Acinar Cell Apoptosis in Serpini2-Deficient Mice Models Pancreatic Insufficiency
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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. -
Analysis of Dynamic Molecular Networks for Pancreatic Ductal
Pan et al. Cancer Cell Int (2018) 18:214 https://doi.org/10.1186/s12935-018-0718-5 Cancer Cell International PRIMARY RESEARCH Open Access Analysis of dynamic molecular networks for pancreatic ductal adenocarcinoma progression Zongfu Pan1†, Lu Li2†, Qilu Fang1, Yiwen Zhang1, Xiaoping Hu1, Yangyang Qian3 and Ping Huang1* Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest solid tumors. The rapid progression of PDAC results in an advanced stage of patients when diagnosed. However, the dynamic molecular mechanism underlying PDAC progression remains far from clear. Methods: The microarray GSE62165 containing PDAC staging samples was obtained from Gene Expression Omnibus and the diferentially expressed genes (DEGs) between normal tissue and PDAC of diferent stages were profled using R software, respectively. The software program Short Time-series Expression Miner was applied to cluster, compare, and visualize gene expression diferences between PDAC stages. Then, function annotation and pathway enrichment of DEGs were conducted by Database for Annotation Visualization and Integrated Discovery. Further, the Cytoscape plugin DyNetViewer was applied to construct the dynamic protein–protein interaction networks and to analyze dif- ferent topological variation of nodes and clusters over time. The phosphosite markers of stage-specifc protein kinases were predicted by PhosphoSitePlus database. Moreover, survival analysis of candidate genes and pathways was per- formed by Kaplan–Meier plotter. Finally, candidate genes were validated by immunohistochemistry in PDAC tissues. Results: Compared with normal tissues, the total DEGs number for each PDAC stage were 994 (stage I), 967 (stage IIa), 965 (stage IIb), 1027 (stage III), 925 (stage IV), respectively. The stage-course gene expression analysis showed that 30 distinct expressional models were clustered. -
Serpins—From Trap to Treatment
MINI REVIEW published: 12 February 2019 doi: 10.3389/fmed.2019.00025 SERPINs—From Trap to Treatment Wariya Sanrattana, Coen Maas and Steven de Maat* Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands Excessive enzyme activity often has pathological consequences. This for example is the case in thrombosis and hereditary angioedema, where serine proteases of the coagulation system and kallikrein-kinin system are excessively active. Serine proteases are controlled by SERPINs (serine protease inhibitors). We here describe the basic biochemical mechanisms behind SERPIN activity and identify key determinants that influence their function. We explore the clinical phenotypes of several SERPIN deficiencies and review studies where SERPINs are being used beyond replacement therapy. Excitingly, rare human SERPIN mutations have led us and others to believe that it is possible to refine SERPINs toward desired behavior for the treatment of enzyme-driven pathology. Keywords: SERPIN (serine proteinase inhibitor), protein engineering, bradykinin (BK), hemostasis, therapy Edited by: Marvin T. Nieman, Case Western Reserve University, United States INTRODUCTION Reviewed by: Serine proteases are the “workhorses” of the human body. This enzyme family is conserved Daniel A. Lawrence, throughout evolution. There are 1,121 putative proteases in the human body, and about 180 of University of Michigan, United States Thomas Renne, these are serine proteases (1, 2). They are involved in diverse physiological processes, ranging from University Medical Center blood coagulation, fibrinolysis, and inflammation to immunity (Figure 1A). The activity of serine Hamburg-Eppendorf, Germany proteases is amongst others regulated by a dedicated class of inhibitory proteins called SERPINs Paulo Antonio De Souza Mourão, (serine protease inhibitors). -
Correlation of Serpin–Protease Expression by Comparative Analysis of Real-Time PCR Profiling Data
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Genomics 88 (2006) 173–184 www.elsevier.com/locate/ygeno Correlation of serpin–protease expression by comparative analysis of real-time PCR profiling data Sunita Badola a, Heidi Spurling a, Keith Robison a, Eric R. Fedyk a, Gary A. Silverman b, ⁎ Jochen Strayle c, Rosana Kapeller a,1, Christopher A. Tsu a, a Millennium Pharmaceuticals, Inc., 40 Landsdowne Street, Cambridge, MA 02139, USA b Department of Pediatrics, University of Pittsburgh School of Medicine, Magee-Women’s Hospital, 300 Halket Street, Pittsburgh, PA 15213, USA c Bayer HealthCare AG, 42096 Wuppertal, Germany Received 2 December 2005; accepted 27 March 2006 Available online 18 May 2006 Abstract Imbalanced protease activity has long been recognized in the progression of disease states such as cancer and inflammation. Serpins, the largest family of endogenous protease inhibitors, target a wide variety of serine and cysteine proteases and play a role in a number of physiological and pathological states. The expression profiles of 20 serpins and 105 serine and cysteine proteases were determined across a panel of normal and diseased human tissues. In general, expression of serpins was highly restricted in both normal and diseased tissues, suggesting defined physiological roles for these protease inhibitors. A high correlation in expression for a particular serpin–protease pair in healthy tissues was often predictive of a biological interaction. The most striking finding was the dramatic change observed in the regulation of expression between proteases and their cognate inhibitors in diseased tissues. -
View Preprint
A peer-reviewed version of this preprint was published in PeerJ on 16 June 2015. View the peer-reviewed version (peerj.com/articles/1026), which is the preferred citable publication unless you specifically need to cite this preprint. Kumar A. 2015. Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ∼500 MY. PeerJ 3:e1026 https://doi.org/10.7717/peerj.1026 Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ~500 MY Abhishek Kumar The serpin superfamily is characterized by proteins that fold into a conserved tertiary structure and exploits a sophisticated and irreversible suicide-mechanism of inhibition. Vertebrate serpins can be conveniently classified into six groups (V1-V6), based on three independent biological features - genomic organization, diagnostic amino acid sites and rare indels. However, this classification system was based on the limited number of mammalian genomes available. In this study, several non-mammalian genomes are used to validate this classification system, using the powerful Bayesian phylogenetic method. PrePrints This method supports the intron and indel based vertebrate classification and proves that serpins have been maintained from lampreys to humans for about 500 MY. Lampreys have less than 10 serpins, which expanded into 36 serpins in humans. The two expanding groups V1 and V2 have SERPINB1/SERPINB6 and SERPINA8/SERPIND1 as the ancestral serpins, respectively. Large clusters of serpins are formed by local duplications of these serpins in tetrapod genomes. Interestingly, the ancestral HCII/SERPIND1 locus (nested within PIK4CA) possesses group V4 serpin (A2APL1, homolog of α2-AP/SERPINF2 ) of lampreys; hence, pointing to the fact that group V4 might have originated from group V2. -
The Transcriptome of Pig Spermatozoa, and Its Role in Fertility
International Journal of Molecular Sciences Article The Transcriptome of Pig Spermatozoa, and Its Role in Fertility Manuel Alvarez-Rodriguez 1,* , Cristina Martinez 1, Dominic Wright 2, Isabel Barranco 3, Jordi Roca 4 and Heriberto Rodriguez-Martinez 1 1 Department of Biomedical & Clinical Sciences (BKV), BKH/Obstetrics & Gynaecology, Faculty of Medicine and Health Sciences, Linköping University, SE-58185 Linköping, Sweden; [email protected] (C.M.); [email protected] (H.R.-M.) 2 Department of Physics, Chemistry and Biology, Faculty of Science and Engineering, Linköping University, SE-58183 Linköping, Sweden; [email protected] 3 Biotechnology of Animal and Human Reproduction (TechnoSperm), Department of Biology, Institute of Food and Agricultural Technology, University of Girona, 17003 Girona, Spain; [email protected] 4 Department of Medicine and Animal Surgery, Faculty of Veterinary Medicine, International Campus for Higher Education and Research “Campus Mare Nostrum”, University of Murcia, 30100 Murcia, Spain; [email protected] * Correspondence: [email protected]; Tel.: +46-(0)729427883 Received: 6 February 2020; Accepted: 24 February 2020; Published: 25 February 2020 Abstract: In the study presented here we identified transcriptomic markers for fertility in the cargo of pig ejaculated spermatozoa using porcine-specific micro-arrays (GeneChip® miRNA 4.0 and GeneChip® Porcine Gene 1.0 ST). We report (i) the relative abundance of the ssc-miR-1285, miR-16, miR-4332, miR-92a, miR-671-5p, miR-4334-5p, miR-425-5p, miR-191, miR-92b-5p and miR-15b miRNAs, and (ii) the presence of 347 up-regulated and 174 down-regulated RNA transcripts in high-fertility breeding boars, based on differences of farrowing rate (FS) and litter size (LS), relative to low-fertility boars in the (Artificial Insemination) AI program. -
A Genomic Analysis of Rat Proteases and Protease Inhibitors
A genomic analysis of rat proteases and protease inhibitors Xose S. Puente and Carlos López-Otín Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, 33006-Oviedo, Spain Send correspondence to: Carlos López-Otín Departamento de Bioquímica y Biología Molecular Facultad de Medicina, Universidad de Oviedo 33006 Oviedo-SPAIN Tel. 34-985-104201; Fax: 34-985-103564 E-mail: [email protected] Proteases perform fundamental roles in multiple biological processes and are associated with a growing number of pathological conditions that involve abnormal or deficient functions of these enzymes. The availability of the rat genome sequence has opened the possibility to perform a global analysis of the complete protease repertoire or degradome of this model organism. The rat degradome consists of at least 626 proteases and homologs, which are distributed into five catalytic classes: 24 aspartic, 160 cysteine, 192 metallo, 221 serine, and 29 threonine proteases. Overall, this distribution is similar to that of the mouse degradome, but significatively more complex than that corresponding to the human degradome composed of 561 proteases and homologs. This increased complexity of the rat protease complement mainly derives from the expansion of several gene families including placental cathepsins, testases, kallikreins and hematopoietic serine proteases, involved in reproductive or immunological functions. These protease families have also evolved differently in the rat and mouse genomes and may contribute to explain some functional differences between these two closely related species. Likewise, genomic analysis of rat protease inhibitors has shown some differences with the mouse protease inhibitor complement and the marked expansion of families of cysteine and serine protease inhibitors in rat and mouse with respect to human. -
The Aggregation-Prone Intracellular Serpin SRP-2 Fails to Transit the ER in Caenorhabditis Elegans
GENETICS | INVESTIGATION The Aggregation-Prone Intracellular Serpin SRP-2 Fails to Transit the ER in Caenorhabditis elegans Richard M. Silverman, Erin E. Cummings, Linda P. O’Reilly, Mark T. Miedel, Gary A. Silverman, Cliff J. Luke, David H. Perlmutter, and Stephen C. Pak1 Departments of Pediatrics and Cell Biology, University of Pittsburgh School of Medicine, Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center and Magee–Womens Hospital Research Institute, Pittsburgh, Pennsylvania 15224 ABSTRACT Familial encephalopathy with neuroserpin inclusions bodies (FENIB) is a serpinopathy that induces a rare form of presenile dementia. Neuroserpin contains a classical signal peptide and like all extracellular serine proteinase inhibitors (serpins) is secreted via the endoplasmic reticulum (ER)–Golgi pathway. The disease phenotype is due to gain-of-function missense mutations that cause neuroserpin to misfold and aggregate within the ER. In a previous study, nematodes expressing a homologous mutation in the endogenous Caenorhabditis elegans serpin, srp-2,werereportedtomodeltheERproteotoxicityinducedbyanallele of mutant neuroserpin. Our results suggest that SRP-2 lacksaclassicalN-terminalsignalpeptideandisamemberofthe intracellular serpin family. Using confocal imaging and an ER colocalization marker, we confirmed that GFP-tagged wild-type SRP-2 localized to the cytosol and not the ER. Similarly, the aggregation- prone SRP-2 mutant formed intracellular inclusions that localized to the cytosol. Interestingly, wild-type SRP-2,targetedtotheERbyfusion to a cleavable N-terminal signal peptide, failedtobesecretedandaccumulatedwithintheERlumen.ThisERretentionphenotypeistypical of other obligate intracellular serpins forced to translocate across the ER membrane. Neuroserpin is a secreted protein that inhibits trypsin- like proteinase. SRP-2 is a cytosolic serpin that inhibits lysosomal cysteine peptidases. We concluded that SRP-2 is neither an ortholog nor a functional homolog of neuroserpin. -
(12) United States Patent (10) Patent No.: US 7,951,382 B2 Gelber Et Al
US007951382B2 (12) United States Patent (10) Patent No.: US 7,951,382 B2 Gelber et al. (45) Date of Patent: May 31, 2011 (54) METHODS FORTREATMENT OF TYPE 2 WO O3,O14151 A2 2/2003 DABETES WO 2004/084797 A2 10, 2004 WO 2005/055956 6, 2005 (75) Inventors: Cohava Gelber, Nokesville, VA (US); W 38885 33.9 Liping Liu, Manassas, VA (US); Zhidong Xie, Manassas, VA (US); OTHER PUBLICATIONS Pranvera Ikonomi, Manassas, VA (US); Antibody Directory (2006), Antichymotrypsin, 3 pages. John R Simms, Haymarket, VA (US); Belagaje et al. (1979) The Journal of Biochemistry 254:5765-5780. Catherine R Auge, Haymarket, VA (US) Better et al. (1988), Science 240: 1041-1043. Boulianne et al. (1984), Nature 312:643-646. (73) Assignee: American Type Culture Collection, Budde et al. (2005), Combinatorial Chemistry & High Throughput Manassas, VA (US) Screening 8:775-781. Burke et al. (1999), Arch. Intern. Med. 159: 1450-1456. (*) Notice: Subject to any disclaimer, the term of this Cabilly et al. (1984) Proc. Natl. Acad. Sci. USA 81:3273-3277. patent is extended or adjusted under 35 Chater et al. (1986) In: Sixth International Symposium on U.S.C. 154(b) by 0 days. Actinomycetales Biology, Akademiai Kaido, Budapest, Hungary pp. 45-54. (21) Appl. No.: 12/759,072 DeLong et al. (1988) Biometrics 44:837-845. Eddy et al. (2003) Diabetes Care 26:3102-31 10. (22) Filed: Apr. 13, 2010 Eddy et al. (2003) Diabetes Care 26:3093-3101. Glover (1985) ed. DNA Cloning vol. II. pp. 143-238, IRL Press. (65) Prior Publication Data Glover (1985) ed. -
UNIVERSITÄTSKLINIKUM HAMBURG-EPPENDORF An
UNIVERSITÄTSKLINIKUM HAMBURG-EPPENDORF Zentrum für Diagnostik / Institut für Neuropathologie Direktor Prof. Dr. med. Markus Glatzel An investigation of interaction between Neuroserpin and its putative targets PC1/3, PC2 and Furin with a YFP-protein complementation assay Dissertation zur Erlangung des Grades eines Doktors der Medizin an der Medizinischen Fakultät der Universität Hamburg. vorgelegt von: Felix Johannes Alfred Wiesmüller aus Regensburg Hamburg 2015 (wird von der Medizinischen Fakultät ausgefüllt) Angenommen von der Medizinischen Fakultät der Universität Hamburg am: 07.12.2015 Veröffentlicht mit Genehmigung der Medizinischen Fakultät der Universität Hamburg. Prüfungsausschuss, der/die Vorsitzende: Prof. Dr. Markus Glatzel Prüfungsausschuss, zweite/r Gutachter/in: Prof. Dr. Hans-Jürgen Kreienkamp Prüfungsausschuss, dritte/r Gutachter/in: 2 Index 1. Introduction ....................................................................................................................... 5 1.1. Neuroserpin .................................................................................................................. 5 1.1.1. Discovery .................................................................................................... 5 1.1.2. Serpin family and serpin kinetics ................................................................ 6 1.1.3. Neuroserpin gene and regulation of expression .......................................... 9 1.1.4. 3D crystal structure .................................................................................. -
Bayesian Phylogeny Analysis of Vertebrate Serpins Illustrates
Bayesian phylogeny analysis of vertebrate serpins illustrates evolutionary conservation of the intron and indels based six groups classification system from lampreys for ∼500 MY Abhishek Kumar Department of Genetics & Molecular Biology in Botany, Institute of Botany, Christian-Albrechts-University at Kiel, Kiel, Germany Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany ABSTRACT The serpin superfamily is characterized by proteins that fold into a conserved tertiary structure and exploits a sophisticated and irreversible suicide-mechanism of inhibition. Vertebrate serpins are classified into six groups (V1–V6), based on three independent biological features—genomic organization, diagnostic amino acid sites and rare indels. However, this classification system was based on the limited number of mammalian genomes available. In this study, several non-mammalian genomes are used to validate this classification system using the powerful Bayesian phylogenetic method. This method supports the intron and indel based vertebrate classification and proves that serpins have been maintained from lampreys to humans for about 500 MY. Lampreys have fewer than 10 serpins, which expand into 36 serpins in humans. The two expanding groups V1 and V2 have SERPINB1/SERPINB6 and SERPINA8/SERPIND1 as the ancestral serpins, respectively. Large clusters of serpins are formed by local duplications of these serpins Submitted 22 March 2015 in tetrapod genomes. Interestingly, the ancestral HCII/SERPIND1 locus (nested Accepted 26 May 2015 within PIK4CA) possesses group V4 serpin (A2APL1, homolog of α2-AP/SERPINF2) Published 16 June 2015 of lampreys; hence, pointing to the fact that group V4 might have originated from Corresponding author group V2. Additionally in this study, details of the phylogenetic history and genomic Abhishek Kumar, ab- characteristics of vertebrate serpins are revisited. -
Key Drug-Targeting Genes in Pancreatic Ductal Adenocarcinoma
www.genesandcancer.com Genes & Cancer, Volume 12, 2021 Research Paper Key drug-targeting genes in pancreatic ductal adenocarcinoma Meena Kishore Sakharkar1, Sarinder Kaur Dhillon2, Mohit Mazumder3 and Jian Yang1 1 Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, Canada 2 Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia 3 School of Life Sciences, Jawaharlal Nehru University, New Delhi, India Correspondence to: Meena Kishore Sakharkar, email: [email protected] and Jian Yang, email: [email protected] Keywords: pancreatic ductal adenocarcinoma; differentially expressed genes; protein-protein interaction network (PPI); fibronec- tin 1; serpin peptidase inhibitor B5 Received: November 11, 2020 Accepted: January 21, 2021 Published: March 11, 2021 Copyright: © 2021 Sakharkar et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal type of cancer. In this study, we undertook a pairwise comparison of gene expression pattern between tumor tissue and its matching adjacent normal tissue for 45 PDAC patients and identified 22 upregulated and 32 downregulated genes. PPI network revealed that fibronectin 1 and serpin peptidase inhibitor B5 were the most interconnected upregulated-nodes. Virtual screening identified bleomycin exhibited reasonably strong binding to both proteins. Effect of bleomycin on cell viability was examined against two PDAC cell lines, AsPC-1 and MIA PaCa-2. AsPC-1 did not respond to bleomycin, however, MIA PaCa-2 responded to bleomycin with an IC50 of 2.6 μM.