Expression Profiling of Metalloproteinases and Their
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Role of Cyclosporine in Gingival Hyperplasia: an in Vitro Study on Gingival Fibroblasts
International Journal of Molecular Sciences Article Role of Cyclosporine in Gingival Hyperplasia: An In Vitro Study on Gingival Fibroblasts 1, , 2, 3 3 Dorina Lauritano * y , Annalisa Palmieri y, Alberta Lucchese , Dario Di Stasio , Giulia Moreo 1 and Francesco Carinci 4 1 Department of Medicine and Surgery, Centre of Neuroscience of Milan, University of Milano-Bicocca, 20126 Milan, Italy; [email protected] 2 Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, via Belmoro 8, 40126 Bologna, Italy; [email protected] 3 Multidisciplinary Department of Medical and Dental Specialties, University of Campania-Luigi Vanvitelli, 80138 Naples, Italy; [email protected] (A.L.); [email protected] (D.D.S.) 4 Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, 44121 Ferrara, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-335-679-0163 These authors contributed equally to this work. y Received: 25 November 2019; Accepted: 13 January 2020; Published: 16 January 2020 Abstract: Background: Gingival hyperplasia could occur after the administration of cyclosporine A. Up to 90% of the patients submitted to immunosuppressant drugs have been reported to suffer from this side effect. The role of fibroblasts in gingival hyperplasia has been widely discussed by literature, showing contrasting results. In order to demonstrate the effect of cyclosporine A on the extracellular matrix component of fibroblasts, we investigated the gene expression profile of human fibroblasts after cyclosporine A administration. Materials and methods: Primary gingival fibroblasts were stimulated with 1000 ng/mL cyclosporine A solution for 16 h. Gene expression levels of 57 genes belonging to the “Extracellular Matrix and Adhesion Molecules” pathway were analyzed using real-time PCR in treated cells, compared to untreated cells used as control. -
Smooth Muscle-Specific MMP17 (MT4-MMP) Defines the Intestinal ECM Niche 2 3 Mara Martín-Alonso1*, Håvard T
bioRxiv preprint doi: https://doi.org/10.1101/2020.06.18.147769; this version posted June 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Smooth muscle-specific MMP17 (MT4-MMP) defines the intestinal ECM niche 2 3 Mara Martín-Alonso1*, Håvard T. Lindholm1,# , Sharif Iqbal2,3,#, Pia Vornewald1#, Sigrid Hoel1, 4 Mirjam J. Damen4, A.F.Maarten Altelaar4, Pekka Katajisto2,3,5, Alicia G. Arroyo6,7, Menno J. 5 Oudhoff1* 6 7 1CEMIR – Centre of Molecular Inflammation Research, Department of Clinical and Molecular 8 Medicine, NTNU – Norwegian University of Science and Technology, 7491 Trondheim, 9 Norway 10 2Institute of Biotechnology, HiLIFE, University of Helsinki, Finland 11 3Molecular and Integrative Bioscience Research Programme, Faculty of Biological and 12 Environmental Sciences, University of Helsinki, Helsinki, Finland 13 4Biomolecular Mass Spectrometry and Proteomics, Utrecht University, Utrecht, The 14 Netherlands 15 5Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden 16 6Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain 17 7Vascular Pathophysiology Area, Centro Nacional de Investigaciones Cardiovasculares 18 (CNIC), Madrid, Spain.CNIC, Madrid, Spain 19 20 #These authors contributed equally to this work 21 *corresponding authors, e-mail: [email protected], [email protected] 22 bioRxiv preprint doi: https://doi.org/10.1101/2020.06.18.147769; this version posted June 18, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. -
Gene Symbol Category ACAN ECM ADAM10 ECM Remodeling-Related ADAM11 ECM Remodeling-Related ADAM12 ECM Remodeling-Related ADAM15 E
Supplementary Material (ESI) for Integrative Biology This journal is (c) The Royal Society of Chemistry 2010 Gene symbol Category ACAN ECM ADAM10 ECM remodeling-related ADAM11 ECM remodeling-related ADAM12 ECM remodeling-related ADAM15 ECM remodeling-related ADAM17 ECM remodeling-related ADAM18 ECM remodeling-related ADAM19 ECM remodeling-related ADAM2 ECM remodeling-related ADAM20 ECM remodeling-related ADAM21 ECM remodeling-related ADAM22 ECM remodeling-related ADAM23 ECM remodeling-related ADAM28 ECM remodeling-related ADAM29 ECM remodeling-related ADAM3 ECM remodeling-related ADAM30 ECM remodeling-related ADAM5 ECM remodeling-related ADAM7 ECM remodeling-related ADAM8 ECM remodeling-related ADAM9 ECM remodeling-related ADAMTS1 ECM remodeling-related ADAMTS10 ECM remodeling-related ADAMTS12 ECM remodeling-related ADAMTS13 ECM remodeling-related ADAMTS14 ECM remodeling-related ADAMTS15 ECM remodeling-related ADAMTS16 ECM remodeling-related ADAMTS17 ECM remodeling-related ADAMTS18 ECM remodeling-related ADAMTS19 ECM remodeling-related ADAMTS2 ECM remodeling-related ADAMTS20 ECM remodeling-related ADAMTS3 ECM remodeling-related ADAMTS4 ECM remodeling-related ADAMTS5 ECM remodeling-related ADAMTS6 ECM remodeling-related ADAMTS7 ECM remodeling-related ADAMTS8 ECM remodeling-related ADAMTS9 ECM remodeling-related ADAMTSL1 ECM remodeling-related ADAMTSL2 ECM remodeling-related ADAMTSL3 ECM remodeling-related ADAMTSL4 ECM remodeling-related ADAMTSL5 ECM remodeling-related AGRIN ECM ALCAM Cell-cell adhesion ANGPT1 Soluble factors and receptors -
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
(P -Value<0.05, Fold Change≥1.4), 4 Vs. 0 Gy Irradiation
Table S1: Significant differentially expressed genes (P -Value<0.05, Fold Change≥1.4), 4 vs. 0 Gy irradiation Genbank Fold Change P -Value Gene Symbol Description Accession Q9F8M7_CARHY (Q9F8M7) DTDP-glucose 4,6-dehydratase (Fragment), partial (9%) 6.70 0.017399678 THC2699065 [THC2719287] 5.53 0.003379195 BC013657 BC013657 Homo sapiens cDNA clone IMAGE:4152983, partial cds. [BC013657] 5.10 0.024641735 THC2750781 Ciliary dynein heavy chain 5 (Axonemal beta dynein heavy chain 5) (HL1). 4.07 0.04353262 DNAH5 [Source:Uniprot/SWISSPROT;Acc:Q8TE73] [ENST00000382416] 3.81 0.002855909 NM_145263 SPATA18 Homo sapiens spermatogenesis associated 18 homolog (rat) (SPATA18), mRNA [NM_145263] AA418814 zw01a02.s1 Soares_NhHMPu_S1 Homo sapiens cDNA clone IMAGE:767978 3', 3.69 0.03203913 AA418814 AA418814 mRNA sequence [AA418814] AL356953 leucine-rich repeat-containing G protein-coupled receptor 6 {Homo sapiens} (exp=0; 3.63 0.0277936 THC2705989 wgp=1; cg=0), partial (4%) [THC2752981] AA484677 ne64a07.s1 NCI_CGAP_Alv1 Homo sapiens cDNA clone IMAGE:909012, mRNA 3.63 0.027098073 AA484677 AA484677 sequence [AA484677] oe06h09.s1 NCI_CGAP_Ov2 Homo sapiens cDNA clone IMAGE:1385153, mRNA sequence 3.48 0.04468495 AA837799 AA837799 [AA837799] Homo sapiens hypothetical protein LOC340109, mRNA (cDNA clone IMAGE:5578073), partial 3.27 0.031178378 BC039509 LOC643401 cds. [BC039509] Homo sapiens Fas (TNF receptor superfamily, member 6) (FAS), transcript variant 1, mRNA 3.24 0.022156298 NM_000043 FAS [NM_000043] 3.20 0.021043295 A_32_P125056 BF803942 CM2-CI0135-021100-477-g08 CI0135 Homo sapiens cDNA, mRNA sequence 3.04 0.043389246 BF803942 BF803942 [BF803942] 3.03 0.002430239 NM_015920 RPS27L Homo sapiens ribosomal protein S27-like (RPS27L), mRNA [NM_015920] Homo sapiens tumor necrosis factor receptor superfamily, member 10c, decoy without an 2.98 0.021202829 NM_003841 TNFRSF10C intracellular domain (TNFRSF10C), mRNA [NM_003841] 2.97 0.03243901 AB002384 C6orf32 Homo sapiens mRNA for KIAA0386 gene, partial cds. -
NIH Public Access Author Manuscript Crit Rev Eukaryot Gene Expr
NIH Public Access Author Manuscript Crit Rev Eukaryot Gene Expr. Author manuscript; available in PMC 2010 July 19. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Crit Rev Eukaryot Gene Expr. 2008 ; 18(3): 251±278. Matrix Metalloproteinase Control of Capillary Morphogenesis Cyrus M Ghajar1, Steven C George1,2, and Andrew J Putnam1,2,3,† 1Department of Biomedical Engineering, University of California, Irvine; Irvine, CA 92697 2Department of Chemical Engineering and Materials Science, University of California, Irvine; Irvine, CA 92697 3Chao Family Comprehensive Cancer Center, University of California, Irvine; Irvine, CA 92697 Abstract Matrix metalloproteinases (MMPs) play crucial roles in a variety of normal (e.g. blood vessel formation, bone development) and pathophysiological (e.g. wound healing, cancer) processes. This is not only due to their ability to degrade the surrounding extracellular matrix (ECM), but also because MMPs function to reveal cryptic matrix binding sites, release matrix-bound growth factors inherent to these processes, and activate a variety of cell surface molecules. The process of blood vessel formation, in particular, is regulated by what is widely classified as the angiogenic switch: a mixture of both pro- and anti-angiogenic factors that function to counteract each other unless the stimuli from one side exceeds the other to disrupt the quiescent state. While it was initially thought that MMPs were strictly pro-angiogenic, new functions for this proteolytic family such as mediating vascular regression and generating matrix fragments with antiangiogenic capacities have been discovered in the last decade. These findings cast MMPs as multi-faceted pro- and anti-angiogenic effectors. -
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 ........................................................................................ -
Importance of Altered Gene Expression of Metalloproteinases 2, 9, and 16 in Acute Myeloid Leukemia: Preliminary Study
Hindawi Journal of Oncology Volume 2021, Article ID 6697975, 8 pages https://doi.org/10.1155/2021/6697975 Research Article Importance of Altered Gene Expression of Metalloproteinases 2, 9, and 16 in Acute Myeloid Leukemia: Preliminary Study Jacek Pietrzak , Marek Mirowski , Rafał S´wiechowski , Damian Wodzin´ ski , Agnieszka Wosiak , Katarzyna Michalska , and Ewa Balcerczak Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Laboratory of Molecular Diagnostics and Pharmacogenomics, Medical University of Lodz, Muszynskiego 1, Lodz 90-151, Poland Correspondence should be addressed to Jacek Pietrzak; [email protected] Received 14 December 2020; Revised 13 April 2021; Accepted 29 April 2021; Published 7 May 2021 Academic Editor: Liren Qian Copyright © 2021 Jacek Pietrzak et al. +is is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Acute myeloid leukemia is a group of hematological neoplasms characterized by a heterogeneous course and high mortality. +e important factor in the neoplastic process is metalloproteinases, proteolytic enzymes capable of degrading various components of the extracellular matrix, which take an active part in modifying the functioning of the cell, including transformation to cancer cell. +ey interact with numerous signaling pathways responsible for the process of cell growth, proliferation, or apoptosis. In the present study, changes in the expression of MMP2, MMP9, and MMP16 genes between patients with AML and people without cancer were examined. +e impact of cytogenetic changes in neoplastic cells on the expression level of MMP2, MMP9, and MMP16 was also assessed, as well as the impact of the altered expression on the effectiveness of the first cycle of remission- inducing therapy. -
Supplementary Table 1 Genes Tested in Qrt-PCR in Nfpas
Supplementary Table 1 Genes tested in qRT-PCR in NFPAs Gene Bank accession Gene Description number ABI assay ID a disintegrin-like and metalloprotease with thrombospondin type 1 motif 7 ADAMTS7 NM_014272.3 Hs00276223_m1 Rho guanine nucleotide exchange factor (GEF) 3 ARHGEF3 NM_019555.1 Hs00219609_m1 BCL2-associated X protein BAX NM_004324 House design Bcl-2 binding component 3 BBC3 NM_014417.2 Hs00248075_m1 B-cell CLL/lymphoma 2 BCL2 NM_000633 House design Bone morphogenetic protein 7 BMP7 NM_001719.1 Hs00233476_m1 CCAAT/enhancer binding protein (C/EBP), alpha CEBPA NM_004364.2 Hs00269972_s1 coxsackie virus and adenovirus receptor CXADR NM_001338.3 Hs00154661_m1 Homo sapiens Dicer1, Dcr-1 homolog (Drosophila) (DICER1) DICER1 NM_177438.1 Hs00229023_m1 Homo sapiens dystonin DST NM_015548.2 Hs00156137_m1 fms-related tyrosine kinase 3 FLT3 NM_004119.1 Hs00174690_m1 glutamate receptor, ionotropic, N-methyl D-aspartate 1 GRIN1 NM_000832.4 Hs00609557_m1 high-mobility group box 1 HMGB1 NM_002128.3 Hs01923466_g1 heterogeneous nuclear ribonucleoprotein U HNRPU NM_004501.3 Hs00244919_m1 insulin-like growth factor binding protein 5 IGFBP5 NM_000599.2 Hs00181213_m1 latent transforming growth factor beta binding protein 4 LTBP4 NM_001042544.1 Hs00186025_m1 microtubule-associated protein 1 light chain 3 beta MAP1LC3B NM_022818.3 Hs00797944_s1 matrix metallopeptidase 17 MMP17 NM_016155.4 Hs01108847_m1 myosin VA MYO5A NM_000259.1 Hs00165309_m1 Homo sapiens nuclear factor (erythroid-derived 2)-like 1 NFE2L1 NM_003204.1 Hs00231457_m1 oxoglutarate (alpha-ketoglutarate) -
Gene Expression Responses in a Cellular Model of Parkinson's Disease
Gene Expression Responses in a Cellular Model of Parkinson's Disease Louis Beverly Brill II Manassas, Virginia B.A., Johns Hopkins University, 1995 A Dissertation presented to the Graduate Faculty of the University of Virginia in Candidacy for the Degree of Doctor of Philosophy Department of Cell Biology University of Virginia May, 2004 Table of Contents Chapter 1 . 1 Chapter 2 . 48 Chapter 3 . 87 Chapter 4 . 123 Chapter 5 . 133 References . 137 Appendix A . 163 Appendix B . 209 Appendix C . 216 Appendix D . 223 Appendix E . 232 Appendix F . 234 Appendix G . 283 Appendix H . 318 Appendix I . 324 Abstract This research represents initial steps towards understanding the relation between changes in gene expression, mitochondrial function and cell death in cell-based models of Parkinson’s disease. The main hypothesis is that rapid gene expression changes in cells exposed to parkinsonian neurotoxins occur, are dependent on mitochondrial status, and directly impact intracellular signaling pathways that determine whether a cell lives or dies. Our cellular model is comprised of SH-SY5Y neuroblastoma cells exposed to the parkinsonian neurotoxin methylpyridinium ion. Transcriptomic changes are evaluated with nylon and glass-based cDNA microarray technology. Cardinal symptoms of Parkinson’s disease, characteristic pathological changes, therapeutic modalities, and current theories on the etiology of the disorder are discussed. Our results verify the existence of mitochondrial-nuclear signaling in the context of electron transport chain deficits, as well as suggesting the vital roles played in this process by previously described intracellular signaling pathways. These results will serve to direct future investigations into gene expression changes relevant to the processes of cell death and cell survival in our cellular model of Parkinson’s disease, and may provide important insights into the pathophysiology of the in vivo disease process. -
Extracellular Matrix Alterations in Metastatic Processes
International Journal of Molecular Sciences Review Extracellular Matrix Alterations in Metastatic Processes Mayra Paolillo * and Sergio Schinelli Department of Drug Sciences, University of Pavia, 27100 Pavia, Italy; [email protected] * Correspondence: [email protected] Received: 17 September 2019; Accepted: 30 September 2019; Published: 7 October 2019 Abstract: The extracellular matrix (ECM) is a complex network of extracellular-secreted macromolecules, such as collagen, enzymes and glycoproteins, whose main functions deal with structural scaffolding and biochemical support of cells and tissues. ECM homeostasis is essential for organ development and functioning under physiological conditions, while its sustained modification or dysregulation can result in pathological conditions. During cancer progression, epithelial tumor cells may undergo epithelial-to-mesenchymal transition (EMT), a morphological and functional remodeling, that deeply alters tumor cell features, leading to loss of epithelial markers (i.e., E-cadherin), changes in cell polarity and intercellular junctions and increase of mesenchymal markers (i.e., N-cadherin, fibronectin and vimentin). This process enhances cancer cell detachment from the original tumor mass and invasiveness, which are necessary for metastasis onset, thus allowing cancer cells to enter the bloodstream or lymphatic flow and colonize distant sites. The mechanisms that lead to development of metastases in specific sites are still largely obscure but modifications occurring in target tissue ECM are being intensively studied. Matrix metalloproteases and several adhesion receptors, among which integrins play a key role, are involved in metastasis-linked ECM modifications. In addition, cells involved in the metastatic niche formation, like cancer associated fibroblasts (CAF) and tumor associated macrophages (TAM), have been found to play crucial roles in ECM alterations aimed at promoting cancer cells adhesion and growth. -
EGFR Activation and Signaling in Cancer Cells Are Enhanced by the Membrane-Bound Metalloprotease MT4-MMP
Published OnlineFirst October 15, 2014; DOI: 10.1158/0008-5472.CAN-13-2994 Cancer Microenvironment and Immunology Research EGFR Activation and Signaling in Cancer Cells Are Enhanced by the Membrane-Bound Metalloprotease MT4-MMP Alexandra Paye1, Alice Truong1, Cassandre Yip1, Jonathan Cimino1, Silvia Blacher1, Carine Munaut1, Didier Cataldo1, Jean Michel Foidart1, Erik Maquoi1, Joelle Collignon2, Philippe Delvenne3, Guy Jerusalem2, Agnes Noel1, and Nor Eddine Sounni1 Abstract MT4-MMP (MMP-17) is a glycosylphosphatidyl inositol–anchored matrix metalloprotease expressed on the surface of cancer cells that promotes tumor growth and metastasis. In this report, we identify MT4-MMP as an important driver of cancer cell proliferation through CDK4 activation and retinoblastoma protein inactivation. We also determine a functional link between MT4-MMP and the growth factor receptor EGFR. Mechanistic experiments revealed direct association of MT4-MMP and its positive effects on EGFR phosphorylation in response to TGFa and EGF in cancer cells. Notably, the effects of MT4-MMP on proliferation and EGFR activation did not rely on metalloprotease activity. Clinically, MT4-MMP and EGFR expressions were correlated in human triple-negative breast cancer specimens. Altogether, our results identify MT4-MMP as a positive modifier of EGFR outside-in signaling that acts to cooperatively drive cancer cell proliferation. Cancer Res; 74(23); 6758–70. Ó2014 AACR. Introduction growth factors binding proteins, or the shedding of receptor – Tumor growth relies on cancer cell properties dysregulation ligands from the cell surface (9 12). Among proteinases that associated with an intense host tissue remodeling. Mitogenic modulate growth factor/growth factor receptor activities or signals consist mainly of growth factors and extracellular bioavailability are the zinc-binding endopeptidase family matrix (ECM) components acting through cell surface recep- including matrix metalloproteinases (MMP) and A disintegrin – tors (1).