1
|
Genome-wide screens identify specific drivers of mutant hTERT promoters. Proc Natl Acad Sci U S A 2022; 119:2105171119. [PMID: 35027447 PMCID: PMC8784157 DOI: 10.1073/pnas.2105171119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 12/31/2022] Open
Abstract
Mutations in hTERT promoter are seen in over 19% of human cancers, irrespective of the cancer type. Understanding the molecular players that regulate Mut-hTERT promoters may help the design of effective targeting strategies to inhibit telomerase reactivation specifically in cancer cells. Our work uses genome-wide functional screens to identify 30 specific regulators of Mut-hTERT promoters. These candidates identified from the screening serve as an excellent resource to understand how telomerase is reactivated and as targets for making inhibitors to telomerase, a key driver of cancer. Cancer-specific hTERT promoter mutations reported in 19% of cancers result in enhanced telomerase activity. Understanding the distinctions between transcriptional regulation of wild-type (WT) and mutant (Mut) hTERT promoters may open up avenues for development of inhibitors which specially block hTERT expression in cancer cells. To comprehensively identify physiological regulators of WT- or Mut-hTERT promoters, we generated several isogenic reporter cells driven by endogenous hTERT loci. Genome-wide CRISPR-Cas9 and small interfering RNA screens using these isogenic reporter lines identified specific regulators of Mut-hTERT promoters. We validate and characterize one of these hits, namely, MED12, a kinase subunit of mediator complex. We demonstrate that MED12 specifically drives expression of hTERT from the Mut-hTERT promoter by mediating long-range chromatin interaction between the proximal Mut-hTERT promoter and T-INT1 distal regulatory region 260 kb upstream. Several hits identified in our screens could serve as potential therapeutic targets, inhibition of which may specifically block Mut-hTERT promoter driven telomerase reactivation in cancers.
Collapse
|
2
|
Haselimashhadi H, Mason JC, Mallon AM, Smedley D, Meehan TF, Parkinson H. OpenStats: A robust and scalable software package for reproducible analysis of high-throughput phenotypic data. PLoS One 2020; 15:e0242933. [PMID: 33378393 PMCID: PMC7773254 DOI: 10.1371/journal.pone.0242933] [Citation(s) in RCA: 4] [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: 05/30/2020] [Accepted: 11/12/2020] [Indexed: 11/19/2022] Open
Abstract
Reproducibility in the statistical analyses of data from high-throughput phenotyping screens requires a robust and reliable analysis foundation that allows modelling of different possible statistical scenarios. Regular challenges are scalability and extensibility of the analysis software. In this manuscript, we describe OpenStats, a freely available software package that addresses these challenges. We show the performance of the software in a high-throughput phenomic pipeline in the International Mouse Phenotyping Consortium (IMPC) and compare the agreement of the results with the most similar implementation in the literature. OpenStats has significant improvements in speed and scalability compared to existing software packages including a 13-fold improvement in computational time to the current production analysis pipeline in the IMPC. Reduced complexity also promotes FAIR data analysis by providing transparency and benefiting other groups in reproducing and re-usability of the statistical methods and results. OpenStats is freely available under a Creative Commons license at www.bioconductor.org/packages/OpenStats.
Collapse
Affiliation(s)
- Hamed Haselimashhadi
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jeremy C. Mason
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ann-Marie Mallon
- MRC Harwell Institute, Harwell Campus, Oxfordshire, United kingdom
| | | | - Terrence F. Meehan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Helen Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| |
Collapse
|
3
|
Zhang XD, Wang D, Sun S, Zhang H. Issues Of Z-factor and an approach to avoid them for quality control in high-throughput screening studies. Bioinformatics 2020; 36:5299-5303. [PMID: 33346821 DOI: 10.1093/bioinformatics/btaa1049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION High throughput screening (HTS) is a vital automation technology in biomedical research in both industry and academia. The well-known z-factor has been widely used as a gatekeeper to assure assay quality in an HTS study. However, many researchers and users may not have realized that z-factor has major issues. RESULTS In this article, the following four major issues are explored and demonstrated so that researchers may use the z-factor appropriately. First, the z-factor violates the Pythagorean Theorem of Statistics. Second, there is no adjustment of sampling error in the application of the z-factor for quality control (QC) in HTS studies. Third, the expectation of the sample-based z-factor does not exist. Fourth, the thresholds in the z-factor based criterion lack a theoretical basis. Here, an approach to avoid these issues was proposed and new QC criteria under homoscedasticity were constructed so that researchers can choose a statistically grounded criterion for QC in the HTS studies. We implemented this approach in an R package and demonstrated its utility in multiple CRISPR/CAS9 or siRNA HTS studies. AVAILABILITY The R package qcSSMDhomo is freely available from GitHub: https://github.com/Karena6688/qcSSMDhomo. The file qcSSMDhomo_1.0.0.tar.gz (for Windows) containing qcSSMDhomo is also available at Bioinformatics online. qcSSMDhomo is distributed under the GNU General Public License. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
| | - Dandan Wang
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Shixue Sun
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau
| | - Heping Zhang
- Department of Biostatistics, Yale University, New Haven, CT06511, USA
| |
Collapse
|
4
|
Yang P, Mathieu C, Kolaitis RM, Zhang P, Messing J, Yurtsever U, Yang Z, Wu J, Li Y, Pan Q, Yu J, Martin EW, Mittag T, Kim HJ, Taylor JP. G3BP1 Is a Tunable Switch that Triggers Phase Separation to Assemble Stress Granules. Cell 2020; 181:325-345.e28. [PMID: 32302571 DOI: 10.1016/j.cell.2020.03.046] [Citation(s) in RCA: 623] [Impact Index Per Article: 155.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 10/23/2019] [Accepted: 03/20/2020] [Indexed: 12/18/2022]
Abstract
The mechanisms underlying ribonucleoprotein (RNP) granule assembly, including the basis for establishing and maintaining RNP granules with distinct composition, are unknown. One prominent type of RNP granule is the stress granule (SG), a dynamic and reversible cytoplasmic assembly formed in eukaryotic cells in response to stress. Here, we show that SGs assemble through liquid-liquid phase separation (LLPS) arising from interactions distributed unevenly across a core protein-RNA interaction network. The central node of this network is G3BP1, which functions as a molecular switch that triggers RNA-dependent LLPS in response to a rise in intracellular free RNA concentrations. Moreover, we show that interplay between three distinct intrinsically disordered regions (IDRs) in G3BP1 regulates its intrinsic propensity for LLPS, and this is fine-tuned by phosphorylation within the IDRs. Further regulation of SG assembly arises through positive or negative cooperativity by extrinsic G3BP1-binding factors that strengthen or weaken, respectively, the core SG network.
Collapse
Affiliation(s)
- Peiguo Yang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cécile Mathieu
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Regina-Maria Kolaitis
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peipei Zhang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - James Messing
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Ugur Yurtsever
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Graduate School of Structure and Dynamics of Living Systems, Université Paris-Saclay, Gif-sur-Yvette, 91190, France
| | - Zemin Yang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jinjun Wu
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yuxin Li
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Qingfei Pan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jiyang Yu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Erik W Martin
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hong Joo Kim
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - J Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| |
Collapse
|
5
|
Raphemot R, Toro-Moreno M, Lu KY, Posfai D, Derbyshire ER. Discovery of Druggable Host Factors Critical to Plasmodium Liver-Stage Infection. Cell Chem Biol 2019; 26:1253-1262.e5. [PMID: 31257182 DOI: 10.1016/j.chembiol.2019.05.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 04/06/2019] [Accepted: 05/22/2019] [Indexed: 11/26/2022]
Abstract
Plasmodium parasites undergo an obligatory and asymptomatic developmental stage within the liver before infecting red blood cells to cause malaria. The hijacked host pathways critical to parasite infection during this hepatic phase remain poorly understood. Here, we implemented a forward genetic screen to identify over 100 host factors within the human druggable genome that are critical to P. berghei infection in hepatoma cells. Notably, we found knockdown of genes involved in protein trafficking pathways to be detrimental to parasite infection. The disruption of protein trafficking modulators, including COPB2 and GGA1, decreases P. berghei parasite size, and an immunofluorescence study suggests that these proteins are recruited to the Plasmodium parasitophorous vacuole in infected hepatocytes. These findings reveal that various host intracellular protein trafficking pathways are subverted by Plasmodium parasites during the liver stage and provide new insights into their manipulation for growth and development.
Collapse
Affiliation(s)
- Rene Raphemot
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Maria Toro-Moreno
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Kuan-Yi Lu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA
| | - Dora Posfai
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA
| | - Emily Rose Derbyshire
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA; Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, NC 27710, USA.
| |
Collapse
|
6
|
Rioualen C, Da Costa Q, Chetrit B, Charafe-Jauffret E, Ginestier C, Bidaut G. HTS-Net: An integrated regulome-interactome approach for establishing network regulation models in high-throughput screenings. PLoS One 2017; 12:e0185400. [PMID: 28949986 PMCID: PMC5614607 DOI: 10.1371/journal.pone.0185400] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/12/2017] [Indexed: 12/28/2022] Open
Abstract
High-throughput RNAi screenings (HTS) allow quantifying the impact of the deletion of each gene in any particular function, from virus-host interactions to cell differentiation. However, there has been less development for functional analysis tools dedicated to RNAi analyses. HTS-Net, a network-based analysis program, was developed to identify gene regulatory modules impacted in high-throughput screenings, by integrating transcription factors-target genes interaction data (regulome) and protein-protein interaction networks (interactome) on top of screening z-scores. HTS-Net produces exhaustive HTML reports for results navigation and exploration. HTS-Net is a new pipeline for RNA interference screening analyses that proves better performance than simple gene rankings by z-scores, by re-prioritizing genes and replacing them in their biological context, as shown by the three studies that we reanalyzed. Formatted input data for the three studied datasets, source code and web site for testing the system are available from the companion web site at http://htsnet.marseille.inserm.fr/. We also compared our program with existing algorithms (CARD and hotnet2).
Collapse
Affiliation(s)
- Claire Rioualen
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Quentin Da Costa
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Bernard Chetrit
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Emmanuelle Charafe-Jauffret
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Christophe Ginestier
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
| | - Ghislain Bidaut
- Aix-Marseille Univ, Marseille, France
- Inserm, U1068, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- Institut Paoli-Calmettes, Marseille, France
- CNRS, UMR7258, Centre de Recherche en Cancérologie de Marseille, Marseille, France
- * E-mail:
| |
Collapse
|
7
|
Bakke J, Wright WC, Zamora AE, Ong SS, Wang YM, Hoyer JD, Brewer CT, Thomas PG, Chen T. Transcription factor ZNF148 is a negative regulator of human muscle differentiation. Sci Rep 2017; 7:8138. [PMID: 28811660 PMCID: PMC5557752 DOI: 10.1038/s41598-017-08267-5] [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: 03/02/2017] [Accepted: 07/06/2017] [Indexed: 01/17/2023] Open
Abstract
Muscle differentiation is a complex process in which muscle progenitor cells undergo determination and eventually cellular fusion. This process is heavily regulated by such master transcription factors as MYOD and members of the MEF2 family. Here, we show that the transcription factor ZNF148 plays a direct role in human muscle cell differentiation. Downregulation of ZNF148 drives the formation of a muscle phenotype with rapid expression of myosin heavy chain, even in proliferative conditions. This phenotype was most likely mediated by the robust and swift upregulation of MYOD and MEF2C.
Collapse
Affiliation(s)
- Jesse Bakke
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - William C Wright
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Anthony E Zamora
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Su Sien Ong
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Yue-Ming Wang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jessica D Hoyer
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Christopher T Brewer
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee, USA. .,Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, Tennessee, USA.
| |
Collapse
|
8
|
Azorsa DO, Turnidge MA, Arora S. Data Analysis for High-Throughput RNAi Screening. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2016; 1470:247-60. [PMID: 27581298 DOI: 10.1007/978-1-4939-6337-9_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
High-throughput RNA interference (HT-RNAi) screening is an effective technology to help identify important genes and pathways involved in a biological process. Analysis of high-throughput RNAi screening data is a critical part of this technology, and many analysis methods have been described. Here, we summarize the workflow and types of analyses commonly used in high-throughput RNAi screening.
Collapse
Affiliation(s)
- David O Azorsa
- Institute of Molecular Medicine, Phoenix Children's Hospital, Phoenix, AZ, USA. .,Department of Child Health, University of Arizona College of Medicine - Phoenix, Phoenix, AZ, USA.
| | - Megan A Turnidge
- Department of Child Health, University of Arizona College of Medicine - Phoenix, Phoenix, AZ, USA.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Shilpi Arora
- Constellation Pharmaceuticals, Cambridge, MA, USA
| |
Collapse
|
9
|
Choma MK, Lumb J, Kozik P, Robinson MS. A Genome-Wide Screen for Machinery Involved in Downregulation of MHC Class I by HIV-1 Nef. PLoS One 2015; 10:e0140404. [PMID: 26466362 PMCID: PMC4605695 DOI: 10.1371/journal.pone.0140404] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/24/2015] [Indexed: 12/02/2022] Open
Abstract
The HIV-1-encoded protein, Nef, plays a key role in the development of AIDS. One of Nef’s functions is to keep MHC class I off the surface of infected cells, a process that requires the host proteins clathrin and AP-1. To identify other proteins involved in this pathway, we carried out a genome-wide siRNA library screen on HeLa cells co-expressing HLA-A2 and an inducible form of Nef. Out of 21,121 siRNA pools, 100 were selected for further analysis, based on their ability to either inhibit or enhance downregulation of MHC-I by Nef. When cells were treated with the same siRNA pools as those used in the screen, 79% produced a similar phenotype. However, when the cells were treated with different siRNA reagents targeting the same genes, only 16% produced a similar phenotype. This indicates that most of the hits found in the original screen are likely to have been off-target, an important concern that is often not taken into account in siRNA screening studies. Nevertheless, we identified novel host factors involved in Nef-induced downregulation of MHC-I, including four genes, MIIP, CAMSAP3, SLC6A3, and KCTD19, where multiple reagents produced a strong inhibitory effect on Nef activity. Other hits slightly below our very high stringency cutoff point may also deserve further study. Thus, our dataset is a valuable resource for scientists investigating the pathogenesis of HIV.
Collapse
Affiliation(s)
- Maja K. Choma
- University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, United Kingdom
| | - Jennifer Lumb
- University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, United Kingdom
| | - Patrycja Kozik
- University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, United Kingdom
| | - Margaret S. Robinson
- University of Cambridge, Cambridge Institute for Medical Research, Cambridge, CB2 0XY, United Kingdom
- * E-mail:
| |
Collapse
|
10
|
Lupberger J, Casanova C, Fischer B, Weiss A, Fofana I, Fontaine N, Fujiwara T, Renaud M, Kopp A, Schuster C, Brino L, Baumert TF, Thoma C. PI4K-beta and MKNK1 are regulators of hepatitis C virus IRES-dependent translation. Sci Rep 2015; 5:13344. [PMID: 26323588 PMCID: PMC4555030 DOI: 10.1038/srep13344] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/22/2015] [Indexed: 12/12/2022] Open
Abstract
Cellular translation is down-regulated by host antiviral responses. Picornaviridae and Flaviviridae including hepatitis C virus (HCV) evade this process using internal ribosomal entry sequences (IRESs). Although HCV IRES translation is a prerequisite for HCV replication, only few host factors critical for IRES activity are known and the global regulator network remains largely unknown. Since signal transduction is an import regulator of viral infections and the host antiviral response we combined a functional RNAi screen targeting the human signaling network with a HCV IRES-specific reporter mRNA assay. We demonstrate that the HCV host cell cofactors PI4K and MKNK1 are positive regulators of HCV IRES translation representing a novel pathway with a functional relevance for the HCV life cycle and IRES-mediated translation of viral RNA.
Collapse
Affiliation(s)
- Joachim Lupberger
- Inserm U1110, Institut de Recherche sur les Maladies Virales et Hépatiques Strasbourg, France.,Université de Strasbourg, France
| | - Claudia Casanova
- Department of Medicine II, University of Freiburg, Freiburg, Germany
| | - Benoit Fischer
- High Throughput Screening platform, IGBMC, UMR7104 CNRS UdS, Inserm, U964, Illkirch, France
| | - Amelie Weiss
- High Throughput Screening platform, IGBMC, UMR7104 CNRS UdS, Inserm, U964, Illkirch, France
| | - Isabel Fofana
- Inserm U1110, Institut de Recherche sur les Maladies Virales et Hépatiques Strasbourg, France.,Université de Strasbourg, France
| | - Nelly Fontaine
- Inserm U1110, Institut de Recherche sur les Maladies Virales et Hépatiques Strasbourg, France.,Université de Strasbourg, France
| | - Toshinobu Fujiwara
- Laboratory of Hygienic Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Mickael Renaud
- High Throughput Screening platform, IGBMC, UMR7104 CNRS UdS, Inserm, U964, Illkirch, France
| | - Arnaud Kopp
- High Throughput Screening platform, IGBMC, UMR7104 CNRS UdS, Inserm, U964, Illkirch, France
| | - Catherine Schuster
- Inserm U1110, Institut de Recherche sur les Maladies Virales et Hépatiques Strasbourg, France.,Université de Strasbourg, France
| | - Laurent Brino
- High Throughput Screening platform, IGBMC, UMR7104 CNRS UdS, Inserm, U964, Illkirch, France
| | - Thomas F Baumert
- Inserm U1110, Institut de Recherche sur les Maladies Virales et Hépatiques Strasbourg, France.,Université de Strasbourg, France.,Institut Hospitalo-Universitaire, Pôle Hépato-digestif, Nouvel Hôpital Civil, Strasbourg, France
| | - Christian Thoma
- Department of Medicine II, University of Freiburg, Freiburg, Germany
| |
Collapse
|
11
|
Rinaldi G, Loukas A, Brindley PJ, Irelan JT, Smout MJ. Viability of developmental stages of Schistosoma mansoni quantified with xCELLigence worm real-time motility assay (xWORM). INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2015; 5:141-8. [PMID: 26288742 PMCID: PMC4534758 DOI: 10.1016/j.ijpddr.2015.07.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/09/2015] [Accepted: 07/13/2015] [Indexed: 12/15/2022]
Abstract
Infection with helminth parasites causes morbidity and mortality in billions of people and livestock worldwide. Where anthelmintic drugs are available, drug resistance is a major problem in livestock parasites, and a looming threat to public health. Monitoring the efficacy of these medicines and screening for new drugs has been hindered by the lack of objective, high-throughput approaches. Several cell monitoring technologies have been adapted for parasitic worms, including video-, fluorescence-, metabolism enzyme- and impedance-based tools that minimize the screening bottleneck. Using the xCELLigence impedance-based system we previously developed a motility-viability assay that is applicable for a range of helminth parasites. Here we have improved substantially the assay by using diverse frequency settings, and have named it the xCELLigence worm real-time motility assay (xWORM). By utilizing strictly standardized mean difference analysis we compared the xWORM output measured with 10, 25 and 50 kHz frequencies to quantify the motility of schistosome adults (human blood flukes) and hatching of schistosome eggs. Furthermore, we have described a novel application of xWORM to monitor movement of schistosome cercariae, the developmental stage that is infectious to humans. For all three stages, 25 kHz was either optimal or near-optimal for monitoring and quantifying schistosome motility. These improvements in methodology sensitivity should enhance the capacity to screen small compound libraries for new drugs both for schistosomes and other helminth pathogens at large. 25 kHz on the xCELLigence system dramatically improves the schistosome xWORM assay. xWORM assay can efficiently determine viability of Schistome adults or eggs. First time cercariae have been incorporated into an automated viability assay. Other helminth monitoring may benefit from alternate xCELLigence frequency options.
Collapse
Affiliation(s)
- Gabriel Rinaldi
- Department of Microbiology, Immunology & Tropical Medicine, and Research Center for the Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, D.C. 20037, USA
| | - Alex Loukas
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, McGregor Rd, Smithfield, Cairns, Queensland 4878, Australia
| | - Paul J. Brindley
- Department of Microbiology, Immunology & Tropical Medicine, and Research Center for the Neglected Diseases of Poverty, School of Medicine and Health Sciences, George Washington University, Washington, D.C. 20037, USA
| | | | - Michael J. Smout
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, McGregor Rd, Smithfield, Cairns, Queensland 4878, Australia
- Corresponding author. James Cook University, Cairns, Queensland 4878, Australia.
| |
Collapse
|
12
|
Ortiz D, Guiguemde WA, Johnson A, Elya C, Anderson J, Clark J, Connelly M, Yang L, Min J, Sato Y, Guy RK, Landfear SM. Identification of Selective Inhibitors of the Plasmodium falciparum Hexose Transporter PfHT by Screening Focused Libraries of Anti-Malarial Compounds. PLoS One 2015; 10:e0123598. [PMID: 25894322 PMCID: PMC4404333 DOI: 10.1371/journal.pone.0123598] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/20/2015] [Indexed: 12/04/2022] Open
Abstract
Development of resistance against current antimalarial drugs necessitates the search for novel drugs that interact with different targets and have distinct mechanisms of action. Malaria parasites depend upon high levels of glucose uptake followed by inefficient metabolic utilization via the glycolytic pathway, and the Plasmodium falciparum hexose transporter PfHT, which mediates uptake of glucose, has thus been recognized as a promising drug target. This transporter is highly divergent from mammalian hexose transporters, and it appears to be a permease that is essential for parasite viability in intra-erythrocytic, mosquito, and liver stages of the parasite life cycle. An assay was developed that is appropriate for high throughput screening against PfHT based upon heterologous expression of PfHT in Leishmania mexicana parasites that are null mutants for their endogenous hexose transporters. Screening of two focused libraries of antimalarial compounds identified two such compounds that are high potency selective inhibitors of PfHT compared to human GLUT1. Additionally, 7 other compounds were identified that are lower potency and lower specificity PfHT inhibitors but might nonetheless serve as starting points for identification of analogs with more selective properties. These results further support the potential of PfHT as a novel drug target.
Collapse
Affiliation(s)
- Diana Ortiz
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, United States of America
| | - W. Armand Guiguemde
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Alex Johnson
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, United States of America
| | - Carolyn Elya
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, United States of America
| | - Johanna Anderson
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, United States of America
| | - Julie Clark
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Michele Connelly
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Lei Yang
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Jaeki Min
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Yuko Sato
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, United States of America
| | - R. Kiplin Guy
- Department of Chemical Biology & Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - Scott M. Landfear
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, OR, United States of America
- * E-mail:
| |
Collapse
|
13
|
Zirin J, Nieuwenhuis J, Samsonova A, Tao R, Perrimon N. Regulators of autophagosome formation in Drosophila muscles. PLoS Genet 2015; 11:e1005006. [PMID: 25692684 PMCID: PMC4334200 DOI: 10.1371/journal.pgen.1005006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 01/15/2015] [Indexed: 01/08/2023] Open
Abstract
Given the diversity of autophagy targets and regulation, it is important to characterize autophagy in various cell types and conditions. We used a primary myocyte cell culture system to assay the role of putative autophagy regulators in the specific context of skeletal muscle. By treating the cultures with rapamycin (Rap) and chloroquine (CQ) we induced an autophagic response, fully suppressible by knockdown of core ATG genes. We screened D. melanogaster orthologs of a previously reported mammalian autophagy protein-protein interaction network, identifying several proteins required for autophagosome formation in muscle cells, including orthologs of the Rab regulators RabGap1 and Rab3Gap1. The screen also highlighted the critical roles of the proteasome and glycogen metabolism in regulating autophagy. Specifically, sustained proteasome inhibition inhibited autophagosome formation both in primary culture and larval skeletal muscle, even though autophagy normally acts to suppress ubiquitin aggregate formation in these tissues. In addition, analyses of glycogen metabolic genes in both primary cultured and larval muscles indicated that glycogen storage enhances the autophagic response to starvation, an important insight given the link between glycogen storage disorders, autophagy, and muscle function. Since the identification of the core autophagy genes in yeast, tissue culture cell lines have been the primary tool to evaluate the role and regulation of autophagy in higher organisms. However, since autophagy is a tissue-specific, context dependent process, stable cell lines can only give a limited view of the autophagic process. Here, we focus on the role of putative autophagy regulators in the specific context of the skeletal muscle, which has one of the most robust autophagy responses in mammals. We describe a fruitfly model of autophagy for skeletal muscles that integrates rapid genetic screening in primary cultured cells with robust in vivo validation in the larval muscle. We screened a set of genes previously linked to the autophagy pathway in humans, and identified both positive and negative regulators of autophagy. Our observation that genes involved in sugar metabolism impact muscle autophagy has important implications for both skeletal and cardiac myopathies associated with aberrant sugar storage. Surprisingly, we found that the proteasome is required to maintain autophagy in the muscle, suggesting that therapeutic treatments aiming to induce autophagy by proteasome inhibition must be carefully calibrated to ensure that the opposite phenotype does not occur.
Collapse
Affiliation(s)
- Jonathan Zirin
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (JZ); (NP)
| | - Joppe Nieuwenhuis
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Anastasia Samsonova
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rong Tao
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (JZ); (NP)
| |
Collapse
|
14
|
Ong SS, Goktug AN, Elias A, Wu J, Saunders D, Chen T. Stability of the human pregnane X receptor is regulated by E3 ligase UBR5 and serine/threonine kinase DYRK2. Biochem J 2014; 459:193-203. [PMID: 24438055 PMCID: PMC3959618 DOI: 10.1042/bj20130558] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The hPXR (human pregnane X receptor), a major chemical toxin sensor, is a ligand-induced transcription factor activated by various xenobiotics and toxins, resulting in the transcriptional up-regulation of detoxifying enzymes. To date, little is known about the upstream regulation of hPXR. Using MS analysis and a kinome-wide siRNA screen, we report that the E3 ligase UBR5 (ubiquitin protein ligase E3 component n-recognin 5) and DYRK2 (dual-specificity tyrosine-phosphorylation-regulated kinase 2) regulate hPXR stability. UBR5 knockdown resulted in accumulation of cellular hPXR and a concomitant increase in hPXR activity, whereas the rescue of UBR5 knockdown decreased the cellular hPXR level and activity. Importantly, UBR5 exerted its effect in concert with the serine/threonine kinase DYRK2, as the knockdown of DYRK2 phenocopied UBR5 knockdown. hPXR was shown to be a substrate for DYRK2, and DYRK2-dependent phosphorylation of hPXR facilitated its subsequent ubiquitination by UBR5. This is the first report of the post-translational regulation of hPXR via phosphorylation-facilitated ubiquitination by DYRK2 and UBR5. The results of the present study reveal the role of the ubiquitin-proteasomal pathway in modulating hPXR activity and indicate that pharmacological inhibitors of the ubiquitin-proteasomal pathway that regulate hPXR stability may negatively affect treatment outcome from unintended hPXR-mediated drug-drug interactions.
Collapse
Affiliation(s)
- Su Sien Ong
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Asli N. Goktug
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Ayesha Elias
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Darren Saunders
- Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst NSW 2010, Australia
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| |
Collapse
|