Kallikrein 4 Is a Proliferative Factor That Is Overexpressed in Prostate Cancer
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Functional Characterization of BC039389-GATM and KLK4
Pflueger et al. BMC Genomics (2015) 16:247 DOI 10.1186/s12864-015-1446-z RESEARCH ARTICLE Open Access Functional characterization of BC039389-GATM and KLK4-KRSP1 chimeric read-through transcripts which are up-regulated in renal cell cancer Dorothee Pflueger1,2, Christiane Mittmann1, Silvia Dehler3, Mark A Rubin4,5, Holger Moch1,2 and Peter Schraml1* Abstract Background: Chimeric read-through RNAs are transcripts originating from two directly adjacent genes (<10 kb) on the same DNA strand. Although they are found in next-generation whole transcriptome sequencing (RNA-Seq) data on a regular basis, investigating them further has usually been refrained from. Therefore, their expression patterns or functions in general, and in oncogenesis in particular, are poorly understood. Results: We used paired-end RNA-Seq and a specifically designed computational data analysis pipeline (FusionSeq) to nominate read-through events in a small discovery set of renal cell carcinomas (RCC) and confirmed them in a larger validation cohort. 324 read-through events were called overall; 22/27 (81%) selected nominees passed validation with conventional PCR and were sequenced at the junction region. We frequently identified various isoforms of a given read-through event. 2/22 read-throughs were up-regulated: BC039389-GATM was higher expressed in RCC compared to benign adjacent kidney; KLK4-KRSP1 was expressed in 46/169 (27%) RCCs, but rarely in normal tissue. KLK4-KRSP1 expression was associated with worse clinical outcome in the patient cohort. In cell lines, both read-throughs influenced molecular mechanisms (i.e. target gene expression or migration/invasion) in a way that counteracted the effect of the respective parent transcript GATM or KLK4. -
Identification of New Substrates and Physiological Relevance
Université de Montréal The Multifaceted Proprotein Convertases PC7 and Furin: Identification of New Substrates and Physiological Relevance Par Stéphanie Duval Biologie Moléculaire, Faculté de médecine Thèse présentée en vue de l’obtention du grade de Philosophiae doctor (Ph.D) en Biologie moléculaire, option médecine cellulaire et moléculaire Avril 2020 © Stéphanie Duval, 2020 Résumé Les proprotéines convertases (PCs) sont responsables de la maturation de plusieurs protéines précurseurs et sont impliquées dans divers processus biologiques importants. Durant les 30 dernières années, plusieurs études sur les PCs se sont traduites en succès cliniques, toutefois les fonctions spécifiques de PC7 demeurent obscures. Afin de comprendre PC7 et d’identifier de nouveaux substrats, nous avons généré une analyse protéomique des protéines sécrétées dans les cellules HuH7. Cette analyse nous a permis d’identifier deux protéines transmembranaires de fonctions inconnues: CASC4 et GPP130/GOLIM4. Au cours de cette thèse, nous nous sommes aussi intéressé au rôle de PC7 dans les troubles comportementaux, grâce à un substrat connu, BDNF. Dans le chapitre premier, je présenterai une revue de la littérature portant entre autres sur les PCs. Dans le chapitre II, l’étude de CASC4 nous a permis de démontrer que cette protéine est clivée au site KR66↓NS par PC7 et Furin dans des compartiments cellulaires acides. Comme CASC4 a été rapporté dans des études de cancer du sein, nous avons généré des cellules MDA- MB-231 exprimant CASC4 de type sauvage et avons démontré une diminution significative de la migration et de l’invasion cellulaire. Ce phénotype est causé notamment par une augmentation du nombre de complexes d’adhésion focale et peut être contrecarré par la surexpression d’une protéine CASC4 mutante ayant un site de clivage optimale par PC7/Furin ou encore en exprimant une protéine contenant uniquement le domaine clivé N-terminal. -
An Overview of the Kallikrein Gene Families in Humans and Other Species: Emerging Candidate Tumour Markers૾
Clinical Biochemistry 36 (2003) 443–452 An overview of the kallikrein gene families in humans and other species: Emerging candidate tumour markers૾ George M. Yousefa,b, Eleftherios P. Diamandisa,b,* aDepartment of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada bDepartment of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada Abstract Kallikreins are serine proteases with diverse physiologic functions. They are represented by multigene families in many animal species, especially in rat and mouse. Recently, the human kallikrein gene family has been fully characterized and includes 15 members, tandemly localized on chromosome 19q13.4. A new definition has now been proposed for kallikreins, which is not based on function but, rather, on close proximity and structural similarities. In this review, we summarize available information about kallikreins in many animal species with special emphasis on human kallikreins. We discuss the common structural features of kallikreins at the DNA, mRNA and protein levels and overview their evolutionary history. Kallikreins are expressed in a wide range of tissues including the salivary gland, endocrine or endocrine-related tissues such as testis, prostate, breast and endometrium and in the central nervous system. Most, if not all, genes are under steroid hormone regulation. Accumulating evidence indicates that kallikreins are involved in many pathologic conditions. Of special interest is the potential role of kallikreins in the central nervous system. In addition, many kallikreins seem to be candidate tumor markers for many malignancies, especially those of endocrine-related organs. © 2003 The Canadian Society of Clinical Chemists. All rights reserved. Keywords: Kallikrein; Tumor markers; Cancer biomarkers; Prostate cancer; Breast cancer; Ovarian cancer; Alzheimer’s disease; Serine proteases; Chromosome 19; Kallikrein evolution; Rodent kallikreins; Hormonally regulated genes 1. -
New Insights Into the Functional Mechanisms and Clinical Applications of the Kallikrein-Related Peptidase Family
MOLECULAR ONCOLOGY 1 (2007) 269–287 available at www.sciencedirect.com www.elsevier.com/locate/molonc Review New insights into the functional mechanisms and clinical applications of the kallikrein-related peptidase family Nashmil Emamia,b, Eleftherios P. Diamandisa,b,* aDepartment of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5G 1L5, Canada bDepartment of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada ABSTRACT ARTICLE INFO Article history: The Kallikrein-related peptidase (KLK) family consists of fifteen conserved serine proteases Received 13 July 2007 that form the largest contiguous cluster of proteases in the human genome. While primar- Received in revised form ily recognized for their clinical utilities as potential disease biomarkers, new compelling 4 September 2007 evidence suggests that this family plays a significant role in various physiological pro- Accepted 7 September 2007 cesses, including skin desquamation, semen liquefaction, neural plasticity, and body fluid Available online 15 September 2007 homeostasis. KLK activation is believed to be mediated through highly organized proteo- lytic cascades, regulated through a series of feedback loops, inhibitors, auto-degradation Keywords: and internal cleavages. Gene expression is mainly hormone-dependent, even though tran- Kallikrein-related peptidases scriptional epigenetic regulation has also been reported. These regulatory mechanisms are PSA integrated with various signaling pathways to mediate multiple functions. Dysregulation of Proteolytic cascades these pathways has been implicated in a large number of neoplastic and non-neoplastic Skin desquamation pathological conditions. This review highlights our current knowledge of structural/ * Corresponding author. Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada. -
Table of Contents
Table of Contents Preface V List of contributing authors VII Table of Contents XI Introduction to Volume 1: Kallikrein-related Peptidases. Characterization, Regulation, and Interactions Within the Protease Web 1 Bibliography 3 1 Genomic Structure of the KLK Locus 5 1.1 Introduction 5 1.2 Kallikreins in rodents 6 1.2.1 The mouse kallikrein gene family 7 1.2.2 The rat kallikrein gene family 8 1.3 Characterization and sequence analysis of the human KLK gene locus 9 1.3.1 Locus overview 9 1.3.2 Repeat elements and pleomorphism 11 1.4 Structural features of the human KLK genes and proteins 12 1.4.1 Common structural features 12 1.5 Sequence variations of human KLK genes 13 1.6 Regulation of KLK activity 14 1.6.1 At the mRNA level 14 1.6.2 Locus control of KLK expression 15 1.6.3 Epigenetic regulation of KLK gene expression 17 1.7 Isoforms and splice variants of human KLKs 18 1.8 Evolution of KLKs 21 Bibliography 22 2 Single Nucleotide Polymorphisms in the Human KLK Locus and Their Implication in Various Diseases 31 2.1 Introduction 31 2.2 KLK SNPs – data-mining from SNPdb and 1000 Genomes 32 2.3 Functional annotations using web-based prediction tools 34 2.4 Experimentally validated functional KLK SNPs 35 2.5 KLK SNP haplotypes and tagging 36 2.6 Malignant and non-malignant diseases and association with KLK SNPs 38 2.6.1 Association studies on high-risk variants in KLK genes 39 XII Table of Contents 2.6.2 Association studies on low-risk variants in KLK genes 39 2.7 Conclusions 71 Bibliography 71 3 Evolution of Kallikrein-related Peptidases 79 -
AACR2006-1686P
Funding Proteinases and Inflammation Network Group grant Kallikrein 14 Signalling through Proteinase-Activated Receptors CIHR operating grant 1,2 3,4 3,4 3,4 5 Alberta Heritage Foundation for Katerina Oikonomopoulou , Kristina K. Hansen , Mahmoud Saifeddine , Illa Tea , Patricia Andrade-Gordon , Medical Research Graeme S. Cottrell6, Nigel W. Bunnett6, Nathalie Vergnolle3, Eleftherios P. Diamandis1,2 and Morley D. Hollenberg3,4 NSERC / CRSNG 1Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto; 2Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto; 3Department of Pharmacology & Therapeutics, and 4Department of Medicine, University of Calgary, Calgary; 5Johnson & Johnson Pharmaceutical Research and Development, Spring House, Pennsylvania, 6Departments of Surgery and Physiology, University of California, San Francisco Kallikrein 14 can selectively disarm PAR (lower concentrations), OVERVIEW Figure 1: Mechanism of PAR activation (activation by proteolysis) 2. Kallikrein 14 can selectively disarm PAR1 (lower concentrations), 2+ Proteinase-activated receptors (PARs): a family of G-protein coupled receptors activated by serine proteinase cleavage site whilst activating PARs 2 and 4; Ca in HEK cells proteinases via a proteolytically revealed ‘tethered ligand’ (Fig. 1). Four family members (Fig. 2); PARs N PAR disarming 1, 2 and 4 signal to cells. N PAR1 dis-arming1 vs. activation Selective activation of PAR4 vs. PARs 1, 2 Human kallikreins (hKs): A 15-member family of secreted serine proteinases implicated in tumour 1 cm Thrombin 1 cm 2 min 2 min TFLLR-NH2 progression and cell survival (Fig. 4). (selective desensitization hK14: a tryptic kallikrein; wide tissue distribution, implicated in breast and ovarian cancer (Fig. 5 and 6). of PAR1) The mechanism of kallikrein action is not yet known: Although some targets have been identified (e.g. -
Solenodon Genome Reveals Convergent Evolution of Venom in Eulipotyphlan Mammals
Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals Nicholas R. Casewella,1, Daniel Petrasb,c, Daren C. Cardd,e,f, Vivek Suranseg, Alexis M. Mychajliwh,i,j, David Richardsk,l, Ivan Koludarovm, Laura-Oana Albulescua, Julien Slagboomn, Benjamin-Florian Hempelb, Neville M. Ngumk, Rosalind J. Kennerleyo, Jorge L. Broccap, Gareth Whiteleya, Robert A. Harrisona, Fiona M. S. Boltona, Jordan Debonoq, Freek J. Vonkr, Jessica Alföldis, Jeremy Johnsons, Elinor K. Karlssons,t, Kerstin Lindblad-Tohs,u, Ian R. Mellork, Roderich D. Süssmuthb, Bryan G. Fryq, Sanjaya Kuruppuv,w, Wayne C. Hodgsonv, Jeroen Kooln, Todd A. Castoed, Ian Barnesx, Kartik Sunagarg, Eivind A. B. Undheimy,z,aa, and Samuel T. Turveybb aCentre for Snakebite Research & Interventions, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA Liverpool, United Kingdom; bInstitut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany; cCollaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA 92093; dDepartment of Biology, University of Texas at Arlington, Arlington, TX 76010; eDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138; fMuseum of Comparative Zoology, Harvard University, Cambridge, MA 02138; gEvolutionary Venomics Lab, Centre for Ecological Sciences, Indian Institute of Science, 560012 Bangalore, India; hDepartment of Biology, Stanford University, Stanford, CA 94305; iDepartment of Rancho La Brea, Natural History Museum of Los Angeles County, Los Angeles, -
Aberrant Human Tissue Kallikrein Levels in the Stratum Corneum and Serum of Patients with Psoriasis: Dependence on Phenotype, Severity and Therapy N
CLINICAL AND LABORATORY INVESTIGATIONS DOI 10.1111/j.1365-2133.2006.07743.x Aberrant human tissue kallikrein levels in the stratum corneum and serum of patients with psoriasis: dependence on phenotype, severity and therapy N. Komatsu,* à K. Saijoh,§ C. Kuk,* F. Shirasaki,à K. Takeharaà and E.P. Diamandis* *Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5G 1L5, Canada àDepartment of Dermatology and §Department of Hygiene, Graduate School of Medical Science, School of Medicine, Kanazawa University, Kanazawa, Japan Summary Correspondence Background Human tissue kallikreins (KLKs) are a family of 15 trypsin-like or Eleftherios P. Diamandis. chymotrypsin-like secreted serine proteases (KLK1–KLK15). Multiple KLKs have E-mail: [email protected] been quantitatively identified in normal stratum corneum (SC) and sweat as can- didate desquamation-related proteases. Accepted for publication 7 November 2006 Objectives To quantify KLK5, KLK6, KLK7, KLK8, KLK10, KLK11, KLK13 and KLK14 in the SC and serum of patients with psoriasis, and their variation Key words between lesional and nonlesional areas and with phenotype, therapy and severity. diagnostic marker, human kallikreins, psoriasis, The overall SC serine protease activities were also measured. serine proteases, stratum corneum, therapy Methods Enzyme-linked immunosorbent assays and enzymatic assays were used. Conflicts of interest Results The lesional SC of psoriasis generally contained significantly higher levels None declared. of all KLKs. KLK6, KLK10 and KLK13 levels were significantly elevated even in the nonlesional SC. The overall trypsin-like, plasmin-like and furin-like activities were significantly elevated in the lesional SC. -
KLK15 Is a Prognostic Marker for Progression?
IJC International Journal of Cancer KLK15 is a prognostic marker for progression-free survival in patients with radical prostatectomy Anja Rabien1, Florian R. Fritzsche2,3, Monika Jung1, Angelika To¨lle1, Eleftherios P. Diamandis4, Kurt Miller1, Klaus Jung1,5, Glen Kristiansen2,3y and Carsten Stephan1,3y 1 Department of Urology, Charite´ - Universita¨tsmedizin Berlin, Campus Charite´ Mitte, Berlin, Germany 2 Institute of Pathology, Charite´ - Universita¨tsmedizin Berlin, Campus Charite´ Mitte, Berlin, Germany 3 Institute of Pathology, Universita¨tsspital Zu¨rich, Zu¨rich, Switzerland 4 Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada 5 Berlin Institute for Urologic Research, Berlin, Germany In search of biomarkers for prostate cancer, we evaluated the expression of the human kallikrein-related peptidase KLK15 in samples of prostatic adenocarcinomas from radical prostatectomies. Twenty-five pairs of cancerous and adjacent normal prostatic tissue were selected by laser capture microdissection. The tissue was used for quantification of KLK15 mRNA by reverse-transcriptase polymerase chain reaction. Immunohistochemical expression of the KLK15 protein in 193 samples of prostatic adenocarcinoma was analysed in relation to clinicopathological parameters of the patients and disease progression. Expression of KLK15 correlated with the pathological tumour stage and Gleason score of the cases, both at mRNA and at protein level. While mRNA expression in the tumour was elevated, the protein level of KLK15 was reduced compared with adjacent normal tissue and to prostatic intraepithelial neoplasia. Univariate Kaplan-Meier analysis showed a significant association of dichotomised KLK15 levels with disease progression defined by prostate-specific antigen relapse (p 5 0.001). -
Human Tissue Kallikrein Expression in the Stratum Corneum and Serum of Atopic Dermatitis Patients
DOI:10.1111/j.1600-0625.2007.00562.x www.blackwellpublishing.com/EXD Original Article Human tissue kallikrein expression in the stratum corneum and serum of atopic dermatitis patients Nahoko Komatsu1,2,3,4, Kiyofumi Saijoh4, Cynthia Kuk1, Amber C. Liu1, Saba Khan1, Fumiaki Shirasaki3, Kazuhiko Takehara3 and Eleftherios P. Diamandis1,2 1Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada; 2Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; 3Department of Dermatology, Graduate School of Medical Science, School of Medicine, Kanazawa University, Kanazawa, Japan; 4Department of Hygiene, Graduate School of Medical Science, School of Medicine, Kanazawa University, Kanazawa, Japan Correspondence: Eleftherios P. Diamandis, MD, PhD, FRCPC, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada, Tel.: +1 416 586 8443, Fax: +1 416 586 8628, e-mail: [email protected] Accepted for publication 9 March 2007 Abstract: Human tissue kallikreins are a family of 15 trypsin- or differ significantly. In the serum of AD patients, KLK8 was chymotrypsin-like secreted serine proteases (KLK1–KLK15). Many significantly elevated and KLK5 and KLK11 were significantly KLKs have been identified in normal stratum corneum (SC) and decreased. However, their serum levels were not modified by sweat, and are candidate desquamation-related proteases. We corticosteroid topical agents. The alterations of KLK levels in the report quantification by enzyme-linked immunosorbent assay SC of AD were more pronounced than those in the serum. KLK7 (ELISA) of KLK5, KLK6, KLK7, KLK8, KLK10, KLK11, KLK13 and in the serum was significantly correlated with eosinophil counts in KLK14 in the SC and serum of atopic dermatitis (AD) patients by the blood of AD patients, while KLK5, KLK8 and KLK11 were ELISA, and examine their variation with clinical phenotype, significantly correlated with LDH in the serum. -
Development and Validation of a Protein-Based Risk Score for Cardiovascular Outcomes Among Patients with Stable Coronary Heart Disease
Supplementary Online Content Ganz P, Heidecker B, Hveem K, et al. Development and validation of a protein-based risk score for cardiovascular outcomes among patients with stable coronary heart disease. JAMA. doi: 10.1001/jama.2016.5951 eTable 1. List of 1130 Proteins Measured by Somalogic’s Modified Aptamer-Based Proteomic Assay eTable 2. Coefficients for Weibull Recalibration Model Applied to 9-Protein Model eFigure 1. Median Protein Levels in Derivation and Validation Cohort eTable 3. Coefficients for the Recalibration Model Applied to Refit Framingham eFigure 2. Calibration Plots for the Refit Framingham Model eTable 4. List of 200 Proteins Associated With the Risk of MI, Stroke, Heart Failure, and Death eFigure 3. Hazard Ratios of Lasso Selected Proteins for Primary End Point of MI, Stroke, Heart Failure, and Death eFigure 4. 9-Protein Prognostic Model Hazard Ratios Adjusted for Framingham Variables eFigure 5. 9-Protein Risk Scores by Event Type This supplementary material has been provided by the authors to give readers additional information about their work. Downloaded From: https://jamanetwork.com/ on 10/02/2021 Supplemental Material Table of Contents 1 Study Design and Data Processing ......................................................................................................... 3 2 Table of 1130 Proteins Measured .......................................................................................................... 4 3 Variable Selection and Statistical Modeling ........................................................................................ -
Supplementary Material Contents
Supplementary Material Contents Immune modulating proteins identified from exosomal samples.....................................................................2 Figure S1: Overlap between exosomal and soluble proteomes.................................................................................... 4 Bacterial strains:..............................................................................................................................................4 Figure S2: Variability between subjects of effects of exosomes on BL21-lux growth.................................................... 5 Figure S3: Early effects of exosomes on growth of BL21 E. coli .................................................................................... 5 Figure S4: Exosomal Lysis............................................................................................................................................ 6 Figure S5: Effect of pH on exosomal action.................................................................................................................. 7 Figure S6: Effect of exosomes on growth of UPEC (pH = 6.5) suspended in exosome-depleted urine supernatant ....... 8 Effective exosomal concentration....................................................................................................................8 Figure S7: Sample constitution for luminometry experiments..................................................................................... 8 Figure S8: Determining effective concentration .........................................................................................................