DOCSLIB.ORG

Single Cell-Derived Clonal Analysis of Human Glioblastoma Links Functional and Genomic Heterogeneity

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Single Cell-Derived Clonal Analysis of Human Glioblastoma Links Functional and Genomic Heterogeneity Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity Mona Meyera,1, Jüri Reimandb,c,1, Xiaoyang Lana,b, Renee Heada, Xueming Zhua, Michelle Kushidaa, Jane Bayanid, Jessica C. Presseye, Anath C. Lionelb,f, Ian D. Clarkea,g, Michael Cusimanoh, Jeremy A. Squirei, Stephen W. Schererb,f, Mark Bernsteinj, Melanie A. Woodine, Gary D. Baderb,c,2, and Peter B. Dirksa,b,k,2 aDivision of Neurosurgery, Program in Developmental and Stem Cell Biology, Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON, Canada M5G 1X8; bDepartment of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8; cThe Donnelly Centre, University of Toronto, Toronto, ON, Canada M5S 3E1 Canada; dDepartment of Transformative Pathology at the Ontario Institute for Cancer Research, Ontario Institute for Cancer Research, Toronto, ON, Canada M5G 0A3; eDepartment of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada M5S 3G5; fThe Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada M5G 1L7; gOntario College of Art and Design, Toronto, ON, Canada M5T 1W1; hDivision of Neurosurgery, St. Michael’s Hospital, Toronto, ON, Canada M5B 1W8; iDepartment of Pathology, Queen’s University, Kingston, ON, Canada K7L 3N6; jDivision of Neurosurgery, Toronto Western Hospital, Toronto, ON, Canada M5T 2S8; and kDepartment of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada M5S 1A8 Edited by Robert A. Weinberg, Whitehead Institute for Biomedical Research; Department of Biology, Massachusetts Institute of Technology, and Ludwig MIT Center for Molecular Oncology, Cambridge, Cambridge, MA, and approved November 24, 2014 (received for review November 7, 2013) Glioblastoma (GBM) is a cancer comprised of morphologically, Understanding the links between genetic and functional genetically, and phenotypically diverse cells. However, an un- behavior of individual GBM clones, derived from single pa- derstanding of the functional significance of intratumoral hetero- tient samples, will be essential to decipher patient-specific geneity is lacking. We devised a method to isolate and functionally molecular mechanisms of GBM progression and therapeutic profile tumorigenic clones from patient glioblastoma samples. resistance. The study of bulk tumors provides a mixture of Individual clones demonstrated unique proliferation and differen- different signals from a heterogeneous set of clones and cur- tiation abilities. Importantly, naïve patient tumors included clones rent single cell approaches are amenable to genomics but not MEDICAL SCIENCES that were temozolomide resistant, indicating that resistance to functional studies. Here, we provide a detailed analysis of single conventional GBM therapy can preexist in untreated tumors at cell derived clones from patient GBM samples using a method a clonal level. Further, candidate therapies for resistant clones were that directly links clonal molecular changes with functional detected with clone-specific drug screening. Genomic analyses properties. Parallel phenotypic and genomic analysis of these revealed genes and pathways that associate with specific functional clones reveals a diverse landscape of functional and genetic behavior of single clones. Our results suggest that functional clonal heterogeneity, as well as insights into drug sensitivity pathways profiling used to identify tumorigenic and drug-resistant tumor in glioblastoma. clones will lead to the discovery of new GBM clone-specific treat- ment strategies. Significance cancer | glioblastoma | clonal heterogeneity | genomic analysis | functional analysis Glioblastoma is an incurable brain tumor. It is characterized by intratumoral phenotypic and genetic heterogeneity, but the functional significance of this heterogeneity is unclear. We lioblastoma (GBM) is the most common and most aggres- devised an integrated functional and genomic strategy to ob- Gsive primary malignant brain tumor in adults. Despite major tain single cell-derived tumor clones directly from patient efforts to improve GBM survival, radiation therapy with concurrent tumors to identify mechanisms of aggressive clone behavior temozolomide (TMZ) chemotherapy achieves only a median sur- and drug resistance. Genomic analysis of single clones iden- vival of 15 months with few long-term survivors. Many patients fail tified genes associated with clonal phenotypes. We predict to respond to TMZ, and treatment of all patients at disease pro- that integration of functional and genomic analysis at a clonal gression uniformly fails. level will be essential for understanding evolution and ther- Glioblastoma is one of the first cancer types systematically apeutic resistance of human cancer, and will lead to the dis- – studied at a genomic and transcriptomic level (1 3). Tran- covery of novel driver mechanisms and clone-specific cancer scriptional profiling of GBM samples has revealed a landscape treatment. of intertumoral heterogeneity with distinct molecular tumor subtypes, although only slight prognostic differences are ap- Author contributions: M.M., J.R., X.L., I.D.C., J.A.S., M.A.W., G.D.B., and P.B.D. designed parent in patients except for a clearly better prognosis in the research; M.M., J.R., X.L., R.H., X.Z., M.K., J.B., J.C.P., I.D.C., M.A.W., and G.D.B. performed CIMP+/IDH1 mutant subgroup (1, 4–6). Increasing evidence research; M.M., J.R., X.L., M.C., M.B., and G.D.B. contributed new reagents/analytic tools; M.M., J.R., X.L., M.K., J.B., J.C.P., A.C.L., I.D.C., J.A.S., S.W.S., M.A.W., G.D.B., and P.B.D. suggests that cancer tissues are more complex than previously analyzed data; M.M., J.R., X.L., G.D.B., and P.B.D. wrote the paper; and P.B.D. originated thought, as tumors comprise considerable intratumoral het- and supervised the study at all stages. erogeneity with mixtures of genetically distinct subclones that The authors declare no conflict of interest. – likely escape therapy and cause disease progression (4, 7 10). This article is a PNAS Direct Submission. In particular, GBM is a cancer type comprised of morpholog- Freely available online through the PNAS open access option. ically and phenotypically diverse cells (11). Recent studies have Data deposition: Gene expression profiles and copy number data are available at ArrayEx- also uncovered genetic diversity apparent in subsamples of in- press, www.ebi.ac.uk/arrayexpress/ (accession nos. E-MTAB-2693 and E-MTAB-2694). – dividual patient GBMs (12 15), and more recently in single 1M.M. and J.R. contributed equally to this work. GBM cells (9). Disease recurrence is associated with muta- 2To whom correspondence may be addressed. Email: [email protected] or peter. tional events that are not shared with the primary tumor sug- [email protected]. gesting evolution from minority populations present at time of This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. initial diagnosis (10). 1073/pnas.1320611111/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1320611111 PNAS Early Edition | 1of6 Downloaded by guest on September 26, 2021 Results independent experiments with clones of different passages, the Single Cell-Derived Clones of Human Glioblastoma Exhibit Functional clones exhibited wide and independent variation in proliferation B SI Appendix Heterogeneity. To enable functional characterization of hetero- and differentiation abilities (Fig. 2 and , Figs. S3 and A–C geneous clones in glioblastoma, we devised a method to isolate S4 ), demonstrating intrinsic distinct functional properties. and grow individual clones from patient tumors using flow We then assessed clonal population response to the conven- cytometry sorting (FACS) and single cell plating in stem cell tional GBM chemotherapeutic agent TMZ (17), in at least three culture conditions (Fig. 1A). We generated 44 individual single independent experiments with clones of different passages. Two tumors contained clones with heterogeneous TMZ responses: 2 cell derived clones from four patient tumors. All tested clones of 8 tested populations in the naïve tumor GBM-472 showed established typical GBM tumors after orthotopic injection in significantly increased resistance to TMZ (P = 0.0011, t test with mice, indicating their tumorigenic potential (SI Appendix, Table Welch correction; clones 472_8, 472_18), whereas 1 clone of 10 in A–D B − S1 and Fig. S1 and Fig. 1 ). the recurrent tumor GBM-482 was relatively sensitive (P < 10 4; We next functionally characterized individual clones. We 482_9; Fig. 2C). We observed only TMZ-resistant clones from identified heterogeneous expression of key GBM proteins phos- the two additional naïve and recurrent tumors. TMZ response phatase and tensin homolog (PTEN), epidermal growth factor and proliferation ability was not significantly correlated (SI Ap- receptor (EGFR), and the constitutively active EGFR deletion pendix, Figs. S5 and S6). Clonal analysis of O6-methylguanin- mutant, EGFRvIII (2, 3, 10, 16), in three tumors, indicating that DNA methyltransferase (MGMT), a common biomarker of TMZ distinct known molecular GBM drivers vary at a clonal level (Fig. resistance in GBM (18), showed variable promoter methylation 2A and SI Appendix,Fig.S2) and suggesting limitations to targeted and protein expression levels that were inconsistent with TMZ therapies based solely on bulk GBM analysis. In identical cul- response (Fig. 2 D and E and SI Appendix,Fig.S7). These data ture conditions
Load more

Recommended publications
  • Accurate Annotation of Human Protein-Coding Small Open Reading Frames
    HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Nat Chem Manuscript Author Biol. Author Manuscript Author manuscript; available in PMC 2020 June 09. Published in final edited form as: Nat Chem Biol. 2020 April ; 16(4): 458–468. doi:10.1038/s41589-019-0425-0. Accurate annotation of human protein-coding small open reading frames Thomas F. Martinez1,*, Qian Chu1, Cynthia Donaldson1, Dan Tan1, Maxim N. Shokhirev2, Alan Saghatelian1,* 1Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, California 92037, USA 2Razavi Newman Integrative Genomics Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, California 92037, USA Abstract Functional protein-coding small open reading frames (smORFs) are emerging as an important class of genes. However, the number of translated smORFs in the human genome is unclear because proteogenomic methods are not sensitive enough, and, as we show, Ribo-Seq strategies require additional measures to ensure comprehensive and accurate smORF annotation. Here, we integrate de novo transcriptome assembly and Ribo-Seq into an improved workflow that overcomes obstacles with previous methods to more confidently annotate thousands of smORFs. Evolutionary conservation analyses suggest that hundreds of smORF-encoded microproteins are likely functional. Additionally, many smORFs are regulated during fundamental biological processes, such as cell stress. Peptides derived from smORFs are also detectable on human leukocyte antigen complexes, revealing smORFs as a source of antigens. Thus, by including additional validation into our smORF annotation workflow, we accurately identify thousands of unannotated translated smORFs that will provide a rich pool of unexplored, functional human genes. Annotation of open reading frames (ORFs) from genome sequencing was initially carried out by locating in-frame start (AUG) and stop codons1–3.
    [Show full text]
  • Thyroid Hormone Influences Brain Gene Expression Programs And
    Molecular Psychiatry https://doi.org/10.1038/s41380-018-0281-4 ARTICLE Thyroid hormone influences brain gene expression programs and behaviors in later generations by altering germ line epigenetic information 1 2,3 1 1 1 M. Elena Martinez ● Christine W. Duarte ● J. Patrizia Stohn ● Aldona Karaczyn ● Zhaofei Wu ● 1 1,3,4 Victoria E DeMambro ● Arturo Hernandez Received: 30 March 2018 / Revised: 16 August 2018 / Accepted: 26 September 2018 © Springer Nature Limited 2018 Abstract Genetic factors do not fully account for the relatively high heritability of neurodevelopmental conditions, suggesting that non-genetic heritable factors contribute to their etiology. To evaluate the potential contribution of aberrant thyroid hormone status to the epigenetic inheritance of neurological phenotypes, we examined genetically normal F2 generation descendants of mice that were developmentally overexposed to thyroid hormone due to a Dio3 mutation. Hypothalamic gene expression profiling in postnatal day 15 F2 descendants on the paternal lineage of ancestral male and female T3-overexposed mice 1234567890();,: 1234567890();,: revealed, respectively, 1089 and 1549 differentially expressed genes. A large number of them, 675 genes, were common to both sets, suggesting comparable epigenetic effects of thyroid hormone on both the male and female ancestral germ lines. Oligodendrocyte- and neuron-specific genes were strongly overrepresented among genes showing, respectively, increased and decreased expression. Altered gene expression extended to other brain regions and was associated in adulthood with decreased anxiety-like behavior, increased marble burying and reduced physical activity. The sperm of T3-overexposed male ancestors revealed significant hypomethylation of CpG islands associated with the promoters of genes involved in the early development of the central nervous system.
    [Show full text]
  • Gene Expression Studies in Depression Development and Treatment
    Mariani et al. Translational Psychiatry (2021) 11:354 https://doi.org/10.1038/s41398-021-01469-6 Translational Psychiatry REVIEW ARTICLE Open Access Gene expression studies in Depression development and treatment: an overview of the underlying molecular mechanisms and biological processes to identify biomarkers Nicole Mariani 1, Nadia Cattane2,CarminePariante 1 and Annamaria Cattaneo 2,3 Abstract A combination of different risk factors, such as genetic, environmental and psychological factors, together with immune system, stress response, brain neuroplasticity and the regulation of neurotransmitters, is thought to lead to the development of major depressive disorder (MDD). A growing number of studies have tried to investigate the underlying mechanisms of MDD by analysing the expression levels of genes involved in such biological processes. These studies have shown that MDD is not just a brain disorder, but also a body disorder, and this is mainly due to the interplay between the periphery and the Central Nervous System (CNS). To this purpose, most of the studies conducted so far have mainly dedicated to the analysis of the gene expression levels using postmortem brain tissue as well as peripheral blood samples of MDD patients. In this paper, we reviewed the current literature on candidate gene expression alterations and the few existing transcriptomics studies in MDD focusing on inflammation, neuroplasticity, neurotransmitters and stress-related genes. Moreover, we focused our attention on studies, which have investigated 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; mRNA levels as biomarkers to predict therapy outcomes. This is important as many patients do not respond to antidepressant medication or could experience adverse side effects, leading to the interruption of treatment.
    [Show full text]
  • Supplementary Material
    Supplementary Material Table S1: Significant downregulated KEGGs pathways identified by DAVID following exposure to five cinnamon- based phenylpropanoids (p < 0.05). p-value Term: Genes (Benjamini) Cytokine-cytokine receptor interaction: FASLG, TNFSF14, CXCL11, IL11, FLT3LG, CCL3L1, CCL3L3, CXCR6, XCR1, 2.43 × 105 RTEL1, CSF2RA, TNFRSF17, TNFRSF14, CCNL2, VEGFB, AMH, TNFRSF10B, INHBE, IFNB1, CCR3, VEGFA, CCR2, IL12A, CCL1, CCL3, CXCL5, TNFRSF25, CCR1, CSF1, CX3CL1, CCL7, CCL24, TNFRSF1B, IL12RB1, CCL21, FIGF, EPO, IL4, IL18R1, FLT1, TGFBR1, EDA2R, HGF, TNFSF8, KDR, LEP, GH2, CCL13, EPOR, XCL1, IFNA16, XCL2 Neuroactive ligand-receptor interaction: OPRM1, THRA, GRIK1, DRD2, GRIK2, TACR2, TACR1, GABRB1, LPAR4, 9.68 × 105 GRIK5, FPR1, PRSS1, GNRHR, FPR2, EDNRA, AGTR2, LTB4R, PRSS2, CNR1, S1PR4, CALCRL, TAAR5, GABRE, PTGER1, GABRG3, C5AR1, PTGER3, PTGER4, GABRA6, GABRA5, GRM1, PLG, LEP, CRHR1, GH2, GRM3, SSTR2, Chlorogenic acid Chlorogenic CHRM3, GRIA1, MC2R, P2RX2, TBXA2R, GHSR, HTR2C, TSHR, LHB, GLP1R, OPRD1 Hematopoietic cell lineage: IL4, CR1, CD8B, CSF1, FCER2, GYPA, ITGA2, IL11, GP9, FLT3LG, CD38, CD19, DNTT, 9.29 × 104 GP1BB, CD22, EPOR, CSF2RA, CD14, THPO, EPO, HLA-DRA, ITGA2B Cytokine-cytokine receptor interaction: IL6ST, IL21R, IL19, TNFSF15, CXCR3, IL15, CXCL11, TGFB1, IL11, FLT3LG, CXCL10, CCR10, XCR1, RTEL1, CSF2RA, IL21, CCNL2, VEGFB, CCR8, AMH, TNFRSF10C, IFNB1, PDGFRA, EDA, CXCL5, TNFRSF25, CSF1, IFNW1, CNTFR, CX3CL1, CCL5, TNFRSF4, CCL4, CCL27, CCL24, CCL25, CCL23, IFNA6, IFNA5, FIGF, EPO, AMHR2, IL2RA, FLT4, TGFBR2, EDA2R,
    [Show full text]
  • Identification of Key Genes and Pathways Involved in Response To
    Deng et al. Biol Res (2018) 51:25 https://doi.org/10.1186/s40659-018-0174-7 Biological Research RESEARCH ARTICLE Open Access Identifcation of key genes and pathways involved in response to pain in goat and sheep by transcriptome sequencing Xiuling Deng1,2†, Dong Wang3†, Shenyuan Wang1, Haisheng Wang2 and Huanmin Zhou1* Abstract Purpose: This aim of this study was to investigate the key genes and pathways involved in the response to pain in goat and sheep by transcriptome sequencing. Methods: Chronic pain was induced with the injection of the complete Freund’s adjuvant (CFA) in sheep and goats. The animals were divided into four groups: CFA-treated sheep, control sheep, CFA-treated goat, and control goat groups (n 3 in each group). The dorsal root ganglions of these animals were isolated and used for the construction of a cDNA= library and transcriptome sequencing. Diferentially expressed genes (DEGs) were identifed in CFA-induced sheep and goats and gene ontology (GO) enrichment analysis was performed. Results: In total, 1748 and 2441 DEGs were identifed in CFA-treated goat and sheep, respectively. The DEGs identi- fed in CFA-treated goats, such as C-C motif chemokine ligand 27 (CCL27), glutamate receptor 2 (GRIA2), and sodium voltage-gated channel alpha subunit 3 (SCN3A), were mainly enriched in GO functions associated with N-methyl- D-aspartate (NMDA) receptor, infammatory response, and immune response. The DEGs identifed in CFA-treated sheep, such as gamma-aminobutyric acid (GABA)-related DEGs (gamma-aminobutyric acid type A receptor gamma 3 subunit [GABRG3], GABRB2, and GABRB1), SCN9A, and transient receptor potential cation channel subfamily V member 1 (TRPV1), were mainly enriched in GO functions related to neuroactive ligand-receptor interaction, NMDA receptor, and defense response.
    [Show full text]
  • Stem Cells and Ion Channels
    Stem Cells International Stem Cells and Ion Channels Guest Editors: Stefan Liebau, Alexander Kleger, Michael Levin, and Shan Ping Yu Stem Cells and Ion Channels Stem Cells International Stem Cells and Ion Channels Guest Editors: Stefan Liebau, Alexander Kleger, Michael Levin, and Shan Ping Yu Copyright © 2013 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in “Stem Cells International.” All articles are open access articles distributed under the Creative Com- mons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Editorial Board Nadire N. Ali, UK Joseph Itskovitz-Eldor, Israel Pranela Rameshwar, USA Anthony Atala, USA Pavla Jendelova, Czech Republic Hannele T. Ruohola-Baker, USA Nissim Benvenisty, Israel Arne Jensen, Germany D. S. Sakaguchi, USA Kenneth Boheler, USA Sue Kimber, UK Paul R. Sanberg, USA Dominique Bonnet, UK Mark D. Kirk, USA Paul T. Sharpe, UK B. Bunnell, USA Gary E. Lyons, USA Ashok Shetty, USA Kevin D. Bunting, USA Athanasios Mantalaris, UK Igor Slukvin, USA Richard K. Burt, USA Pilar Martin-Duque, Spain Ann Steele, USA Gerald A. Colvin, USA EvaMezey,USA Alexander Storch, Germany Stephen Dalton, USA Karim Nayernia, UK Marc Turner, UK Leonard M. Eisenberg, USA K. Sue O’Shea, USA Su-Chun Zhang, USA Marina Emborg, USA J. Parent, USA Weian Zhao, USA Josef Fulka, Czech Republic Bruno Peault, USA Joel C. Glover, Norway Stefan Przyborski, UK Contents Stem Cells and Ion Channels, Stefan Liebau,
    [Show full text]
  • Identification of Differentially Expressed Genes in Human Bladder Cancer Through Genome-Wide Gene Expression Profiling
    521-531 24/7/06 18:28 Page 521 ONCOLOGY REPORTS 16: 521-531, 2006 521 Identification of differentially expressed genes in human bladder cancer through genome-wide gene expression profiling KAZUMORI KAWAKAMI1,3, HIDEKI ENOKIDA1, TOKUSHI TACHIWADA1, TAKENARI GOTANDA1, KENGO TSUNEYOSHI1, HIROYUKI KUBO1, KENRYU NISHIYAMA1, MASAKI TAKIGUCHI2, MASAYUKI NAKAGAWA1 and NAOHIKO SEKI3 1Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima 890-8520; Departments of 2Biochemistry and Genetics, and 3Functional Genomics, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan Received February 15, 2006; Accepted April 27, 2006 Abstract. Large-scale gene expression profiling is an effective CKS2 gene not only as a potential biomarker for diagnosing, strategy for understanding the progression of bladder cancer but also for staging human BC. This is the first report (BC). The aim of this study was to identify genes that are demonstrating that CKS2 expression is strongly correlated expressed differently in the course of BC progression and to with the progression of human BC. establish new biomarkers for BC. Specimens from 21 patients with pathologically confirmed superficial (n=10) or Introduction invasive (n=11) BC and 4 normal bladder samples were studied; samples from 14 of the 21 BC samples were subjected Bladder cancer (BC) is among the 5 most common to microarray analysis. The validity of the microarray results malignancies worldwide, and the 2nd most common tumor of was verified by real-time RT-PCR. Of the 136 up-regulated the genitourinary tract and the 2nd most common cause of genes we detected, 21 were present in all 14 BCs examined death in patients with cancer of the urinary tract (1-7).
    [Show full text]
  • Ion Channels
    UC Davis UC Davis Previously Published Works Title THE CONCISE GUIDE TO PHARMACOLOGY 2019/20: Ion channels. Permalink https://escholarship.org/uc/item/1442g5hg Journal British journal of pharmacology, 176 Suppl 1(S1) ISSN 0007-1188 Authors Alexander, Stephen PH Mathie, Alistair Peters, John A et al. Publication Date 2019-12-01 DOI 10.1111/bph.14749 License https://creativecommons.org/licenses/by/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California S.P.H. Alexander et al. The Concise Guide to PHARMACOLOGY 2019/20: Ion channels. British Journal of Pharmacology (2019) 176, S142–S228 THE CONCISE GUIDE TO PHARMACOLOGY 2019/20: Ion channels Stephen PH Alexander1 , Alistair Mathie2 ,JohnAPeters3 , Emma L Veale2 , Jörg Striessnig4 , Eamonn Kelly5, Jane F Armstrong6 , Elena Faccenda6 ,SimonDHarding6 ,AdamJPawson6 , Joanna L Sharman6 , Christopher Southan6 , Jamie A Davies6 and CGTP Collaborators 1School of Life Sciences, University of Nottingham Medical School, Nottingham, NG7 2UH, UK 2Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Anson Building, Central Avenue, Chatham Maritime, Chatham, Kent, ME4 4TB, UK 3Neuroscience Division, Medical Education Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK 4Pharmacology and Toxicology, Institute of Pharmacy, University of Innsbruck, A-6020 Innsbruck, Austria 5School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, BS8 1TD, UK 6Centre for Discovery Brain Science, University of Edinburgh, Edinburgh, EH8 9XD, UK Abstract The Concise Guide to PHARMACOLOGY 2019/20 is the fourth in this series of biennial publications. The Concise Guide provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties.
    [Show full text]
  • A Scalable Strategy for High-Throughput GFP Tagging of PNAS PLUS Endogenous Human Proteins
    A scalable strategy for high-throughput GFP tagging of PNAS PLUS endogenous human proteins Manuel D. Leonettia,b,1, Sayaka Sekinec,1, Daichi Kamiyamac,2, Jonathan S. Weissmana,b,2, and Bo Huangc,2 aDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94143; bHoward Hughes Medical Institute, University of California, San Francisco, CA 94143; and cDepartment of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143 Contributed by Jonathan S. Weissman, April 28, 2016 (sent for review April 6, 2016; reviewed by Hazen P. Babcock and Pietro De Camilli) A central challenge of the postgenomic era is to comprehensively cost-effective manner; (ii) specificity, limiting tag insertion to the characterize the cellular role of the ∼20,000 proteins encoded in genomic target (ideally in a “scarless” manner that avoids insertion the human genome. To systematically study protein function in a of irrelevant DNA such as selection marker genes); (iii) versatility native cellular background, libraries of human cell lines expressing of the tag, preferably allowing both localization and proteomic proteins tagged with a functional sequence at their endogenous analyses; and (iv) selectability of knockin cells. Recently, a strategy loci would be very valuable. Here, using electroporation of Cas9 based on electroporation of Cas9/single-guide RNA (sgRNA) ri- nuclease/single-guide RNA ribonucleoproteins and taking advan- bonucleoprotein complexes (RNPs) has been reported that enables tage of a split-GFP system, we describe a scalable method for the both scalability and specificity (14,15).Inthisapproach,RNPsare robust, scarless, and specific tagging of endogenous human genes assembled in vitro from purified sgRNA and Cas9, both of which with GFP.
    [Show full text]
  • A Bioinformatics Model of Human Diseases on the Basis Of
    SUPPLEMENTARY MATERIALS A Bioinformatics Model of Human Diseases on the basis of Differentially Expressed Genes (of Domestic versus Wild Animals) That Are Orthologs of Human Genes Associated with Reproductive-Potential Changes Vasiliev1,2 G, Chadaeva2 I, Rasskazov2 D, Ponomarenko2 P, Sharypova2 E, Drachkova2 I, Bogomolov2 A, Savinkova2 L, Ponomarenko2,* M, Kolchanov2 N, Osadchuk2 A, Oshchepkov2 D, Osadchuk2 L 1 Novosibirsk State University, Novosibirsk 630090, Russia; 2 Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; * Correspondence: [email protected]. Tel.: +7 (383) 363-4963 ext. 1311 (M.P.) Supplementary data on effects of the human gene underexpression or overexpression under this study on the reproductive potential Table S1. Effects of underexpression or overexpression of the human genes under this study on the reproductive potential according to our estimates [1-5]. ↓ ↑ Human Deficit ( ) Excess ( ) # Gene NSNP Effect on reproductive potential [Reference] ♂♀ NSNP Effect on reproductive potential [Reference] ♂♀ 1 increased risks of preeclampsia as one of the most challenging 1 ACKR1 ← increased risk of atherosclerosis and other coronary artery disease [9] ← [3] problems of modern obstetrics [8] 1 within a model of human diseases using Adcyap1-knockout mice, 3 in a model of human health using transgenic mice overexpressing 2 ADCYAP1 ← → [4] decreased fertility [10] [4] Adcyap1 within only pancreatic β-cells, ameliorated diabetes [11] 2 within a model of human diseases
    [Show full text]
  • A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response
    A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Adamson, Britt et al. “A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response.” Cell 167, 7 (December 2016): 1867–1882 © 2016 Elsevier Inc As Published http://dx.doi.org/10.1016/J.CELL.2016.11.048 Publisher Elsevier Version Author's final manuscript Citable link http://hdl.handle.net/1721.1/116762 Terms of Use Creative Commons Attribution-NonCommercial-NoDerivs License Detailed Terms http://creativecommons.org/licenses/by-nc-nd/4.0/ HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Cell. Author Manuscript Author manuscript; Manuscript Author available in PMC 2017 December 15. Published in final edited form as: Cell. 2016 December 15; 167(7): 1867–1882.e21. doi:10.1016/j.cell.2016.11.048. A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response Britt Adamson1,2,3,4,*, Thomas M. Norman1,2,3,4,*, Marco Jost1,2,3,4,5, Min Y. Cho1,2,3,4, James K. Nuñez1,2,3,4, Yuwen Chen1,2,3,4, Jacqueline E. Villalta1,2,3,4, Luke A. Gilbert1,2,3,4, Max A. Horlbeck1,2,3,4, Marco Y. Hein1,2,3,4, Ryan A. Pak1,6, Andrew N. Gray5, Carol A. Gross5,7,8, Atray Dixit9,10, Oren Parnas10,11, Aviv Regev10,12, and Jonathan S. Weissman1,2,3,4,† 1Department of Cellular & Molecular Pharmacology,
    [Show full text]
  • NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer
    Florida International University FIU Digital Commons FIU Electronic Theses and Dissertations University Graduate School 11-7-2018 Decipher Mechanisms by which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer Jairo Ramos [email protected] Follow this and additional works at: https://digitalcommons.fiu.edu/etd Part of the Clinical Epidemiology Commons Recommended Citation Ramos, Jairo, "Decipher Mechanisms by which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer" (2018). FIU Electronic Theses and Dissertations. 3872. https://digitalcommons.fiu.edu/etd/3872 This work is brought to you for free and open access by the University Graduate School at FIU Digital Commons. It has been accepted for inclusion in FIU Electronic Theses and Dissertations by an authorized administrator of FIU Digital Commons. For more information, please contact [email protected]. FLORIDA INTERNATIONAL UNIVERSITY Miami, Florida DECIPHER MECHANISMS BY WHICH NUCLEAR RESPIRATORY FACTOR ONE (NRF1) COORDINATES CHANGES IN THE TRANSCRIPTIONAL AND CHROMATIN LANDSCAPE AFFECTING DEVELOPMENT AND PROGRESSION OF INVASIVE BREAST CANCER A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in PUBLIC HEALTH by Jairo Ramos 2018 To: Dean Tomás R. Guilarte Robert Stempel College of Public Health and Social Work This dissertation, Written by Jairo Ramos, and entitled Decipher Mechanisms by Which Nuclear Respiratory Factor One (NRF1) Coordinates Changes in the Transcriptional and Chromatin Landscape Affecting Development and Progression of Invasive Breast Cancer, having been approved in respect to style and intellectual content, is referred to you for judgment.
    [Show full text]