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Lu X, Zhan T, Zhou Q, Yang W, Liu K, Chen Y, Gao R, Hu J, Gu M, Hu S, Jiao XA, Wang X, Liu X, Liu X. The haemagglutinin-neuraminidase protein of velogenic Newcastle disease virus enhances viral infection through NF-κB-mediated programmed cell death. Vet Res 2024; 55:58. [PMID: 38715081 PMCID: PMC11077864 DOI: 10.1186/s13567-024-01312-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/18/2024] [Indexed: 05/12/2024] Open
Abstract
The haemagglutinin-neuraminidase (HN) protein, a vital membrane glycoprotein, plays a pivotal role in the pathogenesis of Newcastle disease virus (NDV). Previously, we demonstrated that a mutation in the HN protein is essential for the enhanced virulence of JS/7/05/Ch, a velogenic variant NDV strain originating from the mesogenic vaccine strain Mukteswar. Here, we explored the effects of the HN protein during viral infection in vitro using three viruses: JS/7/05/Ch, Mukteswar, and an HN-replacement chimeric NDV, JS/MukHN. Through microscopic observation, CCK-8, and LDH release assays, we demonstrated that compared with Mukteswar and JS/MukHN, JS/7/05/Ch intensified the cellular damage and mortality attributed to the mutant HN protein. Furthermore, JS/7/05/Ch induced greater levels of apoptosis, as evidenced by the activation of caspase-3/8/9. Moreover, JS/7/05/Ch promoted autophagy, leading to increased autophagosome formation and autophagic flux. Subsequent pharmacological experiments revealed that inhibition of apoptosis and autophagy significantly impacted virus replication and cell viability in the JS/7/05/Ch-infected group, whereas less significant effects were observed in the other two infected groups. Notably, the mutant HN protein enhanced JS/7/05/Ch-induced apoptosis and autophagy by suppressing NF-κB activation, while it mitigated the effects of NF-κB on NDV infection. Overall, our study offers novel insights into the mechanisms underlying the increased virulence of NDV and serves as a reference for the development of vaccines.
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Affiliation(s)
- Xiaolong Lu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225000, China
| | - Tiansong Zhan
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225000, China
| | - Qiwen Zhou
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225000, China
| | - Wenhao Yang
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225000, China
| | - Kaituo Liu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225000, China
| | - Yu Chen
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225000, China
| | - Ruyi Gao
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225000, China
| | - Jiao Hu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225000, China
- Jiangsu Coinnovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225000, China
| | - Min Gu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225000, China
- Jiangsu Coinnovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225000, China
| | - Shunlin Hu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225000, China
- Jiangsu Coinnovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225000, China
| | - Xin-An Jiao
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225000, China
- Jiangsu Coinnovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225000, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225000, China
| | - Xiaoquan Wang
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225000, China
- Jiangsu Coinnovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225000, China
| | - Xiufan Liu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225000, China.
- Jiangsu Coinnovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225000, China.
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225000, China.
| | - Xiaowen Liu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou, 225000, China.
- Jiangsu Coinnovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, 225000, China.
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Repurposing of a human antibody-based microarray to explore conserved components of the signalome of the parasitic nematode Haemonchus contortus. Parasit Vectors 2022; 15:273. [PMID: 35907892 PMCID: PMC9338626 DOI: 10.1186/s13071-022-05400-w] [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: 05/17/2022] [Accepted: 07/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gaining insight into molecular signalling pathways of socioeconomically important parasitic nematodes has implications for understanding their molecular biology and for developing novel anthelmintic interventions. METHODS Here, we evaluated the use of a human antibody-based microarray to explore conserved elements of the signalome in the barber's pole worm Haemonchus contortus. To do this, we prepared extracts from mixed-sex (female and male) adult worms and third-stage larvae (L3s), incubated these extracts on the antibody microarray and then measured the amounts of antibody-bound proteins ('signal intensity'). RESULTS In total, 878 signals were classified into two distinct categories: signals that were higher for adults than for larvae of H. contortus (n = 376), and signals that were higher for larvae than for adults of this species (n = 502). Following a data-filtering step, high confidence ('specific') signals were obtained for subsequent analyses. In total, 39 pan-specific signals (linked to antibodies that recognise target proteins irrespective of their phosphorylation status) and 65 phosphorylation-specific signals were higher in the adult stage, and 82 pan-specific signals and 183 phosphorylation-specific signals were higher in L3s. Thus, notably more signals were higher in L3s than in the adult worms. Using publicly available information, we then inferred H. contortus proteins that were detected (with high confidence) by specific antibodies directed against human homologues, and revealed relatively high structural conservation between the two species, with some variability for select proteins. We also in silico-matched 763 compound structures (listed in the DrugBank and Kinase SARfari public databases) to four H. contortus proteins (designated HCON_00005760, HCON_00079680, HCON_00013590 and HCON_00105100). CONCLUSIONS We conclude that the present antibody-based microarray provides a useful tool for comparative analyses of signalling pathways between/among developmental stages and/or species, as well as opportunities to explore nematocidal target candidates in H. contortus and related parasites.
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Adderley J, O'Donoghue F, Doerig C, Davis S. MAPPINGS, a tool for network analysis of large phospho-signalling datasets: application to host erythrocyte response to Plasmodium infection. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100149. [PMID: 35909628 PMCID: PMC9325900 DOI: 10.1016/j.crmicr.2022.100149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 05/12/2022] [Accepted: 06/20/2022] [Indexed: 11/17/2022] Open
Abstract
The complexity of signal transduction networks in eukaryotic cells, superimposed to very large datasets generated by “omics” approaches (notably phosphor-proteomics), calls for tools to identify pathways that are mobilised under specific conditions, including infection by intracellular pathogens. This has become a bottleneck in various biology fields, from cancer through developmental biology to infectious diseases. We developed MAPPINGS, a computational tool to extract meaning from large phosphosignalling datasets, and used it to analyse host erythrocyte response to infection with malaria parasites, leading to the identification of host cell pathways that are activated by Plasmodium. MAPPINGS uses random walks to identify chains of phosphorylation events occurring much more or much less frequently than expected, and highlights pathways of phosphorylation that work synergistically, providing a rapid interpretation of the most critical pathways in any phosphosiganlling dataset.
Large datasets of phosphorylation interactions are constantly being generated, but deciphering the complex network structure hidden in these datasets remains challenging. Many phosphorylation interactions occurring in human cells have been identified and constitute the basis for the known phosphorylation interaction network. We overlayed onto this network phosphorylation datasets obtained from an antibody microarray approach aimed at determining changes in phospho-signalling of host erythrocytes, during infection with the malaria parasite Plasmodium falciparum. We designed a pathway analysis tool denoted MAPPINGS that uses random walks to identify chains of phosphorylation events occurring much more or much less frequently than expected. MAPPINGS highlights pathways of phosphorylation that work synergistically, providing a rapid interpretation of the most critical pathways in each dataset. MAPPINGS confirmed several signalling interactions previously shown to be modulated by infection, and revealed additional interactions which could form the basis of numerous future studies. The MAPPINGS analysis strategy described here is widely applicable to comparative phosphorylation datasets in any context, such as response of cells to infection, treatment, or comparison between differentiation stages of any cellular population.
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Affiliation(s)
- Jack Adderley
- School of Health and Biomedical Sciences, RMIT University, Bundoora VIC 3083, Australia
- Corresponding authors.
| | - Finn O'Donoghue
- School of Science, RMIT University, Melbourne, VIC 3053, Australia
| | - Christian Doerig
- School of Health and Biomedical Sciences, RMIT University, Bundoora VIC 3083, Australia
- Corresponding authors.
| | - Stephen Davis
- School of Science, RMIT University, Melbourne, VIC 3053, Australia
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Lee S, Kim S, Koo DJ, Yu J, Cho H, Lee H, Song JM, Kim SY, Min DH, Jeon NL. 3D Microfluidic Platform and Tumor Vascular Mapping for Evaluating Anti-Angiogenic RNAi-Based Nanomedicine. ACS NANO 2021; 15:338-350. [PMID: 33231435 DOI: 10.1021/acsnano.0c05110] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Three-dimensional (3D) visualization of tumor vasculature is a key factor in accurate evaluation of RNA interference (RNAi)-based antiangiogenic nanomedicine, a promising approach for cancer therapeutics. However, this remains challenging because there is not a physiologically relevant in vitro model or precise analytic methodology. To address this limitation, a strategy based on 3D microfluidic angiogenesis-on-a-chip and 3D tumor vascular mapping was developed for evaluating RNAi-based antiangiogenic nanomedicine. We developed a microfluidic model to recapitulate functional 3D angiogenic sprouting when co-cultured with various cancer cell types. This model enabled efficient and rapid assessment of antiangiogenic nanomedicine in treatment of hyper-angiogenic cancer. In addition, tissue-clearing-based whole vascular mapping of tumor xenograft allowed extraction of complex 3D morphological information in diverse quantitative parameters. Using this 3D imaging-based analysis, we observed tumor sub-regional differences in the antiangiogenic effect. Our systematic strategy can help in narrowing down the promising targets of antiangiogenic nanomedicine and then enables deep analysis of complex morphological changes in tumor vasculature, providing a powerful platform for the development of safe and effective nanomedicine for cancer therapeutics.
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Affiliation(s)
- Somin Lee
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Seongchan Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong-Jun Koo
- Program in Neuroscience, Seoul National University, Seoul 08826, Republic of Korea
| | - James Yu
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyeongjun Cho
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyojin Lee
- Biomaterials Research Center, Biomedical Research Division, Korea Institute of Science and Technology, 5 Hwarangno 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Joon Myong Song
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung-Yon Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
- Program in Neuroscience, Seoul National University, Seoul 08826, Republic of Korea
| | - Dal-Hee Min
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Biotherapeutics Convergence Technology, Lemonex Inc., Seoul 08826, Republic of Korea
| | - Noo Li Jeon
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Republic of Korea
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5
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Adderley JD, John von Freyend S, Jackson SA, Bird MJ, Burns AL, Anar B, Metcalf T, Semblat JP, Billker O, Wilson DW, Doerig C. Analysis of erythrocyte signalling pathways during Plasmodium falciparum infection identifies targets for host-directed antimalarial intervention. Nat Commun 2020; 11:4015. [PMID: 32782246 PMCID: PMC7419518 DOI: 10.1038/s41467-020-17829-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/16/2020] [Indexed: 02/08/2023] Open
Abstract
Intracellular pathogens mobilize host signaling pathways of their host cell to promote their own survival. Evidence is emerging that signal transduction elements are activated in a-nucleated erythrocytes in response to infection with malaria parasites, but the extent of this phenomenon remains unknown. Here, we fill this knowledge gap through a comprehensive and dynamic assessment of host erythrocyte signaling during infection with Plasmodium falciparum. We used arrays of 878 antibodies directed against human signaling proteins to interrogate the activation status of host erythrocyte phospho-signaling pathways at three blood stages of parasite asexual development. This analysis reveals a dynamic modulation of many host signalling proteins across parasite development. Here we focus on the hepatocyte growth factor receptor (c-MET) and the MAP kinase pathway component B-Raf, providing a proof of concept that human signaling kinases identified as activated by malaria infection represent attractive targets for antimalarial intervention. Plasmodium infection activates signaling pathways in a-nucleated erythrocytes. Here, Adderley et al. use a comprehensive antibody microarray to show that infection extensively modulates host cell signalling and that the host receptor tyrosine kinase c-MET supports Plasmodium falciparum proliferation.
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Affiliation(s)
- Jack D Adderley
- Centre for Chronic Inflammatory and Infectious and Diseases, Biomedical Sciences Cluster, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, 3083, Australia
| | - Simona John von Freyend
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Sarah A Jackson
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Megan J Bird
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
| | - Amy L Burns
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Burcu Anar
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Tom Metcalf
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jean-Philippe Semblat
- Institut National de la Transfusion Sanguine, Inserm UMR S1134, 75015, Paris, France
| | - Oliver Billker
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK.,Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, SE-901 87, Sweden
| | - Danny W Wilson
- Research Centre for Infectious Diseases, School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia.,Burnet Institute, Melbourne, VIC, 3004, Australia
| | - Christian Doerig
- Centre for Chronic Inflammatory and Infectious and Diseases, Biomedical Sciences Cluster, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, 3083, Australia.
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6
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Haqshenas G, Terradas G, Paradkar PN, Duchemin JB, McGraw EA, Doerig C. A Role for the Insulin Receptor in the Suppression of Dengue Virus and Zika Virus in Wolbachia-Infected Mosquito Cells. Cell Rep 2020; 26:529-535.e3. [PMID: 30650347 DOI: 10.1016/j.celrep.2018.12.068] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 10/25/2018] [Accepted: 12/12/2018] [Indexed: 02/01/2023] Open
Abstract
Wolbachia-infected mosquitoes are refractory to super-infection with arthropod-borne pathogens, but the role of host cell signaling proteins in pathogen-blocking mechanisms remains to be elucidated. Here, we use an antibody microarray approach to provide a comprehensive picture of the signaling response of Aedes aegypti-derived cells to Wolbachia. This approach identifies the host cell insulin receptor as being downregulated by the bacterium. Furthermore, siRNA-mediated knockdown and treatment with a small-molecule inhibitor of the insulin receptor kinase concur to assign a crucial role for this enzyme in the replication of dengue and Zika viruses in cultured mosquito cells. Finally, we show that the production of Zika virus in Wolbachia-free live mosquitoes is impaired by treatment with the selective inhibitor mimicking Wolbachia infection. This study identifies Wolbachia-mediated downregulation of insulin receptor kinase activity as a mechanism contributing to the blocking of super-infection by arboviruses.
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Affiliation(s)
- Gholamreza Haqshenas
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia.
| | - Gerard Terradas
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Prasad N Paradkar
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, VIC, Australia
| | - Jean-Bernard Duchemin
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Geelong, VIC, Australia
| | - Elizabeth A McGraw
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia; Department of Entomology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA.
| | - Christian Doerig
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia.
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7
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Wang T, Ma G, Ang CS, Korhonen PK, Stroehlein AJ, Young ND, Hofmann A, Chang BCH, Williamson NA, Gasser RB. The developmental phosphoproteome of Haemonchus contortus. J Proteomics 2019; 213:103615. [PMID: 31846766 DOI: 10.1016/j.jprot.2019.103615] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/22/2019] [Accepted: 12/13/2019] [Indexed: 12/22/2022]
Abstract
Protein phosphorylation plays essential roles in many cellular processes. Despite recent progress in the genomics, transcriptomics and proteomics of socioeconomically important parasitic nematodes, there is scant phosphoproteomic data to underpin molecular biological discovery. Here, using the phosphopeptide enrichment-based LC-MS/MS and data-independent acquisition (DIA) quantitation, we characterised the first developmental phosphoproteome of the parasitic nematode Haemonchus contortus - one of the most pathogenic parasites of ruminant livestock. Totally, 1804 phosphorylated proteins with 4406 phosphorylation sites ('phosphosites') from different developmental stages/sexes were identified. Bioinformatic analyses of quantified 'phosphosites' exhibited distinctive stage- and sex-specific patterns during development, and identified a subset of phosphoproteins proposed to play crucial roles in processes such as spindle positioning, signal transduction and kinase activity. A sequence-based comparison of the phosphoproteome of H. contortus with those of two free-living nematode species (Caenorhabditis elegans and Pristionchus pacificus) suggested a limited number of common protein phosphorylation events among these species. Our findings infer active roles for protein phosphorylation in the adaptation of a parasitic nematode to a constantly changing external environment. The phosphoproteomic data set for H. contortus provides a basis to better understand phosphorylation and associated biological processes (e.g., regulation of signal transduction), and might enable the discovery of novel anthelmintic targets. SIGNIFICANCE: Here, we report the first phosphoproteome for a socioeconomically parasitic nematode (Haemonchus contortus). This phosphoproteome exhibits distinctive patterns during development, suggesting active roles of post-translational modification in the parasite's adaptation to changing environments within and outside of the host animal. This work sheds a light on the developmental phosphorylation in a parasitic nematode, and could enable the discovery of novel interventions against major pathogens.
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Affiliation(s)
- Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Guangxu Ma
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Andreas J Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Bill C H Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Nicholas A Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
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8
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Haqshenas G, Doerig C. Targeting of host cell receptor tyrosine kinases by intracellular pathogens. Sci Signal 2019; 12:12/599/eaau9894. [PMID: 31530732 DOI: 10.1126/scisignal.aau9894] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Intracellular pathogens use complex and tightly regulated processes to enter host cells. Upon initial interactions with signaling proteins at the surface of target cells, intracellular microbes activate and co-opt specific host signaling pathways that mediate cell surface-cytosol communications to facilitate pathogen internalization. Here, we discuss the roles of host receptor tyrosine kinases (RTKs) in the establishment of productive infections by major intracellular pathogens. We evaluate the gaps in the current understanding of this process and propose a comprehensive approach for assessing the role of host cell signaling in the biology of intracellular microorganisms and viruses. We also discuss RTK-targeting strategies for the treatment of various infections.
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Affiliation(s)
- Gholamreza Haqshenas
- Infection and Immunity, Monash Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia.
| | - Christian Doerig
- Infection and Immunity, Monash Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia. .,Centre for Chronic Infectious and Inflammatory Diseases, School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC 3083, Australia
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9
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Perez S, Kaspi A, Domovitz T, Davidovich A, Lavi-Itzkovitz A, Meirson T, Alison Holmes J, Dai CY, Huang CF, Chung RT, Nimer A, El-Osta A, Yaari G, Stemmer SM, Yu ML, Haviv I, Gal-Tanamy M. Hepatitis C virus leaves an epigenetic signature post cure of infection by direct-acting antivirals. PLoS Genet 2019; 15:e1008181. [PMID: 31216276 PMCID: PMC6602261 DOI: 10.1371/journal.pgen.1008181] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 07/01/2019] [Accepted: 05/08/2019] [Indexed: 02/06/2023] Open
Abstract
The increasing worldwide prevalence of Hepatocellular carcinoma (HCC), characterized by resistance to conventional chemotherapy, poor prognosis and eventually mortality, place it as a prime target for new modes of prevention and treatment. Hepatitis C Virus (HCV) is the predominant risk factor for HCC in the US and Europe. Multiple epidemiological studies showed that sustained virological responses (SVR) following treatment with the powerful direct acting antivirals (DAAs), which have replaced interferon-based regimes, do not eliminate tumor development. We aimed to identify an HCV-specific pathogenic mechanism that persists post SVR following DAAs treatment. We demonstrate that HCV infection induces genome-wide epigenetic changes by performing chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) for histone post-translational modifications that are epigenetic markers for active and repressed chromatin. The changes in histone modifications correlate with reprogramed host gene expression and alter signaling pathways known to be associated with HCV life cycle and HCC. These epigenetic alterations require the presence of HCV RNA or/and expression of the viral proteins in the cells. Importantly, the epigenetic changes induced following infection persist as an "epigenetic signature" after virus eradication by DAAs treatment, as detected using in vitro HCV infection models. These observations led to the identification of an 8 gene signature that is associated with HCC development and demonstrate persistent epigenetic alterations in HCV infected and post SVR liver biopsy samples. The epigenetic signature was reverted in vitro by drugs that inhibit epigenetic modifying enzyme and by the EGFR inhibitor, Erlotinib. This epigenetic "scarring" of the genome, persisting following HCV eradication, suggest a novel mechanism for the persistent pathogenesis of HCV after its eradication by DAAs. Our study offers new avenues for prevention of the persistent oncogenic effects of chronic hepatitis infections using specific drugs to revert the epigenetic changes to the genome.
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Affiliation(s)
- Shira Perez
- Molecular Virology Lab, Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
- Cancer Personalized Medicine and Diagnostic Genomics Lab, Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Antony Kaspi
- Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia
| | - Tom Domovitz
- Molecular Virology Lab, Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Ateret Davidovich
- Molecular Virology Lab, Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Anat Lavi-Itzkovitz
- Molecular Virology Lab, Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat-Gan, Israel
| | - Tomer Meirson
- Drug Discovery Laboratory, Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Jacinta Alison Holmes
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Chia-Yen Dai
- Hepatobiliary Division, Department of Internal Medicine and Hepatitis Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- School of Medicine and Hepatitis Research Center, College of Medicine, and Center for Cancer Research and Center for Liquid Biopsy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chung-Feng Huang
- Hepatobiliary Division, Department of Internal Medicine and Hepatitis Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- School of Medicine and Hepatitis Research Center, College of Medicine, and Center for Cancer Research and Center for Liquid Biopsy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Raymond T. Chung
- Liver Center, Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Assy Nimer
- Internal Medicine Department A, Western Galilee Medical Center, Naharyia, and Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR
| | - Gur Yaari
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat-Gan, Israel
| | - Salomon M. Stemmer
- Davidoff Center, Rabin Medical Center, Beilinson Campus, Petach Tikva, and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ming-Lung Yu
- Hepatobiliary Division, Department of Internal Medicine and Hepatitis Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- School of Medicine and Hepatitis Research Center, College of Medicine, and Center for Cancer Research and Center for Liquid Biopsy, Kaohsiung Medical University, Kaohsiung, Taiwan
- College of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
- * E-mail: (MLY); (IH); (MGT)
| | - Izhak Haviv
- Cancer Personalized Medicine and Diagnostic Genomics Lab, Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
- * E-mail: (MLY); (IH); (MGT)
| | - Meital Gal-Tanamy
- Molecular Virology Lab, Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
- * E-mail: (MLY); (IH); (MGT)
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10
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Meksiriporn B, Ludwicki MB, Stephens EA, Jiang A, Lee HC, Waraho-Zhmayev D, Kummer L, Brandl F, Plückthun A, DeLisa MP. A survival selection strategy for engineering synthetic binding proteins that specifically recognize post-translationally phosphorylated proteins. Nat Commun 2019; 10:1830. [PMID: 31015433 PMCID: PMC6478843 DOI: 10.1038/s41467-019-09854-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 03/28/2019] [Indexed: 02/06/2023] Open
Abstract
There is an urgent need for affinity reagents that target phospho-modified sites on individual proteins; however, generating such reagents remains a significant challenge. Here, we describe a genetic selection strategy for routine laboratory isolation of phospho-specific designed ankyrin repeat proteins (DARPins) by linking in vivo affinity capture of a phosphorylated target protein with antibiotic resistance of Escherichia coli cells. The assay is validated using an existing panel of DARPins that selectively bind the nonphosphorylated (inactive) form of extracellular signal-regulated kinase 2 (ERK2) or its doubly phosphorylated (active) form (pERK2). We then use the selection to affinity-mature a phospho-specific DARPin without compromising its selectivity for pERK2 over ERK2 and to reprogram the substrate specificity of the same DARPin towards non-cognate ERK2. Collectively, these results establish our genetic selection as a useful and potentially generalizable protein engineering tool for studying phospho-specific binding proteins and customizing their affinity and selectivity. Protein phosphorylation helps to control many important cellular activities. Here the authors describe a genetic selection strategy to isolate designed ankyrin repeat proteins that bind specifically to phosphomodified targets.
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Affiliation(s)
- Bunyarit Meksiriporn
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Morgan B Ludwicki
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Erin A Stephens
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Allen Jiang
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Hyeon-Cheol Lee
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Dujduan Waraho-Zhmayev
- Biological Engineering Program, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - Lutz Kummer
- Department of Biochemistry, University of Zürich, 8057, Zürich, Switzerland
| | - Fabian Brandl
- Department of Biochemistry, University of Zürich, 8057, Zürich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, 8057, Zürich, Switzerland
| | - Matthew P DeLisa
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA. .,Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA. .,Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY, 14853, USA.
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11
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Perez S, Gevor M, Davidovich A, Kaspi A, Yamin K, Domovich T, Meirson T, Matityahu A, Brody Y, Stemmer SM, El-Osta A, Haviv I, Onn I, Gal-Tanamy M. Dysregulation of the cohesin subunit RAD21 by Hepatitis C virus mediates host-virus interactions. Nucleic Acids Res 2019; 47:2455-2471. [PMID: 30698808 PMCID: PMC6412124 DOI: 10.1093/nar/gkz052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 12/30/2018] [Accepted: 01/24/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus (HCV) infection is the leading cause of chronic hepatitis, which often results in liver fibrosis, cirrhosis and hepatocellular carcinoma (HCC). HCV possesses an RNA genome and its replication is confined to the cytoplasm. Yet, infection with HCV leads to global changes in gene expression, and chromosomal instability (CIN) in the host cell. The mechanisms by which the cytoplasmic virus affects these nuclear processes are elusive. Here, we show that HCV modulates the function of the Structural Maintenance of Chromosome (SMC) protein complex, cohesin, which tethers remote regions of chromatin. We demonstrate that infection of hepatoma cells with HCV leads to up regulation of the expression of the RAD21 cohesin subunit and changes cohesin residency on the chromatin. These changes regulate the expression of genes associated with virus-induced pathways. Furthermore, siRNA downregulation of viral-induced RAD21 reduces HCV infection. During mitosis, HCV infection induces hypercondensation of chromosomes and the appearance of multi-centrosomes. We provide evidence that the underlying mechanism involves the viral NS3/4 protease and the cohesin regulator, WAPL. Altogether, our results provide the first evidence that HCV induces changes in gene expression and chromosome structure of infected cells by modulating cohesin.
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Affiliation(s)
- Shira Perez
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Cancer Personalized Medicine and Diagnostic Genomics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Michael Gevor
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Ateret Davidovich
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Antony Kaspi
- Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia
| | - Katreena Yamin
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Tom Domovich
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Tomer Meirson
- Cell Migration and Invasion Laboratory, Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Avi Matityahu
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Yehuda Brody
- The Broad institute of Harvard and MIT, Cambridge, MA, USA
| | - Salomon M Stemmer
- Davidoff Center, Rabin Medical Center, Beilinson Campus, Petach Tikva, and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Assam El-Osta
- Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, Australia
- Hong Kong Institute of Diabetes and Obesity, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR
| | - Izhak Haviv
- Cancer Personalized Medicine and Diagnostic Genomics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Itay Onn
- Chromosome Instability and Dynamics Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Meital Gal-Tanamy
- Molecular Virology Lab, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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12
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Atzeni F, Talotta R, Nucera V, Marino F, Gerratana E, Sangari D, Masala IF, Sarzi-Puttini P. Adverse events, clinical considerations and management recommendations in rheumatoid arthritis patients treated with JAK inhibitors. Expert Rev Clin Immunol 2018; 14:945-956. [DOI: 10.1080/1744666x.2018.1504678] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Fabiola Atzeni
- Rheumatology Unit, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Rossella Talotta
- Department of Clinical Pharmacology and Toxicology, University of Milan, Laboratory of Genetics, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Valeria Nucera
- Rheumatology Unit, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Francesca Marino
- Rheumatology Unit, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Elisabetta Gerratana
- Rheumatology Unit, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Donatella Sangari
- Rheumatology Unit, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | | | - Piercarlo Sarzi-Puttini
- Rheumatology Unit, Department of Internal Medicine, ASST-Fatebenefratelli L. Sacco University Hospital, Milan, Italy
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