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model Katherine A.
    [Show full text]
  • Evolutionary Plasticity in Detoxification Gene Modules: the Preservation
    International Journal of Molecular Sciences Article Evolutionary Plasticity in Detoxification Gene Modules: The Preservation and Loss of the Pregnane X Receptor in Chondrichthyes Lineages Elza S. S. Fonseca 1,2, Raquel Ruivo 1 , André M. Machado 1 , Francisca Conrado 1, Boon-Hui Tay 3, Byrappa Venkatesh 3, Miguel M. Santos 1,2 and L. Filipe C. Castro 1,2,* 1 CIIMAR/CIMAR—Interdisciplinary Centre of Marine and Environmental Research, 4450-208 Matosinhos, Portugal; [email protected] (E.S.S.F.); [email protected] (R.R.); [email protected] (A.M.M.); fi[email protected] (F.C.); [email protected] (M.M.S.) 2 FCUP—Faculty of Sciences, Department of Biology, University of Porto, 4150-177 Porto, Portugal 3 Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore; [email protected] (B.-H.T.); [email protected] (B.V.) * Correspondence: fi[email protected]; Tel.: +351-22-3401800 Received: 25 February 2019; Accepted: 6 May 2019; Published: 10 May 2019 Abstract: To appraise how evolutionary processes, such as gene duplication and loss, influence an organism’s xenobiotic sensitivity is a critical question in toxicology. Of particular importance are gene families involved in the mediation of detoxification responses, such as members of the nuclear receptor subfamily 1 group I (NR1I), the pregnane X receptor (PXR), and the constitutive androstane receptor (CAR). While documented in multiple vertebrate genomes, PXR and CAR display an intriguing gene distribution. PXR is absent in birds and reptiles, while CAR shows a tetrapod-specific occurrence.
    [Show full text]
  • 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.
    [Show full text]
  • TMEM106B in Humans and Vac7 and Tag1 in Yeast Are Predicted to Be Lipid Transfer Proteins
    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.12.435176; this version posted March 12, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. TMEM106B in humans and Vac7 and Tag1 in yeast are predicted to be lipid transfer proteins Tim P. Levine* UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, United Kingdom. ORCID 0000-0002-7231-0775 *Corresponding author and lead contact: [email protected] Data availability statement: The data that support this study are freely available in Harvard Dataverse at https://dataverse.harvard.edu/dataverse/LEA_2. Acknowledgements: work was funded by the Higher Education Funding Council for England and the NIHR Moorfields Biomedical Research Centre Conflict of interest disclosure: the author declares that there is no conflict of interest Keywords: Structural bioinformatics, Lipid transfer protein, LEA_2, TMEM106B, Vac7, YLR173W, Endosome, Lysosome Running Title: TMEM106B & Vac7: lipid transfer proteins 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.03.12.435176; this version posted March 12, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract TMEM106B is an integral membrane protein of late endosomes and lysosomes involved in neuronal function, its over-expression being associated with familial frontotemporal lobar degeneration, and under-expression linked to hypomyelination. It has also been identified in multiple screens for host proteins required for productive SARS-CoV2 infection. Because standard approaches to understand TMEM106B at the sequence level find no homology to other proteins, it has remained a protein of unknown function.
    [Show full text]
  • Mouse Tmem106c Knockout Project (CRISPR/Cas9)
    https://www.alphaknockout.com Mouse Tmem106c Knockout Project (CRISPR/Cas9) Objective: To create a Tmem106c knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Tmem106c gene (NCBI Reference Sequence: NM_201359 ; Ensembl: ENSMUSG00000052369 ) is located on Mouse chromosome 15. 8 exons are identified, with the ATG start codon in exon 2 and the TAG stop codon in exon 8 (Transcript: ENSMUST00000064200). Exon 2~8 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 2 starts from about 0.13% of the coding region. Exon 2~8 covers 100.0% of the coding region. The size of effective KO region: ~4867 bp. The KO region does not have any other known gene. Page 1 of 9 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 5 6 7 8 Legends Exon of mouse Tmem106c Knockout region Page 2 of 9 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of start codon is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section downstream of stop codon is aligned with itself to determine if there are tandem repeats.
    [Show full text]
  • Exploring the Relationship Between Gut Microbiota and Major Depressive Disorders
    E3S Web of Conferences 271, 03055 (2021) https://doi.org/10.1051/e3sconf/202127103055 ICEPE 2021 Exploring the Relationship between Gut Microbiota and Major Depressive Disorders Catherine Tian1 1Shanghai American School, Shanghai, China Abstract. Major Depressive Disorder (MDD) is a psychiatric disorder accompanied with a high rate of suicide, morbidity and mortality. With the symptom of an increasing or decreasing appetite, there is a possibility that MDD may have certain connections with gut microbiota, the colonies of microbes which reside in the human digestive system. In recent years, more and more studies started to demonstrate the links between MDD and gut microbiota from animal disease models and human metabolism studies. However, this relationship is still largely understudied, but it is very innovative since functional dissection of this relationship would furnish a new train of thought for more effective treatment of MDD. In this study, by using multiple genetic analytic tools including Allen Brain Atlas, genetic function analytical tools, and MicrobiomeAnalyst, I explored the genes that shows both expression in the brain and the digestive system to affirm that there is a connection between gut microbiota and the MDD. My approach finally identified 7 MDD genes likely to be associated with gut microbiota, implicating 3 molecular pathways: (1) Wnt Signaling, (2) citric acid cycle in the aerobic respiration, and (3) extracellular exosome signaling. These findings may shed light on new directions to understand the mechanism of MDD, potentially facilitating the development of probiotics for better psychiatric disorder treatment. 1 Introduction 1.1 Major Depressive Disorder Major Depressive Disorder (MDD) is a mood disorder that will affect the mood, behavior and other physical parts.
    [Show full text]
  • Anti-TMEM106A (RABBIT) Antibody - 600-401-FH1
    Anti-TMEM106A (RABBIT) Antibody - 600-401-FH1 Code: 600-401-FH1 Size: 100 µg Product Description: Anti-TMEM106A (RABBIT) Antibody - 600-401-FH1 Concentration: 1 mg/mL by UV absorbance at 280 nm PhysicalState: Liquid (sterile filtered) Label Unconjugated Host Rabbit Gene Name TMEM106A Species Reactivity Human, mouse Buffer 0.01 M Sodium Phosphate, 0.25 M Sodium Chloride, pH 7.2 Stabilizer None Preservative 0.02% (w/v) Sodium Azide Storage Condition Store vial at -20° C prior to opening. Aliquot contents and freeze at -20° C or below for extended storage. Avoid cycles of freezing and thawing. Centrifuge product if not completely clear after standing at room temperature. This product is stable for several weeks at 4° C as an undiluted liquid. Dilute only prior to immediate use. Synonyms TMEM106A Antibody, Transmembrane protein 106A Application Note Anti-TMEM106A Antibody has been tested for use in ELISA, Western Blotting, Immunohistochemistry and Immunofluorescence. Specific conditions for reactivity should be optimized by the end user. Expect a band at approximately 29 kDa in Western Blots of specific cell lysates and tissues. Background Transmembrane protein 106A (TMEM106A) is a single-pass transmembrane protein that is closely related to TMEM106B, a protein that is thought to be a novel risk factor for frontotemporal lobar degeneration (FTLD), a group of clinically, pathologically and genetically heterogeneous disorders associated with atrophy in the frontal lobe and temporal lobe of the brain. The actual roles of TMEM106A and TMEM106B are still undetermined; however, as TMEM106B is involved in FTLD, it is possible that TMEM106A may also be a risk factor for FTLD.
    [Show full text]
  • Genetic Regulation of Tmem106b in the Pathogenesis of Frontotemporal Lobar Degeneration
    University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2017 Genetic Regulation Of Tmem106b In The Pathogenesis Of Frontotemporal Lobar Degeneration Michael Gallagher University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Genetics Commons, Molecular Biology Commons, and the Neuroscience and Neurobiology Commons Recommended Citation Gallagher, Michael, "Genetic Regulation Of Tmem106b In The Pathogenesis Of Frontotemporal Lobar Degeneration" (2017). Publicly Accessible Penn Dissertations. 2294. https://repository.upenn.edu/edissertations/2294 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/2294 For more information, please contact [email protected]. Genetic Regulation Of Tmem106b In The Pathogenesis Of Frontotemporal Lobar Degeneration Abstract Neurodegenerative diseases are an emerging global health crisis, with the projected global cost of dementia alone expected to exceed $1 trillion, or >1% of world GDP, by 2018. However, there are no disease-modifying treatments for the major neurodegenerative diseases, such as Alzheimer’s disease, Parkinson’s disease, frontotemporal lobar degeneration (FTLD), and amyotrophic lateral sclerosis. Therefore, there is an urgent need for a better understanding of the pathophysiology underlying these diseases. While genome-wide association studies (GWAS) have identified ~200 genetic ariantsv that are associated with risk of developing neurodegenerative disease, the biological mechanisms underlying these associations are largely unknown. This dissertation investigates the mechanisms by which common genetic variation at TMEM106B, a GWAS-identified risk locus for FTLD, influences disease risk. First, using genetic and clinical data from thirty American and European medical centers, I demonstrate that the TMEM106B locus acts as a genetic modifier of a common Mendelian form of FTLD.
    [Show full text]
  • Evolutionary History of Tibetans Inferred from Whole-Genome Sequencing
    RESEARCH ARTICLE Evolutionary history of Tibetans inferred from whole-genome sequencing Hao Hu1, Nayia Petousi2, Gustavo Glusman3, Yao Yu1, Ryan Bohlender4, Tsewang Tashi5, Jonathan M. Downie6, Jared C. Roach3, Amy M. Cole7, Felipe R. Lorenzo5, Alan R. Rogers4, Mary E. Brunkow3, Gianpiero Cavalleri7, Leroy Hood3, Sama M. Alpatty8, Josef T. Prchal5,6☯, Lynn B. Jorde6☯, Peter A. Robbins9☯, Tatum S. Simonson10☯, Chad D. Huff1☯* 1 Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America, 2 Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, a1111111111 3 Institute for Systems Biology, Seattle, Washington, United States of America, 4 Department of a1111111111 Anthropology, University of Utah, Salt Lake City, Utah, United States of America, 5 Department of Medicine, a1111111111 University of Utah School of Medicine and George E. Wahlin Veterans Administration Medical Center, Salt a1111111111 Lake City, Utah, United States of America, 6 Department of Human Genetics, University of Utah, Salt Lake a1111111111 City, Utah, United States of America, 7 Department of Molecular and Cellular Therapeutics, The Royal College of Surgeons in Ireland, Dublin, Ireland, 8 Skaggs School of Pharmacy and Pharmaceutical Science, UC San Diego, La Jolla, California, United States of America, 9 Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom, 10 Department of Medicine, Division of Physiology, University of California San Diego, La Jolla, California, United States of America OPEN ACCESS ☯ These authors contributed equally to this work. * [email protected] Citation: Hu H, Petousi N, Glusman G, Yu Y, Bohlender R, Tashi T, et al. (2017) Evolutionary history of Tibetans inferred from whole-genome sequencing.
    [Show full text]
  • SUPPLEMENTARY MATERIAL Supplementary Fig. S1. LD Mice Used in This Study Accumulate Polyglucosan Inclusions (Lafora Bodies) in the Brain
    1 SUPPLEMENTARY MATERIAL Supplementary Fig. S1. LD mice used in this study accumulate polyglucosan inclusions (Lafora bodies) in the brain. Samples from the hippocampus of five months old control, Epm2a-/- (lacking laforin) and Epm2b-/- mice (lacking malin) were stained with periodic acid Schiff reagent (PAS staining), which colors polysaccharide granules in red. Bar: 50 m. Supplementary Fig. S2. Principal component analysis (PCA) representing the first two components with the biggest level of phenotypic variability. Samples 1_S1 to 4_S4 corresponded to control, 5_S5, 6_S6 and 8_S8 to Epm2a-/- and 9_S9 to 12_S12 to Epm2b- /- samples, of animals of 16 months of age respectively. Supplementary Table S1. Primers used in this work to validate the expression of the corresponding genes by RT-qPCR. Supplementary Table S2: Genes downregulated more than 0.5 fold in Epm2a-/- and Epm2b-/- mice of 16 months of age. The gene name, false discovery rate (FDR), fold change (FC), description and MGI Id (mouse genome informatics) are indicated. Genes are arranged according to FC. Supplementary Table S3: Genes upregulated more than 1.5 fold in Epm2a-/- mice of 16 months of age. The gene name, false discovery rate (FDR), fold change (FC), description and MGI Id (mouse genome informatics) are indicated. Genes are arranged according to FC. Supplementary Table S4: Genes upregulated more than 1.5 fold in Epm2b-/- mice of 16 months of age. The gene name, false discovery rate (FDR), fold change (FC), description and MGI Id (mouse genome informatics) are indicated. Genes are arranged according to FC. 2 Supplementary Table S5: Genes upregulated in both Epm2a-/- and Epm2b-/- mice of 16 months of age.
    [Show full text]
  • Transmembrane Protein 106A Activates Mouse Peritoneal Macrophages Via the MAPK and NF-Κb Signaling Pathways
    www.nature.com/scientificreports OPEN Transmembrane protein 106a activates mouse peritoneal macrophages via the MAPK and Received: 06 January 2015 Accepted: 30 June 2015 NF-κB signaling pathways Published: 28 July 2015 Hui Dai1, Dong Xu1,2, Jing Su3, Jingyuan Jang1 & Yingyu Chen1,2 The M1 and M2 states of macrophage are the two extremes of a physiologic/phenotypic continuum that is dynamically influenced by environmental signals. Molecular mechanism analysis indicated that they gain M1 and M2-related functions after encountering specific ligands in the tissue environment. Here, we first characterized the previously unknown immunobiological functions of mouse Tmem106a. This protein is abundantly expressed on the surface of mouse macrophages. Activation of Tmem106a by stimulation with anti-Tmem106a upregulated the expression of CD80, CD86, CD69 and MHC II on macrophage, and induced the release of TNF-α, IL-1β, IL-6, CCL2 and NO, but not IL-10. These effects were largely abrogated by pretreatment with siRNA against Tmem106a. Notably, anti-Tmem106a significantly increased iNOS production and phosphorylation of STAT1, and had no effect on the ARGINASE-1 or p-STAT6 level, indicating that anti-Tmem106a activated macrophages and polarized them into M1-like macrophages. Further analysis found that anti-Tmem106a stimulation increased phosphorylation of ERK-1/2, JNK, p38 MAPK, NF-κB p65 and IKKα/β, and promoted nuclear translocation of the cytosolic NF-κB p65 subunit. Collectively, these data suggest that mouse Tmem106a might be a new trigger of macrophage activation and have some influence toward the M1 state through the activation of the MAPKs and NF-κB pathway.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2013/0130246A1 BENSMON Et Al
    US 2013 O130246A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2013/0130246A1 BENSMON et al. (43) Pub. Date: May 23, 2013 (54) METHODS FOR THE DETECTION, (22) Filed: Oct. 31, 2012 VISUALIZATION AND HIGH RESOLUTION PHYSICAL MAPPING OF GENOMIC Related U.S. Application Data REARRANGEMENTS IN BREAST AND OVARAN CANCER GENES AND LOC (60) Provisional application No. 61/553,906, filed on Oct. BRCA1 AND BRCA2 USING GENOMIC 31, 2011. MORSE CODE IN CONJUNCTION WITH MOLECULAR COMBING Publication Classification (71) Applicants: Aaron BENSIMON, Anthony (FR): (51) Int. Cl. Maurizio Ceppi, Issy-Les-Moulineaux CI2O I/68 (2006.01) (FR); Kevin Cheeseman, (52) U.S. Cl. Champigny-Sur-Marne (FR); Emmanuel CPC .................................... CI2O I/6886 (2013.01) Conseiller, Paris (FR); Pierre Walrafen, USPC ......................................................... 435/6.11 Montrouge (FR) (57) ABSTRACT (72) Inventors: Aaron BENSIMON, Anthony (FR): Maurizio Ceppi, Issy-Les-Moulineaux Methods for detecting genomic rearrangements in BRCA1 (FR); Kevin Cheeseman, and BRCA2 genes at high resolution using Molecular Comb Champigny-Sur-Marne (FR); Emmanuel ing and for determining a predisposition to a disease or dis Conseiller, Paris (FR); Pierre Walrafen, order associated with these rearrangements including predis Montrouge (FR) position to ovarian cancer or breast cancer. Primers useful for producing probes for this method and kits for practicing the (21) Appl. No.: 13/665,404 methods. Patent Application Publication May 23, 2013 Sheet 1 of 12 US 2013/0130246 A1 85925 379 o : 98. xxxxxx& 3850,75800 :g i s Patent Application Publication May 23, 2013 Sheet 2 of 12 US 2013/0130246 A1 Fig. 1B 845 3.25° 42950 888 O 3690 73800 O700 147600' S.
    [Show full text]