The Extracellular Matrix Gene Frem1 Is Essential for the Normal Adhesion of the Embryonic Epidermis
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Global Analysis Reveals the Complexity of the Human Glomerular Extracellular Matrix
Global analysis reveals the complexity of the human glomerular extracellular matrix Rachel Lennon,1,2 Adam Byron,1,* Jonathan D. Humphries,1 Michael J. Randles,1,2 Alex Carisey,1 Stephanie Murphy,1,2 David Knight,3 Paul E. Brenchley,2 Roy Zent,4,5 and Martin J. Humphries.1 1Wellcome Trust Centre for Cell-Matrix Research, Faculty of Life Sciences, University of Manchester, Manchester, UK; 2Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK; 3Biological Mass Spectrometry Core Facility, Faculty of Life Sciences, University of Manchester, Manchester, UK; 4Division of Nephrology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; and 5Veterans Affairs Hospital, Nashville, TN, USA. *Present address: Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK. Running title: Proteome of the glomerular matrix Word count: Abstract: 208, main text 2765 Corresponding author: Dr Rachel Lennon, Wellcome Trust Centre for Cell-Matrix Research, Michael Smith Building, University of Manchester, Manchester M13 9PT, UK. Phone: 0044 (0) 161 2755498. Fax: 0044 (0) 161 2755082. Email: [email protected] Abstract The glomerulus contains unique cellular and extracellular matrix (ECM) components, which are required for intact barrier function. Studies of the cellular components have helped to build understanding of glomerular disease; however, the full composition and regulation of glomerular ECM remains poorly understood. Here, we employed mass spectrometry–based proteomics of enriched ECM extracts for a global analysis of human glomerular ECM in vivo and identified a tissue-specific proteome of 144 structural and regulatory ECM proteins. This catalogue includes all previously identified glomerular components, plus many new and abundant components. -
Environmental Influences on Endothelial Gene Expression
ENDOTHELIAL CELL GENE EXPRESSION John Matthew Jeff Herbert Supervisors: Prof. Roy Bicknell and Dr. Victoria Heath PhD thesis University of Birmingham August 2012 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. ABSTRACT Tumour angiogenesis is a vital process in the pathology of tumour development and metastasis. Targeting markers of tumour endothelium provide a means of targeted destruction of a tumours oxygen and nutrient supply via destruction of tumour vasculature, which in turn ultimately leads to beneficial consequences to patients. Although current anti -angiogenic and vascular targeting strategies help patients, more potently in combination with chemo therapy, there is still a need for more tumour endothelial marker discoveries as current treatments have cardiovascular and other side effects. For the first time, the analyses of in-vivo biotinylation of an embryonic system is performed to obtain putative vascular targets. Also for the first time, deep sequencing is applied to freshly isolated tumour and normal endothelial cells from lung, colon and bladder tissues for the identification of pan-vascular-targets. Integration of the proteomic, deep sequencing, public cDNA libraries and microarrays, delivers 5,892 putative vascular targets to the science community. -
High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model
Purdue University Purdue e-Pubs Department of Animal Sciences Faculty Department of Animal Sciences Publications 2016 High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model Chiao-Ling Lo Indiana University School of Medicine Amy C. Lossie Indiana University School of Medicine Tiebing Liang Indiana University School of Medicine Yunlong Liu Indiana University School of Medicine Xiaoling Xuei Indiana University School of Medicine See next page for additional authors Follow this and additional works at: http://docs.lib.purdue.edu/anscpubs Recommended Citation Lo C-L, Lossie AC, Liang T, Liu Y, Xuei X, Lumeng L, et al. (2016) High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model. PLoS Genet 12(8): e1006178. https://doi.org/10.1371/ journal.pgen.1006178 This document has been made available through Purdue e-Pubs, a service of the Purdue University Libraries. Please contact [email protected] for additional information. Authors Chiao-Ling Lo, Amy C. Lossie, Tiebing Liang, Yunlong Liu, Xiaoling Xuei, Lawrence Lumeng, Feng C. Zhou, and William M. Muir This article is available at Purdue e-Pubs: http://docs.lib.purdue.edu/anscpubs/19 RESEARCH ARTICLE High Resolution Genomic Scans Reveal Genetic Architecture Controlling Alcohol Preference in Bidirectionally Selected Rat Model Chiao-Ling Lo1,2, Amy C. Lossie1,3¤, Tiebing Liang1,4, Yunlong Liu1,5, Xiaoling Xuei1,6, Lawrence Lumeng1,4, Feng C. Zhou1,2,7*, William -
Original Article FREM2 Is an Independent Predictor of Poor Survival in Clear Cell Renal Cell Carcinoma-Evidence from the Cancer Genome Atlas (TCGA)
Int J Clin Exp Med 2019;12(12):13741-13748 www.ijcem.com /ISSN:1940-5901/IJCEM0076963 Original Article FREM2 is an independent predictor of poor survival in clear cell renal cell carcinoma-evidence from the cancer genome atlas (TCGA) Weiping Huang, Yongyong Lu, Xixi Huang, Feng Wang, Zhixian Yu Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, Zhejiang Province, China Received February 26, 2018; Accepted October 7, 2018; Epub December 15, 2019; Published December 30, 2019 Abstract: Fraser syndrome protein 1 (FRAS1) and FRAS1 related extracellular matrix protein 1 and 2 (FREM1, FREM2) are a novel group of basement membrane proteins. The relationship between the three gene (FRAS1, FREM1, FREM2) and renal clear cell carcinoma is completely unclear. Thus, in this research, we used the mRNA sequencing data derived from TCGA kidney renal clear cell carcinoma cohort to assess the association of FRAS1, FREM1 and FREM2 with different clinical features. FRAS1, FREM1 and FREM2 mRNA levels were downregulated in KIRC (kidney renal clear cell carcinoma) tissues than normal tissues (FRAS1, P < 0.0001; FREM1, P < 0.0001, FREM2, P = 0.0001), respectively. FRAS1, FREM1 and FREM2 were significantly different in histologic grade, patho- logic stage and pathologic T (all P < 0.001). Low FRAS1, FREM1 and FREM2 expression were correlated to worsen overall survival (all P < 0.01), and Low FREM1 and FREM2 expression had worse relapse-free survival (FREM1, P = 0.0113; FREM2, P = 0.0424). Multivariate Cox regression analysis revealed that FREM2 was an independent prog- nostic factor for overall survival. Taken together, FREM2 expression is an independent predictor of poor survival in renal clear cell carcinoma and is positively associated with advanced stage, high histologic grade. -
Mirna Let-7 from TPO(+) Extracellular Vesicles Is a Potential Marker for a Differential Diagnosis of Follicular Thyroid Nodules
cells Article MiRNA let-7 from TPO(+) Extracellular Vesicles is a Potential Marker for a Differential Diagnosis of Follicular Thyroid Nodules Lidia Zabegina 1,2,3, Inga Nazarova 1,2, Margarita Knyazeva 1,2,3, Nadezhda Nikiforova 1,2, Maria Slyusarenko 1,2, Sergey Titov 4 , Dmitry Vasilyev 1, Ilya Sleptsov 5 and Anastasia Malek 1,2,* 1 Subcellular Technology Lab., N.N. Petrov National Medical Research Center of Oncology, 195251 St. Petersburg, Russia; [email protected] (L.Z.); [email protected] (I.N.); [email protected] (M.K.); [email protected] (N.N.); [email protected] (M.S.); [email protected] (D.V.) 2 Oncosystem Ltd., 121205 Moscow, Russia 3 Institute of Biomedical Systems and Biotechnologies, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia 4 PCR Laboratory; AO Vector-Best, 630117 Novosibirsk, Russia; [email protected] 5 Department of endocrine surgery, Clinic of High Medical Technologies, St. Petersburg State University N.I. Pirogov, 190103 St. Petersburg, Russia; [email protected] * Correspondence: [email protected]; Tel.: +7-960-250-46-80 Received: 19 July 2020; Accepted: 15 August 2020; Published: 18 August 2020 Abstract: Background: The current approaches to distinguish follicular adenomas (FA) and follicular thyroid cancer (FTC) at the pre-operative stage have low predictive value. Liquid biopsy-based analysis of circulating extracellular vesicles (EVs) presents a promising diagnostic method. However, the extreme heterogeneity of plasma EV population hampers the development of new diagnostic tests. We hypothesize that the isolation of EVs with thyroid-specific surface molecules followed by miRNA analysis, may have improved diagnostic potency. -
Supplemental Material Placed on This Supplemental Material Which Has Been Supplied by the Author(S) J Med Genet
BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Med Genet Supplement Supplementary Table S1: GENE MEAN GENE NAME OMIM SYMBOL COVERAGE CAKUT CAKUT ADTKD ADTKD aHUS/TMA aHUS/TMA TUBULOPATHIES TUBULOPATHIES Glomerulopathies Glomerulopathies Polycystic kidneys / Ciliopathies Ciliopathies / kidneys Polycystic METABOLIC DISORDERS AND OTHERS OTHERS AND DISORDERS METABOLIC x x ACE angiotensin-I converting enzyme 106180 139 x ACTN4 actinin-4 604638 119 x ADAMTS13 von Willebrand cleaving protease 604134 154 x ADCY10 adenylate cyclase 10 605205 81 x x AGT angiotensinogen 106150 157 x x AGTR1 angiotensin II receptor, type 1 106165 131 x AGXT alanine-glyoxylate aminotransferase 604285 173 x AHI1 Abelson helper integration site 1 608894 100 x ALG13 asparagine-linked glycosylation 13 300776 232 x x ALG9 alpha-1,2-mannosyltransferase 606941 165 centrosome and basal body associated x ALMS1 606844 132 protein 1 x x APOA1 apolipoprotein A-1 107680 55 x APOE lipoprotein glomerulopathy 107741 77 x APOL1 apolipoprotein L-1 603743 98 x x APRT adenine phosphoribosyltransferase 102600 165 x ARHGAP24 Rho GTPase-Activation protein 24 610586 215 x ARL13B ADP-ribosylation factor-like 13B 608922 195 x x ARL6 ADP-ribosylation factor-like 6 608845 215 ATPase, H+ transporting, lysosomal V0, x ATP6V0A4 605239 90 subunit a4 ATPase, H+ transporting, lysosomal x x ATP6V1B1 192132 163 56/58, V1, subunit B1 x ATXN10 ataxin -
Gene Standard Deviation MTOR 0.12553731 PRPF38A
BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) Gut Gene Standard Deviation MTOR 0.12553731 PRPF38A 0.141472605 EIF2B4 0.154700091 DDX50 0.156333027 SMC3 0.161420017 NFAT5 0.166316903 MAP2K1 0.166585267 KDM1A 0.16904912 RPS6KB1 0.170330192 FCF1 0.170391706 MAP3K7 0.170660513 EIF4E2 0.171572093 TCEB1 0.175363093 CNOT10 0.178975095 SMAD1 0.179164705 NAA15 0.179904998 SETD2 0.180182498 HDAC3 0.183971158 AMMECR1L 0.184195031 CHD4 0.186678211 SF3A3 0.186697697 CNOT4 0.189434633 MTMR14 0.189734199 SMAD4 0.192451524 TLK2 0.192702667 DLG1 0.19336621 COG7 0.193422331 SP1 0.194364189 PPP3R1 0.196430217 ERBB2IP 0.201473001 RAF1 0.206887192 CUL1 0.207514271 VEZF1 0.207579584 SMAD3 0.208159809 TFDP1 0.208834504 VAV2 0.210269344 ADAM17 0.210687138 SMURF2 0.211437666 MRPS5 0.212428684 TMUB2 0.212560675 SRPK2 0.216217428 MAP2K4 0.216345366 VHL 0.219735582 SMURF1 0.221242495 PLCG1 0.221688351 EP300 0.221792349 Sundar R, et al. Gut 2020;0:1–10. doi: 10.1136/gutjnl-2020-320805 BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) Gut MGAT5 0.222050228 CDC42 0.2230598 DICER1 0.225358787 RBX1 0.228272533 ZFYVE16 0.22831803 PTEN 0.228595789 PDCD10 0.228799406 NF2 0.23091035 TP53 0.232683696 RB1 0.232729172 TCF20 0.2346075 PPP2CB 0.235117302 AGK 0.235416298 -
Differential Gene Expression in Oligodendrocyte Progenitor Cells, Oligodendrocytes and Type II Astrocytes
Tohoku J. Exp. Med., 2011,Differential 223, 161-176 Gene Expression in OPCs, Oligodendrocytes and Type II Astrocytes 161 Differential Gene Expression in Oligodendrocyte Progenitor Cells, Oligodendrocytes and Type II Astrocytes Jian-Guo Hu,1,2,* Yan-Xia Wang,3,* Jian-Sheng Zhou,2 Chang-Jie Chen,4 Feng-Chao Wang,1 Xing-Wu Li1 and He-Zuo Lü1,2 1Department of Clinical Laboratory Science, The First Affiliated Hospital of Bengbu Medical College, Bengbu, P.R. China 2Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu, P.R. China 3Department of Neurobiology, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China 4Department of Laboratory Medicine, Bengbu Medical College, Bengbu, P.R. China Oligodendrocyte precursor cells (OPCs) are bipotential progenitor cells that can differentiate into myelin-forming oligodendrocytes or functionally undetermined type II astrocytes. Transplantation of OPCs is an attractive therapy for demyelinating diseases. However, due to their bipotential differentiation potential, the majority of OPCs differentiate into astrocytes at transplanted sites. It is therefore important to understand the molecular mechanisms that regulate the transition from OPCs to oligodendrocytes or astrocytes. In this study, we isolated OPCs from the spinal cords of rat embryos (16 days old) and induced them to differentiate into oligodendrocytes or type II astrocytes in the absence or presence of 10% fetal bovine serum, respectively. RNAs were extracted from each cell population and hybridized to GeneChip with 28,700 rat genes. Using the criterion of fold change > 4 in the expression level, we identified 83 genes that were up-regulated and 89 genes that were down-regulated in oligodendrocytes, and 92 genes that were up-regulated and 86 that were down-regulated in type II astrocytes compared with OPCs. -
RUNNING HEAD: Low Homozygosity in Spanish Sheep
1 RUNNING HEAD: Low homozygosity in Spanish sheep 2 3 Low genome-wide homozygosity in eleven Spanish ovine breeds 4 5 M.G. Luigi 1, T.F. Cardoso 1, 2 , A. Martínez 3, A. Pons 4, L.A. Bermejo 5, J. Jordana 6, J.V. 6 Delgado 3, S. Adán 7, E. Ugarte 8, J. J. Arranz 9, J. Casellas 6 and M. Amills 1, 6 * 7 8 1Department of Animal Genetics, Centre for Research in Agricultural Genomics 9 (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, 10 Bellaterra 08193, Spain; 2CAPES Foundation, Ministry of Education of Brazil, Brasilia 11 D. F., 70.040-020, Brazil; 3Departamento de Genética, Universidad de Córdoba, 12 Córdoba 14071, Spain; 4Unitat de Races Autòctones, Servei de Millora Agrària i 13 Pesquera (SEMILLA), Son Ferriol 07198, Spain; 5Departamento de Ingeniería, 14 Producción y Economía Agrarias, Universidad de La Laguna, 38071 La Laguna, 15 Tenerife, Spain; 6Departament de Ciència Animal i dels Aliments, Facultat de 16 Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; 7Federación 17 de Razas Autóctonas de Galicia (BOAGA), Pazo de Fontefiz, 32152 Coles. Ourense, 18 Spain; 8Neiker-Tecnalia, Campus Agroalimentario de Arkaute, apdo 46 E-01080 19 Vitoria-Gazteiz (Araba), Spain; 9Departamento de Producción Animal, Universidad de 20 León, León 24071, Spain. 21 22 Corresponding author: Marcel Amills. Department of Animal Genetics, Centre for 23 Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus 24 Universitat Autònoma de Barcelona, Bellaterra 08193, Spain. Tel. 34 93 5636600. E- 25 mail: [email protected]. 26 Abstract 27 28 The population of Spanish sheep has decreased from 24 to 15 million heads in 29 the last 75 years due to multiple social and economic factors. -
Ips-Derived Early Oligodendrocyte Progenitor Cells from SPMS Patients Reveal Deficient in Vitro Cell Migration Stimulation
cells Article iPS-Derived Early Oligodendrocyte Progenitor Cells from SPMS Patients Reveal Deficient In Vitro Cell Migration Stimulation Lidia Lopez-Caraballo 1, Jordi Martorell-Marugan 2,3 , Pedro Carmona-Sáez 2,4 and Elena Gonzalez-Munoz 1,5,6,* 1 Laboratory of Cell Reprogramming (LARCEL), Andalusian Centre for Nanomedicine and Biotechnology-BIONAND, 29590 Málaga, Spain; [email protected] 2 Bioinformatics Unit. GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, E-18016 Granada, Spain; [email protected] (J.M.-M.); [email protected] (P.C.-S.) 3 Atrys Health, 08025 Barcelona, Spain 4 Department of Statistics. University of Granada, 18071 Granada, Spain 5 Department of Cell Biology, Genetics and Physiology, University of Málaga, 29071 Málaga, Spain 6 Networking Research Center on Bioengineering, Biomaterials and Nanomedicine, (CIBER-BBN), 29071 Málaga, Spain * Correspondence: [email protected]; Tel.: +34-952367616 Received: 18 June 2020; Accepted: 28 July 2020; Published: 29 July 2020 Abstract: The most challenging aspect of secondary progressive multiple sclerosis (SPMS) is the lack of efficient regenerative response for remyelination, which is carried out by the endogenous population of adult oligoprogenitor cells (OPCs) after proper activation. OPCs must proliferate and migrate to the lesion and then differentiate into mature oligodendrocytes. To investigate the OPC cellular component in SPMS, we developed induced pluripotent stem cells (iPSCs) from SPMS-affected donors and age-matched controls (CT). We confirmed their efficient and similar OPC differentiation capacity, although we reported SPMS-OPCs were transcriptionally distinguishable from their CT counterparts. Analysis of OPC-generated conditioned media (CM) also evinced differences in protein secretion. -
GRIPAP1 / GRASP1 Antibody (N-Terminus) Goat Polyclonal Antibody Catalog # ALS14943
10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 GRIPAP1 / GRASP1 Antibody (N-Terminus) Goat Polyclonal Antibody Catalog # ALS14943 Specification GRIPAP1 / GRASP1 Antibody (N-Terminus) - Product Information Application IHC Primary Accession Q4V328 Reactivity Human Host Goat Clonality Polyclonal Calculated MW 96kDa KDa GRIPAP1 / GRASP1 Antibody (N-Terminus) - Additional Information Gene ID 56850 Anti-GRIPAP1 / GRASP1 antibody IHC of Other Names human brain, cortex. GRIP1-associated protein 1, GRASP-1, GRIPAP1, KIAA1167 Target/Specificity Human GRIPAP1 / GRASP1. This antibody is expected to recognize both reported isoforms (as represented by NP_064522.3; NP_997555.1) Reconstitution & Storage Store at -20°C. Minimize freezing and thawing. Precautions GRIPAP1 / GRASP1 Antibody (N-Terminus) is for research use only and not for use in Anti-GRIPAP1 / GRASP1 antibody IHC of diagnostic or therapeutic procedures. human tonsil. GRIPAP1 / GRASP1 Antibody (N-Terminus) GRIPAP1 / GRASP1 Antibody (N-Terminus) - Protein Information - References Bechtel S.,et al.BMC Genomics Name GRIPAP1 (HGNC:18706) 8:399-399(2007). Ross M.T.,et al.Nature 434:325-337(2005). Synonyms KIAA1167 Hirosawa M.,et al.DNA Res. 6:329-336(1999). Function Lubec G.,et al.Submitted (DEC-2008) to Regulates the endosomal recycling back to UniProtKB. the neuronal plasma membrane, possibly Holt L.J.,et al.Nucleic Acids Res. by connecting early and late recycling 28:72-72(2000). endosomal domains and promoting Page 1/2 10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 segregation of recycling endosomes from early endosomal membranes. -
Anti- Decorin (889C7)
MONOCLONAL ANTIBODY For research use only. Not for clinical diagnosis Catalog No. PRPG-DC-M01 Anti- Decorin (889C7) BACKGROUND Decorin is a ubiquitous smaller ECM proteoglycan that is closely related in structure to another similar proteoglycan, biglycan, and which belongs to the small leucine-rich proteoglycan (SLRP) subfamily. Its core protein may be frequently found associated with the cell surface and normally carries one single chondroitin sulfate or dermatan sulfate chain. Decorin binds to and modulates the signaling of the epidermal growth factor receptor and other members of the ErbB family of receptor tyrosine kinases. It exerts its antitumor activity by a dual mechanism.* Product type Primary antibodies Immunogen Purified bovine decorin Rased in Mouse Myeloma - Clone number 889C7 Isotype IgM Host - Source Hybridoma cell culture Purification - Form Liquid Storage buffer Supernatant supplemented with 0.05% NaN3 Concentration ND Volume 2 mL Label Unlabeled Specificity Decorin Cross reactivity Human, Bovine Other species have not been tested. Storage Store at 4°C for short-term storage and -20°C for prolonged storage Aliquot to avoid cycles of freeze / thaw. Other Data Link : UniProtKB/Swiss-Prot P21793 Application notes IWB, IHC, ELISA Recommended dilutions ・ Western blotting : 1/10 - 1/50 Intact form, smeared band 50-140 kDa; chondrotinase-digested band at 60-70 kDa; reacts poorly with chondroitinase digested decorin ・ Immunohistochemistry : 1/25 - 1/75 (paraffin-embedded) MAb 889C7 stains connective ECMs of a wide range of organs and tissues. Chondroitinase ABC predigestion of the sections alters the staining pattern. ・ ELISA : 1/10 - 1/150 Other applications have not been tested. Optimal dilutions/concentrations should be determined by the end user.