51
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Furlan V, Konc J, Bren U. Inverse Molecular Docking as a Novel Approach to Study Anticarcinogenic and Anti-Neuroinflammatory Effects of Curcumin. Molecules 2018; 23:E3351. [PMID: 30567342 PMCID: PMC6321024 DOI: 10.3390/molecules23123351] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/07/2018] [Accepted: 12/17/2018] [Indexed: 11/16/2022] Open
Abstract
Research efforts are placing an ever increasing emphasis on identifying signal transduction pathways related to the chemopreventive activity of curcumin. Its anticarcinogenic effects are presumably mediated by the regulation of signaling cascades, including nuclear factor κB (NF-κB), activator protein 1 (AP-1), and mitogen-activated protein kinases (MAPK). By modulating signal transduction pathways, curcumin induces apoptosis in malignant cells, thus inhibiting cancer development and progression. Due to the lack of mechanistic insight in the scientific literature, we developed a novel inverse molecular docking protocol based on the CANDOCK algorithm. For the first time, we performed inverse molecular docking of curcumin into a collection of 13,553 available human protein structures from the Protein Data Bank resulting in prioritized target proteins of curcumin. Our predictions were in agreement with the scientific literature and confirmed that curcumin binds to folate receptor β, DNA (cytosine-5)-methyltransferase 3A, metalloproteinase-2, mitogen-activated protein kinase 9, epidermal growth factor receptor and apoptosis-inducing factor 1. We also identified new potential protein targets of curcumin, namely deoxycytidine kinase, NAD-dependent protein deacetylase sirtuin-1 and -2, ecto-5'-nucleotidase, core histone macro-H2A.1, tyrosine-protein phosphatase non-receptor type 11, macrophage colony-stimulating factor 1 receptor, GTPase HRas, aflatoxin B1 aldehyde reductase member 3, aldo-keto reductase family 1 member C3, amiloride-sensitive amine oxidase, death-associated protein kinase 2 and tryptophan-tRNA ligase, that may all play a crucial role in its observed anticancer effects. Moreover, our inverse docking results showed that curcumin potentially binds also to the proteins cAMP-specific 3',5'-cyclic phosphodiesterase 4D and 17-β-hydroxysteroid dehydrogenase type 10, which provides a new explanation for its efficiency in the treatment of Alzheimer's disease. We firmly believe that our computational results will complement and direct future experimental studies on curcumin's anticancer activity as well as on its therapeutic effects against Alzheimer's disease.
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Affiliation(s)
- Veronika Furlan
- Faculty of Chemistry and Chemical Technology, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia.
| | - Janez Konc
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.
| | - Urban Bren
- Faculty of Chemistry and Chemical Technology, University of Maribor, Smetanova 17, SI-2000 Maribor, Slovenia.
- National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.
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52
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Ye CJ, Chen J, Villani AC, Gate RE, Subramaniam M, Bhangale T, Lee MN, Raj T, Raychowdhury R, Li W, Rogel N, Simmons S, Imboywa SH, Chipendo PI, McCabe C, Lee MH, Frohlich IY, Stranger BE, De Jager PL, Regev A, Behrens T, Hacohen N. Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection. Genome Res 2018; 28:1812-1825. [PMID: 30446528 PMCID: PMC6280757 DOI: 10.1101/gr.240390.118] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/09/2018] [Indexed: 02/02/2023]
Abstract
While genetic variants are known to be associated with overall gene abundance in stimulated immune cells, less is known about their effects on alternative isoform usage. By analyzing RNA-seq profiles of monocyte-derived dendritic cells from 243 individuals, we uncovered thousands of unannotated isoforms synthesized in response to influenza infection and type 1 interferon stimulation. We identified more than a thousand quantitative trait loci (QTLs) associated with alternate isoform usage (isoQTLs), many of which are independent of expression QTLs (eQTLs) for the same gene. Compared with eQTLs, isoQTLs are enriched for splice sites and untranslated regions, but depleted of sequences upstream of annotated transcription start sites. Both eQTLs and isoQTLs explain a significant proportion of the disease heritability attributed to common genetic variants. At the ERAP2 locus, we shed light on the function of the gene and how two frequent, highly differentiated haplotypes with intermediate frequencies could be maintained by balancing selection. At baseline and following type 1 interferon stimulation, the major haplotype is associated with low ERAP2 expression caused by nonsense-mediated decay, while the minor haplotype, known to increase Crohn's disease risk, is associated with high ERAP2 expression. In response to influenza infection, we found two uncharacterized isoforms expressed from the major haplotype, likely the result of multiple perfectly linked variants affecting the transcription and splicing at the locus. Thus, genetic variants at a single locus could modulate independent gene regulatory processes in innate immune responses and, in the case of ERAP2, may confer a historical fitness advantage in response to virus.
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Affiliation(s)
- Chun Jimmie Ye
- Institute for Human Genetics, Institute for Health and Computational Sciences, Department of Biostatistics and Epidemiology, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, USA
| | - Jenny Chen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Alexandra-Chloé Villani
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts 02114, USA
| | - Rachel E Gate
- Institute for Human Genetics, Institute for Health and Computational Sciences, Department of Biostatistics and Epidemiology, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, USA.,Biomedical Informatics Program, University of California, San Francisco, California 94143, USA
| | - Meena Subramaniam
- Institute for Human Genetics, Institute for Health and Computational Sciences, Department of Biostatistics and Epidemiology, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143, USA.,Biomedical Informatics Program, University of California, San Francisco, California 94143, USA
| | - Tushar Bhangale
- Genentech Incorporated, South San Francisco, California 94080, USA
| | - Mark N Lee
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts 02114, USA.,Harvard Medical School, Boston, Massachusetts 02116, USA
| | - Towfique Raj
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02116, USA.,Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | | | - Weibo Li
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Noga Rogel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Sean Simmons
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | | | - Cristin McCabe
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Michelle H Lee
- Harvard Medical School, Boston, Massachusetts 02116, USA
| | | | - Barbara E Stranger
- Section of Genetic Medicine, Department of Medicine, Institute for Genomics and Systems Biology, Center for Data Intensive Science, The University of Chicago, Chicago, Illinois 60637, USA
| | - Philip L De Jager
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Harvard Medical School, Boston, Massachusetts 02116, USA.,Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Tim Behrens
- Genentech Incorporated, South San Francisco, California 94080, USA
| | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Medicine, Massachusetts General Hospital Cancer Center, Boston, Massachusetts 02114, USA
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53
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Perlman S, Gallagher T. Not your usual tRNA synthetase: hWARS serves as an enterovirus entry factor. J Clin Invest 2018; 128:4767-4769. [PMID: 30320601 PMCID: PMC6205376 DOI: 10.1172/jci124582] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Enteroviruses, including subtype EV-A71, infect the brain, liver, heart, and other organs, causing a myriad of human diseases. This spectrum of disease is thought to be due, in part, to differential binding to host cells, and additional knowledge of enterovirus cell entry is essential for therapeutic development. In this issue of the JCI, Yeung et al. provide evidence of a novel EV-A71 entry factor, a host-produced tryptophan tRNA synthetase (hWARS), that facilitates entry of multiple subtypes of enteroviruses. hWARS is a cytoplasmic enzyme that is essential for translation but also upregulated and secreted during inflammatory processes. The results of this study support the notion of secreted hWARS as an unconventional virus entry factor that raises interesting questions about mechanisms by which inflammation and a tRNA synthetase facilitate viral pathogenesis.
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Affiliation(s)
- Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa and
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Tom Gallagher
- Department of Microbiology and Immunology, Loyola University, Chicago, Illinois, USA
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54
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Yeung ML, Jia L, Yip CCY, Chan JFW, Teng JLL, Chan KH, Cai JP, Zhang C, Zhang AJ, Wong WM, Kok KH, Lau SKP, Woo PCY, Lo JYC, Jin DY, Shih SR, Yuen KY. Human tryptophanyl-tRNA synthetase is an IFN-γ-inducible entry factor for Enterovirus. J Clin Invest 2018; 128:5163-5177. [PMID: 30153112 DOI: 10.1172/jci99411] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 08/23/2018] [Indexed: 01/08/2023] Open
Abstract
Enterovirus A71 (EV-A71) receptors that have been identified to date cannot fully explain the pathogenesis of EV-A71, which is an important global cause of hand, foot, and mouth disease and life-threatening encephalitis. We identified an IFN-γ-inducible EV-A71 cellular entry factor, human tryptophanyl-tRNA synthetase (hWARS), using genome-wide RNAi library screening. The importance of hWARS in mediating virus entry and infectivity was confirmed by virus attachment, in vitro pulldown, antibody/antigen blocking, and CRISPR/Cas9-mediated deletion. Hyperexpression and plasma membrane translocation of hWARS were observed in IFN-γ-treated semipermissive (human neuronal NT2) and cDNA-transfected nonpermissive (mouse fibroblast L929) cells, resulting in their sensitization to EV-A71 infection. Our hWARS-transduced mouse infection model showed pathological changes similar to those seen in patients with severe EV-A71 infection. Expression of hWARS is also required for productive infection by other human enteroviruses, including the clinically important coxsackievirus A16 (CV-A16) and EV-D68. This is the first report to our knowledge on the discovery of an entry factor, hWARS, that can be induced by IFN-γ for EV-A71 infection. Given that we detected high levels of IFN-γ in patients with severe EV-A71 infection, our findings extend the knowledge of the pathogenicity of EV-A71 in relation to entry factor expression upon IFN-γ stimulation and the therapeutic options for treating severe EV-A71-associated complications.
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Affiliation(s)
- Man Lung Yeung
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Lilong Jia
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Cyril C Y Yip
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Jasper F W Chan
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Jade L L Teng
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kwok-Hung Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jian-Piao Cai
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Chaoyu Zhang
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Anna J Zhang
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Wan-Man Wong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kin-Hang Kok
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China
| | - Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Janice Y C Lo
- Public Health Laboratory Centre, Department of Health, Hong Kong Special Administrative Region, China
| | - Dong-Yan Jin
- School of Biological Sciences, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infection, Chang Gung University, Kwei-Shan Tao-Yuan, Taiwan, Republic of China.,Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Kwei-Shan Tao-Yuan, Taiwan, Republic of China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong Special Administrative Region, China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong Special Administrative Region, China.,The Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Hong Kong Special Administrative Region, China.,University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, China
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55
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Rendleman J, Cheng Z, Maity S, Kastelic N, Munschauer M, Allgoewer K, Teo G, Zhang YBM, Lei A, Parker B, Landthaler M, Freeberg L, Kuersten S, Choi H, Vogel C. New insights into the cellular temporal response to proteostatic stress. eLife 2018; 7:39054. [PMID: 30272558 PMCID: PMC6185107 DOI: 10.7554/elife.39054] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022] Open
Abstract
Maintaining a healthy proteome involves all layers of gene expression regulation. By quantifying temporal changes of the transcriptome, translatome, proteome, and RNA-protein interactome in cervical cancer cells, we systematically characterize the molecular landscape in response to proteostatic challenges. We identify shared and specific responses to misfolded proteins and to oxidative stress, two conditions that are tightly linked. We reveal new aspects of the unfolded protein response, including many genes that escape global translation shutdown. A subset of these genes supports rerouting of energy production in the mitochondria. We also find that many genes change at multiple levels, in either the same or opposing directions, and at different time points. We highlight a variety of putative regulatory pathways, including the stress-dependent alternative splicing of aminoacyl-tRNA synthetases, and protein-RNA binding within the 3’ untranslated region of molecular chaperones. These results illustrate the potential of this information-rich resource.
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Affiliation(s)
- Justin Rendleman
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Zhe Cheng
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Shuvadeep Maity
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Nicolai Kastelic
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Mathias Munschauer
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Kristina Allgoewer
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Guoshou Teo
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Yun Bin Matteo Zhang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Amy Lei
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Brian Parker
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Integrative Research Institute for the Life Sciences, Institute of Biology, Humboldt University, Berlin, Germany
| | | | | | - Hyungwon Choi
- National University of Singapore, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Christine Vogel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, United States
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56
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Halu A, Wang JG, Iwata H, Mojcher A, Abib AL, Singh SA, Aikawa M, Sharma A. Context-enriched interactome powered by proteomics helps the identification of novel regulators of macrophage activation. eLife 2018; 7:37059. [PMID: 30303482 PMCID: PMC6179386 DOI: 10.7554/elife.37059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/30/2018] [Indexed: 02/06/2023] Open
Abstract
The role of pro-inflammatory macrophage activation in cardiovascular disease (CVD) is a complex one amenable to network approaches. While an indispensible tool for elucidating the molecular underpinnings of complex diseases including CVD, the interactome is limited in its utility as it is not specific to any cell type, experimental condition or disease state. We introduced context-specificity to the interactome by combining it with co-abundance networks derived from unbiased proteomics measurements from activated macrophage-like cells. Each macrophage phenotype contributed to certain regions of the interactome. Using a network proximity-based prioritization method on the combined network, we predicted potential regulators of macrophage activation. Prediction performance significantly increased with the addition of co-abundance edges, and the prioritized candidates captured inflammation, immunity and CVD signatures. Integrating the novel network topology with transcriptomics and proteomics revealed top candidate drivers of inflammation. In vitro loss-of-function experiments demonstrated the regulatory role of these proteins in pro-inflammatory signaling. When human cells or tissues are injured, the body triggers a response known as inflammation to repair the damage and protect itself from further harm. However, if the same issue keeps recurring, the tissues become inflamed for longer periods of time, which may ultimately lead to health problems. This is what could be happening in cardiovascular diseases, where long-term inflammation could damage the heart and blood vessels. Many different proteins interact with each other to control inflammation; gaining an insight into the nature of these interactions could help to pinpoint the role of each molecular actor. Researchers have used a combination of unbiased, large-scale experimental and computational approaches to develop the interactome, a map of the known interactions between all proteins in humans. However, interactions between proteins can change between cell types, or during disease. Here, Halu et al. aimed to refine the human interactome and identify new proteins involved in inflammation, especially in the context of cardiovascular disease. Cells called macrophages produce signals that trigger inflammation whey they detect damage in other cells or tissues. The experiments used a technique called proteomics to measure the amounts of all the proteins in human macrophages. Combining these data with the human interactome made it possible to predict new links between proteins known to have a role in inflammation and other proteins in the interactome. Further analysis using other sets of data from macrophages helped identify two new candidate proteins – GBP1 and WARS – that may promote inflammation. Halu et al. then used a genetic approach to deactivate the genes and decrease the levels of these two proteins in macrophages, which caused the signals that encourage inflammation to drop. These findings suggest that GBP1 and WARS regulate the activity of macrophages to promote inflammation. The two proteins could therefore be used as drug targets to treat cardiovascular diseases and other disorders linked to inflammation, but further studies will be needed to precisely dissect how GBP1 and WARS work in humans.
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Affiliation(s)
- Arda Halu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States.,Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Jian-Guo Wang
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Hiroshi Iwata
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Alexander Mojcher
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Ana Luisa Abib
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Sasha A Singh
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Amitabh Sharma
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
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57
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Adam I, Dewi DL, Mooiweer J, Sadik A, Mohapatra SR, Berdel B, Keil M, Sonner JK, Thedieck K, Rose AJ, Platten M, Heiland I, Trump S, Opitz CA. Upregulation of tryptophanyl-tRNA synthethase adapts human cancer cells to nutritional stress caused by tryptophan degradation. Oncoimmunology 2018; 7:e1486353. [PMID: 30524887 PMCID: PMC6279332 DOI: 10.1080/2162402x.2018.1486353] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 05/31/2018] [Accepted: 06/02/2018] [Indexed: 01/19/2023] Open
Abstract
Tryptophan (Trp) metabolism is an important target in immuno-oncology as it represents a powerful immunosuppressive mechanism hijacked by tumors for protection against immune destruction. However, it remains unclear how tumor cells can proliferate while degrading the essential amino acid Trp. Trp is incorporated into proteins after it is attached to its tRNA by tryptophanyl-tRNA synthestases. As the tryptophanyl-tRNA synthestases compete for Trp with the Trp-catabolizing enzymes, the balance between these enzymes will determine whether Trp is used for protein synthesis or is degraded. In human cancers expression of the Trp-degrading enzymes indoleamine-2,3-dioxygenase-1 (IDO1) and tryptophan-2,3-dioxygenase (TDO2) was positively associated with the expression of the tryptophanyl-tRNA synthestase WARS. One mechanism underlying the association between IDO1 and WARS identified in this study is their joint induction by IFNγ released from tumor-infiltrating T cells. Moreover, we show here that IDO1- and TDO2-mediated Trp deprivation upregulates WARS expression by activating the general control non-derepressible-2 (GCN2) kinase, leading to phosphorylation of the eukaryotic translation initiation factor 2α (eIF2α) and induction of activating transcription factor 4 (ATF4). Trp deprivation induced cytoplasmic WARS expression but did not increase nuclear or extracellular WARS levels. GCN2 protected the cells against the effects of Trp starvation and enabled them to quickly make use of Trp for proliferation once it was replenished. Computational modeling of Trp metabolism revealed that Trp deficiency shifted Trp flux towards WARS and protein synthesis. Our data therefore suggest that the upregulation of WARS via IFNγ and/or GCN2-peIF2α-ATF4 signaling protects Trp-degrading cancer cells from excessive intracellular Trp depletion.
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Affiliation(s)
- Isabell Adam
- Brain Cancer Metabolism Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dyah L Dewi
- Brain Cancer Metabolism Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Joram Mooiweer
- Brain Cancer Metabolism Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ahmed Sadik
- Brain Cancer Metabolism Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Soumya R Mohapatra
- Brain Cancer Metabolism Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bianca Berdel
- Brain Cancer Metabolism Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Keil
- DKTK Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jana K Sonner
- DKTK Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kathrin Thedieck
- Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signalling, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department for Neuroscience, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Adam J Rose
- Nutrient Metabolism and Signalling Lab, Department of Biochemistry & Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Michael Platten
- DKTK Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neurology, University Hospital and Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ines Heiland
- Department of Arctic and Marine Biology, UiT Arctic University of Norway, Tromsø, Norway
| | - Saskia Trump
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Christiane A Opitz
- Brain Cancer Metabolism Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Neurology Clinic and National Center for Tumor Diseases, University Hospital of Heidelberg, Heidelberg, Germany
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58
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Lee EY, Kim S, Kim MH. Aminoacyl-tRNA synthetases, therapeutic targets for infectious diseases. Biochem Pharmacol 2018; 154:424-434. [PMID: 29890143 PMCID: PMC7092877 DOI: 10.1016/j.bcp.2018.06.009] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/07/2018] [Indexed: 12/17/2022]
Abstract
Despite remarkable advances in medical science, infection-associated diseases remain among the leading causes of death worldwide. There is a great deal of interest and concern at the rate at which new pathogens are emerging and causing significant human health problems. Expanding our understanding of how cells regulate signaling networks to defend against invaders and retain cell homeostasis will reveal promising strategies against infection. It has taken scientists decades to appreciate that eukaryotic aminoacyl-tRNA synthetases (ARSs) play a role as global cell signaling mediators to regulate cell homeostasis, beyond their intrinsic function as protein synthesis enzymes. Recent discoveries revealed that ubiquitously expressed standby cytoplasmic ARSs sense and respond to danger signals and regulate immunity against infections, indicating their potential as therapeutic targets for infectious diseases. In this review, we discuss ARS-mediated anti-infectious signaling and the emerging role of ARSs in antimicrobial immunity. In contrast to their ability to defend against infection, host ARSs are inevitably co-opted by viruses for survival and propagation. We therefore provide a brief overview of the communication between viruses and the ARS system. Finally, we discuss encouraging new approaches to develop ARSs as therapeutics for infectious diseases.
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Affiliation(s)
- Eun-Young Lee
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon 16229, Republic of Korea; College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Myung Hee Kim
- Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34141, Republic of Korea.
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59
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Miyanokoshi M, Yokosawa T, Wakasugi K. Tryptophanyl-tRNA synthetase mediates high-affinity tryptophan uptake into human cells. J Biol Chem 2018; 293:8428-8438. [PMID: 29666190 DOI: 10.1074/jbc.ra117.001247] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 04/03/2018] [Indexed: 01/08/2023] Open
Abstract
The tryptophan (Trp) transport system has a high affinity and selectivity toward Trp, and has been reported to exist in both human and mouse macrophages. Although this system is highly expressed in interferon-γ (IFN-γ)-treated cells and indoleamine 2,3-dioxygenase 1 (IDO1)-expressing cells, its identity remains incompletely understood. Tryptophanyl-tRNA synthetase (TrpRS) is also highly expressed in IFN-γ-treated cells and also has high affinity and selectivity for Trp. Here, we investigated the effects of human TrpRS expression on Trp uptake into IFN-γ-treated human THP-1 monocytes or HeLa cells. Inhibition of human TrpRS expression by TrpRS-specific siRNAs decreased and overexpression of TrpRS increased Trp uptake into the cells. Of note, the TrpRS-mediated uptake system had more than hundred-fold higher affinity for Trp than the known System L amino acid transporter, promoted uptake of low Trp concentrations, and had very high Trp selectivity. Moreover, site-directed mutagenesis experiments indicated that Trp- and ATP-binding sites, but not tRNA-binding sites, in TrpRS are essential for TrpRS-mediated Trp uptake into the human cells. We further demonstrate that the addition of purified TrpRS to cell culture medium increases Trp uptake into cells. Taken together, our results reveal that TrpRS plays an important role in high-affinity Trp uptake into human cells.
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Affiliation(s)
- Miki Miyanokoshi
- From the Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan and
| | - Takumi Yokosawa
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Keisuke Wakasugi
- From the Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan and .,Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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60
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Ni R, Luo L. A noncanonical function of histidyl-tRNA synthetase: inhibition of vascular hyperbranching during zebrafish development. FEBS Open Bio 2018; 8:722-731. [PMID: 29744287 PMCID: PMC5929932 DOI: 10.1002/2211-5463.12420] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 02/21/2018] [Accepted: 03/14/2018] [Indexed: 11/09/2022] Open
Abstract
Histidyl‐tRNA synthetase (Hars) catalyzes the ligation of histidine residues to cognate tRNA. Here, we demonstrate a noncanonical function of Hars in vascular development in zebrafish. We obtained a novel zebrafish cq34 mutant which exhibited hyperbranching of cranial and intersegmental blood vessels 48 h after fertilization. The gene responsible for this phenotype was identified as hars. We found the increased expression of cdh5 and vegfa in the harscq34 mutant. Knockdown of cdh5 in the mutant reduced disordered connections of the hindbrain capillaries. Inhibition of vascular endothelial growth factor signaling suppressed the abnormal vascular branching observed in the mutant. Moreover, the human HARSmRNA rescued the vascular defects in the cq34 mutant. Thus, the noncanonical function of Hars regulates vascular development, mainly by modulating expression of cdh5 and vegfa.
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Affiliation(s)
- Rui Ni
- Key Laboratory of Freshwater Fish Reproduction and Development Ministry of Education Laboratory of Molecular Developmental Biology School of Life Sciences Southwest University Chongqing China
| | - Lingfei Luo
- Key Laboratory of Freshwater Fish Reproduction and Development Ministry of Education Laboratory of Molecular Developmental Biology School of Life Sciences Southwest University Chongqing China
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61
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Park SR, Kim HJ, Yang SR, Park CH, Lee HY, Hong IS. A novel endogenous damage signal, glycyl tRNA synthetase, activates multiple beneficial functions of mesenchymal stem cells. Cell Death Differ 2018; 25:2023-2036. [PMID: 29666468 DOI: 10.1038/s41418-018-0099-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 02/06/2018] [Accepted: 03/06/2018] [Indexed: 01/06/2023] Open
Abstract
During tissue repair, the injury site releases various bioactive molecules as damage signals to actively recruit stem cells to the damaged region. Despite convincing evidence that mesenchymal stem cells (MSCs) can sense damage signals and promote repair processes, the identity of these signals and how these signals regulate stem cell-mediated tissue repair remain unknown. Glycyl tRNA synthetase (GRS) is a ubiquitously expressed enzyme that catalyzes the first step of protein synthesis in all organisms. In addition to this canonical function, we identified for the first time that GRS is released by damaged tissues or cells in response to various injury signals and may function as a damage signal that activates the proliferative, differentiation, and migratory potential of MSCs, possibly through its identified receptor, cadherin-6 (CDH-6). Binding between GRS and CDH-6 activates survival signals, such as those of the PI3K/Akt and/or FAK/ERK1/2 pathways. More importantly, we also found that MSCs stimulated with GRS show significantly improved homing and differentiation potential and subsequent in vivo therapeutic effects, in a liver fibrosis animal model. Collectively, our findings provide compelling evidence for a novel function of GRS in enhancing the multiple beneficial functions of stem cells via a non-canonical mechanism as a damage signal.
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Affiliation(s)
- Se-Ra Park
- Laboratory of Stem Cell Research, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, 406-840, Republic of Korea.,Department of Molecular Medicine, School of Medicine, Gachon University, Incheon, 406-840, Republic of Korea
| | - Hyun-Jin Kim
- Laboratory of Stem Cell Research, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, 406-840, Republic of Korea.,Department of Molecular Medicine, School of Medicine, Gachon University, Incheon, 406-840, Republic of Korea
| | - Se-Ran Yang
- Department of Thoracic and Cardiovascular Surgery, Kangwon National University, Chuncheon, South Korea
| | - Chan Hum Park
- Department of Otolaryngology-Head and Neck Surgery, Chuncheon Sacred Heart Hospital, Hallym University College of Medicine, Chuncheon, South Korea
| | - Hwa-Yong Lee
- Department of Biomedical Science, Jungwon University, 85 Goesan-eup, Munmu-ro, Goesan-gun, 367-700, Republic of Korea.
| | - In-Sun Hong
- Laboratory of Stem Cell Research, Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon, 406-840, Republic of Korea. .,Department of Molecular Medicine, School of Medicine, Gachon University, Incheon, 406-840, Republic of Korea.
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62
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Halawani D, Gogonea V, DiDonato JA, Pipich V, Yao P, China A, Topbas C, Vasu K, Arif A, Hazen SL, Fox PL. Structural control of caspase-generated glutamyl-tRNA synthetase by appended noncatalytic WHEP domains. J Biol Chem 2018; 293:8843-8860. [PMID: 29643180 DOI: 10.1074/jbc.m117.807503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 03/26/2018] [Indexed: 02/02/2023] Open
Abstract
Aminoacyl-tRNA synthetases are ubiquitous, evolutionarily conserved enzymes catalyzing the conjugation of amino acids onto cognate tRNAs. During eukaryotic evolution, tRNA synthetases have been the targets of persistent structural modifications. These modifications can be additive, as in the evolutionary acquisition of noncatalytic domains, or subtractive, as in the generation of truncated variants through regulated mechanisms such as proteolytic processing, alternative splicing, or coding region polyadenylation. A unique variant is the human glutamyl-prolyl-tRNA synthetase (EPRS) consisting of two fused synthetases joined by a linker containing three copies of the WHEP domain (termed by its presence in tryptophanyl-, histidyl-, and glutamyl-prolyl-tRNA synthetases). Here, we identify site-selective proteolysis as a mechanism that severs the linkage between the EPRS synthetases in vitro and in vivo Caspase action targeted Asp-929 in the third WHEP domain, thereby separating the two synthetases. Using a neoepitope antibody directed against the newly exposed C terminus, we demonstrate EPRS cleavage at Asp-929 in vitro and in vivo Biochemical and biophysical characterizations of the N-terminally generated EPRS proteoform containing the glutamyl-tRNA synthetase and most of the linker, including two WHEP domains, combined with structural analysis by small-angle neutron scattering, revealed a role for the WHEP domains in modulating conformations of the catalytic core and GSH-S-transferase-C-terminal-like (GST-C) domain. WHEP-driven conformational rearrangement altered GST-C domain interactions and conferred distinct oligomeric states in solution. Collectively, our results reveal long-range conformational changes imposed by the WHEP domains and illustrate how noncatalytic domains can modulate the global structure of tRNA synthetases in complex eukaryotic systems.
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Affiliation(s)
- Dalia Halawani
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Valentin Gogonea
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and .,the Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115
| | - Joseph A DiDonato
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Vitaliy Pipich
- the Jülich Center for Neutron Science, Outstation at Maier-Leibnitz Zentrum, Forschungszentrum Jülich, GmbH, Lichtenbergstrasse 1, 85747 Garching, Germany, and
| | - Peng Yao
- the Department of Medicine, Aab Cardiovascular Research Institute, University of Rochester, Rochester, New York 14642
| | - Arnab China
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Celalettin Topbas
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and.,the Department of Chemistry, Cleveland State University, Cleveland, Ohio 44115
| | - Kommireddy Vasu
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Abul Arif
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
| | - Stanley L Hazen
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and.,Center for Cardiovascular Diagnostics and Prevention, and Department of Cardiovascular Medicine, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - Paul L Fox
- From the Department of Cellular and Molecular Medicine, Lerner Research Institute and
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63
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Boczonadi V, Jennings MJ, Horvath R. The role of tRNA synthetases in neurological and neuromuscular disorders. FEBS Lett 2018; 592:703-717. [PMID: 29288497 PMCID: PMC5873386 DOI: 10.1002/1873-3468.12962] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 12/06/2017] [Accepted: 12/21/2017] [Indexed: 12/11/2022]
Abstract
Aminoacyl‐tRNA synthetases (ARSs) are ubiquitously expressed enzymes responsible for charging tRNAs with their cognate amino acids, therefore essential for the first step in protein synthesis. Although the majority of protein synthesis happens in the cytosol, an additional translation apparatus is required to translate the 13 mitochondrial DNA‐encoded proteins important for oxidative phosphorylation. Most ARS genes in these cellular compartments are distinct, but two genes are common, encoding aminoacyl‐tRNA synthetases of glycine (GARS) and lysine (KARS) in both mitochondria and the cytosol. Mutations in the majority of the 37 nuclear‐encoded human ARS genes have been linked to a variety of recessive and dominant tissue‐specific disorders. Current data indicate that impaired enzyme function could explain the pathogenicity, however not all pathogenic ARSs mutations result in deficient catalytic function; thus, the consequences of mutations may arise from other molecular mechanisms. The peripheral nerves are frequently affected, as illustrated by the high number of mutations in cytosolic and bifunctional tRNA synthetases causing Charcot–Marie–Tooth disease (CMT). Here we provide insights on the pathomechanisms of CMT‐causing tRNA synthetases with specific focus on the two bifunctional tRNA synthetases (GARS, KARS).
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Affiliation(s)
- Veronika Boczonadi
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew J Jennings
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Rita Horvath
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
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64
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Sykes EK, McDonald CE, Ghazanfar S, Mactier S, Thompson JF, Scolyer RA, Yang JY, Mann GJ, Christopherson RI. A 14-Protein Signature for Rapid Identification of Poor Prognosis Stage III Metastatic Melanoma. Proteomics Clin Appl 2017; 12:e1700094. [PMID: 29227041 DOI: 10.1002/prca.201700094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/08/2017] [Indexed: 11/10/2022]
Abstract
PURPOSE To validate differences in protein levels between good and poor prognosis American Joint Committee on Cancer (AJCC) stage III melanoma patients and compile a protein panel to stratify patient risk. EXPERIMENTAL DESIGN Protein extracts from melanoma metastases within lymph nodes in patients with stage III disease with good (n = 16, >4 years survival) and poor survival (n = 14, <2 years survival) were analyzed by selected reaction monitoring (SRM). Diagonal Linear Discriminant Analysis (DLDA) was performed to generate a protein biomarker panel. RESULTS SRM analysis identified ten proteins that were differentially abundant between good and poor prognosis stage III melanoma patients. The ten differential proteins were combined with 22 proteins identified in our previous work. A panel of 14 proteins was selected by DLDA that was able to accurately classify patients into prognostic groups based on levels of these proteins. CONCLUSIONS AND CLINICAL RELEVANCE The ten differential proteins identified by SRM have biological significance in cancer progression. The final signature of 14 proteins identified by SRM could be used to identify AJCC stage III melanoma patients likely to have poor outcomes who may benefit from adjuvant systemic therapy.
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Affiliation(s)
- Erin K Sykes
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | | | - Shila Ghazanfar
- School of Mathematics and Statistics, University of Sydney, NSW, Australia
| | - Swetlana Mactier
- School of Life and Environmental Sciences, University of Sydney, NSW, Australia
| | - John F Thompson
- Melanoma Institute Australia, University of Sydney, North Sydney, NSW, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia.,University of Sydney at Westmead Millennium Institute, Westmead, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, University of Sydney, North Sydney, NSW, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Jean Y Yang
- School of Mathematics and Statistics, University of Sydney, NSW, Australia
| | - Graham J Mann
- Melanoma Institute Australia, University of Sydney, North Sydney, NSW, Australia.,University of Sydney at Westmead Millennium Institute, Westmead, NSW, Australia
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65
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Yakobov N, Debard S, Fischer F, Senger B, Becker HD. Cytosolic aminoacyl-tRNA synthetases: Unanticipated relocations for unexpected functions. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:387-400. [PMID: 29155070 DOI: 10.1016/j.bbagrm.2017.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 12/13/2022]
Abstract
Prokaryotic and eukaryotic cytosolic aminoacyl-tRNA synthetases (aaRSs) are essentially known for their conventional function of generating the full set of aminoacyl-tRNA species that are needed to incorporate each organism's repertoire of genetically-encoded amino acids during ribosomal translation of messenger RNAs. However, bacterial and eukaryotic cytosolic aaRSs have been shown to exhibit other essential nonconventional functions. Here we review all the subcellular compartments that prokaryotic and eukaryotic cytosolic aaRSs can reach to exert either a conventional or nontranslational role. We describe the physiological and stress conditions, the mechanisms and the signaling pathways that trigger their relocation and the new functions associated with these relocating cytosolic aaRS. Finally, given that these relocating pools of cytosolic aaRSs participate to a wide range of cellular pathways beyond translation, but equally important for cellular homeostasis, we mention some of the pathologies and diseases associated with the dis-regulation or malfunctioning of these nontranslational functions.
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Affiliation(s)
- Nathaniel Yakobov
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Sylvain Debard
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Frédéric Fischer
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Bruno Senger
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Hubert Dominique Becker
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France.
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66
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Xu X, Zhou H, Zhou Q, Hong F, Vo MN, Niu W, Wang Z, Xiong X, Nakamura K, Wakasugi K, Schimmel P, Yang XL. An alternative conformation of human TrpRS suggests a role of zinc in activating non-enzymatic function. RNA Biol 2017; 15:649-658. [PMID: 28910573 PMCID: PMC6103731 DOI: 10.1080/15476286.2017.1377868] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Tryptophanyl-tRNA synthetase (TrpRS) in vertebrates contains a N-terminal extension in front of the catalytic core. Proteolytic removal of the N-terminal 93 amino acids gives rise to T2-TrpRS, which has potent anti-angiogenic activity mediated through its extracellular interaction with VE-cadherin. Zinc has been shown to have anti-angiogenic effects and can bind to human TrpRS. However, the connection between zinc and the anti-angiogenic function of TrpRS has not been explored. Here we report that zinc binding can induce structural relaxation in human TrpRS to facilitate the proteolytic generation of a T2-TrpRS-like fragment. The zinc-binding site is likely to be contained within T2-TrpRS, and the zinc-bound conformation of T2-TrpRS is mimicked by mutation H130R. We determined the crystal structure of H130R T2-TrpRS at 2.8 Å resolution, which reveals drastically different conformation from that of wild-type (WT) T2-TrpRS. The conformational change creates larger binding surfaces for VE-cadherin as suggested by molecular dynamic simulations. Surface plasmon resonance analysis indicates more than 50-fold increase in binding affinity of H130R T2-TrpRS for VE-cadherin, compared to WT T2-TrpRS. The enhanced interaction is also confirmed by a cell-based binding analysis. These results suggest that zinc plays an important role in activating TrpRS for angiogenesis regulation.
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Affiliation(s)
- Xiaoling Xu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA,Institute of Aging Research, School of Medicine, Hangzhou Normal University, Zhejiang Province, Hangzhou, China,Contact Xiaoling Xu Institute of Aging Research, School of Medicine, Hangzhou Normal University, Room D-615, No.1378 Wenyi West Road, Zhejiang Province, 311121, Hangzhou, China
| | - Huihao Zhou
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Quansheng Zhou
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Fei Hong
- aTyr Pharma, 3545 John Hopkins Court, San Diego, CA, USA
| | - My-Nuong Vo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Wanqiang Niu
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Zhejiang Province, Hangzhou, China
| | - Zhiguo Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Zhejiang Province, Hangzhou, China
| | - Xiaolin Xiong
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Kanaha Nakamura
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Keisuke Wakasugi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Xiang-Lei Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA,Xiang-Lei Yang Department of Molecular Medicine, The Scripps Research Institute, BCC 110 10550 North Torrey Pines Road, La Jolla, CA 92037
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67
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Tsai PC, Soong BW, Mademan I, Huang YH, Liu CR, Hsiao CT, Wu HT, Liu TT, Liu YT, Tseng YT, Lin KP, Yang UC, Chung KW, Choi BO, Nicholson GA, Kennerson ML, Chan CC, De Jonghe P, Cheng TH, Liao YC, Züchner S, Baets J, Lee YC. A recurrent WARS mutation is a novel cause of autosomal dominant distal hereditary motor neuropathy. Brain 2017; 140:1252-1266. [PMID: 28369220 DOI: 10.1093/brain/awx058] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 01/23/2017] [Indexed: 11/14/2022] Open
Abstract
Distal hereditary motor neuropathy is a heterogeneous group of inherited neuropathies characterized by distal limb muscle weakness and atrophy. Although at least 15 genes have been implicated in distal hereditary motor neuropathy, the genetic causes remain elusive in many families. To identify an additional causal gene for distal hereditary motor neuropathy, we performed exome sequencing for two affected individuals and two unaffected members in a Taiwanese family with an autosomal dominant distal hereditary motor neuropathy in which mutations in common distal hereditary motor neuropathy-implicated genes had been excluded. The exome sequencing revealed a heterozygous mutation, c.770A > G (p.His257Arg), in the cytoplasmic tryptophanyl-tRNA synthetase (TrpRS) gene (WARS) that co-segregates with the neuropathy in the family. Further analyses of WARS in an additional 79 Taiwanese pedigrees with inherited neuropathies and 163 index cases from Australian, European, and Korean distal hereditary motor neuropathy families identified the same mutation in another Taiwanese distal hereditary motor neuropathy pedigree with different ancestries and one additional Belgian distal hereditary motor neuropathy family of Caucasian origin. Cell transfection studies demonstrated a dominant-negative effect of the p.His257Arg mutation on aminoacylation activity of TrpRS, which subsequently compromised protein synthesis and reduced cell viability. His257Arg TrpRS also inhibited neurite outgrowth and led to neurite degeneration in the neuronal cell lines and rat motor neurons. Further in vitro analyses showed that the WARS mutation could potentiate the angiostatic activities of TrpRS by enhancing its interaction with vascular endothelial-cadherin. Taken together, these findings establish WARS as a gene whose mutations may cause distal hereditary motor neuropathy and alter canonical and non-canonical functions of TrpRS.
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Affiliation(s)
- Pei-Chien Tsai
- Department of Neurology, Taipei Veterans General Hospital, Taipei 11217, Taiwan.,Department of Neurology, National Yang-Ming University School of Medicine, Taipei 11221, Taiwan.,Brain Research Center, National Yang-Ming University, Taipei 11221, Taiwan
| | - Bing-Wen Soong
- Department of Neurology, Taipei Veterans General Hospital, Taipei 11217, Taiwan.,Department of Neurology, National Yang-Ming University School of Medicine, Taipei 11221, Taiwan.,Brain Research Center, National Yang-Ming University, Taipei 11221, Taiwan.,Institute of Neuroscience, National Yang-Ming University, Taipei 11221, Taiwan
| | - Inès Mademan
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerpen 2610, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerpen 2610, Belgium
| | - Yen-Hua Huang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan.,Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Chia-Rung Liu
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Cheng-Tsung Hsiao
- Department of Neurology, Taipei Veterans General Hospital, Taipei 11217, Taiwan.,Department of Neurology, National Yang-Ming University School of Medicine, Taipei 11221, Taiwan
| | - Hung-Ta Wu
- Department of Neurology, Taipei Veterans General Hospital, Taipei 11217, Taiwan.,Department of Radiology, National Yang-Ming University School of Medicine, Taipei 11221, Taiwan
| | - Tze-Tze Liu
- Genome Research Center, National Yang-Ming University, Taipei 11221, Taiwan
| | - Yo-Tsen Liu
- Department of Neurology, Taipei Veterans General Hospital, Taipei 11217, Taiwan.,Department of Neurology, National Yang-Ming University School of Medicine, Taipei 11221, Taiwan
| | - Yen-Ting Tseng
- Department of Neurology, Taipei Veterans General Hospital, Taipei 11217, Taiwan.,Department of Neurology, National Yang-Ming University School of Medicine, Taipei 11221, Taiwan
| | - Kon-Ping Lin
- Department of Neurology, Taipei Veterans General Hospital, Taipei 11217, Taiwan.,Department of Neurology, National Yang-Ming University School of Medicine, Taipei 11221, Taiwan
| | - Ueng-Cheng Yang
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan.,Center for Systems and Synthetic Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Ki Wha Chung
- Department of Biological Sciences, Kongju National University, Gongju 32588, Korea
| | - Byung-Ok Choi
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Garth A Nicholson
- Northcott Neuroscience Laboratory, ANZAC Research Institute; Molecular Medicine Laboratory, Concord Hospital; Sydney Medical School University of Sydney, NSW 2139, Sydney, Australia
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute; Molecular Medicine Laboratory, Concord Hospital; Sydney Medical School University of Sydney, NSW 2139, Sydney, Australia
| | - Chih-Chiang Chan
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Taipei 10051, Taiwan.,Graduate Institute of Brain and Mind Sciences, National Taiwan University College of Medicine, Taipei 10051, Taiwan
| | - Peter De Jonghe
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerpen 2610, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerpen 2610, Belgium.,Department of Neurology, Antwerp University Hospital, Antwerpen 2650, Belgium
| | - Tzu-Hao Cheng
- Brain Research Center, National Yang-Ming University, Taipei 11221, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Yi-Chu Liao
- Department of Neurology, Taipei Veterans General Hospital, Taipei 11217, Taiwan.,Department of Neurology, National Yang-Ming University School of Medicine, Taipei 11221, Taiwan
| | - Stephan Züchner
- Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL 33136, USA
| | - Jonathan Baets
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerpen 2610, Belgium.,Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerpen 2610, Belgium.,Department of Neurology, Antwerp University Hospital, Antwerpen 2650, Belgium
| | - Yi-Chung Lee
- Department of Neurology, Taipei Veterans General Hospital, Taipei 11217, Taiwan.,Department of Neurology, National Yang-Ming University School of Medicine, Taipei 11221, Taiwan.,Brain Research Center, National Yang-Ming University, Taipei 11221, Taiwan
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68
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Meyer-Schuman R, Antonellis A. Emerging mechanisms of aminoacyl-tRNA synthetase mutations in recessive and dominant human disease. Hum Mol Genet 2017; 26:R114-R127. [PMID: 28633377 PMCID: PMC5886470 DOI: 10.1093/hmg/ddx231] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 06/09/2017] [Accepted: 06/12/2017] [Indexed: 12/29/2022] Open
Abstract
Aminoacyl-tRNA synthetases (ARSs) are responsible for charging amino acids to cognate tRNA molecules, which is the essential first step of protein translation. Interestingly, mutations in genes encoding ARS enzymes have been implicated in a broad spectrum of human inherited diseases. Bi-allelic mutations in ARSs typically cause severe, early-onset, recessive diseases that affect a wide range of tissues. The vast majority of these mutations show loss-of-function effects and impair protein translation. However, it is not clear how a subset cause tissue-specific phenotypes. In contrast, dominant ARS-mediated diseases specifically affect the peripheral nervous system-most commonly causing axonal peripheral neuropathy-and usually manifest later in life. These neuropathies are linked to heterozygosity for missense mutations in five ARS genes, which points to a shared mechanism of disease. However, it is not clear if a loss-of-function mechanism or a toxic gain-of-function mechanism is responsible for ARS-mediated neuropathy, or if a combination of these mechanisms operate on a mutation-specific basis. Here, we review our current understanding of recessive and dominant ARS-mediated disease. We also propose future directions for defining the molecular mechanisms of ARS mutations toward designing therapies for affected patient populations.
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Affiliation(s)
- Rebecca Meyer-Schuman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Anthony Antonellis
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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69
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Lambert CA, Garbacki N, Colige AC. Chemotherapy induces alternative transcription and splicing: Facts and hopes for cancer treatment. Int J Biochem Cell Biol 2017; 91:84-97. [DOI: 10.1016/j.biocel.2017.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 04/04/2017] [Accepted: 04/15/2017] [Indexed: 01/14/2023]
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70
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Abstract
Tumor radiotherapy induces hematopoietic organ damage and reduces thrombocyte counts. Thrombocytopenia is a common disease. Some studies have shown that tRNA synthetase plays not only catalytic tRNA aminoacylation roles, but also functions similarly to cytokines. Recombinant human tyrosyl-tRNA synthetase with a mutated Y341A (rhTyrRS (Y341A)) promotes megakaryocyte migrate from bone marrow to peripheral blood. It would promote megakaryocytes in the lungs adhering to vascular endothelial cells and resulting in the platelet production. The purpose of this research was to investigate the efficacy of rhTyrRS (Y341A) as a therapy for thrombocytopenia and to explore its mechanism of action. We found platelet number was effectively increased by rhTyrRS (Y341A) via platelet count and reticulated platelets (RPs) flow cytometry. We also demonstrated radiation-induced thrombocytopenia could be prevented by rhTyrRS (Y341A). The results of immunohistochemistry and H&E staining showed the number of pulmonary mature megakaryocytes was significantly increased in rhTyrRS (Y341A) treated groups. In transgenic zebrafish larvae, confocal microscopy results showed rhTyrRS (Y341A) promoted the migration and adhesion of megakaryocytes. These results suggested that rhTyrRS (Y341A) promote megakaryocytes in bone marrow migrating to lungs through blood circulation. rhTyrRS (Y341A) may be an effective medicine which could be used to treat patients suffering from thrombocytopenia.
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71
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Nyalwidhe JO, Gallagher GR, Glenn LM, Morris MA, Vangala P, Jurczyk A, Bortell R, Harlan DM, Wang JP, Nadler JL. Coxsackievirus-Induced Proteomic Alterations in Primary Human Islets Provide Insights for the Etiology of Diabetes. J Endocr Soc 2017; 1:1272-1286. [PMID: 29264452 PMCID: PMC5686651 DOI: 10.1210/js.2017-00278] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 09/06/2017] [Indexed: 12/15/2022] Open
Abstract
Enteroviral infections have been associated with the development of type 1 diabetes (T1D), a chronic inflammatory disease characterized by autoimmune destruction of insulin-producing pancreatic beta cells. Cultured human islets, including the insulin-producing beta cells, can be infected with coxsackievirus B4 (CVB4) and thus are useful for understanding cellular responses to infection. We performed quantitative mass spectrometry analysis on cultured primary human islets infected with CVB4 to identify molecules and pathways altered upon infection. Corresponding uninfected controls were included in the study for comparative protein expression analyses. Proteins were significantly and differentially regulated in human islets challenged with virus compared with their uninfected counterparts. Complementary analyses of gene transcripts in CVB4-infected primary islets over a time course validated the induction of RNA transcripts for many of the proteins that were increased in the proteomics studies. Notably, infection with CVB4 results in a considerable decrease in insulin. Genes/proteins modulated during CVB4 infection also include those involved in activation of immune responses, including type I interferon pathways linked to T1D pathogenesis and with antiviral, cell repair, and inflammatory properties. Our study applies proteomics analyses to cultured human islets challenged with virus and identifies target proteins that could be useful in T1D interventions.
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Affiliation(s)
- Julius O Nyalwidhe
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23501.,Leroy T. Canoles Jr. Cancer Research Center, Eastern Virginia Medical School, Norfolk, Virginia 23501
| | - Glen R Gallagher
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Lindsey M Glenn
- Department of Internal Medicine and Strelitz Diabetes Center, Eastern Virginia Medical School, Norfolk, Virginia 23501
| | - Margaret A Morris
- Department of Internal Medicine and Strelitz Diabetes Center, Eastern Virginia Medical School, Norfolk, Virginia 23501
| | - Pranitha Vangala
- Department of Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Agata Jurczyk
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Rita Bortell
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - David M Harlan
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Jennifer P Wang
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Jerry L Nadler
- Department of Internal Medicine and Strelitz Diabetes Center, Eastern Virginia Medical School, Norfolk, Virginia 23501
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72
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Fu CY, Wang PC, Tsai HJ. Competitive binding between Seryl-tRNA synthetase/YY1 complex and NFKB1 at the distal segment results in differential regulation of human vegfa promoter activity during angiogenesis. Nucleic Acids Res 2017; 45:2423-2437. [PMID: 27913726 PMCID: PMC5389716 DOI: 10.1093/nar/gkw1187] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/16/2016] [Indexed: 11/13/2022] Open
Abstract
Vascular endothelial growth factor (VEGF) plays a pivotal role in angiogenesis. Previous studies focused on transcriptional regulation modulated by proximal upstream cis-regulatory elements (CREs) of the human vegfa promoter. However, we hypothesized that distal upstream CREs may also be involved in controlling vegfa transcription. In this study, we found that the catalytic domain of Seryl-tRNA synthetase (SerRS) interacted with transcription factor Yin Yang 1 (YY1) to form a SerRS/YY1 complex that negatively controls vegfa promoter activity through binding distal CREs at -4654 to -4623 of vegfa. Particularly, we demonstrated that the -4654 to -4623 segment, which predominantly controls vegfa promoter activity, is involved in competitive binding between SerRS/YY1 complex and NFKB1. We further showed that VEGFA protein and blood vessel development were reduced by overexpression of either SerRS or YY1, but enhanced by the knockdown of either SerRS or yy1. In contrast, these same parameters were enhanced by overexpression of NFKB1, but reduced by knockdown of nfkb1. Therefore, we suggested that SerRS does not bind DNA directly but form a SerRS/YY1 complex, which functions as a negative effector to regulate vegfa transcription through binding at the distal CREs; while NFKB1 serves as a positive effector through competing with SerRS/YY1 binding at the overlapping CREs.
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Affiliation(s)
- Chuan-Yang Fu
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan.,Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Po-Chun Wang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Huai-Jen Tsai
- Institute of Biomedical Sciences, Mackay Medical College, New Taipei City, Taiwan
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73
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Isolation of bacterial compartments to track movement of protein synthesis factors. Methods 2017; 113:120-126. [PMID: 27887986 DOI: 10.1016/j.ymeth.2016.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 11/19/2016] [Accepted: 11/21/2016] [Indexed: 10/20/2022] Open
Abstract
Aminoacyl-tRNA synthetases (AARSs) comprise an enzyme family that generates and maintains pools of aminoacylated tRNAs, which serve as essential substrates for protein synthesis. Many protein synthesis factors, including tRNA and AARSs also have non-canonical functions. Particularly in mammalian cells, alternate functions of AARSs have been associated with re-distribution in the cell to sites that are removed from translation. Sub-fractionation methods for E. coli were designed and optimized to carefully investigate re-localization of bacterial AARSs and tRNA that might aid in conferring alternate activities. Cell fractionation included isolation of the cytoplasm, periplasm, membrane, outer membrane vesicles, and extracellular media. Specific endogenous proteins and RNAs were probed respectively within each fraction via Western blots using antibodies and by Northern blots with primers to unique regions of the nucleic acid.
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74
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Structural characterization of human aminoacyl-tRNA synthetases for translational and nontranslational functions. Methods 2017; 113:83-90. [DOI: 10.1016/j.ymeth.2016.11.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/14/2016] [Accepted: 11/21/2016] [Indexed: 11/18/2022] Open
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75
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Ahn YH, Park S, Choi JJ, Park BK, Rhee KH, Kang E, Ahn S, Lee CH, Lee JS, Inn KS, Cho ML, Park SH, Park K, Park HJ, Lee JH, Park JW, Kwon NH, Shim H, Han BW, Kim P, Lee JY, Jeon Y, Huh JW, Jin M, Kim S. Secreted tryptophanyl-tRNA synthetase as a primary defence system against infection. Nat Microbiol 2016; 2:16191. [PMID: 27748732 DOI: 10.1038/nmicrobiol.2016.191] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 09/02/2016] [Indexed: 11/09/2022]
Abstract
The N-terminal truncated form of a protein synthesis enzyme, tryptophanyl-tRNA synthetase (mini-WRS), is secreted as an angiostatic ligand. However, the secretion and function of the full-length WRS (FL-WRS) remain unknown. Here, we report that the FL-WRS, but not mini-WRS, is rapidly secreted upon pathogen infection to prime innate immunity. Blood levels of FL-WRS were increased in sepsis patients, but not in those with sterile inflammation. FL-WRS was secreted from monocytes and directly bound to macrophages via a toll-like receptor 4 (TLR4)-myeloid differentiation factor 2 (MD2) complex to induce phagocytosis and chemokine production. Administration of FL-WRS into Salmonella typhimurium-infected mice reduced the levels of bacteria and improved mouse survival, whereas its titration with the specific antibody aggravated the infection. The N-terminal 154-amino-acid eukaryote-specific peptide of WRS was sufficient to recapitulate FL-WRS activity and its interaction mode with TLR4-MD2 is now suggested. Based on these results, secretion of FL-WRS appears to work as a primary defence system against infection, acting before full activation of innate immunity.
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Affiliation(s)
- Young Ha Ahn
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sunyoung Park
- College of Korean Medicine, Daejeon University, Daejeon 34520, Republic of Korea
| | - Jeong June Choi
- College of Korean Medicine, Daejeon University, Daejeon 34520, Republic of Korea
| | - Bo-Kyung Park
- College of Korean Medicine, Daejeon University, Daejeon 34520, Republic of Korea
| | - Kyung Hee Rhee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eunjoo Kang
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon 16229, Republic of Korea
| | - Soyeon Ahn
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Jong Soo Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Kyung-Soo Inn
- Department of Pharmaceutical Science, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Mi-La Cho
- Divison of Rheumatology, Department of Internal Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Sung-Hwan Park
- The Rheumatism Research Center, Catholic Research Institute of Medical Science, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Kyunghee Park
- Division of Allergy and Immunology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.,Institute of Allergy, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hye Jung Park
- Division of Allergy and Immunology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.,Institute of Allergy, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jae-Hyun Lee
- Division of Allergy and Immunology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.,Institute of Allergy, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jung-Won Park
- Division of Allergy and Immunology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.,Institute of Allergy, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Nam Hoon Kwon
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon 16229, Republic of Korea
| | - Hyunbo Shim
- Departments of Bioinspired Science and Life Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Pilhan Kim
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Joo-Youn Lee
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.,Korea Chemical Bank, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Youngho Jeon
- College of Pharmacy, Korea University, Sejong 30019, Republic of Korea
| | - Jin Won Huh
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Mirim Jin
- College of Korean Medicine, Daejeon University, Daejeon 34520, Republic of Korea
| | - Sunghoon Kim
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.,Medicinal Bioconvergence Research Center, Seoul National University, Suwon 16229, Republic of Korea
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76
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Lee CW, Chang KP, Chen YY, Liang Y, Hsueh C, Yu JS, Chang YS, Yu CJ. Overexpressed tryptophanyl-tRNA synthetase, an angiostatic protein, enhances oral cancer cell invasiveness. Oncotarget 2016; 6:21979-92. [PMID: 26110569 PMCID: PMC4673140 DOI: 10.18632/oncotarget.4273] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/05/2015] [Indexed: 12/11/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is one of the most common neoplasms worldwide. Previously, we identified the angiostatic agent tryptophanyl-tRNA synthetase (TrpRS) as a dysregulated protein in OSCC based on a proteomics approach. Herein, we show that TrpRS is overexpressed in OSCC tissues (139/146, 95.2%) compared with adjacent normal tissues and that TrpRS expression positively correlates with tumor stage, overall TNM stage, perineural invasion and tumor depth. Importantly, the TrpRS levels were significantly higher in tumor cells from metastatic lymph nodes than in corresponding primary tumor cells. TrpRS knockdown or treatment with conditioned media obtained from TrpRS-knockdown cells significantly reduced oral cancer cell viability and invasiveness. TrpRS overexpression promoted cell migration and invasion. In addition, the extracellular addition of TrpRS rescued the invasion ability of TrpRS-knockdown cells. Subcellular fractionation and immunofluorescence staining further revealed that TrpRS was distributed on the cell surface, suggesting that secreted TrpRS promotes OSCC progression via an extrinsic pathway. Collectively, our results demonstrated the clinical significance and a novel role of TrpRS in OSCC.
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Affiliation(s)
- Chien-Wei Lee
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Kai-Ping Chang
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Lin-Kou, Tao-Yuan, Taiwan
| | - Yan-Yu Chen
- Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan
| | - Ying Liang
- Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan
| | - Chuen Hsueh
- Department of Pathology, Chang Gung Memorial Hospital, Lin-Kou, Tao-Yuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan.,Pathology Core, Chang Gung University, Tao-Yuan, Taiwan
| | - Jau-Song Yu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan.,Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan
| | - Yu-Sun Chang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan
| | - Chia-Jung Yu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan.,Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan
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77
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Norris EL, Headlam MJ, Dave KA, Smith DD, Bukreyev A, Singh T, Jayakody BA, Chappell KJ, Collins PL, Gorman JJ. Proteoform-Specific Insights into Cellular Proteome Regulation. Mol Cell Proteomics 2016; 15:3297-3320. [PMID: 27451424 PMCID: PMC5054351 DOI: 10.1074/mcp.o116.058438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Indexed: 01/29/2023] Open
Abstract
Knowledge regarding compositions of proteomes at the proteoform level enhances insights into cellular phenotypes. A strategy is described herein for discovery of proteoform-specific information about cellular proteomes. This strategy involved analysis of data obtained by bottom-up mass spectrometry of multiple protein OGE separations on a fraction by fraction basis. The strategy was exemplified using five matched sets of lysates of uninfected and human respiratory syncytial virus-infected A549 cells. Template matching demonstrated that 67.3% of 10475 protein profiles identified focused to narrow pI windows indicative of efficacious focusing. Furthermore, correlation between experimental and theoretical pI gradients indicated reproducible focusing. Based on these observations a proteoform profiling strategy was developed to identify proteoforms, detect proteoform diversity and discover potential proteoform regulation. One component of this strategy involved examination of the focusing profiles for protein groups. A novel concordance analysis facilitated differentiation between proteoforms, including proteoforms generated by alternate splicing and proteolysis. Evaluation of focusing profiles and concordance analysis were applicable to cells from a single and/or multiple biological states. Statistical analyses identified proteoform variation between biological states. Regulation relevant to cellular responses to human respiratory syncytial virus was revealed. Western blotting and Protomap analyses validated the proteoform regulation. Discovery of STAT1, WARS, MX1, and HSPB1 proteoform regulation by human respiratory syncytial virus highlighted the impact of the profiling strategy. Novel truncated proteoforms of MX1 were identified in infected cells and phosphorylation driven regulation of HSPB1 proteoforms was correlated with infection. The proteoform profiling strategy is generally applicable to investigating interactions between viruses and host cells and the analysis of other biological systems.
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Affiliation(s)
| | | | | | - David D Smith
- §Statistics Unit, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Alexander Bukreyev
- ¶Respiratory Virus Section, Laboratory of Infectious Diseases, National Institute for Allergy and Infectious Diseases, NIH, Bethesda, Maryland, and
| | | | | | - Keith J Chappell
- ‖School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Peter L Collins
- ¶Respiratory Virus Section, Laboratory of Infectious Diseases, National Institute for Allergy and Infectious Diseases, NIH, Bethesda, Maryland, and
| | - Jeffrey J Gorman
- From the ‡Protein Discovery Centre and ‖School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
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78
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Abstract
Coronary flow (CF) measured ex vivo is largely determined by capillary density that reflects angiogenic vessel formation in the heart in vivo. Here we exploit this relationship and show that CF in the rat is influenced by a locus on rat chromosome 2 that is also associated with cardiac capillary density. Mitochondrial tryptophanyl-tRNA synthetase (Wars2), encoding an L53F protein variant within the ATP-binding motif, is prioritized as the candidate at the locus by integrating genomic data sets. WARS2(L53F) has low enzyme activity and inhibition of WARS2 in endothelial cells reduces angiogenesis. In the zebrafish, inhibition of wars2 results in trunk vessel deficiencies, disordered endocardial-myocardial contact and impaired heart function. Inhibition of Wars2 in the rat causes cardiac angiogenesis defects and diminished cardiac capillary density. Our data demonstrate a pro-angiogenic function for Wars2 both within and outside the heart that may have translational relevance given the association of WARS2 with common human diseases. Blood supply to the heart is crucial for cardiac function. Here, the authors show that the mitochondrial tryptophanyl-tRNA synthetase, WARS2, drives blood vessel generation in zebrafish and rats and that inhibition of Wars2 diminishes blood vessel growth both within and outside in the heart, suggesting a new target for manipulating angiogenesis.
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79
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Anand S, Madhubala R. Twin Attributes of Tyrosyl-tRNA Synthetase of Leishmania donovani: A HOUSEKEEPING PROTEIN TRANSLATION ENZYME AND A MIMIC OF HOST CHEMOKINE. J Biol Chem 2016; 291:17754-71. [PMID: 27382051 DOI: 10.1074/jbc.m116.727107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Indexed: 12/13/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are housekeeping enzymes essential for protein synthesis. Apart from their parent aminoacylation activity, several aaRSs perform non-canonical functions in diverse biological processes. The present study explores the twin attributes of Leishmania tyrosyl-tRNA synthetase (LdTyrRS) namely, aminoacylation, and as a mimic of host CXC chemokine. Leishmania donovani is a protozoan parasite. Its genome encodes a single copy of tyrosyl-tRNA synthetase. We first tested the canonical aminoacylation role of LdTyrRS. The recombinant protein was expressed, and its kinetic parameters were determined by aminoacylation assay. To study the physiological role of LdTyrRS in Leishmania, gene deletion mutations were attempted via targeted gene replacement. The heterozygous mutants showed slower growth kinetics and exhibited attenuated virulence. LdTyrRS appears to be an essential gene as the chromosomal null mutants did not survive. Our data also highlights the non-canonical function of L. donovani tyrosyl-tRNA synthetase. We show that LdTyrRS protein is present in the cytoplasm and exits from the parasite cytoplasm into the extracellular medium. The released LdTyrRS functions as a neutrophil chemoattractant. We further show that LdTyrRS specifically binds to host macrophages with its ELR (Glu-Leu-Arg) peptide motif. The ELR-CXCR2 receptor interaction mediates this binding. This interaction triggers enhanced secretion of the proinflammatory cytokines TNF-α and IL-6 by host macrophages. Our data indicates a possible immunomodulating role of LdTyrRS in Leishmania infection. This study provides a platform to explore LdTyrRS as a potential target for drug development.
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Affiliation(s)
- Sneha Anand
- From the School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rentala Madhubala
- From the School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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80
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Xu G, Zou WQ, Du SJ, Wu MJ, Xiang TX, Luo ZG. Mechanism of dihydroartemisinin-induced apoptosis in prostate cancer PC3 cells: An iTRAQ-based proteomic analysis. Life Sci 2016; 157:1-11. [PMID: 27234895 DOI: 10.1016/j.lfs.2016.05.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 04/18/2016] [Accepted: 05/23/2016] [Indexed: 10/21/2022]
Abstract
AIMS Prostate cancer (PCa) is one of the most common cancers in men in the world. Advanced PCa, especially castration-resistant PCa (CRPC), is difficult to cure. There is an urgent need to develop novel agents for CPRC. Dihydroartemisinin (DHA) is a semisynthetic derivative of artemisinin and is a well-known antimalarial drug. DHA has been documented to be a potential anticancer agent for PCa. However, the mechanisms underlying the anticancer activity of DHA are still unknown. MAIN METHODS Proteomics analysis based on iTRAQ technology was performed to determine the protein profile changes in human prostate cancer PC3 cells treated by DHA, and apoptosis was detected by flow cytometry and transmission electron microscopy. KEY FINDINGS DHA induced obvious apoptosis in PC3 cells. Using iTRAQ technology, we found 86 differentially expressed proteins linked to the cytotoxicity of DHA in PC3 cells. Gene ontology analysis showed the differentially expressed proteins were mainly associated with the protein synthesis and translation. Protein interaction network analysis and KEGG pathway analysis revealed altered aminoacyl-tRNA biosynthesis and metabolic pathways. Moreover, one candidate protein, heat shock protein HSP70 (HSPA1A), was identified by western blot analysis. SIGNIFICANCE Our results indicate that multiple mechanisms involved in the anticancer activity of DHA in PC3 cells. Decreased HSP70 expression may have an important role in DHA-induced apoptosis in PC3 cells. Our data also provide novel insights into the anticancer mechanisms of DHA.
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Affiliation(s)
- Ge Xu
- Institute of Life Science, Chongqing Medical University, Chongqing 400016, China
| | - Wen-Qin Zou
- Institute of Life Science, Chongqing Medical University, Chongqing 400016, China
| | - Shi-Juan Du
- Institute of Life Science, Chongqing Medical University, Chongqing 400016, China
| | - Ming-Jun Wu
- Institute of Life Science, Chongqing Medical University, Chongqing 400016, China
| | - Ting-Xiu Xiang
- Artron BioResearch Inc., 3938 North Fraser Way, Burnaby, BC, V5J 5H6, Canada
| | - Zi-Guo Luo
- Institute of Life Science, Chongqing Medical University, Chongqing 400016, China.
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81
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Identification of a residue crucial for the angiostatic activity of human mini tryptophanyl-tRNA synthetase by focusing on its molecular evolution. Sci Rep 2016; 6:24750. [PMID: 27094087 PMCID: PMC4837363 DOI: 10.1038/srep24750] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/04/2016] [Indexed: 11/28/2022] Open
Abstract
Human tryptophanyl-tRNA synthetase (TrpRS) exists in two forms: a full-length TrpRS and a mini TrpRS. We previously found that human mini, but not full-length, TrpRS is an angiostatic factor. Moreover, it was shown that the interaction between mini TrpRS and the extracellular domain of vascular endothelial (VE)-cadherin is crucial for its angiostatic activity. However, the molecular mechanism of the angiostatic activity of human mini TrpRS is only partly understood. In the present study, we investigated the effects of truncated (mini) form of TrpRS proteins from human, bovine, or zebrafish on vascular endothelial growth factor (VEGF)-stimulated chemotaxis of human umbilical vein endothelial cells (HUVECs). We show that both human and bovine mini TrpRSs inhibited VEGF-induced endothelial migration, whereas zebrafish mini TrpRS did not. Next, to identify residues crucial for the angiostatic activity of human mini TrpRS, we prepared several site-directed mutants based on amino acid sequence alignments among TrpRSs from various species and demonstrated that a human mini K153Q TrpRS mutant cannot inhibit VEGF-stimulated HUVEC migration and cannot bind to the extracellular domain of VE-cadherin. Taken together, we conclude that the Lys153 residue of human mini TrpRS is a VE-cadherin binding site and is therefore crucial for its angiostatic activity.
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82
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Cao Z, Wang H, Mao X, Luo L. Noncanonical function of threonyl-tRNA synthetase regulates vascular development in zebrafish. Biochem Biophys Res Commun 2016; 473:67-72. [DOI: 10.1016/j.bbrc.2016.03.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 03/13/2016] [Indexed: 01/09/2023]
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83
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Nguyen DN, Jiang P, Stensballe A, Bendixen E, Sangild PT, Chatterton DEW. Bovine lactoferrin regulates cell survival, apoptosis and inflammation in intestinal epithelial cells and preterm pig intestine. J Proteomics 2016; 139:95-102. [PMID: 26996464 DOI: 10.1016/j.jprot.2016.03.020] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/14/2016] [Accepted: 03/11/2016] [Indexed: 01/08/2023]
Abstract
UNLABELLED Bovine lactoferrin (bLF) may modulate neonatal intestinal inflammation. Previous studies in intestinal epithelial cells (IECs) indicated that moderate bLF doses enhance proliferation whereas high doses trigger inflammation. To further elucidate cellular mechanisms, we profiled the porcine IEC proteome after stimulation with bLF at 0, 0.1, 1 and 10g/L by LC-MS-based proteomics. Key pathways were analyzed in the intestine of formula-fed preterm pigs with and without supplementation of 10g/L bLF. Levels of 123 IEC proteins were altered by bLF. Low bLF doses (0.1-1g/L) up-regulated 11 proteins associated with glycolysis, energy metabolism and protein synthesis, indicating support of cell survival. In contrast, a high bLF dose (10g/L) up-regulated three apoptosis-inducing proteins, down-regulated five anti-apoptotic and proliferation-inducing proteins and 15 proteins related to energy and amino acid metabolism, and altered three proteins enhancing the hypoxia inducible factor-1 (HIF-1) pathway. In the preterm pig intestine, bLF at 10g/L decreased villus height/crypt depth ratio and up-regulated the Bax/Bcl-2 ratio and HIF-1α, indicating elevated intestinal apoptosis and inflammation. In conclusion, bLF dose-dependently affects IECs via metabolic, apoptotic and inflammatory pathways. It is important to select an appropriate dose when feeding neonates with bLF to avoid detrimental effects exerted by excessive doses. BIOLOGICAL SIGNIFICANCE The present work elucidates dose-dependent effects of bLF on the proteomic changes of IECs in vitro supplemented with data from a preterm pig study confirming detrimental effects of enteral feeding with the highest dose of bLF (10g/L). The study contributes to further understanding on mechanisms that bLF, as an important milk protein, can regulate the homeostasis of the immature intestine. Results from this study urge neonatologists to carefully consider the dose of bLF to supplement into infant formula used for preterm neonates.
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Affiliation(s)
- Duc Ninh Nguyen
- Comparative Pediatrics and Nutrition, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, DK-1958, Denmark; Department of Food Science, University of Copenhagen, DK-1958, Denmark
| | - Pingping Jiang
- Comparative Pediatrics and Nutrition, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, DK-1958, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, DK-9220, Denmark
| | - Emøke Bendixen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000, Denmark
| | - Per T Sangild
- Comparative Pediatrics and Nutrition, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, DK-1958, Denmark
| | - Dereck E W Chatterton
- Comparative Pediatrics and Nutrition, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, DK-1958, Denmark; Department of Food Science, University of Copenhagen, DK-1958, Denmark.
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84
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Malissovas N, Griffin LB, Antonellis A, Beis D. Dimerization is required for GARS-mediated neurotoxicity in dominant CMT disease. Hum Mol Genet 2016; 25:1528-42. [PMID: 27008886 DOI: 10.1093/hmg/ddw031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 02/01/2016] [Indexed: 01/25/2023] Open
Abstract
Charcot-Marie-Tooth (CMT) disease is a genetically heterogeneous group of peripheral neuropathies. Mutations in several aminoacyl-tRNA synthetase (ARS) genes have been implicated in inherited CMT disease. There are 12 reported CMT-causing mutations dispersed throughout the primary sequence of the human glycyl-tRNA synthetase (GARS). While there is strong genetic evidence linking GARS mutations to CMT disease, the molecular pathology underlying the neuromuscular and sensory phenotypes is still not fully understood. In particular, it is unclear whether the mutations result in a toxic gain of function, a partial loss of activity related to translation, or a combination of these mechanisms. We identified a zebrafish allele of gars (gars(s266)). Homozygous mutant embryos carry a C->A transversion, that changes a threonine to a lysine, in a residue next to a CMT-associated human mutation. We show that the neuromuscular phenotype observed in animals homozygous for T209K Gars (T130K in GARS) is due to a loss of dimerization of the mutated protein. Furthermore, we show that the loss of function, dimer-deficient and human disease-associated G319R Gars (G240R in GARS) mutant protein is unable to rescue the above phenotype. Finally, we demonstrate that another human disease-associated mutant G605R Gars (G526 in GARS) dimerizes with the remaining wild-type protein in animals heterozygous for the T209K Gars and reduces the function enough to elicit a neuromuscular phenotype. Our data indicate that dimerization is required for the dominant neurotoxicity of disease-associated GARS mutations and provide a rapid, tractable model for studying newly identified GARS variants for a role in human disease.
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Affiliation(s)
- Nikos Malissovas
- Developmental Biology, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 11527 Athens, Greece, Medical School, University of Crete, Greece
| | - Laurie B Griffin
- Cellular and Molecular Biology Program, Medical Scientist Training Program
| | - Anthony Antonellis
- Cellular and Molecular Biology Program, Department of Human Genetics, and Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Dimitris Beis
- Developmental Biology, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 11527 Athens, Greece,
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85
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Castranova D, Davis AE, Lo BD, Miller MF, Paukstelis PJ, Swift MR, Pham VN, Torres-Vázquez J, Bell K, Shaw KM, Kamei M, Weinstein BM. Aminoacyl-Transfer RNA Synthetase Deficiency Promotes Angiogenesis via the Unfolded Protein Response Pathway. Arterioscler Thromb Vasc Biol 2016; 36:655-62. [PMID: 26821951 DOI: 10.1161/atvbaha.115.307087] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/07/2016] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Understanding the mechanisms regulating normal and pathological angiogenesis is of great scientific and clinical interest. In this report, we show that mutations in 2 different aminoacyl-transfer RNA synthetases, threonyl tRNA synthetase (tars(y58)) or isoleucyl tRNA synthetase (iars(y68)), lead to similar increased branching angiogenesis in developing zebrafish. APPROACH AND RESULTS The unfolded protein response pathway is activated by aminoacyl-transfer RNA synthetase deficiencies, and we show that unfolded protein response genes atf4, atf6, and xbp1, as well as the key proangiogenic ligand vascular endothelial growth factor (vegfaa), are all upregulated in tars(y58) and iars(y68) mutants. Finally, we show that the protein kinase RNA-like endoplasmic reticulum kinase-activating transcription factor 4 arm of the unfolded protein response pathway is necessary for both the elevated vegfaa levels and increased angiogenesis observed in tars(y58) mutants. CONCLUSIONS Our results suggest that endoplasmic reticulum stress acts as a proangiogenic signal via unfolded protein response pathway-dependent upregulation of vegfaa.
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Affiliation(s)
- Daniel Castranova
- From the Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD (D.C., A.E.D., B.D.L., M.F.M., M.R.S., V.N.P., J.T.-V., K.B., K.M.S., M.K., B.M.W.); and Department of Chemistry and Biochemistry, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park (P.J.P.)
| | - Andrew E Davis
- From the Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD (D.C., A.E.D., B.D.L., M.F.M., M.R.S., V.N.P., J.T.-V., K.B., K.M.S., M.K., B.M.W.); and Department of Chemistry and Biochemistry, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park (P.J.P.)
| | - Brigid D Lo
- From the Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD (D.C., A.E.D., B.D.L., M.F.M., M.R.S., V.N.P., J.T.-V., K.B., K.M.S., M.K., B.M.W.); and Department of Chemistry and Biochemistry, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park (P.J.P.)
| | - Mayumi F Miller
- From the Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD (D.C., A.E.D., B.D.L., M.F.M., M.R.S., V.N.P., J.T.-V., K.B., K.M.S., M.K., B.M.W.); and Department of Chemistry and Biochemistry, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park (P.J.P.)
| | - Paul J Paukstelis
- From the Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD (D.C., A.E.D., B.D.L., M.F.M., M.R.S., V.N.P., J.T.-V., K.B., K.M.S., M.K., B.M.W.); and Department of Chemistry and Biochemistry, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park (P.J.P.)
| | - Matthew R Swift
- From the Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD (D.C., A.E.D., B.D.L., M.F.M., M.R.S., V.N.P., J.T.-V., K.B., K.M.S., M.K., B.M.W.); and Department of Chemistry and Biochemistry, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park (P.J.P.)
| | - Van N Pham
- From the Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD (D.C., A.E.D., B.D.L., M.F.M., M.R.S., V.N.P., J.T.-V., K.B., K.M.S., M.K., B.M.W.); and Department of Chemistry and Biochemistry, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park (P.J.P.)
| | - Jesús Torres-Vázquez
- From the Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD (D.C., A.E.D., B.D.L., M.F.M., M.R.S., V.N.P., J.T.-V., K.B., K.M.S., M.K., B.M.W.); and Department of Chemistry and Biochemistry, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park (P.J.P.)
| | - Kameha Bell
- From the Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD (D.C., A.E.D., B.D.L., M.F.M., M.R.S., V.N.P., J.T.-V., K.B., K.M.S., M.K., B.M.W.); and Department of Chemistry and Biochemistry, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park (P.J.P.)
| | - Kenna M Shaw
- From the Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD (D.C., A.E.D., B.D.L., M.F.M., M.R.S., V.N.P., J.T.-V., K.B., K.M.S., M.K., B.M.W.); and Department of Chemistry and Biochemistry, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park (P.J.P.)
| | - Makoto Kamei
- From the Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD (D.C., A.E.D., B.D.L., M.F.M., M.R.S., V.N.P., J.T.-V., K.B., K.M.S., M.K., B.M.W.); and Department of Chemistry and Biochemistry, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park (P.J.P.)
| | - Brant M Weinstein
- From the Program in Genomics of Differentiation, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD (D.C., A.E.D., B.D.L., M.F.M., M.R.S., V.N.P., J.T.-V., K.B., K.M.S., M.K., B.M.W.); and Department of Chemistry and Biochemistry, College of Computer, Mathematical, and Natural Sciences, University of Maryland, College Park (P.J.P.).
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86
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Zeng R, Wang M, You GY, Yue RZ, Chen YC, Zeng Z, Liu R, Qiang O, Zhang L. Effect of Mini-Tyrosyl-tRNA Synthetase/Mini-Tryptophanyl-tRNA Synthetase on Angiogenesis in Rhesus Monkeys after Acute Myocardial Infarction. Cardiovasc Ther 2016; 34:4-12. [PMID: 26400816 DOI: 10.1111/1755-5922.12161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Rui Zeng
- Department of Cardiology; West China Hospital; School of Clinic Medicine; Sichuan University; Chengdu China
| | - Mian Wang
- Department of Cardiology; West China Hospital; School of Clinic Medicine; Sichuan University; Chengdu China
| | - Gui-ying You
- Department of Cardiology; West China Hospital; School of Clinic Medicine; Sichuan University; Chengdu China
| | - Rong-zheng Yue
- Department of Nephrology; West China Hospital; School of Clinic Medicine; Sichuan University; Chengdu China
| | - Yu-cheng Chen
- Department of Cardiology; West China Hospital; School of Clinic Medicine; Sichuan University; Chengdu China
| | - Zhi Zeng
- Department of Cardiology; West China Hospital; School of Clinic Medicine; Sichuan University; Chengdu China
| | - Rui Liu
- Laboratory of Peptides Related with Human Diseases; National Laboratory of Biomedicine; Sichuan University; Chengdu China
| | - Ou Qiang
- Laboratory of Peptides Related with Human Diseases; National Laboratory of Biomedicine; Sichuan University; Chengdu China
| | - Li Zhang
- Department of Cardiology; West China Hospital; School of Clinic Medicine; Sichuan University; Chengdu China
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87
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Park BS, Yeo SG, Jung J, Jeong NY. A novel therapeutic target for peripheral nerve injury-related diseases: aminoacyl-tRNA synthetases. Neural Regen Res 2015; 10:1656-62. [PMID: 26692865 PMCID: PMC4660761 DOI: 10.4103/1673-5374.167766] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Aminoacyl-tRNA synthetases (AminoARSs) are essential enzymes that perform the first step of protein synthesis. Beyond their original roles, AminoARSs possess non-canonical functions, such as cell cycle regulation and signal transduction. Therefore, AminoARSs represent a powerful pharmaceutical target if their non-canonical functions can be controlled. Using AminoARSs-specific primers, we screened mRNA expression in the spinal cord dorsal horn of rats with peripheral nerve injury created by sciatic nerve axotomy. Of 20 AminoARSs, we found that phenylalanyl-tRNA synthetase beta chain (FARSB), isoleucyl-tRNA synthetase (IARS) and methionyl-tRNA synthetase (MARS) mRNA expression was increased in spinal dorsal horn neurons on the injured side, but not in glial cells. These findings suggest the possibility that FARSB, IARS and MARS, as a neurotransmitter, may transfer abnormal sensory signals after peripheral nerve damage and become a new target for drug treatment.
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Affiliation(s)
- Byung Sun Park
- Department of Anatomy and Neurobiology, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Seung Geun Yeo
- Department of Otolaryngolgy, Head and Neck Surgery, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Junyang Jung
- Department of Anatomy and Neurobiology, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
| | - Na Young Jeong
- Department of Anatomy and Cell Biology, College of Medicine, Dong-A University, Busan, Republic of Korea
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88
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Casas-Tintó S, Lolo FN, Moreno E. Active JNK-dependent secretion of Drosophila Tyrosyl-tRNA synthetase by loser cells recruits haemocytes during cell competition. Nat Commun 2015; 6:10022. [DOI: 10.1038/ncomms10022] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/27/2015] [Indexed: 12/23/2022] Open
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89
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Fang P, Guo M. Evolutionary Limitation and Opportunities for Developing tRNA Synthetase Inhibitors with 5-Binding-Mode Classification. Life (Basel) 2015; 5:1703-25. [PMID: 26670257 PMCID: PMC4695845 DOI: 10.3390/life5041703] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/30/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that catalyze the transfer of amino acids to their cognate tRNAs as building blocks for translation. Each of the aaRS families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. In addition, aaRSs in higher species have evolved important non-translational functions. These translational and non-translational functions of aaRS are attractive for developing antibacterial, antifungal, and antiparasitic agents and for treating other human diseases. The interplay between amino acids, tRNA, ATP, EF-Tu and non-canonical binding partners, had shaped each family with distinct pattern of key sites for regulation, with characters varying among species across the path of evolution. These sporadic variations in the aaRSs offer great opportunity to target these essential enzymes for therapy. Up to this day, growing numbers of aaRS inhibitors have been discovered and developed. Here, we summarize the latest developments and structural studies of aaRS inhibitors, and classify them with distinct binding modes into five categories.
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Affiliation(s)
- Pengfei Fang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Min Guo
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
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90
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Transcript Expression Data from Human Islets Links Regulatory Signals from Genome-Wide Association Studies for Type 2 Diabetes and Glycemic Traits to Their Downstream Effectors. PLoS Genet 2015; 11:e1005694. [PMID: 26624892 PMCID: PMC4666611 DOI: 10.1371/journal.pgen.1005694] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 10/30/2015] [Indexed: 01/01/2023] Open
Abstract
The intersection of genome-wide association analyses with physiological and functional data indicates that variants regulating islet gene transcription influence type 2 diabetes (T2D) predisposition and glucose homeostasis. However, the specific genes through which these regulatory variants act remain poorly characterized. We generated expression quantitative trait locus (eQTL) data in 118 human islet samples using RNA-sequencing and high-density genotyping. We identified fourteen loci at which cis-exon-eQTL signals overlapped active islet chromatin signatures and were coincident with established T2D and/or glycemic trait associations. At some, these data provide an experimental link between GWAS signals and biological candidates, such as DGKB and ADCY5. At others, the cis-signals implicate genes with no prior connection to islet biology, including WARS and ZMIZ1. At the ZMIZ1 locus, we show that perturbation of ZMIZ1 expression in human islets and beta-cells influences exocytosis and insulin secretion, highlighting a novel role for ZMIZ1 in the maintenance of glucose homeostasis. Together, these findings provide a significant advance in the mechanistic insights of T2D and glycemic trait association loci.
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91
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Mirando AC, Fang P, Williams TF, Baldor LC, Howe AK, Ebert AM, Wilkinson B, Lounsbury KM, Guo M, Francklyn CS. Aminoacyl-tRNA synthetase dependent angiogenesis revealed by a bioengineered macrolide inhibitor. Sci Rep 2015; 5:13160. [PMID: 26271225 PMCID: PMC4536658 DOI: 10.1038/srep13160] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 07/16/2015] [Indexed: 11/23/2022] Open
Abstract
Aminoacyl-tRNA synthetases (AARSs) catalyze an early step in protein synthesis, but also regulate diverse physiological processes in animal cells. These include angiogenesis, and human threonyl-tRNA synthetase (TARS) represents a potent pro-angiogenic AARS. Angiogenesis stimulation can be blocked by the macrolide antibiotic borrelidin (BN), which exhibits a broad spectrum toxicity that has discouraged deeper investigation. Recently, a less toxic variant (BC194) was identified that potently inhibits angiogenesis. Employing biochemical, cell biological, and biophysical approaches, we demonstrate that the toxicity of BN and its derivatives is linked to its competition with the threonine substrate at the molecular level, which stimulates amino acid starvation and apoptosis. By separating toxicity from the inhibition of angiogenesis, a direct role for TARS in vascular development in the zebrafish could be demonstrated. Bioengineered natural products are thus useful tools in unmasking the cryptic functions of conventional enzymes in the regulation of complex processes in higher metazoans.
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Affiliation(s)
| | - Pengfei Fang
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida
| | | | | | - Alan K Howe
- Department of Pharmacology, University of Vermont
| | | | - Barrie Wilkinson
- Isomerase Therapeutics Ltd, Science Village, Chesterford Research Park, Cambridge CB10 1XL, UK
| | | | - Min Guo
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida
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92
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Millar JA, Valdés R, Kacharia FR, Landfear SM, Cambronne ED, Raghavan R. Coxiella burnetii and Leishmania mexicana residing within similar parasitophorous vacuoles elicit disparate host responses. Front Microbiol 2015; 6:794. [PMID: 26300862 PMCID: PMC4528172 DOI: 10.3389/fmicb.2015.00794] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/21/2015] [Indexed: 12/24/2022] Open
Abstract
Coxiella burnetii is a bacterium that thrives in an acidic parasitophorous vacuole (PV) derived from lysosomes. Leishmania mexicana, a eukaryote, has also independently evolved to live in a morphologically similar PV. As Coxiella and Leishmania are highly divergent organisms that cause different diseases, we reasoned that their respective infections would likely elicit distinct host responses despite producing phenotypically similar parasite-containing vacuoles. The objective of this study was to investigate, at the molecular level, the macrophage response to each pathogen. Infection of THP-1 (human monocyte/macrophage) cells with Coxiella and Leishmania elicited disparate host responses. At 5 days post-infection, when compared to uninfected cells, 1057 genes were differentially expressed (746 genes up-regulated and 311 genes down-regulated) in C. burnetii infected cells, whereas 698 genes (534 genes up-regulated and 164 genes down-regulated) were differentially expressed in L. mexicana infected cells. Interestingly, of the 1755 differentially expressed genes identified in this study, only 126 genes (~7%) are common to both infections. We also discovered that 1090 genes produced mRNA isoforms at significantly different levels under the two infection conditions, suggesting that alternate proteins encoded by the same gene might have important roles in host response to each infection. Additionally, we detected 257 micro RNAs (miRNAs) that were expressed in THP-1 cells, and identified miRNAs that were specifically expressed during Coxiella or Leishmania infections. Collectively, this study identified host mRNAs and miRNAs that were influenced by Coxiella and/or Leishmania infections, and our data indicate that although their PVs are morphologically similar, Coxiella and Leishmania have evolved different strategies that perturb distinct host processes to create and thrive within their respective intracellular niches.
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Affiliation(s)
- Jess A Millar
- Department of Biology and Center for Life in Extreme Environments, Portland State University, Portland, OR USA
| | - Raquel Valdés
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR USA
| | - Fenil R Kacharia
- Department of Biology and Center for Life in Extreme Environments, Portland State University, Portland, OR USA
| | - Scott M Landfear
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR USA
| | - Eric D Cambronne
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR USA
| | - Rahul Raghavan
- Department of Biology and Center for Life in Extreme Environments, Portland State University, Portland, OR USA
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Campone M, Valo I, Jézéquel P, Moreau M, Boissard A, Campion L, Loussouarn D, Verriele V, Coqueret O, Guette C. Prediction of Recurrence and Survival for Triple-Negative Breast Cancer (TNBC) by a Protein Signature in Tissue Samples. Mol Cell Proteomics 2015. [PMID: 26209610 DOI: 10.1074/mcp.m115.048967] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
To date, there is no available targeted therapy for patients who are diagnosed with triple-negative breast cancers (TNBC). The aim of this study was to identify a new specific target for specific treatments. Frozen primary tumors were collected from 83 adjuvant therapy-naive TNBC patients. These samples were used for global proteome profiling by iTRAQ-OFFGEL-LC-MS/MS approach in two series: a training cohort (n = 42) and a test set (n = 41). Patients who remains free of local or distant metastasis for a minimum of 5 years after surgery were classified in the no-relapse group; the others were in the relapse group. OPLS and Kaplan-Meier analyses were performed to select candidate markers, which were validated by immunohistochemistry. Three proteins were identified in the training set and validated in the test set by Kaplan-Meier method and immunohistochemistry (IHC): TrpRS as a good prognostic markers and DP and TSP1 as bad prognostic markers. We propose the establishment of an IHC test to calculate the score of TrpRS, DP, and TSP1 in TNBC tumors to evaluate the degree of aggressiveness of the tumors. Finally, we propose that DP and TSP1 could provide therapeutic targets for specific treatments.
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Affiliation(s)
- Mario Campone
- ‡René Gauducheau ICO Cancer Center, Inserm U892, CNRS 6299, Bd J. Monod, 44805 Saint Herblain Cedex, France; §Paul Papin ICO Cancer Center, Inserm U892, CNRS 6299, 2 rue Moll, 49933 Angers Cedex 9, France
| | - Isabelle Valo
- §Paul Papin ICO Cancer Center, Inserm U892, CNRS 6299, 2 rue Moll, 49933 Angers Cedex 9, France
| | - Pascal Jézéquel
- ‡René Gauducheau ICO Cancer Center, Inserm U892, CNRS 6299, Bd J. Monod, 44805 Saint Herblain Cedex, France
| | - Marie Moreau
- ¶Angers University, 4 Boulevard de Lavoisier, Angers, 49000, France
| | - Alice Boissard
- §Paul Papin ICO Cancer Center, Inserm U892, CNRS 6299, 2 rue Moll, 49933 Angers Cedex 9, France
| | - Loic Campion
- ‡René Gauducheau ICO Cancer Center, Inserm U892, CNRS 6299, Bd J. Monod, 44805 Saint Herblain Cedex, France
| | - Delphine Loussouarn
- ‖INSERM U892, CNRS 6299, IRT-UN, 8 quai Moncousu, 44007 Nantes Cedex, France
| | - Véronique Verriele
- §Paul Papin ICO Cancer Center, Inserm U892, CNRS 6299, 2 rue Moll, 49933 Angers Cedex 9, France
| | - Olivier Coqueret
- §Paul Papin ICO Cancer Center, Inserm U892, CNRS 6299, 2 rue Moll, 49933 Angers Cedex 9, France; ¶Angers University, 4 Boulevard de Lavoisier, Angers, 49000, France
| | - Catherine Guette
- §Paul Papin ICO Cancer Center, Inserm U892, CNRS 6299, 2 rue Moll, 49933 Angers Cedex 9, France;
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94
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Regulation of angiogenesis by aminoacyl-tRNA synthetases. Int J Mol Sci 2014; 15:23725-48. [PMID: 25535072 PMCID: PMC4284789 DOI: 10.3390/ijms151223725] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 12/11/2014] [Accepted: 12/12/2014] [Indexed: 02/06/2023] Open
Abstract
In addition to their canonical roles in translation the aminoacyl-tRNA synthetases (ARSs) have developed secondary functions over the course of evolution. Many of these activities are associated with cellular survival and nutritional stress responses essential for homeostatic processes in higher eukaryotes. In particular, six ARSs and one associated factor have documented functions in angiogenesis. However, despite their connection to this process, the ARSs are mechanistically distinct and exhibit a range of positive or negative effects on aspects of endothelial cell migration, proliferation, and survival. This variability is achieved through the appearance of appended domains and interplay with inflammatory pathways not found in prokaryotic systems. Complete knowledge of the non-canonical functions of ARSs is necessary to understand the mechanisms underlying the physiological regulation of angiogenesis.
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95
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Datt M, Sharma A. Novel and unique domains in aminoacyl-tRNA synthetases from human fungal pathogens Aspergillus niger, Candida albicans and Cryptococcus neoformans. BMC Genomics 2014; 15:1069. [PMID: 25479903 PMCID: PMC4301749 DOI: 10.1186/1471-2164-15-1069] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 11/20/2014] [Indexed: 12/15/2022] Open
Abstract
Background Some species of fungi can cause serious human diseases, particularly to immuno-compromised individuals. Opportunistic fungal infections are a leading cause of mortality, and present an emerging challenge that requires development of new and effective therapeutics. Aminoacyl-tRNA synthetases (aaRSs) are indispensable components of cellular protein translation machinery and can be targeted for discovery of novel anti-fungal agents. Results Validation of aaRSs as potential drug targets in pathogenic microbes prompted us to investigate the genomic distribution of aaRSs within three fungi that infect humans – A. niger, C. albicans and C. neoformans. Hidden Markov Models were built for aaRSs and related proteins to search for homologues in these fungal genomes. Here, we provide a detailed and comprehensive annotation for 3 fungal genome aaRSs and their associated proteins. We delineate predicted localizations, subdomain architectures and prevalence of unusual motifs within these aaRSs. Several fungal aaRSs have unique domain appendages of unknown function e.g. A. niger AsxRS and C. neoformans TyrRS have additional domains that are absent from human homologs. Conclusions Detailed comparisons of fungal aaRSs with human homologs suggest key differences that could be exploited for specific drug targeting. Our cataloging and structural analyses provide a comprehensive foundation for experimentally dissecting fungal aaRSs that may enable development of new anti-fungal agents. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1069) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Amit Sharma
- Structural and Computational Biology group, International Center for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India.
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96
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Park BS, Jo HW, Jung J. Expression profile of aminoacyl-tRNA synthetases in dorsal root ganglion neurons after peripheral nerve injury. J Mol Histol 2014; 46:115-22. [PMID: 25467976 DOI: 10.1007/s10735-014-9601-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 11/26/2014] [Indexed: 12/15/2022]
Abstract
Aminoacyl-tRNA synthetases (AminoARSs) are essential enzymes involved in acylating tRNA with amino acids. In addition to the typical functions of AminoARSs, various non-canonical functions have been reported, such as involvement in cellular regulatory processes and signal transduction. Here, to explore the cellular changes in sensory neurons after nerve injury, we evaluated AARS mRNA expression in rat dorsal root ganglia (DRG) neurons using AminoARS-specific primers. Of 20 AminoARSs, we found that expression of lysyl-tRNA synthetase (KARS) and glutaminyl-tRNA synthetase (QARS) was decreased in the DRG injured side. We observed decreased KARS and QARS expression in DRG neuronal cell bodies, but not in satellite cells. Therefore, we suggest the possibility that KARS and QARS may act as signaling molecules to transfer abnormal sensory signals to the spinal dorsal horn after peripheral nerve damage. Therefore, KARS and QARS may represent powerful pharmaceutical targets via control of their non-canonical functions.
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Affiliation(s)
- Byung Sun Park
- Department of Anatomy and Neurobiology, School of Medicine, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 130-701, Republic of Korea
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97
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Ling Z, Yanling Z, Zhe F, Kui C, Xiushi Z, Min Y, Wei M. Recombinant human tyrosyl-tRNA synthetase, a novel thrombopoietic agent. Eur J Pharmacol 2014; 738:293-300. [DOI: 10.1016/j.ejphar.2014.05.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 05/26/2014] [Accepted: 05/28/2014] [Indexed: 12/21/2022]
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98
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Wellman TL, Eckenstein M, Wong C, Rincon M, Ashikaga T, Mount SL, Francklyn CS, Lounsbury KM. Threonyl-tRNA synthetase overexpression correlates with angiogenic markers and progression of human ovarian cancer. BMC Cancer 2014; 14:620. [PMID: 25163878 PMCID: PMC4155084 DOI: 10.1186/1471-2407-14-620] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 08/20/2014] [Indexed: 12/11/2022] Open
Abstract
Background Ovarian tumors create a dynamic microenvironment that promotes angiogenesis and reduces immune responses. Our research has revealed that threonyl-tRNA synthetase (TARS) has an extracellular angiogenic activity separate from its function in protein synthesis. The objective of this study was to test the hypothesis that TARS expression in clinical samples correlates with angiogenic markers and ovarian cancer progression. Methods Protein and mRNA databases were explored to correlate TARS expression with ovarian cancer. Serial sections of paraffin embedded ovarian tissues from 70 patients diagnosed with epithelial ovarian cancer and 12 control patients were assessed for expression of TARS, vascular endothelial growth factor (VEGF) and PECAM using immunohistochemistry. TARS secretion from SK-OV-3 human ovarian cancer cells was measured. Serum samples from 31 tissue-matched patients were analyzed by ELISA for TARS, CA-125, and tumor necrosis factor-α (TNF-α). Results There was a strong association between the tumor expression of TARS and advancing stage of epithelial ovarian cancer (p < 0.001). TARS expression and localization were also correlated with VEGF (p < 0.001). A significant proportion of samples included heavy TARS staining of infiltrating leukocytes which also correlated with stage (p = 0.017). TARS was secreted by ovarian cancer cells, and patient serum TARS was related to tumor TARS and angiogenic markers, but did not achieve significance with respect to stage. Multivariate Cox proportional hazard models revealed a surprising inverse relationship between TARS expression and mortality risk in late stage disease (p = 0.062). Conclusions TARS expression is increased in epithelial ovarian cancer and correlates with markers of angiogenic progression. These findings and the association of TARS with disease survival provide clinical validation that TARS is associated with angiogenesis in ovarian cancer. These results encourage further study of TARS as a regulator of the tumor microenvironment and possible target for diagnosis and/or treatment in ovarian cancer. Electronic supplementary material The online version of this article (doi:10.1186/1471-2407-14-620) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Karen M Lounsbury
- Departments of Pharmacology, University of Vermont, College of Medicine, Burlington, Vermont 05405, USA.
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99
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Lo WS, Gardiner E, Xu Z, Lau CF, Wang F, Zhou JJ, Mendlein JD, Nangle LA, Chiang KP, Yang XL, Au KF, Wong WH, Guo M, Zhang M, Schimmel P. Human tRNA synthetase catalytic nulls with diverse functions. Science 2014; 345:328-32. [PMID: 25035493 PMCID: PMC4188629 DOI: 10.1126/science.1252943] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Genetic efficiency in higher organisms depends on mechanisms to create multiple functions from single genes. To investigate this question for an enzyme family, we chose aminoacyl tRNA synthetases (AARSs). They are exceptional in their progressive and accretive proliferation of noncatalytic domains as the Tree of Life is ascended. Here we report discovery of a large number of natural catalytic nulls (CNs) for each human AARS. Splicing events retain noncatalytic domains while ablating the catalytic domain to create CNs with diverse functions. Each synthetase is converted into several new signaling proteins with biological activities "orthogonal" to that of the catalytic parent. We suggest that splice variants with nonenzymatic functions may be more general, as evidenced by recent findings of other catalytically inactive splice-variant enzymes.
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Affiliation(s)
- Wing-Sze Lo
- IAS HKUST-Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. Pangu Biopharma, Edinburgh Tower, The Landmark, 15 Queen's Road Central, Hong Kong, China
| | - Elisabeth Gardiner
- The Scripps Laboratories for tRNA Synthetase Research, The Scripps Research Institute, 10650 North Torrey Pines Road, La Jolla, CA 92037, USA. aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA 92121, USA
| | - Zhiwen Xu
- IAS HKUST-Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. Pangu Biopharma, Edinburgh Tower, The Landmark, 15 Queen's Road Central, Hong Kong, China
| | - Ching-Fun Lau
- IAS HKUST-Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. Pangu Biopharma, Edinburgh Tower, The Landmark, 15 Queen's Road Central, Hong Kong, China
| | - Feng Wang
- IAS HKUST-Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. Pangu Biopharma, Edinburgh Tower, The Landmark, 15 Queen's Road Central, Hong Kong, China
| | - Jie J Zhou
- IAS HKUST-Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. Pangu Biopharma, Edinburgh Tower, The Landmark, 15 Queen's Road Central, Hong Kong, China
| | - John D Mendlein
- aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA 92121, USA
| | - Leslie A Nangle
- aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA 92121, USA
| | - Kyle P Chiang
- aTyr Pharma, 3545 John Hopkins Court, Suite 250, San Diego, CA 92121, USA
| | - Xiang-Lei Yang
- IAS HKUST-Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. The Scripps Laboratories for tRNA Synthetase Research, The Scripps Research Institute, 10650 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Kin-Fai Au
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
| | - Min Guo
- The Scripps Laboratories for tRNA Synthetase Research, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Mingjie Zhang
- IAS HKUST-Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Paul Schimmel
- IAS HKUST-Scripps R&D Laboratory, Institute for Advanced Study, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China. The Scripps Laboratories for tRNA Synthetase Research, The Scripps Research Institute, 10650 North Torrey Pines Road, La Jolla, CA 92037, USA. The Scripps Laboratories for tRNA Synthetase Research, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
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100
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Lang Y, Zhang Y, Zhan L, Feng Z, Zhou X, Yu M, Mo W. Expression, purification, and characterization of rhTyrRS. BMC Biotechnol 2014; 14:64. [PMID: 25027604 PMCID: PMC4118627 DOI: 10.1186/1472-6750-14-64] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 07/09/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aminoacyl-tRNA synthetases (AARSs) catalyze the first step of protein synthesis. Emerging evidence indicates that AARSs may have additional functions, playing a role in signal transduction pathways regulating thrombopoiesis and inflammation. Recombinant human tyrosyl-tRNA synthetase (rhTyrRS) is engineered with a single amino acid substitution that unmasks its cytokine activity. An industrial production method that provides high yield as well as high purity, quality, and potency of this protein is required for preclinical research. RESULTS We expressed codon-optimized rhTyrRS in Escherichia coli under fermentation conditions. Soluble protein was purified by a three-step purification method using cation exchange chromatography, gel filtration chromatography, and anion exchange chromatography. We also established a method to test the biological activity of rhTyrRS by measuring aminoacylation and IL-8 release in rhTyrRS-treated HL-60 cells. CONCLUSIONS The characterization of purified rhTyrRS indicated that this protein can be used in pharmacodynamic and pharmacokinetic studies.
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Affiliation(s)
| | | | | | | | | | - Min Yu
- The Key Laboratory of Molecular Medicine, Ministry of Education, Fudan University, Shanghai, P,R, China.
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