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Harnessing Gene Expression Profiles for the Identification of Ex Vivo Drug
cancers Article Harnessing Gene Expression Profiles for the Identification of Ex Vivo Drug Response Genes in Pediatric Acute Myeloid Leukemia David G.J. Cucchi 1 , Costa Bachas 1 , Marry M. van den Heuvel-Eibrink 2,3, Susan T.C.J.M. Arentsen-Peters 3, Zinia J. Kwidama 1, Gerrit J. Schuurhuis 1, Yehuda G. Assaraf 4, Valérie de Haas 3 , Gertjan J.L. Kaspers 3,5 and Jacqueline Cloos 1,* 1 Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands; [email protected] (D.G.J.C.); [email protected] (C.B.); [email protected] (Z.J.K.); [email protected] (G.J.S.) 2 Department of Pediatric Oncology/Hematology, Erasmus MC–Sophia Children’s Hospital, 3015 CN Rotterdam, The Netherlands; [email protected] 3 Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; [email protected] (S.T.C.J.M.A.-P.); [email protected] (V.d.H.); [email protected] (G.J.L.K.) 4 The Fred Wyszkowski Cancer Research, Laboratory, Department of Biology, Technion-Israel Institute of Technology, 3200003 Haifa, Israel; [email protected] 5 Emma’s Children’s Hospital, Amsterdam UMC, Vrije Universiteit Amsterdam, Pediatric Oncology, 1081 HV Amsterdam, The Netherlands * Correspondence: [email protected] Received: 21 April 2020; Accepted: 12 May 2020; Published: 15 May 2020 Abstract: Novel treatment strategies are of paramount importance to improve clinical outcomes in pediatric AML. Since chemotherapy is likely to remain the cornerstone of curative treatment of AML, insights in the molecular mechanisms that determine its cytotoxic effects could aid further treatment optimization. -
Nus a Thesis Submitted
EPAS1 REGULATION AND FUNCTION IN THE HUMAN TROPHOBLAST NORHAM ERLYANI BTE ABDUL HAMID B.Sc. (Hons.), NUS A THESIS SUBMITTED FOR THE DEGREE OF DOCTOR OF PHILOSOPHY NUS GRADUATE SCHOOL FOR INTEGRATIVE SCIENCES AND ENGINEERING NATIONAL UNIVERSITY OF SINGAPORE 2013 ACKNOWLEDGEMENTS Writing this doctoral dissertation has been most challenging and it would not have been possible without the support of many people. First of all, my gratitude goes to A*STAR, NGS, and GIS for giving me the opportunity to pursue the Doctor of Philosophy. I would like to thank A/P Paul Robson for being a tremendous mentor, and for his invaluable guidance. Under his care, I was able to develop and grow into an independent researcher. His unyielding encouragement gave me confidence to pursue the work I have achieved today. For always pointing me in the right direction and having the student’s best interest at heart, I must thank the panel of advisors at GIS as well as my thesis advisory committee; A/P Neil Clarke, Asst. Prof. Tara Huber, Asst. Prof. Thilo Hagen, and Dr. Shyam Prabhakar. I owe special thanks to my co-workers, Dr. Wishva Herath and Dr. Li Juntao. Their indispensable expertise in Bioinformatics is deeply appreciated, without which much of the data would have been rendered unintelligible to me. To my peers Mehran Rahmani, Nani Djunaidi, and Tapan Mistri, I thank you all for the sharing of ideas as well as laboratory material. Together, we can conquer the PhD! Additionally, I would also like to extend my thanks to Sun Lili, Jameelah Sheikh, Woon Chow Thai, and all members of the lab for their support and cooperation, ensuring research in the Robson lab proceeds as smoothly as possible. -
DNA Methylation Variants at HIF3A Locus, B-Vitamin Intake, and Long-Term Weight Change: Gene-Diet Interactions in Two U.S
3146 Diabetes Volume 64, September 2015 Tao Huang,1 Yan Zheng,1 Qibin Qi,2 Min Xu,3 Sylvia H. Ley,1 Yanping Li,1 Jae H. Kang,4 Janey Wiggs,5 Louis R. Pasquale,4,5 Andrew T. Chan,6 Eric B. Rimm,1,4,7 David J. Hunter,1,7 JoAnn E. Manson,4,7,8 Walter C. Willett,1,4,7 Frank B. Hu,1,4,7 and Lu Qi1,4 DNA Methylation Variants at HIF3A Locus, B-Vitamin Intake, and Long-term Weight Change: Gene-Diet Interactions in Two U.S. Cohorts Diabetes 2015;64:3146–3154 | DOI: 10.2337/db15-0264 The first epigenome-wide association study of BMI not induced by changes in the DNA sequence (1). Increasing identified DNA methylation at an HIF3A locus associated evidence indicates that DNA methylation plays a pivotal role with BMI. We tested the hypothesis that DNA methylation in regulating body adiposity (2–5). In a recent large-scale variants are associated with BMI according to intake of epigenome-wide association study, Dick et al. (4) found B vitamins. In two large cohorts, we found significant inter- that DNA methylation at HIF3A was associated with BMI. actions between the DNA methylation–associated HIF3A However, genetic variants in this locus were not associated single nucleotide polymorphism (SNP) rs3826795 and in- with BMI, although they were associated with HIF3A meth- take of B vitamins on 10-year changes in BMI. The asso- ylationlevelsinbloodandadiposeandskintissues.The ciation between rs3826795 and BMI changes consistently authors suggested that the association between HIF3A meth- increased across the tertiles of total vitamin B and B 2 12 ylation and BMI might not be operating by the Mendelian intake (all P for interaction <0.01). -
1 Metabolic Dysfunction Is Restricted to the Sciatic Nerve in Experimental
Page 1 of 255 Diabetes Metabolic dysfunction is restricted to the sciatic nerve in experimental diabetic neuropathy Oliver J. Freeman1,2, Richard D. Unwin2,3, Andrew W. Dowsey2,3, Paul Begley2,3, Sumia Ali1, Katherine A. Hollywood2,3, Nitin Rustogi2,3, Rasmus S. Petersen1, Warwick B. Dunn2,3†, Garth J.S. Cooper2,3,4,5* & Natalie J. Gardiner1* 1 Faculty of Life Sciences, University of Manchester, UK 2 Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK 3 Centre for Endocrinology and Diabetes, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, UK 4 School of Biological Sciences, University of Auckland, New Zealand 5 Department of Pharmacology, Medical Sciences Division, University of Oxford, UK † Present address: School of Biosciences, University of Birmingham, UK *Joint corresponding authors: Natalie J. Gardiner and Garth J.S. Cooper Email: [email protected]; [email protected] Address: University of Manchester, AV Hill Building, Oxford Road, Manchester, M13 9PT, United Kingdom Telephone: +44 161 275 5768; +44 161 701 0240 Word count: 4,490 Number of tables: 1, Number of figures: 6 Running title: Metabolic dysfunction in diabetic neuropathy 1 Diabetes Publish Ahead of Print, published online October 15, 2015 Diabetes Page 2 of 255 Abstract High glucose levels in the peripheral nervous system (PNS) have been implicated in the pathogenesis of diabetic neuropathy (DN). However our understanding of the molecular mechanisms which cause the marked distal pathology is incomplete. Here we performed a comprehensive, system-wide analysis of the PNS of a rodent model of DN. -
Supplemental Materials ZNF281 Enhances Cardiac Reprogramming
Supplemental Materials ZNF281 enhances cardiac reprogramming by modulating cardiac and inflammatory gene expression Huanyu Zhou, Maria Gabriela Morales, Hisayuki Hashimoto, Matthew E. Dickson, Kunhua Song, Wenduo Ye, Min S. Kim, Hanspeter Niederstrasser, Zhaoning Wang, Beibei Chen, Bruce A. Posner, Rhonda Bassel-Duby and Eric N. Olson Supplemental Table 1; related to Figure 1. Supplemental Table 2; related to Figure 1. Supplemental Table 3; related to the “quantitative mRNA measurement” in Materials and Methods section. Supplemental Table 4; related to the “ChIP-seq, gene ontology and pathway analysis” and “RNA-seq” and gene ontology analysis” in Materials and Methods section. Supplemental Figure S1; related to Figure 1. Supplemental Figure S2; related to Figure 2. Supplemental Figure S3; related to Figure 3. Supplemental Figure S4; related to Figure 4. Supplemental Figure S5; related to Figure 6. Supplemental Table S1. Genes included in human retroviral ORF cDNA library. Gene Gene Gene Gene Gene Gene Gene Gene Symbol Symbol Symbol Symbol Symbol Symbol Symbol Symbol AATF BMP8A CEBPE CTNNB1 ESR2 GDF3 HOXA5 IL17D ADIPOQ BRPF1 CEBPG CUX1 ESRRA GDF6 HOXA6 IL17F ADNP BRPF3 CERS1 CX3CL1 ETS1 GIN1 HOXA7 IL18 AEBP1 BUD31 CERS2 CXCL10 ETS2 GLIS3 HOXB1 IL19 AFF4 C17ORF77 CERS4 CXCL11 ETV3 GMEB1 HOXB13 IL1A AHR C1QTNF4 CFL2 CXCL12 ETV7 GPBP1 HOXB5 IL1B AIMP1 C21ORF66 CHIA CXCL13 FAM3B GPER HOXB6 IL1F3 ALS2CR8 CBFA2T2 CIR1 CXCL14 FAM3D GPI HOXB7 IL1F5 ALX1 CBFA2T3 CITED1 CXCL16 FASLG GREM1 HOXB9 IL1F6 ARGFX CBFB CITED2 CXCL3 FBLN1 GREM2 HOXC4 IL1F7 -
HIF3A Antibody Product Type
PRODUCT INFORMATION Product name:HIF3A antibody Product type: Primary antibodies Description: Rabbit polyclonal to HIF3A Immunogen:3 synthetic peptides (human) conjugated to KLH Reacts with: Human, Mouse Tested applications: ELISA, WB & IF GENE INFORMATION Gene Symbol:HIF3A Gene Name:hypoxia inducible factor 3, alpha subunit Ensembl ID:ENSG00000124440 Entrez GeneID:64344 GenBank Accession number:AK027725 Omim ID:609976 SwissProt:Q9Y2N7 Molecular weight of HIF3A: 72.4kDa Function:Involved in adaptive response to hypoxia. Suppresses hypoxiainducible expression of HIF1A and EPAS1. Binds to core DNA sequence 5'TACGTG3' within the hypoxia response element (HRE) of target gene promoters. The complex HIF3AARNT activates the transcription of reporter genes driven by HRE. Isoform 4 has a dominant negative function of inactivating HIF1Amediated transcription. Isoform 4 attenuates the binding of HIF1A to hypoxiaresponsive elements (HRE), thus inhibiting HREdriven transcription. Hypoxia induces downregulation of isoform 4, leading to activation of HIF1A in hypoxia. Conversely, upon restoring normoxia, the expression of isoform 4 increases and thereby secure an inhibition of HIF1A activity. Isoform 4 may be a negative regulator of hypoxiainducible gene expression in the kidney and may be involved in renal tumorigenesis. Functions as an inhibitor of angiogenesis in the cornea Expected subcellular localization:Nucleus. Cytoplasm. Note: In the nuclei of all periportal and perivenous hepatocytes. In the distal perivenous zone, detected in the cytoplasm of the hepatocytes Summary:The protein encoded by this gene is the alpha3 subunit of one of several alpha/betasubunit heterodimeric transcription factors that regulate many adaptive responses to low oxygen tension (hypoxia). -
Role of RUNX1 in Aberrant Retinal Angiogenesis Jonathan D
Page 1 of 25 Diabetes Identification of RUNX1 as a mediator of aberrant retinal angiogenesis Short Title: Role of RUNX1 in aberrant retinal angiogenesis Jonathan D. Lam,†1 Daniel J. Oh,†1 Lindsay L. Wong,1 Dhanesh Amarnani,1 Cindy Park- Windhol,1 Angie V. Sanchez,1 Jonathan Cardona-Velez,1,2 Declan McGuone,3 Anat O. Stemmer- Rachamimov,3 Dean Eliott,4 Diane R. Bielenberg,5 Tave van Zyl,4 Lishuang Shen,1 Xiaowu Gai,6 Patricia A. D’Amore*,1,7 Leo A. Kim*,1,4 Joseph F. Arboleda-Velasquez*1 Author affiliations: 1Schepens Eye Research Institute/Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, 20 Staniford St., Boston, MA 02114 2Universidad Pontificia Bolivariana, Medellin, Colombia, #68- a, Cq. 1 #68305, Medellín, Antioquia, Colombia 3C.S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital, 55 Fruit St., Boston, MA 02114 4Retina Service, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, 243 Charles St., Boston, MA 02114 5Vascular Biology Program, Boston Children’s Hospital, Department of Surgery, Harvard Medical School, 300 Longwood Ave., Boston, MA 02115 6Center for Personalized Medicine, Children’s Hospital Los Angeles, Los Angeles, 4650 Sunset Blvd, Los Angeles, CA 90027, USA 7Department of Pathology, Harvard Medical School, 25 Shattuck St., Boston, MA 02115 Corresponding authors: Joseph F. Arboleda-Velasquez: [email protected] Ph: (617) 912-2517 Leo Kim: [email protected] Ph: (617) 912-2562 Patricia D’Amore: [email protected] Ph: (617) 912-2559 Fax: (617) 912-0128 20 Staniford St. Boston MA, 02114 † These authors contributed equally to this manuscript Word Count: 1905 Tables and Figures: 4 Diabetes Publish Ahead of Print, published online April 11, 2017 Diabetes Page 2 of 25 Abstract Proliferative diabetic retinopathy (PDR) is a common cause of blindness in the developed world’s working adult population, and affects those with type 1 and type 2 diabetes mellitus. -
Mir-17-92 Fine-Tunes MYC Expression and Function to Ensure
ARTICLE Received 31 Mar 2015 | Accepted 22 Sep 2015 | Published 10 Nov 2015 DOI: 10.1038/ncomms9725 OPEN miR-17-92 fine-tunes MYC expression and function to ensure optimal B cell lymphoma growth Marija Mihailovich1, Michael Bremang1, Valeria Spadotto1, Daniele Musiani1, Elena Vitale1, Gabriele Varano2,w, Federico Zambelli3, Francesco M. Mancuso1,w, David A. Cairns1,w, Giulio Pavesi3, Stefano Casola2 & Tiziana Bonaldi1 The synergism between c-MYC and miR-17-19b, a truncated version of the miR-17-92 cluster, is well-documented during tumor initiation. However, little is known about miR-17-19b function in established cancers. Here we investigate the role of miR-17-19b in c-MYC-driven lymphomas by integrating SILAC-based quantitative proteomics, transcriptomics and 30 untranslated region (UTR) analysis upon miR-17-19b overexpression. We identify over one hundred miR-17-19b targets, of which 40% are co-regulated by c-MYC. Downregulation of a new miR-17/20 target, checkpoint kinase 2 (Chek2), increases the recruitment of HuR to c- MYC transcripts, resulting in the inhibition of c-MYC translation and thus interfering with in vivo tumor growth. Hence, in established lymphomas, miR-17-19b fine-tunes c-MYC activity through a tight control of its function and expression, ultimately ensuring cancer cell homeostasis. Our data highlight the plasticity of miRNA function, reflecting changes in the mRNA landscape and 30 UTR shortening at different stages of tumorigenesis. 1 Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy. 2 Units of Genetics of B cells and lymphomas, IFOM, FIRC Institute of Molecular Oncology Foundation, Milan 20139, Italy. -
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 -
Molecular Genetics in Neuroblastoma Prognosis
children Review Molecular Genetics in Neuroblastoma Prognosis Margherita Lerone 1, Marzia Ognibene 1 , Annalisa Pezzolo 2 , Giuseppe Martucciello 3,4 , Federico Zara 1,4, Martina Morini 5,*,† and Katia Mazzocco 6,† 1 Unit of Medical Genetics, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; [email protected] (M.L.); [email protected] (M.O.); [email protected] (F.Z.) 2 IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; [email protected] 3 Department of Pediatric Surgery, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; [email protected] 4 Dipartimento di Neuroscienze, Riabilitazione, Oftalmologia, Genetica e Scienze Materno-Infantili, University of Genova, 16132 Genova, Italy 5 Laboratory of Molecular Biology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy 6 Department of Pathology, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-010-5636-2633 † Authors share senior authorship. Abstract: In recent years, much research has been carried out to identify the biological and genetic characteristics of the neuroblastoma (NB) tumor in order to precisely define the prognostic subgroups for improving treatment stratification. This review will describe the major genetic features and the recent scientific advances, focusing on their impact on diagnosis, prognosis, and therapeutic solutions in NB clinical management. Keywords: neuroblastoma; genetics; TRK; liquid biopsy; exosomes; telomere maintenance; hypoxia Citation: Lerone, M.; Ognibene, M.; Pezzolo, A.; Martucciello, G.; Zara, F.; 1. Introduction Morini, M.; Mazzocco, K. Molecular Genetics in Neuroblastoma Prognosis. Neuroblastoma (NB) is a pediatric heterogeneous disease with a median age of Children 2021, 8, 456. https:// 17 months at diagnosis, which can evolve with a benign course or fatal illness, with a doi.org/10.3390/children8060456 natural history ranging from a benign course to a terminal illness [1–3]. -
Β-Catenin Signaling Dynamics Regulate Cell Fate in Differentiating Neural Stem Cells
β-Catenin signaling dynamics regulate cell fate in differentiating neural stem cells Alyssa B. Rosenblooma, Marcin Tarczynski a, Nora Lama, Ravi S. Kaneb,1, Lukasz J. Bugaja,c,1, and David V. Schaffera,d,e,f,1 aDepartment of Bioengineering, University of California, Berkeley, CA 94720; bSchool of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332; cDepartment of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104; dDepartment of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720; eDepartment of Molecular and Cell Biology, University of California, Berkeley, CA 94720; and fHelen Wills Neuroscience Institute, University of California, Berkeley, CA 94720 Edited by Randall T. Moon, University of Washington, Seattle, WA, and approved September 21, 2020 (received for review May 4, 2020) Stem cells undergo differentiation in complex and dynamic environ- of how signaling dynamics impact cellular function. Optogenetics ments wherein instructive signals fluctuate on various timescales. has recently emerged as a field in which light—which can readily Thus, cells must be equipped to properly respond to the timing of be varied in intensity, space, and time—is harnessed to precisely signals, for example, to distinguish sustained signaling from transient modulate cell-signaling pathways. In this approach, light-sensitive noise. However, how stem cells respond to dynamic variations in proteins are engineered to interface with specific signaling path- differentiation cues is not well characterized. Here, we use optoge- ways, and the subsequent introduction of such an optogenetic netic activation of β-catenin signaling to probe the dynamic responses construct into cells renders the signaling pathway responsive to of differentiating adult neural stem cells (NSCs). -
Single-Cell Analysis Uncovers Fibroblast Heterogeneity
ARTICLE https://doi.org/10.1038/s41467-020-17740-1 OPEN Single-cell analysis uncovers fibroblast heterogeneity and criteria for fibroblast and mural cell identification and discrimination ✉ Lars Muhl 1,2 , Guillem Genové 1,2, Stefanos Leptidis 1,2, Jianping Liu 1,2, Liqun He3,4, Giuseppe Mocci1,2, Ying Sun4, Sonja Gustafsson1,2, Byambajav Buyandelger1,2, Indira V. Chivukula1,2, Åsa Segerstolpe1,2,5, Elisabeth Raschperger1,2, Emil M. Hansson1,2, Johan L. M. Björkegren 1,2,6, Xiao-Rong Peng7, ✉ Michael Vanlandewijck1,2,4, Urban Lendahl1,8 & Christer Betsholtz 1,2,4 1234567890():,; Many important cell types in adult vertebrates have a mesenchymal origin, including fibro- blasts and vascular mural cells. Although their biological importance is undisputed, the level of mesenchymal cell heterogeneity within and between organs, while appreciated, has not been analyzed in detail. Here, we compare single-cell transcriptional profiles of fibroblasts and vascular mural cells across four murine muscular organs: heart, skeletal muscle, intestine and bladder. We reveal gene expression signatures that demarcate fibroblasts from mural cells and provide molecular signatures for cell subtype identification. We observe striking inter- and intra-organ heterogeneity amongst the fibroblasts, primarily reflecting differences in the expression of extracellular matrix components. Fibroblast subtypes localize to discrete anatomical positions offering novel predictions about physiological function(s) and regulatory signaling circuits. Our data shed new light on the diversity of poorly defined classes of cells and provide a foundation for improved understanding of their roles in physiological and pathological processes. 1 Karolinska Institutet/AstraZeneca Integrated Cardio Metabolic Centre, Blickagången 6, SE-14157 Huddinge, Sweden.