The GUDMAP Database – an Online Resource for Genitourinary Research Simon D
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Targeted Exome Sequencing Provided Comprehensive Genetic Diagnosis of Congenital Anomalies of the Kidney and Urinary Tract
Journal of Clinical Medicine Article Targeted Exome Sequencing Provided Comprehensive Genetic Diagnosis of Congenital Anomalies of the Kidney and Urinary Tract 1,2, 3,4, 3 1,5 Yo Han Ahn y, Chung Lee y, Nayoung K. D. Kim , Eujin Park , Hee Gyung Kang 1,2,6,* , Il-Soo Ha 1,2,6, Woong-Yang Park 3,4,7 and Hae Il Cheong 1,2,6 1 Department of Pediatrics, Seoul National University College of Medicine, Seoul 03080, Korea; [email protected] (Y.H.A.); [email protected] (E.P.); [email protected] (I.-S.H.); [email protected] (H.I.C.) 2 Department of Pediatrics, Seoul National University Children’s Hospital, Seoul 03080, Korea 3 Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea; [email protected] (C.L.); [email protected] (N.K.D.K.); [email protected] (W.-Y.P.) 4 Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Korea 5 Department of Pediatrics, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07441, Korea 6 Kidney Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul 03080, Korea 7 Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea * Correspondence: [email protected] These authors equally contributed to this article. y Received: 31 January 2020; Accepted: 8 March 2020; Published: 10 March 2020 Abstract: Congenital anomalies of the kidney and urinary tract (CAKUT) are the most common cause of chronic kidney disease in children. -
UPK1B Antibody / Uroplakin 1B [Clone UPK1B/3081] (V8152)
UPK1B Antibody / Uroplakin 1B [clone UPK1B/3081] (V8152) Catalog No. Formulation Size V8152-100UG 0.2 mg/ml in 1X PBS with 0.1 mg/ml BSA (US sourced) and 0.05% sodium azide 100 ug V8152-20UG 0.2 mg/ml in 1X PBS with 0.1 mg/ml BSA (US sourced) and 0.05% sodium azide 20 ug V8152SAF-100UG 1 mg/ml in 1X PBS; BSA free, sodium azide free 100 ug Bulk quote request Availability 1-3 business days Species Reactivity Human Format Purified Clonality Monoclonal (mouse origin) Isotype Mouse IgG2b, kappa Clone Name UPK1B/3081 Purity Protein G affinity chromatography UniProt O75841 Localization Cell surface Applications Immunohistochemistry (FFPE) : 1-2ug/ml Limitations This UPK1B antibody is available for research use only. IHC staining of FFPE human urothelial carcinoma with UPK1B antibody. HIER: boil tissue sections in pH 9 10mM Tris with 1mM EDTA for 20 min and allow to cool before testing. IHC staining of FFPE human urothelial carcinoma with UPK1B antibody. HIER: boil tissue sections in pH 9 10mM Tris with 1mM EDTA for 20 min and allow to cool before testing. IHC staining of FFPE human urothelial carcinoma with UPK1B antibody. HIER: boil tissue sections in pH 9 10mM Tris with 1mM EDTA for 20 min and allow to cool before testing. Analysis of HuProt(TM) microarray containing more than 19,000 full-length human proteins using UPK1B antibody (clone UPK1B/3081). These results demonstrate the foremost specificity of the UPK1B/3081 mAb. Z- and S- score: The Z-score represents the strength of a signal that an antibody (in combination with a fluorescently-tagged anti-IgG secondary Ab) produces when binding to a particular protein on the HuProt(TM) array. -
Supplementary Materials
Supplementary materials Supplementary Table S1: MGNC compound library Ingredien Molecule Caco- Mol ID MW AlogP OB (%) BBB DL FASA- HL t Name Name 2 shengdi MOL012254 campesterol 400.8 7.63 37.58 1.34 0.98 0.7 0.21 20.2 shengdi MOL000519 coniferin 314.4 3.16 31.11 0.42 -0.2 0.3 0.27 74.6 beta- shengdi MOL000359 414.8 8.08 36.91 1.32 0.99 0.8 0.23 20.2 sitosterol pachymic shengdi MOL000289 528.9 6.54 33.63 0.1 -0.6 0.8 0 9.27 acid Poricoic acid shengdi MOL000291 484.7 5.64 30.52 -0.08 -0.9 0.8 0 8.67 B Chrysanthem shengdi MOL004492 585 8.24 38.72 0.51 -1 0.6 0.3 17.5 axanthin 20- shengdi MOL011455 Hexadecano 418.6 1.91 32.7 -0.24 -0.4 0.7 0.29 104 ylingenol huanglian MOL001454 berberine 336.4 3.45 36.86 1.24 0.57 0.8 0.19 6.57 huanglian MOL013352 Obacunone 454.6 2.68 43.29 0.01 -0.4 0.8 0.31 -13 huanglian MOL002894 berberrubine 322.4 3.2 35.74 1.07 0.17 0.7 0.24 6.46 huanglian MOL002897 epiberberine 336.4 3.45 43.09 1.17 0.4 0.8 0.19 6.1 huanglian MOL002903 (R)-Canadine 339.4 3.4 55.37 1.04 0.57 0.8 0.2 6.41 huanglian MOL002904 Berlambine 351.4 2.49 36.68 0.97 0.17 0.8 0.28 7.33 Corchorosid huanglian MOL002907 404.6 1.34 105 -0.91 -1.3 0.8 0.29 6.68 e A_qt Magnogrand huanglian MOL000622 266.4 1.18 63.71 0.02 -0.2 0.2 0.3 3.17 iolide huanglian MOL000762 Palmidin A 510.5 4.52 35.36 -0.38 -1.5 0.7 0.39 33.2 huanglian MOL000785 palmatine 352.4 3.65 64.6 1.33 0.37 0.7 0.13 2.25 huanglian MOL000098 quercetin 302.3 1.5 46.43 0.05 -0.8 0.3 0.38 14.4 huanglian MOL001458 coptisine 320.3 3.25 30.67 1.21 0.32 0.9 0.26 9.33 huanglian MOL002668 Worenine -
Local Immune Response in Bladder Pain Syndrome/Interstitial Cystitis ESSIC Type 3C
Int Urogynecol J DOI 10.1007/s00192-013-2112-0 ORIGINAL ARTICLE Local immune response in bladder pain syndrome/interstitial cystitis ESSIC type 3C Marianne Gamper & Volker Viereck & Jakob Eberhard & Jochen Binder & Carlo Moll & JoEllen Welter & René Moser Received: 4 January 2013 /Accepted: 6 April 2013 # The Author(s) 2013. This article is published with open access at Springerlink.com Abstract polymerase chain reaction (RT-qPCR), immunohistochem- Introduction and hypothesis Bladder pain syndrome/interstitial istry was performed on bladder tissue and urinary immuno- cystitis (BPS/IC) is identified based on subjective symptoms globulins G and A were quantified by enzyme-linked which lead to heterogeneous patient populations. Previous immunosorbent assay. Statistical analyses included the studies using gene expression arrays for BPS/IC with Kruskal-Wallis test for non-parametric data and post hoc Hunner’s lesions [European Society for the Study of tests identified differences between groups. Interstitial Cystitis (ESSIC) type 3C], a subtype of the condition Results High expression of T- and B-cell markers (CTLA4, discernible by cystoscopy, have revealed characteristic immune CD20, CD79A, IGH@), low expression of urothelial responses and urothelial abnormalities. This current study markers (KRT20, UPK1B, UPK3A), focal lymphoid aggre- aimed to further characterize this subtype using a gene expres- gates in the submucosa and high immunoglobulin concen- sion panel. We hypothesized that B-cell activation with high tration in urine were found exclusively in BPS/IC ESSIC levels of urinary antibody concentration would be found. type 3C patients. Results for OAB were in intermediate Methods Cold-cup bladder biopsies, catheterized urine and ranges between the other two groups and UPK1B even blood were collected from 15 BPS/IC ESSIC type 3C pa- reached significantly lower expression when compared to tients, 11 non-inflammatory overactive bladder (OAB) pa- healthy controls. -
Liquid Biopsy Biomarkers in Urine: a Route Towards Molecular Diagnosis and Personalized Medicine of Bladder Cancer
Journal of Personalized Medicine Review Liquid Biopsy Biomarkers in Urine: A Route towards Molecular Diagnosis and Personalized Medicine of Bladder Cancer Matteo Ferro 1,† , Evelina La Civita 2,†, Antonietta Liotti 2, Michele Cennamo 2, Fabiana Tortora 3 , Carlo Buonerba 4,5, Felice Crocetto 6 , Giuseppe Lucarelli 7 , Gian Maria Busetto 8 , Francesco Del Giudice 9 , Ottavio de Cobelli 1,10, Giuseppe Carrieri 9, Angelo Porreca 11, Amelia Cimmino 12,* and Daniela Terracciano 2,* 1 Department of Urology of European Institute of Oncology (IEO), IRCCS, Via Ripamonti 435, 20141 Milan, Italy; [email protected] (M.F.); [email protected] (O.d.C.) 2 Department of Translational Medical Sciences, University of Naples “Federico II”, 80131 Naples, Italy; [email protected] (E.L.C.); [email protected] (A.L.); [email protected] (M.C.) 3 Institute of Protein Biochemistry, National Research Council, 80131 Naples, Italy; [email protected] 4 CRTR Rare Tumors Reference Center, AOU Federico II, 80131 Naples, Italy; [email protected] 5 Environment & Health Operational Unit, Zoo-Prophylactic Institute of Southern Italy, 80055 Portici, Italy 6 Department of Neurosciences, Sciences of Reproduction and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy; [email protected] 7 Department of Emergency and Organ Transplantation, Urology, Andrology and Kidney Transplantation Unit, University of Bari, 70124 Bari, Italy; [email protected] 8 Department of Urology and Organ Transplantation, -
A Transcriptomic Atlas of Aged Human Microglia
ARTICLE DOI: 10.1038/s41467-018-02926-5 OPEN A transcriptomic atlas of aged human microglia Marta Olah1,2, Ellis Patrick 3, Alexandra-Chloe Villani2,4, Jishu Xu 2, Charles C. White2, Katie J. Ryan5, Paul Piehowski 6, Alifiya Kapasi6, Parham Nejad2, Maria Cimpean 5, Sarah Connor1,2, Christina J. Yung1, Michael Frangieh5, Allison McHenry5, Wassim Elyaman1,2, Vlad Petyuk 6, Julie A. Schneider7, David A. Bennett7, Philip L. De Jager 1,2 & Elizabeth M. Bradshaw1,2 With a rapidly aging global human population, finding a cure for late onset neurodegenerative diseases has become an urgent enterprise. However, these efforts are hindered by the lack of 1234567890():,; understanding of what constitutes the phenotype of aged human microglia—the cell type that has been strongly implicated by genetic studies in the pathogenesis of age-related neuro- degenerative disease. Here, we establish the set of genes that is preferentially expressed by microglia in the aged human brain. This HuMi_Aged gene set captures a unique phenotype, which we confirm at the protein level. Furthermore, we find this gene set to be enriched in susceptibility genes for Alzheimer’s disease and multiple sclerosis, to be increased with advancing age, and to be reduced by the protective APOEε2 haplotype. APOEε4 has no effect. These findings confirm the existence of an aging-related microglial phenotype in the aged human brain and its involvement in the pathological processes associated with brain aging. 1 Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York City, NY 10032, USA. 2 Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA. -
Single-Cell Transcriptomes Reveal a Complex Cellular Landscape in the Middle Ear and Differential Capacities for Acute Response to Infection
fgene-11-00358 April 9, 2020 Time: 15:55 # 1 ORIGINAL RESEARCH published: 15 April 2020 doi: 10.3389/fgene.2020.00358 Single-Cell Transcriptomes Reveal a Complex Cellular Landscape in the Middle Ear and Differential Capacities for Acute Response to Infection Allen F. Ryan1*, Chanond A. Nasamran2, Kwang Pak1, Clara Draf1, Kathleen M. Fisch2, Nicholas Webster3 and Arwa Kurabi1 1 Departments of Surgery/Otolaryngology, UC San Diego School of Medicine, VA Medical Center, La Jolla, CA, United States, 2 Medicine/Center for Computational Biology & Bioinformatics, UC San Diego School of Medicine, VA Medical Center, La Jolla, CA, United States, 3 Medicine/Endocrinology, UC San Diego School of Medicine, VA Medical Center, La Jolla, CA, United States Single-cell transcriptomics was used to profile cells of the normal murine middle ear. Clustering analysis of 6770 transcriptomes identified 17 cell clusters corresponding to distinct cell types: five epithelial, three stromal, three lymphocyte, two monocyte, Edited by: two endothelial, one pericyte and one melanocyte cluster. Within some clusters, Amélie Bonnefond, Institut National de la Santé et de la cell subtypes were identified. While many corresponded to those cell types known Recherche Médicale (INSERM), from prior studies, several novel types or subtypes were noted. The results indicate France unexpected cellular diversity within the resting middle ear mucosa. The resolution of Reviewed by: Fabien Delahaye, uncomplicated, acute, otitis media is too rapid for cognate immunity to play a major Institut Pasteur de Lille, France role. Thus innate immunity is likely responsible for normal recovery from middle ear Nelson L. S. Tang, infection. The need for rapid response to pathogens suggests that innate immune The Chinese University of Hong Kong, China genes may be constitutively expressed by middle ear cells. -
The Regulation of Self-Renewal in Normal Human Urothelial Cells
The Regulation of Self-Renewal in Normal Human Urothelial Cells Lisa A. Kirkwood PhD University of York Department of Biology April 2012 Abstract The urinary tract is lined by a mitotically-quiescent, but highly regenerative epithelium, the urothelium. The mechanisms regulating urothelial regeneration are incompletely understood although autocrine stimulation of the Epidermal Growth Factor Receptor (EGFR) signalling pathway has been implicated. The hypothesis developed in this thesis is that urothelial homeostasis is regulated through resolution of interactive signal transduction networks downstream of local environmental cues, such as cell:cell contact. Here, canonical Wnt signalling was examined as a candidate key pathway due to the pivotal role of β-catenin in both nuclear transcription and intercellular adherens junctions. Normal human urothelial (NHU) cells isolated from surgical biopsies were grown as finite cell lines in monolayer culture. mRNA analysis from proliferating cultures inferred all components for a functional autocrine-activated canonical Wnt cascade were present. In proliferating cells, β-catenin was nuclear and Axin2 expression provided an objective hallmark of β-catenin/TCF transcription factor activity. This endogenous activity was not mediated by Wnt receptor activation, as Wnt ligand was produced in inactive (non-palmitylated) form in serum-free culture, but instead -catenin activation was driven via EGFR- mediated phosphorylation of GSK3 and inhibition of the β-catenin destruction complex. In quiescent, contact–inhibited cultures, β-catenin was seen to re- localise to the adherens junctions and GSK3β activity was re-established. Knock-down of β-catenin using RNA interference led to significant changes in p-ERK and p-AKT activity as well as an increase in E-cadherin protein expression. -
Comprehensive Analysis Reveals Novel Gene Signature in Head and Neck Squamous Cell Carcinoma: Predicting Is Associated with Poor Prognosis in Patients
5892 Original Article Comprehensive analysis reveals novel gene signature in head and neck squamous cell carcinoma: predicting is associated with poor prognosis in patients Yixin Sun1,2#, Quan Zhang1,2#, Lanlin Yao2#, Shuai Wang3, Zhiming Zhang1,2 1Department of Breast Surgery, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China; 2School of Medicine, Xiamen University, Xiamen, China; 3State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China Contributions: (I) Conception and design: Y Sun, Q Zhang; (II) Administrative support: Z Zhang; (III) Provision of study materials or patients: Y Sun, Q Zhang; (IV) Collection and assembly of data: Y Sun, L Yao; (V) Data analysis and interpretation: Y Sun, S Wang; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors. #These authors contributed equally to this work. Correspondence to: Zhiming Zhang. Department of Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, China. Email: [email protected]. Background: Head and neck squamous cell carcinoma (HNSC) remains an important public health problem, with classic risk factors being smoking and excessive alcohol consumption and usually has a poor prognosis. Therefore, it is important to explore the underlying mechanisms of tumorigenesis and screen the genes and pathways identified from such studies and their role in pathogenesis. The purpose of this study was to identify genes or signal pathways associated with the development of HNSC. Methods: In this study, we downloaded gene expression profiles of GSE53819 from the Gene Expression Omnibus (GEO) database, including 18 HNSC tissues and 18 normal tissues. -
Expanded Encyclopaedias of DNA Elements in the Human and Mouse Genomes
Article https://doi.org/10.1038/s41586-020-2493-4 Supplementary information Expanded encyclopaedias of DNA elements in the human and mouse genomes In the format provided by the The ENCODE Project Consortium, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Charles B. authors and unedited Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A. Davis, Alexander Dobin, Rajinder Kaul, Jessica Halow, Eric L. Van Nostrand, Peter Freese, David U. Gorkin, Yin Shen, Yupeng He, Mark Mackiewicz, Florencia Pauli-Behn, Brian A. Williams, Ali Mortazavi, Cheryl A. Keller, Xiao-Ou Zhang, Shaimae I. Elhajjajy, Jack Huey, Diane E. Dickel, Valentina Snetkova, Xintao Wei, Xiaofeng Wang, Juan Carlos Rivera-Mulia, Joel Rozowsky, Jing Zhang, Surya B. Chhetri, Jialing Zhang, Alec Victorsen, Kevin P. White, Axel Visel, Gene W. Yeo, Christopher B. Burge, Eric Lécuyer, David M. Gilbert, Job Dekker, John Rinn, Eric M. Mendenhall, Joseph R. Ecker, Manolis Kellis, Robert J. Klein, William S. Noble, Anshul Kundaje, Roderic Guigó, Peggy J. Farnham, J. Michael Cherry ✉, Richard M. Myers ✉, Bing Ren ✉, Brenton R. Graveley ✉, Mark B. Gerstein ✉, Len A. Pennacchio ✉, Michael P. Snyder ✉, Bradley E. Bernstein ✉, Barbara Wold ✉, Ross C. Hardison ✉, Thomas R. Gingeras ✉, John A. Stamatoyannopoulos ✉ & Zhiping Weng ✉ Nature | www.nature.com/nature Nature | www.nature.com | 1 Expanded Encyclopedias of DNA Elements in the Human and Mouse Genomes Supplementary Information Guide Supplementary Notes 6 Supplementary Note 1. Defining and classifying candidate cis-regulatory elements (cCREs) 6 Supplementary Note 2. Testing various epigenetic signals for predicting enhancers and promoters. 11 Supplementary Note 3. Contribution of ENCODE Phase III data to the Registry of cCREs. -
A Validation and Extended Description of the Lund Taxonomy for Urothelial
www.nature.com/scientificreports OPEN A validation and extended description of the Lund taxonomy for urothelial carcinoma using the Received: 11 July 2017 Accepted: 19 February 2018 TCGA cohort Published: xx xx xxxx Nour-al-dain Marzouka1, Pontus Eriksson1, Carlos Rovira1, Fredrik Liedberg2, Gottfrid Sjödahl2 & Mattias Höglund1 Global gene expression analysis has been a major tool for urothelial carcinoma subtype discovery. This approach has revealed extensive complexity both in intrinsic features of the tumor cells and in the microenvironment. However, global gene expression cannot distinguish between gene expression signals originating from the tumor cells proper and from normal cells in the biopsy. Here, we use a large cohort of advanced urothelial carcinomas for which both gene expression data and extensive immunohistochemistry are available to create a supervised mRNA expression centroid classifer. This classifer identifes the major Lund taxonomy tumor cell phenotypes as defned by IHC. We apply this classifer to the independent TCGA dataset and show excellent associations between identifed subtypes and genomic features. We validate a progressed version of Urothelial-like A (UroA-Prog) that shows FGFR3 mutations and CDKN2A deletions, and we show that the variant Urothelial-like C is almost devoid of FGFR3 mutations. We show that Genomically Unstable tumors are very distinct from Urothelial-like tumors at the genomic level, and that tumors classifed as Basal/SCC-like all complied with the established defnition for Basal/SCC-like tumors. We identify the Mesenchymal-like and Small- cell/Neuroendocrine-like subtypes, and demonstrate that patients with UroB and Sc/NE-like tumors show the worst overall survival. -
1 a Framework to Identify Modifier Genes in Patients With
bioRxiv preprint doi: https://doi.org/10.1101/117978; this version posted March 18, 2017. 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 4.0 International license. A framework to identify modifier genes in patients with Phelan-McDermid syndrome Short running title: Mapping modifier genes in Phelan-McDermid Syndrome Anne-Claude Tabet1,2,3,4¶, Thomas Rolland2,3,4¶, Marie Ducloy2,3,4, Jonathan Lévy1, Julien Buratti2,3,4, Alexandre Mathieu2,3,4, Damien Haye1, Laurence Perrin1, Céline Dupont1, Sandrine Passemard1, Yline Capri1, Alain Verloes1, Séverine Drunat1, Boris Keren5, Cyril Mignot6, Isabelle Marey7, Aurélia Jacquette7, Sandra Whalen7, Eva Pipiras8, Brigitte Benzacken8, Sandra Chantot-Bastaraud9, Alexandra Afenjar10, Delphine Héron10, Cédric Le Caignec11, Claire Beneteau11, Olivier Pichon11, Bertrand Isidor11, Albert David11, Jean-Michel Dupont12, Stephan Kemeny13, Laetitia Gouas13, Philippe Vago13, Anne-Laure Mosca-Boidron14, Laurence Faivre15, Chantal Missirian16, Nicole Philip16, Damien Sanlaville17, Patrick Edery18, Véronique Satre19, Charles Coutton19, Françoise Devillard19, Klaus Dieterich20, Marie-Laure Vuillaume21, Caroline Rooryck21, Didier Lacombe21, Lucile Pinson22, Vincent Gatinois22, Jacques Puechberty22, Jean Chiesa23, James Lespinasse24, Christèle Dubourg25, Chloé Quelin25, Mélanie Fradin25, Hubert Journel26, Annick Toutain27, Dominique Martin28, Abdelamdjid Benmansour1,