Supplementary Table S5. List of All the Peptides That Were Included in the Peptide Biomarker Panels for Detecting Primary UBC
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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. -
Propranolol-Mediated Attenuation of MMP-9 Excretion in Infants with Hemangiomas
Supplementary Online Content Thaivalappil S, Bauman N, Saieg A, Movius E, Brown KJ, Preciado D. Propranolol-mediated attenuation of MMP-9 excretion in infants with hemangiomas. JAMA Otolaryngol Head Neck Surg. doi:10.1001/jamaoto.2013.4773 eTable. List of All of the Proteins Identified by Proteomics This supplementary material has been provided by the authors to give readers additional information about their work. © 2013 American Medical Association. All rights reserved. Downloaded From: https://jamanetwork.com/ on 10/01/2021 eTable. List of All of the Proteins Identified by Proteomics Protein Name Prop 12 mo/4 Pred 12 mo/4 Δ Prop to Pred mo mo Myeloperoxidase OS=Homo sapiens GN=MPO 26.00 143.00 ‐117.00 Lactotransferrin OS=Homo sapiens GN=LTF 114.00 205.50 ‐91.50 Matrix metalloproteinase‐9 OS=Homo sapiens GN=MMP9 5.00 36.00 ‐31.00 Neutrophil elastase OS=Homo sapiens GN=ELANE 24.00 48.00 ‐24.00 Bleomycin hydrolase OS=Homo sapiens GN=BLMH 3.00 25.00 ‐22.00 CAP7_HUMAN Azurocidin OS=Homo sapiens GN=AZU1 PE=1 SV=3 4.00 26.00 ‐22.00 S10A8_HUMAN Protein S100‐A8 OS=Homo sapiens GN=S100A8 PE=1 14.67 30.50 ‐15.83 SV=1 IL1F9_HUMAN Interleukin‐1 family member 9 OS=Homo sapiens 1.00 15.00 ‐14.00 GN=IL1F9 PE=1 SV=1 MUC5B_HUMAN Mucin‐5B OS=Homo sapiens GN=MUC5B PE=1 SV=3 2.00 14.00 ‐12.00 MUC4_HUMAN Mucin‐4 OS=Homo sapiens GN=MUC4 PE=1 SV=3 1.00 12.00 ‐11.00 HRG_HUMAN Histidine‐rich glycoprotein OS=Homo sapiens GN=HRG 1.00 12.00 ‐11.00 PE=1 SV=1 TKT_HUMAN Transketolase OS=Homo sapiens GN=TKT PE=1 SV=3 17.00 28.00 ‐11.00 CATG_HUMAN Cathepsin G OS=Homo -
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. -
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. -
Figure S1. Representative Report Generated by the Ion Torrent System Server for Each of the KCC71 Panel Analysis and Pcafusion Analysis
Figure S1. Representative report generated by the Ion Torrent system server for each of the KCC71 panel analysis and PCaFusion analysis. (A) Details of the run summary report followed by the alignment summary report for the KCC71 panel analysis sequencing. (B) Details of the run summary report for the PCaFusion panel analysis. A Figure S1. Continued. Representative report generated by the Ion Torrent system server for each of the KCC71 panel analysis and PCaFusion analysis. (A) Details of the run summary report followed by the alignment summary report for the KCC71 panel analysis sequencing. (B) Details of the run summary report for the PCaFusion panel analysis. B Figure S2. Comparative analysis of the variant frequency found by the KCC71 panel and calculated from publicly available cBioPortal datasets. For each of the 71 genes in the KCC71 panel, the frequency of variants was calculated as the variant number found in the examined cases. Datasets marked with different colors and sample numbers of prostate cancer are presented in the upper right. *Significantly high in the present study. Figure S3. Seven subnetworks extracted from each of seven public prostate cancer gene networks in TCNG (Table SVI). Blue dots represent genes that include initial seed genes (parent nodes), and parent‑child and child‑grandchild genes in the network. Graphical representation of node‑to‑node associations and subnetwork structures that differed among and were unique to each of the seven subnetworks. TCNG, The Cancer Network Galaxy. Figure S4. REVIGO tree map showing the predicted biological processes of prostate cancer in the Japanese. Each rectangle represents a biological function in terms of a Gene Ontology (GO) term, with the size adjusted to represent the P‑value of the GO term in the underlying GO term database. -
Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in -
Nephronectin As a Matrix Effector in Cancer
cancers Review Nephronectin as a Matrix Effector in Cancer Synnøve Norvoll Magnussen 1,* , Jimita Toraskar 2,3 , Elin Hadler-Olsen 1,4, Tonje S. Steigedal 2,3 and Gunbjørg Svineng 1 1 Department of Medical Biology, Faculty of Health Sciences, UiT—The Arctic University of Norway, 9037 Tromsø, Norway; [email protected] (E.H.-O.); [email protected] (G.S.) 2 Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway; [email protected] (J.T.); [email protected] (T.S.S.) 3 Cancer Clinic, St. Olavs Hospital HF, 7006 Trondheim, Norway 4 The Public Dental Health Service Competence Center of Northern Norway, 9271 Tromsø, Norway * Correspondence: [email protected] Simple Summary: The extracellular matrix provides an important scaffold for cells and tissues of multicellular organisms. The scaffold not only provides a secure anchorage point, but also functions as a reservoir for signalling molecules, sequestered and released when necessary. A dysregulated extracellular matrix may therefore modulate cellular behaviour, as seen during cancer progression. The extracellular matrix protein nephronectin was discovered two decades ago and found to regulate important embryonic developmental processes. Loss of either nephronectin or its receptor, integrin α8β1, leads to underdeveloped kidneys. Recent findings show that nephronectin is also dysregulated in breast cancer and plays a role in promoting metastasis. To enable therapeutic intervention, it is important to fully understand the role of nephronectin and its receptors in cancer progression. In Citation: Magnussen, S.N.; this review, we summarise the literature on nephronectin, analyse the structure and domain-related Toraskar, J.; Hadler-Olsen, E.; functions of nephronectin and link these functions to potential roles in cancer progression. -
LOXL2-Mediated H3K4 Oxidation Reduces Chromatin Accessibility in Triple-Negative Breast Cancer Cells
Oncogene (2020) 39:79–121 https://doi.org/10.1038/s41388-019-0969-1 ARTICLE LOXL2-mediated H3K4 oxidation reduces chromatin accessibility in triple-negative breast cancer cells 1 1 2 1 1 1 J. P. Cebrià-Costa ● L. Pascual-Reguant ● A. Gonzalez-Perez ● G. Serra-Bardenys ● J. Querol ● M. Cosín ● 1,3 4 4 2 5 6 G. Verde ● R. A. Cigliano ● W. Sanseverino ● S. Segura-Bayona ● A. Iturbide ● D. Andreu ● 1 1,7 1 1,7,8,9 10 6,10 P. Nuciforo ● C. Bernado-Morales ● V. Rodilla ● J. Arribas ● J. Yelamos ● A. Garcia de Herreros ● 2 1 T. H. Stracker ● S. Peiró Received: 28 January 2019 / Revised: 8 July 2019 / Accepted: 9 August 2019 / Published online: 28 August 2019 © The Author(s) 2019. This article is published with open access Abstract Oxidation of H3 at lysine 4 (H3K4ox) by lysyl oxidase-like 2 (LOXL2) generates an H3 modification with an unknown physiological function. We find that LOXL2 and H3K4ox are higher in triple-negative breast cancer (TNBC) cell lines and patient-derived xenografts (PDXs) than those from other breast cancer subtypes. ChIP-seq revealed that H3K4ox is located primarily in heterochromatin, where it is involved in chromatin compaction. Knocking down LOXL2 reduces H3K4ox levels 1234567890();,: 1234567890();,: and causes chromatin decompaction, resulting in a sustained activation of the DNA damage response (DDR) and increased susceptibility to anticancer agents. This critical role that LOXL2 and oxidized H3 play in chromatin compaction and DDR suggests that functionally targeting LOXL2 could be a way to sensitize TNBC cells to conventional therapy. -
Supplementary Table S2. List of Genes with Expression That Is Positively Correlated (Pearson Correlation Coefficient P>0.3)
Supplementary Table S2. List of genes with expression that is positively correlated (Pearson correlation coefficient p>0.3) with HOXA9 expression in the study by Sun et al (1). Most HOXA genes (indicated by bold face) show highly significant positive correlation with HOXA9 expression, except for HOXA6 and HOXA13, similar to our findings in the UCSF and MDA tumor sets. Note that HOXA11, which did not demonstrate a statistically significant positive correlation with HOXA9 expression in both the UCSF and MDA tumor sets, demonstrates a substantially lower correlation coefficient relative to the other HOXA genes that positively correlate with HOXA9 expression in the study by Sun et al. These data were obtained from the online ONCOMINE database (www.oncomine.org) (2) searching for transcripts positively correlated with HOXA9 expression. Gene Name Gene Symbol Reporter ID Correlation (p) homeobox A9 HOXA9 214651_s_at .7682 homeobox A9 HOXA9 209905_at .7682 homeobox A10 HOXA10 213150_at .6058 homeobox A7 HOXA7 235753_at .6058 homeobox A10 HOXA10 213147_at .6058 homeobox A7 HOXA7 206847_s_at .6058 homeobox A4 HOXA4 206289_at .5741 homeobox A2 HOXA2 1557051_s_at .5379 homeobox A1 HOXA1 214639_s_at .5379 homeobox A3 HOXA3 235521_at .5379 homeobox B2 HOXB2 205453_at .5379 homeobox B3 HOXB3 228904_at .5379 EST EST 1555907_at .5379 homeobox A4 HOXA4 230080_at .5379 homeobox A2 HOXA2 228642_at .5379 homeobox A2 HOXA2 1557050_at .5379 homeobox A5 HOXA5 213844_at .5379 homeobox A2 HOXA2 214457_at .5113 homeobox B7 HOXB7 204778_x_at .5042 homeobox C6 HOXC6 -
Us 2018 / 0305689 A1
US 20180305689A1 ( 19 ) United States (12 ) Patent Application Publication ( 10) Pub . No. : US 2018 /0305689 A1 Sætrom et al. ( 43 ) Pub . Date: Oct. 25 , 2018 ( 54 ) SARNA COMPOSITIONS AND METHODS OF plication No . 62 /150 , 895 , filed on Apr. 22 , 2015 , USE provisional application No . 62/ 150 ,904 , filed on Apr. 22 , 2015 , provisional application No. 62 / 150 , 908 , (71 ) Applicant: MINA THERAPEUTICS LIMITED , filed on Apr. 22 , 2015 , provisional application No. LONDON (GB ) 62 / 150 , 900 , filed on Apr. 22 , 2015 . (72 ) Inventors : Pål Sætrom , Trondheim (NO ) ; Endre Publication Classification Bakken Stovner , Trondheim (NO ) (51 ) Int . CI. C12N 15 / 113 (2006 .01 ) (21 ) Appl. No. : 15 /568 , 046 (52 ) U . S . CI. (22 ) PCT Filed : Apr. 21 , 2016 CPC .. .. .. C12N 15 / 113 ( 2013 .01 ) ; C12N 2310 / 34 ( 2013. 01 ) ; C12N 2310 /14 (2013 . 01 ) ; C12N ( 86 ) PCT No .: PCT/ GB2016 /051116 2310 / 11 (2013 .01 ) $ 371 ( c ) ( 1 ) , ( 2 ) Date : Oct . 20 , 2017 (57 ) ABSTRACT The invention relates to oligonucleotides , e . g . , saRNAS Related U . S . Application Data useful in upregulating the expression of a target gene and (60 ) Provisional application No . 62 / 150 ,892 , filed on Apr. therapeutic compositions comprising such oligonucleotides . 22 , 2015 , provisional application No . 62 / 150 ,893 , Methods of using the oligonucleotides and the therapeutic filed on Apr. 22 , 2015 , provisional application No . compositions are also provided . 62 / 150 ,897 , filed on Apr. 22 , 2015 , provisional ap Specification includes a Sequence Listing . SARNA sense strand (Fessenger 3 ' SARNA antisense strand (Guide ) Mathew, Si Target antisense RNA transcript, e . g . NAT Target Coding strand Gene Transcription start site ( T55 ) TY{ { ? ? Targeted Target transcript , e . -
Distinct Transcriptomes Define Rostral and Caudal 5Ht Neurons
DISTINCT TRANSCRIPTOMES DEFINE ROSTRAL AND CAUDAL 5HT NEURONS by CHRISTI JANE WYLIE Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy Dissertation Advisor: Dr. Evan S. Deneris Department of Neurosciences CASE WESTERN RESERVE UNIVERSITY May, 2010 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the thesis/dissertation of ______________________________________________________ candidate for the ________________________________degree *. (signed)_______________________________________________ (chair of the committee) ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ (date) _______________________ *We also certify that written approval has been obtained for any proprietary material contained therein. TABLE OF CONTENTS TABLE OF CONTENTS ....................................................................................... iii LIST OF TABLES AND FIGURES ........................................................................ v ABSTRACT ..........................................................................................................vii CHAPTER 1 INTRODUCTION ............................................................................................... 1 I. Serotonin (5-hydroxytryptamine, 5HT) ....................................................... 1 A. Discovery.............................................................................................. -
Gene Expression Profiles of Multiple Independent Cadmium- And
Gene Expression Profiles of Multiple Independent Cadmium‐ and Arsenite‐ Transformed Human Urothelial Cells: Specific Gene Signatures in a Sea of Heterogeneity. Scott Garrett Department of Pathology School of Medicine and Health Sciences University of North Dakota Grand Forks ND Problems in Cancer Research • Environmental causation of cancer – President’s Cancer Panel 2008‐09, Reducing Environmental Cancer Risk, “Environmentally caused cancer are ggyrossly underestimated..” • Desperate need for diagnostic and prognostic markers of cancer. – Screening for common cancers – Prognostic markers for predicting cancer that need aggressive treatments from those that don’t • Also, need to understand carcinogenesis for prevention and treatment. Bladder Cancer Has a High Environmental Etiology • Aromatic amine dyes in bladder cancer was the first environmental etiology in cancer. • Nearly 50% of BC thought to be caused by cigarette smoking • Suscept ibility due to concentration of carcinogens in urine. Arsenite (As+3) & Cadmium (Cd+2) • Arsenite in drinking water linked to BC in South Asia • Confirmed in animal models • Arsenite, 1St in priority as a toxic substance (ATSDR). • Cadmium has also been linked to BC, albeit much weaker, but: – Cigarette smoking is a major source of cadmium Overall Experimental Approach Long‐Term Cultured Cells Transformed Cells Metal Exposure Tranf & assess Discover Induced or tumor behavior Transfect or Repressed Gene knockdown & assess cell behavior Gene X Human Tissues Assess correlation to tumor grade Mechanism of