Loss of α2-6 Sialylation Promotes the Transformation Of
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HPSE2 Gene Heparanase 2 (Inactive)
HPSE2 gene heparanase 2 (inactive) Normal Function The HPSE2 gene provides instructions for making a protein called heparanase 2. Little is known about this protein, but its structure is similar to that of another protein called heparanase 1. Heparanase 1 is an enzyme that splits (cleaves) molecules called heparan sulfate proteoglycans (HSPGs) by removing the heparan sulfate portion (the side chain). HSPGs are important parts of the lattice of proteins and other molecules outside the cell (extracellular matrix) and of basement membranes, which are thin, sheet-like structures that separate and support cells in many tissues. Cleavage of HSPGs by heparanase 1 may lead to changes in the basement membrane or extracellular matrix that allow cell movement or release of substances from the cell. The specific function of the heparanase 2 enzyme is not well understood, but studies suggest that it may block the action of heparanase 1. Health Conditions Related to Genetic Changes Migraine MedlinePlus Genetics provides information about Migraine Ochoa syndrome At least nine HPSE2 gene mutations have been identified in people with Ochoa syndrome (also called urofacial syndrome), a disorder that causes urinary problems and unusual facial expressions. These mutations result in changes in the heparanase 2 protein that likely prevent it from functioning. The connection between HPSE2 gene mutations and the features of Ochoa syndrome are unclear. Because the areas of the brain that control facial expression and urination are in close proximity, some researchers have suggested that the genetic changes may lead to an abnormality in this brain region that may account for the symptoms of Ochoa syndrome. -
Urinary Tract Effects of HPSE2 Mutations
BRIEF COMMUNICATION www.jasn.org Urinary Tract Effects of HPSE2 Mutations † Helen M. Stuart,* Neil A. Roberts,* Emma N. Hilton,* Edward A. McKenzie, Sarah B. Daly,* † ‡ Kristen D. Hadfield,* Jeffery S. Rahal,* Natalie J. Gardiner, Simon W. Tanley, | Malcolm A. Lewis,* Emily Sites,§ Brad Angle,§ Cláudia Alves, Teresa Lourenço,¶ Márcia Rodrigues,¶ Angelina Calado,** Marta Amado,** Nancy Guerreiro,** Inês Serras,** †† †† || Christian Beetz , Rita-Eva Varga , Mesrur Selcuk Silay,§§ John M. Darlow, ¶¶ || || ††† Mark G. Dobson , ¶¶ David E. Barton , *** Manuela Hunziker,¶¶ Prem Puri,¶¶*** ‡‡‡ Sally A. Feather, Judith A. Goodship ,§§§ Timothy H.J. Goodship ,§§§ Heather J. ||| BRIEF COMMUNICATION Lambert ,§§§ Heather J. Cordell ,§§§ the UK VUR Study Group, Anand Saggar, †††† Maria Kinali ,¶¶¶, the 4C Study Group, Christian Lorenz ,**** Kristina Moeller, |||| Franz Schaefer,§§§§ Aysun K. Bayazit , Stefanie Weber,¶¶¶¶ William G. Newman ,* and Adrian S. Woolf * Due to the number of contributing authors, the affiliations are listed at the end of this article. ABSTRACT Urofacial syndrome (UFS) is an autosomal recessive congenital disease featuring grimacing grimacing and dysmorphic bladders. and incomplete bladder emptying. Mutations of HPSE2, encoding heparanase 2, a Considering these and previously pub- heparanase 1 inhibitor, occur in UFS, but knowledge about the HPSE2 mutation spec- lished mutations4–7 (Figure 1A), it is clear trum is limited. Here, seven UFS kindreds with HPSE2 mutations are presented, that pathogenic HPSE2 mutations are including one with deleted asparagine 254, suggesting a role for this amino acid, found across the gene’s coding region. which is conserved in vertebrate orthologs. HPSE2 mutations were absent in 23 non- Most (i.e., nonsense or frameshift muta- neurogenic neurogenic bladder probands and, of 439 families with nonsyndromic tions) would cause loss of function, but a vesicoureteric reflux, only one carried a putative pathogenic HPSE2 variant. -
Supplemental Figure 1. Vimentin
Double mutant specific genes Transcript gene_assignment Gene Symbol RefSeq FDR Fold- FDR Fold- FDR Fold- ID (single vs. Change (double Change (double Change wt) (single vs. wt) (double vs. single) (double vs. wt) vs. wt) vs. single) 10485013 BC085239 // 1110051M20Rik // RIKEN cDNA 1110051M20 gene // 2 E1 // 228356 /// NM 1110051M20Ri BC085239 0.164013 -1.38517 0.0345128 -2.24228 0.154535 -1.61877 k 10358717 NM_197990 // 1700025G04Rik // RIKEN cDNA 1700025G04 gene // 1 G2 // 69399 /// BC 1700025G04Rik NM_197990 0.142593 -1.37878 0.0212926 -3.13385 0.093068 -2.27291 10358713 NM_197990 // 1700025G04Rik // RIKEN cDNA 1700025G04 gene // 1 G2 // 69399 1700025G04Rik NM_197990 0.0655213 -1.71563 0.0222468 -2.32498 0.166843 -1.35517 10481312 NM_027283 // 1700026L06Rik // RIKEN cDNA 1700026L06 gene // 2 A3 // 69987 /// EN 1700026L06Rik NM_027283 0.0503754 -1.46385 0.0140999 -2.19537 0.0825609 -1.49972 10351465 BC150846 // 1700084C01Rik // RIKEN cDNA 1700084C01 gene // 1 H3 // 78465 /// NM_ 1700084C01Rik BC150846 0.107391 -1.5916 0.0385418 -2.05801 0.295457 -1.29305 10569654 AK007416 // 1810010D01Rik // RIKEN cDNA 1810010D01 gene // 7 F5 // 381935 /// XR 1810010D01Rik AK007416 0.145576 1.69432 0.0476957 2.51662 0.288571 1.48533 10508883 NM_001083916 // 1810019J16Rik // RIKEN cDNA 1810019J16 gene // 4 D2.3 // 69073 / 1810019J16Rik NM_001083916 0.0533206 1.57139 0.0145433 2.56417 0.0836674 1.63179 10585282 ENSMUST00000050829 // 2010007H06Rik // RIKEN cDNA 2010007H06 gene // --- // 6984 2010007H06Rik ENSMUST00000050829 0.129914 -1.71998 0.0434862 -2.51672 -
Implications in Parkinson's Disease
Journal of Clinical Medicine Review Lysosomal Ceramide Metabolism Disorders: Implications in Parkinson’s Disease Silvia Paciotti 1,2 , Elisabetta Albi 3 , Lucilla Parnetti 1 and Tommaso Beccari 3,* 1 Laboratory of Clinical Neurochemistry, Department of Medicine, University of Perugia, Sant’Andrea delle Fratte, 06132 Perugia, Italy; [email protected] (S.P.); [email protected] (L.P.) 2 Section of Physiology and Biochemistry, Department of Experimental Medicine, University of Perugia, Sant’Andrea delle Fratte, 06132 Perugia, Italy 3 Department of Pharmaceutical Sciences, University of Perugia, Via Fabretti, 06123 Perugia, Italy; [email protected] * Correspondence: [email protected] Received: 29 January 2020; Accepted: 20 February 2020; Published: 21 February 2020 Abstract: Ceramides are a family of bioactive lipids belonging to the class of sphingolipids. Sphingolipidoses are a group of inherited genetic diseases characterized by the unmetabolized sphingolipids and the consequent reduction of ceramide pool in lysosomes. Sphingolipidoses include several disorders as Sandhoff disease, Fabry disease, Gaucher disease, metachromatic leukodystrophy, Krabbe disease, Niemann Pick disease, Farber disease, and GM2 gangliosidosis. In sphingolipidosis, lysosomal lipid storage occurs in both the central nervous system and visceral tissues, and central nervous system pathology is a common hallmark for all of them. Parkinson’s disease, the most common neurodegenerative movement disorder, is characterized by the accumulation and aggregation of misfolded α-synuclein that seem associated to some lysosomal disorders, in particular Gaucher disease. This review provides evidence into the role of ceramide metabolism in the pathophysiology of lysosomes, highlighting the more recent findings on its involvement in Parkinson’s disease. Keywords: ceramide metabolism; Parkinson’s disease; α-synuclein; GBA; GLA; HEX A-B; GALC; ASAH1; SMPD1; ARSA * Correspondence [email protected] 1. -
Differences Between Human and Chimpanzee Genomes and Their Implications in Gene Expression, Protein Functions and Biochemical Properties of the Two Species Maria V
Suntsova and Buzdin BMC Genomics 2020, 21(Suppl 7):535 https://doi.org/10.1186/s12864-020-06962-8 REVIEW Open Access Differences between human and chimpanzee genomes and their implications in gene expression, protein functions and biochemical properties of the two species Maria V. Suntsova1 and Anton A. Buzdin1,2,3,4* From 11th International Young Scientists School “Systems Biology and Bioinformatics”–SBB-2019 Novosibirsk, Russia. 24-28 June 2019 Abstract Chimpanzees are the closest living relatives of humans. The divergence between human and chimpanzee ancestors dates to approximately 6,5–7,5 million years ago. Genetic features distinguishing us from chimpanzees and making us humans are still of a great interest. After divergence of their ancestor lineages, human and chimpanzee genomes underwent multiple changes including single nucleotide substitutions, deletions and duplications of DNA fragments of different size, insertion of transposable elements and chromosomal rearrangements. Human-specific single nucleotide alterations constituted 1.23% of human DNA, whereas more extended deletions and insertions cover ~ 3% of our genome. Moreover, much higher proportion is made by differential chromosomal inversions and translocations comprising several megabase-long regions or even whole chromosomes. However, despite of extensive knowledge of structural genomic changes accompanying human evolution we still cannot identify with certainty the causative genes of human identity. Most structural gene-influential changes happened at the level of expression regulation, which in turn provoked larger alterations of interactome gene regulation networks. In this review, we summarized the available information about genetic differences between humans and chimpanzees and their potential functional impacts on differential molecular, anatomical, physiological and cognitive peculiarities of these species. -
Broad and Thematic Remodeling of the Surface Glycoproteome on Isogenic
bioRxiv preprint doi: https://doi.org/10.1101/808139; this version posted October 17, 2019. 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. Broad and thematic remodeling of the surface glycoproteome on isogenic cells transformed with driving proliferative oncogenes Kevin K. Leung1,5, Gary M. Wilson2,5, Lisa L. Kirkemo1, Nicholas M. Riley2,4, Joshua J. Coon2,3, James A. Wells1* 1Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA, USA Departments of Chemistry2 and Biomolecular Chemistry3, University of Wisconsin- Madison, Madison, WI, 53706, USA 4Present address Department of Chemistry, Stanford University, Stanford, CA, 94305, USA 5These authors contributed equally *To whom correspondence should be addressed bioRxiv preprint doi: https://doi.org/10.1101/808139; this version posted October 17, 2019. 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. Abstract: The cell surface proteome, the surfaceome, is the interface for engaging the extracellular space in normal and cancer cells. Here We apply quantitative proteomics of N-linked glycoproteins to reveal how a collection of some 700 surface proteins is dramatically remodeled in an isogenic breast epithelial cell line stably expressing any of six of the most prominent proliferative oncogenes, including the receptor tyrosine kinases, EGFR and HER2, and downstream signaling partners such as KRAS, BRAF, MEK and AKT. -
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. -
(12) United States Patent (10) Patent No.: US 8,323,640 B2 Sakuraba Et Al
USOO8323640B2 (12) United States Patent (10) Patent No.: US 8,323,640 B2 Sakuraba et al. (45) Date of Patent: *Dec. 4, 2012 (54) HIGHLY FUNCTIONAL ENZYME HAVING OTHER PUBLICATIONS O-GALACTOSIDASE ACTIVITY Broun et al., Catalytic plasticity of fatty acid modification enzymes (75) Inventors: Hitoshi Sakuraba, Abiko (JP); Youichi underlying chemical diversity of plant lipids. Science, 1998, vol. 282: Tajima, Tokyo (JP); Mai Ito, Tokyo 1315-1317. (JP); Seiichi Aikawa, Tokyo (JP); Cameron ER. Recent advances in transgenic technology. 1997, vol. T: 253-265. Fumiko Aikawa, Tokyo (JP) Chica et al., Semi-rational approaches to engineering enzyme activ (73) Assignees: Tokyo Metropolitan Organization For ity: combining the benefits of directed evolution and rational design. Curr, opi. Biotechnol., 2005, vol. 16:378-384. Medical Research, Tokyo (JP); Altif Couzin et al. As Gelsinger case ends, Gene therapy Suffers another Laboratories, Tokyo (JP) blow. Science, 2005, vol. 307: 1028. Devos et al., Practical Limits of Function prediction. Proteins: Struc (*) Notice: Subject to any disclaimer, the term of this ture, Function, and Genetics. 2000, vol. 41: 98-107. patent is extended or adjusted under 35 Donsante et al., AAV vector integration sites in mouse hapatocellular U.S.C. 154(b) by 0 days. carcinoma. Science, 2007. vol. 317: 477. Juengst ET., What next for human gene therapy? BMJ., 2003, vol. This patent is Subject to a terminal dis 326: 1410-1411. claimer. Kappel et al., Regulating gene expression in transgenic animals. Current Opinion in Biotechnology 1992, vol. 3: 548-553. (21) Appl. No.: 13/052,632 Kimmelman J. Recent developments in gene transfer: risk and eth ics. -
Understanding the Molecular Pathobiology of Acid Ceramidase Deficiency
Understanding the Molecular Pathobiology of Acid Ceramidase Deficiency By Fabian Yu A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Institute of Medical Science University of Toronto © Copyright by Fabian PS Yu 2018 Understanding the Molecular Pathobiology of Acid Ceramidase Deficiency Fabian Yu Doctor of Philosophy Institute of Medical Science University of Toronto 2018 Abstract Farber disease (FD) is a devastating Lysosomal Storage Disorder (LSD) caused by mutations in ASAH1, resulting in acid ceramidase (ACDase) deficiency. ACDase deficiency manifests along a broad spectrum but in its classical form patients die during early childhood. Due to the scarcity of cases FD has largely been understudied. To circumvent this, our lab previously generated a mouse model that recapitulates FD. In some case reports, patients have shown signs of visceral involvement, retinopathy and respiratory distress that may lead to death. Beyond superficial descriptions in case reports, there have been no in-depth studies performed to address these conditions. To improve the understanding of FD and gain insights for evaluating future therapies, we performed comprehensive studies on the ACDase deficient mouse. In the visual system, we reported presence of progressive uveitis. Further tests revealed cellular infiltration, lipid buildup and extensive retinal pathology. Mice developed retinal dysplasia, impaired retinal response and decreased visual acuity. Within the pulmonary system, lung function tests revealed a decrease in lung compliance. Mice developed chronic lung injury that was contributed by cellular recruitment, and vascular leakage. Additionally, we report impairment to lipid homeostasis in the lungs. ii To understand the liver involvement in FD, we characterized the pathology and performed transcriptome analysis to identify gene and pathway changes. -
Down Regulation of Membrane-Bound Neu3 Constitutes a New
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Publications of the IAS Fellows IJC International Journal of Cancer Down regulation of membrane-bound Neu3 constitutes a new potential marker for childhood acute lymphoblastic leukemia and induces apoptosis suppression of neoplastic cells Chandan Mandal1, Cristina Tringali2, Susmita Mondal1, Luigi Anastasia2, Sarmila Chandra3, Bruno Venerando2 and Chitra Mandal1 1 Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, A Unit of Council of Scientific and Industrial Research, Govt of India, 4, Raja S. C. Mullick Road, Kolkata 700032, India 2 Department of Medical Chemistry, Biochemistry and Biotechnology, University of Milan, and IRCCS Policlinico San Donato, San Donato, Milan, Italy 3 Department of Hematology, Kothari Medical Centre, Kolkata 700027, India Membrane-linked sialidase Neu3 is a key enzyme for the extralysosomal catabolism of gangliosides. In this respect, it regulates pivotal cell surface events, including trans-membrane signaling, and plays an essential role in carcinogenesis. In this report, we demonstrated that acute lymphoblastic leukemia (ALL), lymphoblasts (primary cells from patients and cell lines) are characterized by a marked down-regulation of Neu3 in terms of both gene expression (230 to 40%) and enzymatic activity toward ganglioside GD1a (225.6 to 30.6%), when compared with cells from healthy controls. Induced overexpression of Neu3 in the ALL-cell line, MOLT-4, led to a significant increase of ceramide (166%) and to a parallel decrease of lactosylceramide (255%). These events strongly guided lymphoblasts to apoptosis, as we assessed by the decrease in Bcl2/ Bax ratio, the accumulation of Neu3 transfected cells in the sub G0–G1 phase of the cell cycle, the enhanced annexin-V positivity, the higher cleavage of procaspase-3. -
Yeast Genome Gazetteer P35-65
gazetteer Metabolism 35 tRNA modification mitochondrial transport amino-acid metabolism other tRNA-transcription activities vesicular transport (Golgi network, etc.) nitrogen and sulphur metabolism mRNA synthesis peroxisomal transport nucleotide metabolism mRNA processing (splicing) vacuolar transport phosphate metabolism mRNA processing (5’-end, 3’-end processing extracellular transport carbohydrate metabolism and mRNA degradation) cellular import lipid, fatty-acid and sterol metabolism other mRNA-transcription activities other intracellular-transport activities biosynthesis of vitamins, cofactors and RNA transport prosthetic groups other transcription activities Cellular organization and biogenesis 54 ionic homeostasis organization and biogenesis of cell wall and Protein synthesis 48 plasma membrane Energy 40 ribosomal proteins organization and biogenesis of glycolysis translation (initiation,elongation and cytoskeleton gluconeogenesis termination) organization and biogenesis of endoplasmic pentose-phosphate pathway translational control reticulum and Golgi tricarboxylic-acid pathway tRNA synthetases organization and biogenesis of chromosome respiration other protein-synthesis activities structure fermentation mitochondrial organization and biogenesis metabolism of energy reserves (glycogen Protein destination 49 peroxisomal organization and biogenesis and trehalose) protein folding and stabilization endosomal organization and biogenesis other energy-generation activities protein targeting, sorting and translocation vacuolar and lysosomal -
Supplementary Information Biocementation of Soil by Calcite/Aragonite Precipitation Using Pseudomonas Azotoformans and Citrobact
Electronic Supplementary Material (ESI) for RSC Advances. This journal is © The Royal Society of Chemistry 2019 Supplementary Information Biocementation of soil by calcite/aragonite precipitation using Pseudomonas azotoformans and Citrobacter freundii derived enzymes Heba Abdel-Aleem1, Tarek Dishisha1, Amal Saafan2, Abduallah A. AbouKhadra3 and Yasser Gaber1,4,* 1Department of Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University, 62511, Beni-Suef, Egypt 2Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Menoufia university, Shebeen El-kom, Egypt 3Department of Civil Engineering, Facutly of Engineering, Beni-Suef University, 62511, Beni- Suef, Egypt 4Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Mutah University, Al-karak, 61710, Jordan *Corresponding author: E-mail: [email protected] Tel. int +20 82 216 2133 ; Fax. int +20 82 216 2133 1 Supplementary Table 1: strains identified using BCL card (Gram positive spore forming bacilli) Sample/test A1 B1 B2 Y1a Y2a BXYL - - - - - BXYL (betaxylosidase), LysA - - - - - LysA (L- lysine arylamidase), AspA - - - + - AspA (L aspartate arylamidase), LeuA + + + + + LeuA (leucine arylamidase), PheA - + - - - PheA (phenylalanine arylamidase), ProA - - - + - ProA (L-proline arylamidase), BGAL - - - - - BGAL (beta galactosidase), PyrA + + + + + PyrA (L-pyrrolydonyl arylamidase), AGAL - - - - - AGAL (alpha galactosidase), AlaA - - - + - AlaA (alanine arylamidase), TyrA - - - - - TyrA (tyrosine arylamidase), BNAG + + + + + BNAG (beta-N-acetyl