DOCSLIB.ORG

Open Full Page

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Open Full Page Published OnlineFirst January 12, 2016; DOI: 10.1158/0008-5472.CAN-15-1859 Cancer Tumor and Stem Cell Biology Research Formation of Renal Cysts and Tumors in Vhl/Trp53-Deficient Mice Requires HIF1a and HIF2a Desir ee Schonenberger€ 1, Sabine Harlander1,2, Michal Rajski1, Robert A. Jacobs1,2,3, Anne-Kristine Lundby1,2, Mojca Adlesic1, Tomas Hejhal1, Peter J. Wild4, Carsten Lundby1,2, and Ian J. Frew1,2 Abstract The von Hippel–Lindau (VHL) tumor suppressor gene is inac- chondrial abundance and oxidative capacity, glycogen accu- tivated in the majority of clear cell renal cell carcinomas (ccRCC), mulation, and acquisition of a clear cell phenotype in Vhl- but genetic ablation of Vhl alone in mouse models is insufficient deficient renal epithelial cells. HIF1a, but not HIF2a, induced to recapitulate human tumorigenesis. One function of pVHL is to Warburg-like metabolism characterized by increased glycoly- regulate the stability of the hypoxia-inducible factors (HIF), sis, decreased oxygen consumption, and decreased ATP pro- which become constitutively activated in the absence of pVHL. duction in mouse embryonic fibroblasts, providing insights In established ccRCC, HIF1a has been implicated as a renal tumor into the cellular changes potentially occurring in Vhl mutant suppressor, whereas HIF2a is considered an oncoprotein. In this renal cells before ccRCC formation. Importantly, deletion of study, we investigated the contributions of HIF1a and HIF2a to either Hif1a or Hif2a completely prevented the formation of ccRCC initiation in the context of Vhl deficiency. We found that renal cysts and tumors in Vhl/Trp53 mutant mice. These find- deleting Vhl plus Hif1a or Hif2a specifically in the renal ings argue that both HIF1a and HIF2a exert protumorigenic epithelium did not induce tumor formation. However, HIF1a functions during the earliest stages of cyst and tumor forma- and HIF2a differentially regulated cell proliferation, mito- tion in the kidney. Cancer Res; 76(7); 1–12. Ó2016 AACR. Introduction autochthonous mouse models that fully reproduce all of the characteristic morphologic and invasive properties of human Clear cell renal cell carcinoma (ccRCC) is the most frequent ccRCC; however, consistent with the hypothesis that multiple renal malignancy, and up to 92% of ccRCC tumors harbor cooperating mutations are required for ccRCC development, biallelic inactivation of the von Hippel–Lindau (VHL) tumor kidney epithelial cell–specific codeletion of Vhl with Pten (6), or suppressor gene (1). VHL mutations occur at the earliest stage with Kif3a to genetically ablate primary cilia (7), caused the of tumor formation (2). The absence of pVHL function is clearly formation of simple and atypical cystic lesions that are similar necessary for the growth of fully transformed ccRCC cell lines as to the ccRCC precursor cystic lesions found in the kidneys of xenografts (3). However, the fact that the frequency of VHL patients with inherited VHL disease. Deletion of Vhl together with mutant single epithelial cells vastly outweighs the number of homozygous loss of Trp53 (8) or with heterozygous loss of Bap1 ccRCC tumors in kidneys of familial VHL disease patients (4) and (9) gave rise to very similar phenotypes, including simple and the absence of tumors in a variety of renal epithelial cell–specific atypical cystic lesions as well as tumors containing cells that Vhl knockout mice (reviewed in ref. 5) argues that ccRCC forma- display cytoplasmic clearing and elevated mTORC1 activity, reca- tion requires mutations in addition to VHL. There are currently no pitulating many of the cellular and molecular changes that are characteristic of human ccRCC. pVHL controls many biological activities, including regulation 1Institute of Physiology, University of Zurich, Zurich, Switzerland. 2Zurich Center for Integrative Human Physiology, University of Zurich, of the stability of the hypoxia-inducible transcription factors a Zurich, Switzerland. 3Health and Physical Education, School of Teach- (HIF1a, HIF2a, and HIF3a, collectively HIFa; ref. 10), regulation ing and Learning, Western Carolina University, Cullowhee, North Car- of NF-kB activity (11), maintenance of the primary cilium (12), olina. 4Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland. activation of p53 (13), secretion of extracellular matrix compo- nents (14), promotion of DNA double-strand repair (15), regu- Note: Supplementary data for this article are available at Cancer Research Online (http://cancerres.aacrjournals.org/). lation of the plane of cellular division (16, 17), and suppression of aneuploidy (16, 18). The combined loss of several or all of pVHL's D. Schonenberger,€ S. Harlander, and M. Rajski contributed equally to this article. functions could contribute to tumor initiation and progression. Corresponding Author: Ian J. Frew, University of Zurich, Winterthurerstrasse Loss of function mutations of VHL occur in ccRCC mutually 190, CH-8057 Zurich, Switzerland. Phone: 41-44-635-5004; Fax: 41-44-635- exclusively to rarer mutations in TCEB1, encoding Elongin C, 6814; E-mail: [email protected] and collectively these cause constitutive stabilization of HIFa in doi: 10.1158/0008-5472.CAN-15-1859 up to 95% of ccRCC tumors (1), implying that HIFa activation is a Ó2016 American Association for Cancer Research. major oncogenic driving force in ccRCC. HIF1a and HIF2a appear www.aacrjournals.org OF1 Downloaded from cancerres.aacrjournals.org on September 29, 2021. © 2016 American Association for Cancer Research. Published OnlineFirst January 12, 2016; DOI: 10.1158/0008-5472.CAN-15-1859 Schonenberger€ et al. to play opposite roles in determining the aggressiveness of estab- mice. Littermate mice that lacked the Cre transgene served as wild- lished ccRCCs; HIF1a inhibits, whereas HIF2a promotes tumor type controls. formation in ccRCC xenografts (19–21), copy loss of the chro- mosomal locus harboring the HIF1A gene predicts poor patient Immunohistochemistry a a outcome (22), and sporadic ccRCCs expressing HIF1 and HIF2 Immunohistochemistry and immunofluorescence of formalin- exhibit lower proliferation rates than ccRCCs expressing only fixed paraffin-embedded tissues were performed as previously a a HIF2 (23). ccRCC cell lines frequently express only HIF2 and described (6, 8) using antibodies listed in Supplementary Materi- a do not express functional HIF1 due to biallelic alterations of the als and Methods. HIF1A locus (24). Knockdown of HIF1A in ccRCC cell lines that express both HIF1a and HIF2a promotes xenograft tumor for- Respirometry mation (24). These studies argue that whereas HIF2a activity is Biopsies (1 mm3) of renal cortex and medulla were assayed for tumor promoting, there is a selection against HIF1a expression or oxygen consumption following the addition of different respira- activity during the progression of some cases of ccRCC. On the tory substrates and inhibitors using high-resolution respirometry other hand, because HIF1a is strongly expressed in single and (Oxygraph-2k, OROBOROS INSTRUMENTS Corp) according to multicellular clusters of VHL-null cells and in cystic lesions in VHL the protocol described in Supplementary Materials and Methods. patients (4), and because transgenic overexpression of HIF1a in mouse proximal tubular epithelial cells causes a clear cell appear- ance, increased proliferation, and a disorganized tubular mor- Microarrays phology (25), and because many human ccRCCs express HIF1a Primary adult mouse renal epithelial cells were cultured for 3 and HIF1a target genes (26), it may also be argued that HIF1a days and infected with Adeno-GFP (Vector Biolabs, 1060) or plays an important role in promoting ccRCC development. These Adeno-Cre (Vector Biolabs, 1700) as described (8). mRNA studies have largely focused on fully transformed, genetically was isolated 4 days after adenovirus infection, and Cy3- and complex ccRCC cell lines derived from advanced tumors, and it Cy5-labeled cDNA from GFP and Cre samples was competitively remains unclear if and how HIF1a and HIF2a contribute to the hybridized to Mouse GE 4 Â 44 K v2 Microarrays (Agilent). Dye earliest stages of initiation of ccRCC. swap experiments were used to control potential dye-specific An early event following VHL mutation is likely to be a hybridization effects. Analysis using R/Bioconductor package profound alteration of cellular metabolic pathways. Numerous limma was based on the average fold expression level changes HIF1a and/or HIF2a-dependent metabolic changes occur in (Cre/GFP) of three independent biologic experiments. Microarray ccRCC cell lines, including elevated glucose uptake and conver- data are accessible through GEO number GSE75745. sion to lactate with a concomitant reduction in mitochondrial oxidation of pyruvate, reduced mitochondrial biogenesis, Histological stains reduced mitochondrial complex I activity, altered cytochrome c Hematoxylin and eosin (H&E) and periodic acid-Schiff (PAS) oxidase activity, increased pentose phosphate pathway flux, stains were conducted using standard protocols. For the visual- decreased oxidative glutaminolysis, and increased lipogenesis ization of lipids, frozen kidney sections were fixed with 10% through reductive glutamine metabolism (27–38). Because formalin for 15 minutes, washed in tap water, equilibrated in 60% ccRCC cell lines have complex genetic backgrounds that arose isopropanol, and stained with Oil Red O (3 mg/mL in 60% during tumor evolution, it is possible that some of these meta- isopropanol) overnight at 4C. After
Load more

Recommended publications
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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).
    [Show full text]
  • 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.
    [Show full text]
  • 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
    [Show full text]
  • 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).
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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
    [Show full text]
  • 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].
    [Show full text]
  • 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).
    [Show full text]
  • 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.
    [Show full text]