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Schmok JC, Jain M, Street LA, Tankka AT, Schafer D, Her HL, Elmsaouri S, Gosztyla ML, Boyle EA, Jagannatha P, Luo EC, Kwon EJ, Jovanovic M, Yeo GW. Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion. Nat Biotechnol 2024; 42:1429-1441. [PMID: 38168984 PMCID: PMC11389820 DOI: 10.1038/s41587-023-02014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 09/29/2023] [Indexed: 01/05/2024]
Abstract
RNA-binding proteins (RBPs) modulate alternative splicing outcomes to determine isoform expression and cellular survival. To identify RBPs that directly drive alternative exon inclusion, we developed tethered function luciferase-based splicing reporters that provide rapid, scalable and robust readouts of exon inclusion changes and used these to evaluate 718 human RBPs. We performed enhanced cross-linking immunoprecipitation, RNA sequencing and affinity purification-mass spectrometry to investigate a subset of candidates with no prior association with splicing. Integrative analysis of these assays indicates surprising roles for TRNAU1AP, SCAF8 and RTCA in the modulation of hundreds of endogenous splicing events. We also leveraged our tethering assays and top candidates to identify potent and compact exon inclusion activation domains for splicing modulation applications. Using these identified domains, we engineered programmable fusion proteins that outperform current artificial splicing factors at manipulating inclusion of reporter and endogenous exons. This tethering approach characterizes the ability of RBPs to induce exon inclusion and yields new molecular parts for programmable splicing control.
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Affiliation(s)
- Jonathan C Schmok
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Manya Jain
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lena A Street
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Alex T Tankka
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Danielle Schafer
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Hsuan-Lin Her
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sara Elmsaouri
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Maya L Gosztyla
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Evan A Boyle
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Pratibha Jagannatha
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - En-Ching Luo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ester J Kwon
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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Daakour S, Nelson DR, Fu W, Jaiswal A, Dohai B, Alzahmi AS, Koussa J, Huang X, Shen Y, Twizere JC, Salehi-Ashtiani K. Adaptive Evolution Signatures in Prochlorococcus: Open Reading Frame (ORF)eome Resources and Insights from Comparative Genomics. Microorganisms 2024; 12:1720. [PMID: 39203562 PMCID: PMC11357015 DOI: 10.3390/microorganisms12081720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/30/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
Prochlorococcus, a cyanobacteria genus of the smallest and most abundant oceanic phototrophs, encompasses ecotype strains adapted to high-light (HL) and low-light (LL) niches. To elucidate the adaptive evolution of this genus, we analyzed 40 Prochlorococcus marinus ORFeomes, including two cornerstone strains, MED4 and NATL1A. Employing deep learning with robust statistical methods, we detected new protein family distributions in the strains and identified key genes differentiating the HL and LL strains. The HL strains harbor genes (ABC-2 transporters) related to stress resistance, such as DNA repair and RNA processing, while the LL strains exhibit unique chlorophyll adaptations (ion transport proteins, HEAT repeats). Additionally, we report the finding of variable, depth-dependent endogenous viral elements in the 40 strains. To generate biological resources to experimentally study the HL and LL adaptations, we constructed the ORFeomes of two representative strains, MED4 and NATL1A synthetically, covering 99% of the annotated protein-coding sequences of the two species, totaling 3976 cloned, sequence-verified open reading frames (ORFs). These comparative genomic analyses, paired with MED4 and NATL1A ORFeomes, will facilitate future genotype-to-phenotype mappings and the systems biology exploration of Prochlorococcus ecology.
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Affiliation(s)
- Sarah Daakour
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - David R. Nelson
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - Weiqi Fu
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Department of Marine Science, Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Ashish Jaiswal
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - Bushra Dohai
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Helmholtz Center Munich, Institute of Network Biology (INET), German Research Center for Environmental Health, 85764 Munich, Germany
| | - Amnah Salem Alzahmi
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Laboratory of Viral Interactomes Networks, Unit of Molecular & Computational Biology, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Liège, 4000 Liège, Belgium
| | - Joseph Koussa
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Department of Biology, New York University, New York, NY 10012, USA
- Department of Chemical and Biological Sciences, Montgomery College, Germantown, MD 20850, USA
| | - Xiaoluo Huang
- Genome Synthesis and Editing Platform, China National GeneBank (CNGB), BGI-Research, Shenzhen 518120, China; (X.H.); (Y.S.)
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Beijing 100045, China
| | - Yue Shen
- Genome Synthesis and Editing Platform, China National GeneBank (CNGB), BGI-Research, Shenzhen 518120, China; (X.H.); (Y.S.)
| | - Jean-Claude Twizere
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Laboratory of Viral Interactomes Networks, Unit of Molecular & Computational Biology, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Liège, 4000 Liège, Belgium
| | - Kourosh Salehi-Ashtiani
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
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Gillespie W, Zhang Y, Ruiz OE, Cerda J, Ortiz-Guzman J, Turner WD, Largoza G, Sherman M, Mosser LE, Fujimoto E, Chien CB, Kwan KM, Arenkiel BR, Devine WP, Wythe JD. Multisite Assembly of Gateway Induced Clones (MAGIC): a flexible cloning toolbox with diverse applications in vertebrate model systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.13.603267. [PMID: 39026881 PMCID: PMC11257631 DOI: 10.1101/2024.07.13.603267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Here we present the Multisite Assembly of Gateway Induced Clones (MAGIC) system, which harnesses site-specific recombination-based cloning via Gateway technology for rapid, modular assembly of between 1 and 3 "Entry" vector components, all into a fourth, standard high copy "Destination" plasmid backbone. The MAGIC toolkit spans a range of in vitro and in vivo uses, from directing tunable gene expression, to driving simultaneous expression of microRNAs and fluorescent reporters, to enabling site-specific recombinase-dependent gene expression. All MAGIC system components are directly compatible with existing multisite gateway Tol2 systems currently used in zebrafish, as well as existing eukaryotic cell culture expression Destination plasmids, and available mammalian lentiviral and adenoviral Destination vectors, allowing rapid cross-species experimentation. Moreover, herein we describe novel vectors with flanking piggyBac transposon elements for stable genomic integration in vitro or in vivo when used with piggyBac transposase. Collectively, the MAGIC system facilitates transgenesis in cultured mammalian cells, electroporated mouse and chick embryos, as well as in injected zebrafish embryos, enabling the rapid generation of innovative DNA constructs for biological research due to a shared, common plasmid platform.
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Aublin-Gex A, Jacolin F, Diaz O, Jacquemin C, Marçais A, Walzer T, Lotteau V, Vidalain PO, Perrin-Cocon L. Tethering of hexokinase 2 to mitochondria promotes resistance of liver cancer cells to natural killer cell cytotoxicity. Eur J Immunol 2024:e2350954. [PMID: 38837415 DOI: 10.1002/eji.202350954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/07/2024]
Abstract
Hexokinases (HKs) control the first step of glucose catabolism. A switch of expression from liver HK (glucokinase, GCK) to the tumor isoenzyme HK2 is observed in hepatocellular carcinoma progression. Our prior work revealed that HK isoenzyme switch in hepatocytes not only regulates hepatic metabolic functions but also modulates innate immunity and sensitivity to Natural Killer (NK) cell cytotoxicity. This study investigates the impact of HK2 expression and its mitochondrial binding on the resistance of human liver cancer cells to NK-cell-induced cytolysis. We have shown that HK2 expression induces resistance to NK cell cytotoxicity in a process requiring mitochondrial binding of HK2. Neither HK2 nor GCK expression affects target cells' ability to activate NK cells. In contrast, mitochondrial binding of HK2 reduces effector caspase 3/7 activity both at baseline and upon NK-cell activation. Furthermore, HK2 tethering to mitochondria enhances their resistance to cytochrome c release triggered by tBID. These findings indicate that HK2 mitochondrial binding in liver cancer cells is an intrinsic resistance factor to cytolysis and an escape mechanism from immune surveillance.
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Affiliation(s)
- Anne Aublin-Gex
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Florentine Jacolin
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Olivier Diaz
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Clémence Jacquemin
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Antoine Marçais
- CIRI, Centre International de Recherche en Infectiologie, Team Lymphocyte activation and signaling, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Thierry Walzer
- CIRI, Centre International de Recherche en Infectiologie, Team Lymphocyte activation and signaling, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Vincent Lotteau
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Pierre-Olivier Vidalain
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Laure Perrin-Cocon
- CIRI, Centre International de Recherche en Infectiologie, Team Viral Infection, Metabolism and Immunity, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
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5
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Trepte P, Secker C, Olivet J, Blavier J, Kostova S, Maseko SB, Minia I, Silva Ramos E, Cassonnet P, Golusik S, Zenkner M, Beetz S, Liebich MJ, Scharek N, Schütz A, Sperling M, Lisurek M, Wang Y, Spirohn K, Hao T, Calderwood MA, Hill DE, Landthaler M, Choi SG, Twizere JC, Vidal M, Wanker EE. AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor. Mol Syst Biol 2024; 20:428-457. [PMID: 38467836 PMCID: PMC10987651 DOI: 10.1038/s44320-024-00019-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 03/13/2024] Open
Abstract
Protein-protein interactions (PPIs) offer great opportunities to expand the druggable proteome and therapeutically tackle various diseases, but remain challenging targets for drug discovery. Here, we provide a comprehensive pipeline that combines experimental and computational tools to identify and validate PPI targets and perform early-stage drug discovery. We have developed a machine learning approach that prioritizes interactions by analyzing quantitative data from binary PPI assays or AlphaFold-Multimer predictions. Using the quantitative assay LuTHy together with our machine learning algorithm, we identified high-confidence interactions among SARS-CoV-2 proteins for which we predicted three-dimensional structures using AlphaFold-Multimer. We employed VirtualFlow to target the contact interface of the NSP10-NSP16 SARS-CoV-2 methyltransferase complex by ultra-large virtual drug screening. Thereby, we identified a compound that binds to NSP10 and inhibits its interaction with NSP16, while also disrupting the methyltransferase activity of the complex, and SARS-CoV-2 replication. Overall, this pipeline will help to prioritize PPI targets to accelerate the discovery of early-stage drug candidates targeting protein complexes and pathways.
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Affiliation(s)
- Philipp Trepte
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany.
- Brain Development and Disease, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, 1030, Vienna, Austria.
| | - Christopher Secker
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany.
- Zuse Institute Berlin, Berlin, Germany.
| | - Julien Olivet
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Structural Biology Unit, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Katholieke Universiteit Leuven, 3000, Leuven, Belgium
| | - Jeremy Blavier
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium
| | - Simona Kostova
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Sibusiso B Maseko
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium
| | - Igor Minia
- RNA Biology and Posttranscriptional Regulation, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125, Berlin, Germany
| | - Eduardo Silva Ramos
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Patricia Cassonnet
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN (GMVR), Institut Pasteur, Centre National de la Recherche Scientifique (CNRS), Université de Paris, Paris, France
| | - Sabrina Golusik
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Martina Zenkner
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Stephanie Beetz
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Mara J Liebich
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Nadine Scharek
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Anja Schütz
- Protein Production & Characterization, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Marcel Sperling
- Multifunctional Colloids and Coating, Fraunhofer Institute for Applied Polymer Research (IAP), 14476, Potsdam-Golm, Germany
| | - Michael Lisurek
- Structural Chemistry and Computational Biophysics, Leibniz-Institut für Molekulare Pharmakologie (FMP), 13125, Berlin, Germany
| | - Yang Wang
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kerstin Spirohn
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Markus Landthaler
- RNA Biology and Posttranscriptional Regulation, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, 13125, Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, 13125, Berlin, Germany
| | - Soon Gang Choi
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, Interdisciplinary Cluster for Applied Genoproteomics (GIGA)-Molecular Biology of Diseases, University of Liège, 4000, Liège, Belgium.
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium.
- Laboratory of Algal Synthetic and Systems Biology, Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.
| | - Erich E Wanker
- Proteomics and Molecular Mechanisms of Neurodegenerative Diseases, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany.
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6
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Mao ND, Xu Y, Che H, Yao X, Gao Y, Wang C, Deng H, Hui Z, Zhang H, Ye XY. Design, synthesis and biological evaluation of novel 1,2,4a,5-tetrahydro-4H-benzo[b][1,4]oxazino[4,3-d][1,4]oxazine-based AAK1 inhibitors with anti-viral property against SARS-CoV-2. Eur J Med Chem 2024; 268:116232. [PMID: 38377825 DOI: 10.1016/j.ejmech.2024.116232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/09/2024] [Accepted: 02/10/2024] [Indexed: 02/22/2024]
Abstract
Coronavirus entry into host cells hinges on the interaction between the spike glycoprotein of the virus and the cell-surface receptor angiotensin-converting enzyme 2 (ACE2), initiating the subsequent clathrin-mediated endocytosis (CME) pathway. AP-2-associated protein kinase 1 (AAK1) holds a pivotal role in this pathway, regulating CME by modulating the phosphorylation of the μ subunit of adaptor protein 2 (AP2M1). Herein, we report a series of novel AAK1 inhibitors based on previously reported 1,2,4a,5-tetrahydro-4H-benzo[b] [1,4]oxazino[4,3-d] [1,4]oxazine scaffold. Among 23 synthesized compounds, compound 12e is the most potent one with an IC50 value of 9.38 ± 0.34 nM against AAK1. The in vitro antiviral activity of 12e against SARS-CoV-2 was evaluated using a model involving SARS-CoV-2 pseudovirus infecting hACE2-HEK293 host cells. The results revealed that 12e was superior in vitro antiviral activity against SARS-CoV-2 entry into host cells when compared to SGC-AAK1-1 and LX9211, and its activity was comparable to that of a related and reference compound 8. Mechanistically, all AAK1 inhibitors attenuated AAK1-induced phosphorylation of AP2M1 threonine 156 and disrupted the direct interaction between AP2M1 and ACE2, ultimately inhibiting SARS-CoV-2 infection. Notably, compounds 8 and 12e exhibited a more potent effect in suppressing the phosphorylation of AP2M1 T156 and the interaction between AP2M1 and ACE2. In conclusion, novel AAK1 inhibitor 12e demonstrates significant efficacy in suppressing SARS-CoV-2 infection, and holds promise as a potential candidate for developing novel antiviral drugs against SARS-CoV-2 and other coronavirus infections.
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Affiliation(s)
- Nian-Dong Mao
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China; School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Yueying Xu
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Hao Che
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Xia Yao
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Yuan Gao
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Chenchen Wang
- School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Haowen Deng
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China
| | - Zi Hui
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
| | - Hang Zhang
- School of Basic Medical Science, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
| | - Xiang-Yang Ye
- School of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China; School of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, 311121, China.
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7
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Kirchenwitz M, Halfen J, von Peinen K, Prettin S, Kollasser J, Zur Lage S, Blankenfeldt W, Brakebusch C, Rottner K, Steffen A, Stradal TEB. RhoB promotes Salmonella survival by regulating autophagy. Eur J Cell Biol 2023; 102:151358. [PMID: 37703749 DOI: 10.1016/j.ejcb.2023.151358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/05/2023] [Accepted: 08/29/2023] [Indexed: 09/15/2023] Open
Abstract
Salmonella enterica serovar Typhimurium manipulates cellular Rho GTPases for host cell invasion by effector protein translocation via the Type III Secretion System (T3SS). The two Guanine nucleotide exchange (GEF) mimicking factors SopE and -E2 and the inositol phosphate phosphatase (PiPase) SopB activate the Rho GTPases Rac1, Cdc42 and RhoA, thereby mediating bacterial invasion. S. Typhimurium lacking these three effector proteins are largely invasion-defective. Type III secretion is crucial for both early and later phases of the intracellular life of S. Typhimurium. Here we investigated whether and how the small GTPase RhoB, known to localize on endomembrane vesicles and at the invasion site of S. Typhimurium, contributes to bacterial invasion and to subsequent steps relevant for S. Typhimurium lifestyle. We show that RhoB is significantly upregulated within hours of Salmonella infection. This effect depends on the presence of the bacterial effector SopB, but does not require its phosphatase activity. Our data reveal that SopB and RhoB bind to each other, and that RhoB localizes on early phagosomes of intracellular S. Typhimurium. Whereas both SopB and RhoB promote intracellular survival of Salmonella, RhoB is specifically required for Salmonella-induced upregulation of autophagy. Finally, in the absence of RhoB, vacuolar escape and cytosolic hyper-replication of S. Typhimurium is diminished. Our findings thus uncover a role for RhoB in Salmonella-induced autophagy, which supports intracellular survival of the bacterium and is promoted through a positive feedback loop by the Salmonella effector SopB.
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Affiliation(s)
- Marco Kirchenwitz
- Department of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Jessica Halfen
- Department of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Kristin von Peinen
- Department of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Silvia Prettin
- Department of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Jana Kollasser
- Department of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Susanne Zur Lage
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Wulf Blankenfeldt
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Cord Brakebusch
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Klemens Rottner
- Department of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany; Division of Molecular Cell Biology, Zoological Institute, Technische Universität Braunschweig, Spielmannstrasse 7, 38106 Braunschweig, Germany
| | - Anika Steffen
- Department of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Theresia E B Stradal
- Department of Cell Biology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany.
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8
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Bosch JA, Keith N, Escobedo F, Fisher WW, LaGraff JT, Rabasco J, Wan KH, Weiszmann R, Hu Y, Kondo S, Brown JB, Perrimon N, Celniker SE. Molecular and functional characterization of the Drosophila melanogaster conserved smORFome. Cell Rep 2023; 42:113311. [PMID: 37889754 PMCID: PMC10843857 DOI: 10.1016/j.celrep.2023.113311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/24/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
Short polypeptides encoded by small open reading frames (smORFs) are ubiquitously found in eukaryotic genomes and are important regulators of physiology, development, and mitochondrial processes. Here, we focus on a subset of 298 smORFs that are evolutionarily conserved between Drosophila melanogaster and humans. Many of these smORFs are conserved broadly in the bilaterian lineage, and ∼182 are conserved in plants. We observe remarkably heterogeneous spatial and temporal expression patterns of smORF transcripts-indicating wide-spread tissue-specific and stage-specific mitochondrial architectures. In addition, an analysis of annotated functional domains reveals a predicted enrichment of smORF polypeptides localizing to mitochondria. We conduct an embryonic ribosome profiling experiment and find support for translation of 137 of these smORFs during embryogenesis. We further embark on functional characterization using CRISPR knockout/activation, RNAi knockdown, and cDNA overexpression, revealing diverse phenotypes. This study underscores the importance of identifying smORF function in disease and phenotypic diversity.
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Affiliation(s)
- Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nathan Keith
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Felipe Escobedo
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - William W Fisher
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - James Thai LaGraff
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jorden Rabasco
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kenneth H Wan
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Richard Weiszmann
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Shu Kondo
- Laboratory of Invertebrate Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - James B Brown
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Susan E Celniker
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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9
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Balmas E, Sozza F, Bottini S, Ratto ML, Savorè G, Becca S, Snijders KE, Bertero A. Manipulating and studying gene function in human pluripotent stem cell models. FEBS Lett 2023; 597:2250-2287. [PMID: 37519013 DOI: 10.1002/1873-3468.14709] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
Human pluripotent stem cells (hPSCs) are uniquely suited to study human development and disease and promise to revolutionize regenerative medicine. These applications rely on robust methods to manipulate gene function in hPSC models. This comprehensive review aims to both empower scientists approaching the field and update experienced stem cell biologists. We begin by highlighting challenges with manipulating gene expression in hPSCs and their differentiated derivatives, and relevant solutions (transfection, transduction, transposition, and genomic safe harbor editing). We then outline how to perform robust constitutive or inducible loss-, gain-, and change-of-function experiments in hPSCs models, both using historical methods (RNA interference, transgenesis, and homologous recombination) and modern programmable nucleases (particularly CRISPR/Cas9 and its derivatives, i.e., CRISPR interference, activation, base editing, and prime editing). We further describe extension of these approaches for arrayed or pooled functional studies, including emerging single-cell genomic methods, and the related design and analytical bioinformatic tools. Finally, we suggest some directions for future advancements in all of these areas. Mastering the combination of these transformative technologies will empower unprecedented advances in human biology and medicine.
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Affiliation(s)
- Elisa Balmas
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Federica Sozza
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Sveva Bottini
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Maria Luisa Ratto
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Giulia Savorè
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Silvia Becca
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Kirsten Esmee Snijders
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Alessandro Bertero
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
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10
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Chowdhury I, Dashi G, Keskitalo S. CMGC Kinases in Health and Cancer. Cancers (Basel) 2023; 15:3838. [PMID: 37568654 PMCID: PMC10417348 DOI: 10.3390/cancers15153838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/18/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
CMGC kinases, encompassing cyclin-dependent kinases (CDKs), mitogen-activated protein kinases (MAPKs), glycogen synthase kinases (GSKs), and CDC-like kinases (CLKs), play pivotal roles in cellular signaling pathways, including cell cycle regulation, proliferation, differentiation, apoptosis, and gene expression regulation. The dysregulation and aberrant activation of these kinases have been implicated in cancer development and progression, making them attractive therapeutic targets. In recent years, kinase inhibitors targeting CMGC kinases, such as CDK4/6 inhibitors and BRAF/MEK inhibitors, have demonstrated clinical success in treating specific cancer types. However, challenges remain, including resistance to kinase inhibitors, off-target effects, and the need for better patient stratification. This review provides a comprehensive overview of the importance of CMGC kinases in cancer biology, their involvement in cellular signaling pathways, protein-protein interactions, and the current state of kinase inhibitors targeting these kinases. Furthermore, we discuss the challenges and future perspectives in targeting CMGC kinases for cancer therapy, including potential strategies to overcome resistance, the development of more selective inhibitors, and novel therapeutic approaches, such as targeting protein-protein interactions, exploiting synthetic lethality, and the evolution of omics in the study of the human kinome. As our understanding of the molecular mechanisms and protein-protein interactions involving CMGC kinases expands, so too will the opportunities for the development of more selective and effective therapeutic strategies for cancer treatment.
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Affiliation(s)
- Iftekhar Chowdhury
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland; (I.C.)
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Giovanna Dashi
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland; (I.C.)
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Salla Keskitalo
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland; (I.C.)
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
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11
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Cross-talk between mutant p53 and p62/SQSTM1 augments cancer cell migration by promoting the degradation of cell adhesion proteins. Proc Natl Acad Sci U S A 2022; 119:e2119644119. [PMID: 35439056 PMCID: PMC9173583 DOI: 10.1073/pnas.2119644119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Missense mutations in the TP53 gene, encoding the p53 tumor suppressor, are very frequent in human cancer. Some of those mutations, particularly the more common (“hotspot”) ones, not only abrogate p53’s tumor suppressor activities but also endow the mutant protein with oncogenic gain of function (GOF). We report that p53R273H, the most common p53 mutant in pancreatic cancer, interacts with the SQSTM1/p62 protein to accelerate the degradation of cell adhesion proteins. This enables pancreatic cancer cells to detach from the epithelial sheet and engage in individualized cell migration, probably augmenting metastatic spread. By providing insights into mechanisms that underpin mutant p53 GOF, this study may suggest ways to interfere with the progression of cancers bearing particular p53 mutants. Missense mutations in the p53 tumor suppressor abound in human cancer. Common (“hotspot”) mutations endow mutant p53 (mutp53) proteins with oncogenic gain of function (GOF), including enhanced cell migration and invasiveness, favoring cancer progression. GOF is usually attributed to transcriptional effects of mutp53. To elucidate transcription-independent effects of mutp53, we characterized the protein interactome of the p53R273H mutant in cells derived from pancreatic ductal adenocarcinoma (PDAC), where p53R273H is the most frequent p53 mutant. We now report that p53R273H, but not the p53R175H hotspot mutant, interacts with SQSTM1/p62 and promotes cancer cell migration and invasion in a p62-dependent manner. Mechanistically, the p53R273H-p62 axis drives the proteasomal degradation of several cell junction–associated proteins, including the gap junction protein Connexin 43, facilitating scattered cell migration. Concordantly, down-regulation of Connexin 43 augments PDAC cell migration, while its forced overexpression blunts the promigratory effect of the p53R273H-p62 axis. These findings define a mechanism of mutp53 GOF.
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12
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Schor S, Pu S, Nicolaescu V, Azari S, Kõivomägi M, Karim M, Cassonnet P, Saul S, Neveu G, Yueh A, Demeret C, Skotheim JM, Jacob Y, Randall G, Einav S. The cargo adapter protein CLINT1 is phosphorylated by the Numb-associated kinase BIKE and mediates dengue virus infection. J Biol Chem 2022; 298:101956. [PMID: 35452674 PMCID: PMC9133654 DOI: 10.1016/j.jbc.2022.101956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 11/25/2022] Open
Abstract
The signaling pathways and cellular functions regulated by the four Numb-associated kinases are largely unknown. We reported that AAK1 and GAK control intracellular trafficking of RNA viruses and revealed a requirement for BIKE in early and late stages of dengue virus (DENV) infection. However, the downstream targets phosphorylated by BIKE have not yet been identified. Here, to identify BIKE substrates, we conducted a barcode fusion genetics-yeast two-hybrid screen and retrieved publicly available data generated via affinity-purification mass spectrometry. We subsequently validated 19 of 47 putative BIKE interactors using mammalian cell-based protein-protein interaction assays. We found that CLINT1, a cargo-specific adapter implicated in bidirectional Golgi-to-endosome trafficking, emerged as a predominant hit in both screens. Our experiments indicated that BIKE catalyzes phosphorylation of a threonine 294 CLINT1 residue both in vitro and in cell culture. Our findings revealed that CLINT1 phosphorylation mediates its binding to the DENV nonstructural 3 protein and subsequently promotes DENV assembly and egress. Additionally, using live-cell imaging we revealed that CLINT1 cotraffics with DENV particles and is involved in mediating BIKE's role in DENV infection. Finally, our data suggest that additional cellular BIKE interactors implicated in the host immune and stress responses and the ubiquitin proteasome system might also be candidate phosphorylation substrates of BIKE. In conclusion, these findings reveal cellular substrates and pathways regulated by the understudied Numb-associated kinase enzyme BIKE, a mechanism for CLINT1 regulation, and control of DENV infection via BIKE signaling, with potential implications for cell biology, virology, and host-targeted antiviral design.
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Affiliation(s)
- Stanford Schor
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University, California, USA
| | - Szuyuan Pu
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University, California, USA
| | - Vlad Nicolaescu
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Siavash Azari
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University, California, USA
| | | | - Marwah Karim
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University, California, USA
| | - Patricia Cassonnet
- Department of Virology, Molecular Genetics of RNA Virus Genetics (GMVR), Pasteur Institute, National Center for Scientific Research, and Paris Diderot University, Paris, France
| | - Sirle Saul
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University, California, USA
| | - Gregory Neveu
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University, California, USA
| | - Andrew Yueh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Caroline Demeret
- Department of Virology, Molecular Genetics of RNA Virus Genetics (GMVR), Pasteur Institute, National Center for Scientific Research, and Paris Diderot University, Paris, France
| | - Jan M Skotheim
- Department of Biology, Stanford University, California, USA
| | - Yves Jacob
- Department of Virology, Molecular Genetics of RNA Virus Genetics (GMVR), Pasteur Institute, National Center for Scientific Research, and Paris Diderot University, Paris, France
| | - Glenn Randall
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Shirit Einav
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University, California, USA; Chan Zuckerberg Biohub, San Francisco, California, USA.
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13
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Shon H, Matveeva EA, Jull EC, Hu Y, Coupet TA, Lee YS. Evidence Supporting Substrate Channeling between Domains of Human PAICS: A Time-Course Analysis of 13C-Bicarbonate Incorporation. Biochemistry 2022; 61:575-582. [PMID: 35285625 PMCID: PMC8988938 DOI: 10.1021/acs.biochem.1c00803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human phosphoribosylaminoimidazole carboxylase phosphoribosylaminoimdiazole succinocarboxamide synthetase (PAICS) is a dual activity enzyme catalyzing two consecutive reactions in de novo purine nucleotide synthesis. Crystallographic structures of recombinant human PAICS suggested the channeling of 4-carboxy-5-aminoimidazole-1-ribose-5'-phosphate (CAIR) between two active sites of PAICS, while a prior work of an avian PAICS suggested otherwise. Here, we present time-course mass spectrometric data supporting the channeling of CAIR between domains of recombinant human PAICS. Time-course mass spectral analysis showed that CAIR added to the bulk solution (CAIRbulk) is decarboxylated and re-carboxylated before the accumulation of succinyl-5-aminoimidazole-4-carboxamide-1-ribose-5'-phosphate (SAICAR). An experiment with 13C-bicarbonate showed that SAICAR production was proportional to re-carboxylated CAIR instead of total CAIR or CAIRbulk. This result indicates that the SAICAR synthase domain selectively uses enzyme-made CAIR over CAIRbulk, which is consistent with the channeling model. This channeling between PAICS domains may be a part of a larger channeling process in de novo purine nucleotide synthesis.
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Affiliation(s)
- Hyungjoo Shon
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Elena A Matveeva
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Ella C Jull
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
| | - Yijia Hu
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tiffany A Coupet
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Young-Sam Lee
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky 40536, United States
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14
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Dunham B, Ganapathiraju MK. Benchmark Evaluation of Protein-Protein Interaction Prediction Algorithms. Molecules 2021; 27:41. [PMID: 35011283 PMCID: PMC8746451 DOI: 10.3390/molecules27010041] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
Protein-protein interactions (PPIs) perform various functions and regulate processes throughout cells. Knowledge of the full network of PPIs is vital to biomedical research, but most of the PPIs are still unknown. As it is infeasible to discover all of them experimentally due to technical and resource limitations, computational prediction of PPIs is essential and accurately assessing the performance of algorithms is required before further application or translation. However, many published methods compose their evaluation datasets incorrectly, using a higher proportion of positive class data than occuring naturally, leading to exaggerated performance. We re-implemented various published algorithms and evaluated them on datasets with realistic data compositions and found that their performance is overstated in original publications; with several methods outperformed by our control models built on 'illogical' and random number features. We conclude that these methods are influenced by an over-characterization of some proteins in the literature and due to scale-free nature of PPI network and that they fail when tested on all possible protein pairs. Additionally, we found that sequence-only-based algorithms performed worse than those that employ functional and expression features. We present a benchmark evaluation of many published algorithms for PPI prediction. The source code of our implementations and the benchmark datasets created here are made available in open source.
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15
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Kramme C, Plesa AM, Wang HH, Wolf B, Smela MP, Guo X, Kohman RE, Chatterjee P, Church GM. MegaGate: A toxin-less gateway molecular cloning tool. STAR Protoc 2021; 2:100907. [PMID: 34746865 PMCID: PMC8551244 DOI: 10.1016/j.xpro.2021.100907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Gateway cloning employs the use of the ccdb toxin and has low colony numbers, making it difficult to apply at scale to clone libraries of cDNA vectors. In this protocol, we describe MegaGate, a toxin-less Gateway technology capable of robust cDNA library cloning that is efficient, cheap, and scalable. MegaGate eliminates the ccdb toxin used in Gateway recombinase cloning and instead utilizes meganuclease-mediated digestion to eliminate background vectors during cloning and is 99.8% efficient with high colony numbers. For complete details on the use and execution of this protocol, please refer to Kramme et al. (2021).
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Affiliation(s)
- Christian Kramme
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Alexandru M. Plesa
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Helen H. Wang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Bennett Wolf
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Merrick Pierson Smela
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Xiaoge Guo
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Richie E. Kohman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Pranam Chatterjee
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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16
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Gu Y, Li G, Wang P, Guo Y, Li J. A simple and precise method (Y2H-in-frame-seq) improves yeast two-hybrid screening with cDNA libraries. J Genet Genomics 2021; 49:595-598. [PMID: 34864215 DOI: 10.1016/j.jgg.2021.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 10/19/2022]
Affiliation(s)
- Yinghui Gu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Guannan Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Ping Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yan Guo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jingrui Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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17
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Stieglitz JT, Potts KA, Van Deventer JA. Broadening the Toolkit for Quantitatively Evaluating Noncanonical Amino Acid Incorporation in Yeast. ACS Synth Biol 2021; 10:3094-3104. [PMID: 34730946 DOI: 10.1021/acssynbio.1c00370] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genetic code expansion is a powerful approach for advancing critical fields such as biological therapeutic discovery. However, the machinery for genetically encoding noncanonical amino acids (ncAAs) is only available in limited plasmid formats, constraining potential applications. In extreme cases, the introduction of two separate plasmids, one containing an orthogonal translation system (OTS) to facilitate ncAA incorporation and a second for expressing a ncAA-containing protein of interest, is not possible due to a lack of the available selection markers. One strategy to circumvent this challenge is to express the OTS and protein of interest from a single vector. For what we believe is the first time in yeast, we describe here several sets of single plasmid systems (SPSs) for performing genetic code manipulation and compare the ncAA incorporation capabilities of these plasmids against the capabilities of previously described dual plasmid systems (DPSs). For both dual fluorescent protein reporters and yeast display reporters tested with multiple OTSs and ncAAs, measured ncAA incorporation efficiencies with SPSs were determined to be equal to efficiencies determined with DPSs. Click chemistry on yeast cells displaying ncAA-containing proteins was also shown to be feasible in both formats, although differences in reactivity between formats suggest the need for caution when using such approaches. Additionally, we investigated whether these reporters would support the separation of yeast strains known to exhibit distinct ncAA incorporation efficiencies. Model sorts conducted with mixtures of two strains transformed with the same SPS or DPS both led to the enrichment of a strain known to support a higher efficiency ncAA incorporation, suggesting that these reporters will be suitable for conducting screens for strains exhibiting enhanced ncAA incorporation efficiencies. Overall, our results confirm that SPSs are well behaved in yeast and provide a convenient alternative to DPSs. SPSs are expected to be invaluable for conducting high-throughput investigations of the effects of genetic or genomic changes on ncAA incorporation efficiency and, more fundamentally, the eukaryotic translation apparatus.
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Affiliation(s)
- Jessica T. Stieglitz
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - Kelly A. Potts
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
| | - James A. Van Deventer
- Chemical and Biological Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
- Biomedical Engineering Department, Tufts University, Medford, Massachusetts 02155, United States
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18
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Kramme C, Plesa AM, Wang HH, Wolf B, Smela MP, Guo X, Kohman RE, Chatterjee P, Church GM. An integrated pipeline for mammalian genetic screening. CELL REPORTS METHODS 2021; 1:100082. [PMID: 35474898 PMCID: PMC9017118 DOI: 10.1016/j.crmeth.2021.100082] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022]
Abstract
With the recent advancements in genome editing, next-generation sequencing (NGS), and scalable cloning techniques, scientists can now conduct genetic screens at unprecedented levels of scale and precision. With such a multitude of technologies, there is a need for a simple yet comprehensive pipeline to enable systematic mammalian genetic screening. In this study, we develop unique algorithms for target identification and a toxin-less Gateway cloning tool, termed MegaGate, for library cloning which, when combined with existing genetic perturbation methods and NGS-coupled readouts, enable versatile engineering of relevant mammalian cell lines. Our integrated pipeline for sequencing-based target ascertainment and modular perturbation screening (STAMPScreen) can thus be utilized for a host of cell state engineering applications.
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Affiliation(s)
- Christian Kramme
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Alexandru M. Plesa
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Helen H. Wang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Bennett Wolf
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Merrick Pierson Smela
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Xiaoge Guo
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Richie E. Kohman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Pranam Chatterjee
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
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19
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Alharatani R, Ververi A, Beleza-Meireles A, Ji W, Mis E, Patterson QT, Griffin JN, Bhujel N, Chang CA, Dixit A, Konstantino M, Healy C, Hannan S, Neo N, Cash A, Li D, Bhoj E, Zackai EH, Cleaver R, Baralle D, McEntagart M, Newbury-Ecob R, Scott R, Hurst JA, Au PYB, Hosey MT, Khokha M, Marciano DK, Lakhani SA, Liu KJ. Novel truncating mutations in CTNND1 cause a dominant craniofacial and cardiac syndrome. Hum Mol Genet 2021; 29:1900-1921. [PMID: 32196547 PMCID: PMC7372553 DOI: 10.1093/hmg/ddaa050] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 03/12/2020] [Accepted: 03/17/2020] [Indexed: 12/18/2022] Open
Abstract
CTNND1 encodes the p120-catenin (p120) protein, which has a wide range of functions, including the maintenance of cell–cell junctions, regulation of the epithelial-mesenchymal transition and transcriptional signalling. Due to advances in next-generation sequencing, CTNND1 has been implicated in human diseases including cleft palate and blepharocheilodontic (BCD) syndrome albeit only recently. In this study, we identify eight novel protein-truncating variants, six de novo, in 13 participants from nine families presenting with craniofacial dysmorphisms including cleft palate and hypodontia, as well as congenital cardiac anomalies, limb dysmorphologies and neurodevelopmental disorders. Using conditional deletions in mice as well as CRISPR/Cas9 approaches to target CTNND1 in Xenopus, we identified a subset of phenotypes that can be linked to p120-catenin in epithelial integrity and turnover, and additional phenotypes that suggest mesenchymal roles of CTNND1. We propose that CTNND1 variants have a wider developmental role than previously described and that variations in this gene underlie not only cleft palate and BCD but may be expanded to a broader velocardiofacial-like syndrome.
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Affiliation(s)
- Reham Alharatani
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London SE1 9RT, UK.,Paediatric Dentistry, Centre of Oral, Clinical and Translational Science, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London SE5 9RS, UK
| | - Athina Ververi
- Department of Clinical Genetics, Great Ormond Street Hospital Trust, London WC1N 3JH, UK
| | - Ana Beleza-Meireles
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London SE1 9RT, UK.,Department of Clinical Genetics, Guy's and St. Thomas' NHS Foundation Trust, London SE1 9RT, UK
| | - Weizhen Ji
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Emily Mis
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Quinten T Patterson
- Departments of Internal Medicine and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-8856, USA
| | - John N Griffin
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London SE1 9RT, UK.,Pediatric Genomics Discovery Program, Departments of Genetics and Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nabina Bhujel
- South Thames Cleft Service, Guy's and St. Thomas' NHS Foundation Trust, London SE1 7EH, UK
| | - Caitlin A Chang
- Department of Medical Genetics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, AB, Canada
| | - Abhijit Dixit
- Nottingham University Hospitals NHS Trust, Nottingham NG5 1PB, UK
| | - Monica Konstantino
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Christopher Healy
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London SE1 9RT, UK
| | - Sumayyah Hannan
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London SE1 9RT, UK
| | - Natsuko Neo
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London SE1 9RT, UK.,Tokyo Medical and Dental University, Tokyo, Japan
| | - Alex Cash
- South Thames Cleft Service, Guy's and St. Thomas' NHS Foundation Trust, London SE1 7EH, UK
| | - Dong Li
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elizabeth Bhoj
- Department of Pediatrics, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elaine H Zackai
- Department of Pediatrics, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ruth Cleaver
- Peninsula Clinical Genetics Service, Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO17 1BJ, UK
| | - Meriel McEntagart
- Department of Clinical Genetics, St George's Hospital, London SW17 0RE, UK
| | - Ruth Newbury-Ecob
- Clinical Genetics, University Hospital Bristol NHS Foundation Trust, Bristol BS2 8EG, UK
| | - Richard Scott
- Department of Clinical Genetics, Great Ormond Street Hospital Trust, London WC1N 3JH, UK
| | - Jane A Hurst
- Department of Clinical Genetics, Great Ormond Street Hospital Trust, London WC1N 3JH, UK
| | - Ping Yee Billie Au
- Department of Medical Genetics, Cumming School of Medicine, Alberta Children's Hospital Research Institute, University of Calgary, AB, Canada
| | - Marie Therese Hosey
- Paediatric Dentistry, Centre of Oral, Clinical and Translational Science, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London SE5 9RS, UK
| | - Mustafa Khokha
- Pediatric Genomics Discovery Program, Departments of Genetics and Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Denise K Marciano
- Departments of Internal Medicine and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-8856, USA
| | - Saquib A Lakhani
- Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Karen J Liu
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London SE1 9RT, UK
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20
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Uehara H, Zhang X, Pereira F, Narendran S, Choi S, Bhuvanagiri S, Liu J, Ravi Kumar S, Bohner A, Carroll L, Archer B, Zhang Y, Liu W, Gao G, Ambati J, Jun AS, Ambati BK. Start codon disruption with CRISPR/Cas9 prevents murine Fuchs' endothelial corneal dystrophy. eLife 2021; 10:e55637. [PMID: 34100716 PMCID: PMC8216720 DOI: 10.7554/elife.55637] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/07/2021] [Indexed: 12/17/2022] Open
Abstract
A missense mutation of collagen type VIII alpha 2 chain (COL8A2) gene leads to early-onset Fuchs' endothelial corneal dystrophy (FECD), which progressively impairs vision through the loss of corneal endothelial cells. We demonstrate that CRISPR/Cas9-based postnatal gene editing achieves structural and functional rescue in a mouse model of FECD. A single intraocular injection of an adenovirus encoding both the Cas9 gene and guide RNA (Ad-Cas9-Col8a2gRNA) efficiently knocked down mutant COL8A2 expression in corneal endothelial cells, prevented endothelial cell loss, and rescued corneal endothelium pumping function in adult Col8a2 mutant mice. There were no adverse sequelae on histology or electroretinography. Col8a2 start codon disruption represents a non-surgical strategy to prevent vision loss in early-onset FECD. As this demonstrates the ability of Ad-Cas9-gRNA to restore the phenotype in adult post-mitotic cells, this method may be widely applicable to adult-onset diseases, even in tissues affected with disorders of non-reproducing cells.
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Affiliation(s)
- Hironori Uehara
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of OregonEugene, ORUnited States
| | - Xiaohui Zhang
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of OregonEugene, ORUnited States
| | - Felipe Pereira
- Department of Ophthalmology, University of VirginiaCharlottesvilleUnited States
| | - Siddharth Narendran
- Department of Ophthalmology, University of VirginiaCharlottesvilleUnited States
| | - Susie Choi
- Moran Eye Center, Department of Ophthalmology and Visual Sciences, University of UtahSalt Lake CityUnited States
| | - Sai Bhuvanagiri
- Moran Eye Center, Department of Ophthalmology and Visual Sciences, University of UtahSalt Lake CityUnited States
| | - Jinlu Liu
- Moran Eye Center, Department of Ophthalmology and Visual Sciences, University of UtahSalt Lake CityUnited States
| | - Sangeetha Ravi Kumar
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of OregonEugene, ORUnited States
| | - Austin Bohner
- Moran Eye Center, Department of Ophthalmology and Visual Sciences, University of UtahSalt Lake CityUnited States
| | - Lara Carroll
- Moran Eye Center, Department of Ophthalmology and Visual Sciences, University of UtahSalt Lake CityUnited States
| | - Bonnie Archer
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of OregonEugene, ORUnited States
| | - Yue Zhang
- Division of Epidemiology, Department of Internal Medicine, University of UtahSalt Lake CityUnited States
| | - Wei Liu
- Division of Epidemiology, Department of Internal Medicine, University of UtahSalt Lake CityUnited States
| | - Guangping Gao
- Gene Therapy Center, Department of Microbiology and Physiological Science Systems, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Jayakrishna Ambati
- Department of Ophthalmology, University of VirginiaCharlottesvilleUnited States
| | - Albert S Jun
- Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Balamurali K Ambati
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of OregonEugene, ORUnited States
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21
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The transcriptional landscape of Venezuelan equine encephalitis virus (TC-83) infection. PLoS Negl Trop Dis 2021; 15:e0009306. [PMID: 33788849 PMCID: PMC8041203 DOI: 10.1371/journal.pntd.0009306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 04/12/2021] [Accepted: 03/12/2021] [Indexed: 01/10/2023] Open
Abstract
Venezuelan Equine Encephalitis Virus (VEEV) is a major biothreat agent that naturally causes outbreaks in humans and horses particularly in tropical areas of the western hemisphere, for which no antiviral therapy is currently available. The host response to VEEV and the cellular factors this alphavirus hijacks to support its effective replication or evade cellular immune responses are largely uncharacterized. We have previously demonstrated tremendous cell-to-cell heterogeneity in viral RNA (vRNA) and cellular transcript levels during flaviviral infection using a novel virus-inclusive single-cell RNA-Seq approach. Here, we used this unbiased, genome-wide approach to simultaneously profile the host transcriptome and vRNA in thousands of single cells during infection of human astrocytes with the live-attenuated vaccine strain of VEEV (TC-83). Host transcription was profoundly suppressed, yet “superproducer cells” with extremely high vRNA abundance emerged during the first viral life cycle and demonstrated an altered transcriptome relative to both uninfected cells and cells with high vRNA abundance harvested at later time points. Additionally, cells with increased structural-to-nonstructural transcript ratio exhibited upregulation of intracellular membrane trafficking genes at later time points. Loss- and gain-of-function experiments confirmed pro- and antiviral activities in both vaccine and virulent VEEV infections among the products of transcripts that positively or negatively correlated with vRNA abundance, respectively. Lastly, comparison with single cell transcriptomic data from other viruses highlighted common and unique pathways perturbed by infection across evolutionary scales. This study provides a high-resolution characterization of the VEEV (TC-83)-host interplay, identifies candidate targets for antivirals, and establishes a comparative single-cell approach to study the evolution of virus-host interactions. Little is known about the host response to Venezuelan Equine Encephalitis Virus (VEEV) and the cellular factors this alphavirus hijacks to support effective replication or evade cellular immune responses. Monitoring dynamics of host and viral RNA (vRNA) during viral infection at a single-cell level can provide insight into the virus-host interplay at a high resolution. Here, a single-cell RNA sequencing technology that detects host and viral RNA was used to investigate the interactions between TC-83, the vaccine strain of VEEV, and the human host during the course of infection of U-87 MG cells (human astrocytoma). Virus abundance and host transcriptome were heterogeneous across cells from the same culture. Subsets of differentially expressed genes, positively or negatively correlating with vRNA abundance, were identified and subsequently in vitro validated as candidate proviral and antiviral factors, respectively, in TC-83 and/or virulent VEEV infections. In the first replication cycle, “superproducer” cells exhibited rapid increase in vRNA abundance and unique gene expression patterns. At later time points, cells with increased structural-to-nonstructural transcript ratio demonstrated upregulation of intracellular membrane trafficking genes. Lastly, comparing the VEEV dataset with published datasets on other RNA viruses revealed unique and overlapping responses across viral clades. Overall, this study improves the understanding of VEEV-host interactions, reveals candidate targets for antiviral approaches, and establishes a comparative single-cell approach to study the evolution of virus-host interactions.
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22
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Terai H, Hamamoto J, Emoto K, Masuda T, Manabe T, Kuronuma S, Kobayashi K, Masuzawa K, Ikemura S, Nakayama S, Kawada I, Suzuki Y, Takeuchi O, Suzuki Y, Ohtsuki S, Yasuda H, Soejima K, Fukunaga K. SHOC2 Is a Critical Modulator of Sensitivity to EGFR-TKIs in Non-Small Cell Lung Cancer Cells. Mol Cancer Res 2020; 19:317-328. [PMID: 33106373 DOI: 10.1158/1541-7786.mcr-20-0664] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/16/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022]
Abstract
EGFR mutation-positive patients with non-small cell lung cancer (NSCLC) respond well to treatment with EGFR-tyrosine kinase inhibitors (EGFR-TKI); however, treatment with EGFR-TKIs is not curative, owing to the presence of residual cancer cells with intrinsic or acquired resistance to this class of drugs. Additional treatment targets that may enhance the efficacy of EGFR-TKIs remain elusive. Using a CRISPR/Cas9-based screen, we identified the leucine-rich repeat scaffold protein SHOC2 as a key modulator of sensitivity to EGFR-TKI treatment. On the basis of in vitro assays, we demonstrated that SHOC2 expression levels strongly correlate with the sensitivity to EGFR-TKIs and that SHOC2 affects the sensitivity to EGFR-TKIs in NSCLC cells via SHOC2/MRAS/PP1c and SHOC2/SCRIB signaling. The potential SHOC2 inhibitor celastrol phenocopied SHOC2 depletion. In addition, we confirmed that SHOC2 expression levels were important for the sensitivity to EGFR-TKIs in vivo. Furthermore, IHC showed the accumulation of cancer cells that express high levels of SHOC2 in lung cancer tissues obtained from patients with NSCLC who experienced acquired resistance to EGFR-TKIs. These data indicate that SHOC2 may be a therapeutic target for patients with NSCLC or a biomarker to predict sensitivity to EGFR-TKI therapy in EGFR mutation-positive patients with NSCLC. Our findings may help improve treatment strategies for patients with NSCLC harboring EGFR mutations. IMPLICATIONS: This study showed that SHOC2 works as a modulator of sensitivity to EGFR-TKIs and the expression levels of SHOC2 can be used as a biomarker for sensitivity to EGFR-TKIs.
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Affiliation(s)
- Hideki Terai
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan. .,Division of Bioregulatory Medicine, Department of Pharmacology, Kitasato University, Tokyo, Japan.,Department of Respiratory Medicine, Kitasato University, Kitasato Institute Hospital, Tokyo, Japan.,Clinical and Translational Research Center, Keio University School of Medicine, Tokyo, Japan
| | - Junko Hamamoto
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan.,Division of Bioregulatory Medicine, Department of Pharmacology, Kitasato University, Tokyo, Japan
| | - Katsura Emoto
- Division of Diagnostic Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Takeshi Masuda
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Tadashi Manabe
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Satoshi Kuronuma
- Biomedical Laboratory, Department of Research, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Keigo Kobayashi
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Keita Masuzawa
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Shinnosuke Ikemura
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan.,Keio Cancer Center, Keio University School of Medicine, Tokyo, Japan
| | - Sohei Nakayama
- Department of Respiratory Medicine, Kitasato University, Kitasato Institute Hospital, Tokyo, Japan
| | - Ichiro Kawada
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yusuke Suzuki
- Department of Respiratory Medicine, Kitasato University, Kitasato Institute Hospital, Tokyo, Japan
| | - Osamu Takeuchi
- Biomedical Laboratory, Department of Research, Kitasato University Kitasato Institute Hospital, Tokyo, Japan
| | - Yukio Suzuki
- Division of Bioregulatory Medicine, Department of Pharmacology, Kitasato University, Tokyo, Japan.,Department of Respiratory Medicine, Kitasato University, Kitasato Institute Hospital, Tokyo, Japan
| | - Sumio Ohtsuki
- Department of Pharmaceutical Microbiology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hiroyuki Yasuda
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kenzo Soejima
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan.,Clinical and Translational Research Center, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
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23
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Kim DK, Knapp JJ, Kuang D, Chawla A, Cassonnet P, Lee H, Sheykhkarimli D, Samavarchi-Tehrani P, Abdouni H, Rayhan A, Li R, Pogoutse O, Coyaud É, van der Werf S, Demeret C, Gingras AC, Taipale M, Raught B, Jacob Y, Roth FP. A Comprehensive, Flexible Collection of SARS-CoV-2 Coding Regions. G3 (BETHESDA, MD.) 2020; 10:3399-3402. [PMID: 32763951 PMCID: PMC7467003 DOI: 10.1534/g3.120.401554] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 07/22/2020] [Indexed: 01/07/2023]
Abstract
The world is facing a global pandemic of COVID-19 caused by the SARS-CoV-2 coronavirus. Here we describe a collection of codon-optimized coding sequences for SARS-CoV-2 cloned into Gateway-compatible entry vectors, which enable rapid transfer into a variety of expression and tagging vectors. The collection is freely available. We hope that widespread availability of this SARS-CoV-2 resource will enable many subsequent molecular studies to better understand the viral life cycle and how to block it.
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Affiliation(s)
- Dae-Kyum Kim
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Jennifer J Knapp
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Da Kuang
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Aditya Chawla
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Patricia Cassonnet
- Unité de Génétique Moléculaire des Virus à ARN, Département Virologie, Institut Pasteur, Paris, France
- UMR3569, Centre National de la Recherche Scientifique, Paris, France
- Université de Paris, Paris, France
| | - Hunsang Lee
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Dayag Sheykhkarimli
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | | | - Hala Abdouni
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Ashyad Rayhan
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Roujia Li
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Oxana Pogoutse
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Étienne Coyaud
- Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
| | - Sylvie van der Werf
- Unité de Génétique Moléculaire des Virus à ARN, Département Virologie, Institut Pasteur, Paris, France
- UMR3569, Centre National de la Recherche Scientifique, Paris, France
- Université de Paris, Paris, France
| | - Caroline Demeret
- Unité de Génétique Moléculaire des Virus à ARN, Département Virologie, Institut Pasteur, Paris, France
- UMR3569, Centre National de la Recherche Scientifique, Paris, France
- Université de Paris, Paris, France
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Mikko Taipale
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Brian Raught
- Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Yves Jacob
- Unité de Génétique Moléculaire des Virus à ARN, Département Virologie, Institut Pasteur, Paris, France
- UMR3569, Centre National de la Recherche Scientifique, Paris, France
- Université de Paris, Paris, France
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
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24
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Park SS, Ponce-Balbuena D, Kuick R, Guerrero-Serna G, Yoon J, Mellacheruvu D, Conlon KP, Basrur V, Nesvizhskii AI, Jalife J, Rual JF. Kir2.1 Interactome Mapping Uncovers PKP4 as a Modulator of the Kir2.1-Regulated Inward Rectifier Potassium Currents. Mol Cell Proteomics 2020; 19:1436-1449. [PMID: 32541000 PMCID: PMC8143648 DOI: 10.1074/mcp.ra120.002071] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Indexed: 12/27/2022] Open
Abstract
Kir2.1, a strong inward rectifier potassium channel encoded by the KCNJ2 gene, is a key regulator of the resting membrane potential of the cardiomyocyte and plays an important role in controlling ventricular excitation and action potential duration in the human heart. Mutations in KCNJ2 result in inheritable cardiac diseases in humans, e.g. the type-1 Andersen-Tawil syndrome (ATS1). Understanding the molecular mechanisms that govern the regulation of inward rectifier potassium currents by Kir2.1 in both normal and disease contexts should help uncover novel targets for therapeutic intervention in ATS1 and other Kir2.1-associated channelopathies. The information available to date on protein-protein interactions involving Kir2.1 channels remains limited. Additional efforts are necessary to provide a comprehensive map of the Kir2.1 interactome. Here we describe the generation of a comprehensive map of the Kir2.1 interactome using the proximity-labeling approach BioID. Most of the 218 high-confidence Kir2.1 channel interactions we identified are novel and encompass various molecular mechanisms of Kir2.1 function, ranging from intracellular trafficking to cross-talk with the insulin-like growth factor receptor signaling pathway, as well as lysosomal degradation. Our map also explores the variations in the interactome profiles of Kir2.1WTversus Kir2.1Δ314-315, a trafficking deficient ATS1 mutant, thus uncovering molecular mechanisms whose malfunctions may underlie ATS1 disease. Finally, using patch-clamp analysis, we validate the functional relevance of PKP4, one of our top BioID interactors, to the modulation of Kir2.1-controlled inward rectifier potassium currents. Our results validate the power of our BioID approach in identifying functionally relevant Kir2.1 interactors and underline the value of our Kir2.1 interactome as a repository for numerous novel biological hypotheses on Kir2.1 and Kir2.1-associated diseases.
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Affiliation(s)
- Sung-Soo Park
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Daniela Ponce-Balbuena
- Department of Internal Medicine and Center for Arrhythmia Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Rork Kuick
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Guadalupe Guerrero-Serna
- Department of Internal Medicine and Center for Arrhythmia Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Justin Yoon
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | | | - Kevin P Conlon
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - José Jalife
- Department of Internal Medicine and Center for Arrhythmia Research, University of Michigan, Ann Arbor, Michigan, USA
- Fundación Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
| | - Jean-François Rual
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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25
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Luo EC, Nathanson JL, Tan FE, Schwartz JL, Schmok JC, Shankar A, Markmiller S, Yee BA, Sathe S, Pratt GA, Scaletta DB, Ha Y, Hill DE, Aigner S, Yeo GW. Large-scale tethered function assays identify factors that regulate mRNA stability and translation. Nat Struct Mol Biol 2020; 27:989-1000. [PMID: 32807991 DOI: 10.1038/s41594-020-0477-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 07/02/2020] [Indexed: 02/07/2023]
Abstract
The molecular functions of the majority of RNA-binding proteins (RBPs) remain unclear, highlighting a major bottleneck to a full understanding of gene expression regulation. Here, we develop a plasmid resource of 690 human RBPs that we subject to luciferase-based 3'-untranslated-region tethered function assays to pinpoint RBPs that regulate RNA stability or translation. Enhanced UV-cross-linking and immunoprecipitation of these RBPs identifies thousands of endogenous mRNA targets that respond to changes in RBP level, recapitulating effects observed in tethered function assays. Among these RBPs, the ubiquitin-associated protein 2-like (UBAP2L) protein interacts with RNA via its RGG domain and cross-links to mRNA and rRNA. Fusion of UBAP2L to RNA-targeting CRISPR-Cas9 demonstrates programmable translational enhancement. Polysome profiling indicates that UBAP2L promotes translation of target mRNAs, particularly global regulators of translation. Our tethering survey allows rapid assignment of the molecular activity of proteins, such as UBAP2L, to specific steps of mRNA metabolism.
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Affiliation(s)
- En-Ching Luo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jason L Nathanson
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Frederick E Tan
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joshua L Schwartz
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jonathan C Schmok
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Archana Shankar
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sebastian Markmiller
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gabriel A Pratt
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Duy B Scaletta
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yuanchi Ha
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA.,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA. .,Stem Cell Program, University of California, San Diego, La Jolla, CA, USA. .,Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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26
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Nollet EA, Cardo-Vila M, Ganguly SS, Tran JD, Schulz VV, Cress A, Corey E, Miranti CK. Androgen receptor-induced integrin α6β1 and Bnip3 promote survival and resistance to PI3K inhibitors in castration-resistant prostate cancer. Oncogene 2020; 39:5390-5404. [PMID: 32565538 PMCID: PMC7395876 DOI: 10.1038/s41388-020-1370-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 11/09/2022]
Abstract
The androgen receptor (AR) is the major driver of prostate cancer growth and survival. However, almost all patients relapse with castration resistant disease (CRPC) when treated with anti-androgen therapy. In CRPC, AR is often aberrantly activated independent of androgen. Targeting survival pathways downstream of AR could be a viable strategy to overcome CRPC. Surprisingly, little is known about how AR drives prostate cancer survival. Furthermore, CRPC tumors in which Pten is lost are also resistant to eradication by PI3K inhibitors. We sought to identify the mechanism by which AR drives tumor survival in CRPC to identify ways to overcome resistance to PI3K inhibition. We found that integrin α6β1 and Bnip3 are selectively elevated in CRPC downstream of AR. While integrin α6 promotes survival and is a direct transcriptional target of AR, the ability of AR to induce Bnip3 is dependent on adhesion to laminin and integrin α6β1-dependent nuclear translocation of HIF1α. Integrin α6β1 and Bnip3 were found to promote survival of CRPC cells selectively on laminin through the induction of autophagy and mitophagy. Furthermore, blocking Bnip3 or integrin α6β1 restored sensitivity to PI3K inhibitors in Pten-negative CRPC. We identified an AR driven pathway that cooperates with laminin and hypoxia to drive resistance to PI3K inhibitors. These findings can help explain in part why PI3K inhibitors have failed in clinical trials to overcome AR-dependent CRPC.
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Affiliation(s)
| | - Marina Cardo-Vila
- Department of Cellular and Molecular Medicine and Prostate Cancer Research Program at University of Arizona Cancer Center, Tucson, AZ, USA
| | - Sourik S Ganguly
- Department of Cellular and Molecular Medicine and Prostate Cancer Research Program at University of Arizona Cancer Center, Tucson, AZ, USA
| | - Jack D Tran
- Department of Cellular and Molecular Medicine and Prostate Cancer Research Program at University of Arizona Cancer Center, Tucson, AZ, USA
| | | | - Anne Cress
- Department of Cellular and Molecular Medicine and Prostate Cancer Research Program at University of Arizona Cancer Center, Tucson, AZ, USA
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Cindy K Miranti
- Van Andel Research Institute, Grand Rapids, MI, USA. .,Department of Cellular and Molecular Medicine and Prostate Cancer Research Program at University of Arizona Cancer Center, Tucson, AZ, USA.
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27
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A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. Proc Natl Acad Sci U S A 2020; 117:11836-11842. [PMID: 32398372 DOI: 10.1073/pnas.1918068117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we develop PCR-mediated Linkage of barcoded Adapters To nucleic acid Elements for sequencing (PLATE-seq) that serves as a general tool to rapidly sequence thousands of DNA elements. We validate its utility by generating the ORFeome for Oryza sativa covering 2,300 genes and constructing a high-quality protein-protein interactome map consisting of 322 interactions between 289 proteins, expanding the known interactions in rice by roughly 50%. Our work paves the way for high-throughput profiling of protein-protein interactions in a wide range of organisms.
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28
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Sheynkman GM, Tuttle KS, Laval F, Tseng E, Underwood JG, Yu L, Dong D, Smith ML, Sebra R, Willems L, Hao T, Calderwood MA, Hill DE, Vidal M. ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms. Nat Commun 2020; 11:2326. [PMID: 32393825 PMCID: PMC7214433 DOI: 10.1038/s41467-020-16174-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 04/16/2020] [Indexed: 01/02/2023] Open
Abstract
Most human protein-coding genes are expressed as multiple isoforms, which greatly expands the functional repertoire of the encoded proteome. While at least one reliable open reading frame (ORF) model has been assigned for every coding gene, the majority of alternative isoforms remains uncharacterized due to (i) vast differences of overall levels between different isoforms expressed from common genes, and (ii) the difficulty of obtaining full-length transcript sequences. Here, we present ORF Capture-Seq (OCS), a flexible method that addresses both challenges for targeted full-length isoform sequencing applications using collections of cloned ORFs as probes. As a proof-of-concept, we show that an OCS pipeline focused on genes coding for transcription factors increases isoform detection by an order of magnitude when compared to unenriched samples. In short, OCS enables rapid discovery of isoforms from custom-selected genes and will accelerate mapping of the human transcriptome.
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Affiliation(s)
- Gloria M Sheynkman
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA. .,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA. .,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Katharine S Tuttle
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Biochemistry, Northeastern University, Boston, MA, 02115, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute of Data Science and Genomic Technology, New York, NY, 10029, USA
| | - Florent Laval
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Laboratory of Molecular Biology, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium.,Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, University of Liège, 4000, Liège, Belgium
| | | | | | - Liang Yu
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, China
| | - Da Dong
- School of Computer Science and Technology, Xidian University, Xi'an, 710071, China
| | - Melissa L Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute of Data Science and Genomic Technology, New York, NY, 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Icahn Institute of Data Science and Genomic Technology, New York, NY, 10029, USA
| | - Luc Willems
- Laboratory of Molecular Biology, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium.,Laboratory of Molecular and Cellular Epigenetics, GIGA-Cancer, University of Liège, 4000, Liège, Belgium
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA. .,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA. .,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
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29
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Kumar S, Barouch-Bentov R, Xiao F, Schor S, Pu S, Biquand E, Lu A, Lindenbach BD, Jacob Y, Demeret C, Einav S. MARCH8 Ubiquitinates the Hepatitis C Virus Nonstructural 2 Protein and Mediates Viral Envelopment. Cell Rep 2020; 26:1800-1814.e5. [PMID: 30759391 PMCID: PMC7053169 DOI: 10.1016/j.celrep.2019.01.075] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 11/07/2018] [Accepted: 01/18/2019] [Indexed: 02/07/2023] Open
Abstract
The mechanisms that regulate envelopment of HCV and other viruses that bud intracellularly and/or lack late-domain motifs are largely unknown. We reported that K63 polyubiquitination of the HCV nonstructural (NS) 2 protein mediates HRS (ESCRT-0 component) binding and envelopment. Nevertheless, the ubiquitin signaling that governs NS2 ubiquitination remained unknown. Here, we map the NS2 interactome with the ubiquitin proteasome system (UPS) via mammalian cell-based screens. NS2 interacts with E3 ligases, deubiquitinases, and ligase regulators, some of which are candidate proviral or antiviral factors. MARCH8, a RING-finger E3 ligase, catalyzes K63-linked NS2 polyubiquitination in vitro and in HCV-infected cells. MARCH8 is required for infection with HCV, dengue, and Zika viruses and specifically mediates HCV envelopment. Our data reveal regulation of HCV envelopment via ubiquitin signaling and both a viral protein substrate and a ubiquitin K63-linkage of the understudied MARCH8, with potential implications for cell biology, virology, and host-targeted antiviral design. The mechanisms that regulate intracellular viral envelopment are unknown. Kumar et al. report that MARCH8 catalyzes K63-linked polyubiquitination of the HCV nonstructural 2 protein and subsequently ESCRT recruitment and HCV envelopment. MARCH8 is required for infection with other Flaviviridae family members, thereby representing a potential host target for antiviral strategies.
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Affiliation(s)
- Sathish Kumar
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rina Barouch-Bentov
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Fei Xiao
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Stanford Schor
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Szuyuan Pu
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elise Biquand
- Département de Virologie, Unité de Génétique Moléculaire des Virus ARN (GMVR), Institut Pasteur, Centre National de la Recherche Scientifique; Université Paris Diderot, Paris, France
| | - Albert Lu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Yves Jacob
- Département de Virologie, Unité de Génétique Moléculaire des Virus ARN (GMVR), Institut Pasteur, Centre National de la Recherche Scientifique; Université Paris Diderot, Paris, France
| | - Caroline Demeret
- Département de Virologie, Unité de Génétique Moléculaire des Virus ARN (GMVR), Institut Pasteur, Centre National de la Recherche Scientifique; Université Paris Diderot, Paris, France
| | - Shirit Einav
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
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30
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Agrotis A, von Chamier L, Oliver H, Kiso K, Singh T, Ketteler R. Human ATG4 autophagy proteases counteract attachment of ubiquitin-like LC3/GABARAP proteins to other cellular proteins. J Biol Chem 2019; 294:12610-12621. [PMID: 31315929 PMCID: PMC6709618 DOI: 10.1074/jbc.ac119.009977] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Indexed: 01/01/2023] Open
Abstract
Microtubule-associated protein 1 light chain 3 α (LC3)/GABA type A receptor-associated protein (GABARAP) comprises a family of ubiquitin-like proteins involved in (macro)autophagy, an important intracellular degradation pathway that delivers cytoplasmic material to lysosomes via double-membrane vesicles called autophagosomes. The only currently known cellular molecules covalently modified by LC3/GABARAP are membrane phospholipids such as phosphatidylethanolamine in the autophagosome membrane. Autophagy-related 4 cysteine peptidase (ATG4) proteases process inactive pro-LC3/GABARAP before lipidation, and the same proteases can also deconjugate LC3/GABARAP from lipids. To determine whether LC3/GABARAP has other molecular targets, here we generated a pre-processed LC3B mutant (Q116P) that is resistant to ATG4-mediated deconjugation. Upon expression in human cells and when assessed by immunoblotting under reducing and denaturing conditions, deconjugation-resistant LC3B accumulated in multiple forms and at much higher molecular weights than free LC3B. We observed a similar accumulation when pre-processed versions of all mammalian LC3/GABARAP isoforms were expressed in ATG4-deficient cell lines, suggesting that LC3/GABARAP can attach also to other larger molecules. We identified ATG3, the E2-like enzyme involved in LC3/GABARAP lipidation, as one target of conjugation with multiple copies of LC3/GABARAP. We show that LC3B-ATG3 conjugates are distinct from the LC3B-ATG3 thioester intermediate formed before lipidation, and we biochemically demonstrate that ATG4B can cleave LC3B-ATG3 conjugates. Finally, we determined ATG3 residue Lys-243 as an LC3B modification site. Overall, we provide the first cellular evidence that mammalian LC3/GABARAP post-translationally modifies proteins akin to ubiquitination ("LC3ylation"), with ATG4 proteases acting like deubiquitinating enzymes to counteract this modification ("deLC3ylation").
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Affiliation(s)
- Alexander Agrotis
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Lucas von Chamier
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Harriet Oliver
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Koshiro Kiso
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Tanya Singh
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Robin Ketteler
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
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31
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Agrotis A, Pengo N, Burden JJ, Ketteler R. Redundancy of human ATG4 protease isoforms in autophagy and LC3/GABARAP processing revealed in cells. Autophagy 2019; 15:976-997. [PMID: 30661429 PMCID: PMC6526816 DOI: 10.1080/15548627.2019.1569925] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Macroautophagy/autophagy is a cellular degradation pathway that delivers cytoplasmic material to lysosomes via double-membrane organelles called autophagosomes. Lipidation of ubiquitin-like LC3/GABARAP proteins on the autophagosome membrane is important for autophagy. The cysteine protease ATG4 executes 2 LC3/GABARAP processing events: priming of newly synthesized pro-LC3/GABARAP to enable subsequent lipidation, and delipidation/deconjugation of lipidated LC3/GABARAP (the exact purpose of which is unclear in mammals). Four ATG4 isoforms (ATG4A to ATG4D) exist in mammals; however, the functional redundancy of these proteins in cells is poorly understood. Here we show that human HAP1 and HeLa cells lacking ATG4B exhibit a severe but incomplete defect in LC3/GABARAP processing and autophagy. By further genetic depletion of ATG4 isoforms using CRISPR-Cas9 and siRNA we uncover that ATG4A, ATG4C and ATGD all contribute to residual priming activity, which is sufficient to enable lipidation of endogenous GABARAPL1 on autophagic structures. We also demonstrate that expressing high levels of pre-primed LC3B in ATG4-deficient cells can rescue a defect in autophagic degradation of the cargo receptor SQSTM1/p62, suggesting that delipidation by human ATG4 is not essential for autophagosome formation and fusion with lysosomes. Overall, our study provides a comprehensive characterization of ATG4 isoform function during autophagy in human cells. Abbreviations: Atg: autophagy-related; baf A1: bafilomycin A1; CASP3: caspase 3; CLEM: correlative light and electron microscopy; CMV: cytomegalovirus; CRISPR: clustered regularly interspaced short palindromic repeats; DKO: double knockout; EGFP: enhanced green fluorescent protein; GABARAP: GABA type A receptor-associated protein; GABARAPL1: GABA type A receptor-associated protein like 1; GABARAPL2: GABA type A receptor-associated protein like 2; GFP: green fluorescent protein; HB: homogenization buffer; KO: knockout; LAMP1: lysosomal associated membrane protein 1; LIR: LC3 interacting region; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MFN2: mitofusin 2; N.A.: numerical aperture; NEM: N-ethylmaleimide; PDHA1: pyruvate dehydrogenase E1 alpha 1 subunit; PLD: phospholipase D; PE: phosphatidylethanolamine; RLUC: Renilla luciferase; SQSTM1: sequestosome 1; TEM: transmission electron microscopy; TKO: triple knockout; ULK1: unc-51 like autophagy activating kinase 1; VCL: vinculin; WT: wild-type
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Affiliation(s)
- Alexander Agrotis
- a MRC Laboratory for Molecular Cell Biology , University College London , London , UK
| | - Niccolo Pengo
- a MRC Laboratory for Molecular Cell Biology , University College London , London , UK
| | - Jemima J Burden
- a MRC Laboratory for Molecular Cell Biology , University College London , London , UK
| | - Robin Ketteler
- a MRC Laboratory for Molecular Cell Biology , University College London , London , UK
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32
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Reece-Hoyes JS, Walhout AJM. Identifying Interactors from an Activation Domain Prey Library. Cold Spring Harb Protoc 2018; 2018:2018/7/pdb.prot094987. [PMID: 29967273 DOI: 10.1101/pdb.prot094987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In yeast hybrid assays, the process of identifying preys that interact with the bait of interest involves several steps. First, in this protocol, the bait yeast strain is transformed with a library of activation domain (AD)-prey clones and plated on selective media containing 3-aminotriazole (3AT). This selects transformants containing an AD-prey clone that induces HIS3 reporter expression. Second, these "HIS-positive" colonies are analyzed for LacZ induction (and, optionally, URA3 induction in yeast two-hybrid (Y2H) assays). Third, yeast PCR is used on these "double-positive" colonies to amplify the insert from the AD-prey plasmid. Fourth, some of this PCR product is used to perform a gap-repair retest to confirm the interaction in fresh bait-strain yeast, and the remainder is used for DNA sequencing to determine prey identity for those that successfully retest. Finally, interactions are carefully examined to filter out likely false-positive interactions. This protocol takes 20-43 d plus sequence confirmation to complete.
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33
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Reece-Hoyes JS, Walhout AJM. Gateway-Compatible Yeast One-Hybrid and Two-Hybrid Assays. Cold Spring Harb Protoc 2018; 2018:2018/7/pdb.top094953. [PMID: 29967278 DOI: 10.1101/pdb.top094953] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In the first section of this introduction, we provide background information for yeast two-hybrid (Y2H) assays that provide a genetic method for the identification and analysis of binary protein-protein interactions and that are complementary to biochemical methods such as immunoprecipitation. In the second section, we discuss yeast one-hybrid (Y1H) assays that provide a "gene-centered" (DNA-to-protein) genetic method to identify and study protein-DNA interactions between cis-regulatory elements and transcription factors (TFs). This method is complementary to "TF-centered" (protein-to-DNA) biochemical methods such as chromatin immunoprecipitation.
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34
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Ordureau A, Paulo JA, Zhang W, Ahfeldt T, Zhang J, Cohn EF, Hou Z, Heo JM, Rubin LL, Sidhu SS, Gygi SP, Harper JW. Dynamics of PARKIN-Dependent Mitochondrial Ubiquitylation in Induced Neurons and Model Systems Revealed by Digital Snapshot Proteomics. Mol Cell 2018; 70:211-227.e8. [PMID: 29656925 DOI: 10.1016/j.molcel.2018.03.012] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/21/2018] [Accepted: 03/08/2018] [Indexed: 11/24/2022]
Abstract
Flux through kinase and ubiquitin-driven signaling systems depends on the modification kinetics, stoichiometry, primary site specificity, and target abundance within the pathway, yet we rarely understand these parameters and their spatial organization within cells. Here we develop temporal digital snapshots of ubiquitin signaling on the mitochondrial outer membrane in embryonic stem cell-derived neurons, and we model HeLa cell systems upon activation of the PINK1 kinase and PARKIN ubiquitin ligase by proteomic counting of ubiquitylation and phosphorylation events. We define the kinetics and site specificity of PARKIN-dependent target ubiquitylation, and we demonstrate the power of this approach to quantify pathway modulators and to mechanistically define the role of PARKIN UBL phosphorylation in pathway activation in induced neurons. Finally, through modulation of pS65-Ub on mitochondria, we demonstrate that Ub hyper-phosphorylation is inhibitory to mitophagy receptor recruitment, indicating that pS65-Ub stoichiometry in vivo is optimized to coordinate PARKIN recruitment via pS65-Ub and mitophagy receptors via unphosphorylated chains.
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Affiliation(s)
- Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Wei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Tim Ahfeldt
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02132, USA
| | - Jiuchun Zhang
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Erin F Cohn
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Zhonggang Hou
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jin-Mi Heo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Lee L Rubin
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02132, USA
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, and Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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35
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Zanini F, Pu SY, Bekerman E, Einav S, Quake SR. Single-cell transcriptional dynamics of flavivirus infection. eLife 2018; 7:32942. [PMID: 29451494 PMCID: PMC5826272 DOI: 10.7554/elife.32942] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/08/2018] [Indexed: 12/25/2022] Open
Abstract
Dengue and Zika viral infections affect millions of people annually and can be complicated by hemorrhage and shock or neurological manifestations, respectively. However, a thorough understanding of the host response to these viruses is lacking, partly because conventional approaches ignore heterogeneity in virus abundance across cells. We present viscRNA-Seq (virus-inclusive single cell RNA-Seq), an approach to probe the host transcriptome together with intracellular viral RNA at the single cell level. We applied viscRNA-Seq to monitor dengue and Zika virus infection in cultured cells and discovered extreme heterogeneity in virus abundance. We exploited this variation to identify host factors that show complex dynamics and a high degree of specificity for either virus, including proteins involved in the endoplasmic reticulum translocon, signal peptide processing, and membrane trafficking. We validated the viscRNA-Seq hits and discovered novel proviral and antiviral factors. viscRNA-Seq is a powerful approach to assess the genome-wide virus-host dynamics at single cell level.
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Affiliation(s)
- Fabio Zanini
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Szu-Yuan Pu
- Division of Infectious Diseases, Department of Medicine, Stanford University School of Medicine, Stanford, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | - Elena Bekerman
- Division of Infectious Diseases, Department of Medicine, Stanford University School of Medicine, Stanford, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | - Shirit Einav
- Division of Infectious Diseases, Department of Medicine, Stanford University School of Medicine, Stanford, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, United States.,Department of Applied Physics, Stanford University, Stanford, United States.,Chan Zuckerberg Biohub, San Francisco, United States
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36
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Wolf B, Balestra FR, Spahr A, Gönczy P. ZYG-1 promotes limited centriole amplification in the C. elegans seam lineage. Dev Biol 2018; 434:221-230. [PMID: 29307730 DOI: 10.1016/j.ydbio.2018.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/08/2017] [Accepted: 01/01/2018] [Indexed: 11/27/2022]
Abstract
Genome stability relies notably on the integrity of centrosomes and on the mitotic spindle they organize. Structural and numerical centrosome aberrations are frequently observed in human cancer, and there is increasing evidence that centrosome amplification can promote tumorigenesis. Here, we use C. elegans seam cells as a model system to analyze centrosome homeostasis in the context of a stereotyped stem like lineage. We found that overexpression of the Plk4-related kinase ZYG-1 leads to the formation of one supernumerary centriolar focus per parental centriole during the cell cycle that leads to the sole symmetric division in the seam lineage. In the following cell cycle, such supernumerary foci function as microtubule organizing centers, but do not cluster during mitosis, resulting in the formation of a multipolar spindle and then aneuploid daughter cells. Intriguingly, we found also that supernumerary centriolar foci do not assemble in the asymmetric cell divisions that precedes or that follows the symmetric seam cell division, despite the similar presence of GFP::ZYG-1. Furthermore, we established that supernumerary centrioles form earlier during development in animals depleted of the heterochronic gene lin-14, in which the symmetric division is precocious. Conversely, supernumerary centrioles are essentially not observed in animals depleted of lin-28, in which the symmetric division is lacking. These findings lead us to conclude that ZYG-1 promotes limited centriole amplification solely during the symmetric division in the C. elegans seam lineage.
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Affiliation(s)
- Benita Wolf
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Fernando R Balestra
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Antoine Spahr
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Pierre Gönczy
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
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37
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Abstract
A complete understanding of human cancer variants requires new methods to systematically and efficiently assess the functional effects of genomic mutations at a large scale. Here, we describe a set of tools to rapidly clone and stratify thousands of cancer mutations at base resolution. This protocol provides a massively parallel pipeline to achieve high stringency and throughput. The approach includes high-throughput generation of mutant clones by Gateway, confirmation of variant identity by barcoding and next-generation sequencing, and stratification of cancer variants by multiplexed interaction profiling. Compared with alternative site-directed mutagenesis methods, our protocol requires less sequencing effort and enables robust statistical calling of allele-specific effects. To ensure the precision of variant interaction profiling, we further describe two complementary methods-a high-throughput enhanced yeast two-hybrid (HT-eY2H) assay and a mammalian-cell-based Gaussia princeps luciferase protein-fragment complementation assay (GPCA). These independent assays with standard controls validate mutational interaction profiles with high quality. This protocol provides experimentally derived guidelines for classifying candidate cancer alleles emerging from whole-genome or whole-exome sequencing projects as 'drivers' or 'passengers'. For ∼100 genomic mutations, the protocol-including target primer design, variant library construction, and sequence verification-can be completed within as little as 2-3 weeks, and cancer variant stratification can be completed within 2 weeks.
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38
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The Enterococcus faecalis virulence factor ElrA interacts with the human Four-and-a-Half LIM Domains Protein 2. Sci Rep 2017; 7:4581. [PMID: 28676674 PMCID: PMC5496941 DOI: 10.1038/s41598-017-04875-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 05/22/2017] [Indexed: 12/22/2022] Open
Abstract
The commensal bacterium Enterococcus faecalis is a common cause of nosocomial infections worldwide. The increasing prevalence of multi-antibiotic resistant E. faecalis strains reinforces this public health concern. Despite numerous studies highlighting several pathology-related genetic traits, the molecular mechanisms of E. faecalis virulence remain poorly understood. In this work, we studied 23 bacterial proteins that could be considered as virulence factors or involved in the Enterococcus interaction with the host. We systematically tested their interactions with human proteins using the Human ORFeome library, a set of 12,212 human ORFs, in yeast. Among the thousands of tested interactions, one involving the E. faecalis virulence factor ElrA and the human protein FHL2 was evidenced by yeast two-hybrid and biochemically confirmed. Further molecular characterizations allowed defining an FHL2-interacting domain (FID) of ElrA. Deletion of the FID led to an attenuated in vivo phenotype of the mutated strain clearly indicating that this interaction is likely to contribute to the multifactorial virulence of this opportunistic pathogen. Altogether, our results show that FHL2 is the first host cellular protein directly targeted by an E. faecalis virulence factor and that this interaction is involved in Enterococcus pathogenicity.
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39
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Jo M, Chung AY, Yachie N, Seo M, Jeon H, Nam Y, Seo Y, Kim E, Zhong Q, Vidal M, Park HC, Roth FP, Suk K. Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target. Genome Res 2017; 27:1487-1500. [PMID: 28596290 PMCID: PMC5580709 DOI: 10.1101/gr.211649.116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 06/06/2017] [Indexed: 12/13/2022]
Abstract
To understand disease mechanisms, a large-scale analysis of human–yeast genetic interactions was performed. Of 1305 human disease genes assayed, 20 genes exhibited strong toxicity in yeast. Human–yeast genetic interactions were identified by en masse transformation of the human disease genes into a pool of 4653 homozygous diploid yeast deletion mutants with unique barcode sequences, followed by multiplexed barcode sequencing to identify yeast toxicity modifiers. Subsequent network analyses focusing on amyotrophic lateral sclerosis (ALS)-associated genes, such as optineurin (OPTN) and angiogenin (ANG), showed that the human orthologs of the yeast toxicity modifiers of these ALS genes are enriched for several biological processes, such as cell death, lipid metabolism, and molecular transport. When yeast genetic interaction partners held in common between human OPTN and ANG were validated in mammalian cells and zebrafish, MAP2K5 kinase emerged as a potential drug target for ALS therapy. The toxicity modifiers identified in this study may deepen our understanding of the pathogenic mechanisms of ALS and other devastating diseases.
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Affiliation(s)
- Myungjin Jo
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, Kyungpook National University School of Medicine, Daegu, 41944, Korea
| | - Ah Young Chung
- Department of Biomedical Sciences, Korea University Ansan Hospital, Ansan-si, Gyeonggi-do, 425-707, Korea
| | - Nozomu Yachie
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto and Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Minchul Seo
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, Kyungpook National University School of Medicine, Daegu, 41944, Korea
| | - Hyejin Jeon
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, Kyungpook National University School of Medicine, Daegu, 41944, Korea
| | - Youngpyo Nam
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, Kyungpook National University School of Medicine, Daegu, 41944, Korea
| | - Yeojin Seo
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, Kyungpook National University School of Medicine, Daegu, 41944, Korea
| | - Eunmi Kim
- Department of Biomedical Sciences, Korea University Ansan Hospital, Ansan-si, Gyeonggi-do, 425-707, Korea
| | - Quan Zhong
- Department of Biological Sciences, Wright State University, Dayton, Ohio 45435, USA
| | - Marc Vidal
- Department of Biological Sciences, Wright State University, Dayton, Ohio 45435, USA
| | - Hae Chul Park
- Department of Biomedical Sciences, Korea University Ansan Hospital, Ansan-si, Gyeonggi-do, 425-707, Korea
| | - Frederick P Roth
- Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto and Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada.,Canadian Institute for Advanced Research, Toronto, Ontario M5G 1Z8, Canada
| | - Kyoungho Suk
- Department of Pharmacology, Brain Science and Engineering Institute, and Department of Biomedical Sciences, BK21 Plus KNU Biomedical Convergence Program, Kyungpook National University School of Medicine, Daegu, 41944, Korea
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40
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Lu H, Villafane N, Dogruluk T, Grzeskowiak CL, Kong K, Tsang YH, Zagorodna O, Pantazi A, Yang L, Neill NJ, Kim YW, Creighton CJ, Verhaak RG, Mills GB, Park PJ, Kucherlapati R, Scott KL. Engineering and Functional Characterization of Fusion Genes Identifies Novel Oncogenic Drivers of Cancer. Cancer Res 2017; 77:3502-3512. [PMID: 28512244 DOI: 10.1158/0008-5472.can-16-2745] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 03/07/2017] [Accepted: 04/27/2017] [Indexed: 01/22/2023]
Abstract
Oncogenic gene fusions drive many human cancers, but tools to more quickly unravel their functional contributions are needed. Here we describe methodology permitting fusion gene construction for functional evaluation. Using this strategy, we engineered the known fusion oncogenes, BCR-ABL1, EML4-ALK, and ETV6-NTRK3, as well as 20 previously uncharacterized fusion genes identified in The Cancer Genome Atlas datasets. In addition to confirming oncogenic activity of the known fusion oncogenes engineered by our construction strategy, we validated five novel fusion genes involving MET, NTRK2, and BRAF kinases that exhibited potent transforming activity and conferred sensitivity to FDA-approved kinase inhibitors. Our fusion construction strategy also enabled domain-function studies of BRAF fusion genes. Our results confirmed other reports that the transforming activity of BRAF fusions results from truncation-mediated loss of inhibitory domains within the N-terminus of the BRAF protein. BRAF mutations residing within this inhibitory region may provide a means for BRAF activation in cancer, therefore we leveraged the modular design of our fusion gene construction methodology to screen N-terminal domain mutations discovered in tumors that are wild-type at the BRAF mutation hotspot, V600. We identified an oncogenic mutation, F247L, whose expression robustly activated the MAPK pathway and sensitized cells to BRAF and MEK inhibitors. When applied broadly, these tools will facilitate rapid fusion gene construction for subsequent functional characterization and translation into personalized treatment strategies. Cancer Res; 77(13); 3502-12. ©2017 AACR.
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Affiliation(s)
- Hengyu Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Nicole Villafane
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas
| | - Turgut Dogruluk
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Caitlin L Grzeskowiak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Kathleen Kong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yiu Huen Tsang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Oksana Zagorodna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Angeliki Pantazi
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lixing Yang
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Nicholas J Neill
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Young Won Kim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Chad J Creighton
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Roel G Verhaak
- The Jackson Laboratory, Genomic Medicine, Farmington, Connecticut
| | - Gordon B Mills
- Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Peter J Park
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Raju Kucherlapati
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas. .,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
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41
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Luck K, Sheynkman GM, Zhang I, Vidal M. Proteome-Scale Human Interactomics. Trends Biochem Sci 2017; 42:342-354. [PMID: 28284537 DOI: 10.1016/j.tibs.2017.02.006] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 02/10/2017] [Accepted: 02/16/2017] [Indexed: 01/28/2023]
Abstract
Cellular functions are mediated by complex interactome networks of physical, biochemical, and functional interactions between DNA sequences, RNA molecules, proteins, lipids, and small metabolites. A thorough understanding of cellular organization requires accurate and relatively complete models of interactome networks at proteome scale. The recent publication of four human protein-protein interaction (PPI) maps represents a technological breakthrough and an unprecedented resource for the scientific community, heralding a new era of proteome-scale human interactomics. Our knowledge gained from these and complementary studies provides fresh insights into the opportunities and challenges when analyzing systematically generated interactome data, defines a clear roadmap towards the generation of a first reference interactome, and reveals new perspectives on the organization of cellular life.
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Affiliation(s)
- Katja Luck
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Gloria M Sheynkman
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Ivy Zhang
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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42
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Bekerman E, Neveu G, Shulla A, Brannan J, Pu SY, Wang S, Xiao F, Barouch-Bentov R, Bakken RR, Mateo R, Govero J, Nagamine CM, Diamond MS, De Jonghe S, Herdewijn P, Dye JM, Randall G, Einav S. Anticancer kinase inhibitors impair intracellular viral trafficking and exert broad-spectrum antiviral effects. J Clin Invest 2017; 127:1338-1352. [PMID: 28240606 DOI: 10.1172/jci89857] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/30/2016] [Indexed: 01/09/2023] Open
Abstract
Global health is threatened by emerging viral infections, which largely lack effective vaccines or therapies. Targeting host pathways that are exploited by multiple viruses could offer broad-spectrum solutions. We previously reported that AAK1 and GAK, kinase regulators of the host adaptor proteins AP1 and AP2, are essential for hepatitis C virus (HCV) infection, but the underlying mechanism and relevance to other viruses or in vivo infections remained unknown. Here, we have discovered that AP1 and AP2 cotraffic with HCV particles in live cells. Moreover, we found that multiple viruses, including dengue and Ebola, exploit AAK1 and GAK during entry and infectious virus production. In cultured cells, treatment with sunitinib and erlotinib, approved anticancer drugs that inhibit AAK1 or GAK activity, or with more selective compounds inhibited intracellular trafficking of HCV and multiple unrelated RNA viruses with a high barrier to resistance. In murine models of dengue and Ebola infection, sunitinib/erlotinib combination protected against morbidity and mortality. We validated sunitinib- and erlotinib-mediated inhibition of AAK1 and GAK activity as an important mechanism of antiviral action. Additionally, we revealed potential roles for additional kinase targets. These findings advance our understanding of virus-host interactions and establish a proof of principle for a repurposed, host-targeted approach to combat emerging viruses.
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43
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Mehla J, Caufield JH, Sakhawalkar N, Uetz P. A Comparison of Two-Hybrid Approaches for Detecting Protein-Protein Interactions. Methods Enzymol 2017; 586:333-358. [PMID: 28137570 DOI: 10.1016/bs.mie.2016.10.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Two-hybrid systems are one of the most popular, preferred, cost effective, and scalable in vivo genetic approaches for screening protein-protein interactions. A number of variants of yeast and bacterial two-hybrid systems exist, rendering them ideal for modern, flexible proteomics-driven studies. For mapping protein interactions at genome scales (that is, constructing an interactome), the yeast two-hybrid system has been extensively tested and is preferred over bacterial two-hybrid systems, given that users have created more resources such as a variety of vectors and other modifications. Each system has its own advantages and limitations and thus needs to be compared directly. For instance, the bacterial two-hybrid method seems a better fit than the yeast two-hybrid system to screen membrane-associated proteins. In this chapter, we provide detailed protocols for yeast and bacterial two-hybrid systems as well as a comparison of outcomes for each approach using our own and published data.
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Affiliation(s)
- J Mehla
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, United States.
| | - J H Caufield
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, United States
| | - N Sakhawalkar
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, United States
| | - P Uetz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, United States.
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44
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Bradley M, Ramirez I, Cheung K, Gholkar AA, Torres JZ. Inducible LAP-tagged Stable Cell Lines for Investigating Protein Function, Spatiotemporal Localization and Protein Interaction Networks. J Vis Exp 2016. [PMID: 28060263 PMCID: PMC5226453 DOI: 10.3791/54870] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Multi-protein complexes, rather than single proteins acting in isolation, often govern molecular pathways regulating cellular homeostasis. Based on this principle, the purification of critical proteins required for the functioning of these pathways along with their native interacting partners has not only allowed the mapping of the protein constituents of these pathways, but has also provided a deeper understanding of how these proteins coordinate to regulate these pathways. Within this context, understanding a protein's spatiotemporal localization and its protein-protein interaction network can aid in defining its role within a pathway, as well as how its misregulation may lead to disease pathogenesis. To address this need, several approaches for protein purification such as tandem affinity purification (TAP) and localization and affinity purification (LAP) have been designed and used successfully. Nevertheless, in order to apply these approaches to pathway-scale proteomic analyses, these strategies must be supplemented with modern technological developments in cloning and mammalian stable cell line generation. Here, we describe a method for generating LAP-tagged human inducible stable cell lines for investigating protein subcellular localization and protein-protein interaction networks. This approach has been successfully applied to the dissection of multiple cellular pathways including cell division and is compatible with high-throughput proteomic analyses.
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Affiliation(s)
- Michelle Bradley
- Department of Chemistry and Biochemistry, University of California, Los Angeles
| | - Ivan Ramirez
- Department of Chemistry and Biochemistry, University of California, Los Angeles
| | - Keith Cheung
- Department of Chemistry and Biochemistry, University of California, Los Angeles
| | - Ankur A Gholkar
- Department of Chemistry and Biochemistry, University of California, Los Angeles
| | - Jorge Z Torres
- Department of Chemistry and Biochemistry, University of California, Los Angeles; Molecular Biology Institute, University of California, Los Angeles; Jonsson Comprehensive Cancer Center, University of California, Los Angeles;
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45
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Fuxman Bass JI, Reece-Hoyes JS, Walhout AJ. Gene-Centered Yeast One-Hybrid Assays. Cold Spring Harb Protoc 2016; 2016:2016/12/pdb.top077669. [PMID: 27934693 PMCID: PMC5443116 DOI: 10.1101/pdb.top077669] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
An important question when studying gene regulation is which transcription factors (TFs) interact with which cis-regulatory elements, such as promoters and enhancers. Addressing this issue in complex multicellular organisms is challenging as several hundreds of TFs and thousands of regulatory elements must be considered in the context of different tissues and physiological conditions. Yeast one-hybrid (Y1H) assays provide a powerful "gene-centered" method to identify the TFs that can bind a DNA sequence of interest. In this introduction, we describe the basic principles of the Y1H assay and its advantages and disadvantages and briefly discuss how it is complementary to "TF-centered" methods that identify protein-DNA interactions for a known protein of interest.
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Affiliation(s)
- Juan I. Fuxman Bass
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - John S. Reece-Hoyes
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Albertha J.M. Walhout
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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46
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Howard TP, Vazquez F, Tsherniak A, Hong AL, Rinne M, Aguirre AJ, Boehm JS, Hahn WC. Functional Genomic Characterization of Cancer Genomes. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2016; 81:237-246. [PMID: 27815544 DOI: 10.1101/sqb.2016.81.031070] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
International efforts to sequence cancer genomes now provide an overview of the major genetic alterations that occur in most human cancers. These studies have identified many highly recurrent alterations in specific cancer subtypes but have also identified mutations that occur at lower frequency and unstudied variants of known cancer-associated genes. To elucidate the function of such cancer alleles, we have developed several approaches to systematically interrogate genomic changes found in human tumors. In general, we have taken two complementary approaches. In the first approach, we focus on perturbing genes identified as mutated, amplified, or deleted by cancer genome annotation efforts, whereas in the second, we have taken an unbiased approach to identify genes that are essential for cancer cell proliferation or survival in cell lines that are extensively annotated to identify context-specific essential genes. These studies begin to allow us to define a cancer dependencies map.
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Affiliation(s)
- Thomas P Howard
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Francisca Vazquez
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Aviad Tsherniak
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Andrew L Hong
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142.,Boston Children's Hospital, Boston, Massachusetts 02115
| | - Mik Rinne
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Andrew J Aguirre
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - Jesse S Boehm
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
| | - William C Hahn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142
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47
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Barouch-Bentov R, Neveu G, Xiao F, Beer M, Bekerman E, Schor S, Campbell J, Boonyaratanakornkit J, Lindenbach B, Lu A, Jacob Y, Einav S. Hepatitis C Virus Proteins Interact with the Endosomal Sorting Complex Required for Transport (ESCRT) Machinery via Ubiquitination To Facilitate Viral Envelopment. mBio 2016; 7:e01456-16. [PMID: 27803188 PMCID: PMC5090039 DOI: 10.1128/mbio.01456-16] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/07/2016] [Indexed: 02/07/2023] Open
Abstract
Enveloped viruses commonly utilize late-domain motifs, sometimes cooperatively with ubiquitin, to hijack the endosomal sorting complex required for transport (ESCRT) machinery for budding at the plasma membrane. However, the mechanisms underlying budding of viruses lacking defined late-domain motifs and budding into intracellular compartments are poorly characterized. Here, we map a network of hepatitis C virus (HCV) protein interactions with the ESCRT machinery using a mammalian-cell-based protein interaction screen and reveal nine novel interactions. We identify HRS (hepatocyte growth factor-regulated tyrosine kinase substrate), an ESCRT-0 complex component, as an important entry point for HCV into the ESCRT pathway and validate its interactions with the HCV nonstructural (NS) proteins NS2 and NS5A in HCV-infected cells. Infectivity assays indicate that HRS is an important factor for efficient HCV assembly. Specifically, by integrating capsid oligomerization assays, biophysical analysis of intracellular viral particles by continuous gradient centrifugations, proteolytic digestion protection, and RNase digestion protection assays, we show that HCV co-opts HRS to mediate a late assembly step, namely, envelopment. In the absence of defined late-domain motifs, K63-linked polyubiquitinated lysine residues in the HCV NS2 protein bind the HRS ubiquitin-interacting motif to facilitate assembly. Finally, ESCRT-III and VPS/VTA1 components are also recruited by HCV proteins to mediate assembly. These data uncover involvement of ESCRT proteins in intracellular budding of a virus lacking defined late-domain motifs and a novel mechanism by which HCV gains entry into the ESCRT network, with potential implications for other viruses. IMPORTANCE Viruses commonly bud at the plasma membrane by recruiting the host ESCRT machinery via conserved motifs termed late domains. The mechanism by which some viruses, such as HCV, bud intracellularly is, however, poorly characterized. Moreover, whether envelopment of HCV and other viruses lacking defined late domains is ESCRT mediated and, if so, what the entry points into the ESCRT pathway are remain unknown. Here, we report the interaction network of HCV with the ESCRT machinery and a critical role for HRS, an ESCRT-0 complex component, in HCV envelopment. Viral protein ubiquitination was discovered to be a signal for HRS binding and HCV assembly, thereby functionally compensating for the absence of late domains. These findings characterize how a virus lacking defined late domains co-opts ESCRT to bud intracellularly. Since the ESCRT machinery is essential for the life cycle of multiple viruses, better understanding of this virus-host interplay may yield targets for broad-spectrum antiviral therapies.
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Affiliation(s)
- Rina Barouch-Bentov
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Gregory Neveu
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Fei Xiao
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Melanie Beer
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Elena Bekerman
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Stanford Schor
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Joseph Campbell
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Jim Boonyaratanakornkit
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Brett Lindenbach
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, USA
| | - Albert Lu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - Yves Jacob
- Département de Virologie, Unité de Génétique Moléculaire des Virus ARN (GMVR), Institut Pasteur, Centre national de la recherche scientifique, and Université Paris Diderot, Paris, France
| | - Shirit Einav
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
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Vordenbäumen S, Lueking A, Budde P, Zucht HD, Goehler H, Brinks R, Fischer-Betz R, Richter J, Bleck E, Detert J, Langer HE, Sörgel A, Burmester GR, Schulz-Knappe P, Schneider M. Sequential high-content profiling of the IgG-autoantibody repertoire reveals novel antigens in rheumatoid arthritis. Arthritis Res Ther 2016; 18:235. [PMID: 27729089 PMCID: PMC5059912 DOI: 10.1186/s13075-016-1135-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 09/20/2016] [Indexed: 12/29/2022] Open
Abstract
Background The aim was to identify novel diagnostic autoantibody candidates for rheumatoid arthritis (RA) by comprehensive screening for autoreactivity. Method We incubated 5892 recombinant proteins coupled to fluorescent beads, with patients’ sera for the detection of IgG-autoantibodies in three independent patient cohorts: A (n = 72 patients with established RA); B/B- (n = 116 patients with early RA (B) and n = 51 CCP-negative patients with early RA from B (B-)); and C (n = 184 patients with early seronegative RA), in comparison to matched healthy controls. Intersects of significantly increased autoantibodies as determined by the Mann-Whitney test were sought. Result Screening of 5892 antigens in RA cohorts A and B, or the seronegative cohorts B- and C revealed intersects of 23 and 13 significantly increased autoantibodies, respectively. Reactivity to three antigens was increased in all cohorts tested: N-acetylglucosamine-1-phosphate transferase, gamma subunit (GNPTG), heterogeneous nuclear ribonucleoprotein A1-like 2 (HNRNPA1), and insulin-like growth factor binding protein 2 (IGFBP2). Conclusions Comprehensive sequential screening for autoantibodies reveals novel candidates for diagnostic markers in both seropositive and seronegative RA and suggests new fields of research into the pathogenesis of RA.
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Affiliation(s)
- Stefan Vordenbäumen
- Department Rheumatology & Hiller Research Unit Rheumatology, Heinrich-Heine-University, Moorenstr. 5, Düsseldorf, 40225, Germany.
| | | | | | | | | | - Ralph Brinks
- Department Rheumatology & Hiller Research Unit Rheumatology, Heinrich-Heine-University, Moorenstr. 5, Düsseldorf, 40225, Germany.,German Diabetes Center, Institute for Biometry and Epidemiology, Düsseldorf, Germany
| | - Rebecca Fischer-Betz
- Department Rheumatology & Hiller Research Unit Rheumatology, Heinrich-Heine-University, Moorenstr. 5, Düsseldorf, 40225, Germany
| | - Jutta Richter
- Department Rheumatology & Hiller Research Unit Rheumatology, Heinrich-Heine-University, Moorenstr. 5, Düsseldorf, 40225, Germany
| | - Ellen Bleck
- Department Rheumatology & Hiller Research Unit Rheumatology, Heinrich-Heine-University, Moorenstr. 5, Düsseldorf, 40225, Germany
| | - Jacqueline Detert
- Department Rheumatology and Clinical Immunology, Charité - University Medicine Berlin, Berlin, Germany
| | - Hans-Eckhard Langer
- Rheumatology, Clinical Immunology and Osteololgy at Evangelisches Krankenhaus, Düsseldorf, Germany
| | - Anne Sörgel
- Department Rheumatology & Hiller Research Unit Rheumatology, Heinrich-Heine-University, Moorenstr. 5, Düsseldorf, 40225, Germany
| | - Gerd-Rüdiger Burmester
- Department Rheumatology and Clinical Immunology, Charité - University Medicine Berlin, Berlin, Germany
| | | | - Matthias Schneider
- Department Rheumatology & Hiller Research Unit Rheumatology, Heinrich-Heine-University, Moorenstr. 5, Düsseldorf, 40225, Germany
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49
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Sullivan AE, Peet DJ, Whitelaw ML. MAGED1 is a novel regulator of a select subset of bHLH PAS transcription factors. FEBS J 2016; 283:3488-502. [PMID: 27472814 DOI: 10.1111/febs.13824] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 07/19/2016] [Accepted: 07/27/2016] [Indexed: 01/04/2023]
Abstract
Transcription factors of the basic helix-loop-helix (bHLH) PER-ARNT-SIM (PAS) family generally have critical and nonredundant biological roles, but some bHLH PAS proteins compete for common cofactors or recognise similar DNA elements. Identifying factors that regulate function of bHLH PAS proteins, particularly in cells where multiple family members are coexpressed, is important for understanding bHLH PAS factor biology. This study identifies and characterises a novel interaction between melanoma-associated antigen D1 (MAGED1) and select members of the bHLH PAS transcription factor family. MAGED1 binds and positively regulates the transcriptional activity of family members SIM1, SIM2, NPAS4 and ARNT2, but does not interact with AhR, HIF1α and ARNT. This interaction is mediated by PAS repeat regions which also form the interface for bHLH PAS dimerisation, and accordingly MAGED1 is not found in complex with bHLH PAS dimers. We show that MAGED1 does not affect bHLH PAS protein levels and cannot be acting as a coactivator of transcriptionally active heterodimers, but rather appears to interact with nascent bHLH PAS proteins in the cytoplasm to enhance their function prior to nuclear import. As a selective regulator, MAGED1 may play an important role in the biology of these specific factors and in general bHLH PAS protein dynamics.
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Affiliation(s)
- Adrienne E Sullivan
- Department of Molecular and Cellular Biology, University of Adelaide, Australia.
| | - Daniel J Peet
- Department of Molecular and Cellular Biology, University of Adelaide, Australia
| | - Murray L Whitelaw
- Department of Molecular and Cellular Biology, University of Adelaide, Australia
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50
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Fowler DK, Stewart S, Seredick S, Eisen JS, Stankunas K, Washbourne P. A MultiSite Gateway Toolkit for Rapid Cloning of Vertebrate Expression Constructs with Diverse Research Applications. PLoS One 2016; 11:e0159277. [PMID: 27500400 PMCID: PMC4976983 DOI: 10.1371/journal.pone.0159277] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/29/2016] [Indexed: 11/19/2022] Open
Abstract
Recombination-based cloning is a quick and efficient way to generate expression vectors. Recent advancements have provided powerful recombinant DNA methods for molecular manipulations. Here, we describe a novel collection of three-fragment MultiSite Gateway cloning system-compatible vectors providing expanded molecular tools for vertebrate research. The components of this toolkit encompass a broad range of uses such as fluorescent imaging, dual gene expression, RNA interference, tandem affinity purification, chemically-inducible dimerization and lentiviral production. We demonstrate examples highlighting the utility of this toolkit for producing multi-component vertebrate expression vectors with diverse primary research applications. The vectors presented here are compatible with other Gateway toolkits and collections, facilitating the rapid generation of a broad range of innovative DNA constructs for biological research.
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Affiliation(s)
- Daniel K. Fowler
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Scott Stewart
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Steve Seredick
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Judith S. Eisen
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Kryn Stankunas
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Philip Washbourne
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, Oregon, United States of America
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