1
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Wu CT, Lidsky PV, Xiao Y, Cheng R, Lee IT, Nakayama T, Jiang S, He W, Demeter J, Knight MG, Turn RE, Rojas-Hernandez LS, Ye C, Chiem K, Shon J, Martinez-Sobrido L, Bertozzi CR, Nolan GP, Nayak JV, Milla C, Andino R, Jackson PK. SARS-CoV-2 replication in airway epithelia requires motile cilia and microvillar reprogramming. Cell 2023; 186:112-130.e20. [PMID: 36580912 PMCID: PMC9715480 DOI: 10.1016/j.cell.2022.11.030] [Citation(s) in RCA: 58] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 09/15/2022] [Accepted: 11/23/2022] [Indexed: 12/04/2022]
Abstract
How SARS-CoV-2 penetrates the airway barrier of mucus and periciliary mucins to infect nasal epithelium remains unclear. Using primary nasal epithelial organoid cultures, we found that the virus attaches to motile cilia via the ACE2 receptor. SARS-CoV-2 traverses the mucus layer, using motile cilia as tracks to access the cell body. Depleting cilia blocks infection for SARS-CoV-2 and other respiratory viruses. SARS-CoV-2 progeny attach to airway microvilli 24 h post-infection and trigger formation of apically extended and highly branched microvilli that organize viral egress from the microvilli back into the mucus layer, supporting a model of virus dispersion throughout airway tissue via mucociliary transport. Phosphoproteomics and kinase inhibition reveal that microvillar remodeling is regulated by p21-activated kinases (PAK). Importantly, Omicron variants bind with higher affinity to motile cilia and show accelerated viral entry. Our work suggests that motile cilia, microvilli, and mucociliary-dependent mucus flow are critical for efficient virus replication in nasal epithelia.
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Affiliation(s)
- Chien-Ting Wu
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Center for Clinical Sciences Research, 269 Campus Drive, Stanford, CA, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, Room S572E, Box 2280, San Francisco, CA, USA
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, Room S572E, Box 2280, San Francisco, CA, USA
| | - Ran Cheng
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Center for Clinical Sciences Research, 269 Campus Drive, Stanford, CA, USA; Department of Biology, Stanford University, Stanford, CA, USA
| | - Ivan T Lee
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Tsuguhisa Nakayama
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA; Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Sizun Jiang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Wei He
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Center for Clinical Sciences Research, 269 Campus Drive, Stanford, CA, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Center for Clinical Sciences Research, 269 Campus Drive, Stanford, CA, USA
| | - Miguel G Knight
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, Room S572E, Box 2280, San Francisco, CA, USA
| | - Rachel E Turn
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Center for Clinical Sciences Research, 269 Campus Drive, Stanford, CA, USA
| | - Laura S Rojas-Hernandez
- Department of Pediatric Pulmonary Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Chengjin Ye
- Disease Intervention and Prevention and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Kevin Chiem
- Disease Intervention and Prevention and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Judy Shon
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Luis Martinez-Sobrido
- Disease Intervention and Prevention and Population Health Programs, Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jayakar V Nayak
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA; Department of Otolaryngology, VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Carlos Milla
- Department of Pediatric Pulmonary Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, Room S572E, Box 2280, San Francisco, CA, USA.
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Center for Clinical Sciences Research, 269 Campus Drive, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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2
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Janas JA, Zhang L, Luu JH, Demeter J, Meng L, Marro SG, Mall M, Mooney NA, Schaukowitch K, Ng YH, Yang N, Huang Y, Neumayer G, Gozani O, Elias JE, Jackson PK, Wernig M. Tip60-mediated H2A.Z acetylation promotes neuronal fate specification and bivalent gene activation. Mol Cell 2022; 82:4627-4646.e14. [PMID: 36417913 PMCID: PMC9779922 DOI: 10.1016/j.molcel.2022.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 08/28/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
Cell lineage specification is accomplished by a concerted action of chromatin remodeling and tissue-specific transcription factors. However, the mechanisms that induce and maintain appropriate lineage-specific gene expression remain elusive. Here, we used an unbiased proteomics approach to characterize chromatin regulators that mediate the induction of neuronal cell fate. We found that Tip60 acetyltransferase is essential to establish neuronal cell identity partly via acetylation of the histone variant H2A.Z. Despite its tight correlation with gene expression and active chromatin, loss of H2A.Z acetylation had little effect on chromatin accessibility or transcription. Instead, loss of Tip60 and acetyl-H2A.Z interfered with H3K4me3 deposition and activation of a unique subset of silent, lineage-restricted genes characterized by a bivalent chromatin configuration at their promoters. Altogether, our results illuminate the mechanisms underlying bivalent chromatin activation and reveal that H2A.Z acetylation regulates neuronal fate specification by establishing epigenetic competence for bivalent gene activation and cell lineage transition.
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Affiliation(s)
- Justyna A Janas
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lichao Zhang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jacklyn H Luu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Lingjun Meng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Samuele G Marro
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Moritz Mall
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nancie A Mooney
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Katie Schaukowitch
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yi Han Ng
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nan Yang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yuhao Huang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gernot Neumayer
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Joshua E Elias
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter K Jackson
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marius Wernig
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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3
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Jiang S, Chan CN, Rovira-Clavé X, Chen H, Bai Y, Zhu B, McCaffrey E, Greenwald NF, Liu C, Barlow GL, Weirather JL, Oliveria JP, Nakayama T, Lee IT, Matter MS, Carlisle AE, Philips D, Vazquez G, Mukherjee N, Busman-Sahay K, Nekorchuk M, Terry M, Younger S, Bosse M, Demeter J, Rodig SJ, Tzankov A, Goltsev Y, McIlwain DR, Angelo M, Estes JD, Nolan GP. Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments. Immunity 2022; 55:1118-1134.e8. [PMID: 35447093 PMCID: PMC9220319 DOI: 10.1016/j.immuni.2022.03.020] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 10/13/2021] [Accepted: 03/25/2022] [Indexed: 12/12/2022]
Abstract
Understanding the mechanisms of HIV tissue persistence necessitates the ability to visualize tissue microenvironments where infected cells reside; however, technological barriers limit our ability to dissect the cellular components of these HIV reservoirs. Here, we developed protein and nucleic acid in situ imaging (PANINI) to simultaneously quantify DNA, RNA, and protein levels within these tissue compartments. By coupling PANINI with multiplexed ion beam imaging (MIBI), we measured over 30 parameters simultaneously across archival lymphoid tissues from healthy or simian immunodeficiency virus (SIV)-infected nonhuman primates. PANINI enabled the spatial dissection of cellular phenotypes, functional markers, and viral events resulting from infection. SIV infection induced IL-10 expression in lymphoid B cells, which correlated with local macrophage M2 polarization. This highlights a potential viral mechanism for conditioning an immunosuppressive tissue environment for virion production. The spatial multimodal framework here can be extended to decipher tissue responses in other infectious diseases and tumor biology.
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Affiliation(s)
- Sizun Jiang
- Department of Pathology, Stanford University, Stanford, CA, USA; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | - Chi Ngai Chan
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | | | - Han Chen
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yunhao Bai
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Bokai Zhu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Erin McCaffrey
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Candace Liu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Graham L Barlow
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Jason L Weirather
- Center of Immuno-Oncology, Dana-Faber Cancer Institute, Boston, MA, USA
| | - John Paul Oliveria
- Department of Pathology, Stanford University, Stanford, CA, USA; Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Tsuguhisa Nakayama
- Department of Pathology, Stanford University, Stanford, CA, USA; Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Ivan T Lee
- Department of Pathology, Stanford University, Stanford, CA, USA; Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthias S Matter
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Anne E Carlisle
- Center of Immuno-Oncology, Dana-Faber Cancer Institute, Boston, MA, USA
| | - Darci Philips
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Gustavo Vazquez
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Kathleen Busman-Sahay
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Michael Nekorchuk
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Margaret Terry
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Skyler Younger
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA
| | - Marc Bosse
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Janos Demeter
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Scott J Rodig
- Department of Pathology, Brigham & Women's Hospital, Boston, MA, USA
| | - Alexandar Tzankov
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Yury Goltsev
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Michael Angelo
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Jacob D Estes
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, USA; Division of Pathobiology & Immunology, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA.
| | - Garry P Nolan
- Department of Pathology, Stanford University, Stanford, CA, USA.
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4
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Yao Y, Du Jiang P, Chao BN, Cagdas D, Kubo S, Balasubramaniyam A, Zhang Y, Shadur B, NaserEddin A, Folio LR, Schwarz B, Bohrnsen E, Zheng L, Lynberg M, Gottlieb S, Leney-Greene MA, Park AY, Tezcan I, Akdogan A, Gocmen R, Onder S, Rosenberg A, Soilleux EJ, Johnson E, Jackson PK, Demeter J, Chauvin SD, Paul F, Selbach M, Bulut H, Clatworthy MR, Tuong ZK, Zhang H, Stewart BJ, Bosio CM, Stepensky P, Clare S, Ganesan S, Pascall JC, Daumke O, Butcher GW, McMichael AJ, Simon AK, Lenardo MJ. GIMAP6 regulates autophagy, immune competence, and inflammation in mice and humans. J Exp Med 2022; 219:213217. [PMID: 35551368 PMCID: PMC9111091 DOI: 10.1084/jem.20201405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/18/2022] [Accepted: 03/16/2022] [Indexed: 11/26/2022] Open
Abstract
Inborn errors of immunity (IEIs) unveil regulatory pathways of human immunity. We describe a new IEI caused by mutations in the GTPase of the immune-associated protein 6 (GIMAP6) gene in patients with infections, lymphoproliferation, autoimmunity, and multiorgan vasculitis. Patients and Gimap6−/− mice show defects in autophagy, redox regulation, and polyunsaturated fatty acid (PUFA)–containing lipids. We find that GIMAP6 complexes with GABARAPL2 and GIMAP7 to regulate GTPase activity. Also, GIMAP6 is induced by IFN-γ and plays a critical role in antibacterial immunity. Finally, we observed that Gimap6−/− mice died prematurely from microangiopathic glomerulosclerosis most likely due to GIMAP6 deficiency in kidney endothelial cells.
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Affiliation(s)
- Yikun Yao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ping Du Jiang
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Brittany N Chao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD.,Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Deniz Cagdas
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Satoshi Kubo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Arasu Balasubramaniyam
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Yu Zhang
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Bella Shadur
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel.,The Garvan Institute of Medical Research, Immunology Division, Darlinghurst, Sydney, Australia.,St Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, Australia
| | - Adeeb NaserEddin
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Les R Folio
- Clinical Center, National Institutes of Health, Bethesda, MD
| | - Benjamin Schwarz
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Eric Bohrnsen
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Lixin Zheng
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Matthew Lynberg
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Simone Gottlieb
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Michael A Leney-Greene
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Ann Y Park
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ilhan Tezcan
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ali Akdogan
- Division of Rheumatology, Department of Internal Medicine, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Rahsan Gocmen
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Sevgen Onder
- Department of Pathology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Avi Rosenberg
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD.,Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
| | | | - Errin Johnson
- The Dunn School of Pathology, South Parks Road, Oxford, UK
| | - Peter K Jackson
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Janos Demeter
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Samuel D Chauvin
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Florian Paul
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Matthias Selbach
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Haydar Bulut
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Zewen K Tuong
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Hanlin Zhang
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Catharine M Bosio
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Polina Stepensky
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Simon Clare
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - John C Pascall
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Oliver Daumke
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Geoffrey W Butcher
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Andrew J McMichael
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anna Katharina Simon
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
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5
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Kotmayer L, László T, Kiss R, Hegyi LL, Mikala G, Farkas P, Balogh A, Masszi T, Demeter J, Weisinger J, Alizadeh H, Gergely L, Sulák A, Egyed M, Plander M, Pettendi P, Lévai D, Schneider T, Pauker Z, Masszi A, Szász R, Bödör C, Alpár D. P615: BCL2 RESISTANCE MUTATIONS IN A REAL-WORLD COHORT OF PATIENTS WITH VENETOCLAX-TREATED CHRONIC LYMPHOCYTIC LEUKAEMIA. Hemasphere 2022. [DOI: 10.1097/01.hs9.0000845348.59055.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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6
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Mascharak S, Talbott HE, Januszyk M, Griffin M, Chen K, Davitt MF, Demeter J, Henn D, Bonham CA, Foster DS, Mooney N, Cheng R, Jackson PK, Wan DC, Gurtner GC, Longaker MT. Multi-omic analysis reveals divergent molecular events in scarring and regenerative wound healing. Cell Stem Cell 2022; 29:315-327.e6. [DOI: 10.1016/j.stem.2021.12.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 07/01/2021] [Accepted: 12/22/2021] [Indexed: 02/01/2023]
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7
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Chen CK, Cheng R, Demeter J, Chen J, Weingarten-Gabbay S, Jiang L, Snyder MP, Weissman JS, Segal E, Jackson PK, Chang HY. Structured elements drive extensive circular RNA translation. Mol Cell 2021; 81:4300-4318.e13. [PMID: 34437836 PMCID: PMC8567535 DOI: 10.1016/j.molcel.2021.07.042] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 06/03/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022]
Abstract
The human genome encodes tens of thousands circular RNAs (circRNAs) with mostly unknown functions. Circular RNAs require internal ribosome entry sites (IRES) if they are to undergo translation without a 5' cap. Here, we develop a high-throughput screen to systematically discover RNA sequences that can direct circRNA translation in human cells. We identify more than 17,000 endogenous and synthetic sequences as candidate circRNA IRES. 18S rRNA complementarity and a structured RNA element positioned on the IRES are important for driving circRNA translation. Ribosome profiling and peptidomic analyses show extensive IRES-ribosome association, hundreds of circRNA-encoded proteins with tissue-specific distribution, and antigen presentation. We find that circFGFR1p, a protein encoded by circFGFR1 that is downregulated in cancer, functions as a negative regulator of FGFR1 oncoprotein to suppress cell growth during stress. Systematic identification of circRNA IRES elements may provide important links among circRNA regulation, biological function, and disease.
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Affiliation(s)
- Chun-Kan Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ran Cheng
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jin Chen
- Department of Pharmacology and Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shira Weingarten-Gabbay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lihua Jiang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Departments of Dermatology and Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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8
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Wu CT, Hilgendorf KI, Bevacqua RJ, Hang Y, Demeter J, Kim SK, Jackson PK. Discovery of ciliary G protein-coupled receptors regulating pancreatic islet insulin and glucagon secretion. Genes Dev 2021; 35:1243-1255. [PMID: 34385262 PMCID: PMC8415323 DOI: 10.1101/gad.348261.121] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 07/02/2021] [Indexed: 01/17/2023]
Abstract
Multiple G protein-coupled receptors (GPCRs) are expressed in pancreatic islet cells, but the majority have unknown functions. We observed specific GPCRs localized to primary cilia, a prominent signaling organelle, in pancreatic α and β cells. Loss of cilia disrupts β-cell endocrine function, but the molecular drivers are unknown. Using functional expression, we identified multiple GPCRs localized to cilia in mouse and human islet α and β cells, including FFAR4, PTGER4, ADRB2, KISS1R, and P2RY14. Free fatty acid receptor 4 (FFAR4) and prostaglandin E receptor 4 (PTGER4) agonists stimulate ciliary cAMP signaling and promote glucagon and insulin secretion by α- and β-cell lines and by mouse and human islets. Transport of GPCRs to primary cilia requires TULP3, whose knockdown in primary human and mouse islets relocalized ciliary FFAR4 and PTGER4 and impaired regulated glucagon or insulin secretion, without affecting ciliary structure. Our findings provide index evidence that regulated hormone secretion by islet α and β cells is controlled by ciliary GPCRs providing new targets for diabetes.
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Affiliation(s)
- Chien-Ting Wu
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Keren I Hilgendorf
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Romina J Bevacqua
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Yan Hang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Seung K Kim
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Medicine, Stanford University, Stanford, California 94305, USA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
- Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Medicine, Stanford University, Stanford, California 94305, USA
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9
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Wu CT, Lidsky PV, Xiao Y, Lee IT, Cheng R, Nakayama T, Jiang S, Demeter J, Bevacqua RJ, Chang CA, Whitener RL, Stalder AK, Zhu B, Chen H, Goltsev Y, Tzankov A, Nayak JV, Nolan GP, Matter MS, Andino R, Jackson PK. SARS-CoV-2 infects human pancreatic β cells and elicits β cell impairment. Cell Metab 2021; 33:1565-1576.e5. [PMID: 34081912 PMCID: PMC8130512 DOI: 10.1016/j.cmet.2021.05.013] [Citation(s) in RCA: 185] [Impact Index Per Article: 61.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 04/01/2021] [Accepted: 05/07/2021] [Indexed: 01/08/2023]
Abstract
Emerging evidence points toward an intricate relationship between the pandemic of coronavirus disease 2019 (COVID-19) and diabetes. While preexisting diabetes is associated with severe COVID-19, it is unclear whether COVID-19 severity is a cause or consequence of diabetes. To mechanistically link COVID-19 to diabetes, we tested whether insulin-producing pancreatic β cells can be infected by SARS-CoV-2 and cause β cell depletion. We found that the SARS-CoV-2 receptor, ACE2, and related entry factors (TMPRSS2, NRP1, and TRFC) are expressed in β cells, with selectively high expression of NRP1. We discovered that SARS-CoV-2 infects human pancreatic β cells in patients who succumbed to COVID-19 and selectively infects human islet β cells in vitro. We demonstrated that SARS-CoV-2 infection attenuates pancreatic insulin levels and secretion and induces β cell apoptosis, each rescued by NRP1 inhibition. Phosphoproteomic pathway analysis of infected islets indicates apoptotic β cell signaling, similar to that observed in type 1 diabetes (T1D). In summary, our study shows SARS-CoV-2 can directly induce β cell killing.
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Affiliation(s)
- Chien-Ting Wu
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ivan T Lee
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Ran Cheng
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA, USA
| | - Tsuguhisa Nakayama
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA; Department of Otorhinolaryngology, Jikei University School of Medicine, Tokyo, Japan
| | - Sizun Jiang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Romina J Bevacqua
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Charles A Chang
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Robert L Whitener
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anna K Stalder
- Institute of Pathology, University of Basel, Schönbeinstrasse 40, 4003 Basel, Switzerland
| | - Bokai Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Han Chen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yury Goltsev
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexandar Tzankov
- Institute of Pathology, University of Basel, Schönbeinstrasse 40, 4003 Basel, Switzerland
| | - Jayakar V Nayak
- Department of Otolaryngology-Head and Neck Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Garry P Nolan
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthias S Matter
- Institute of Pathology, University of Basel, Schönbeinstrasse 40, 4003 Basel, Switzerland.
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA.
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA.
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10
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Nano PR, Johnson TK, Kudo T, Mooney NA, Ni J, Demeter J, Jackson PK, Chen JK. Structure-activity mapping of ARHGAP36 reveals regulatory roles for its GAP homology and C-terminal domains. PLoS One 2021; 16:e0251684. [PMID: 33999959 PMCID: PMC8128262 DOI: 10.1371/journal.pone.0251684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/01/2021] [Indexed: 11/24/2022] Open
Abstract
ARHGAP36 is an atypical Rho GTPase-activating protein (GAP) family member that drives both spinal cord development and tumorigenesis, acting in part through an N-terminal motif that suppresses protein kinase A and activates Gli transcription factors. ARHGAP36 also contains isoform-specific N-terminal sequences, a central GAP-like module, and a unique C-terminal domain, and the functions of these regions remain unknown. Here we have mapped the ARHGAP36 structure-activity landscape using a deep sequencing-based mutagenesis screen and truncation mutant analyses. Using this approach, we have discovered several residues in the GAP homology domain that are essential for Gli activation and a role for the C-terminal domain in counteracting an N-terminal autoinhibitory motif that is present in certain ARHGAP36 isoforms. In addition, each of these sites modulates ARHGAP36 recruitment to the plasma membrane or primary cilium. Through comparative proteomics, we also have identified proteins that preferentially interact with active ARHGAP36, and we demonstrate that one binding partner, prolyl oligopeptidase-like protein, is a novel ARHGAP36 antagonist. Our work reveals multiple modes of ARHGAP36 regulation and establishes an experimental framework that can be applied towards other signaling proteins.
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Affiliation(s)
- Patricia R. Nano
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Taylor K. Johnson
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Takamasa Kudo
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Nancie A. Mooney
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jun Ni
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Janos Demeter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Peter K. Jackson
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - James K. Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Chemistry, Stanford University, Stanford, California, United States of America
- * E-mail:
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11
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Zaro BW, Noh JJ, Mascetti VL, Demeter J, George B, Zukowska M, Gulati GS, Sinha R, Flynn RA, Banuelos A, Zhang A, Wilkinson AC, Jackson P, Weissman IL. Proteomic analysis of young and old mouse hematopoietic stem cells and their progenitors reveals post-transcriptional regulation in stem cells. eLife 2020; 9:e62210. [PMID: 33236985 PMCID: PMC7688314 DOI: 10.7554/elife.62210] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
The balance of hematopoietic stem cell (HSC) self-renewal and differentiation is critical for a healthy blood supply; imbalances underlie hematological diseases. The importance of HSCs and their progenitors have led to their extensive characterization at genomic and transcriptomic levels. However, the proteomics of hematopoiesis remains incompletely understood. Here we report a proteomics resource from mass spectrometry of mouse young adult and old adult mouse HSCs, multipotent progenitors and oligopotent progenitors; 12 cell types in total. We validated differential protein levels, including confirmation that Dnmt3a protein levels are undetected in young adult mouse HSCs until forced into cycle. Additionally, through integrating proteomics and RNA-sequencing datasets, we identified a subset of genes with apparent post-transcriptional repression in young adult mouse HSCs. In summary, we report proteomic coverage of young and old mouse HSCs and progenitors, with broader implications for understanding mechanisms for stem cell maintenance, niche interactions and fate determination.
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Affiliation(s)
- Balyn W Zaro
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Joseph J Noh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Victoria L Mascetti
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of MedicineStanfordUnited States
| | - Benson George
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Monika Zukowska
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Gunsagar S Gulati
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Ryan A Flynn
- Department of Chemistry, Stanford UniversityStanfordUnited States
| | - Allison Banuelos
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Allison Zhang
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
| | - Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
| | - Peter Jackson
- Baxter Laboratory, Department of Microbiology and Immunology and Department of Pathology, Stanford University School of MedicineStanfordUnited States
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of MedicineStanfordUnited States
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of MedicineStanfordUnited States
- Department of Developmental Biology and the Stanford UC-Berkeley Stem Cell InstituteStanfordUnited States
- Department of Pathology, Stanford University School of MedicineStanfordUnited States
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12
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Schürch CM, Bhate SS, Barlow GL, Phillips DJ, Noti L, Zlobec I, Chu P, Black S, Demeter J, McIlwain DR, Kinoshita S, Samusik N, Goltsev Y, Nolan GP. Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front. Cell 2020; 183:838. [PMID: 33125896 PMCID: PMC7658307 DOI: 10.1016/j.cell.2020.10.021] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Schürch CM, Bhate SS, Barlow GL, Phillips DJ, Noti L, Zlobec I, Chu P, Black S, Demeter J, McIlwain DR, Kinoshita S, Samusik N, Goltsev Y, Nolan GP. Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front. Cell 2020; 182:1341-1359.e19. [PMID: 32763154 PMCID: PMC7479520 DOI: 10.1016/j.cell.2020.07.005] [Citation(s) in RCA: 324] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 04/22/2020] [Accepted: 07/08/2020] [Indexed: 12/21/2022]
Abstract
Antitumoral immunity requires organized, spatially nuanced interactions between components of the immune tumor microenvironment (iTME). Understanding this coordinated behavior in effective versus ineffective tumor control will advance immunotherapies. We re-engineered co-detection by indexing (CODEX) for paraffin-embedded tissue microarrays, enabling simultaneous profiling of 140 tissue regions from 35 advanced-stage colorectal cancer (CRC) patients with 56 protein markers. We identified nine conserved, distinct cellular neighborhoods (CNs)-a collection of components characteristic of the CRC iTME. Enrichment of PD-1+CD4+ T cells only within a granulocyte CN positively correlated with survival in a high-risk patient subset. Coupling of tumor and immune CNs, fragmentation of T cell and macrophage CNs, and disruption of inter-CN communication was associated with inferior outcomes. This study provides a framework for interrogating how complex biological processes, such as antitumoral immunity, occur through concerted actions of cells and spatial domains.
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Affiliation(s)
- Christian M Schürch
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Salil S Bhate
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Graham L Barlow
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Darci J Phillips
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Dermatology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Luca Noti
- Institute of Pathology, University of Bern, 3008 Bern, Switzerland
| | - Inti Zlobec
- Institute of Pathology, University of Bern, 3008 Bern, Switzerland
| | - Pauline Chu
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah Black
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David R McIlwain
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shigemi Kinoshita
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nikolay Samusik
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yury Goltsev
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Garry P Nolan
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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14
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Coles GL, Cristea S, Webber JT, Levin RS, Moss SM, He A, Sangodkar J, Hwang YC, Arand J, Drainas AP, Mooney NA, Demeter J, Spradlin JN, Mauch B, Le V, Shue YT, Ko JH, Lee MC, Kong C, Nomura DK, Ohlmeyer M, Swaney DL, Krogan NJ, Jackson PK, Narla G, Gordan JD, Shokat KM, Sage J. Unbiased Proteomic Profiling Uncovers a Targetable GNAS/PKA/PP2A Axis in Small Cell Lung Cancer Stem Cells. Cancer Cell 2020; 38:129-143.e7. [PMID: 32531271 PMCID: PMC7363571 DOI: 10.1016/j.ccell.2020.05.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 02/18/2020] [Accepted: 05/04/2020] [Indexed: 12/23/2022]
Abstract
Using unbiased kinase profiling, we identified protein kinase A (PKA) as an active kinase in small cell lung cancer (SCLC). Inhibition of PKA activity genetically, or pharmacologically by activation of the PP2A phosphatase, suppresses SCLC expansion in culture and in vivo. Conversely, GNAS (G-protein α subunit), a PKA activator that is genetically activated in a small subset of human SCLC, promotes SCLC development. Phosphoproteomic analyses identified many PKA substrates and mechanisms of action. In particular, PKA activity is required for the propagation of SCLC stem cells in transplantation studies. Broad proteomic analysis of recalcitrant cancers has the potential to uncover targetable signaling networks, such as the GNAS/PKA/PP2A axis in SCLC.
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Affiliation(s)
- Garry L Coles
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Sandra Cristea
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - James T Webber
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Rebecca S Levin
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Steven M Moss
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Andy He
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jaya Sangodkar
- Division of Genetic Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Yeonjoo C Hwang
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Julia Arand
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Alexandros P Drainas
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Nancie A Mooney
- Baxter Laboratory, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Jessica N Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brandon Mauch
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Vicky Le
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Yan Ting Shue
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julie H Ko
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Myung Chang Lee
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Christina Kong
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael Ohlmeyer
- Icahn School of Medicine at Mount Sinai, New York, NY, USA; Atux Iskay LLC, Plainsboro, New Jersey, NJ 08536, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; David J. Gladstone Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA; David J. Gladstone Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Peter K Jackson
- Baxter Laboratory, Stanford University, Stanford, CA 94305, USA; Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Goutham Narla
- Division of Genetic Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - John D Gordan
- Department of Medicine, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA 94158, USA
| | - Kevan M Shokat
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Julien Sage
- Department of Pediatrics, Stanford University, 265 Campus Drive, Stanford, CA 94305-5457, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
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15
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Kelly M, Han K, Kostyrko K, Mooney N, Jeng E, Demeter J, Sweet-Cordero A, Bassik M, Jackson PK. Abstract B25: Combined proteomic and genetic interaction mapping reveals new Ras pathway effectors and regulators. Mol Cancer Res 2020. [DOI: 10.1158/1557-3125.ras18-b25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Despite intensive study, no drugs in clinical use specifically target KRAS-mutant tumors. Uncharacterized feedback pathways and unmapped compensatory pathways, including compensation among paralogs, hinder our ability to target Ras effector pathways, requiring a better catalogue of pathways upstream and downstream of Ras. We used tandem affinity purification of Kras, Hras and Nras, their activated alleles and key proteins with known regulatory (GEFs, GAPs) or effectors (Raf, RalGDS1, RIN1/2) in both 293 cells and A549 NSCLC cells to generate a high-confidence protein-protein interaction (PPI) network of 220 proteins showing 1,400 physical interactions. The network was used to design an sgRNA library (10 sgRNAs/gene) and screen Cas9-expressing A549 cells for strong growth dependencies. These data were then used to select 120 genes and construct a 2-gene tandem sgRNA library of highest relevance to the Ras pathway (with 60 control sgRNAs). This 2-gene sgRNA library was tested in A549 and H23 NSCLC lines for quantitative single and two gene-dependent quantitative changes in growth, showing 100s of strong synthetic lethals among 14K pairwise tests. These genetic interactions in conjunction with PPIs and TCGA data identify extensive coupling between Raf/MEK/ERK kinases, Ral and Rap GTPases, the Rap1GDS1 small GTPase controller, and RADIL cell adhesion pathways. The screen identified new candidate effector pathways for cell adhesion, Rap GTPase regulation, and protein processing, including new understudied Kras direct effectors RADIL, RGL1/2/3, and RIN1/2. Additional 20 x 20 custom libraries were screened in a broader panel of Kras-mutant versus other NSCLC lines. These screens revealed systematic Kras-dependent synthetic lethality among components of the MAP kinase pathway (ERK1/ERK2, ERK1/RAF1, MEK1/MEK2 etc.) and other interactions between the MAPK pathway and components of the Ral and Rap GTPase, RADIL cell adhesion pathways and RIN1-dependent macropinocytosis pathways. Using the recent Kras G12C inhibitor in H23 cells, we have validated that sgRNA knockouts of these Kras effector affect these specific, new pathways: cell adhesion via RADIL, growth signaling via Rap1GDS1 and RhoA, and macropinocytosis via the Rab5 GEF RIN1. Application of the Kras inhibitor ARS-853 shows much-reduced effects on specific Kras effector pathways in cells deleted for these specific effectors, showing these effectors are highly coupled to Kras. Our systematic data reveal new genetic vulnerabilities and target candidates with potential for new therapeutics.
Citation Format: Marcus Kelly, Kyuho Han, Kaja Kostyrko, Nancie Mooney, Edwin Jeng, Janos Demeter, Alejandro Sweet-Cordero, Michael Bassik, Peter K. Jackson. Combined proteomic and genetic interaction mapping reveals new Ras pathway effectors and regulators [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr B25.
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Affiliation(s)
| | | | - Kaja Kostyrko
- 2University of California San Francisco, San Francisco, CA
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16
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Hilgendorf KI, Johnson CT, Mezger A, Rice SL, Norris AM, Demeter J, Greenleaf WJ, Reiter JF, Kopinke D, Jackson PK. Omega-3 Fatty Acids Activate Ciliary FFAR4 to Control Adipogenesis. Cell 2019; 179:1289-1305.e21. [PMID: 31761534 DOI: 10.1016/j.cell.2019.11.005] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 09/23/2019] [Accepted: 10/31/2019] [Indexed: 10/25/2022]
Abstract
Adult mesenchymal stem cells, including preadipocytes, possess a cellular sensory organelle called the primary cilium. Ciliated preadipocytes abundantly populate perivascular compartments in fat and are activated by a high-fat diet. Here, we sought to understand whether preadipocytes use their cilia to sense and respond to external cues to remodel white adipose tissue. Abolishing preadipocyte cilia in mice severely impairs white adipose tissue expansion. We discover that TULP3-dependent ciliary localization of the omega-3 fatty acid receptor FFAR4/GPR120 promotes adipogenesis. FFAR4 agonists and ω-3 fatty acids, but not saturated fatty acids, trigger mitosis and adipogenesis by rapidly activating cAMP production inside cilia. Ciliary cAMP activates EPAC signaling, CTCF-dependent chromatin remodeling, and transcriptional activation of PPARγ and CEBPα to initiate adipogenesis. We propose that dietary ω-3 fatty acids selectively drive expansion of adipocyte numbers to produce new fat cells and store saturated fatty acids, enabling homeostasis of healthy fat tissue.
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Affiliation(s)
- Keren I Hilgendorf
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Carl T Johnson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Stem Cell and Regenerative Medicine Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anja Mezger
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Selena L Rice
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Alessandra M Norris
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Jeremy F Reiter
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Daniel Kopinke
- Department of Biochemistry and Biophysics, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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17
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Hsu J, Arand J, Chaikovsky A, Mooney NA, Demeter J, Brison CM, Oliverio R, Vogel H, Rubin SM, Jackson PK, Sage J. E2F4 regulates transcriptional activation in mouse embryonic stem cells independently of the RB family. Nat Commun 2019; 10:2939. [PMID: 31270324 PMCID: PMC6610666 DOI: 10.1038/s41467-019-10901-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/06/2019] [Indexed: 01/22/2023] Open
Abstract
E2F transcription factors are central regulators of cell division and cell fate decisions. E2F4 often represents the predominant E2F activity in cells. E2F4 is a transcriptional repressor implicated in cell cycle arrest and whose repressive activity depends on its interaction with members of the RB family. Here we show that E2F4 is important for the proliferation and the survival of mouse embryonic stem cells. In these cells, E2F4 acts in part as a transcriptional activator that promotes the expression of cell cycle genes. This role for E2F4 is independent of the RB family. Furthermore, E2F4 functionally interacts with chromatin regulators associated with gene activation and we observed decreased histone acetylation at the promoters of cell cycle genes and E2F targets upon loss of E2F4 in RB family-mutant cells. Taken together, our findings uncover a non-canonical role for E2F4 that provide insights into the biology of rapidly dividing cells. E2F transcription factors are regulators of cell division and cell fate decisions. Here the authors show that E2F4 is important for proliferation and survival of mouse ESCs, independent of the RB family, and that E2F4 interacts with chromatin regulators associated with gene activation.
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Affiliation(s)
- Jenny Hsu
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Julia Arand
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Andrea Chaikovsky
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Nancie A Mooney
- Baxter Laboratory, Department of Microbiology & Immunology, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology & Immunology, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Caileen M Brison
- Department of Chemistry and Biochemistry, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Romane Oliverio
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Hannes Vogel
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.,Department of Pathology, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Julien Sage
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA. .,Department of Genetics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.
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18
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Dreyling M, Santoro A, Leppä S, Demeter J, Follows G, Lenz G, Kim W, Mollica L, Nagler A, Phipps Diong C, Provencio M, Magagnoli M, Munoz J, Hiemeyer F, Liu L, Miriyala A, Rodrigues L, Garcia-Vargas J, Childs B, Zinzani P. EFFICACY AND SAFETY IN HIGH-RISK RELAPSED OR REFRACTORY INDOLENT FOLLICULAR LYMPHOMA PATIENTS TREATED WITH COPANLISIB. Hematol Oncol 2019. [DOI: 10.1002/hon.57_2631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- M. Dreyling
- Department of Medicine III; University Hospital (LMU); Munich Germany
| | - A. Santoro
- Cancer Center; Humanitas Clinical and Research Center; Rozzano Italy
| | - S. Leppä
- Comprehensive Cancer Center; Helsinki University Hospital; Helsinki Finland
| | - J. Demeter
- First Department of Internal Medicine; Semmelweis University; Budapest Hungary
| | - G.A. Follows
- Haematology; Cambridge University Hospitals NHS Foundation Trust; Cambridge United Kingdom
| | - G. Lenz
- Translational Oncology; University Hospital Münster; Münster Germany
| | - W.S. Kim
- Hematology and Oncology; Sungkyunkwan University School of Medicine, Samsung Medical Center; Seoul Republic of Korea
| | - L. Mollica
- Clinical Research in Hematology and Clinical Oncology; Maisonneuve-Rosemont Hospital Research Centre; Montréal Quebec Canada
| | - A. Nagler
- Chaim Sheba Medical Center; Tel Aviv University; Tel HaShomer Israel
| | - C. Phipps Diong
- Department of Haematology; Singapore General Hospital; Bukit Merah Singapore
| | - M. Provencio
- Medical Oncology; Health Research Institute, Hospital Universitario Puerta de Hierro, Universidad Autónoma de Madrid; Madrid Spain
| | - M. Magagnoli
- Cancer Center; Humanitas Clinical and Research Center; Rozzano Italy
| | - J. Munoz
- Hematology and Oncology; Banner MD Anderson Cancer Center Clinic; Gilbert United States
| | - F. Hiemeyer
- Pharmaceutical Division; Bayer AG; Berlin Germany
| | - L. Liu
- Oncology; Bayer HealthCare Pharmaceuticals, Inc.; Whippany United States
| | - A. Miriyala
- Oncology; Bayer HealthCare Pharmaceuticals, Inc.; Whippany United States
| | | | - J. Garcia-Vargas
- Oncology; Bayer HealthCare Pharmaceuticals, Inc.; Whippany United States
| | - B.H. Childs
- Oncology; Bayer HealthCare Pharmaceuticals, Inc.; Whippany United States
| | - P.L. Zinzani
- Institute of Hematology “Seràgnoli”; University of Bologna; Bologna Italy
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19
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Zinzani P, Santoro A, Leppä S, Demeter J, Follows G, Lenz G, Kim W, Mollica L, Nagler A, Phipps Diong C, Provencio M, Magagnoli M, Munoz J, Miriyala A, Liu L, Zhang M, Garcia-Vargas J, Childs B, Dreyling M. SAFETY ANALYSIS OF PATIENTS WITH A MEDICAL HISTORY OF RESPIRATORY DISORDERS TREATED WITH COPANLISIB FROM THE CHRONOS-1 STUDY IN RELAPSED OR REFRACTORY INDOLENT B-CELL LYMPHOMA. Hematol Oncol 2019. [DOI: 10.1002/hon.58_2631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- P.L. Zinzani
- Institute of Hematology “Seràgnoli”; University of Bologna; Bologna Italy
| | - A. Santoro
- Cancer Center; Humanitas Clinical and Research Center; Rozzano Italy
| | - S. Leppä
- Comprehensive Cancer Center; Helsinki University Hospital; Helsinki Finland
| | - J. Demeter
- First Department of Internal Medicine; Semmelweis University; Budapest Hungary
| | - G.A. Follows
- Haematology; Cambridge University Hospitals NHS Foundation Trust; Cambridge United Kingdom
| | - G. Lenz
- Translational Oncology; University Hospital Münster; Münster Germany
| | - W.S. Kim
- Samsung Medical Center; Sungkyunkwan University School of Medicine; Seoul Republic of Korea
| | - L. Mollica
- Clinical Research in Hematology and Clinical Oncology; Maisonneuve-Rosemont Hospital Research Centre; Montréal, Quebec Canada
| | - A. Nagler
- Chaim Sheba Medical Center; Tel Aviv University; Tel HaShomer Israel
| | - C. Phipps Diong
- Department of Haematology; Singapore General Hospital; Bukit Merah Singapore
| | - M. Provencio
- Health Research Institute; Hospital Universitario Puerta de Hierro, Universidad Autónoma de Madrid; Madrid Spain
| | - M. Magagnoli
- Cancer Center; Humanitas Clinical and Research Center; Rozzano Italy
| | - J. Munoz
- Hematology and Oncology; Banner MD Anderson Cancer Center Clinic; Gilbert United States
| | - A. Miriyala
- Oncology; Bayer HealthCare Pharmaceuticals, Inc.; Whippany United States
| | - L. Liu
- Oncology; Bayer HealthCare Pharmaceuticals, Inc.; Whippany United States
| | - M. Zhang
- Oncology; Bayer HealthCare Pharmaceuticals, Inc.; Whippany United States
| | - J. Garcia-Vargas
- Oncology; Bayer HealthCare Pharmaceuticals, Inc.; Whippany United States
| | - B.H. Childs
- Oncology; Bayer HealthCare Pharmaceuticals, Inc.; Whippany United States
| | - M. Dreyling
- Department of Medicine III; University Hospital (LMU); Munich Germany
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20
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Lin CH, Wang Z, Duque-Afonso J, Wong SHK, Demeter J, Loktev AV, Somervaille TCP, Jackson PK, Cleary ML. Oligomeric self-association contributes to E2A-PBX1-mediated oncogenesis. Sci Rep 2019; 9:4915. [PMID: 30894657 PMCID: PMC6426973 DOI: 10.1038/s41598-019-41393-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 03/04/2019] [Indexed: 11/16/2022] Open
Abstract
The PBX1 homeodomain transcription factor is converted by t(1;19) chromosomal translocations in acute leukemia into the chimeric E2A-PBX1 oncoprotein. Fusion with E2A confers potent transcriptional activation and constitutive nuclear localization, bypassing the need for dimerization with protein partners that normally stabilize and regulate import of PBX1 into the nucleus, but the mechanisms underlying its oncogenic activation are incompletely defined. We demonstrate here that E2A-PBX1 self-associates through the PBX1 PBC-B domain of the chimeric protein to form higher-order oligomers in t(1;19) human leukemia cells, and that this property is required for oncogenic activity. Structural and functional studies indicate that self-association facilitates the binding of E2A-PBX1 to DNA. Mutants unable to self-associate are transformation defective, however their oncogenic activity is rescued by the synthetic oligomerization domain of FKBP, which confers conditional transformation properties on E2A-PBX1. In contrast to self-association, PBX1 protein domains that mediate interactions with HOX DNA-binding partners are dispensable. These studies suggest that oligomeric self-association may compensate for the inability of monomeric E2A-PBX1 to stably bind DNA and circumvents protein interactions that otherwise modulate PBX1 stability, nuclear localization, DNA binding, and transcriptional activity. The unique dependence on self-association for E2A-PBX1 oncogenic activity suggests potential approaches for mechanism-based targeted therapies.
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MESH Headings
- Basic Helix-Loop-Helix Transcription Factors/genetics
- Basic Helix-Loop-Helix Transcription Factors/metabolism
- Carcinogenesis/genetics
- Cell Line, Tumor
- Chromosomes, Human, Pair 1/chemistry
- Chromosomes, Human, Pair 19/chemistry
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Gene Expression Regulation, Neoplastic
- HEK293 Cells
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Pre-B-Cell Leukemia Transcription Factor 1/genetics
- Pre-B-Cell Leukemia Transcription Factor 1/metabolism
- Protein Binding
- Protein Multimerization
- Protein Stability
- Tacrolimus Binding Proteins/genetics
- Tacrolimus Binding Proteins/metabolism
- Transcription, Genetic
- Translocation, Genetic
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Affiliation(s)
- Chiou-Hong Lin
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Zhong Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, 510006, China
| | - Jesús Duque-Afonso
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Hematology and Oncology, University Medical Center Freiburg, Freiburg, Germany
| | - Stephen Hon-Kit Wong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Janos Demeter
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Alexander V Loktev
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Tim C P Somervaille
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester, M20 4GJ, UK
| | - Peter K Jackson
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Michael L Cleary
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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21
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Szakonyi J, Medvecz M, Wikonkál N, Holló P, Hídvégi B, Demeter J, Csomor J, Szepesi Á, Marschalkó M. Lymphoproliferative diseases among patients treated with biologicals: a case study and single center survey. Eur J Cancer 2019. [DOI: 10.1016/s0959-8049(19)30633-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Provencio Pulla M, Santoro A, Mollica L, Leppä S, Follows G, Lenz G, Kim W, Nagler A, Panayiotidis P, Demeter J, Özcan M, Kosinova M, Bouabdallah K, Morschhauser F, Ishida T, Huang L, Garcia-Vargas J, Childs B, Zinzani P, Dreyling M. Copanlisib treatment in patients with relapsed or refractory indolent B-cell lymphoma: Subgroup analyses from the CHRONOS-1 study. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx373.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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23
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Kanie T, Abbott KL, Mooney NA, Plowey ED, Demeter J, Jackson PK. The CEP19-RABL2 GTPase Complex Binds IFT-B to Initiate Intraflagellar Transport at the Ciliary Base. Dev Cell 2017. [PMID: 28625565 DOI: 10.1016/j.devcel.2017.05.016] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Highly conserved intraflagellar transport (IFT) protein complexes direct both the assembly of primary cilia and the trafficking of signaling molecules. IFT complexes initially accumulate at the base of the cilium and periodically enter the cilium, suggesting an as-yet-unidentified mechanism that triggers ciliary entry of IFT complexes. Using affinity-purification and mass spectrometry of interactors of the centrosomal and ciliopathy protein, CEP19, we identify CEP350, FOP, and the RABL2B GTPase as proteins organizing the first known mechanism directing ciliary entry of IFT complexes. We discover that CEP19 is recruited to the ciliary base by the centriolar CEP350/FOP complex and then specifically captures GTP-bound RABL2B, which is activated via its intrinsic nucleotide exchange. Activated RABL2B then captures and releases its single effector, the intraflagellar transport B holocomplex, from the large pool of pre-docked IFT-B complexes, and thus initiates ciliary entry of IFT.
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Affiliation(s)
- Tomoharu Kanie
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Keene Louis Abbott
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nancie Ann Mooney
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Edward Douglas Plowey
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Peter Kent Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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24
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Dreyling M, Santoro A, Mollica L, Leppä S, Follows G, Lenz G, Kim W, Nagler A, Panayiotidis P, Demeter J, Özcan M, Kosinova M, Bouabdallah K, Morschhauser F, Stevens D, Trevarthen D, Giurescu M, Liu L, Koechert K, Peña C, Cupit L, Yin S, Hiemeyer F, Garcia-Vargas J, Childs B, Zinzani P. COPANLISIB IN PATIENTS WITH RELAPSED OR REFRACTORY INDOLENT B-CELL LYMPHOMA (CHRONOS-1). Hematol Oncol 2017. [DOI: 10.1002/hon.2437_107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- M. Dreyling
- Medizinische Klinik und Poliklinik III; Klinikum der Universität München-Grosshadern; Munich Germany
| | - A. Santoro
- Department of Oncology and Hematology, Humanitas Cancer Center; Humanitas Clinical and Research Institute; Rozzano MI Italy
| | - L. Mollica
- Department of Hematology; Hôpital Maisonneuve-Rosemont-Montreal; Montreal Quebec Canada
| | - S. Leppä
- Department of Oncology; Helsinki University Central Hospital Cancer Center; Helsinki Finland
| | - G.A. Follows
- Department of Haematology; Cambridge University Hospitals NHS Foundation Trust Addenbrooke's Hospital; Cambridge UK
| | - G. Lenz
- Translational Oncology; University Hospital Münster; Münster Germany
| | - W. Kim
- Division of Hematology and Oncology, Department of Medicine; Sungkyunkwan University School of Medicine, Samsung Medical Center; Seoul Republic of Korea
| | - A. Nagler
- Hematology Division; Chaim Sheba Medical Center- Tel Aviv University; Tel-Hashomer Israel
| | - P. Panayiotidis
- Division of Hematology; Laikon University Hospital, National and Kapodistrian University of Athens; Athens Greece
| | - J. Demeter
- First Department of Internal Medicine, Division of Haematology; Semmelweis University; Budapest Hungary
| | - M. Özcan
- Department of Hematology; Ankara University School of Medicine; Ankara Turkey
| | - M. Kosinova
- Department of Hematology; Kemerovo Regional Clinical Hospital; Kemerovo Russian Federation
| | - K. Bouabdallah
- Service d'Hématologie et de Thérapie Cellulaire; University Hospital of Bordeaux; Pessac France
| | - F. Morschhauser
- Department of Hematology; CHRU - Hôpital Claude Huriez; Lille France
| | - D.A. Stevens
- Medical Oncology; Norton Cancer Institute; Louisville-KY USA
| | - D. Trevarthen
- Medical Oncology; Comprehensive Cancer Care and Research Institute of Colorado; Englewood-CO USA
| | - M. Giurescu
- Pharmaceutical Division, Bayer AG; Berlin Germany
| | - L. Liu
- Biomarkers; Bayer HealthCare Pharmaceuticals Inc; Whippany-NJ USA
| | - K. Koechert
- Pharmaceutical Division, Bayer AG; Berlin Germany
| | - C. Peña
- Biomarkers; Bayer HealthCare Pharmaceuticals Inc; Whippany-NJ USA
| | - L. Cupit
- Clinical Development; Bayer HealthCare Pharmaceuticals Inc; Whippany-NJ USA
| | - S. Yin
- Clinical Development; Bayer HealthCare Pharmaceuticals Inc; Whippany-NJ USA
| | - F. Hiemeyer
- Pharmaceutical Division, Bayer AG; Berlin Germany
| | - J. Garcia-Vargas
- Clinical Development; Bayer HealthCare Pharmaceuticals Inc; Whippany-NJ USA
| | - B.H. Childs
- Clinical Development; Bayer HealthCare Pharmaceuticals Inc; Whippany-NJ USA
| | - P. Zinzani
- Department of Hematology; Institute of Hematology "L. e A. Seràgnoli"- University of Bologna; Bologna Italy
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Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag K, Demeter J, Engel S, Hellerstedt ST, Karra K, Hitz BC, Nash RS, Paskov K, Sheppard T, Skrzypek M, Weng S, Wong E, Michael Cherry J. Integration of new alternative reference strain genome sequences into the Saccharomyces genome database. Database (Oxford) 2016; 2016:baw074. [PMID: 27252399 PMCID: PMC4888754 DOI: 10.1093/database/baw074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 04/22/2016] [Indexed: 12/14/2022]
Abstract
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. To provide a wider scope of genetic and phenotypic variation in yeast, the genome sequences and their corresponding annotations from 11 alternative S. cerevisiae reference strains have been integrated into SGD. Genomic and protein sequence information for genes from these strains are now available on the Sequence and Protein tab of the corresponding Locus Summary pages. We illustrate how these genome sequences can be utilized to aid our understanding of strain-specific functional and phenotypic differences. Database URL:www.yeastgenome.org
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Affiliation(s)
- Giltae Song
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Gail Binkley
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Kyla Dalusag
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Janos Demeter
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Stacia Engel
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Kalpana Karra
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Benjamin C Hitz
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Robert S Nash
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Kelley Paskov
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Travis Sheppard
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Marek Skrzypek
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Shuai Weng
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Edith Wong
- Department of Genetics, Stanford University, Stanford, CA, USA
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26
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Sheppard TK, Hitz BC, Engel SR, Song G, Balakrishnan R, Binkley G, Costanzo MC, Dalusag KS, Demeter J, Hellerstedt ST, Karra K, Nash RS, Paskov KM, Skrzypek MS, Weng S, Wong ED, Cherry JM. The Saccharomyces Genome Database Variant Viewer. Nucleic Acids Res 2015; 44:D698-702. [PMID: 26578556 PMCID: PMC4702884 DOI: 10.1093/nar/gkv1250] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/02/2015] [Indexed: 11/18/2022] Open
Abstract
The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is the authoritative community resource for the Saccharomyces cerevisiae reference genome sequence and its annotation. In recent years, we have moved toward increased representation of sequence variation and allelic differences within S. cerevisiae. The publication of numerous additional genomes has motivated the creation of new tools for their annotation and analysis. Here we present the Variant Viewer: a dynamic open-source web application for the visualization of genomic and proteomic differences. Multiple sequence alignments have been constructed across high quality genome sequences from 11 different S. cerevisiae strains and stored in the SGD. The alignments and summaries are encoded in JSON and used to create a two-tiered dynamic view of the budding yeast pan-genome, available at http://www.yeastgenome.org/variant-viewer.
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Affiliation(s)
- Travis K Sheppard
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Benjamin C Hitz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stacia R Engel
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Giltae Song
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rama Balakrishnan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gail Binkley
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maria C Costanzo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kyla S Dalusag
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Janos Demeter
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sage T Hellerstedt
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kalpana Karra
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert S Nash
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kelley M Paskov
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marek S Skrzypek
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shuai Weng
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Edith D Wong
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - J Michael Cherry
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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27
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Song G, Dickins BJA, Demeter J, Engel S, Gallagher J, Choe K, Dunn B, Snyder M, Cherry JM. Correction: AGAPE (Automated Genome Analysis PipelinE) for Pan-Genome Analysis of Saccharomyces cerevisiae. PLoS One 2015; 10:e0129184. [PMID: 26017550 PMCID: PMC4446291 DOI: 10.1371/journal.pone.0129184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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28
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Song G, Dickins BJA, Demeter J, Engel S, Dunn B, Cherry JM. AGAPE (Automated Genome Analysis PipelinE) for pan-genome analysis of Saccharomyces cerevisiae. PLoS One 2015; 10:e0120671. [PMID: 25781462 PMCID: PMC4363492 DOI: 10.1371/journal.pone.0120671] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 01/25/2015] [Indexed: 11/24/2022] Open
Abstract
The characterization and public release of genome sequences from thousands of organisms is expanding the scope for genetic variation studies. However, understanding the phenotypic consequences of genetic variation remains a challenge in eukaryotes due to the complexity of the genotype-phenotype map. One approach to this is the intensive study of model systems for which diverse sources of information can be accumulated and integrated. Saccharomyces cerevisiae is an extensively studied model organism, with well-known protein functions and thoroughly curated phenotype data. To develop and expand the available resources linking genomic variation with function in yeast, we aim to model the pan-genome of S. cerevisiae. To initiate the yeast pan-genome, we newly sequenced or re-sequenced the genomes of 25 strains that are commonly used in the yeast research community using advanced sequencing technology at high quality. We also developed a pipeline for automated pan-genome analysis, which integrates the steps of assembly, annotation, and variation calling. To assign strain-specific functional annotations, we identified genes that were not present in the reference genome. We classified these according to their presence or absence across strains and characterized each group of genes with known functional and phenotypic features. The functional roles of novel genes not found in the reference genome and associated with strains or groups of strains appear to be consistent with anticipated adaptations in specific lineages. As more S. cerevisiae strain genomes are released, our analysis can be used to collate genome data and relate it to lineage-specific patterns of genome evolution. Our new tool set will enhance our understanding of genomic and functional evolution in S. cerevisiae, and will be available to the yeast genetics and molecular biology community.
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Affiliation(s)
- Giltae Song
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
| | - Benjamin J. A. Dickins
- School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Janos Demeter
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Stacia Engel
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Barbara Dunn
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - J. Michael Cherry
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
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29
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Marton I, Pósfai É, Borbényi Z, Bödör C, Papp G, Demeter J, Korom I, Varga E, Bata-Csörgő Z. Therapeutic challenge during the long-term follow-up of a patient with indolent systemic mastocytosis with extensive cutaneous involvement. Eur Rev Med Pharmacol Sci 2015; 19:1607-1609. [PMID: 26004600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
From a dermatological aspect, it posed a considerable challenge the skin-limited form of mastocytosis, urticaria pigmentosa and indolent systemic mastocytosis (ISM) with cutaneous lesions. Despite the favourable prognosis, lifelong dermatological control is needed, during which the average symptomatic therapy does not always seem adequate. We report here the case of a female ISM patient with recurrent cutaneous symptoms that impaired her quality of life, with a follow-up time of 27 years. During this long follow-up period, the cutaneous lesions could be controlled by antihistamines, leukotriene antagonists, glucocorticoids, local immunosuppressants or local UV radiation for only relatively short periods. Imatinib mesylate was, therefore, introduced in an attempt to control the cutaneous lesions. Tyrosine kinase inhibition is an unusual dermatological therapeutic option. This case illustrates that imatinib mesylate was a good choice with which to achieve a reduction of the skin lesions in this KIT D816V mutation-negative disease: it led to a temporary appreciable improvement of the patient's quality of life.
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Affiliation(s)
- I Marton
- 2nd Department of Medicine and Cardiology Centre, Medical Faculty, Albert Szent-Györgyi Clinical Centre, University of Szeged, Szeged, Hungary.
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30
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Meldal BHM, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S. The complex portal--an encyclopaedia of macromolecular complexes. Nucleic Acids Res 2014; 43:D479-84. [PMID: 25313161 PMCID: PMC4384031 DOI: 10.1093/nar/gku975] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The IntAct molecular interaction database has created a new, free, open-source, manually curated resource, the Complex Portal (www.ebi.ac.uk/intact/complex), through which protein complexes from major model organisms are being collated and made available for search, viewing and download. It has been built in close collaboration with other bioinformatics services and populated with data from ChEMBL, MatrixDB, PDBe, Reactome and UniProtKB. Each entry contains information about the participating molecules (including small molecules and nucleic acids), their stoichiometry, topology and structural assembly. Complexes are annotated with details about their function, properties and complex-specific Gene Ontology (GO) terms. Consistent nomenclature is used throughout the resource with systematic names, recommended names and a list of synonyms all provided. The use of the Evidence Code Ontology allows us to indicate for which entries direct experimental evidence is available or if the complex has been inferred based on homology or orthology. The data are searchable using standard identifiers, such as UniProt, ChEBI and GO IDs, protein, gene and complex names or synonyms. This reference resource will be maintained and grow to encompass an increasing number of organisms. Input from groups and individuals with specific areas of expertise is welcome.
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Affiliation(s)
- Birgit H M Meldal
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Oscar Forner-Martinez
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Maria C Costanzo
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5477, USA
| | - Jose Dana
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Janos Demeter
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5477, USA
| | - Marine Dumousseau
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Selina S Dwight
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5477, USA
| | - Anna Gaulton
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Luana Licata
- Department of Biology, University of Rome, Tor Vergata, Rome 00133, Italy
| | - Anna N Melidoni
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Sylvie Ricard-Blum
- UMR 5086 CNRS, Université Lyon1, Institut de Biologie et Chimie des Protéines, 7 passage du Vercors, 69367 Lyon Cedex 07, France
| | - Bernd Roechert
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland
| | - Marek S Skyzypek
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5477, USA
| | - Manu Tiwari
- Stammzellbiologie, Institut für Anatomie und Zellbiologie, GZMB Universitätsmedizin Göttingen, Ernst-Caspari-Haus, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Sameer Velankar
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Edith D Wong
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5477, USA
| | - Henning Hermjakob
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Sandra Orchard
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
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31
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Véber O, Wilde A, Demeter J, Tamás G, Mucsi I, Tabák AG. The effect of steroid pulse therapy on carbohydrate metabolism in multiple myeloma patients: a randomized crossover observational clinical study. J Endocrinol Invest 2014; 37:345-51. [PMID: 24682910 DOI: 10.1007/s40618-013-0027-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 11/18/2013] [Indexed: 10/25/2022]
Abstract
BACKGROUND Hyperglycemia is a common, but not well-characterized side effect of glucocorticoid treatment. AIM To study the effect of pulse dexamethasone treatment on carbohydrate metabolism among multiple myeloma patients. MATERIAL/SUBJECTS AND METHODS A randomized crossover observational study in a teaching hospital with nine myeloma patients (one male, two with known type 2 diabetes (KDM), mean age 69.0 ± 6.7 years) were investigated using a standard 75 g Oral Glucose Tolerance Test (patients without KDM) and a 3-day continuous glucose monitoring (CGM--all patients) during and between dexamethasone cycles. RESULTS During dexamethasone treatment patients had elevated 2-h postload glucose (12.8 ± 4.7 vs. 8.7 ± 3.2 mmol/L, P = 0.024) but similar fasting glucose (6.3 ± 1.4 vs. 5.1 ± 0.5 mmol/L, P = 0.112). Estimated hourly mean interstitial glucose values based on linear mixed models showed an increase of 0.03 [SE 0.01] mmol/L per hour from 5.0 [0.4] in patients without KDM and followed a quadratic curve from 5.0 [0.4] mmol/L at midnight to 7.5 [0.5] mmol/L at 12:00 h in patients with KDM during control periods. During dexamethasone treatment glucose was similar to control periods between 02:00 and 12:00 h in the non-KDM group, where they followed a cubic trajectory from 5.3 [0.4] mmol/L at 04:00 h to 7.3 [0.4] mmol/L at 18:00 h. In contrast, interstitial glucose was increased by at least 7.9 [0.3] mmol/L throughout the day in KDM patients during dexamethasone treatment and increased from 13.6 [0.5] mmol/L at midnight to 17.5 [0.5] mmol/L at 17:00 h. CONCLUSIONS During pulse steroid therapy of myeloma patients without KDM afternoon and evening glucose measurements may be the optimal tools to characterize glucose metabolism.
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Affiliation(s)
- O Véber
- Institute of Behavioural Sciences, Semmelweis University Faculty of Medicine, Budapest, Hungary
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32
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Hu JC, Sherlock G, Siegele DA, Aleksander SA, Ball CA, Demeter J, Gouni S, Holland TA, Karp PD, Lewis JE, Liles NM, McIntosh BK, Mi H, Muruganujan A, Wymore F, Thomas PD, Altman T. PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. Nucleic Acids Res 2013; 42:D677-84. [PMID: 24285306 PMCID: PMC3965092 DOI: 10.1093/nar/gkt1203] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
PortEco (http://porteco.org) aims to collect, curate and provide data and analysis tools to support basic biological research in Escherichia coli (and eventually other bacterial systems). PortEco is implemented as a ‘virtual’ model organism database that provides a single unified interface to the user, while integrating information from a variety of sources. The main focus of PortEco is to enable broad use of the growing number of high-throughput experiments available for E. coli, and to leverage community annotation through the EcoliWiki and GONUTS systems. Currently, PortEco includes curated data from hundreds of genome-wide RNA expression studies, from high-throughput phenotyping of single-gene knockouts under hundreds of annotated conditions, from chromatin immunoprecipitation experiments for tens of different DNA-binding factors and from ribosome profiling experiments that yield insights into protein expression. Conditions have been annotated with a consistent vocabulary, and data have been consistently normalized to enable users to find, compare and interpret relevant experiments. PortEco includes tools for data analysis, including clustering, enrichment analysis and exploration via genome browsers. PortEco search and data analysis tools are extensively linked to the curated gene, metabolic pathway and regulation content at its sister site, EcoCyc.
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Affiliation(s)
- James C Hu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA, Department of Genetics, Stanford University, Stanford, CA 94305, USA, Department of Biology, Texas A&M University, College Station, TX, 77843, USA, Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA and Deptartment of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
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33
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Vastagh I, Palásti Á, Aradi G, Tóth A, Várallyay G, Rudas G, Demeter J, Csomor J, Aberle S, Budka H, Bereczki D, Kovács G. Six-year survival of progressive multifocal leukoencephalopathy associated with follicular lymphoma. J Neurol Sci 2013. [DOI: 10.1016/j.jns.2013.07.2137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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34
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Demeter J, Teichert A, Kiefer K, Wallacher D, Ryll H, Menéndez E, Paramanik D, Steitz R, Van Haesendonck C, Vantomme A, Temst K. Simultaneous polarized neutron reflectometry and anisotropic magnetoresistance measurements. Rev Sci Instrum 2011; 82:033902. [PMID: 21456758 DOI: 10.1063/1.3541839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A novel experimental facility to carry out simultaneous polarized neutron reflectometry (PNR) and anisotropic magnetoresistance (AMR) measurements is presented. Performing both techniques at the same time increases their strength considerably. The proof of concept of this method is demonstrated on a CoO/Co bilayer exchange bias system. Although information on the same phenomena, such as the coercivity or the reversal mechanism, can be separately obtained from either of these techniques, the simultaneous application optimizes the consistency between both. In this way, possible differences in experimental conditions, such as applied magnetic field amplitude and orientation, sample temperature, magnetic history, etc., can be ruled out. Consequently, only differences in the fundamental sensitivities of the techniques can cause discrepancies in the interpretation between the two. The almost instantaneous information obtained from AMR can be used to reveal time-dependent effects during the PNR acquisition. Moreover, the information inferred from the AMR measurements can be used for optimizing the experimental conditions for the PNR measurements in a more efficient way than with the PNR measurements alone.
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Affiliation(s)
- J Demeter
- Instituut voor Kern- en Stralingsfysica and INPAC, K.U.Leuven, Celestijnenlaan 200D, B-3001 Leuven, Belgium.
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35
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Fodor A, Hoffer I, Krenács L, Bagdi E, Csomor J, Matolcsy A, Molnár M, Eid H, Nagy Z, Demeter J. 45 High frequency and prognostic importance of autoimmune hemolytic anemia in splenic marginal zone lymphoma. EJC Suppl 2010. [DOI: 10.1016/s1359-6349(10)70716-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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36
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Holterhus PM, Bebermeier JH, Werner R, Demeter J, Richter-Unruh A, Cario G, Appari M, Siebert R, Riepe F, Brooks JD, Hiort O. Disorders of sex development expose transcriptional autonomy of genetic sex and androgen-programmed hormonal sex in human blood leukocytes. BMC Genomics 2009; 10:292. [PMID: 19570224 PMCID: PMC2713997 DOI: 10.1186/1471-2164-10-292] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Accepted: 07/01/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gender appears to be determined by independent programs controlled by the sex-chromosomes and by androgen-dependent programming during embryonic development. To enable experimental dissection of these components in the human, we performed genome-wide profiling of the transcriptomes of peripheral blood mononuclear cells (PBMC) in patients with rare defined "disorders of sex development" (DSD, e.g., 46, XY-females due to defective androgen biosynthesis) compared to normal 46, XY-males and 46, XX-females. RESULTS A discrete set of transcripts was directly correlated with XY or XX genotypes in all individuals independent of male or female phenotype of the external genitalia. However, a significantly larger gene set in the PBMC only reflected the degree of external genital masculinization independent of the sex chromosomes and independent of concurrent post-natal sex steroid hormone levels. Consequently, the architecture of the transcriptional PBMC-"sexes" was either male, female or even "intersex" with a discordant alignment of the DSD individuals' genetic and hormonal sex signatures. CONCLUSION A significant fraction of gene expression differences between males and females in the human appears to have its roots in early embryogenesis and is not only caused by sex chromosomes but also by long-term sex-specific hormonal programming due to presence or absence of androgen during the time of external genital masculinization. Genetic sex and the androgen milieu during embryonic development might therefore independently modulate functional traits, phenotype and diseases associated with male or female gender as well as with DSD conditions.
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37
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Appari M, Werner R, Wünsch L, Cario G, Demeter J, Hiort O, Riepe F, Brooks JD, Holterhus PM. Apolipoprotein D (APOD) is a putative biomarker of androgen receptor function in androgen insensitivity syndrome. J Mol Med (Berl) 2009; 87:623-32. [PMID: 19330472 DOI: 10.1007/s00109-009-0462-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Revised: 02/24/2009] [Accepted: 03/04/2009] [Indexed: 01/24/2023]
Abstract
Androgen insensitivity syndrome (AIS) is the most common cause of disorders of sex development usually caused by mutations in the androgen receptor (AR) gene. AIS is characterized by a poor genotype-phenotype correlation, and many patients with clinically presumed AIS do not seem to have mutations in the AR gene. We therefore aimed at identifying a biomarker enabling the assessment of the cellular function of the AR as a transcriptional activator. In the first step, we used complementary DNA (cDNA) microarrays for a genome-wide screen for androgen-regulated genes in two normal male primary scrotal skin fibroblast strains compared to two labia majora fibroblast strains from 46,XY females with complete AIS (CAIS). Apolipoprotein D (APOD) and two further transcripts were significantly upregulated by dihydrotestosterone (DHT) in scrotum fibroblasts, while CAIS labia majora cells were unresponsive. Microarray data were well correlated with quantitative real-time polymerase chain reaction (qRT-PCR; R = 0.93). Subsequently, we used qRT-PCR in independent new cell cultures and confirmed the significant DHT-dependent upregulation of APOD in five normal scrotum strains [13.5 +/- 8.2 (SD)-fold] compared with three CAIS strains (1.2 +/- 0.7-fold, p = 0.028; t test) and six partial androgen insensitivity syndrome strains (2 +/- 1.3-fold, p = 0.034; t test). Moreover, two different 17ss-hydroxysteroid dehydrogenase III deficiency labia majora strains showed APOD induction in the range of normal scrotum (9.96 +/- 1.4-fold), supporting AR specificity. Therefore, qRT-PCR of APOD messenger RNA transcription in primary cultures of labioscrotal skin fibroblasts is a promising tool for assessing AR function, potentially allowing a function-based diagnostic evaluation of AIS in the future.
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Affiliation(s)
- Mahesh Appari
- Department of Pediatrics, University-Hospital Schleswig-Holstein, Christian Albrechts University of Kiel, Germany.
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Hubble J, Demeter J, Jin H, Mao M, Nitzberg M, Reddy TBK, Wymore F, Zachariah ZK, Sherlock G, Ball CA. Implementation of GenePattern within the Stanford Microarray Database. Nucleic Acids Res 2008; 37:D898-901. [PMID: 18953035 PMCID: PMC2686537 DOI: 10.1093/nar/gkn786] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Hundreds of researchers across the world use the Stanford Microarray Database (SMD; http://smd.stanford.edu/) to store, annotate, view, analyze and share microarray data. In addition to providing registered users at Stanford access to their own data, SMD also provides access to public data, and tools with which to analyze those data, to any public user anywhere in the world. Previously, the addition of new microarray data analysis tools to SMD has been limited by available engineering resources, and in addition, the existing suite of tools did not provide a simple way to design, execute and share analysis pipelines, or to document such pipelines for the purposes of publication. To address this, we have incorporated the GenePattern software package directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. In this article, we describe our implementation of the GenePattern microarray analysis software package into the SMD code base. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability.
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Affiliation(s)
- Jeremy Hubble
- Department of Genetics, Stanford University School of Medicine, CA 94305, USA
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Holterhus PM, Deppe U, Werner R, Richter-Unruh A, Bebermeier JH, Wünsch L, Krege S, Schweikert HU, Demeter J, Riepe F, Hiort O, Brooks JD. Intrinsic androgen-dependent gene expression patterns revealed by comparison of genital fibroblasts from normal males and individuals with complete and partial androgen insensitivity syndrome. BMC Genomics 2007; 8:376. [PMID: 17945006 PMCID: PMC2212662 DOI: 10.1186/1471-2164-8-376] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 10/18/2007] [Indexed: 01/22/2023] Open
Abstract
Background To better understand the molecular programs of normal and abnormal genital development, clear-cut definition of androgen-dependent gene expression patterns, without the influence of genotype (46, XX vs. 46, XY), is warranted. Previously, we have identified global gene expression profiles in genital-derived fibroblasts that differ between 46, XY males and 46, XY females with complete androgen insensitivity syndrome (CAIS) due to inactivating mutations of the androgen receptor (AR). While these differences could be due to cell autonomous changes in gene expression induced by androgen programming, recent work suggests they could also be influenced by the location from which the fibroblasts were harvested (topology). To minimize the influence of topology, we compared gene expression patterns of fibroblasts derived from identical urogenital anlagen: the scrotum in normally virilized 46, XY males and the labia majora from completely feminized 46, XY individuals with CAIS. Results 612 transcripts representing 440 unique genes differed significantly in expression levels between scrotum and CAIS labia majora, suggesting the effects of androgen programming. While some genes coincided with those we had identified previously (TBX3, IGFBP5, EGFR, CSPG2), a significant number did not, implying that topology had influenced gene expression in our previous experiments. Supervised clustering of gene expression data derived from a large set of fibroblast cultures from individuals with partial AIS revealed that the new, topology controlled data set better classified the specimens. Conclusion Inactivating mutations of the AR, in themselves, appear to induce lasting changes in gene expression in cultured fibroblasts, independent of topology and genotype. Genes identified are likely to be relevant candidates to decipher androgen-dependent normal and abnormal genital development.
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Affiliation(s)
- Paul-Martin Holterhus
- Department of Pediatrics, University-Hospital Schleswig-Holstein, Campus Kiel, Schwanenweg 20, Kiel, Germany.
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Marschalkó M, Csomor J, Eros N, Szigeti A, Hársing J, Szakonyi J, Désaknai M, Matolcsy A, Demeter J, Kárpáti S. Coexistence of primary cutaneous anaplastic large cell lymphoma and mycosis fungoides in a patient with B-cell chronic lymphocytic leukaemia. Br J Dermatol 2007; 157:1291-3. [PMID: 17927791 DOI: 10.1111/j.1365-2133.2007.08226.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Demeter J, Balassa K, D¨om¨ot¨or M, Egyed M, Gasztonyi Z, Aryab H, Gurzó M, Iványi J, Klucsik Z, Sréter L, Nagy Z. P166 Experience with the use of yttrium-90 ibritumomab tiuxetan (Zevalin) in relapsed follicular lymphoma. Blood Rev 2007. [DOI: 10.1016/s0268-960x(07)70245-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Balassa K, B¨od¨or C, Vonnák E, Kovacs T, Matolcsy A, Demeter J. P118 Familial polycythaemia vera in a Hungarian family. Blood Rev 2007. [DOI: 10.1016/s0268-960x(07)70196-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Hajdu M, Sebestyén A, Barna G, Reiniger L, Jánosi J, Sréter L, Várkonyi J, Demeter J, Kopper L. Activity of the notch-signalling pathway in circulating human chronic lymphocytic leukaemia cells. Scand J Immunol 2007; 65:271-5. [PMID: 17309782 DOI: 10.1111/j.1365-3083.2006.01897.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dysregulation of the Notch-pathway has been implicated in the pathogenesis of chronic lymphocytic leukaemia (B-CLL). We characterized the mRNA expression of Notch pathway elements in circulating normal B- and B-CLL cells, and compared expression profiles with clinical and prognostic data. Similar expression profiles were found in normal B-cells and B-CLL cells, however, most B-CLL samples showed lower Hairy/Enhancer of Split-1 expression than normal B-cells, which suggests that the pathway is not over-activated in B-CLL. The expression of Notch-pathway genes did not correlate with other prognostic factors of B-CLL. The importance of Notch-signalling in CLL cells in lymphatic tissue microenvironments remains to be determined.
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Affiliation(s)
- M Hajdu
- I Department of Pathology and Experimental Cancer Research, Budapest, Hungary.
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Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, Jin H, Maier D, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G, Ball CA. The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res 2006; 35:D766-70. [PMID: 17182626 PMCID: PMC1781111 DOI: 10.1093/nar/gkl1019] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The Stanford Microarray Database (SMD; ) is a research tool and archive that allows hundreds of researchers worldwide to store, annotate, analyze and share data generated by microarray technology. SMD supports most major microarray platforms, and is MIAME-supportive and can export or import MAGE-ML. The primary mission of SMD is to be a research tool that supports researchers from the point of data generation to data publication and dissemination, but it also provides unrestricted access to analysis tools and public data from 300 publications. In addition to supporting ongoing research, SMD makes its source code fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD. In this article, we describe several data analysis tools implemented in SMD and we discuss features of our software release.
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Affiliation(s)
- Janos Demeter
- Department of Biochemistry, Stanford University School of MedicineStanford, CA, USA
| | - Catherine Beauheim
- Department of Genetics, Stanford University School of MedicineStanford, CA, USA
| | | | | | - Heng Jin
- Department of Biochemistry, Stanford University School of MedicineStanford, CA, USA
| | - Donald Maier
- Department of Biochemistry, Stanford University School of MedicineStanford, CA, USA
| | - John C. Matese
- Lewis-Sigler Institute for Integrative Genomics, Princeton UniversityPrinceton, NJ, USA
| | - Michael Nitzberg
- Department of Biochemistry, Stanford University School of MedicineStanford, CA, USA
| | - Farrell Wymore
- Department of Biochemistry, Stanford University School of MedicineStanford, CA, USA
| | | | - Patrick O. Brown
- Department of Biochemistry, Stanford University School of MedicineStanford, CA, USA
- Howard Hughes Medical InstituteStanford, CA, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of MedicineStanford, CA, USA
| | - Catherine A. Ball
- Department of Biochemistry, Stanford University School of MedicineStanford, CA, USA
- To whom correspondence should be addressed. Tel: +1 650 724 3028; Fax: +1 650 724 3701;
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Bebermeier JH, Brooks JD, DePrimo SE, Werner R, Deppe U, Demeter J, Hiort O, Holterhus PM. Cell-line and tissue-specific signatures of androgen receptor-coregulator transcription. J Mol Med (Berl) 2006; 84:919-31. [PMID: 16932916 DOI: 10.1007/s00109-006-0081-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2005] [Accepted: 03/31/2006] [Indexed: 10/24/2022]
Abstract
Normal genital skin fibroblasts (GSF) and the human prostate carcinoma cell line LNCaP have been used widely as cell culture models of genital origin to study androgen receptor (AR) signaling. We demonstrate that LNCaP shows a reproducible response to androgens as assessed using cDNA-microarrays representing approximately 32,000 unique human genes, whereas several independent GSF strains are virtually unresponsive. We show that LNCaP cells express markedly higher AR protein levels likely contributing to the observed differences of androgen responsiveness. However, previous data suggested that AR-expression levels alone do not determine androgen responsiveness of human GSF compared to LNCaP. We hypothesized that cell-specific differences in expression levels of AR coregulators might contribute to differences in androgen responsiveness and might be found by comparing LNCaP and GSFs. Using the Canadian McGill-database of AR coregulators ( http://www.mcgill.ca/androgendb ), we identified 61 AR-coregulator genes represented by 282 transcripts on our microarray platform that was used to measure transcript profiles of LNCaP and GSF cells. Baseline expression levels of 48 AR-coregulator transcripts representing 33 distinct genes showed significant differences between GSF and LNCaP, four of which we confirmed by reverse transcriptase polymerase chain reaction. Compared to LNCaP, GSFs displayed significant upregulation of AR coregulators that can function as repressors of AR-transactivation, such as caveolin 1. Analysis of a recently published comprehensive dataset of 115 microarrays representing 35 different human tissues revealed tissue-specific signatures of AR coregulators that segregated with ontogenetically related groups of tissues (e.g., lymphatic system and genital tissues, brain). Our data demonstrate the existence of cell-line and tissue-specific expression patterns of molecules with documented AR coregulatory functions. Therefore, differential expression patterns of AR coregulators could modify tissue-specificity and diversity of androgen actions in development, physiology, and disease.
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Affiliation(s)
- Jan-Hendrik Bebermeier
- Department of Pediatric and Adolescent Medicine, University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
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Garner CE, Sumner SCJ, Davis JG, Burgess JP, Yueh Y, Demeter J, Zhan Q, Valentine J, Jeffcoat AR, Burka LT, Mathews JM. Metabolism and disposition of 1-bromopropane in rats and mice following inhalation or intravenous administration. Toxicol Appl Pharmacol 2006; 215:23-36. [PMID: 16513153 DOI: 10.1016/j.taap.2006.01.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Revised: 01/20/2006] [Accepted: 01/25/2006] [Indexed: 11/18/2022]
Abstract
Workplace exposure to 1-bromopropane (1-BrP) can potentially occur during its use in spray adhesives, fats, waxes, and resins. 1-BrP may be used to replace ozone depleting solvents, resulting in an increase in its annual production in the US, which currently exceeds 1 million pounds. The potential for human exposure to 1-BrP and the reports of adverse effects associated with potential occupational exposure to high levels of 1-BrP have increased the need for the development of biomarkers of exposure and an improved understanding of 1-BrP metabolism and disposition. In this study, the factors influencing the disposition and biotransformation of 1-BrP were examined in male F344 rats and B6C3F1 mice following inhalation exposure (800 ppm) or intravenous administration (5, 20, and 100 mg/kg). [1,2,3-(13)C]1-BrP and [1-(14)C]1-BrP were administered to enable characterization of urinary metabolites using NMR spectroscopy, LC-MS/MS, and HPLC coupled radiochromatography. Exhaled breath volatile organic chemicals (VOC), exhaled CO(2), urine, feces, and tissues were collected for up to 48 h post-administration for determination of radioactivity distribution. Rats and mice exhaled a majority of the administered dose as either VOC (40-72%) or (14)CO(2) (10-30%). For rats, but not mice, the percentage of the dose exhaled as VOC increased between the mid ( approximately 50%) and high ( approximately 71%) dose groups; while the percentage of the dose exhaled as (14)CO(2) decreased (19 to 10%). The molar ratio of exhaled (14)CO(2) to total released bromide, which decreased as dose increased, demonstrated that the proportion of 1-BrP metabolized via oxidation relative to pathways dependent on glutathione conjugation is inversely proportional to dose in the rat. [(14)C]1-BrP equivalents were recovered in urine (13-17%, rats; 14-23% mice), feces (<2%), or retained in the tissues and carcass (<6%) of rats and mice administered i.v. 5 to 100 mg/kg [(14)C]1-BrP. Metabolites characterized in urine of rats and mice include N-acetyl-S-propylcysteine, N-acetyl-3-(propylsulfinyl)alanine, N-acetyl-S-(2-hydroxypropyl)cysteine, 1-bromo-2-hydroxypropane-O-glucuronide, N-acetyl-S-(2-oxopropyl)cysteine, and N-acetyl-3-[(2-oxopropyl)sulfinyl]alanine. These metabolites may be formed following oxidation of 1-bromopropane to 1-bromo-2-propanol and bromoacetone and following subsequent glutathione conjugation with either of these compounds. Rats pretreated with 1-aminobenzotriazole (ABT), a potent inhibitor of P450 excreted less in urine (down 30%), exhaled as (14)CO2 (down 80%), or retained in liver (down 90%), with a concomitant increase in radioactivity expired as VOC (up 52%). Following ABT pretreatment, rat urinary metabolites were reduced in number from 10 to 1, N-acetyl-S-propylcysteine, which accounted for >90% of the total urinary radioactivity in ABT pretreated rats. Together, these data demonstrate a role for cytochrome P450 and glutathione in the dose-dependent metabolism and disposition of 1-BrP in the rat.
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Affiliation(s)
- C E Garner
- Department of Drug Metabolism and Disposition, RTI International, Research Triangle Park, NC 27709, USA.
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Ferreri AJ, Ponzoni M, Guidoboni M, Cortelazzo S, Demeter J, Zallio F, Palmas A, Politi L, Doglioni C, Dolcetti R. Chlamydia psittaci (Cp)-eradicating therapy with doxycycline is an active treatment against ocular adnexa MALT lymphoma (OAML): Final results of a multicentre prospective trial. J Clin Oncol 2006. [DOI: 10.1200/jco.2006.24.18_suppl.7559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
7559 Background: An association between OAML and Cp infection has been reported. Preliminary data suggest that patients (pts) with Cp-related OAML could achieve lymphoma regression after eradicating therapy with doxycycline, while data on the activity of this strategy in Cp-negative OAML are not available. Methods: In this multicentre prospective trial, 27 consecutive pts with OAML and measurable disease, at diagnosis (n = 15) or relapse, were treated with doxycycline 100 mg, bid orally, for 3 weeks. Objective response was the primary endpoint. The presence of Cp DNA in lymphoma samples was evaluated by TETR-PCR. Results: Tolerability was excellent in all pts but one. At a median follow-up of 13 mo. (range 3–45), response was complete (CR) in 6 pts and partial in 7 (ORR = 48%; 95% CI:30%-66%); three pts had a response <50%, 9 had stable disease (3–13 mo.), two had progressive disease. Response was slow; 5 pts achieved the best response only after one year of follow-up (median time to the best response: 6 mo.). TETR-PCR resulted positive in 11 (41%) pts and negative in 16. Lymphoma regression was observed in both PCR-positive and -negative pts (64% vs. 38%; p = 0.25), with a CR rate of 36% and 13% (p = 0.18), respectively. Response rate was similar between pts with conjunctival and intra-orbital lymphomas (43% vs. 54%, p = 0.71). The three pts with regional lymphadenopathies and three of the 5 pts with bilateral OAL achieved objective response (4 CRs), which lasted 3+, 13+, 16+, 22+, 26+, and 37 mo. In relapsed pts, objective response was observed in 3 of 5 previously irradiated pts and in 5 of 7 non-irradiated pts (p = 0.99). Twenty pts are failure-free, with a 2-yr FFS of 66±12%. Conclusions: Doxycycline is a fast, cheap and safe therapy, able to induce durable regression in 64% of Cp-related OAML. This antibiotic is a valid alternative against OAML, even in pts with multiple failures, involving previously irradiated areas or regional lymph nodes. We report for the first time responses also in PCR-negative OAML; this finding stimulates the development of more sensitive and specific methods for Cp detection and the study of potential associations with other infectious agents responsive to doxycycline. No significant financial relationships to disclose.
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Affiliation(s)
- A. J. Ferreri
- San Raffaele H Scientific Institute, Milan, Italy; Centro di Riferimento Oncologico, Aviano, Italy; Ospedale Riuniti di Bergamo, Bergamo, Italy; Semmelweis University, Budapest, Hungary; Istituto Nazionale dei Tumori, Milan, Italy; Ospedale San Francesco, Nuoro, Italy
| | - M. Ponzoni
- San Raffaele H Scientific Institute, Milan, Italy; Centro di Riferimento Oncologico, Aviano, Italy; Ospedale Riuniti di Bergamo, Bergamo, Italy; Semmelweis University, Budapest, Hungary; Istituto Nazionale dei Tumori, Milan, Italy; Ospedale San Francesco, Nuoro, Italy
| | - M. Guidoboni
- San Raffaele H Scientific Institute, Milan, Italy; Centro di Riferimento Oncologico, Aviano, Italy; Ospedale Riuniti di Bergamo, Bergamo, Italy; Semmelweis University, Budapest, Hungary; Istituto Nazionale dei Tumori, Milan, Italy; Ospedale San Francesco, Nuoro, Italy
| | - S. Cortelazzo
- San Raffaele H Scientific Institute, Milan, Italy; Centro di Riferimento Oncologico, Aviano, Italy; Ospedale Riuniti di Bergamo, Bergamo, Italy; Semmelweis University, Budapest, Hungary; Istituto Nazionale dei Tumori, Milan, Italy; Ospedale San Francesco, Nuoro, Italy
| | - J. Demeter
- San Raffaele H Scientific Institute, Milan, Italy; Centro di Riferimento Oncologico, Aviano, Italy; Ospedale Riuniti di Bergamo, Bergamo, Italy; Semmelweis University, Budapest, Hungary; Istituto Nazionale dei Tumori, Milan, Italy; Ospedale San Francesco, Nuoro, Italy
| | - F. Zallio
- San Raffaele H Scientific Institute, Milan, Italy; Centro di Riferimento Oncologico, Aviano, Italy; Ospedale Riuniti di Bergamo, Bergamo, Italy; Semmelweis University, Budapest, Hungary; Istituto Nazionale dei Tumori, Milan, Italy; Ospedale San Francesco, Nuoro, Italy
| | - A. Palmas
- San Raffaele H Scientific Institute, Milan, Italy; Centro di Riferimento Oncologico, Aviano, Italy; Ospedale Riuniti di Bergamo, Bergamo, Italy; Semmelweis University, Budapest, Hungary; Istituto Nazionale dei Tumori, Milan, Italy; Ospedale San Francesco, Nuoro, Italy
| | - L. Politi
- San Raffaele H Scientific Institute, Milan, Italy; Centro di Riferimento Oncologico, Aviano, Italy; Ospedale Riuniti di Bergamo, Bergamo, Italy; Semmelweis University, Budapest, Hungary; Istituto Nazionale dei Tumori, Milan, Italy; Ospedale San Francesco, Nuoro, Italy
| | - C. Doglioni
- San Raffaele H Scientific Institute, Milan, Italy; Centro di Riferimento Oncologico, Aviano, Italy; Ospedale Riuniti di Bergamo, Bergamo, Italy; Semmelweis University, Budapest, Hungary; Istituto Nazionale dei Tumori, Milan, Italy; Ospedale San Francesco, Nuoro, Italy
| | - R. Dolcetti
- San Raffaele H Scientific Institute, Milan, Italy; Centro di Riferimento Oncologico, Aviano, Italy; Ospedale Riuniti di Bergamo, Bergamo, Italy; Semmelweis University, Budapest, Hungary; Istituto Nazionale dei Tumori, Milan, Italy; Ospedale San Francesco, Nuoro, Italy
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Dairkee SH, Nicolau M, Champion S, Ji Y, Sayeed A, Meng Z, Demeter J, Jeffrey SS. Immortalization-associated gene signature in breast cancer. Breast Cancer Res 2005. [PMCID: PMC4233551 DOI: 10.1186/bcr1130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Ball CA, Awad IAB, Demeter J, Gollub J, Hebert JM, Hernandez-Boussard T, Jin H, Matese JC, Nitzberg M, Wymore F, Zachariah ZK, Brown PO, Sherlock G. The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res 2005; 33:D580-2. [PMID: 15608265 PMCID: PMC539960 DOI: 10.1093/nar/gki006] [Citation(s) in RCA: 150] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The Stanford Microarray Database (SMD) (http://smd.stanford.edu) is a research tool for hundreds of Stanford researchers and their collaborators. In addition, SMD functions as a resource for the entire biological research community by providing unrestricted access to microarray data published by SMD users and by disseminating its source code. In addition to storing GenePix (Axon Instruments) and ScanAlyze output from spotted microarrays, SMD has recently added the ability to store, retrieve, display and analyze the complete raw data produced by several additional microarray platforms and image analysis software packages, so that we can also now accept data from Affymetrix GeneChips (MAS5/GCOS or dChip), Agilent Catalog or Custom arrays (using Agilent's Feature Extraction software) or data created by SpotReader (Niles Scientific). We have implemented software that allows us to accept MAGE-ML documents from array manufacturers and to submit MIAME-compliant data in MAGE-ML format directly to ArrayExpress and GEO, greatly increasing the ease with which data from SMD can be published adhering to accepted standards and also increasing the accessibility of published microarray data to the general public. We have introduced a new tool to facilitate data sharing among our users, so that datasets can be shared during, before or after the completion of data analysis. The latest version of the source code for the complete database package was released in November 2004 (http://smd.stanford.edu/download/), allowing researchers around the world to deploy their own installations of SMD.
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Affiliation(s)
- Catherine A Ball
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
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Shah PH, MacFarlane RC, Bhattacharya D, Matese JC, Demeter J, Stroup SE, Singh U. Comparative genomic hybridizations of Entamoeba strains reveal unique genetic fingerprints that correlate with virulence. Eukaryot Cell 2005; 4:504-15. [PMID: 15755913 PMCID: PMC1087797 DOI: 10.1128/ec.4.3.504-515.2005] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2004] [Accepted: 12/21/2004] [Indexed: 11/20/2022]
Abstract
Variable phenotypes have been identified for Entamoeba species. Entamoeba histolytica is invasive and causes colitis and liver abscesses but only in approximately 10% of infected individuals; 90% remain asymptomatically colonized. Entamoeba dispar, a closely related species, is avirulent. To determine the extent of genetic diversity among Entamoeba isolates and potential genotype-phenotype correlations, we have developed an E. histolytica genomic DNA microarray and used it to genotype strains of E. histolytica and E. dispar. On the basis of the identification of divergent genetic loci, all strains had unique genetic fingerprints. Comparison of divergent genetic regions allowed us to distinguish between E. histolytica and E. dispar, identify novel genetic regions usable for strain and species typing, and identify a number of genes restricted to virulent strains. Among the four E. histolytica strains, a strain with attenuated virulence was the most divergent and phylogenetically distinct strain, raising the intriguing possibility that genetic subtypes of E. histolytica may be partially responsible for the observed variability in clinical outcomes. This microarray-based genotyping assay can readily be applied to the study of E. histolytica clinical isolates to determine genetic diversity and potential genotypic-phenotypic associations.
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Affiliation(s)
- Preetam H Shah
- Department of Medicine, Division of Infectious Diseases, Stanford University School of Medicine, Stanford, CA, USA
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