Demethylation of TIMP2 and TIMP3 Inhibit Cell Proliferation, Migration and Invasion in Pituitary Adenoma
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A Single-Cell Transcriptional Atlas Identifies Extensive Heterogeneity in the Cellular Composition of Tendons
bioRxiv preprint doi: https://doi.org/10.1101/801266; this version posted October 10, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. A single-cell transcriptional atlas identifies extensive heterogeneity in the cellular composition of tendons Jacob B Swanson1, Andrea J De Micheli2, Nathaniel P Disser1, Leandro M Martinez1, Nicholas R Walker1,3, Benjamin D Cosgrove2, Christopher L Mendias1,3,* 1Hospital for Special Surgery, New York, NY, USA 2Meining School of Biomedical Engineering, Cornell University, Ithaca, NY, USA 3Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA *Corresponding Author Christopher Mendias, PhD Hospital for Special Surgery 535 E 70th St New York, NY 10021 USA +1 212-606-1785 [email protected] Keywords: tenocyte; tendon fibroblast; pericyte; single-cell RNA sequencing bioRxiv preprint doi: https://doi.org/10.1101/801266; this version posted October 10, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.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. Abstract Tendon is a dense, hypocellular connective tissue that transmits forces between muscles and bones. Cellular heterogeneity is increasingly recognized as an important factor in the biological basis of tissue homeostasis and disease, but little is known about the diversity of cells that populate tendon. Our objective was to explore the heterogeneity of cells in mouse Achilles tendons using single-cell RNA sequencing. We identified 13 unique cell types in tendons, including 4 previously undescribed populations of fibroblasts. -
The Diverse Roles of TIMP-3: Insights Into Degenerative Diseases of the Senescent Retina and Brain
cells Review The Diverse Roles of TIMP-3: Insights into Degenerative Diseases of the Senescent Retina and Brain Jennifer M. Dewing 1, Roxana O. Carare 1, Andrew J. Lotery 1,2 and J. Arjuna Ratnayaka 1,* 1 Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, MP806, Tremona Road, Southampton SO16 6YD, UK; [email protected] (J.M.D.); [email protected] (R.O.C.); [email protected] (A.J.L.) 2 Eye Unit, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK * Correspondence: [email protected]; Tel.: +44-238120-8183 Received: 13 November 2019; Accepted: 19 December 2019; Published: 21 December 2019 Abstract: Tissue inhibitor of metalloproteinase-3 (TIMP-3) is a component of the extracellular environment, where it mediates diverse processes including matrix regulation/turnover, inflammation and angiogenesis. Rare TIMP-3 risk alleles and mutations are directly linked with retinopathies such as age-related macular degeneration (AMD) and Sorsby fundus dystrophy, and potentially, through indirect mechanisms, with Alzheimer’s disease. Insights into TIMP-3 activities may be gleaned from studying Sorsby-linked mutations. However, recent findings do not fully support the prevailing hypothesis that a gain of function through the dimerisation of mutated TIMP-3 is responsible for retinopathy. Findings from Alzheimer’s patients suggest a hitherto poorly studied relationship between TIMP-3 and the Alzheimer’s-linked amyloid-beta (Aβ) proteins that warrant further scrutiny. This may also have implications for understanding AMD as aged/diseased retinae contain high levels of Aβ. Findings from TIMP-3 knockout and mutant knock-in mice have not led to new treatments, particularly as the latter does not satisfactorily recapitulate the Sorsby phenotype. -
Suramin Inhibits Osteoarthritic Cartilage Degradation by Increasing Extracellular Levels
Molecular Pharmacology Fast Forward. Published on August 10, 2017 as DOI: 10.1124/mol.117.109397 This article has not been copyedited and formatted. The final version may differ from this version. MOL #109397 Suramin inhibits osteoarthritic cartilage degradation by increasing extracellular levels of chondroprotective tissue inhibitor of metalloproteinases 3 (TIMP-3). Anastasios Chanalaris, Christine Doherty, Brian D. Marsden, Gabriel Bambridge, Stephen P. Wren, Hideaki Nagase, Linda Troeberg Arthritis Research UK Centre for Osteoarthritis Pathogenesis, Kennedy Institute of Downloaded from Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7FY, UK (A.C., C.D., G.B., H.N., L.T.); Alzheimer’s Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK (S.P.W.); Structural Genomics Consortium, molpharm.aspetjournals.org University of Oxford, Old Road Campus Research Building, Old Road Campus, Roosevelt Drive, Headington, Oxford, OX3 7DQ (BDM). at ASPET Journals on September 29, 2021 1 Molecular Pharmacology Fast Forward. Published on August 10, 2017 as DOI: 10.1124/mol.117.109397 This article has not been copyedited and formatted. The final version may differ from this version. MOL #109397 Running title: Repurposing suramin to inhibit osteoarthritic cartilage loss. Corresponding author: Linda Troeberg Address: Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7FY, UK Phone number: +44 (0)1865 612600 E-mail: [email protected] Downloaded -
Investigation of COVID-19 Comorbidities Reveals Genes and Pathways Coincident with the SARS-Cov-2 Viral Disease
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.21.306720; this version posted September 21, 2020. 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-ND 4.0 International license. Title: Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease. Authors: Mary E. Dolan1*,2, David P. Hill1,2, Gaurab Mukherjee2, Monica S. McAndrews2, Elissa J. Chesler2, Judith A. Blake2 1 These authors contributed equally and should be considered co-first authors * Corresponding author [email protected] 2 The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA Abstract: The emergence of the SARS-CoV-2 virus and subsequent COVID-19 pandemic initiated intense research into the mechanisms of action for this virus. It was quickly noted that COVID-19 presents more seriously in conjunction with other human disease conditions such as hypertension, diabetes, and lung diseases. We conducted a bioinformatics analysis of COVID-19 comorbidity-associated gene sets, identifying genes and pathways shared among the comorbidities, and evaluated current knowledge about these genes and pathways as related to current information about SARS-CoV-2 infection. We performed our analysis using GeneWeaver (GW), Reactome, and several biomedical ontologies to represent and compare common COVID- 19 comorbidities. Phenotypic analysis of shared genes revealed significant enrichment for immune system phenotypes and for cardiovascular-related phenotypes, which might point to alleles and phenotypes in mouse models that could be evaluated for clues to COVID-19 severity. -
Prognostic Significance of TIMP-1 in Non-Small Cell Lung Cancer
ANTICANCER RESEARCH 31: 4031-4038 (2011) Prognostic Significance of TIMP-1 in Non-small Cell Lung Cancer MARTIN PESTA1, VLASTIMIL KULDA2, RADEK KUCERA1, MILOS PESEK3, JINDRA VRZALOVA1, VACLAV LISKA4, LADISLAV PECEN1, VLADISLAV TRESKA4, JARMIL SAFRANEK4, MARKETA PRAZAKOVA1, ONDREJ VYCITAL4, JAN BRUHA4, LUBOS HOLUBEC5 and ONDREJ TOPOLCAN1 Departments of 1Internal Medicine II and 2Biochemistry, Faculty of Medicine in Pilsen, Charles University in Prague, Czech Republic; 3TRN Clinic, University Hospital and Medical Faculty in Pilsen, Czech Republic; Departments of 4Surgery and 5Oncology, University Teaching Hospital, Pilsen, Czech Republic Abstract. Tissue inhibitor of metalloproteinases 1 (TIMP1) the mortality 48.7/100 000 per year (1). Non-small cell lung regulates not only extracellular matrix catabolism but the cancer (NSCLC) accounts for 80% of all cases (2). major effect in tumor tissue is promotion of cell growth and Although there are tumor markers routinely used for solid anti-apoptotic activity. The aim of our study was to evaluate tumors, some of them having become gold standards (3), plasma TIMP1 levels and tissue TIMP1 mRNA expression as there is still an effort being made to search for new ones. prognostic markers in NSCLC patients. Patients and Tissue inhibitor of metalloproteinases 1 (TIMP1) has been Methods: We studied a group of 108 patients with NSCLC studied intensively over the last ten years and in colorectal who had undergone lung surgery. Estimation of TIMP1 cancer it seems to be promising as a prognostic marker in mRNA was performed by quantitative polymerase chain clinical use (4). A Danish-Australian endoscopy study group reaction (qPCR) and estimation of plasma TIMP1 protein on colorectal cancer detection is trying to use TIMP1 as a using enzyme-linked immunosorbent assay (ELISA). -
A Rare Penetrant TIMP3 Mutation Confers Relatively Late Onset Choroidal Neovascularisation Which Can Mimic Age-Related Macular D
Eye (2016) 30, 488–491 © 2016 Macmillan Publishers Limited All rights reserved 0950-222X/16 www.nature.com/eye 1,2 3 3 1,2 CASE SERIES A rare penetrant A Warwick , J Gibson , R Sood and A Lotery TIMP3 mutation confers relatively late onset choroidal neovascularisation which can mimic age-related macular degeneration Abstract world.1 Genetic predisposition is thought to play a role and to date 19 genetic loci have been Purpose To perform a genotype–phenotype correlation for three patients heterozygous for associated at a genome-wide level with an 2 a missense mutation in the tissue inhibitor of increased risk of developing AMD. ’ metalloproteinase 3 (TIMP3) gene. Sorsby s fundus dystrophy (SFD) is a rare autosomal dominant fundus dystrophy caused 1Clinical Neurosciences Methods Retrospective, observational case Research Group, Clinical series. The medical records and photographs by mutations in the tissue inhibitor of TIMP3 3 and Experimental Sciences, were reviewed for three patients diagnosed at metalloproteinase 3 ( ) gene. It shares Faculty of Medicine, the time with neovascular age-related macular similar clinical features with AMD, including University of choroidal neovascularisation (CNV), although Southampton, degeneration (AMD). All were later found to Southampton, UK carry a predicted C113G mutation in the TIMP3 the age of onset is typically younger in the fourth gene, other known mutations in which are decade of life. 2Eye Unit, University associated with Sorsby’sfundusdystrophy. We report the clinical phenotypes of three Southampton NHS Trust, Results All three patients developed drusen patients diagnosed at Southampton Eye Unit Southampton, UK and bilateral choroidal neovascularisation with with bilateral neovascular AMD before the subsequent disciform scarring and atrophy. -
Gene Regulation Underlies Environmental Adaptation in House Mice
Downloaded from genome.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Research Gene regulation underlies environmental adaptation in house mice Katya L. Mack,1 Mallory A. Ballinger,1 Megan Phifer-Rixey,2 and Michael W. Nachman1 1Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, California 94720, USA; 2Department of Biology, Monmouth University, West Long Branch, New Jersey 07764, USA Changes in cis-regulatory regions are thought to play a major role in the genetic basis of adaptation. However, few studies have linked cis-regulatory variation with adaptation in natural populations. Here, using a combination of exome and RNA- seq data, we performed expression quantitative trait locus (eQTL) mapping and allele-specific expression analyses to study the genetic architecture of regulatory variation in wild house mice (Mus musculus domesticus) using individuals from five pop- ulations collected along a latitudinal cline in eastern North America. Mice in this transect showed clinal patterns of variation in several traits, including body mass. Mice were larger in more northern latitudes, in accordance with Bergmann’s rule. We identified 17 genes where cis-eQTLs were clinal outliers and for which expression level was correlated with latitude. Among these clinal outliers, we identified two genes (Adam17 and Bcat2) with cis-eQTLs that were associated with adaptive body mass variation and for which expression is correlated with body mass both within and between populations. Finally, we per- formed a weighted gene co-expression network analysis (WGCNA) to identify expression modules associated with measures of body size variation in these mice. -
Matrisome-Associated Gene Expression Patterns Correlating with TIMP2 in Cancer David Peeney1*, Yu Fan2, Trinh Nguyen 2, Daoud Meerzaman2 & William G
www.nature.com/scientificreports OPEN Matrisome-Associated Gene Expression Patterns Correlating with TIMP2 in Cancer David Peeney1*, Yu Fan2, Trinh Nguyen 2, Daoud Meerzaman2 & William G. Stetler-Stevenson 1 Remodeling of the extracellular matrix (ECM) to facilitate invasion and metastasis is a universal hallmark of cancer progression. However, a defnitive therapeutic target remains to be identifed in this tissue compartment. As major modulators of ECM structure and function, matrix metalloproteinases (MMPs) are highly expressed in cancer and have been shown to support tumor progression. MMP enzymatic activity is inhibited by the tissue inhibitor of metalloproteinase (TIMP1–4) family of proteins, suggesting that TIMPs may possess anti-tumor activity. TIMP2 is a promiscuous MMP inhibitor that is ubiquitously expressed in normal tissues. In this study, we address inconsistencies in the literature regarding the role of TIMP2 in tumor progression by analyzing co-expressed genes in tumor vs. normal tissue. Utilizing data from The Cancer Genome Atlas and Genotype-Tissue expression studies, focusing on breast and lung carcinomas, we analyzed the correlation between TIMP2 expression and the transcriptome to identify a list of genes whose expression is highly correlated with TIMP2 in tumor tissues. Bioinformatic analysis of the identifed gene list highlights a core of matrix and matrix- associated genes that are of interest as potential modulators of TIMP2 function, thus ECM structure, identifying potential tumor microenvironment biomarkers and/or therapeutic targets for further study. Matrix metalloproteinases (MMPs) are a family of zinc-dependent endopeptidases that are the major mediators of extracellular matrix (ECM) breakdown and turnover. Humans express 23 MMPs and these play a critical role in tissue development, homeostasis and disease progression. -
Influence of LPS, TNF, TGF-ß1 and IL-4 on the Expression of Mmps, Timps and Selected Cytokines in Rat Synovial Membranes Incubated in Vitro
127-137.qxd 18/11/2010 09:29 Ì ™ÂÏ›‰·127 INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 27: 127-137, 2011 127 Influence of LPS, TNF, TGF-ß1 and IL-4 on the expression of MMPs, TIMPs and selected cytokines in rat synovial membranes incubated in vitro ANNA HYC, ANNA OSIECKA-IWAN, JUSTYNA NIDERLA-BIELINSKA and STANISLAW MOSKALEWSKI Department of Histology and Embryology, Medical University of Warsaw, Chalubinskiego 5 St., PL02-004 Warsaw, Poland Received July 30, 2010; Accepted September 28, 2010 DOI: 10.3892/ijmm.2010.550 Abstract. Synovial membranes are formed by four main Introduction types of cells, i.e. fibroblasts, macrophages, epitheliocytes and adipocytes. To study the combined effect of various The synovial membrane defined in anatomy textbooks as the factors on these cell populations, synovial membranes vascular connective tissue which produces the synovial fluid dissected from rat knee joints were incubated in control (1) is composed of the synovial lining and the subsynovium medium or medium with lipopolysaccharide (LPS), TNF, (2). The synovial lining, also called the synovial intima (3), TGF-ß1 or IL-4 for 12 h. LPS stimulated TNF secretion and consists of macrophage-like type A cells and fibroblast-like both agents stimulated secretion of IL-6. TGF-ß1 slightly B cells (4-6). It is supported by the highly vascularized increased IL-6 secretion. LPS increased the mRNA levels of subsynovium, consisting of loose alveolar tissue, dense fibrous IL-6, IL-1ß, TGF-ß1, MMP1a, MMP1b, MMP3, MMP9, tissue and fat pad (2). MMP13, MMP14, TIMP1 and TIMP3 while the mRNA Most of the studies on the cells present in the synovial levels of MMP2, TIMP2 and TIMP4 were significantly membrane deal with the cells forming the synovial lining decreased. -
Matrix Metalloproteinase9 As the Protein Target in Anti-Breast Cancer
Adhipandito et al. Future Journal of Pharmaceutical Sciences (2019) 5:1 Future Journal of https://doi.org/10.1186/s43094-019-0001-1 Pharmaceutical Sciences REVIEW Open Access Matrix metalloproteinase9 as the protein target in anti-breast cancer drug discovery: an approach by targeting hemopexin domain Christophorus Fideluno Adhipandito1, Diana Putri Kartika Sari Ludji1, Eko Aprilianto1, Riris Istighfari Jenie2, Belal Al-Najjar3 and Maywan Hariono1* Abstract Background: The discovery and development of anticancer still remain a challenge especially regarding the problem of cancer cell selectivity. Matrix metalloproteinase (MMP) was broadly studied as one of the protein targets to stop cancer angiogenesis as well as its cell migration. Main text: The MMP degrades extracellular matrix (ECM) such as collagen and gelatin which are important to control the cell migration from one to other sites. In cancer, this cell migration is regarded with metastasis, which is essential for the formation of new blood vessels called angiogenesis. The most common target in MMP, i.e. the catalytic site, is currently reported as being the non-selective target for inhibitor compounds that inhibit all MMPs but is associated with adverse side effects. Hemopexin, especially in MMP9 (PEX9) was found to be different from other domains in the MMP family which could potentially be the next target for anticancer due to the availability of its crystal structure in the Protein Data Bank (PDB). Conclusion: The PEX9 crystal structure was resolved as a homodimer connected by a hydrophobic area between two blades along the β-propeller which its structure and function for computational drug modelling can be studied. -
NEDD9 Depletion Leads to MMP14 Inactivation by TIMP2 and Prevents Invasion and Metastasis
Published OnlineFirst November 7, 2013; DOI: 10.1158/1541-7786.MCR-13-0300 Molecular Cancer Cell Death and Survival Research NEDD9 Depletion Leads to MMP14 Inactivation by TIMP2 and Prevents Invasion and Metastasis Sarah L. McLaughlin1, Ryan J. Ice1, Anuradha Rajulapati1, Polina Y. Kozyulina2, Ryan H. Livengood5, Varvara K. Kozyreva1, Yuriy V. Loskutov1, Mark V. Culp4, Scott A. Weed1,3, Alexey V. Ivanov1,2 and Elena N. Pugacheva1,2 Abstract The scaffolding protein NEDD9 is an established prometastatic marker in several cancers. Nevertheless, the molecular mechanisms of NEDD9-drivenmetastasisincancersremainill-defined. Here, using a compre- hensive breast cancer tissue microarray, it was shown that increased levels of NEDD9 protein significantly correlated with the transition from carcinoma in situ to invasive carcinoma. Similarly, it was shown that NEDD9 overexpression is a hallmark of highly invasive breast cancer cells. Moreover, NEDD9 expression is crucial for the protease-dependent mesenchymal invasion of cancer cells at the primary site but not at the metastatic site. Depletion of NEDD9 is sufficient to suppress invasion of tumor cells in vitro and in vivo, leading to decreased circulating tumor cells and lung metastases in xenograft models. Mechanistically, NEDD9 localized to invasive pseudopods and was required for local matrix degradation. Depletion of NEDD9 impaired invasion of cancer cells through inactivation of membrane-bound matrix metalloproteinase MMP14 by excess TIMP2 on the cell surface. Inactivation of MMP14 is accompanied by reduced collagenolytic activity of soluble metalloproteinases MMP2 and MMP9. Reexpression of NEDD9 is sufficient to restore the activity of MMP14 and the invasive properties of breast cancer cells in vitro and in vivo. -
Changes in Gene and Protein Expression of Metalloproteinase-2 and -9 and Their Inhibitors TIMP2 and TIMP3 in Different Parts of Fluoride-Exposed Rat Brain
International Journal of Molecular Sciences Article Changes in Gene and Protein Expression of Metalloproteinase-2 and -9 and Their Inhibitors TIMP2 and TIMP3 in Different Parts of Fluoride-Exposed Rat Brain Agnieszka Łukomska 1 , Irena Baranowska-Bosiacka 2, Karolina Dec 3, Anna Pilutin 4, Maciej Tarnowski 5 , Karolina Jakubczyk 3 , Wojciech Zwierełło˙ 1 , Marta Skórka-Majewicz 1 , Dariusz Chlubek 2 and Izabela Gutowska 1,* 1 Department of Medical Chemistry, Pomeranian Medical University, Powsta´nców Wlkp. 72 Av., 70-111 Szczecin, Poland; [email protected] (A.Ł.); [email protected] (W.Z.);˙ [email protected] (M.S.-M.) 2 Department of Biochemistry, Pomeranian Medical University, Powsta´nców Wlkp. 72 Av., 70-111 Szczecin, Poland; [email protected] (I.B.-B.); [email protected] (D.C.) 3 Department of Human Nutrition and Metabolomic, Pomeranian Medical University, Broniewskiego 24 Str., 71-460 Szczecin, Poland; [email protected] (K.D.); [email protected] (K.J.) 4 Department of Histology and Embryology, Pomeranian Medical University, Powsta´nców Wlkp. 72 Av., 70-111 Szczecin, Poland; [email protected] 5 Department of Physiology, Pomeranian Medical University, Powsta´nców Wlkp. 72 Av., 70-111 Szczecin, Poland; [email protected] * Correspondence: [email protected] Abstract: Fluoride (F) exposure decreases brain receptor activity and neurotransmitter production. Citation: Łukomska, A.; A recent study has shown that chronic fluoride exposure during childhood can affect cognitive func- Baranowska-Bosiacka, I.; Dec, K.; tion and decrease intelligence quotient, but the mechanism of this phenomenon is still incomplete. Pilutin, A.; Tarnowski, M.; Jakubczyk, Extracellular matrix (ECM) and its enzymes are one of the key players of neuroplasticity which is es- K.; Zwierełło,˙ W.; Skórka-Majewicz, sential for cognitive function development.