DOCSLIB.ORG

Urine Proteomic Profiling in Patients with Nephrolithiasis and Cystinuria

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Urine Proteomic Profiling in Patients with Nephrolithiasis and Cystinuria International Urology and Nephrology (2019) 51:593–599 https://doi.org/10.1007/s11255-018-2044-1 UROLOGY - ORIGINAL PAPER Urine proteomic profiling in patients with nephrolithiasis and cystinuria Larisa Kovacevic1 · Joseph A. Caruso2 · Hong Lu1 · Natalija Kovacevic1,3 · Yegappan Lakshmanan1 · Nicholas J. Carruthers2 · David S. Goldfarb4 Received: 11 September 2018 / Accepted: 23 November 2018 / Published online: 5 December 2018 © Springer Nature B.V. 2018 Abstract Purpose The purpose of the study was to assess the differences in the concentration and function of urinary proteins between patients with cystine stones (CYS) and healthy controls (HC). We postulated that CYS and HC groups would demonstrate different proteomic profiles. Methods A pilot study was performed comparing urinary proteomes of 10 patients with CYS and 10 age- and gender- matched HC, using liquid chromatography-mass spectrometry. Proteins which met the selection criteria (i) ≥ 2 unique pep- tide identifications; (ii) ≥ twofold difference in protein abundance; and (iii) ≤ 0.05 p value for the Fisher’s Exact Test were analyzed using Gene Ontology classifications. Results Of the 2097 proteins identified by proteomic analysis, 398 proteins were significantly different between CYS and HC. Of those, 191 were involved in transport processes and 61 in inflammatory responses. The majority were vesicle- mediated transport proteins (78.5%), and 1/3 of them were down-regulated; of those, 12 proteins were involved in endosomal transport (including 6 charged multivesicular body proteins (CHMP) and 3 vacuolar sorting-associated proteins) and 9 in transmembrane transport. Myosin-2 and two actin-related proteins were significantly up-regulated in the vesicle-mediated transport group. Conclusion We provide proteomic evidence of impaired endocytosis, dysregulation of actin and myosin cytoskeleton, and inflammation in CYS. Endosomal transport proteins were down-regulated mainly through defective CHMP. These findings may contribute to further understanding of the pathogenesis of CYS, potentially affecting its management. Keywords Nephrolithiasis · Cystinuria · Urine · Proteomics Introduction Cystinuria is a rare genetic disease that is characterized by impaired transport of cystine and dibasic amino acids in the Electronic supplementary material The online version of this proximal renal tubule [1]. About half of all cases are trans- article (https ://doi.org/10.1007/s1125 5-018-2044-1) contains mitted in an autosomal recessive fashion, caused by muta- supplementary material, which is available to authorized users. tions in the SLC3A1 gene. This gene encodes rBAT, one of * Larisa Kovacevic the two protein components of the neutral and basic amino [email protected] acid transporter [2]. The other half are autosomal dominant with incomplete penetrance, caused by mutations in SLC7A9 1 Department of Pediatric Urology, Children’s Hospital gene, which encodes the light component, the catalytic pro- of Michigan, 3901 Beaubien Blvd, Detroit, MI 48201, USA tein, of the transporter, b0,+ AT. 2 Institute of Environmental Health Sciences, Wayne State Patients with cystinuria often present with kidney stones University, Detroit, MI, USA owing to the low solubility of cystine in urine. Their likeli- 3 Vattikuti Urology Institute, Henri Ford Hospital, Detroit, MI, hood of forming stones is about 50% [3]. Cystine stones are USA large and bilateral in the majority of cases. Even though 4 Nephrology Division, New York University Langone cystine stones represent only 1–2% of all cases with stones, Medical Center, New York, NY, USA Vol.:(0123456789)1 3 594 International Urology and Nephrology (2019) 51:593–599 the morbidity is high due to increased recurrence rate, need HC group consisted of 10 age- and gender-matched vol- for multiple surgeries and the risk of developing chronic unteer individuals. Random mid-stream fresh urine samples kidney disease [4]. Renal function in patients with cystine were collected after a detailed history and physical examina- kidney stones is reduced compared to those with non-cystine tion was performed. The HC participants denied history of stones [5], but the cause of this decline is not entirely clear. kidney stones, had normal urinalysis by dipstick and were The gene mutations identified in cystinuria cannot fully not taking any medications. The urine was obtained for rou- explain kidney stone activity. It has been shown that not all tine urinalysis for clinical care, and would have then been patients with two mutated SLC3A1 genes will form a stone. discarded; it was sent to the proteomics laboratory without Additionally, patients with identical SLC3A1 or SLC7A9 any personal health identification information. Under these genotypes may have onset of stone disease at different ages circumstances, analysis of the urine is not considered human and with different severity. Therefore, other unidentified fac- subjects research. tors seem to contribute to kidney stone formation. These factors may include endogenous proteins that could serve Sample collection and preparation as promoters or inhibitors of cystine precipitation, aggrega- tion or epithelial adherence. Proteomics allows simultaneous Random mid-stream fresh urine samples were obtained in examination of the patterns of multiple urinary proteins and sterile cups, prepared within 3 h of collection (centrifuged has become one of the most promising tools in nephrology at 2500 rpm for 15 min) at both institutions and stored as and urology [6, 7]. Using a proteomic approach, we aimed recommended by standardized protocols (developed by the to assess the differences in the concentration and function of Human Urine and Kidney Proteome Project, HUKPP, and urinary proteins between cystinuria and renal stones (CYS) the European Urine and Kidney Proteomics, EuroKUP Initi- and healthy controls (HC). We postulated that CYS and HC atives) until use [8]. Following preparation at NYU, de-iden- groups would demonstrate different proteomic profiles. We tified urine specimens and data were sent to our institution. also presumed that CYS patients would have a significant Aliquots were stored at − 80 °C until all urine specimens number of proteins involved in abnormal cellular processes were received and processed for proteomic analysis. Each including stress, inflammation and immune response, as well aliquot was used just once. Proteins in each sample were as others yet to be identified. concentrated in a Centricon-type filter. Albumin and IgG were removed by anti-HAS/IgG resin (Sartorius). Protein concentration in each sample was measured by the BCA Methods protein assay (Pierce). Protein digestion and tandem mass tag (TMT) We compared urinary proteomes of 10 patients with CYS labeling and 10 age- and gender-matched HC, using liquid chroma- tography-mass spectrometry (LC–MS/MS). For HC and CYS groups, 10 µg of depleted urine protein from 10 individual samples were pooled together for 100 µg Patient selection total, and then dried. Samples were resuspended in 10 µl of 1% SDS, and denatured for 5 min at 95 °C. Samples were We prospectively enrolled 10 consecutive patients with CYS reduced with 2 mM DTT in 50 mM TEAB for 30 min at (35.4 ± 11.2 years, 5 males and 5 females) who presented 65 °C, followed by alkylation with 6 mM iodoacetamide for routine follow-up visit at New York University Langone for 30 min at RT. Proteins were digested with 2 µg trypsin Medical Center 9 patients), and at Children’s Hospital of overnight at 37 °C. Each sample was uniquely labeled using Michigan (1 patient). All were established patients with an isobaric TMT tag (Pierce, 1.2 mg) in 50% acetonitrile cystinuria who had a history of nephrolithiasis. The diagno- for 1 h at RT, followed by quenching with 0.5% hydroxy- sis of cystinuria was made when a stone composed of cystine lamine. Samples were purified over detergent-removal col- was obtained, and confirmed when urine cystine levels were umns (Pierce) and dried. found to be higher than 75 mg in a 24-h urine collection analyzed by Litholink Corporation (LabCorp, Chicago, IL). 2D LC–MS/MS Random mid-stream fresh urine samples were collected from all participants. At the time of urine collection, patients Peptides were resuspended in 5% acetonitrile/0.1% formic were asymptomatic (i.e., were not experiencing episodes of acid/0.005% trifluoroacetic acid and desalted/separated urinary tract obstruction and/or urinary tract infections), and over a 5-µm reverse phase PLRP-S column (Agilent) using were not taking antibiotics. The patients were taking citrate mobile phases A (2% acetonitrile) and B (98% acetonitrile), (9/10), tiopronin (5/10), or d-penicillamine (2/10). with both buffers adjusted to pH 10.0 using ammonium 1 3 International Urology and Nephrology (2019) 51:593–599 595 hydroxide. Thirty first dimension fractions were collected Results using a TriVersa NanoMate (Advion) system paired to a LTQ-XL mass spectrometer (Thermo). Second dimension Patient’s characteristics peptide separation was performed using reverse phase chro- matography (Acclaim PepMap RSLC column, Thermo) Serum creatinine values were available in 6 out of the 10 under acidic conditions (0.1% formic acid) with an EASY CYS patients, with a mean of 1.09 ± 0.31 mg/dl (range nLC-1000 uHPLC system (Thermo). Peptides were sepa- 0.71–1.59 mg/dl). Mean eGFR for these patients was rated over a 90-min gradient and analyzed with an OrbiTrap 92 ± 38.1 ml/min/1.73 m2 (range 46–146 ml/min/1.73 m2). Fusion mass spectrometer (Thermo). MS1 scans were per- The data regarding comorbidities were available only in formed in profile mode in the orbitrap at 120,000 resolution. 1 patient and included obesity. However, CYS was repre- Data-dependent MS2 acquisitions were triggered on the top sented by a relatively young group of people who, besides 10 most abundant ions (charge states 2–7) and fragmented having cystinuria, are relatively healthy. None of the HC using CID at 35% collision energy in the linear ion trap. had any comorbidities and their serum creatinine concen- Dynamic exclusion was turned on (40 s).
Load more

Recommended publications
  • Isyte: Integrated Systems Tool for Eye Gene Discovery
    Lens iSyTE: Integrated Systems Tool for Eye Gene Discovery Salil A. Lachke,1,2,3,4 Joshua W. K. Ho,1,4,5 Gregory V. Kryukov,1,4,6 Daniel J. O’Connell,1 Anton Aboukhalil,1,7 Martha L. Bulyk,1,8,9 Peter J. Park,1,5,10 and Richard L. Maas1 PURPOSE. To facilitate the identification of genes associated ther investigation. Extension of this approach to other ocular with cataract and other ocular defects, the authors developed tissue components will facilitate eye disease gene discovery. and validated a computational tool termed iSyTE (integrated (Invest Ophthalmol Vis Sci. 2012;53:1617–1627) DOI: Systems Tool for Eye gene discovery; http://bioinformatics. 10.1167/iovs.11-8839 udel.edu/Research/iSyTE). iSyTE uses a mouse embryonic lens gene expression data set as a bioinformatics filter to select candidate genes from human or mouse genomic regions impli- ven with the advent of high-throughput sequencing, the cated in disease and to prioritize them for further mutational Ediscovery of genes associated with congenital birth defects and functional analyses. such as eye defects remains a challenge. We sought to develop METHODS. Microarray gene expression profiles were obtained a straightforward experimental approach that could facilitate for microdissected embryonic mouse lens at three key devel- the identification of candidate genes for developmental disor- opmental time points in the transition from the embryonic day ders, and, as proof-of-principle, we chose defects involving the (E)10.5 stage of lens placode invagination to E12.5 lens primary ocular lens. Opacification of the lens results in cataract, a leading cause of blindness that affects 77 million persons and fiber cell differentiation.
    [Show full text]
  • Proteome Analysis of the HIV-1 Gag Interactome
    Virology 460-461 (2014) 194–206 Contents lists available at ScienceDirect Virology journal homepage: www.elsevier.com/locate/yviro Proteome analysis of the HIV-1 Gag interactome Christine E. Engeland a, Nigel P. Brown b, Kathleen Börner a,b, Michael Schümann c, Eberhard Krause c, Lars Kaderali d, Gerd A. Müller e, Hans-Georg Kräusslich a,n a Department of Infectious Diseases, Virology, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany b Bioquant, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany c Leibniz-Institut für Molekulare Pharmakologie, Robert-Rössle-Straße 10, D-13125 Berlin, Germany d Institute for Medical Informatics and Biometry (IMB), Medical Faculty Carl Gustav Carus, Dresden University of Technology, Fetscherstraße 74, D-01307 Dresden, Germany e Molecular Oncology, Medical School, University of Leipzig, Semmelweisstraße 14, D-04103 Leipzig, Germany article info abstract Article history: Human immunodeficiency virus Gag drives assembly of virions in infected cells and interacts with host Received 20 January 2014 factors which facilitate or restrict viral replication. Although several Gag-binding proteins have been Returned to author for revisions characterized, understanding of virus–host interactions remains incomplete. In a series of six affinity 6 February 2014 purification screens, we have identified protein candidates for interaction with HIV-1 Gag. Proteins Accepted 19 April 2014 previously found in virions or identified in siRNA screens for host factors influencing HIV-1 replication Available online 10 June 2014 were recovered. Helicases, translation factors, cytoskeletal and motor proteins, factors involved in RNA Keywords: degradation and RNA interference were enriched in the interaction data. Cellular networks of HIV Gag cytoskeleton, SR proteins and tRNA synthetases were identified.
    [Show full text]
  • Role of RUNX1 in Aberrant Retinal Angiogenesis Jonathan D
    Page 1 of 25 Diabetes Identification of RUNX1 as a mediator of aberrant retinal angiogenesis Short Title: Role of RUNX1 in aberrant retinal angiogenesis Jonathan D. Lam,†1 Daniel J. Oh,†1 Lindsay L. Wong,1 Dhanesh Amarnani,1 Cindy Park- Windhol,1 Angie V. Sanchez,1 Jonathan Cardona-Velez,1,2 Declan McGuone,3 Anat O. Stemmer- Rachamimov,3 Dean Eliott,4 Diane R. Bielenberg,5 Tave van Zyl,4 Lishuang Shen,1 Xiaowu Gai,6 Patricia A. D’Amore*,1,7 Leo A. Kim*,1,4 Joseph F. Arboleda-Velasquez*1 Author affiliations: 1Schepens Eye Research Institute/Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, 20 Staniford St., Boston, MA 02114 2Universidad Pontificia Bolivariana, Medellin, Colombia, #68- a, Cq. 1 #68305, Medellín, Antioquia, Colombia 3C.S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital, 55 Fruit St., Boston, MA 02114 4Retina Service, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles St., Boston, MA 02114 5Vascular Biology Program, Boston Children’s Hospital, Department of Surgery, Harvard Medical School, 300 Longwood Ave., Boston, MA 02115 6Center for Personalized Medicine, Children’s Hospital Los Angeles, Los Angeles, 4650 Sunset Blvd, Los Angeles, CA 90027, USA 7Department of Pathology, Harvard Medical School, 25 Shattuck St., Boston, MA 02115 Corresponding authors: Joseph F. Arboleda-Velasquez: [email protected] Ph: (617) 912-2517 Leo Kim: [email protected] Ph: (617) 912-2562 Patricia D’Amore: [email protected] Ph: (617) 912-2559 Fax: (617) 912-0128 20 Staniford St. Boston MA, 02114 † These authors contributed equally to this manuscript Word Count: 1905 Tables and Figures: 4 Diabetes Publish Ahead of Print, published online April 11, 2017 Diabetes Page 2 of 25 Abstract Proliferative diabetic retinopathy (PDR) is a common cause of blindness in the developed world’s working adult population, and affects those with type 1 and type 2 diabetes mellitus.
    [Show full text]
  • Analysis of the Indacaterol-Regulated Transcriptome in Human Airway
    Supplemental material to this article can be found at: http://jpet.aspetjournals.org/content/suppl/2018/04/13/jpet.118.249292.DC1 1521-0103/366/1/220–236$35.00 https://doi.org/10.1124/jpet.118.249292 THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS J Pharmacol Exp Ther 366:220–236, July 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Analysis of the Indacaterol-Regulated Transcriptome in Human Airway Epithelial Cells Implicates Gene Expression Changes in the s Adverse and Therapeutic Effects of b2-Adrenoceptor Agonists Dong Yan, Omar Hamed, Taruna Joshi,1 Mahmoud M. Mostafa, Kyla C. Jamieson, Radhika Joshi, Robert Newton, and Mark A. Giembycz Departments of Physiology and Pharmacology (D.Y., O.H., T.J., K.C.J., R.J., M.A.G.) and Cell Biology and Anatomy (M.M.M., R.N.), Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada Received March 22, 2018; accepted April 11, 2018 Downloaded from ABSTRACT The contribution of gene expression changes to the adverse and activity, and positive regulation of neutrophil chemotaxis. The therapeutic effects of b2-adrenoceptor agonists in asthma was general enriched GO term extracellular space was also associ- investigated using human airway epithelial cells as a therapeu- ated with indacaterol-induced genes, and many of those, in- tically relevant target. Operational model-fitting established that cluding CRISPLD2, DMBT1, GAS1, and SOCS3, have putative jpet.aspetjournals.org the long-acting b2-adrenoceptor agonists (LABA) indacaterol, anti-inflammatory, antibacterial, and/or antiviral activity. Numer- salmeterol, formoterol, and picumeterol were full agonists on ous indacaterol-regulated genes were also induced or repressed BEAS-2B cells transfected with a cAMP-response element in BEAS-2B cells and human primary bronchial epithelial cells by reporter but differed in efficacy (indacaterol $ formoterol .
    [Show full text]
  • Supplementary Figures and Tables
    SUPPLEMENTARY DATA Supplementary Figure 1. Isolation and culture of endothelial cells from surgical specimens of FVM. (A) Representative pre-surgical fundus photograph of a right eye exhibiting a FVM encroaching on the optic nerve (dashed line) causing tractional retinal detachment with blot hemorrhages throughout retina (arrow heads). (B) Magnetic beads (arrows) allow for separation and culturing of enriched cell populations from surgical specimens (scale bar = 100 μm). (C) Cultures of isolated cells stained positively for CD31 representing a successfully isolated enriched population (scale bar = 40 μm). ©2017 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db16-1035/-/DC1 SUPPLEMENTARY DATA Supplementary Figure 2. Efficient siRNA knockdown of RUNX1 expression and function demonstrated by qRT-PCR, Western Blot, and scratch assay. (A) RUNX1 siRNA induced a 60% reduction of RUNX1 expression measured by qRT-PCR 48 hrs post-transfection whereas expression of RUNX2 and RUNX3, the two other mammalian RUNX orthologues, showed no significant changes, indicating specificity of our siRNA. Functional inhibition of Runx1 signaling was demonstrated by a 330% increase in insulin-like growth factor binding protein-3 (IGFBP3) RNA expression level, a known target of RUNX1 inhibition. Western blot demonstrated similar reduction in protein levels. (B) siRNA- 2’s effect on RUNX1 was validated by qRT-PCR and western blot, demonstrating a similar reduction in both RNA and protein. Scratch assay demonstrates functional inhibition of RUNX1 by siRNA-2. ns: not significant, * p < 0.05, *** p < 0.001 ©2017 American Diabetes Association. Published online at http://diabetes.diabetesjournals.org/lookup/suppl/doi:10.2337/db16-1035/-/DC1 SUPPLEMENTARY DATA Supplementary Table 1.
    [Show full text]
  • Supporting Information
    Supporting Information Whittle et al. 10.1073/pnas.0812894106 SI Text range based on analysis on 1.5% agarose gels after reversal of In Vitro Genomic Selection. Recombinant NFI-1-GST fusion pro- cross-linking. DNA-protein complexes were precipitated with tein was immobilized on Glutathione Sepharose 4B (Amersham) anti-NFI immune serum (5 ␮l) or preimmune serum (5 ␮l) as a and C. elegans genomic DNA was used for in vitro genomic control and 5% of the input sample was set aside. Samples were selection. The fusion protein contained the NFI-1 DNA-binding processed using the ChIP assay kit (Upstate). Following reversal domain and a short downstream region. For NFI-1-GST Sepha- of the cross-links, RNase A and Proteinase K treatments, the rose preparation, 400 ml of induced DH5␣ cells expressing immunoprecipitated DNA was purified using phenol-chloro- NFI-1-GST (plasmid pGEXNFI-1) was extracted in buffer L (25 form, precipitated with ethanol, and dissolved in 50 ␮l of DNase, mM Hepes pH 7.5, 10% sucrose, 0.35 M NaCl, 5 mM DTT, 1 mM Rnase-free water. For ChIP-chip, samples were amplified by PMSF, 0.1% Nonidet P-40 and 2 mg/ml of lysozyme). The extract either ligation mediated PCR (5) or a modified Whole Genome (35 ml) was flash-frozen in 5-ml aliquots and stored at –70 °C. To Amplification protocol [Sigma; (6)] as previously described. immobilize NFI-1-GST protein on Glutathione Sepharose 4B, 5 ml of cell extract was incubated with 65 ␮l (bed volume) of Microarrays and Data Extraction.
    [Show full text]
  • A Peripheral Blood Gene Expression Signature to Diagnose Subclinical Acute Rejection
    CLINICAL RESEARCH www.jasn.org A Peripheral Blood Gene Expression Signature to Diagnose Subclinical Acute Rejection Weijia Zhang,1 Zhengzi Yi,1 Karen L. Keung,2 Huimin Shang,3 Chengguo Wei,1 Paolo Cravedi,1 Zeguo Sun,1 Caixia Xi,1 Christopher Woytovich,1 Samira Farouk,1 Weiqing Huang,1 Khadija Banu,1 Lorenzo Gallon,4 Ciara N. Magee,5 Nader Najafian,5 Milagros Samaniego,6 Arjang Djamali ,7 Stephen I. Alexander,2 Ivy A. Rosales,8 Rex Neal Smith,8 Jenny Xiang,3 Evelyne Lerut,9 Dirk Kuypers,10,11 Maarten Naesens ,10,11 Philip J. O’Connell,2 Robert Colvin,8 Madhav C. Menon,1 and Barbara Murphy1 Due to the number of contributing authors, the affiliations are listed at the end of this article. ABSTRACT Background In kidney transplant recipients, surveillance biopsies can reveal, despite stable graft function, histologic features of acute rejection and borderline changes that are associated with undesirable graft outcomes. Noninvasive biomarkers of subclinical acute rejection are needed to avoid the risks and costs associated with repeated biopsies. Methods We examined subclinical histologic and functional changes in kidney transplant recipients from the prospective Genomics of Chronic Allograft Rejection (GoCAR) study who underwent surveillance biopsies over 2 years, identifying those with subclinical or borderline acute cellular rejection (ACR) at 3 months (ACR-3) post-transplant. We performed RNA sequencing on whole blood collected from 88 indi- viduals at the time of 3-month surveillance biopsy to identify transcripts associated with ACR-3, developed a novel sequencing-based targeted expression assay, and validated this gene signature in an independent cohort.
    [Show full text]
  • In This Table Protein Name, Uniprot Code, Gene Name P-Value
    Supplementary Table S1: In this table protein name, uniprot code, gene name p-value and Fold change (FC) for each comparison are shown, for 299 of the 301 significantly regulated proteins found in both comparisons (p-value<0.01, fold change (FC) >+/-0.37) ALS versus control and FTLD-U versus control. Two uncharacterized proteins have been excluded from this list Protein name Uniprot Gene name p value FC FTLD-U p value FC ALS FTLD-U ALS Cytochrome b-c1 complex P14927 UQCRB 1.534E-03 -1.591E+00 6.005E-04 -1.639E+00 subunit 7 NADH dehydrogenase O95182 NDUFA7 4.127E-04 -9.471E-01 3.467E-05 -1.643E+00 [ubiquinone] 1 alpha subcomplex subunit 7 NADH dehydrogenase O43678 NDUFA2 3.230E-04 -9.145E-01 2.113E-04 -1.450E+00 [ubiquinone] 1 alpha subcomplex subunit 2 NADH dehydrogenase O43920 NDUFS5 1.769E-04 -8.829E-01 3.235E-05 -1.007E+00 [ubiquinone] iron-sulfur protein 5 ARF GTPase-activating A0A0C4DGN6 GIT1 1.306E-03 -8.810E-01 1.115E-03 -7.228E-01 protein GIT1 Methylglutaconyl-CoA Q13825 AUH 6.097E-04 -7.666E-01 5.619E-06 -1.178E+00 hydratase, mitochondrial ADP/ATP translocase 1 P12235 SLC25A4 6.068E-03 -6.095E-01 3.595E-04 -1.011E+00 MIC J3QTA6 CHCHD6 1.090E-04 -5.913E-01 2.124E-03 -5.948E-01 MIC J3QTA6 CHCHD6 1.090E-04 -5.913E-01 2.124E-03 -5.948E-01 Protein kinase C and casein Q9BY11 PACSIN1 3.837E-03 -5.863E-01 3.680E-06 -1.824E+00 kinase substrate in neurons protein 1 Tubulin polymerization- O94811 TPPP 6.466E-03 -5.755E-01 6.943E-06 -1.169E+00 promoting protein MIC C9JRZ6 CHCHD3 2.912E-02 -6.187E-01 2.195E-03 -9.781E-01 Mitochondrial 2-
    [Show full text]
  • Characterization of the Macrophage Transcriptome in Glomerulonephritis-Susceptible and -Resistant Rat Strains
    Genes and Immunity (2011) 12, 78–89 & 2011 Macmillan Publishers Limited All rights reserved 1466-4879/11 www.nature.com/gene ORIGINAL ARTICLE Characterization of the macrophage transcriptome in glomerulonephritis-susceptible and -resistant rat strains K Maratou1, J Behmoaras2, C Fewings1, P Srivastava1, Z D’Souza1, J Smith3, L Game4, T Cook2 and T Aitman1 1Physiological Genomics and Medicine Group, MRC Clinical Sciences Centre, Imperial College London, London, UK; 2Centre for Complement and Inflammation Research, Imperial College London, London, UK; 3Renal Section, Imperial College London, London, UK and 4Genomics Laboratory, MRC Clinical Sciences Centre, London, UK Crescentic glomerulonephritis (CRGN) is a major cause of rapidly progressive renal failure for which the underlying genetic basis is unknown. Wistar–Kyoto (WKY) rats show marked susceptibility to CRGN, whereas Lewis rats are resistant. Glomerular injury and crescent formation are macrophage dependent and mainly explained by seven quantitative trait loci (Crgn1–7). Here, we used microarray analysis in basal and lipopolysaccharide (LPS)-stimulated macrophages to identify genes that reside on pathways predisposing WKY rats to CRGN. We detected 97 novel positional candidates for the uncharacterized Crgn3–7. We identified 10 additional secondary effector genes with profound differences in expression between the two strains (45-fold change, o1% false discovery rate) for basal and LPS-stimulated macrophages. Moreover, we identified eight genes with differentially expressed alternatively spliced isoforms, by using an in-depth analysis at the probe level that allowed us to discard false positives owing to polymorphisms between the two rat strains. Pathway analysis identified several common linked pathways, enriched for differentially expressed genes, which affect macrophage activation.
    [Show full text]
  • Chromosome Mis-Segregation and Cytokinesis Failure in Trisomic
    RESEARCH ARTICLE elifesciences.org Chromosome mis-segregation and cytokinesis failure in trisomic human cells Joshua M Nicholson1,2, Joana C Macedo3,4,5, Aaron J Mattingly1†, Darawalee Wangsa6, Jordi Camps6‡, Vera Lima7, Ana M Gomes3, Sofia Doria´ 7, Thomas Ried6, Elsa Logarinho3,4,5*, Daniela Cimini1,2* 1Department of Biological Sciences, Virginia Tech, Blacksburg, United States; 2Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, United States; 3Aging and Aneuploidy Laboratory, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal; 4Instituto de Investigac¸a˜ o e Inovac¸a˜ oemSaude-i3S,´ Universidade do Porto, Porto, Portugal; 5Cell Division Unit, Department of Experimental Biology, Faculdade de Medicina, Universidade do Porto, Porto, Portugal; 6Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, United States; 7Department of Genetics, Faculdade de Medicina, *For correspondence: elsa. [email protected] (EL); Universidade do Porto, Porto, Portugal [email protected] (DC) Present address: †Cell and Tissue Biology, School of Dentistry, Abstract Cancer cells display aneuploid karyotypes and typically mis-segregate chromosomes at University of California, San high rates, a phenotype referred to as chromosomal instability (CIN). To test the effects of Francisco, San Francisco, United aneuploidy on chromosome segregation and other mitotic phenotypes we used the colorectal cancer States; ‡Gastrointestinal and cell line DLD1 (2n = 46) and two variants with trisomy 7 or 13 (DLD1+7 and DLD1+13), as well as Pancreatic Oncology Group, euploid and trisomy 13 amniocytes (AF and AF+13). We found that trisomic cells displayed higher Hospital Clınic,´ Centro de Investigacion´ Biomedica´ en Red rates of chromosome mis-segregation compared to their euploid counterparts.
    [Show full text]
  • Genomic and Transcriptome Analysis Revealing an Oncogenic Functional Module in Meningiomas
    Neurosurg Focus 35 (6):E3, 2013 ©AANS, 2013 Genomic and transcriptome analysis revealing an oncogenic functional module in meningiomas XIAO CHANG, PH.D.,1 LINGLING SHI, PH.D.,2 FAN GAO, PH.D.,1 JONATHAN RUssIN, M.D.,3 LIYUN ZENG, PH.D.,1 SHUHAN HE, B.S.,3 THOMAS C. CHEN, M.D.,3 STEVEN L. GIANNOTTA, M.D.,3 DANIEL J. WEISENBERGER, PH.D.,4 GAbrIEL ZADA, M.D.,3 KAI WANG, PH.D.,1,5,6 AND WIllIAM J. MAck, M.D.1,3 1Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, California; 2GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China; 3Department of Neurosurgery, Keck School of Medicine, University of Southern California, Los Angeles, California; 4USC Epigenome Center, Keck School of Medicine, University of Southern California, Los Angeles, California; 5Department of Psychiatry, Keck School of Medicine, University of Southern California, Los Angeles, California; and 6Division of Bioinformatics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California Object. Meningiomas are among the most common primary adult brain tumors. Although typically benign, roughly 2%–5% display malignant pathological features. The key molecular pathways involved in malignant trans- formation remain to be determined. Methods. Illumina expression microarrays were used to assess gene expression levels, and Illumina single- nucleotide polymorphism arrays were used to identify copy number variants in benign, atypical, and malignant me- ningiomas (19 tumors, including 4 malignant ones). The authors also reanalyzed 2 expression data sets generated on Affymetrix microarrays (n = 68, including 6 malignant ones; n = 56, including 3 malignant ones).
    [Show full text]
  • Unveiling Ubiquitination As a New Regulatory Mechanism of the ESCRT-III Protein CHMP1B Xènia Crespo-Yañez
    Unveiling Ubiquitination as a New Regulatory Mechanism of the ESCRT-III Protein CHMP1B Xènia Crespo-Yañez To cite this version: Xènia Crespo-Yañez. Unveiling Ubiquitination as a New Regulatory Mechanism of the ESCRT-III Pro- tein CHMP1B. Cellular Biology. Université Grenoble Alpes, 2017. English. NNT : 2017GREAV035. tel-01684692 HAL Id: tel-01684692 https://tel.archives-ouvertes.fr/tel-01684692 Submitted on 15 Jan 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE Pour obtenir le grade de DOCTEUR DE LA COMMUNAUTE UNIVERSITE GRENOBLE ALPES Spécialité : Biologie Cellulaire Arrêté ministériel : 25 mai 2016 Présentée par Xènia CRESPO-YAÑEZ Thèse dirigée par Marie-Odile FAUVARQUE préparée au sein du Laboratoire Biologie à Grande Echelle, Institut de Biosciences et Biotechnologies de Grenoble, CEA Grenoble dans l'École Doctorale de Chimie et Sciences du Vivant Découverte de l'ubiquitination en tant que nouveau mécanisme de régulation de la protéine ESCRT-III CHMP1B Thèse soutenue publiquement le 13 octobre 2017 devant le jury composé de : Mme Christel BROU Directrice de recherche, Institut Pasteur, Examinatrice M. Pierre COSSON Professeur, Université de Genève, Rapporteur M. Jean-René HUYNH Directeur de recherche, Collège de France, Rapporteur Mme Marie-Odile FAUVARQUE Directrice de recherche, CEA, Directrice de thèse M.
    [Show full text]