DOCSLIB.ORG

Chromophobe Renal Cell Carcinoma with and Without Sarcomatoid Change: a Clinicopathological, Comparative Genomic Hybridization, and Whole-Exome Sequencing Study

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Chromophobe Renal Cell Carcinoma with and Without Sarcomatoid Change: a Clinicopathological, Comparative Genomic Hybridization, and Whole-Exome Sequencing Study Am J Transl Res 2015;7(11):2482-2499 www.ajtr.org /ISSN:1943-8141/AJTR0014993 Original Article Chromophobe renal cell carcinoma with and without sarcomatoid change: a clinicopathological, comparative genomic hybridization, and whole-exome sequencing study Yuan Ren1*, Kunpeng Liu1*, Xueling Kang3, Lijuan Pang1, Yan Qi1, Zhenyan Hu1, Wei Jia1, Haijun Zhang1, Li Li1, Jianming Hu1, Weihua Liang1, Jin Zhao1, Hong Zou1*, Xianglin Yuan2, Feng Li1* 1Department of Pathology, School of Medicine, First Affiliated Hospital, Shihezi University, Key Laboratory of Xinjiang Endemic and Ethnic Diseases, Ministry of Education of China, Shihezi, China; 2Tongji Hospital Cancer Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; 3Department of Pathology, Shanghai General Hospital, Shanghai, China. *Equal contributors. Received August 24, 2015; Accepted October 13, 2015; Epub November 15, 2015; Published November 30, 2015 Abstract: Chromophobe renal cell carcinomas (CRCC) with and without sarcomatoid change have different out- comes; however, fewstudies have compared their genetic profiles. Therefore, we identified the genomic alteration- sin CRCC common type (CRCC C) (n=8) and CRCC with sarcomatoid change (CRCC S) (n=4) using comparative genomic hybridization (CGH) and whole-exome sequencing. The CGH profiles showed that the CRCC C group had more chromosomal losses (72 vs. 18) but fewer chromosomal gains (23 vs. 57) than the CRCC S group. Losses of chromosomes 1p, 8p21-23, 10p16-20, 10p12-ter, 13p20-30, and 17p13 and gains of chromosomes 1q11, 1q21-23, 1p13-15, 2p23-24, and 3p21-ter differed between the groups. Whole-exome sequencing showed that the mutational status of 270 genes differed between CRCC (n=12) and normal renal tissues (n=18). In the functional enrichment analysis, the missense-mutated genes were classified into 6 biological processes (38 functions) and 5 pathways. The biological processes included cell adhesion, cell motility, ATP metabolism, sensory perception, carbo- hydrate and lipid metabolism and transport. The pathways included ATP-binding cassette transporter, extracellular matrix-receptor interaction, olfactory transduction, chondroitin sulfate biosynthesis, and hypertrophic cardiomyopa- thy. Whole-exome sequencing analysis revealed that the missense mutation statuses of 49 genes differed between the CRCC C and CRCC S groups. Furthermore, genetic alterations in metastasis suppressor 1, serine peptidase in- hibitor Kazal type 8, transient receptor potential cation channel super family M member 6, Rh family B glycoprotein, and mannose receptor C type 1 were located in different chromosomal regions. These alterations may provide clues regarding CRCC tumorigenesis and provide a basis for future targeted therapies. Keywords: Chromophobe renal cell carcinoma, chromophobe renal cell carcinoma with sarcomatoid change, com- parative genomic hybridization, whole-exome sequencing, genetic alteration Introduction being diagnosed at TNM stages III and IV, and with a median survival time of only 19 months Renal cell carcinoma (RCC) accounts for 2-3% [3-5]. Sarcomatoid RCCs account for about of all adult malignancies and is the seventh and 1-8% of all renal neoplasms; however, it is not a twelfth most common malignancy in men and distinct histological entity, as it arises from all women, respectively [1]. Chromophobe renal subtypes of RCC [6, 7]. Molecular genetic test- cell carcinoma (CRCC) is the third most com- ing is of great importance for the CRCC and mon histological subtype of RCC and carries CRCC S diagnosis and prognosis and may help a better prognosis than conventional RCC guide treatment. However, little is currently [2]. However, CRCC with sarcomatoid change known about genetic alterations in CRCC S, and (CRCC S) is associated with poor clinical out- few molecular genetics studies have compared comes, with most cases of sarcomatoid RCCs CRCC and CRCC S. Furthermore, until recently, A comparative genetic study of CRCC with and without sarcomatoid change whole-genome sequencing of CRCC has been standard phenol/chloroform extraction meth- little investigated. Therefore, we here identified od. DNA quality was checked on a 1% agarose and compared the genomic alterations in CRCC gel, and the amount of extracted DNA was mea- common type (CRCC C; 8 cases) and CRCC S (4 sured spectrophotometrically at 260 nm (impu- cases) using comparative genomic hybridiza- rity and the DNA to non-DNA ratio were also tion (CGH) and whole-exome sequencing. crosschecked at 280 nm). Extractions were stored at -80°C until nick translation labeling. Material and methods Comparative genomic hybridization (CGH) Ethics statement CGH was performed using a commercially avail- Ethical approval was obtained from Institutional able kit according to the manufacturer’s proto- Ethics Review Board (IERB), The First Affiliated col (Vysis Inc., Downers Grove, IL, USA). Briefly, Hospital, Shihezi University School of Medicine tumor DNA was labeled with fluorescein isothio- and all participants provided written informed cyanate (FITC), while the normal reference DNA consent for themselves. was labeled with cyanine 3 (Cy3). The hybridiza- tion mixture consisted of approximately 200 ng Specimens Spectrum Green-labeled test DNA and 200 ng Spectrum Red-labeled total genomic reference Paraffin-embedded CRCC (n=12) and normal DNA coprecipitated with 10 μg human Cot-1 renal tissues (n=18) were obtained from the DNA (Invitrogen, Carlsbad, CA, USA) and was archives of the Department of Pathology, dissolved in hybridization buffer before hybrid- School of Medicine, Shihezi University. The clin- ization to metaphase chromosomes. The probe icopathological data of these cases were col- mixtures were denatured at 73°C for 5 min and lected from the patients’ medical records after then competitively hybridized to the denatured obtaining patient consent and approval by normal metaphase chromosomes in a 37°C the Institutional Research Ethics Committee. humidified chamber for 3 days. After washing, CRCCs were classified according to the 2004 the chromosomes were counterstained with World Health Organization Classification of 4’6-diamidino-2-phenylindoledihydrochloride Renal Tumors, 2010 American Joint Committee (DAPI) II (Vysis Inc.) and embedded in an an- on Cancer guidelines, and International Union ti-fading agent to reduce photobleaching. To against Cancer tumor/lymph node metastasis/ provide a control in case of artifacts, normal distal metastasis (TNM) classification system. female DNA (labeled green) was used as a neg- Immunohistochemistry ative control. DNA extracted from the MPE600 breast cancer cell line was used as a positive Paraffin-embedded CRCC tissue sections we- control (labeled green). Threshold levels of re stained using the 2-step Envision method 1.25 and 0.8 were used to score gains and (Dako, Glostrup, Denmark). The following pri- losses, respectively. High-level amplification mary antibodies were used: cluster of differ- was indicated by a ratio greater than 1.5. All entiation (CD) 10 (GT200410, 1:100), cytokera- centromeres, chromosome p35-36, and het- tin (CK) AE1/3 (AE1/AE3, 1:100), vimentin erochromatic regions of chromosomes Y, 16, (Vim3B4, 1:100), CD117 (104D2, 1:300), 19, and 22 were excluded from further analysis P504S (13H4, 1:100), and CK7 (OV-TL12/30, because these regions can yield unreliable 1:50) (all from Dako). Briefly, thetissue sections hybridization owing to incompletely suppressed were incubated with primary antibodies acco- repetitive DNA sequences. rding to the manufacturer’s instructions. Im- munodetection was performed using 3,3’-dia- Whole-exome sequencing minobenzidine as the chromogenic horseradish peroxidase substrate, followed by hematoxylin DNA (1 μg) extracted from CRCC tissues (n=12) counterstaining. and normal renal tissues (n=18) were labeled with Illumina reagents and hybridized to Human DNA extraction Exome BeadChips (Illumina, San Diego, CA, USA). Illumina Expression Console software Total DNA was extracted from CRCC (n=12) and was used to perform the quality assessment. normal renal (n=18) tissue samples using a The significance analysis of microarrays algo- 2483 Am J Transl Res 2015;7(11):2482-2499 A comparative genetic study of CRCC with and without sarcomatoid change Table 1. Clinical characteristic of the 12 CRCC cases Case Age (y)/Sex Diagnosis Stage (tumor diameter, comment) Follow-up 1 52/M CRCC C PT2M0N0 stage 2 (7.5 cm, primary) Alive 2 36/M CRCC C PT1M0N0 stage 1 (6 cm, primary) Alive 3 56/F CRCC C pT1M0N0 stage 1 (5 cm, primary) Alive 4 53/M CRCC C pT3M0N0 stage 3 (20 cm, primary) Died 5 years after the operation 5 55/F CRCC C pT1M0N0 stage 1 (6.5 cm, primary) Alive 6 25/M CRCC C pT2M0N0 stage 2 (8 cm, primary) Alive 7 64/M CRCC C pT1M0N0 stage 1 (5.5 cm primary) Alive 8 60/M CRCC C pT2M0N0 stage 2 (8.5 cm, primary) Alive 9 39/M CRCC S pT3M0N1 stage 3 (15 cm, primary, 3/4 lymph nodes positive) Developed brain metastasis and died 1 month after the operation 10 52/F CRCC S pT3M0N1 stage 3 (15 cm, primary, 1/4 lymph nodes positive) Died 3 years after the operation 11 36/F CRCC S pT2M1N0 stage 4 (9.5 cm, primary, lung metastasis) Died 8 months after the operation 12 72/F CRCC S pT2M1N1 stage 4 (8.2 cm, primary, bone metastasis, 1/5 lymph nodes positive) Died 1 year after the operation Abbreviations: CRCC, chromophobe renal cell carcinoma; CRCC C, CRCC common type; CRCC S, CRCC with sarcomatoid change; F, female; M, male. Table 3. Chromosome aberrations in the 12 cases of CRCC
Load more

Recommended publications
  • Genetic Variation Across the Human Olfactory Receptor Repertoire Alters Odor Perception
    bioRxiv preprint doi: https://doi.org/10.1101/212431; this version posted November 1, 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. Genetic variation across the human olfactory receptor repertoire alters odor perception Casey Trimmer1,*, Andreas Keller2, Nicolle R. Murphy1, Lindsey L. Snyder1, Jason R. Willer3, Maira Nagai4,5, Nicholas Katsanis3, Leslie B. Vosshall2,6,7, Hiroaki Matsunami4,8, and Joel D. Mainland1,9 1Monell Chemical Senses Center, Philadelphia, Pennsylvania, USA 2Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, New York, USA 3Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, USA 4Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA 5Department of Biochemistry, University of Sao Paulo, Sao Paulo, Brazil 6Howard Hughes Medical Institute, New York, New York, USA 7Kavli Neural Systems Institute, New York, New York, USA 8Department of Neurobiology and Duke Institute for Brain Sciences, Duke University Medical Center, Durham, North Carolina, USA 9Department of Neuroscience, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA *[email protected] ABSTRACT The human olfactory receptor repertoire is characterized by an abundance of genetic variation that affects receptor response, but the perceptual effects of this variation are unclear. To address this issue, we sequenced the OR repertoire in 332 individuals and examined the relationship between genetic variation and 276 olfactory phenotypes, including the perceived intensity and pleasantness of 68 odorants at two concentrations, detection thresholds of three odorants, and general olfactory acuity.
    [Show full text]
  • Database Tool the Systematic Annotation of the Three Main GPCR
    Database, Vol. 2010, Article ID baq018, doi:10.1093/database/baq018 ............................................................................................................................................................................................................................................................................................. Database tool The systematic annotation of the three main Downloaded from https://academic.oup.com/database/article-abstract/doi/10.1093/database/baq018/406672 by guest on 15 January 2019 GPCR families in Reactome Bijay Jassal1, Steven Jupe1, Michael Caudy2, Ewan Birney1, Lincoln Stein2, Henning Hermjakob1 and Peter D’Eustachio3,* 1European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK, 2Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada and 3New York University School of Medicine, New York, NY 10016, USA *Corresponding author: Tel: +212 263 5779; Fax: +212 263 8166; Email: [email protected] Submitted 14 April 2010; Revised 14 June 2010; Accepted 13 July 2010 ............................................................................................................................................................................................................................................................................................. Reactome is an open-source, freely available database of human biological pathways and processes. A major goal of our work is to provide an integrated view of cellular signalling processes that spans from ligand–receptor
    [Show full text]
  • SNP Genotypes of Olfactory Receptor Genes Associated with Olfactory Ability in German Shepherd Dogs
    SHORT COMMUNICATION doi: 10.1111/age.12389 SNP genotypes of olfactory receptor genes associated with olfactory ability in German Shepherd dogs † ‡ – M. Yang*, G.-J. Geng , W. Zhang , L. Cui§, H.-X. Zhang and J.-L. Zheng‡ † *Police-dog Technology Department, National Police University of China, Shenyang, Liaoning 110034, China. Technology Department, ‡ Shenyang Traffic Police Detachment, Shenyang, Liaoning 110001, China. Forensic Medicine Department, National Police University of China, Shenyang, Liaoning 110854, China. §Document Inspection Department, National Police University of China, Shenyang, Liaoning – 110854, China. Mark Inspection Department, National Police University of China, Shenyang, Liaoning 110854, China. Summary To find out the relationship between SNP genotypes of canine olfactory receptor genes and olfactory ability, 28 males and 20 females from German Shepherd dogs in police service were scored by odor detection tests and analyzed using the Beckman GenomeLab SNPstream. The representative 22 SNP loci from the exonic regions of 12 olfactory receptor genes were investigated, and three kinds of odor (human, ice drug and trinitrotoluene) were detected. The results showed that the SNP genotypes at the OR10H1-like:c.632C>T, OR10H1-like:c.770A>T, OR2K2-like:c.518G>A, OR4C11-like: c.511T>G and OR4C11-like:c.692G>A loci had a statistically significant effect on the scenting abilities (P < 0.001). The kind of odor influenced the performances of the dogs (P < 0.001). In addition, there were interactions between genotype and the kind of odor at the following loci: OR10H1-like:c.632C>T, OR10H1-like:c.770A>T, OR4C11-like:c.511T>G and OR4C11-like:c.692G>A(P< 0.001).
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Cellular and Molecular Signatures in the Disease Tissue of Early
    Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of
    [Show full text]
  • Supplementary Methods
    Heterogeneous Contribution of Microdeletions in the Development of Common Generalized and Focal epilepsies. SUPPLEMENTARY METHODS Epilepsy subtype extended description. Genetic Gereralized Epilepsy (GGE): Features unprovoked tonic and/or clonic seizures, originated inconsistently at some focal point within the brain that rapidly generalizes engaging bilateral distributed spikes and waves discharges on the electroencephalogram. This generalization can include cortical and sub cortical structures but not necessarily the entire cortex[1]. GGE is the most common group of epilepsies accounting for 20% of all cases[2]. It is characterized by an age-related onset and a strong familial aggregation and heritability which allows the assumption of a genetic cause. Although genetic associations have been identified, a broad spectrum of causes is acknowledged and remains largely unsolved [3]. Rolandic Epilepsy (RE): Commonly known also as Benign Epilepsy with Centrotemporal Spikes (BECTS), hallmarks early onset diagnosis (mean onset = 7 years old) with brief, focal hemifacial or oropharyngeal sensorimotor seizures alongside speech arrest and secondarily generalized tonic– clonic seizures, which mainly occur during sleep[4]. Rolandic epilepsy features a broad spectrum of less benign related syndromes called atypical Rolandic epilepsy (ARE), including benign partial epilepsy (ABPE), Landau–Kleffner syndrome(LKS) and epileptic encephalopathy with continuous spike-and-waves during sleep (CSWSS)[5]. Together they are the most common childhood epilepsy with a prevalence of 0.2–0.73/1000 (i.e. _1/2500)[6]. Adult Focal Epilepsy (AFE). Focal epilepsy is characterized by sporadic events of seizures originated within a specific brain region and restricted to one hemisphere. Although they can exhibit more than one network of wave discharges on the electroencephalogram, and different degrees of spreading, they feature a consistent site of origin.
    [Show full text]
  • Whole Exome Sequencing in Families at High Risk for Hodgkin Lymphoma: Identification of a Predisposing Mutation in the KDR Gene
    Hodgkin Lymphoma SUPPLEMENTARY APPENDIX Whole exome sequencing in families at high risk for Hodgkin lymphoma: identification of a predisposing mutation in the KDR gene Melissa Rotunno, 1 Mary L. McMaster, 1 Joseph Boland, 2 Sara Bass, 2 Xijun Zhang, 2 Laurie Burdett, 2 Belynda Hicks, 2 Sarangan Ravichandran, 3 Brian T. Luke, 3 Meredith Yeager, 2 Laura Fontaine, 4 Paula L. Hyland, 1 Alisa M. Goldstein, 1 NCI DCEG Cancer Sequencing Working Group, NCI DCEG Cancer Genomics Research Laboratory, Stephen J. Chanock, 5 Neil E. Caporaso, 1 Margaret A. Tucker, 6 and Lynn R. Goldin 1 1Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 2Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 3Ad - vanced Biomedical Computing Center, Leidos Biomedical Research Inc.; Frederick National Laboratory for Cancer Research, Frederick, MD; 4Westat, Inc., Rockville MD; 5Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; and 6Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA ©2016 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol.2015.135475 Received: August 19, 2015. Accepted: January 7, 2016. Pre-published: June 13, 2016. Correspondence: [email protected] Supplemental Author Information: NCI DCEG Cancer Sequencing Working Group: Mark H. Greene, Allan Hildesheim, Nan Hu, Maria Theresa Landi, Jennifer Loud, Phuong Mai, Lisa Mirabello, Lindsay Morton, Dilys Parry, Anand Pathak, Douglas R. Stewart, Philip R. Taylor, Geoffrey S. Tobias, Xiaohong R. Yang, Guoqin Yu NCI DCEG Cancer Genomics Research Laboratory: Salma Chowdhury, Michael Cullen, Casey Dagnall, Herbert Higson, Amy A.
    [Show full text]
  • Deep Sequencing of the Human Retinae Reveals the Expression of Odorant Receptors
    fncel-11-00003 January 20, 2017 Time: 14:24 # 1 CORE Metadata, citation and similar papers at core.ac.uk Provided by Frontiers - Publisher Connector ORIGINAL RESEARCH published: 24 January 2017 doi: 10.3389/fncel.2017.00003 Deep Sequencing of the Human Retinae Reveals the Expression of Odorant Receptors Nikolina Jovancevic1*, Kirsten A. Wunderlich2, Claudia Haering1, Caroline Flegel1, Désirée Maßberg1, Markus Weinrich1, Lea Weber1, Lars Tebbe2, Anselm Kampik3, Günter Gisselmann1, Uwe Wolfrum2, Hanns Hatt1† and Lian Gelis1† 1 Department of Cell Physiology, Ruhr-University Bochum, Bochum, Germany, 2 Department of Cell and Matrix Biology, Johannes Gutenberg University of Mainz, Mainz, Germany, 3 Department of Ophthalmology, Ludwig Maximilian University of Munich, Munich, Germany Several studies have demonstrated that the expression of odorant receptors (ORs) occurs in various tissues. These findings have served as a basis for functional studies that demonstrate the potential of ORs as drug targets for a clinical application. To the best of our knowledge, this report describes the first evaluation of the mRNA expression of ORs and the localization of OR proteins in the human retina that set a Edited by: stage for subsequent functional analyses. RNA-Sequencing datasets of three individual Hansen Wang, University of Toronto, Canada neural retinae were generated using Next-generation sequencing and were compared Reviewed by: to previously published but reanalyzed datasets of the peripheral and the macular Ewald Grosse-Wilde, human retina and to reference tissues. The protein localization of several ORs was Max Planck Institute for Chemical Ecology (MPG), Germany investigated by immunohistochemistry. The transcriptome analyses detected an average Takaaki Sato, of 14 OR transcripts in the neural retina, of which OR6B3 is one of the most highly National Institute of Advanced expressed ORs.
    [Show full text]
  • New Tests 2 Test Updates 4 CPT Code Updates 11 Deleted Tests 11 Diagnostics Update Volume XXI, No
    Volume XXI, No. 6 JUNE 2021 MONTHLY TEST UPDATES Diagnostics Update New Tests 2 Test Updates 4 CPT Code Updates 11 Deleted Tests 11 Diagnostics Update Volume XXI, No. 6 | JUNE 2021 New Tests Use Anti-DFS70 antibodies may help identify individuals who do not have an Anti-Carbamylated Protein (CarP) Antibody 520311 ANA-associated Autoimmune Rheumatic Disease (AARD) especially in the absence of significant clinical findings.1 Anti-DFS70 Ab, especially when positive CPT 83516 in isolation (i.e. in the absence of AARD-associated autoantibodies), may Synonyms Anti-CarP antigen antibody; RA marker prevent unnecessary referrals and examinations of ANA-positive individuals.2 Special Instructions This test has not been approved for NY state clients. Limitations This test should be used with clinical findings and other Specimen Serum autoimmune testing; it cannot be used alone to rule out autoimmune disease. Volume 1 mL This test was developed and its performance characteristics determined Minimum Volume 0.5 mL by Labcorp. It has not been cleared or approved by the Food and Drug Container Red-top tube; serum from red-top tube; serum from a gel tube; or Administration. serum gel tube Methodology Enzyme-linked immunosorbent assay (ELISA) Collection Separate serum from cells within one hour of collection. Transfer to a Additional Information Anti-DFS70 antibodies target the dense fine speckled plastic transport tube before shipping. protein of 70 kDa which is identical to Lens Epithelium-Derived Growth Factor Storage Instructions Refrigerate or freeze. or transcription co-activator p75 (LEDGFp75). They are detectable in 2% to 22% Stability of healthy individuals and in less than 1% of patients with AARD are of unknown Temperature Period clinical significance.
    [Show full text]
  • Pflugers Final
    CORE Metadata, citation and similar papers at core.ac.uk Provided by Serveur académique lausannois A comprehensive analysis of gene expression profiles in distal parts of the mouse renal tubule. Sylvain Pradervand2, Annie Mercier Zuber1, Gabriel Centeno1, Olivier Bonny1,3,4 and Dmitri Firsov1,4 1 - Department of Pharmacology and Toxicology, University of Lausanne, 1005 Lausanne, Switzerland 2 - DNA Array Facility, University of Lausanne, 1015 Lausanne, Switzerland 3 - Service of Nephrology, Lausanne University Hospital, 1005 Lausanne, Switzerland 4 – these two authors have equally contributed to the study to whom correspondence should be addressed: Dmitri FIRSOV Department of Pharmacology and Toxicology, University of Lausanne, 27 rue du Bugnon, 1005 Lausanne, Switzerland Phone: ++ 41-216925406 Fax: ++ 41-216925355 e-mail: [email protected] and Olivier BONNY Department of Pharmacology and Toxicology, University of Lausanne, 27 rue du Bugnon, 1005 Lausanne, Switzerland Phone: ++ 41-216925417 Fax: ++ 41-216925355 e-mail: [email protected] 1 Abstract The distal parts of the renal tubule play a critical role in maintaining homeostasis of extracellular fluids. In this review, we present an in-depth analysis of microarray-based gene expression profiles available for microdissected mouse distal nephron segments, i.e., the distal convoluted tubule (DCT) and the connecting tubule (CNT), and for the cortical portion of the collecting duct (CCD) (Zuber et al., 2009). Classification of expressed transcripts in 14 major functional gene categories demonstrated that all principal proteins involved in maintaining of salt and water balance are represented by highly abundant transcripts. However, a significant number of transcripts belonging, for instance, to categories of G protein-coupled receptors (GPCR) or serine-threonine kinases exhibit high expression levels but remain unassigned to a specific renal function.
    [Show full text]
  • Single Cell Derived Clonal Analysis of Human Glioblastoma Links
    SUPPLEMENTARY INFORMATION: Single cell derived clonal analysis of human glioblastoma links functional and genomic heterogeneity ! Mona Meyer*, Jüri Reimand*, Xiaoyang Lan, Renee Head, Xueming Zhu, Michelle Kushida, Jane Bayani, Jessica C. Pressey, Anath Lionel, Ian D. Clarke, Michael Cusimano, Jeremy Squire, Stephen Scherer, Mark Bernstein, Melanie A. Woodin, Gary D. Bader**, and Peter B. Dirks**! ! * These authors contributed equally to this work.! ** Correspondence: [email protected] or [email protected]! ! Supplementary information - Meyer, Reimand et al. Supplementary methods" 4" Patient samples and fluorescence activated cell sorting (FACS)! 4! Differentiation! 4! Immunocytochemistry and EdU Imaging! 4! Proliferation! 5! Western blotting ! 5! Temozolomide treatment! 5! NCI drug library screen! 6! Orthotopic injections! 6! Immunohistochemistry on tumor sections! 6! Promoter methylation of MGMT! 6! Fluorescence in situ Hybridization (FISH)! 7! SNP6 microarray analysis and genome segmentation! 7! Calling copy number alterations! 8! Mapping altered genome segments to genes! 8! Recurrently altered genes with clonal variability! 9! Global analyses of copy number alterations! 9! Phylogenetic analysis of copy number alterations! 10! Microarray analysis! 10! Gene expression differences of TMZ resistant and sensitive clones of GBM-482! 10! Reverse transcription-PCR analyses! 11! Tumor subtype analysis of TMZ-sensitive and resistant clones! 11! Pathway analysis of gene expression in the TMZ-sensitive clone of GBM-482! 11! Supplementary figures and tables" 13" "2 Supplementary information - Meyer, Reimand et al. Table S1: Individual clones from all patient tumors are tumorigenic. ! 14! Fig. S1: clonal tumorigenicity.! 15! Fig. S2: clonal heterogeneity of EGFR and PTEN expression.! 20! Fig. S3: clonal heterogeneity of proliferation.! 21! Fig.
    [Show full text]
  • Supplementary Table 1
    Supplementary Table 1. 492 genes are unique to 0 h post-heat timepoint. The name, p-value, fold change, location and family of each gene are indicated. Genes were filtered for an absolute value log2 ration 1.5 and a significance value of p ≤ 0.05. Symbol p-value Log Gene Name Location Family Ratio ABCA13 1.87E-02 3.292 ATP-binding cassette, sub-family unknown transporter A (ABC1), member 13 ABCB1 1.93E-02 −1.819 ATP-binding cassette, sub-family Plasma transporter B (MDR/TAP), member 1 Membrane ABCC3 2.83E-02 2.016 ATP-binding cassette, sub-family Plasma transporter C (CFTR/MRP), member 3 Membrane ABHD6 7.79E-03 −2.717 abhydrolase domain containing 6 Cytoplasm enzyme ACAT1 4.10E-02 3.009 acetyl-CoA acetyltransferase 1 Cytoplasm enzyme ACBD4 2.66E-03 1.722 acyl-CoA binding domain unknown other containing 4 ACSL5 1.86E-02 −2.876 acyl-CoA synthetase long-chain Cytoplasm enzyme family member 5 ADAM23 3.33E-02 −3.008 ADAM metallopeptidase domain Plasma peptidase 23 Membrane ADAM29 5.58E-03 3.463 ADAM metallopeptidase domain Plasma peptidase 29 Membrane ADAMTS17 2.67E-04 3.051 ADAM metallopeptidase with Extracellular other thrombospondin type 1 motif, 17 Space ADCYAP1R1 1.20E-02 1.848 adenylate cyclase activating Plasma G-protein polypeptide 1 (pituitary) receptor Membrane coupled type I receptor ADH6 (includes 4.02E-02 −1.845 alcohol dehydrogenase 6 (class Cytoplasm enzyme EG:130) V) AHSA2 1.54E-04 −1.6 AHA1, activator of heat shock unknown other 90kDa protein ATPase homolog 2 (yeast) AK5 3.32E-02 1.658 adenylate kinase 5 Cytoplasm kinase AK7
    [Show full text]