Placental Secretome Characterization Identifies Candidates for Pregnancy
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MEG8 Regulates Tissue Factor Pathway Inhibitor 2 (TFPI2) Expression in the Endothelium
MEG8 regulates Tissue Factor Pathway Inhibitor 2 (TFPI2) expression in the endothelium Veerle Kremer VU Medical Center, Amsterdam UMC Diewertje I. Bink VU Medical Center, Amsterdam UMC Laura Stanicek VU Medical Center, Amsterdam UMC Eva van Ingen Leiden University Medical Center Sarah Hilderink VU Medical Center, Amsterdam UMC Anne Yaël Nossent Leiden University Medical Center Reinier A. Boon ( [email protected] ) VU Medical Center, Amsterdam UMC Research Article Keywords: human umbilical vein endothelial cells (HUVECs), Tissue Factor Pathway Inhibitor 2 (TFPI2) Posted Date: August 13th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-800527/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/19 Abstract A large portion of the genome is transcribed into non-coding RNA, which does not encode protein. Many long non-coding RNAs (lncRNAs) have been shown to be involved in important regulatory processes such as genomic imprinting and chromatin modication. The 14q32 locus contains many non-coding RNAs such as Maternally Expressed Gene 8 (MEG8). We observed an induction of this gene in ischemic heart disease. We investigated the role of MEG8 specically in endothelial function as well as the underlying mechanism. We hypothesized that MEG8 plays an important role in cardiovascular disease via epigenetic regulation of gene expression. Experiments were performed in human umbilical vein endothelial cells (HUVECs). In vitro silencing of MEG8 resulted in impaired angiogenic sprouting. More specically, total sprout length was reduced as was proliferation, while migration was unaffected. We performed RNA sequencing to assess changes in gene expression after loss of MEG8. -
Protein Interaction Network of Alternatively Spliced Isoforms from Brain Links Genetic Risk Factors for Autism
ARTICLE Received 24 Aug 2013 | Accepted 14 Mar 2014 | Published 11 Apr 2014 DOI: 10.1038/ncomms4650 OPEN Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism Roser Corominas1,*, Xinping Yang2,3,*, Guan Ning Lin1,*, Shuli Kang1,*, Yun Shen2,3, Lila Ghamsari2,3,w, Martin Broly2,3, Maria Rodriguez2,3, Stanley Tam2,3, Shelly A. Trigg2,3,w, Changyu Fan2,3, Song Yi2,3, Murat Tasan4, Irma Lemmens5, Xingyan Kuang6, Nan Zhao6, Dheeraj Malhotra7, Jacob J. Michaelson7,w, Vladimir Vacic8, Michael A. Calderwood2,3, Frederick P. Roth2,3,4, Jan Tavernier5, Steve Horvath9, Kourosh Salehi-Ashtiani2,3,w, Dmitry Korkin6, Jonathan Sebat7, David E. Hill2,3, Tong Hao2,3, Marc Vidal2,3 & Lilia M. Iakoucheva1 Increased risk for autism spectrum disorders (ASD) is attributed to hundreds of genetic loci. The convergence of ASD variants have been investigated using various approaches, including protein interactions extracted from the published literature. However, these datasets are frequently incomplete, carry biases and are limited to interactions of a single splicing isoform, which may not be expressed in the disease-relevant tissue. Here we introduce a new interactome mapping approach by experimentally identifying interactions between brain-expressed alternatively spliced variants of ASD risk factors. The Autism Spliceform Interaction Network reveals that almost half of the detected interactions and about 30% of the newly identified interacting partners represent contribution from splicing variants, emphasizing the importance of isoform networks. Isoform interactions greatly contribute to establishing direct physical connections between proteins from the de novo autism CNVs. Our findings demonstrate the critical role of spliceform networks for translating genetic knowledge into a better understanding of human diseases. -
Environmental Influences on Endothelial Gene Expression
ENDOTHELIAL CELL GENE EXPRESSION John Matthew Jeff Herbert Supervisors: Prof. Roy Bicknell and Dr. Victoria Heath PhD thesis University of Birmingham August 2012 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. ABSTRACT Tumour angiogenesis is a vital process in the pathology of tumour development and metastasis. Targeting markers of tumour endothelium provide a means of targeted destruction of a tumours oxygen and nutrient supply via destruction of tumour vasculature, which in turn ultimately leads to beneficial consequences to patients. Although current anti -angiogenic and vascular targeting strategies help patients, more potently in combination with chemo therapy, there is still a need for more tumour endothelial marker discoveries as current treatments have cardiovascular and other side effects. For the first time, the analyses of in-vivo biotinylation of an embryonic system is performed to obtain putative vascular targets. Also for the first time, deep sequencing is applied to freshly isolated tumour and normal endothelial cells from lung, colon and bladder tissues for the identification of pan-vascular-targets. Integration of the proteomic, deep sequencing, public cDNA libraries and microarrays, delivers 5,892 putative vascular targets to the science community. -
Supplementary Data
SUPPLEMENTARY DATA A cyclin D1-dependent transcriptional program predicts clinical outcome in mantle cell lymphoma Santiago Demajo et al. 1 SUPPLEMENTARY DATA INDEX Supplementary Methods p. 3 Supplementary References p. 8 Supplementary Tables (S1 to S5) p. 9 Supplementary Figures (S1 to S15) p. 17 2 SUPPLEMENTARY METHODS Western blot, immunoprecipitation, and qRT-PCR Western blot (WB) analysis was performed as previously described (1), using cyclin D1 (Santa Cruz Biotechnology, sc-753, RRID:AB_2070433) and tubulin (Sigma-Aldrich, T5168, RRID:AB_477579) antibodies. Co-immunoprecipitation assays were performed as described before (2), using cyclin D1 antibody (Santa Cruz Biotechnology, sc-8396, RRID:AB_627344) or control IgG (Santa Cruz Biotechnology, sc-2025, RRID:AB_737182) followed by protein G- magnetic beads (Invitrogen) incubation and elution with Glycine 100mM pH=2.5. Co-IP experiments were performed within five weeks after cell thawing. Cyclin D1 (Santa Cruz Biotechnology, sc-753), E2F4 (Bethyl, A302-134A, RRID:AB_1720353), FOXM1 (Santa Cruz Biotechnology, sc-502, RRID:AB_631523), and CBP (Santa Cruz Biotechnology, sc-7300, RRID:AB_626817) antibodies were used for WB detection. In figure 1A and supplementary figure S2A, the same blot was probed with cyclin D1 and tubulin antibodies by cutting the membrane. In figure 2H, cyclin D1 and CBP blots correspond to the same membrane while E2F4 and FOXM1 blots correspond to an independent membrane. Image acquisition was performed with ImageQuant LAS 4000 mini (GE Healthcare). Image processing and quantification were performed with Multi Gauge software (Fujifilm). For qRT-PCR analysis, cDNA was generated from 1 µg RNA with qScript cDNA Synthesis kit (Quantabio). qRT–PCR reaction was performed using SYBR green (Roche). -
Comparative Analysis of Human Chromosome 7Q21 and Mouse
Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Letter Comparative analysis of human chromosome 7q21 and mouse proximal chromosome 6 reveals a placental-specific imprinted gene, TFPI2/Tfpi2, which requires EHMT2 and EED for allelic-silencing David Monk,1,6 Alexandre Wagschal,2 Philippe Arnaud,2 Pari-Sima Mu¨ller,3 Layla Parker-Katiraee,4 Déborah Bourc’his,5 Stephen W. Scherer,4 Robert Feil,2 Philip Stanier,1 and Gudrun E. Moore1 1Institute of Child Health, London WC1N 1EH, United Kingdom; 2Institute of Molecular Genetics, CNRS UMR-5535 and University of Montpellier-II, 34293 Montpellier, France; 3Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom; 4Center for Applied Genomics, The Hospital for Sick Children, Toronto M5G 1L7, Canada; 5Inserm U741, F-75251 Paris Cedex 05, France Genomic imprinting is a developmentally important mechanism that involves both differential DNA methylation and allelic histone modifications. Through detailed comparative characterization, a large imprinted domain mapping to chromosome 7q21 in humans and proximal chromosome 6 in mice was redefined. This domain is organized around a maternally methylated CpG island comprising the promoters of the adjacent PEG10 and SGCE imprinted genes. Examination of Dnmt3l−/+ conceptuses shows that imprinted expression for all genes of the cluster depends upon the germline methylation at this putative “imprinting control region” (ICR). Similarly as for other ICRs, we find its DNA-methylated allele to be associated with trimethylation of lysine 9 on histone H3 (H3K9me3) and trimethylation of lysine 20 on histone H4 (H4K20me3), whereas the transcriptionally active paternal allele is enriched in H3K4me2 and H3K9 acetylation. -
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 -
A Novel Resveratrol Analog: Its Cell Cycle Inhibitory, Pro-Apoptotic and Anti-Inflammatory Activities on Human Tumor Cells
A NOVEL RESVERATROL ANALOG : ITS CELL CYCLE INHIBITORY, PRO-APOPTOTIC AND ANTI-INFLAMMATORY ACTIVITIES ON HUMAN TUMOR CELLS A dissertation submitted to Kent State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy by Boren Lin May 2006 Dissertation written by Boren Lin B.S., Tunghai University, 1996 M.S., Kent State University, 2003 Ph. D., Kent State University, 2006 Approved by Dr. Chun-che Tsai , Chair, Doctoral Dissertation Committee Dr. Bryan R. G. Williams , Co-chair, Doctoral Dissertation Committee Dr. Johnnie W. Baker , Members, Doctoral Dissertation Committee Dr. James L. Blank , Dr. Bansidhar Datta , Dr. Gail C. Fraizer , Accepted by Dr. Robert V. Dorman , Director, School of Biomedical Sciences Dr. John R. Stalvey , Dean, College of Arts and Sciences ii TABLE OF CONTENTS LIST OF FIGURES……………………………………………………………….………v LIST OF TABLES……………………………………………………………………….vii ACKNOWLEDGEMENTS….………………………………………………………….viii I INTRODUCTION….………………………………………………….1 Background and Significance……………………………………………………..1 Specific Aims………………………………………………………………………12 II MATERIALS AND METHODS.…………………………………………….16 Cell Culture and Compounds…….……………….…………………………….….16 MTT Cell Viability Assay………………………………………………………….16 Trypan Blue Exclusive Assay……………………………………………………...18 Flow Cytometry for Cell Cycle Analysis……………..……………....……………19 DNA Fragmentation Assay……………………………………………...…………23 Caspase-3 Activity Assay………………………………...……….….…….………24 Annexin V-FITC Staining Assay…………………………………..…...….………28 NF-kappa B p65 Activity Assay……………………………………..………….…29 -
The Chemical Defensome of Five Model Teleost Fish
www.nature.com/scientificreports OPEN The chemical defensome of fve model teleost fsh Marta Eide1,5, Xiaokang Zhang2,3,5, Odd André Karlsen1, Jared V. Goldstone4, John Stegeman4, Inge Jonassen2 & Anders Goksøyr1* How an organism copes with chemicals is largely determined by the genes and proteins that collectively function to defend against, detoxify and eliminate chemical stressors. This integrative network includes receptors and transcription factors, biotransformation enzymes, transporters, antioxidants, and metal- and heat-responsive genes, and is collectively known as the chemical defensome. Teleost fsh is the largest group of vertebrate species and can provide valuable insights into the evolution and functional diversity of defensome genes. We have previously shown that the xenosensing pregnane x receptor (pxr, nr1i2) is lost in many teleost species, including Atlantic cod (Gadus morhua) and three-spined stickleback (Gasterosteus aculeatus), but it is not known if compensatory mechanisms or signaling pathways have evolved in its absence. In this study, we compared the genes comprising the chemical defensome of fve fsh species that span the teleosteii evolutionary branch often used as model species in toxicological studies and environmental monitoring programs: zebrafsh (Danio rerio), medaka (Oryzias latipes), Atlantic killifsh (Fundulus heteroclitus), Atlantic cod, and three-spined stickleback. Genome mining revealed evolved diferences in the number and composition of defensome genes that can have implication for how these species sense and respond to environmental pollutants, but we did not observe any candidates of compensatory mechanisms or pathways in cod and stickleback in the absence of pxr. The results indicate that knowledge regarding the diversity and function of the defensome will be important for toxicological testing and risk assessment studies. -
High Mutation Frequency of the PIGA Gene in T Cells Results In
High Mutation Frequency of the PIGA Gene in T Cells Results in Reconstitution of GPI A nchor−/CD52− T Cells That Can Give Early Immune Protection after This information is current as Alemtuzumab-Based T Cell−Depleted of October 1, 2021. Allogeneic Stem Cell Transplantation Floris C. Loeff, J. H. Frederik Falkenburg, Lois Hageman, Wesley Huisman, Sabrina A. J. Veld, H. M. Esther van Egmond, Marian van de Meent, Peter A. von dem Borne, Hendrik Veelken, Constantijn J. M. Halkes and Inge Jedema Downloaded from J Immunol published online 2 February 2018 http://www.jimmunol.org/content/early/2018/02/02/jimmun ol.1701018 http://www.jimmunol.org/ Supplementary http://www.jimmunol.org/content/suppl/2018/02/02/jimmunol.170101 Material 8.DCSupplemental Why The JI? Submit online. by guest on October 1, 2021 • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2018 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Published February 2, 2018, doi:10.4049/jimmunol.1701018 The Journal of Immunology High Mutation Frequency of the PIGA Gene in T Cells Results in Reconstitution of GPI Anchor2/CD522 T Cells That Can Give Early Immune Protection after Alemtuzumab- Based T Cell–Depleted Allogeneic Stem Cell Transplantation Floris C. -
IFN-Γ Selectively Suppresses a Subset of TLR4-Activated Genes and Enhancers to Potentiate M1-Like Macrophage Polarization
bioRxiv preprint doi: https://doi.org/10.1101/437160; this version posted October 7, 2018. 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. IFN-γ selectively suppresses a subset of TLR4-activated genes and enhancers to potentiate M1-like macrophage polarization Kyuho Kang1,2, Sung Ho Park1, Keunsoo Kang3 and Lionel B. Ivashkiv1,4 1 Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY 10021 2 Department of Biology, Chungbuk National University, Cheongju 28644, Republic of Korea 3 Department of Microbiology, Dankook University, Cheonan 31116, Republic of Korea 4 Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021 *Correspondence to: Lionel B. Ivashkiv, Hospital for Special Surgery, 535 East 70th Street, New York, NY 10021; Tel: 212-606-1653; Fax: 212-774-2301; Email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/437160; this version posted October 7, 2018. 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 Complete polarization of macrophages towards an M1-like proinflammatory and antimicrobial state requires combined action of IFN-γ and LPS. Synergistic activation of canonical inflammatory NF-κB target genes by IFN-γ and LPS is well appreciated, but less is known about whether IFN-γ negatively regulates components of the LPS response, and how this affects polarization. -
Demographic History and Genetic Adaptation in the Himalayan
Demographic History and Genetic Adaptation in the Himalayan Region Inferred from Genome-Wide SNP Genotypes of 49 Populations Elena Arciero,†,1 Thirsa Kraaijenbrink,†,2 Asan,†,3 Marc Haber,1 Massimo Mezzavilla,1,4 Qasim Ayub,1,5,6 Wei Wang,3 Zhaxi Pingcuo,7 Huanming Yang,3,8 Jian Wang,3,8 Mark A. Jobling,9 George van Driem,10 Yali Xue,1 Peter de Knijff,*,2 and Chris Tyler-Smith*,1 1The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom Downloaded from https://academic.oup.com/mbe/article-abstract/35/8/1916/4999976 by Leiden University / LUMC user on 22 July 2019 2Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands 3BGI-Shenzhen, Shenzhen, China 4Division of Experimental Genetics, Sidra Medical and Research Center, Doha, Qatar 5Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia Genomics Facility, Selangor Darul Ehsan, Malaysia 6School of Science, Monash University Malaysia, Selangor Darul Ehsan, Malaysia 7The Third People’s Hospital of the TibetAutonomousRegion,Lhasa,China 8James D. Watson Institute of Genome Science, Hangzhou, China 9Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom 10Institute of Linguistics, University of Bern, Bern, Switzerland †These authors contributed equally to this work. *Corresponding authors: E-mails: [email protected]; [email protected]. Associate editor: Rasmus Nielsen Abstract We genotyped 738 individuals belonging to 49 populations from Nepal, Bhutan, North India, or Tibet at over 500,000 SNPs, and analyzed the genotypes in the context of available worldwide population data in order to investigate the demographic history of the region and the genetic adaptations to the harsh environment. -
A Comparative Genomics Approach to Using High-Throughput
The University of Maine DigitalCommons@UMaine Honors College 5-2013 A Comparative Genomics Approach to Using High-Throughput Gene Expression Data to Study Limb Regeneration in Ambystoma Mexicanum and Danio Rerio: Developing a More Completely Annotated Database Justin Bolinger University of Maine - Main Follow this and additional works at: https://digitalcommons.library.umaine.edu/honors Part of the Comparative and Evolutionary Physiology Commons, Genomics Commons, and the Molecular Genetics Commons Recommended Citation Bolinger, Justin, "A Comparative Genomics Approach to Using High-Throughput Gene Expression Data to Study Limb Regeneration in Ambystoma Mexicanum and Danio Rerio: Developing a More Completely Annotated Database" (2013). Honors College. 116. https://digitalcommons.library.umaine.edu/honors/116 This Honors Thesis is brought to you for free and open access by DigitalCommons@UMaine. It has been accepted for inclusion in Honors College by an authorized administrator of DigitalCommons@UMaine. For more information, please contact [email protected]. A COMPARATIVE GENOMICS APPROACH TO USING HIGH-THROUGHPUT GENE EXPRESSION DATA TO STUDY LIMB REGENERATION IN AMBYSTOMA MEXICANUM AND DANIO RERIO: DEVELOPING A MORE COMPLETELY ANNOTATED DATABASE by Justin Bolinger A Thesis Submitted in Partial Fulfillment of the Requirements for a Degree with Honors (Chemical Engineering) The Honors College University of Maine at Orono May 2013 Advisory Committee: Keith Hutchison, Department of Biochemistry and Molecular Biology, Advisor Benjamin King, Staff Scientist, Mount Desert Island Biological Laboratory, co-Advisor John Hwalek, Department of Chemical Engineering François Amar, Department of Chemistry Kevin Roberge, Department of Physics and Astronomy ABSTRACT Axolotl (Ambystoma mexicanum) and the zebrafish (Danio rerio) represent organisms extensively studied because of their remarkable capability of fully regenerating completely functional tissues after a traumatic event takes place.